commit 61734d3da08b88a5c35a7c57c20644e122fa5e36 Author: Pedro Costa Date: Wed Sep 30 16:43:17 2020 +0000 typo fixes (#1427) Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/AmrLevel.rst Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/Fortran.rst Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/IO.rst Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LoadBalancing.rst commit c75c4a65ec50580504f87e6ea7cbd4d314644a17 Author: Weiqun Zhang Date: Tue Sep 29 21:55:31 2020 -0700 Signed distance function (#1425) ## Summary * Add FillImpFunc to fill MultiFab with the value of implicit function * average_down_nodal: optional argument to specify the safety of mfiter * Add FillSignedDistance to fill MultiFab with signed distance. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_MultiFabUtil.H Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp commit ea9f8208cd820326cbd38d65307ae7f1181b48fb Author: Andrew Myers Date: Tue Sep 29 14:53:33 2020 -0700 Call sync at the end of the particle transformation functions. (#1424) The `ParticleTransformations` test was broken on Tulip. The problem was missing `synchronize` statements in the test code itself. However, it is safer if these functions perform the synchronization internally. The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ParticleTransformation.H commit 23f2eb2dc97b56038d38b4079ee161800c8e40c2 Author: mic84 Date: Tue Sep 29 12:41:26 2020 -0700 Doc: update documentation on CMake+CUDA (#1421) * Doc: update documentation on CMake+CUDA * Update Docs/sphinx_documentation/source/GPU.rst Co-authored-by: Axel Huebl * Update Docs/sphinx_documentation/source/GPU.rst Co-authored-by: Axel Huebl * CMake: bump up minimum required CUDA version * Doc: update doc Co-authored-by: Axel Huebl Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/GPU.rst Tools/CMake/AMReX_SetupCUDA.cmake commit f9a441ae372198bf6efe3af6eaca3b967ee3291c Author: Weiqun Zhang Date: Tue Sep 29 09:16:03 2020 -0700 Fix 1D CUDA compilation failure due to #1332 (#1423) The most vexing parse in C++ strikes again. This closes #1422. Src/Base/AMReX_GpuLaunchMacrosG.H commit b7ef5a650d7e3accb9f698b7ec929c87cbf24711 Author: Weiqun Zhang Date: Tue Sep 29 08:24:51 2020 -0700 Remove the call to set device flags. (#1417) ## Summary This is no longer needed and may result in failure due to that the device has already been set and initialized in another code. ## Additional background Exa-Wind has a code that uses both Kokkos and AMReX. It seems that the call to cudaSetDeviceFlags fails because of that. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_GpuDevice.cpp commit ef6789d593814c78ce1de0456fb5fa524a1f9c13 Author: Andrew Myers Date: Mon Sep 28 17:30:23 2020 -0700 Fix new bug in clearNeighhborsGPU (#1420) * Fix new bug in clearNeighhborsGPU * fix typo Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit c4116b67f7f176229a749bc818b7610a61a9a2f8 Author: Andrew Myers Date: Mon Sep 28 14:17:55 2020 -0700 these functions need to be marked __host__ __device__ to compile with HIP (#1419) Src/Particle/AMReX_ParticleUtil.H commit e4f0bcd12845e81daa8c13d9839e9662c26bfd08 Author: Andrew Myers Date: Mon Sep 28 13:11:30 2020 -0700 Define ParticleTile in AddParticles (#1409) * Remove GetPosition and SetPosition from ParIter * define the particle tile before adding particles to it Src/Particle/AMReX_ParticleContainerI.H commit aadf8eb8711b816d3234745a98c6170918bca7c3 Author: Andrew Myers Date: Mon Sep 28 13:09:33 2020 -0700 Generalize clearNeighbors for multiple levels and remove faulty assertions. (#1418) * Generalize clearNeighbors for multiple levels and remove faulty assertions. * also fix cpu version Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 3a9381141a1fe78180be578e7b0e1b24a7532171 Author: Andrew Myers Date: Fri Sep 25 14:15:18 2020 -0700 fix decltype for the case where have a random engine (#1414) Src/Particle/AMReX_ParticleTransformation.H commit d7ed0d7a41d92ecfb0a4cee2ff023597e5e9f875 Author: Andrew Myers Date: Fri Sep 25 14:15:09 2020 -0700 always clear neighbor particles before calling Redistribute() (#1415) Src/Particle/AMReX_NeighborParticles.H commit 4a4d585621b0fa34980464baab0466b5e09bc781 Author: asalmgren Date: Fri Sep 25 09:50:37 2020 -0700 1) remove flags setCGVerbose and setCGMaxIter since those are more accurately called (#1413) setBottomVerbose and setBottomMaxIter. The "setCG..." flags are misleading since they actually apply to non-CG bottom solvers as well. 2) add documentation in the Linear Solvers section about "maxorder" -- this was not previously documented. Docs/sphinx_documentation/source/LinearSolvers.rst Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.H Tests/LinearSolvers/MLMG/inputs Tests/LinearSolvers/MLMG/inputs.boxes Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/advance.cpp Tutorials/LinearSolvers/ABecLaplacian_F/inputs Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-abeclap-lev Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-poisson-com Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp Tutorials/LinearSolvers/MultiComponent/inputs Tutorials/LinearSolvers/MultiComponent/main.cpp Tutorials/LinearSolvers/Nodal_Projection_EB/inputs_3d Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp Tutorials/SDC/MISDC_ADR_2d/Source/main.cpp commit bd7c2b8db69b4a3cdb40bf3f23bf8eea952d5071 Author: Pedro Costa Date: Fri Sep 25 16:13:23 2020 +0000 typo fixes (#1411) ## Summary some small typos I found while reading the documentation ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Co-authored-by: Weiqun Zhang Docs/sphinx_documentation/source/Basics.rst commit 9499db8a1f406d1691b845f203c3a15c5f28c744 Author: Andrew Myers Date: Fri Sep 25 08:43:04 2020 -0700 Remove GetPosition and SetPosition from ParIter (#1408) These were added for WarpX, but they are not used any more. The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ParIter.H commit 9f43ecbb0df8e37e4d0aa9511f76cc5e91c52d9d Author: Andrew Myers Date: Thu Sep 24 13:58:32 2020 -0700 filterParticles and filterAndTransformParticles need to take callables with and without RNG (#1407) The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_WriteBinaryParticleData.H commit 605e276d42d660eaf28e8a7f68636d30f624738f Author: Axel Huebl Date: Thu Sep 24 08:10:29 2020 -0700 ParallelDescriptor: Check MPI If Self (#1406) ## Summary Only check the requested MPI Threading level if AMReX also initialized MPI. Follow-up to #1351 ## Additional background ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_ParallelDescriptor.cpp commit 3cad68f7a504044186d0caa20649197d2794aa8b Author: Donald E. Willcox Date: Wed Sep 23 18:02:34 2020 -0700 Enable compilation on Cori interactive nodes (#1405) ## Summary This enables compilation in Cori interactive jobs. Previously, in interactive jobs on Cori Haswell and KNL, `hostname -f` returned a string like `nid00018` so we were loading `Make.unknown`, causing compilation failure. @WeiqunZhang suggested checking the `NERSC_HOST` environment variable instead, which is defined on Cori login, interactive (Haswell & KNL), and GPU nodes. This PR moves the check in `Make.machines` for Cori to follow the logic for Cori GPU, and we check if `NERSC_HOST` is set to `cori`. I've tested this works on Haswell & KNL interactive jobs and that we are still setting `which_computer` correctly on Cori GPU. ## Additional background ## Checklist The proposed changes: - [X] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/Make.machines commit 2b31386adec5efda010ff08261d5f0658027e96c Author: Weiqun Zhang Date: Wed Sep 23 17:23:48 2020 -0700 DPCPP: use C++17 and disable mkl warnings (#1404) * DPCPP: use C++17 and disable mkl warnings * Explicitly use C++17 because MKL contains C++17 codes. Co-authored-by: Axel Huebl Src/Base/AMReX_Random.H Src/Base/AMReX_RandomEngine.H Tools/GNUMake/comps/dpcpp.mak commit 766a2385cf37e97291f7e0d4fa5ebe1ed55f7fe5 Author: Axel Huebl Date: Wed Sep 23 16:32:19 2020 -0700 Docs: C++17 & Particle SP (#1403) Update the build docs for GNUmake: - single precision for particles - typo in `USE_DPCPP` option - add C++17 option Equivalent CMake options are up-to-date, so no change is needed. Docs/sphinx_documentation/source/BuildingAMReX.rst commit fbee3e3a3b1ebd912dbe6c1b6bb29d36d10ab153 Author: mic84 Date: Wed Sep 23 16:16:11 2020 -0700 CMake: enforce C++17 as minimum C++ standard for ENABLE_DPCPP=ON (#1402) Tools/CMake/AMReX_Config.cmake commit 577c8221804b5a2185c0356d6ab46e538722b9d1 Author: Weiqun Zhang Date: Wed Sep 23 14:47:56 2020 -0700 Use RNG in Particle I/O filter (#1401) In order to support the use of RNG in particle I/O filters, we need to be able to call two types of filter functions. The new type has a RandomEngine argument. Src/Particle/AMReX_WriteBinaryParticleData.H commit e9007d6832efe63e94ff180d97f2212cad9e13ac Author: Pedro Costa Date: Wed Sep 23 17:58:05 2020 +0000 nitpicking :) (#1400) ## Summary typo fix ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Docs/sphinx_documentation/source/Basics.rst commit 5f85756e8523423913bd46a7d318def6f1889103 Author: Weiqun Zhang Date: Wed Sep 23 10:31:10 2020 -0700 Update dpcpp flags (#1399) * -fsycl-unnamed-lambda is enabled by default now. So we do not need to pass the flag anymore. * Early optimizations are enabled by default in beta09. This makes a lot of tests crash. So we disable it with -fno-sycl-early-optimizations. Tools/CMake/AMReXSYCL.cmake Tools/GNUMake/comps/dpcpp.mak commit f75ae5897d699a0fa4835818b5d5ab83535e5be8 Author: mic84 Date: Wed Sep 23 08:09:22 2020 -0700 NodalProjector: fix comments (#1396) Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 804f844b0634e5fde9fd52a36c12fcb3069fcc66 Author: kngott <30483578+kngott@users.noreply.github.com> Date: Tue Sep 22 15:11:36 2020 -0700 Fix inaccurate assertion. (#1395) Src/Base/AMReX_BoxList.cpp commit a18b88f27ca0b5c69cd935d7af3011d954322d9a Author: mic84 Date: Tue Sep 22 13:47:12 2020 -0700 CMake: remove LinearSolvers/MultiComponent from tutorials (#1394) Tutorials/LinearSolvers/MultiComponent/CMakeLists.txt commit 784f23144d3edda49ff812e6c601ca3ec1468372 Author: Weiqun Zhang Date: Tue Sep 22 13:33:25 2020 -0700 Fix function type for HIP (#1393) Currently in HIP we do not have a way to do SNFINAE based on whether the function is callable on host or not. So we have to replace the device lambda with host and device lambda. Src/Base/AMReX_MultiFab.cpp commit 9198b1b9a7f7f77ff04261aada6284301db77391 Author: Weiqun Zhang Date: Mon Sep 21 21:08:18 2020 -0700 DPCPP support for mulitple GPUs (#1392) Src/Base/AMReX_GpuDevice.cpp commit d6eadf8c32ae211febeaa2aa1e6e1df5a70807cb Author: Weiqun Zhang Date: Mon Sep 21 20:21:53 2020 -0700 Intall intel-oneapi-mkl-devel in CI (#1391) .github/workflows/dependencies/dependencies_dpcpp.sh commit 9a272a1701dbedd1f0b993720f157cf340d12f33 Author: Weiqun Zhang Date: Mon Sep 21 13:52:33 2020 -0700 Random Number Generation on Device (#1363) In order to support RNG on device with DPC++, we have to change the API because DPC++ does not support global device variables. We introduce a new ParallelForRNG function that takes a device lambda with an extra RandomEngine argument. Random numbers can be generated by calling amrex::Random(RandomEngine const&). To maintain backward compatibility in the short term, the old way of calling `amrex::Random()` on device is kept. But it will be removed soon because no locking is needed in the new way unlike in `Random()`. Note that only the device version of `amrex::Random()` is deprecated. Src/Base/AMReX_Extension.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_RandomEngine.H Src/Base/AMReX_Reduce.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/AsyncOut/multifab/main.cpp Tests/GPU/RandomNumberGeneration/inputs Tests/GPU/RandomNumberGeneration/main.cpp Tests/Particles/ParallelContext/main.cpp Tests/Particles/Redistribute/main.cpp Tutorials/GPU/ParallelReduce/main.cpp commit 3c8dad86006c5ef256884733bff99b9806be46d4 Author: Andrew Myers Date: Mon Sep 21 13:51:30 2020 -0700 Remove redundant particle test (#1389) The same functionality is already tested in `Tests/Particles/Redistribute`. The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tests/Particles/GNUmakefile Tests/Particles/Make.package Tests/Particles/main.cpp Tests/Particles/test.py commit 1e35d0d50287bc32a02a94b03466a750c9e491d1 Author: Axel Huebl Date: Mon Sep 21 10:24:23 2020 -0700 CMake & DPC++: Avoid Flag Deduplication (#1388) ## Summary Avoid deduplication of `-mlong-double-64 -Xclang -mlong-double-64` into `-mlong-double-64 -Xclang`. Update the apt package name, which was changed by upstream for beta09. Refs.: - https://gitlab.kitware.com/cmake/cmake/-/issues/15826 - https://gitlab.kitware.com/cmake/cmake/-/merge_requests/1841 ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate .github/workflows/dependencies/dependencies_dpcpp.sh Tools/CMake/AMReXSYCL.cmake commit 1cec808bc2f814033350b09f01f4b64a9112f2cd Author: Weiqun Zhang Date: Mon Sep 21 08:33:10 2020 -0700 More on Gpu kernel fusing (#1332) ## Summary * Add Gpu::KernelInfo argument to ParallelFor to allow the user to indicate whether the kernel is an candidate for fusing. * For MFIter, if the local size is less or equal to 3, the fuse region is turned on and small kernels marked fusable will be fused. * Add launch macros for fusing. * Add fusing to a number of functions used by linear solvers. Note that there are a lot more amrex functions need to be updated for fusing. * Optimize reduction for bottom solve. * Consolidate memcpy in communication functions. * Option to use device memory in communication kernels for packing and unpacking buffers. But it's currently turned off because the performance was not improved in testing. In fact, it was worse than using pinned memory. But this might change in the future. So the option is kept. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuFuse.H Src/Base/AMReX_GpuFuse.cpp Src/Base/AMReX_GpuKernelInfo.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_Reduce.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 626b5f55c1c3d143e918f5e5e95cb231e497e896 Author: Weiqun Zhang Date: Mon Sep 21 08:29:39 2020 -0700 Make max GPU streams runtime parameter (#1386) ## Summary Add a new runtime parameter, amrex.max_gpu_streams. ## Additional background This can be used to work around a HIP compiler bug by setting `amrex.max_gpu_streams=1`. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 50e3994bb3cb3d4fdd1a680ae10176bc99dcd4d5 Author: Weiqun Zhang Date: Sun Sep 20 13:40:05 2020 -0700 Switch to `use mpi` from `include 'mpif.h'` (#1385) Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 816ef0b6d37580fc86c5c1119ecdfa7288cf83e5 Author: Weiqun Zhang Date: Sun Sep 20 13:31:59 2020 -0700 Fix a typo in Advection_F make file (#1384) ## Summary ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tutorials/FortranInterface/Advection_F/Source/Src_3d/Make.package commit 35a0533f8726e3741a5bc7cadc68d9e6926a6893 Author: Weiqun Zhang Date: Sun Sep 20 13:31:24 2020 -0700 Fix tensor solver with periodic boundaries (#1383) ## Summary Remove erroneous calls to EnforcePeriodicity. When coarse/fine boundary meets periodic boundary with fine grids form an L-shape, the uncovered fine ghost cell at the corner is actually "multi-valued". That is the cells with the same indices has different values in different boxes. That's why calling EnforcePeriodicity is erroneous. For CPU runs, this bug introduces deterministic errors, but the solver still converges. For GPU runs, this causes convergence issues too because EnforcePeriodicity is not deterministic when the values inside domain are not consistent. ## Additional background ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [x] changes answers in the test suite to more than roundoff level - [x] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 7c5cce3687a5b663355b1a367f0734760dcb4a0b Author: Andrew Myers Date: Fri Sep 18 17:15:53 2020 -0700 Remove old / obsolete / non-test tests. (#1381) Tests/Algoim/CMakeLists.txt Tests/Algoim/GNUmakefile Tests/Algoim/Make.package Tests/Algoim/main.cpp Tests/BBIOBenchmark/BBIOTest.cpp Tests/BBIOBenchmark/BBIOTestDriver.cpp Tests/BBIOBenchmark/CMakeLists.txt Tests/BBIOBenchmark/GNUmakefile Tests/BBIOBenchmark/README Tests/BaseFabTesting/CMakeLists.txt Tests/BaseFabTesting/GNUmakefile Tests/BaseFabTesting/Make.package Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp Tests/C_BaseLib/AMRPROFTEST_F.H Tests/C_BaseLib/AMRProfTestBL.cpp Tests/C_BaseLib/CMakeLists.txt Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/TPROFILER.F Tests/C_BaseLib/TPROFILER_F.H Tests/C_BaseLib/fillfab.f Tests/C_BaseLib/mt19937int.out Tests/C_BaseLib/t8BIT.cpp Tests/C_BaseLib/tBA.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tDM.cpp Tests/C_BaseLib/tDir.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tFillFab.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tMFcopy.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tRABcast.cpp Tests/C_BaseLib/tRan.cpp Tests/C_BaseLib/tUMap.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tVisMF2.cpp Tests/C_BaseLib/tread.cpp Tests/DataServicesTest0/CMakeLists.txt Tests/DataServicesTest0/DataServicesTest0.cpp Tests/DataServicesTest0/GNUmakefile Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile Tests/GPU/CudaGraphs/BuildingGraphs/Make.package Tests/GPU/CudaGraphs/BuildingGraphs/inputs_3d Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp Tests/GPU/CudaGraphs/BuildingGraphs/run.corigpu Tests/GPU/CudaGraphs/CrazyGraphs/GNUmakefile Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp Tests/GPU/CudaGraphs/CrazyGraphs/run.corigpu Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile Tests/GPU/CudaGraphs/GraphBoundary/Make.package Tests/GPU/CudaGraphs/GraphBoundary/Prob.H Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d Tests/GPU/CudaGraphs/GraphBoundary/main.cpp Tests/GPU/CudaGraphs/GraphBoundary/profile.sh Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu Tests/GPU/CudaGraphs/GraphBoundary/run.summit Tests/GPU/CudaGraphs/GraphInitTest/GNUmakefile Tests/GPU/CudaGraphs/GraphInitTest/Make.package Tests/GPU/CudaGraphs/GraphInitTest/inputs_3d Tests/GPU/CudaGraphs/GraphInitTest/main.cpp Tests/GPU/CudaGraphs/GraphReuseCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphReuseCopy/Make.package Tests/GPU/CudaGraphs/GraphReuseCopy/inputs_3d Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp Tests/GPU/CudaGraphs/GraphReuseCopy/run.corigpu Tests/GPU/CudaGraphs/GraphWithMemcpy/GNUmakefile Tests/GPU/CudaGraphs/GraphWithMemcpy/Make.package Tests/GPU/CudaGraphs/GraphWithMemcpy/inputs_3d Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp Tests/GPU/CudaGraphs/GraphWithMemcpy/run.corigpu Tests/GPU/CudaGraphs/Readme.txt Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile Tests/GPU/CuptiTest/Exec/CUDA/Make.package Tests/GPU/CuptiTest/Exec/CUDA/myfunc.H Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H Tests/GPU/CuptiTest/Make.CUPTI Tests/GPU/CuptiTest/Source/Make.package Tests/GPU/CuptiTest/Source/main.cpp Tests/GPU/Locking/GNUmakefile Tests/GPU/Locking/Make.package Tests/GPU/Locking/inputs Tests/GPU/Locking/main.cpp Tests/GPU/libamrex_CUDA/GNUmakefile Tests/GPU/libamrex_CUDA/README.md Tests/GPU/libamrex_CUDA/main.cpp Tests/IOBenchmark/GNUmakefile Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/README Tests/IOBenchmark/inputs Tests/IOBenchmark/inputs.dirname Tests/IOBenchmark/inputs.dss Tests/IOBenchmark/inputs.dssmf Tests/IOBenchmark/inputs.nft Tests/IOBenchmark/inputs.small Tests/MKDir/GNUmakefile Tests/MKDir/MKDir.cpp Tests/NoFort/GNUmakefile Tests/NoFort/Make.package Tests/NoFort/main.cpp Tests/PnetCDFBenchmark/GNUmakefile Tests/PnetCDFBenchmark/Make.package Tests/PnetCDFBenchmark/ReadMe Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.H Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp Tests/PnetCDFBenchmark/inputs Tests/PnetCDFBenchmark/main.cpp Tests/ProfTests/HeatEquation_EX1_C/Exec/GNUmakefile Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_2d Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_3d Tests/ProfTests/HeatEquation_EX1_C/Source/Make.package Tests/ProfTests/HeatEquation_EX1_C/Source/advance.cpp Tests/ProfTests/HeatEquation_EX1_C/Source/advance_2d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/advance_3d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/main.cpp Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc.H Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc_F.H Tests/ProfTests/ThirdParty/Exec/GNUmakefile Tests/ProfTests/ThirdParty/Exec/inputs_2d Tests/ProfTests/ThirdParty/Exec/inputs_3d Tests/ProfTests/ThirdParty/Source/Make.package Tests/ProfTests/ThirdParty/Source/advance.cpp Tests/ProfTests/ThirdParty/Source/advance_2d.f90 Tests/ProfTests/ThirdParty/Source/advance_3d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_2d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_3d.f90 Tests/ProfTests/ThirdParty/Source/main.cpp Tests/ProfTests/ThirdParty/Source/myfunc.H Tests/ProfTests/ThirdParty/Source/myfunc_F.H Tests/SinglePrecision/GNUmakefile Tests/SinglePrecision/Make.package Tests/SinglePrecision/main.cpp Tests/Slice/GNUmakefile Tests/Slice/Make.package Tests/Slice/inputs Tests/Slice/main.H Tests/Slice/main.cpp Tests/SliceWithInterp/inputs Tests/SliceWithInterp/main.cpp Tests/Stream/GNUmakefile Tests/Stream/Make.package Tests/Stream/inputs Tests/Stream/main.cpp Tests/ThirdPartyLib/GNUmakefile Tests/ThirdPartyLib/Readme Tests/ThirdPartyLib/bar.F90 Tests/ThirdPartyLib/foo.cpp Tests/ThirdPartyLib/main.c Tests/TypeCheck/GNUmakefile Tests/TypeCheck/Make.package Tests/TypeCheck/f.f90 Tests/TypeCheck/f_F.H Tests/Vectorization/GNUmakefile Tests/Vectorization/Make.package Tests/Vectorization/kc.H Tests/Vectorization/kc.cpp Tests/Vectorization/kdecl.H Tests/Vectorization/kf.F90 Tests/Vectorization/main.cpp commit 28a454d7ea1f696dd721834b9b4e668294bf50b5 Author: mic84 Date: Fri Sep 18 16:23:04 2020 -0700 CMake: enable testing via CTest. (#1362) .github/workflows/linux.yml CMakeLists.txt Tests/Algoim/CMakeLists.txt Tests/AsyncOut/multifab/CMakeLists.txt Tests/BBIOBenchmark/CMakeLists.txt Tests/BaseFabTesting/CMakeLists.txt Tests/CMakeLists.txt Tests/C_BaseLib/CMakeLists.txt Tests/DataServicesTest0/CMakeLists.txt Tests/FillBoundaryComparison/CMakeLists.txt Tests/Particles/NeighborParticles/CMakeLists.txt Tests/Particles/ParticleMesh/CMakeLists.txt Tests/Particles/ParticleReduce/CMakeLists.txt Tests/Particles/ParticleTransformations/CMakeLists.txt Tests/Particles/Redistribute/CMakeLists.txt Tests/complementIn/CMakeLists.txt commit 9831ee93eb844ce43a37c8b3af138cc57e893964 Author: Andrew Myers Date: Fri Sep 18 15:58:59 2020 -0700 Remove reliance on managed memory from AMReX_ParticleCommunication.H/.cpp (#1380) Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit eb2b7fd5419a4b2e89d32c6ec0ac8e7bfd59df69 Author: Andrew Myers Date: Fri Sep 18 10:25:48 2020 -0700 fix signed vs. unsigned issue in AMReX_ParticleCommunication.cpp (#1379) Src/Particle/AMReX_ParticleCommunication.cpp commit 6fbd2868a38396391260c0ac61f23c5eac5d6d6b Author: Weiqun Zhang Date: Fri Sep 18 07:24:18 2020 -0700 Fix #1375 (#1378) A Bug was introduced in #1375. The host vector should have an initial size. Src/Particle/AMReX_ParticleTile.H commit 6ce92531fd1fb5fce70506ddd214aacf0db06501 Author: Weiqun Zhang Date: Thu Sep 17 19:09:33 2020 -0700 DPC++ & HIP: NumberOfParticles on device (#1377) ## Summary For DPC++ and HIP, we have to run NumberOfParticles on device. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ParticleContainerI.H commit e4023270d871f6850f9fe8ff744745e7d74fdaac Author: Weiqun Zhang Date: Thu Sep 17 18:30:12 2020 -0700 Put static constexpr members back to ParticleTile (#1376) ## Summary They should not be removed in #1375. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ParticleTile.H commit 4b2f5fa1fc7d13c150a41f74ff33b5fbe4395bdf Author: Weiqun Zhang Date: Thu Sep 17 17:21:44 2020 -0700 Avoid accessing device memory directly on host (#1375) ## Summary ParticleLocator and ParticleTile contain vectors using device memory. To remove the dependency on unified memory we avoid accessing them directly on the host. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleTile.H commit 39f32bd4f9f6d9f0a9455f7f1790337a780a1e09 Author: Andrew Myers Date: Thu Sep 17 11:34:21 2020 -0700 Add explicit syncs to InitParticles in the Test routines. (#1374) The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tests/Particles/AsyncIO/main.cpp Tests/Particles/NeighborParticles/MDParticleContainer.cpp Tests/Particles/ParallelContext/main.cpp Tests/Particles/ParticleReduce/main.cpp Tests/Particles/ParticleTransformations/main.cpp Tests/Particles/Redistribute/main.cpp commit 3cf2461f97ba66b8da5d62cacf35b43ab6584b67 Author: Weiqun Zhang Date: Thu Sep 17 09:48:48 2020 -0700 User defined literals in DPC++ (#1366) It is now supported in beta09 with `-Xclang -mlong-double-64`. Src/Base/AMReX_REAL.H Tools/CMake/AMReXSYCL.cmake Tools/GNUMake/comps/dpcpp.mak commit 5a2d460801039b79a9d90ac2bf116c186d1220f9 Author: mic84 Date: Wed Sep 16 19:02:22 2020 -0700 GNUMake: remove unused define for HIP compilation (#1372) * GNUMake: remove unused AMREX_HIP_PLATFORM define * GNUMake: rename HIP_PLATFORM to HIP_COMPILER for consistency Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 59036167c676ae1acc31b18e061f99573af36111 Author: Axel Huebl Date: Wed Sep 16 17:09:11 2020 -0700 .gitignore: build/ (#1373) ## Summary besides our currently assumed temporary build directories, a temporar build/ directory is quite common in CMake (although discouraged to build inside the tree at all, but this is safe enough). ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate .gitignore commit ea27c4008901d88fa41af08592bbd2355f23f569 Author: Mark Meredith Date: Wed Sep 16 17:38:46 2020 -0400 Fix uninitialized compiler warnings for: xslope yslope zslope (#1371) ## Summary Getting compiler warnings when building MFiX-Exa file that includes `AMReX_EB_slopes_K.H` ## Additional background Building with GCC 7.5.0: ``` ../src/convection/mfix_slopes.cpp: In member function 'void mfix::mfix_compute_slopes(int, amrex::Real, amrex::MultiFab&, const amrex::Vector&, const amrex::Vector&, const amrex::Vector&, int, std::map, amrex::PODVector > >&)': ../src/convection/mfix_slopes.cpp:235:52: error: 'zslope' may be used uninitialized in this function [-Werror=maybe-uninitialized] zs_fab(i,j,k,slopes_comp+n) = eb_slopes[2]; ../src/convection/mfix_slopes.cpp:216:52: error: 'yslope' may be used uninitialized in this function [-Werror=maybe-uninitialized] ys_fab(i,j,k,slopes_comp+n) = eb_slopes[1]; ../src/convection/mfix_slopes.cpp:197:52: error: 'xslope' may be used uninitialized in this function [-Werror=maybe-uninitialized] xs_fab(i,j,k,slopes_comp+n) = eb_slopes[0]; ``` ## Checklist The proposed changes: - [X] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Co-authored-by: Mark Meredith Src/EB/AMReX_EB_slopes_K.H commit 7aacbd10c8b6b0cf463d04d3418783587090467f Author: mic84 Date: Tue Sep 15 17:41:31 2020 -0700 CMake: remove duplicate sources (#1370) Src/Base/CMakeLists.txt commit 940a9499bb7c5c4f1aa209d4e501d34e20eeafff Author: mic84 Date: Tue Sep 15 14:50:59 2020 -0700 CMake: re-organize tutorials (#1333) * CMake: begin refactoring tutorials * CMake: refactor Tutorials/Basic * CMake: setup_tutorials is now able to figure out include paths by itself * CMake: add optional arguments ot setup_tutorial * CMake: refactor Tutorials/Amr * CMake: refactor Tutorials/LinearSolvers * CMake: add tutorials in Tutorials/EB * Tutorials: change name of file for consistency with 2D case * CMake: refactor Tutorials/FortranInterface * CMake: refactor Tutorials/Particles * CMake: forgot to refactor Tutorials/LinearSolvers/NodeTensorLap/ * CMake: update CI * CMake: some clean-up * CMake: forgot to update the CI for win and mac * CMake: add missing F_interfaces sources to build set * CMake: 2D setup for tutorials * CMake: 1D setup for tutorials * CMake: EB is made avaialble only if DIM>1 * CMake: exclude MPI-only tutorials from build if ENABLE_MPI=OFF * CMake: some turotorials need Fortran enabled * CMake: exclude CUDA-unaware tutorials from CUDA builds * CMake: this should fix the Windows CI * CMake: add tutorials in Tutorials/ForkJoin * CMake: fix mispelled variable * CMAke: Particles/CellSortedParticles tutorial is not CUDA-ready * CMake: change naming scheme for tutorials target to avoid conflicts * CMake: add tutorials in Tutorials/Blueprint * CMake: replace option ENABLE_TUTORIALS with AMReX_BUILD_TUTORIALS * Update Tools/CMake/AMReX_Options.cmake * Update Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt * CMake: this is not needed anymore * CMake: must use setup_target_for_cuda_compilation * CMake: fix build setup for Particles/ElectromagneticPIC * CMake: add tutorials in Tutorials/GPU * Fix EBCNS particles tutorials. The syntax for reductions has changed since itwas written. * CMake: improvements to setup_tutorials() * CMake: document how to build tutorials Co-authored-by: Axel Huebl .github/workflows/linux.yml .github/workflows/macos.yml .github/workflows/windows.yml CMakeLists.txt Docs/sphinx_documentation/source/BuildingAMReX.rst Src/F_Interfaces/CMakeLists.txt Tools/CMake/AMReX_Options.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_CF/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_F/CMakeLists.txt Tutorials/Basic/HeatEquation_EX2_C/CMakeLists.txt Tutorials/Basic/HeatEquation_EX2_CF/CMakeLists.txt Tutorials/Basic/HeatEquation_EX3_C/CMakeLists.txt Tutorials/Basic/HelloWorld_C/CMakeLists.txt Tutorials/Basic/HelloWorld_F/CMakeLists.txt Tutorials/Basic/PrefixSum_MultiFab/CMakeLists.txt Tutorials/Basic/main_C/CMakeLists.txt Tutorials/Basic/main_F/CMakeLists.txt Tutorials/Blueprint/AssignMultiLevelDensity/CMakeLists.txt Tutorials/Blueprint/CellSortedParticles/CMakeLists.txt Tutorials/Blueprint/HeatEquation_EX1_C/CMakeLists.txt Tutorials/CMakeLists.txt Tutorials/EB/CNS/CMakeLists.txt Tutorials/EB/Donut/CMakeLists.txt Tutorials/EB/GeometryGeneration/CMakeLists.txt Tutorials/EB/LevelSet/CMakeLists.txt Tutorials/EB/MacProj/CMakeLists.txt Tutorials/EB/Poisson/CMakeLists.txt Tutorials/ForkJoin/MLMG/CMakeLists.txt Tutorials/ForkJoin/Simple/CMakeLists.txt Tutorials/FortranInterface/Advection_F/CMakeLists.txt Tutorials/FortranInterface/Advection_F/Source/Src_3d/Make.package Tutorials/FortranInterface/Advection_F/Source/Src_3d/advect_3d_mod.F90 Tutorials/FortranInterface/Advection_octree_F/CMakeLists.txt Tutorials/FortranInterface/Advection_octree_F2/CMakeLists.txt Tutorials/GPU/CNS/CMakeLists.txt Tutorials/GPU/EBCNS/CMakeLists.txt Tutorials/GPU/EBCNS/Source/CNS.cpp Tutorials/GPU/EBCNS/Source/CNS_K.H Tutorials/GPU/Launch/CMakeLists.txt Tutorials/GPU/ParallelReduce/CMakeLists.txt Tutorials/GPU/ParallelScan/CMakeLists.txt Tutorials/LinearSolvers/ABecLaplacian_C/CMakeLists.txt Tutorials/LinearSolvers/ABecLaplacian_F/CMakeLists.txt Tutorials/LinearSolvers/MAC_Projection_EB/CMakeLists.txt Tutorials/LinearSolvers/MultiComponent/CMakeLists.txt Tutorials/LinearSolvers/NodalPoisson/CMakeLists.txt Tutorials/LinearSolvers/Nodal_Projection_EB/CMakeLists.txt Tutorials/LinearSolvers/NodeTensorLap/CMakeLists.txt Tutorials/Particles/CellSortedParticles/CMakeLists.txt Tutorials/Particles/ElectromagneticPIC/CMakeLists.txt Tutorials/Particles/ElectrostaticPIC/CMakeLists.txt Tutorials/Particles/NeighborList/CMakeLists.txt commit a2284e9368e079dd4030ec9e0c41512f191848cf Author: Andrew Myers Date: Tue Sep 15 08:31:16 2020 -0700 Reorder struct (#1368) This reverts a breaking change introduced in 1337. The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particle.H commit 8929086e08058ac61d096414363341485afec34b Author: Andrew Myers Date: Mon Sep 14 08:30:11 2020 -0700 Implement Particle in a way that does not involve UB. (#1337) Src/Particle/AMReX_Particle.H Tests/Particles/Redistribute/main.cpp commit 6fa3cc67ed0997e12877cdf3b5baf6d594d1c538 Author: WeiqunZhang Date: Mon Sep 14 07:56:41 2020 -0700 Updates for oneAPI beta09 (#1365) Src/Base/AMReX_GpuQualifiers.H Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/dpcpp.mak commit 82339abdc742453d076d0bfeca7d9ed4e479eb0c Author: WeiqunZhang Date: Sat Sep 12 18:24:06 2020 -0700 Revert "DPCPP Beta09: Package Broken (#1361)" (#1364) This reverts commit 198a4958cc2cbfd5a7e1d639d5ff750489104df6. The workaround does not work with #1363 because of mkl. We have now temporarily removed dpc++ from the list of required checks. So we can revert this change now. Once the packages are fixed, we will make the check require again. .github/workflows/linux.yml commit 5175acf9efc2e8aeb37fc581480aba034a1fbb3f Author: Candace Gilet Date: Fri Sep 11 12:55:43 2020 -0400 amrex::EB_average_down(): Fix indexing error. (#1360) Src/EB/AMReX_EBMultiFabUtil.cpp commit 198a4958cc2cbfd5a7e1d639d5ff750489104df6 Author: Axel Huebl Date: Fri Sep 11 07:55:44 2020 -0700 DPCPP Beta09: Package Broken (#1361) ## Summary The Ubuntu packages seem to forget the `env/var.sh` activation scripts for the compiler packages for beta09. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate .github/workflows/linux.yml commit de4aab4f20ebffa862a0f9c29daa2717d8abcbd3 Author: Andrew Myers Date: Thu Sep 10 17:00:08 2020 -0700 only add one copy of the ghost particle regardless of how many isects we have (#1359) Src/Particle/AMReX_ParticleContainerI.H commit fe4c98e749e40c65f03046a3efc9df5f948ced69 Author: WeiqunZhang Date: Thu Sep 10 13:47:36 2020 -0700 SetBoxArray (#1310) If SetBoxArray is called in Level 0's MakeNewLevelFromScrach, the set BoxArray will be used. This makes it consistent with the behavior of SetDistributionMap. Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit b1fcd62bd7f98fce1be98313307697d61320687d Author: WeiqunZhang Date: Thu Sep 10 13:46:42 2020 -0700 Remove duplicated alias. (#1311) Src/Base/AMReX_GpuAllocators.H commit a1eafe7ab57324e7b574ab5b636ba0fc98ea7635 Author: asalmgren Date: Wed Sep 9 19:36:15 2020 -0700 Logic wasn't quite right for the calculation in amrex_calc_slopes_ext… (#1358) …dir_eb routine of slope not seeing EB cells that is adjacent to and tangential to ext_dir boundary ## Summary Previous commit of AMReX_EB_slopes.cpp had messed up the logic for calcluation of the slope in amrex_calc_slopes_extdir_eb routine in cells not seeing any EB but next to ext_dir bondary and tangential to boundary ## Additional background ## Checklist The proposed changes: - [X] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/EB/AMReX_EB_slopes_K.H commit 27c21a0c56623022a9b012c0ec2ec837e4971366 Author: WeiqunZhang Date: Wed Sep 9 19:03:25 2020 -0700 Gpu::single_task (#1357) Add a new version that uses the current default stream. Src/Base/AMReX_GpuLaunchFunctsG.H commit 6b032b4188e77e2b089e21c74586f5a2e6c1e5d2 Author: asalmgren Date: Wed Sep 9 08:48:34 2020 -0700 Add non-EB slopes and extend the generality of EB slope routines in 2D and 3D (#1350) ## Summary This commit adds a file with the non-EB slope routines, and updates the EB-aware routines to correctly compute slopes where an EB boundary intersects an hoextrap/extdir face, e.g. inflow. This does not assume the geometry intersects without a slant. This has been tested in 2D and 3D (with a function f(x,y,z) = 10 + 5 x + 2 y + 3 z specified at cell centroids) and with slanted cylinders intersecting inflow in each coordinate direction. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_Slopes_K.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_EB_slopes_K.H commit 7cc452c65185efbb07e6503cb79206d10c0dc35c Author: Axel Huebl Date: Wed Sep 9 08:40:32 2020 -0700 Async IO: Check Runtime Threading (#1351) ## Summary Even if `AMREX_MPI_THREAD_MULTIPLE` is defined at compile time, applications might provide their own MPI init routines and/or MPI implementations, runtime arguments or environment arguments can influence the actually provided MPI thread safety level at runtime. Therefore, we need to check the MPI thread safety level again at runtime where we require a certain minimum. ## Additional background WarpX PR: https://github.com/ECP-WarpX/WarpX/pull/1298 ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_AsyncOut.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit f542f98d72c2cd651a0eae4d092c12239976db3f Author: Axel Huebl Date: Wed Sep 9 08:31:53 2020 -0700 Docs: MPI_THREAD_MULTIPLE (#1355) ## Summary Add GNUmake and CMake docs about control of `MPI_THREAD_MULTIPLE`. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [x] are described in the proposed changes to the AMReX documentation, if appropriate Docs/sphinx_documentation/source/BuildingAMReX.rst commit a9aa65cc3841375b762324fe79516f5cfdee7364 Author: Andrew Myers Date: Tue Sep 8 17:17:57 2020 -0700 also use atomics in the particle_dx != dx case (#1356) Src/Particle/AMReX_Particle_mod_K.H commit c59619f5ff32a78494b0b2328914fe108254844c Author: Andrew Myers Date: Tue Sep 8 15:53:07 2020 -0700 Fix EM pic tutorial - the syntax for reductions has changed since it was written. (#1354) Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit 96d1381e1f20adf48df84ff4f16601c887dac239 Author: WeiqunZhang Date: Tue Sep 8 12:34:35 2020 -0700 USE_EB (#1349) Changes to make AMR codes compiled with EB but not building any Geometry work as if it is all regular. Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil_I.H commit a2aebd24854b5d375899a44156603f4bc9c85a64 Author: Andrew Myers Date: Tue Sep 8 10:49:03 2020 -0700 Always recompute offset, dx, and inv_dx, and the roundoff_domain when either the ProbDomain or Domain is changed. (#1353) Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit cd075c81967aca29a17a52af3f41310a8426b121 Author: Axel Huebl Date: Tue Sep 8 08:13:49 2020 -0700 Fallthrough: ICC Warning (#1352) ## Summary `gnu::fallthrough` is not defined with ICC 20.2.1.20200602 and throws a warning at compile-time in ParamsParse. ## Additional background ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_Extension.H commit 9ec96e6f9b286ccd26a61a910f0fb97a08a377fe Author: Brian Friesen Date: Sun Sep 6 09:19:33 2020 -0700 bcf/hpcsdk-updates (#1348) ## Summary This PR fixes two wrong compile/link flags in the NVIDIA HPC SDK which are documented in #1347. ## Additional background The wrong/missing flags are documented in #1347. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/comps/hpcsdk.mak commit 31421f70c3cf73ae2cc9aaa4e7e024f554a69e20 Author: asalmgren Date: Fri Sep 4 17:35:28 2020 -0700 Add slopes routines (#1346) * Add the calculation of slopes using a least squares fit when the values in each cell are defined to be at cell centroids. * Add to the description of each routine * EB_SLOPES_K_H --> AMREX_EB_SLOPES_K_H Src/EB/AMReX_EB_slopes_K.H Src/EB/CMakeLists.txt Src/EB/Make.package commit 7e0d7196dd1e8ac91625030622b360cbcafa21ce Author: WeiqunZhang Date: Fri Sep 4 17:27:40 2020 -0700 No inline for assertion (#1345) It is recommended that assertion calls on device are not inlined because of performance issues. Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Extension.H Src/Base/AMReX_GpuDevice.cpp commit a7166b92dc0b58b1ed96110ed2a43341513dcdd3 Author: WeiqunZhang Date: Fri Sep 4 16:21:32 2020 -0700 Fix mkconfig.py (#1344) ## Summary In the script, Intel, Cray and PGI should be quoted as string. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/libamrex/mkconfig.py commit de8a23ac50146b732aeaadf874ead2cae93753c8 Author: Andrew Myers Date: Fri Sep 4 14:43:29 2020 -0700 Add -Xcudafe --diag_suppress=esa_on_defaulted_function_ignored to suppress spurious warnings from nvcc. (#1342) Tools/CMake/AMReX_SetupCUDA.cmake Tools/GNUMake/comps/nvcc.mak commit d8747f753f9f5524aba04e1a70fee3d1665654bd Author: Axel Huebl Date: Fri Sep 4 13:39:44 2020 -0700 CI: Move DPC++ dependencies (#1336) Move install script into unified location. ## Summary ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate .github/workflows/dependencies/dependencies_dpcpp.sh .github/workflows/linux.yml commit b9e746e447e896aa0df049845d573e11f7db10ab Author: Rajeev Jain Date: Fri Sep 4 15:36:46 2020 -0500 Update AMReX_multifab_mod.F90 (#1339) #1338 The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 2ae64e7f472e81000c25ca97eb7587f4d43d0960 Author: Andrew Myers Date: Fri Sep 4 13:35:18 2020 -0700 PR 1324 did not account for runtime-added components (#1341) The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ParticleContainerI.H commit e34912f3bc26d532fa9c3ee608ec5e50c4ce26f9 Author: WeiqunZhang Date: Thu Sep 3 10:29:23 2020 -0700 update CHANGES for 20.09 (#1334) CHANGES commit c7cef052978eb509972a8f2c6b43771f22cf4fff Author: Andrew Myers Date: Wed Sep 2 19:11:10 2020 -0700 Add support for extended particle range to the Fortran interfaces (#1331) * add support for extended particle range to the Fortran interfaces * replace c_long -> amrex_long for Windows support Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Prob_2d.f90 Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Prob_3d.f90 commit 64e772795b9f9b09db11e4fbdf30552331850965 Author: WeiqunZhang Date: Wed Sep 2 16:43:45 2020 -0700 Avoid divide-by-zero in 2D EB (#1319) Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp commit 3d65510d12ef10fe2a7d4b0d0bf9164615689597 Author: WeiqunZhang Date: Wed Sep 2 16:34:45 2020 -0700 EB smoother (#1330) * EB smoother In #1327, the interpolation coefficients for EB stencil in cell-centered linear solvers were fixed. Here, the EB smoother is also updated to use the correct coefficients. * fix order in interpolation coefficient * Reduce max order to 2 for cut cells. * If using hypre or petsc for EB solver, reduce order to 2. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 4128f25ffa247802ab93e8fae7133b80a5e3d59f Author: Roberto Porcu <53792251+rporcu@users.noreply.github.com> Date: Wed Sep 2 14:21:45 2020 -0400 Gpu synchronization is needed to avoid deadlock situations (#1328) Src/Particle/AMReX_ParticleCommunication.H commit 65f25c7db1ba2f88654cff8e91d24cf3ff45b075 Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com> Date: Tue Sep 1 17:26:10 2020 -0700 Fix bug to correctly compute the interp_coeff array (#1327) Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H commit d5e29d965070a36c6e232ef114d1f5bd88b701e3 Author: WeiqunZhang Date: Tue Sep 1 17:02:51 2020 -0700 EB extend_domain_face (#1321) ## Summary When there are a lot of ghost cells, extend_domain_face option could fail in the current development branch. This PR fixes it. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Docs/sphinx_documentation/source/Basics.rst Src/EB/AMReX_EB2_Level.H commit e4444fa80264ae716f9cadd4d7e8847fcf3d833b Author: Andrew Myers Date: Tue Sep 1 17:02:26 2020 -0700 Add explicit default copy ctors for ParticleIDWrapper and ParticleCPUWrapper (#1323) This should fix a warning with DPC++. Src/Particle/AMReX_Particle.H commit 98b73e64bfcc839ba168b3e423d4d2f8e4914c28 Author: Klaus Date: Tue Sep 1 19:01:42 2020 -0500 Add parameter that stores OpenMP support version (#1325) ## Summary Add a parameter to `AMReX_omp_mod` that can be used by Fortran code to check whether AMReX was built with OpenMP support, and, if yes, what the version number (_OPENMP) was at the time AMReX was compiled. ## Additional background The name of the parameter is `amrex_omp_support`, the type is (default kind) integer. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new **(mini)**-capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Co-authored-by: Klaus Weide <> Src/Base/AMReX_omp_mod.F90 commit 1ffbfc1caab2dae19db0e7fa27202938300f9ced Author: Andrew Myers Date: Tue Sep 1 17:00:43 2020 -0700 Use Long for maxnextid in plot and checkfiles to accomodate the expanded range. (#1326) The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ParticleHDF5.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_WriteBinaryParticleData.H commit 57d5bfeb97b03ce037714a08260d78660b6774be Author: WeiqunZhang Date: Tue Sep 1 16:46:23 2020 -0700 ParticleContainer: communicate_real_comp and commuicate_int_comp (#1324) Having both host and device copies of these two so that we do not rely on unified memory. Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit b7479f0a662a9b256f1e42d1cd3c628457a53c1c Author: mic84 Date: Tue Sep 1 11:15:35 2020 -0700 CMake: re-write genex evaluation functions (#1287) * CMake: start adding genex evaluation functions * CMake: more genex evaluation functions * CMake: add support for more genex types * CMake: finalize new function to evaluate genex * CMake: slighly change the interface of function eval_genex * CMake: deploy eval_genex. * CMake: set MSVC required flags using regex * CMake: final improvements to new genex evaluation helpers Tools/CMake/AMReXBuildInfo.cmake Tools/CMake/AMReXGenexHelpers.cmake Tools/CMake/AMReXInstallHelpers.cmake Tools/CMake/AMReXTargetHelpers.cmake Tools/CMake/AMReXTypecheck.cmake Tools/CMake/AMReX_Config.cmake commit 6dd02ab17f06478d7fbea8e91ba274f932004801 Author: Andrew Myers Date: Thu Aug 27 19:08:59 2020 -0700 Need another overload of the operator= for ParticleIDWrapper and ParticleCPUWrapper. (#1317) The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_Particle.H commit 5e9dbc1dd2fb8675de53bc42bd8b3d13f9eacb88 Author: Andrew Myers Date: Thu Aug 27 11:12:18 2020 -0700 Extend the number of unique particles per cpu we can have at once. (#1315) Currently, we use two signed integers to store id numbers for each particle as well as the rank it was generated on. This allows unique combinations of 'id', and 'cpu' numbers to be generated without any communication between ranks. However, this does waste some space, since it's unlikely that 2**31-1 MPI ranks will be used any time soon, while the same limit for the id has actually been overflowed in real-world WarpX simulations. To address this, in this PR, we still use 64 bits to represent the combination of (id, cpu), but we devote 40 bits to the id and only 24 to the cpu. This allows ~0.5 trillion unique particles on each of 16.7 million MPI ranks, which should be good enough for the foreseeable future. The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleContainerI.H commit d48f68f1a641084009e597d955ce3036d36b1755 Author: WeiqunZhang Date: Wed Aug 26 09:00:42 2020 -0700 Add ParmParse parameters to Tutorials/GPU/Launch (#1314) Tutorials/GPU/Launch/main.cpp commit 655f10afbc68b5c4279d2ca78c7add8b449f71e4 Author: WeiqunZhang Date: Tue Aug 25 15:57:40 2020 -0700 HIP: printf works now on device (#1312) ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_GpuPrint.H commit 02530bc8a600e2a3589b875208f372dd2e462a31 Author: Klaus Date: Tue Aug 25 15:44:05 2020 -0500 Add get_pmap method to amrex_distromap (Fortran) (#1307) ## Summary Add a new method to the `amrex_distromap` type in F_Interfaces. `get_pmap` fills a caller-owned array of PEs. Changes to make this more elegant are welcome. ## Additional background We need something like this in order to actually look into a distribution mapping computed by AMReX from Fortran code. (Currently this functionality is desired for Implementing a parallel restart capability from FLASH checkpoint files in FLASH.) ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Co-authored-by: Klaus Weide <> Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_mod.F90 commit 7b72e38bbbe63d2039a5e0ef7a4833792c99beff Author: kngott <30483578+kngott@users.noreply.github.com> Date: Tue Aug 25 12:04:39 2020 -0700 Nsight documentation fix. (#1309) * Fix Nsight docs. * Missing syntax. Docs/sphinx_documentation/source/External_Profiling_Tools.rst commit 51c4a990b42e37d84cc0c2b8055403d351febbb2 Author: Klaus Date: Tue Aug 25 12:25:42 2020 -0500 Fix instruction for local development branch (#1305) ## Summary Just a simple one-word doc change ## Additional background I tried to follow instructions in `CONTRIBUTING.md` and found that the `git pull` command as documented before this change resulted in an error message. ## Checklist The proposed changes: - [x] fix a bug in AMReX documentation Co-authored-by: Klaus Weide <> CONTRIBUTING.md commit a34e8e42d52b7725552ea97e5e089a90b96833cc Author: WeiqunZhang Date: Mon Aug 24 19:22:19 2020 -0700 Modify the use of HOST and HOSTNAME in make system (#1303) ## Summary PR #1275 fixed a bug in the use of `HOST` and `HOSTNAME` in the make system. However, the fix broke on Summit because `HOSTNAME` on Summit login nodes is set to something like `login1`. We now set `host_name` to `hostname -f` and `host_name_short` to `hostname -s` command, which is the behavior before the fix in #1275. We add a new make variable `host_name_env` that is set to `HOSTNAME` and `HOST` from the environment and use it for tulip. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/Make.machines commit e82080e322f238435f925da35fb8bae36365269d Author: Marc Day Date: Mon Aug 24 18:00:46 2020 -0700 Move declaration of Array4 object (#1302) ## Summary The autogen function for refinement tagging on physical box doesn't make use of a field, but the controller was trying to make an Array4 using the field that doesn't exist in this case. This fix moves the declaration down into a place where the data is guaranteed to exist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/AmrCore/AMReX_ErrorList.cpp commit 21269eff092d0a03aff9269b1200c0e408fde90e Author: Andrew Myers Date: Mon Aug 24 12:31:26 2020 -0700 Remove early exit for the 1 box case in RedistributeGPU. (#1301) This early exit had a bug in that it did not properly remove invalid particles. The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit bb831b49bbb3b853a18ee0e16d955aafe251da7d Author: WeiqunZhang Date: Sat Aug 22 21:04:40 2020 -0700 add Scan::InclusiveSum and ExclusiveSum for CPU (#1299) ## Summary Add Scan::InclusiveSum and ExclusiveSum for CPU to avoid ifdef. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_Scan.H commit 91f387dad9f57dfa884b4e5d03b88ff18f7b8c12 Author: WeiqunZhang Date: Sat Aug 22 16:00:51 2020 -0700 Turn on AsyncOut by default for HIP (#1298) ## Summary Currently for HIP, The_Arena allocates device memory. We turn on AsyncOut by default so that we can write plotfiles and VisMF files. In the long term, we should also fix VisMF::Write so that it can work with device memory. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_AsyncOut.cpp commit ba556dfe28afaa6704ea049f8200a8b53cffd888 Author: mxxw Date: Sat Aug 22 09:29:21 2020 -0700 removed AMREX_NOEXCEPT from main.cpp:L139 to avoid 'error: expected b… (#1297) removed AMREX_NOEXCEPT from main.cpp:L139 to avoid 'error: expected body of lambda expression' ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tutorials/GPU/ParallelReduce/main.cpp commit ab300111b705486f10782f1966020907d9f66b66 Author: jmsexton03 Date: Fri Aug 21 14:58:25 2020 -0400 Add check for empty probin_file in Amr::restart (#1295) ## Summary This adds the same empty check in Amr::restart that is used in Amr::InitializeInit ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Amr/AMReX_Amr.cpp commit a70adecd122ef1a4441cabd0f6356f53389e606b Author: mic84 Date: Fri Aug 21 11:33:50 2020 -0700 CMake: fix typo in source file name (#1296) Tutorials/Basic/HeatEquation_EX1_F/CMakeLists.txt commit 373cb8ac3143e1252ccd9b181280d355e9399f8a Author: WeiqunZhang Date: Fri Aug 21 08:06:10 2020 -0700 Fix a few warnings (#1293) Src/Base/AMReX_FBI.H Src/Base/AMReX_GpuPrint.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_Reduce.H Src/Particle/AMReX_ParticleContainerI.H commit 1aef797d0dd5a701c696d02165237c2c8e39771c Author: WeiqunZhang Date: Thu Aug 20 20:19:30 2020 -0700 Extern HIP device function (#1294) ## Summary We now need to use __attribute__((weak)) for extern HIP device function, otherwise we get undefined hidden symbol error. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_GpuQualifiers.H commit ce5e0d4bf4b27a88fc3eb6a2dab137b6b25e2bbb Author: jmsexton03 Date: Thu Aug 20 23:19:02 2020 -0400 Update Sundials interface, documentation, and build to be version agnostic (#1289) ## Summary Updates the make system to use SUNDIALS_ROOT and USE_SUNDIALS Updates the documentation regarding sundials and tutorials Removes some CVODE/SUNDIALS tutorials This will require applications to update their make variables ## Additional background Co-authored-by: Balos, Cody Joe ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [x] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Co-authored-by: Balos, Cody Joe Co-authored-by: Michele Rosso Docs/sphinx_documentation/source/CVODE_top.rst Docs/sphinx_documentation/source/External_Frameworks_Chapter.rst Docs/sphinx_documentation/source/SUNDIALS.rst Docs/sphinx_documentation/source/SUNDIALS3.rst Docs/sphinx_documentation/source/SUNDIALS_CVODE.rst Docs/sphinx_documentation/source/SUNDIALS_top.rst Docs/sphinx_tutorials/source/CVODE_Tutorial.rst Docs/sphinx_tutorials/source/SUNDIALS_Tutorial.rst Src/CMakeLists.txt Src/Extern/SUNDIALS/CMakeLists.txt Src/Extern/SUNDIALS/Make.package Src/Extern/SUNDIALS/arkode_interface.f90 Src/Extern/SUNDIALS/cvode_interface.f90 Src/Extern/SUNDIALS3/CMakeLists.txt Src/Extern/SUNDIALS3/Make.package Src/Extern/SUNDIALS3/arkode_interface.f90 Src/Extern/SUNDIALS3/cvode_interface.f90 Src/Extern/SUNDIALS3/farkode.f90 Src/Extern/SUNDIALS3/fcvode.f90 Src/Extern/SUNDIALS3/fnvector_serial.f90 Src/Extern/SUNDIALS3/fnvector_serial_fprefix.f90 Src/Extern/SUNDIALS3/fsunlinsol_dense.f90 Src/Extern/SUNDIALS3/fsunmat_dense.f90 Src/Extern/SUNDIALS4/CMakeLists.txt Src/Extern/SUNDIALS4/Make.package Src/Extern/SUNDIALS4/arkode_interface.f90 Src/Extern/SUNDIALS4/cvode_interface.f90 Src/Extern/SUNDIALS4/farkode_arkstep_mod.f90 Src/Extern/SUNDIALS4/farkode_mod.f90 Src/Extern/SUNDIALS4/fcvode_mod.f90 Src/Extern/SUNDIALS4/fnvector_mod.f90 Src/Extern/SUNDIALS4/fnvector_serial_mod.f90 Src/Extern/SUNDIALS4/fsundials_types_mod.f90 Src/Extern/SUNDIALS4/fsunlinsol_dense_mod.f90 Src/Extern/SUNDIALS4/fsunlinsol_mod.f90 Src/Extern/SUNDIALS4/fsunmatrix_dense_mod.f90 Src/Extern/SUNDIALS4/fsunmatrix_mod.f90 Tools/CMake/AMReXThirdPartyLibraries.cmake Tools/CMake/FindSUNDIALS.cmake Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.sundials Tools/GNUMake/packages/Make.sundials3 Tools/GNUMake/packages/Make.sundials4 Tutorials/CVODE/EX1_F/GNUmakefile Tutorials/CVODE/EX1_F/Make.package Tutorials/CVODE/EX1_F/inputs Tutorials/CVODE/EX1_F/integrate_ode.f90 Tutorials/CVODE/EX1_F/main.cpp Tutorials/CVODE/EX1_F/myfunc_F.H Tutorials/CVODE/EX1_F/ode_mod.f90 Tutorials/CVODE/EX2_F/GNUmakefile Tutorials/CVODE/EX2_F/Make.package Tutorials/CVODE/EX2_F/inputs Tutorials/CVODE/EX2_F/integrate_ode_no_jac.f90 Tutorials/CVODE/EX2_F/integrate_ode_with_jac.f90 Tutorials/CVODE/EX2_F/main.cpp Tutorials/CVODE/EX2_F/myfunc_F.H Tutorials/CVODE/EX2_F/ode_mod.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX1/CMakeLists.txt Tutorials/CVODE/SUNDIALS3_finterface/EX1/main.cpp Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/ark_analytic_fp.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/cv_analytic_fp.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/cv_analytic_fp.out Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.out Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.out Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.out Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/GNUmakefile Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/Make.package Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/ark_analytic_f2003.f90 Tutorials/SUNDIALS/EX-CUSOLVER/GNUmakefile Tutorials/SUNDIALS/EX-CUSOLVER/Make.CVODE Tutorials/SUNDIALS/EX-CUSOLVER/Make.package Tutorials/SUNDIALS/EX-CUSOLVER/README.md Tutorials/SUNDIALS/EX-CUSOLVER/extern_probin.template Tutorials/SUNDIALS/EX-CUSOLVER/inputs Tutorials/SUNDIALS/EX-CUSOLVER/inputs_128 Tutorials/SUNDIALS/EX-CUSOLVER/inputs_256 Tutorials/SUNDIALS/EX-CUSOLVER/inputs_32 Tutorials/SUNDIALS/EX-CUSOLVER/inputs_64 Tutorials/SUNDIALS/EX-CUSOLVER/main.cpp Tutorials/SUNDIALS/EX-CUSOLVER/make_cuda.sh Tutorials/SUNDIALS/EX-CUSOLVER/make_cuda_cusolver.sh Tutorials/SUNDIALS/EX-CUSOLVER/make_serial.sh Tutorials/SUNDIALS/EX-CUSOLVER/react_cuda.cpp Tutorials/SUNDIALS/EX-CUSOLVER/react_cuda_cusolver.cpp Tutorials/SUNDIALS/EX-CUSOLVER/react_serial.cpp Tutorials/SUNDIALS/EX-CUSOLVER/react_system.F90 Tutorials/SUNDIALS/EX-CUSOLVER/react_utils.F90 Tutorials/SUNDIALS/EX-CUSOLVER/test_react.H Tutorials/SUNDIALS/EX-CUSOLVER/test_react_F.H Tutorials/SUNDIALS/EX1_C/CMakeLists.txt Tutorials/SUNDIALS/EX1_C/GNUmakefile Tutorials/SUNDIALS/EX1_C/Make.package Tutorials/SUNDIALS/EX1_C/SetIC.f90 Tutorials/SUNDIALS/EX1_C/inputs Tutorials/SUNDIALS/EX1_C/inputs_2box Tutorials/SUNDIALS/EX1_C/inputs_non_vectorized Tutorials/SUNDIALS/EX1_C/main.cpp Tutorials/SUNDIALS/EX1_C/myfunc_F.H Tutorials/SUNDIALS/EX1_CUDA/GNUmakefile Tutorials/SUNDIALS/EX1_CUDA/Make.package Tutorials/SUNDIALS/EX1_CUDA/SetIC.f90 Tutorials/SUNDIALS/EX1_CUDA/inputs Tutorials/SUNDIALS/EX1_CUDA/main.cpp Tutorials/SUNDIALS/EX1_CUDA/myfunc_F.H Tutorials/SUNDIALS/EX1_CUDA/ode_mod.f90 Tutorials/SUNDIALS/EX1_F/GNUmakefile Tutorials/SUNDIALS/EX1_F/Make.package Tutorials/SUNDIALS/EX1_F/inputs Tutorials/SUNDIALS/EX1_F/integrate_ode.f90 Tutorials/SUNDIALS/EX1_F/main.cpp Tutorials/SUNDIALS/EX1_F/myfunc_F.H Tutorials/SUNDIALS/EX1_F/ode_mod.f90 Tutorials/SUNDIALS/EX2_F/GNUmakefile Tutorials/SUNDIALS/EX2_F/Make.package Tutorials/SUNDIALS/EX2_F/inputs Tutorials/SUNDIALS/EX2_F/integrate_ode_no_jac.f90 Tutorials/SUNDIALS/EX2_F/integrate_ode_with_jac.f90 Tutorials/SUNDIALS/EX2_F/main.cpp Tutorials/SUNDIALS/EX2_F/myfunc_F.H Tutorials/SUNDIALS/EX2_F/ode_mod.f90 commit 418f90d6f6620008edc0385ce6f487cb555ae1fb Author: Candace Gilet Date: Thu Aug 20 21:15:56 2020 -0400 Fix typo (#1292) ## Summary Fix a typo in AMReX_extrapolater_3D_K.H ## Additional background ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Amr/AMReX_extrapolater_3D_K.H commit f38919982f59b25f49b9b2a4c948f20677f144e7 Author: asalmgren Date: Thu Aug 20 16:26:04 2020 -0700 Un-comment lines which should not have been commented (#1291) ## Summary ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tests/LinearSolvers/EBTensor/MyTest.cpp commit df022f23e57792da09feed9b9db74dc60e6d4847 Author: WeiqunZhang Date: Thu Aug 20 14:14:12 2020 -0700 Skip MPI checking when doing make clean etc. (#1290) ## Summary When we do `make clean`, `make realclean` etc., we do not need to check MPI. This can avoid unnecessary errors. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/sites/Make.unknown commit 924ec34c858335848b9514590f41d221990f209d Author: kngott <30483578+kngott@users.noreply.github.com> Date: Thu Aug 20 13:55:11 2020 -0700 Get rid of incorrect comment. (#1288) ## Summary Just deleting this old, spurious comment before I forget about it. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/Make.defs commit 7c35abbcdf3882d0b83c5746a23c5f2eca24a2dc Author: WeiqunZhang Date: Thu Aug 20 10:20:27 2020 -0700 Physical locations in pltofiles (#1286) Normally, the integer index of a Geometry's Domain starts with 0. But if not, the physical location of boxes stored in plotfiles is incorrect, because the RealBox constructor we use takes the physical location of index 0. So we need to shift the box before using RealBox. Src/Base/AMReX_PlotFileUtil.cpp commit 0748356f06fadf2f6caef6542f48d15c3e9391bc Author: WeiqunZhang Date: Thu Aug 20 08:20:26 2020 -0700 Misc. updates for ROCm 3.6.0 (#1285) ## Summary ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Dim3.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_GpuAssert.H Src/Base/AMReX_GpuComplex.H Src/Base/AMReX_GpuPrint.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Math.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_PlotFileDataImpl.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_RealVect.H Tools/GNUMake/comps/hip.mak Tutorials/Basic/HeatEquation_EX2_C/Source/mykernel.H Tutorials/GPU/CNS/Source/CNS_K.H commit e33b6cd8b866c2f8f34a16491316f912960922c0 Author: Marc Day Date: Wed Aug 19 17:56:11 2020 -0700 Add section to Make.unknown for intel mpi (#1284) ## Summary Avoid another site-specific make setting by adding generic id for Intel MPI - seems to work for UT Austin's TACC center computer, Stampede2, for example. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/sites/Make.unknown commit c35f7aad31ec34f55f3dcfab9b42f19a31224a18 Author: mic84 Date: Wed Aug 19 15:55:31 2020 -0700 CMake: re-factor third party libraries setup (#1252) ## Summary Centralize setup of all parallel backends dependencies. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/CMakeLists.txt Src/Extern/Conduit/CMakeLists.txt Src/Extern/HYPRE/CMakeLists.txt Src/Extern/PETSc/CMakeLists.txt Src/Extern/SENSEI/CMakeLists.txt Src/Extern/SUNDIALS4/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReXThirdPartyLibraries.cmake Tools/CMake/AMReX_Config.cmake commit 547e0f040a8ec6c03b73a4a001eaa34fd369121e Author: asalmgren Date: Wed Aug 19 12:43:32 2020 -0700 1) replace gpu_regtest flag by plot_error flag (which can be used on … (#1283) …CPU or GPU) 2) add analogous 2D test problem -- also with analytical solution ## Summary ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [X] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tests/LinearSolvers/EBTensor/Make.package Tests/LinearSolvers/EBTensor/MyTest.cpp Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp Tests/LinearSolvers/EBTensor/MyTest_2D_K.H Tests/LinearSolvers/EBTensor/MyTest_3D_K.H Tests/LinearSolvers/EBTensor/inputs Tests/LinearSolvers/EBTensor/inputs.rt.2d commit 5a81f883ec4d83fbe4c31c8e18db023deade5623 Author: Jon Rood Date: Wed Aug 19 10:36:34 2020 -0600 Add use of CUDA_HOME to Make.nrel. (#1282) ## Summary We set `CUDA_HOME` on machines at NREL so this adds its use to `Make.nrel`. This is mostly so that `-lnvToolsExt` will happen automatically for us when using the tiny profiler. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/sites/Make.nrel commit 192f638662e02c660e98bca5970c5e75b4c535b5 Author: WeiqunZhang Date: Wed Aug 19 06:58:12 2020 -0700 fcompare (#1281) ## Summary Remove unimplemented option from help message. Print more information on which files have NaNs if there are. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/Plotfile/fcompare.cpp commit 33fdf6bbc80eacca651766697e991c21bae8d32d Author: WeiqunZhang Date: Tue Aug 18 19:55:11 2020 -0700 HIP: exp (#1280) ## Summary ROCm 3.6 has fixed std::exp. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H commit 2d258baa734c8929035a1a2523d87695881c2008 Author: WeiqunZhang Date: Tue Aug 18 19:54:47 2020 -0700 Fix a bug in VisMF::AsyncWrite (#1279) ## Summary When not writing ghost cells, we need to make sure the header has the correct number of ghost cells that is zero. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_VisMF.cpp commit cb2cdfafde7c00f62e951d7060552c71167856b1 Author: WeiqunZhang Date: Tue Aug 18 17:21:46 2020 -0700 Updates for Tulip (#1278) ## Summary * Force DEBUG=FALSE for HIP to avoid a compiler bug. * Modify makefile so that the dependency files are not dumped in the current directory. * Add support for MPI. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/sites/Make.frontier-coe commit ce38e4b385fdd54f8bb67f254904802ceacc4079 Author: WeiqunZhang Date: Tue Aug 18 15:15:54 2020 -0700 OMP CI (#1277) Add an OMP CI test. .github/workflows/linux.yml commit 8688f76e033b5868762c178fe4dc20ef2930032a Author: WeiqunZhang Date: Tue Aug 18 14:57:39 2020 -0700 Fix typo for OMP (#1276) The typo was introduced in #1274. Src/AmrCore/AMReX_TagBox.cpp commit b0735b5e604305f226b42816d9f0d3c882ff3c4c Author: WeiqunZhang Date: Tue Aug 18 14:34:07 2020 -0700 Fix Make.machines (#1275) The tests on environment variables HOSTNAME and HOST were incorrect. Tools/GNUMake/Make.machines commit f71d122d0ed6831ae946e108116a88bee9b563d7 Author: WeiqunZhang Date: Tue Aug 18 14:02:54 2020 -0700 TagBoxArray::hasTags (#1274) In #1258, TagBoxArray::numtags was removed. However, IAMR still needs it. So a new function, hasTags, is added for IAMR. Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp commit 6478336784067131d857a3f219220b6b00127751 Author: WeiqunZhang Date: Mon Aug 17 21:19:11 2020 -0700 TagBoxArray on GPU (#1258) # Summary TagBoxArray functions can now run on GPU now. We no longer rely on unified memory for TagBoxArray functions. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_AsyncOut.cpp Src/Base/AMReX_GpuAtomic.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_Scan.H commit 3235db6b295923ed454cc1bbdfe6ce3b6964e93c Author: mxxw Date: Mon Aug 17 16:36:17 2020 -0700 Make.machines (#1273) ## Summary ensure host_name_short is always defined in Tools/GNUMake/Make.machines ## Additional background ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/Make.machines commit 8b66f47e906c53cd0127531d97fd65508d8eb9f9 Author: WeiqunZhang Date: Mon Aug 17 10:32:21 2020 -0700 DPC++: Missing synchronize() (#1268) Missing Gpu::synnhronize() call after host to device memcpy. Src/Base/AMReX_Reduce.H commit addfc7d6f35604f43893d836c891138b373757d2 Author: WeiqunZhang Date: Mon Aug 17 10:02:25 2020 -0700 Should use std::forward. (#1267) Src/Base/AMReX_FabArrayUtility.H commit 2c45e058537a3bffd212e13968e6df6562f01bc3 Author: WeiqunZhang Date: Mon Aug 17 09:51:32 2020 -0700 Advection_AmrCore Tutorial (#1266) Remove redundant MPI_Allreduce and cleanup. Tutorials/Amr/Advection_AmrCore/Source/AdvancePhiAtLevel.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 2d16fa694c4e08cc6ce922d31da730d4ab116985 Author: WeiqunZhang Date: Mon Aug 17 09:03:24 2020 -0700 amrex::Math::abs for beta8 on DG1 (#1271) ## Summary Due to a compiler bug (I believe), we have to modify amrex::Math::abs for beta8 on DG1. ## Additional background After spending many hours debugging Tutorial/Amr/Adevection_AmrCore/ on DG1, it is found that `MultiFab::norm0` does not return the correct result, because of the use of `amrex::Math::abs`. After making the change in this PR, the test now produces correct results with AMR. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_Math.H commit b4128deaff6e9ec9a91b605271f1aa972a1d3809 Author: mxxw Date: Sun Aug 16 18:21:43 2020 -0700 add support for additional AMD GPU SKUs and incl. poplar and redwood … (#1270) #1168 Summary Changed Tools/GNUMake/sites/Make.frontier-coe to 1. add support for additional AMD GPU SKUs; 2. include poplar and redwood in the list of frontier-coe machines ## Additional background Changed ifeq ($(which_computer),$(filter $(which_computer),tulip)) ifeq ($(USE_HIP),TRUE) CXXFLAGS += --amdgpu-target=gfx906 HIPCC_FLAGS += --amdgpu-target=gfx906 endif endif to ifeq (,$(filter $(which_computer),poplar redwood tulip)) $(error Unknown Frontier CoE computer, $(which_computer)) else ifeq ($(USE_HIP),TRUE) CXXFLAGS += --amdgpu-target=gfx906,gfx908 HIPCC_FLAGS += --amdgpu-target=gfx906,gfx908 endif endif For AMD GPUs, the compile target should be exact to avoid runtime errors, i.e., one should generally not assume that a binary targeting an older GPU will always run correctly on a newer GPU. However, building "fat binaries" is possible, so that one does, typically, not need one separate binary specifically built for each AMD GPU SKU available on the platform. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/sites/Make.frontier-coe commit cf4e666a7268d83dffcbb8559c1608fbee067b7c Author: mxxw Date: Sun Aug 16 18:21:02 2020 -0700 updated Make.machines to include new frontier-coe machines and change… (#1265) …d 'hostname -f' command to 'hostname' ## Summary updated Make.machines: 1. added poplar and redwood to frontier-coe machines; 2. changed name string matching for frontier-coe to only yield exact matches (filter); hence, !="" means exact match; 3. changed `hostname -f` command (which includes the domain) to `hostname` to avoid false negatives, e.g., not recognizing `hostname -f`==tulip.cm.cluster as tulip; ## Additional background ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/Make.machines commit bfaa57db45438d795293032609286d5c3146d8a3 Author: mxxw Date: Sun Aug 16 16:58:39 2020 -0700 fixed bug in matching of COMP_VERSION to correctly treat CCE > 9 (#1269) ## Summary changed Tools/GNUMake/comps/cray.mak to fix bugs in the matching of $(COMP_VERSION) in order to correctly treat CCE version > 9 ## Additional background Starting with version 9, the Cray CCE C and C++ compilers changed to being clang/LLVM based which makes it necessary to change some flags compared to CCE versions <=8. (This change does not apply to the Cray Fortran compiler versions.) However, the original version check of COMP_VERSION = $(shell echo $(CRAY_CC_VERSION) | cut -f 1 -d .) in combination with the tests of "ifeq ($(COMP_VERSION),9)" differentiated only between V9 and non-V9, which it assumed to be V8. Howerver, now, we have V10 while V11 is being tested, all of which would be treated like V8, which is incorrect. To address this issue the compiler version classification is now done with ifeq ($(shell expr $(COMP_VERSION) \>= 9), 1) CCE_GE_V9 := TRUE else CCE_GE_V9 := FALSE endif and it is tested with ifeq ($(CCE_GE_V9),TRUE) ## Checklist The proposed changes: - [X] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/comps/cray.mak commit 3896fae0158d1456e238845250bda4264d5980d7 Author: asalmgren Date: Sun Aug 16 16:17:37 2020 -0700 Change default max_level in AmrCore tutorial from 0 to 2. (#1264) Tutorials/Amr/Advection_AmrCore/Exec/inputs commit ac2128cc218ea5ba8124f2c78c808cccf1fab1f9 Author: asalmgren Date: Fri Aug 14 17:33:32 2020 -0700 Replace amrcore tutorial (#1253) ## Summary This replaces the existing tutorial with the more general, all C++ one developed for ATPESC 2020. This version works for CPU and GPU (compile-time option), in 2D and 3D (compile-time option), with and without subcycling (run-time option). A .md file is also included in the directory which walks a new user through how to run this code and what to experiment with to understand AMR. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [x] are described in the proposed changes to the AMReX documentation, if appropriate Co-authored-by: Weiqun Zhang Docs/sphinx_tutorials/source/AMR_Tutorial.rst Src/Base/AMReX_Box.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrCore/Exec/GNUmakefile Tutorials/Amr/Advection_AmrCore/Exec/GNUmakefile_movie Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv Tutorials/Amr/Advection_AmrCore/Exec/Make.package Tutorials/Amr/Advection_AmrCore/Exec/Prob.H Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/Exec/inputs Tutorials/Amr/Advection_AmrCore/Exec/inputs_for_scaling Tutorials/Amr/Advection_AmrCore/Exec/paraview_amr101.py Tutorials/Amr/Advection_AmrCore/README Tutorials/Amr/Advection_AmrCore/README.md Tutorials/Amr/Advection_AmrCore/Source/AdvancePhiAllLevels.cpp Tutorials/Amr/Advection_AmrCore/Source/AdvancePhiAtLevel.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore/Source/DefineVelocity.cpp Tutorials/Amr/Advection_AmrCore/Source/Kernels.H Tutorials/Amr/Advection_AmrCore/Source/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_K/Adv_K.H Tutorials/Amr/Advection_AmrCore/Source/Src_K/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_K/compute_flux_2D_K.H Tutorials/Amr/Advection_AmrCore/Source/Src_K/compute_flux_3D_K.H Tutorials/Amr/Advection_AmrCore/Source/Src_K/slope_K.H Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrCore/Source/Tagging.H Tutorials/Amr/Advection_AmrCore/Source/bc_fill.H Tutorials/Amr/Advection_AmrCore/Source/bc_fill_nd.F90 Tutorials/Amr/Advection_AmrCore/Source/face_velocity.H Tutorials/Amr/Advection_AmrCore/Source/main.cpp Tutorials/GPU/Advection_AmrCore/CMakeLists.txt Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/GPU/Advection_AmrCore/README Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H Tutorials/GPU/Advection_AmrCore/Source/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/bc_fill.H Tutorials/GPU/Advection_AmrCore/Source/main.cpp commit 192fa35ab4195456ba122bce5585e901d51e4b6d Author: WeiqunZhang Date: Fri Aug 14 16:12:46 2020 -0700 Rocm36 (#1263) ## Summary Update make system for hip-clang. Remove some hip workarounds. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFabUtility.H Src/Base/AMReX_Extension.H Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuElixir.cpp Src/Base/AMReX_GpuError.H Src/Base/AMReX_GpuLaunch.H Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 6c36b5ffcf2c7fb97a9cf2ee7a2d6951c5dc1064 Author: WeiqunZhang Date: Fri Aug 14 10:32:50 2020 -0700 Tensor solver and extension of EB domain face (#1262) ## Summary ParmParse parameter eb2.extend_domain_face is now true by default. The reason for the change is that for most applications it's hard to imagine one would want it to be false. It will also solve the EB tensor solver issue when there is a cut cell just outside the domain abutting a covered valid cell. Recent changes to the tensor solvers are incorrect and are reverted here. They are incorrect because the ghost cells in the modified functions actually have values at the cell centered. Although the users put domain face values in the ghost cells, that is not what the solver does. The solver stores the boundary values in boundary registers. Before the stencil is being applied, bc function is called to fill the ghost cells with properly interpolated or extrapolated values so that the stencil operations are just like working on normal interior cells. Revert "Correcting tensor cross terms computation for periodic bcs (#1254)" This reverts commit 1197adc5be6144bae9e362c114ca16b879006180. Revert "Changing computation at inflow/outflow for tensor solve (#1235)" This reverts commit b391885e918d63fa1741f954d2792e31426a6204. Revert "Changing computation at outflow for the EBTensor (#1187)" This reverts commit 9cd538802ea5b3ab7e6db10d6046933e937aa449. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [x] changes answers in the test suite to more than roundoff level - [x] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_Level.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 5f7a29477108d74834fc0d19ca966e8ea7b6a16f Author: Andrew Myers Date: Thu Aug 13 13:25:13 2020 -0700 reuse the tiling machinary in SortParticlesByBin. (#1257) Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H commit 1652a9da291f96dfa8c1f522a6ddf281b2ad252c Author: asalmgren Date: Thu Aug 13 10:26:44 2020 -0700 Fix formatting (1261) ## Summary ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Docs/sphinx_documentation/source/Basics.rst commit 4c6040c0a3f5c96a2f26592d54f0284dfb524b8b Author: asalmgren Date: Thu Aug 13 08:34:56 2020 -0700 Add text about how to set default value in the code by passing name (#1260) of routine to amrex::Initialize(...) Docs/sphinx_documentation/source/Basics.rst commit 04d0eecf4a09bcdb584368d89e931fb7a1978580 Author: WeiqunZhang Date: Wed Aug 12 17:36:04 2020 -0700 nvcc -MM (#1259) ## Summary `-MM` is not supported for nvcc <= 10.0. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tools/GNUMake/comps/nvcc.mak commit e915f9e20be15cc070d4aa023474c8cc2f92840c Author: Andrew Myers Date: Wed Aug 12 12:16:23 2020 -0700 Domain precision (#1209) Due to issues with pointing point precision, there are points inside the `ProbDomain()` that do not map to cells inside the `Domain()` box when binned using something like the `getParticleCell` function. This PR adds an additional domain, the "RoundoffDomain()", to the Geometry object. Points inside the roundoff domain are always sure to map to cells inside `Domain()`. The bounds are calculated when the Geometry object is constructed using bisection. This helps solve a number of issues that can happen when you have particles very close to the domain boundaries. While I have tested this with Nyx and WarpX, there is a chance that there could be a downstream effect on other codes. If the bisection fails when setting the roundoff domain on some problem, then we may need to adjust some tolerances. Src/Base/AMReX_Algorithm.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Particle/AMReX_ParticleContainerI.H commit 19db258fdd76dd5631d8205d8078623c6b97037b Author: Axel Huebl Date: Wed Aug 12 10:40:28 2020 -0700 CI: Fix oneAPI Activation (#1208) now located at `/opt/intel/oneapi/setvars.sh` Tools/CMake/AMReXSYCL.cmake Tools/GNUMake/comps/dpcpp.mak commit 4d4ef3e9b950639f2da9cafe2ee7fa3d572e227c Author: Andrew Myers Date: Wed Aug 12 10:27:34 2020 -0700 Give HDF5 benchmark option to read in a set of realistic grids. (#1236) This should lead to more useful measurements for Castro. The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [x] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Tests/HDF5Benchmark/inputs Tests/HDF5Benchmark/main.cpp commit d89d48026e077f251408c2652c6ee2e5c5f80d51 Author: Mu-Hua Chien Date: Wed Aug 12 13:26:02 2020 -0400 fix semicoarsening bugs for nodal solver (#1255) ## Summary Fix a semicoarsening bug for nodal solver. ## Additional background In avgdown coefficient, there is a place use coarsen ratio instead of the mg_coarsen_ratio_vec. Also, build the semi_avgdown for nodal solver. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 1628d314b33143c6747bd2b44a99426bd1ac3d09 Author: kngott <30483578+kngott@users.noreply.github.com> Date: Wed Aug 12 10:22:46 2020 -0700 Fixes for Amrvis warnings from gcc 7.5 with DEBUG=TRUE, DIM=2 and DIM=3. (#1256) ## Summary Warnings from compiling Amrvis using GCC 7.5 with DEBUG=TRUE, DIM=2 and DIM=3. (Build on dogora). Primarily ignore_unused, commenting out function parameter declarations and a few manual type casts. Some unique warning adjustments as well (e.g. a shadowed BL_PROFILER). To be paired with a matching PR in the Amrvis repo. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BoxList.cpp Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/ProfParser/BLProfParser.y Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 1197adc5be6144bae9e362c114ca16b879006180 Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com> Date: Tue Aug 11 14:02:22 2020 -0700 Correcting tensor cross terms computation for periodic bcs (#1254) ## Summary Correcting tensor cross terms computation for periodic bcs ## Additional background Fixing a bug introduced in PR #1235. Now it computes in the correct way the cross terms in the tensor solve for problems with periodic bcs. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [x] changes answers in the test suite to more than roundoff level - [x] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit a4ab677faf1279d20d7feb6f42263bcc7b1468f4 Author: WeiqunZhang Date: Mon Aug 10 17:35:07 2020 -0700 Fix bug in FPinfo for EB (#1241) PR #1224 introduced a bug that affects FillPatch on nodal grids for EB. When there is only one ghost cell, the fine patch grids might be degenerate in the sense that some boxes are only 1 node wide. In that case, we cannot build cell-centered EBCellFlags unless there are ghost cells. Src/Base/AMReX_FabArrayBase.cpp commit 46b75867f5106fa363563a230e64a078a3cacc00 Author: Andrew Myers Date: Mon Aug 10 14:00:15 2020 -0700 Fix curly brace warning with clang (#1251) Src/Base/AMReX_Machine.cpp commit a1c997e6ca9d3ad58b18881ef9f319334a2db161 Author: Andrew Myers Date: Mon Aug 10 14:00:05 2020 -0700 fix some warnings that arise in the redistribute test (#1250) Tests/Particles/Redistribute/main.cpp commit c99e8ac4af561a960b98e7995d8fbb291aa70865 Author: Andrew Myers Date: Mon Aug 10 13:49:52 2020 -0700 Remove _rt and _prt from the particle code, for reasons explained in PR 1243. (#1249) Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 480d1fffe7c7ff7bddcca356ce656f1cecd7f308 Author: WeiqunZhang Date: Mon Aug 10 13:41:07 2020 -0700 Remove Perilla (#1248) Remove Perilla because it's incompatible with our GPU strategy and it's no longer being maintained. Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/make_api.py Docs/sphinx_documentation/source/AsyncIter.rst Docs/sphinx_documentation/source/AsyncIter_Chapter.rst Docs/sphinx_documentation/source/index.rst Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/Amr/Make.package Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.cpp Src/AmrTask/AMFIter/AMReX_Connections.H Src/AmrTask/AMFIter/Makefile Src/AmrTask/Amr/AMReX_AmrLevelTask.H Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/AmrTask/Amr/Make.package Src/AmrTask/Amr/Makefile Src/AmrTask/AmrCore/AMReX_FillPatchUtil.H Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrTask/Makefile Src/AmrTask/arch.common Src/AmrTask/arch/arch.mpi.generic Src/AmrTask/arch/arch.serial Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_AbstractTask.cpp Src/AmrTask/graph/AMReX_Affinity.H Src/AmrTask/graph/AMReX_Affinity.cpp Src/AmrTask/graph/AMReX_DataTypes.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/graph/AMReX_TaskGraph.cpp Src/AmrTask/graph/Makefile Src/AmrTask/graph/RTS.H Src/AmrTask/make_defaults/Cori Src/AmrTask/make_defaults/Edison Src/AmrTask/make_defaults/Summit-dev Src/AmrTask/rts_impls/MPI_Generic/Makefile Src/AmrTask/rts_impls/MPI_Generic/README Src/AmrTask/rts_impls/MPI_Generic/mylock.h Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/rts_impls/MPI_Generic/rts_graphimpl.H Src/AmrTask/rts_impls/MPI_Generic/rts_taskimpl.H Src/AmrTask/rts_impls/README Src/AmrTask/rts_impls/Serial/Makefile Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/rts_impls/Serial/rts_graphimpl.H Src/AmrTask/rts_impls/Serial/rts_taskimpl.H Src/AmrTask/rts_impls/Utils/dl_malloc.c Src/AmrTask/rts_impls/Utils/dl_malloc.h Src/AmrTask/rts_impls/Utils/sysInfo.C Src/AmrTask/rts_impls/Utils/sysInfo.H Src/AmrTask/rts_impls/mpi/Make.package Src/AmrTask/rts_impls/mpi/PackageQueue.H Src/AmrTask/rts_impls/mpi/PackageQueue.cpp Src/AmrTask/rts_impls/mpi/Perilla.H Src/AmrTask/rts_impls/mpi/Perilla.cpp Src/AmrTask/rts_impls/mpi/PerillaConfig.H Src/AmrTask/rts_impls/mpi/PerillaRts.H Src/AmrTask/rts_impls/mpi/PerillaRts.cpp Src/AmrTask/rts_impls/mpi/perilla.mak Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi_omp/Barrier.H Src/AmrTask/rts_impls/mpi_omp/Barrier.cpp Src/AmrTask/rts_impls/mpi_omp/LocalConnection.H Src/AmrTask/rts_impls/mpi_omp/Make.package Src/AmrTask/rts_impls/mpi_omp/PackageQueue.H Src/AmrTask/rts_impls/mpi_omp/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_omp/Perilla.H Src/AmrTask/rts_impls/mpi_omp/Perilla.cpp Src/AmrTask/rts_impls/mpi_omp/PerillaConfig.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_omp/RGIter.H Src/AmrTask/rts_impls/mpi_omp/RGIter.cpp 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Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Adv_3d.f90 Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Make.package Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/compute_flux_3d.f90 Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/slope_3d.f90 Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Adv_nd.f90 Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Make.package Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Tagging_nd.f90 Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/tagging_params.f90 Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Source/main.cpp commit b391885e918d63fa1741f954d2792e31426a6204 Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com> Date: Mon Aug 10 11:17:32 2020 -0700 Changing computation at inflow/outflow for tensor solve (#1235) ## Summary Computation at inflow boundaries for the MLEBTensor and inflow/outflow for MLTensor has been changed. ## Additional background At outflow the tensor solve uses extrapolated values from the interior cell to the outflow face. At inflow, the tensor solve uses boundary data, evaluated at the face, that has been stored in the ghost cell next to the inflow face. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [x] changes answers in the test suite to more than roundoff level - [x] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit ad1b75d9557fddf126f67be4b802327c1a4415e5 Author: asalmgren Date: Mon Aug 10 10:46:17 2020 -0700 Remove sensei tutorials (#1247) * Remove SENSEI tutorials. * Update tutorial documentation since we no longer have SENSEI tutorials 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Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/SENSEI/Advection_AmrCore/README Tutorials/SENSEI/Advection_AmrCore/README_SENSEI.md Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/SENSEI/Advection_AmrCore/Source/Make.package Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 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Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/probin Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/histogram.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/histogram_python.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/iso_extract.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/read_adios2_bp4_default.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/read_adios2_sst_default.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_adios2_bp4.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_adios2_sst.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/SENSEI/Advection_AmrLevel/README Tutorials/SENSEI/Advection_AmrLevel/README_SENSEI.md Tutorials/SENSEI/Advection_AmrLevel/Source/Adv_F.H Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/SENSEI/Advection_AmrLevel/Source/LevelBldAdv.cpp Tutorials/SENSEI/Advection_AmrLevel/Source/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/main.cpp Tutorials/SENSEI/README.md commit 63d386514d5167d5849d11e0cc6dbb146c46a37b Author: WeiqunZhang Date: Sun Aug 9 20:22:25 2020 -0700 oneAPI Beta 8 (#1243) In beta8, C++11 user defined literals are broken because of the use of long double. We have implemented a workaround by overloading operator "" _rt with `const char*` argument and our own `atof`. But, because Clang does not evaluate the new version of the operator at compile time, we now avoid using `_rt` in AMReX. In the long term, we may have to remove it entirely if the long double issue is not resolved in DPC++. With the workaround, we can enable the DPC++ CI test again. .github/workflows/linux.yml Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_extrapolater_2D_K.H Src/Amr/AMReX_extrapolater_3D_K.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_Dim3.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_REAL.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_Scan.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/EB/AMReX_algoim_K.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H Tutorials/Basic/HeatEquation_EX1_CF/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_CF/Source/main.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/RT/cns_prob_parm.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob_parm.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_parm.H Tutorials/GPU/CNS/Source/CNS_parm.cpp Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/CNS/Source/main.cpp commit e3f25aa6b9ed74229d203110fa59fb2d0e815bdf Author: WeiqunZhang Date: Sun Aug 9 20:21:44 2020 -0700 Fix a bug in Tutorials/GPU/CNS (#1245) Fix a bug in deriving velocity and a number of warnings for Tutorials/GPU/CNS. Src/Base/AMReX_FBI.H Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_derive.cpp commit cd0a8034f389b40882900b3faa92d84beed13201 Author: WeiqunZhang Date: Sun Aug 9 20:21:04 2020 -0700 FPE trap in DPC++ (#1244) Due to a bug in DPC++ compiler, we disable fpe trapping. Src/Base/AMReX.cpp commit a2eecef9c2efab1548ad14d6b5083f14451441bb Author: drangara <69211175+drangara@users.noreply.github.com> Date: Sun Aug 9 16:34:44 2020 -0400 Small volfrac (#1228) ## Summary When extend_domain_face is set to true we do the following: If we set a cell that lies on one of the 6 faces of the domain as covered because its volfrac is less than the small_volfrac , we are forcing the corresponding ghost cells on that face to also be covered. ## Additional background ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [x] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_Level.H commit d8d270056e953904c04d3ae3221006389128531e Author: Jon Rood Date: Sun Aug 9 10:30:38 2020 -0600 Remove error message for unknown MPI in Make.nrel since we want to be able to use MPT for MPI. (#1242) Tools/GNUMake/sites/Make.nrel commit 09db04bf308dbfe797baa19b9118466f545ee16c Author: Andrew Myers Date: Fri Aug 7 16:39:17 2020 -0700 fix some warnings that arise when USE_SINGLE_PRECISION_PARTICLES=TRUE but PRECISION=DOUBLE (#1240) Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 881397d57f8fee10dc24db747e07a7bb3685d4ec Author: WeiqunZhang Date: Fri Aug 7 16:23:35 2020 -0700 GNU Make dependency (#1239) Use `-MM` instead of `-M` to generate dependency in GNU Make system, because we do not need to include dependency on headers in the system header directories. Tools/GNUMake/Make.defs commit b4ba4429672be4589d535b7e6c83272fee5fdfe3 Author: WeiqunZhang Date: Fri Aug 7 13:51:41 2020 -0700 Oversetmask (#1232) Switch the overset mask convention to that 1 means unknown and 0 means known. The new convention is more convenient for AMR-Wind. Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Tests/LinearSolvers/CellOverset/MyTest.cpp Tests/LinearSolvers/NodalOverset/MyTest.cpp Tests/LinearSolvers/TensorOverset/MyTest.cpp commit cd71ce08c17edb1aeeaa89d00bb9b072713c26a8 Author: WeiqunZhang Date: Fri Aug 7 13:40:39 2020 -0700 Remove old solvers (#1238) Src/LinearSolvers/C_CellMG and C_TensorMG are removed. They have been superseded by Src/LinearSolvers/MLMG. Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG/AMReX_lo_bctypes.fi Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG/OpenSource.txt Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H Src/LinearSolvers/C_CellMG4/Make.package Src/LinearSolvers/C_CellMG4/OpenSource.txt Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D1.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D2.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D3.F Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_3D.F Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/DV_2D.mF Src/LinearSolvers/C_TensorMG/DV_3D1.mF Src/LinearSolvers/C_TensorMG/DV_3D2.mF Src/LinearSolvers/C_TensorMG/DV_3D3.mF Src/LinearSolvers/C_TensorMG/DV_3D4.mF Src/LinearSolvers/C_TensorMG/Format.m Src/LinearSolvers/C_TensorMG/Make.package Src/LinearSolvers/C_TensorMG/OpenSource.txt Src/LinearSolvers/C_TensorMG/Optimize.m Src/LinearSolvers/C_TensorMG/amrex_tmg_util.F90 Src/LinearSolvers/C_TensorMG/visc2d.m Src/LinearSolvers/C_TensorMG/visc2d.ma Src/LinearSolvers/C_TensorMG/visc2d.nb Src/LinearSolvers/C_TensorMG/visc3d.m Src/LinearSolvers/C_TensorMG/visc3d.ma Src/LinearSolvers/C_TensorMG/visc3d.nb Tests/LinearSolvers/C_CellMG/COEF_2D.F Tests/LinearSolvers/C_CellMG/COEF_3D.F Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile.dumpi Tests/LinearSolvers/C_CellMG/MACOPERATOR_2D.F Tests/LinearSolvers/C_CellMG/MACOPERATOR_3D.F Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/Palette Tests/LinearSolvers/C_CellMG/amrvis.defaults Tests/LinearSolvers/C_CellMG/dumpi/NOTE Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.4096core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.512core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.64core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.8core Tests/LinearSolvers/C_CellMG/inputs.2d Tests/LinearSolvers/C_CellMG/inputs.3d Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_CellMG/vpramps.dat Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package Tests/LinearSolvers/C_TensorMG/Palette Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/amrvis.defaults Tests/LinearSolvers/C_TensorMG/inputs Tests/LinearSolvers/C_TensorMG/inputs2D Tests/LinearSolvers/C_TensorMG/inputs3D Tests/LinearSolvers/C_TensorMG/inputs8 Tests/LinearSolvers/C_TensorMG/main_2D.F Tests/LinearSolvers/C_TensorMG/main_3D.F Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/C_TensorMG/probin Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/C_TensorMG/vpramps.dat Tools/CompileTesting/compiletesting.py commit 6de33d5b79d614dcdd3c7f4923676c7e8ad503dd Author: mic84 Date: Fri Aug 7 12:25:10 2020 -0700 MacProjector: allow for re-use of the object and enhance multi-level algorithm. (#1225) * MacProjector: build RHS each time project() is called * MacProjector: average down velocities before and after projection Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit b9ed579c052acac1fb73ced3ac2e9e63b17b3046 Author: Andrew Myers Date: Fri Aug 7 11:59:09 2020 -0700 Fix unused variable warnings in AMReX_LinOp.* (#1237) The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp commit 53d32def6b48c00270f97f4efd6251aa55cb6e7a Author: Candace Gilet Date: Thu Aug 6 17:06:06 2020 -0400 Fix typo. (#1234) ## Summary Fix a typo in AMReX_extrapolater_3D_K.H ## Additional background Some IAMR runs were crashing with out of bounds errors. This fixes those, and brings this C version in agreement with what the old F90 version was doing. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Amr/AMReX_extrapolater_3D_K.H commit fe8cc5f3facab97cd39df5c06f6a3e2cc43ab378 Author: asalmgren Date: Thu Aug 6 11:15:56 2020 -0700 Fix AMREX_HOME in Tests and Tutorials only (#1233) * 1) Replace all instances of "AMREX_HOME ?=" by "AMREX_HOME =" in Tests and Tutorials only. Since these exist within the amrex directory structure the default should be that they always use the amrex they are part of, not the one set by the user's environment variable 2) Replace all instances of BoxLib/BOXLIB/boxlib by AMReX. Tests/Algoim/GNUmakefile Tests/AsyncOut/multifab/GNUmakefile Tests/BBIOBenchmark/GNUmakefile Tests/BaseFabTesting/GNUmakefile Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile Tests/GPU/CudaGraphs/GraphInitTest/GNUmakefile Tests/GPU/CudaGraphs/GraphReuseCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphWithMemcpy/GNUmakefile Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile Tests/GPU/Fuse/GNUmakefile Tests/GPU/Locking/GNUmakefile Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/Vector/GNUmakefile Tests/GPU/libamrex_CUDA/GNUmakefile Tests/HDF5Benchmark/GNUmakefile Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/CellOverset/GNUmakefile Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBTensor/GNUmakefile Tests/LinearSolvers/EBflux_grad/GNUmakefile Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/NodalOverset/GNUmakefile Tests/LinearSolvers/NodeEB/GNUmakefile Tests/LinearSolvers/TensorOverset/GNUmakefile Tests/MKDir/GNUmakefile Tests/NoFort/GNUmakefile Tests/Particles/AssignDensity/GNUmakefile Tests/Particles/AssignMultiLevelDensity/GNUmakefile Tests/Particles/AsyncIO/GNUmakefile Tests/Particles/GNUmakefile Tests/Particles/GhostsAndVirtuals/GNUmakefile Tests/Particles/InitFromAscii/GNUmakefile Tests/Particles/Intersection/GNUmakefile Tests/Particles/NeighborParticles/GNUmakefile Tests/Particles/ParallelContext/GNUmakefile Tests/Particles/ParticleIterator/GNUmakefile Tests/Particles/ParticleMesh/GNUmakefile Tests/Particles/ParticleReduce/GNUmakefile Tests/Particles/ParticleTransformations/GNUmakefile Tests/Particles/Redistribute/GNUmakefile Tests/Particles/SparseBins/GNUmakefile Tests/Particles/TypeDescriptor/GNUmakefile Tests/PnetCDFBenchmark/GNUmakefile Tests/ProfTests/HeatEquation_EX1_C/Exec/GNUmakefile Tests/ProfTests/ThirdParty/Exec/GNUmakefile Tests/SinglePrecision/GNUmakefile Tests/Slice/GNUmakefile Tests/Stream/GNUmakefile Tests/TypeCheck/GNUmakefile Tests/Vectorization/GNUmakefile Tests/complementIn/GNUmakefile Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/UniformVelocity/GNUmakefile Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/README Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_2d/Adv_2d.f90 Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Source/Src_3d/Adv_3d.f90 Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/UniformVelocity/GNUmakefile Tutorials/AmrTask/MiniApps/Adv_phaseAsync/README 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Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile Tutorials/SDC/MISDC_ADR_2d/Exec/GNUmakefile Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 commit 888e804b77fad6754368396bb728e3ec491ed610 Author: Andrew Myers Date: Wed Aug 5 13:23:09 2020 -0700 use rvalues for functions that take callables (#1231) Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_SparseBins.H commit 30fe5a59e9730683a28f7291ae96310d9560d917 Author: Michael Zingale Date: Wed Aug 5 12:32:34 2020 -0400 add asserts for bounds checking to Array1D and Array2D (#1230) ## Summary Array1D and Array2D did not check if the index was in bounds. This adds an `AMREX_ASSERT` that catches out of bounds issues when compiled with `DEBUG = TRUE`. ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_Array.H commit e2dac9c4e6fa2a4163ec778b4958af843077069c Author: WeiqunZhang Date: Tue Aug 4 16:12:50 2020 -0700 Optimization of the construction of SFC (#1227) ## Summary The Morton numbers are explicitly computed and stored in SFCTokens. This speeds up the sorting in making space filling curve significantly. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Print.H commit 9d76c3732bd03111c0279630761e5439e70c9b49 Author: Andrew Myers Date: Tue Aug 4 15:00:39 2020 -0700 Refactoring of particle buffer map (#1229) Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_ParticleUtil.H commit d570a8c6647abc85a32cbcbe4af886fa2dde3782 Author: WeiqunZhang Date: Tue Aug 4 11:13:27 2020 -0700 Ignore unused indices in AMREX_LOOP_3D and 4D (#1226) Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_Loop.H commit f706d8aceb4272eb3e8f700cf77150cf4967aa20 Author: WeiqunZhang Date: Tue Aug 4 09:20:57 2020 -0700 Optimization of FPinfo and complementIn (#1224) ## Summary Use simplified BoxArray in FPinfo and parallelize FPinfo. Add parallel version of BoxList::parallelComplementIn and use it in AmrMesh::MakeNewGrids. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_FillPatchUtil_I.H Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 99d2227371a6a47e40b8175ee0f73f97ecf3aa59 Author: Lucas Esclapez <13371051+esclapez@users.noreply.github.com> Date: Tue Aug 4 08:41:54 2020 -0700 Feature extrapolator gpu (#1222) ## Summary Move the Amr/Extrapolater used in IAMR/PeleLM to C++/GPU compliant. ## Additional background The Extrapolater allows to fill ghost cells with first order extrapolation from interior cells. ## Checklist The C++ version does not introduce any changes to the results and passed CI compilation tests. The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [X] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_extrapolater_1D_K.H Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2D_K.H Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3D_K.H Src/Amr/AMReX_extrapolater_3d.f90 Src/Amr/AMReX_extrapolater_K.H Src/Amr/CMakeLists.txt Src/Amr/Make.package commit 294435b79bddc3106249a15c64bd7b4322c19024 Author: Andrew Myers Date: Mon Aug 3 14:11:17 2020 -0700 Less surprising behavior for the ok() method of FabArray. (#1223) This makes the `ok()` method of FabArray return `false` instead of crashing if the `define()` method has yet to be called. We allow FabArray and its derived classes to be default constructed, which places them in a unusable state until the the `define` method has been called. We also provide an `ok()` method, which according to its doxygen strings returns whether the FabArray is well-defined. Currently, this method will crash with a not-particularly instructive error message if it is called on a default-constructed-but-not-defined FabArray. This pull request changes it to return `false` instead, which I'd argue is more intuitive - if it's legal to construct a FabArray and define it later, then it should be legal to test whether that has been done or not. I have also updated the doxygen string for the method in question. Even if we want this to crash instead of returning `false`, it should do so with its own assertion and a clear error message. The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [x] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_FabArray.H commit a918cdabf2bd5f5991fe69494593634f1fced2b4 Author: WeiqunZhang Date: Mon Aug 3 13:16:49 2020 -0700 Optimization of regrid (#1199) ## Summary New BoxList::maxSize function that keeps Boxes after chopping in an order that is easy to merge them back into original Box. New BoxList::order_simplify function that assumes the BoxList is in the order that we only need to search the next Box in the list. Cache simplified BoxList inside BoxArray. Use simplified BoxArray in FPinfo. This commit will make most regression tests fail because it changes the grids. But if the comparison is done with `fcompare....ex -a`, it should only change answers at roundoff level unless the test is very sensitive. Src/AmrCore/AMReX_AmrMesh.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_FabArrayBase.cpp commit 4c50993ce86e8f6c54c50b93cbbb1aab92d42edd Author: Brandon Runnels Date: Mon Aug 3 12:29:18 2020 -0600 Fillboundary (#1171) This pull request fixes the problem of edge nodes not getting filled properly when filling multiple layers of ghost nodes. This occurs when there are overlapping ghost nodes on a coarse/fine boundary. (See issue #568) Summary of changes to AMreX: - Added a `BoxArray::complementIn` function that takes a box _list_ and returns the complement box list. - Added an additional boolean argument `multi_ghost` to all `FillBoundary` functions that gets passed (eventually) to `define_fb`. In all cases, a default value of `false` is supplied. - Modified `define_fb` to include the missing ghost nodes in the list of `send_tags`. (This uses the new `complementIn` function.) Summery of changes to `LinearSolver/MultiComponent` tutorial: - Removed the `realFillBoundary` function, replaced with `FillBoundary(false,true) - Modified `main.cpp` so that it can be compiled and run (non-trivially) in 2D as well as 3D. Diagram of the problem that this PR fixes: ![FillBoundaryIllustration](https://user-images.githubusercontent.com/6371567/88218141-d9982980-cc1c-11ea-84f7-194934dfed73.png) Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tutorials/LinearSolvers/MultiComponent/inputs Tutorials/LinearSolvers/MultiComponent/main.cpp commit 28ceb92eae33e7b7797831bed85ad6242fdcf317 Author: Brian Friesen Date: Mon Aug 3 11:25:41 2020 -0700 Tools: add NVIDIA HPC SDK as a compiler (#1131) HPC SDK replaced PGI after PGI 20.4, so we should get it working now. Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/hpcsdk.mak commit 273cf0cc0c2b26d1f81147a5a00ceb26bd17184c Author: asalmgren Date: Sun Aug 2 14:09:09 2020 -0700 The average_down_faces calls between AMR levels in the linear solvers need to see periodicity (#1221) The average_down_faces calls between AMR levels need to use the interfaces that sees the periodicity. This requires adding that functionality to EB_average_down_faces (it has already been added to non-EB average_down_faces.) ## Summary Recently we added the functionality for an average_down_faces call to average fine data from one side to average not only onto the face under it but also onto the face on the other side of the domain if periodic in that direction. This PR 1) extends that functionality to the EB_average_down_faces call and 2) uses this new functionality when averaging down face-based coefficients between AMR levels in the cell-centered linear solvers. ## Checklist The proposed changes: - [X] fix a bug or incorrect behavior in AMReX - [X] add new capabilities to AMReX - [X] changes answers in the test suite to more than roundoff level - [X] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 9cd538802ea5b3ab7e6db10d6046933e937aa449 Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com> Date: Sun Aug 2 14:00:12 2020 -0700 Changing computation at outflow for the EBTensor (#1187) Computation at outflow boundaries for the EBTensor has been changed to not take into account cells outside the domain. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit ccaebccf710600e2e28510f8ba43b760a10a918b Author: asalmgren Date: Sun Aug 2 13:16:56 2020 -0700 Fix the calculation of divu at inflow face in nodal projection so that it does not use tangential velocities on an inflow face (#1219) ## Summary Mathematically the nodal projection should only see the normal velocity at inflow faces, but it was coded so that it would use non-zero tangential velocities at inflow in the calculation of divu. Most users never set tangential velocities to anything but zero, but if they did, this would give an incorrect divergence. ## Additional background ## Checklist The proposed changes: - [X] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [X] changes answers in the test suite to more than roundoff level - [X] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 9ed2833df8a110f0ea43e901da96a93f0686a031 Author: Marc Day Date: Sat Aug 1 18:48:08 2020 -0700 Remove instructions....not needed and clutters Slack notices (#1218) ## Summary Although the instructions were commented out in the formatted PR text, they clutter up the Slack notices, and aren't really necessary anyway. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate .github/pull_request_template.md commit 20d9b4a451bc2ee8a9133fa618e46ffd479c6807 Author: WeiqunZhang Date: Sat Aug 1 12:58:03 2020 -0700 20.08 (#1220) ## Summary Update CHANGES for 20.08 ## Additional background ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate CHANGES commit 2dad6e2975931107be98205086eb11969e937ed1 Author: WeiqunZhang Date: Thu Jul 30 22:53:09 2020 -0700 Average down faces (#1216) New average_down_faces functions that take coarse Geometry and average down periodically. Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 1476ea3ef4a3dc6bae80b241d85657c0fc5d9d31 Author: WeiqunZhang Date: Wed Jul 29 18:30:43 2020 -0700 fix angle brackets pr template (#1215) ## Summary The `-->` in the html comment part of the PR template closes the comment and leaves the words after that and before the actual closing `-->` visible. This is fixed. The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate .github/pull_request_template.md commit d8cdfd9eda11126954ac549c57eec8723e97f21b Author: WeiqunZhang Date: Wed Jul 29 18:26:27 2020 -0700 Fix warnings for DPC++ (#1214) ## Summary - Add more warnings flags to dpcpp. - Fix warnings for DPC++. - Fix a bug in DPC++ version of ReduceLogicalOr. ## Checklist The proposed changes: - [x] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate Src/Base/AMReX_BlockMutex.H Src/Base/AMReX_BlockMutex.cpp Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuAtomic.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_Reduce.H Src/Base/AMReX_parstream.cpp Tools/GNUMake/comps/dpcpp.mak Tools/GNUMake/comps/llvm.mak commit 2dc11c2ffd58a4e3f50d691a856446db0dfde8c5 Author: kngott <30483578+kngott@users.noreply.github.com> Date: Wed Jul 29 09:01:50 2020 -0700 Update the documentation for NSight tools. (#1163) Created a skeleton in External Profiling for documenting AMReX specific implementations of the NSight package. Also updated the run.corigpu script with new data from the Hackathon. Docs/sphinx_documentation/source/External_Profiling_Tools.rst Docs/sphinx_documentation/source/External_Profiling_Tools_Chapter.rst Tutorials/GPU/run.corigpu Tutorials/GPU/run.script Tutorials/GPU/run.summit commit 94961adbaf07c228eaae7c3ee3536f1ee338a3ce Author: Houjun Date: Tue Jul 28 17:12:15 2020 -0700 Fix a bug with HDF5 boxcenter data (#1213) * Fix a bug that causes wrong value assignment for the boxcenter dataset Co-authored-by: Houjun Tang Src/Base/AMReX_PlotFileUtil.cpp commit 1a4780d8ef5fb2fa7948ab926c942ea551690e60 Author: Marc Day Date: Tue Jul 28 14:25:29 2020 -0700 Add PR template file (#1211) ## Sumary Following CASTRO's lead, this template for PRs will pre-fill PR messages with suggested text. Hitting "Preview" in the PR window will format the message nicely. ## Checklist The proposed changes: - [ ] fix a bug or incorrect behavior in AMReX - [ ] add new capabilities to AMReX - [ ] changes answers in the test suite to more than roundoff level - [ ] are likely to significantly affect the results of downstream AMReX users - [ ] are described in the proposed changes to the AMReX documentation, if appropriate .github/pull_request_template.md commit 97a6fa2f59f2985a4f67adbd8d431a50f8a35590 Author: Andrew Myers Date: Tue Jul 28 13:14:02 2020 -0700 Turn off CI for DPC++ right now, since it's currently broken. (#1210) * turn off the DPC++ CI workflow for now, as it is broken in beta 8 * note that this is borked right now .github/workflows/linux.yml commit e4da66c8e01efa09257e6362688c8a7c4e3bd1dd Author: asalmgren Date: Mon Jul 27 17:27:16 2020 -0700 Docs hypre fix (#1207) Docs/sphinx_documentation/source/LinearSolvers.rst commit 9db726812c87a2138ee2b2a831d3363824f1c633 Author: Axel Huebl Date: Mon Jul 27 12:59:33 2020 -0700 CMake: NVCC/cudafe Error Numbers (#1206) Activate this fancy, undocumented flag to show error numbers in NVCC. This is great if one wants to suppress (or report) them and should be standard. Tools/CMake/AMReX_SetupCUDA.cmake commit ffe8d2e06bf276cbe382b658223ea3b4d78b89e7 Author: WeiqunZhang Date: Mon Jul 27 11:16:17 2020 -0700 fix periodic boundary bug in #1204 (#1205) Src/AmrCore/AMReX_TagBox.cpp commit d731f8ba3a26c74febfae7d42862617e01112534 Author: WeiqunZhang Date: Sun Jul 26 18:05:50 2020 -0700 EB outside domain (#1201) * EB outside domain Add a runtime parameter `eb2.extend_domain_face` to control EB generation outside the domain. The default is false. That is the implicit function will be used for cells outside the domain. This preserves the current behavior. If it is set to true, the geometry information is then extrapolated from domain faces. * fix fillFab for EB_levelset Src/Base/AMReX_Algorithm.H Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IndexSpaceI.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB_levelset.H commit 931ac6fb4a03faed44918731ecb383368ba0cfe2 Author: WeiqunZhang Date: Sun Jul 26 15:06:25 2020 -0700 Fix bug in #1156 (#1204) In #1156, newly generated grids were not always properly nested because the tags in ghost cells were discarded. This is fixed and an assertion is added. Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 6812ea39f6739eae11d4cfaf9ac28940e77df0ae Author: Max Katz Date: Sun Jul 26 09:22:22 2020 -0700 Fix CellConservativeProtected bug from #1184 (#1203) * Fix CellConservativeProtected bug from #1184 * Fix comment Src/AmrCore/AMReX_Interpolater.cpp commit 1dbf5d7a5939e2b9bdb41627716fe392f168c5e0 Author: WeiqunZhang Date: Sat Jul 25 20:43:52 2020 -0700 GNU Make option to turn warnings into errors (#1198) Add `WARN_ERROR` (with default of `FALSE`) to the GNU Make system to turn warnings into errors for GCC and Clang. Add `WARN_ERROR` to the 2d and 3d CIs using GNU Make. .github/workflows/linux.yml Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/llvm.mak commit b9b0196728b93353a34f1152337f88a701ff6fde Author: WeiqunZhang Date: Sat Jul 25 16:14:04 2020 -0700 udpate branch name due to regression_testing branch name change (#1200) Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/source/Testing.rst commit 8ce4756814f2064eae003a5c414e914f60a69960 Author: Andrew Myers Date: Fri Jul 24 19:12:29 2020 -0700 Fix some more clang warnings (#1197) Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_Box.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_Machine.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_ParallelReduce.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_linop_fi.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_TracerParticles.cpp commit c013c29ad1e9e7da23431a6f4b5c1ab47cc059a4 Author: WeiqunZhang Date: Fri Jul 24 18:27:53 2020 -0700 Gcc7 no array bounds (#1196) * Wno-array-bounds for gcc 7 * [[gnu::fallthrought]] is available for gcc >= 7 only. Test the result of dynamic_cast. Src/Base/AMReX_Extension.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tools/GNUMake/comps/gnu.mak commit c9ca46b45b96ce1507e74a0bcafe545de802e5c0 Author: Andrew Myers Date: Fri Jul 24 16:24:55 2020 -0700 Remove anonymous struct, which is not standard. Note that this is a b… (#1191) Src/Particle/AMReX_Particle.H commit 660da8bb839c47a6aa530b9611006c1d3fb8c50f Author: WeiqunZhang Date: Fri Jul 24 14:42:28 2020 -0700 fix a wrong clang flag (#1194) * fix a wrong clang flag * fix a warning Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tools/GNUMake/comps/llvm.mak commit 572648806d3aeaac06406637b13802c975171b24 Author: WeiqunZhang Date: Fri Jul 24 12:45:45 2020 -0700 fix clang warnings (#1193) Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_FillPatchUtil_I.H Src/AmrCore/AMReX_Interpolater.H Src/Base/AMReX_Array.H Src/Base/AMReX_Extension.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_PODVector.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_Tuple.H Src/Boundary/AMReX_Mask.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/Particle/AMReX_BinIterator.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tools/GNUMake/comps/llvm.mak commit a4947448f775cbc027a9b0b6a639e70a74caae9f Author: Andrew Myers Date: Fri Jul 24 11:49:35 2020 -0700 fix a parameter shadowing warning coming from VisMF::RemoveFiles with gcc (#1192) Src/Base/AMReX_VisMF.cpp commit 1fe53cb2852b162a9d7f37a2147e4e4e651d1c2f Author: WeiqunZhang Date: Fri Jul 24 11:07:38 2020 -0700 fix more warnings and add CI for building 3d with configure (#1184) * fix more warnings and add CI for building 3d with configure * make ignore_unused constexpr and force inline * add AMREX_FALLTHROUGH * fix more warnings * enable xsdk in ci and test no_fortran * remove constexpr from ignore_unused for C++11 * use Clang for 2d ci * disable mpi for the 2d ci with clang .github/workflows/linux.yml Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX.H Src/Base/AMReX_Array4.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BlockMutex.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Extension.H Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_Machine.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelReduce.H Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_Reduce.H Src/Base/AMReX_Utility.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_AllRegular.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_utils.cpp Src/EB/AMReX_algoim.cpp Src/EB/AMReX_distFcnElement.cpp Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/Base/AMReX_FPhysBC.cpp Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/Projections/AMReX_MacProjector.cpp Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H commit 5dbcd14861f7656df4e2b2d5a588a00b7ad5c8ef Author: Andrew Myers Date: Fri Jul 24 11:03:38 2020 -0700 rewrite these loops in a way that silences a gcc warning about potential null deferences (#1190) Src/Particle/AMReX_ParticleTile.H commit fb413521ab2ebd9fa7614c1434a4c913a3516b06 Author: Andrew Myers Date: Fri Jul 24 09:38:49 2020 -0700 Make aggregation type and buffer static member data of ParticleContainer. This silences a warning about unused variables. (#1189) Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 2acea22a9390f3a691d7c2b721aa0b03c5f44129 Author: asalmgren Date: Fri Jul 24 09:38:04 2020 -0700 D_DECL --> AMREX_D_DECL (#1188) Src/AmrCore/AMReX_ErrorList.cpp commit 0c180badf2333e18101fefbe900794fb24964e51 Author: Axel Huebl Date: Fri Jul 24 09:32:02 2020 -0700 CI: Clang 6 C++17 SP NOMPI (#1181) Add a Clang build to CI that also covers single precision (SP). .github/workflows/dependencies/dependencies_clang6.sh .github/workflows/linux.yml commit 92418c3a0256c66a365a6ee4f61510a4308348a9 Author: WeiqunZhang Date: Thu Jul 23 22:23:50 2020 -0700 Communication buffers (#1186) Use The_Cpu_Arena (BArena) instead of The_Pinned_Arena (CArena) for communication buffers to avoid the CArena fragmentation issue with the type of problems that allocate increasingly larger memory in a contiguous chunk during simulation. CArena then cannot effective use previous allocation chunks because they are slightly smaller. The fix is for CPU build only. We still need to have a strategy for this for GPU build. Src/Base/AMReX_FabArrayBase.cpp commit 9f29a86876fb1c8ada03cb121a10869211ea9bba Author: Mu-Hua Chien Date: Fri Jul 24 00:42:19 2020 -0400 Fix a bug for Nodal semicoarsening (#1185) * set up starting point * Fix the problem of semicoarsening in yz direction and restore MyTest.cpp and input-rt * fix a bug in 2d * commit for debuggin failure in tridiagonal solve * fix a bug when doing semicoarsening with short x Co-authored-by: Kan Bok-Hua Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp commit 84276f6176ca64a8df617b33c9e82a5915d72396 Author: WeiqunZhang Date: Thu Jul 23 20:28:15 2020 -0700 Add some supports for nghost vector in Fortran multifab (#1099) * Support nghost vector in Fortran multifab * nghost vector version of amrex_multifab%copy Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit e010fa881d837acd0824156323c1ff8aa44d67c5 Author: Axel Huebl Date: Thu Jul 23 19:55:28 2020 -0700 Wreorder: ErrorList (#1182) Fix: ``` AMReX_ErrorList.H:434:47: warning: field 'm_ngrow' will be initialized after field 'm_info' [-Wreorder] ``` Src/AmrCore/AMReX_ErrorList.H commit 370bccc3f3b148bde0ec9377697d5db31b4bb946 Author: Axel Huebl Date: Thu Jul 23 15:21:08 2020 -0700 Fix c++11 float narrowing (#1180) Fix a compile issue with DPC++ (SP) and AppleClang (DP): ``` Src/AmrCore/AMReX_ErrorList.cpp:318:52: error: non-constant-expression cannot be narrowed from type 'double' to 'float' in initializer list [-Wc++11-narrowing] ``` Src/AmrCore/AMReX_ErrorList.cpp commit 3b0aec5d0286b533835d1a245acd4afbc0a3067a Author: Andrew Myers Date: Thu Jul 23 14:06:11 2020 -0700 reimplement SortParticlesByCell() in terms of SortParticlesByBin(), reducing code duplication. (#1172) Src/Particle/AMReX_ParticleContainerI.H commit e1b7a288e50553150610baeabca3d6fe12e29d58 Author: Andrew Myers Date: Thu Jul 23 14:05:10 2020 -0700 Test for ghost and virtual particles (#1179) Tests/Particles/GhostsAndVirtuals/GNUmakefile Tests/Particles/GhostsAndVirtuals/Make.package Tests/Particles/GhostsAndVirtuals/inputs Tests/Particles/GhostsAndVirtuals/main.cpp commit bba8d3fa1c0bba29289caeb314ec19d6188ab84e Author: Max Katz Date: Thu Jul 23 13:41:09 2020 -0700 Switch to nvtxRangePush() and nvtxRangePop() in TinyProfiler (#1177) Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 2abcbb8bd30239dc4278cf8bbd717e1af5ab13d1 Author: Andrew Myers Date: Thu Jul 23 13:35:27 2020 -0700 fix enable_if and typedef (#1178) Src/Particle/AMReX_ParticleTile.H commit f031488e07d10d409f7fbffe52f073de055eafc9 Author: WeiqunZhang Date: Thu Jul 23 12:00:46 2020 -0700 Fused GPU kernel launches (#1135) * First pass of fused launches * fuse 4D kernels too * fuse 1D kernels too * consolidate cudaMemcpy * Fuser singleton * add a test for fuse * add more assertion on not in omp parallel region * move the varidic version of launch_global back to GpuLaunch.H because it depends on other funcitons not in GpuLaunchGlobal.H * fix comment * fix a couple of bugs * do the not-in-omp-parallel assertion only if there are fused kernels to launch * add recommended threshold for kernel fusing * missing include guard Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuFuse.H Src/Base/AMReX_GpuFuse.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchGlobal.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/Fuse/GNUmakefile Tests/GPU/Fuse/Make.package Tests/GPU/Fuse/main.cpp commit 685886a14096b5180dbb9f3e039f0d44272c8be2 Author: WeiqunZhang Date: Thu Jul 23 11:56:17 2020 -0700 update DPC++ wishlist (#1175) Docs/Notes/DPCPPWishlist.md commit 411ea9b9467f9443b8d455a98deca43b1f7233ce Author: WeiqunZhang Date: Thu Jul 23 11:55:49 2020 -0700 WARN_ALL (#1176) * WARN_ALL Add WARN_ALL option to GNUMake system to turn on more compiler warnings for gcc and clang. The default is FALSE. Fix a couple of bugs found by the warning and a number of warnings. * add WARN_ALL to documentation Docs/sphinx_documentation/source/BuildingAMReX.rst Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_EArena.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_FilCC_C.cpp Src/Base/AMReX_FilND_C.cpp Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuElixir.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PODVector.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_Random.cpp Src/Base/AMReX_Reduce.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_VisMF.cpp Src/Boundary/AMReX_InterpBndryData.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/llvm.mak commit 38e3dfb14e30c6ed05a5335185fd746d0b23ba4b Author: WeiqunZhang Date: Thu Jul 23 08:58:17 2020 -0700 fix documentation format (#1174) Docs/sphinx_documentation/source/Basics.rst commit e1cffba53407ce934add479ea73145e0ee815024 Author: Marc Day Date: Wed Jul 22 20:49:28 2020 -0700 Add alternative error tagging class (#1166) * Add alternative error tagging class * Address PR comments Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_ErrorList.cpp commit 8e535d480ab2eb3f180aeb5078d6525ec24d8a21 Author: Andrew Myers Date: Wed Jul 22 13:41:35 2020 -0700 Make ghost particles support soa data (#1053) Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParIter.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_Particles.H commit 5fa8dc1d70d58c04c7170dfbe85a02c954a8c071 Author: jmsexton03 Date: Wed Jul 22 16:07:27 2020 -0400 Fix HDF5 dataset id precision for single precision particles (#1173) Fixes segfault in amrex/Tests/HDF5Benchmark for USE_HDF5=TRUE USE_CUDA=TRUE USE_SINGLE_PRECISION_PARTICLES=TRUE Src/Particle/AMReX_ParticleHDF5.H commit 39d03b864f3bad3de32988eb5351000447075344 Author: WeiqunZhang Date: Wed Jul 22 10:49:16 2020 -0700 update CONTRIBUTING.md on how to fix git commits to have a clean history (#1164) * update CONTRIBUTING.md on how to fix git commits to have a clean history Co-authored-by: Axel Huebl CONTRIBUTING.md commit 5fa55019e580a70aa8c1a8f3f9c908f2d24ed5c2 Author: Mu-Hua Chien Date: Wed Jul 22 12:24:24 2020 -0400 Semicoarsening nodal (#1158) Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest.H commit ecb5c574f5eebd2c63080b0f561f44db9fd27581 Author: WeiqunZhang Date: Wed Jul 22 08:06:01 2020 -0700 Fix bug in #1159 (#1168) Src/Base/AMReX_DistributionMapping.cpp commit f87409ca66f212fa81315fcb77318f4a9131f63d Author: mic84 Date: Wed Jul 22 00:58:15 2020 -0700 CMake: implement ability to export build tree (#1149) * CMake: define C++ required flags as a property of target amrex * CMake: fix handling of typechecker. Just found out that: 1) We did not install typechecker 2) We do not need the typechecker path in the config file anymore * CMake: enable exporting of build-tree * CMake: linking against Flags_CXX_REQUIRED not needed anymore * CMake: MSVC preprocessor flags must the public * CMake: one more instance of Flags_CXX_REQUIRED to get rid of * CMake: clean-up and add some comments * Update Tools/CMake/AMReXInstallHelpers.cmake Co-authored-by: Axel Huebl Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReXFlagsTargets.cmake Tools/CMake/AMReXInstallHelpers.cmake Tools/CMake/AMReX_Config.cmake commit cc05b20149176b6260a903d84e89e5c073f49759 Author: WeiqunZhang Date: Tue Jul 21 19:43:13 2020 -0700 add comments to hash version of RemoveDuplicates (#1162) Src/Base/AMReX_Vector.H commit a8db2cdf5be4e62e901b68913f1b192dde6fea8c Author: Neil Carlson Date: Tue Jul 21 19:54:57 2020 -0600 Reset amrex_geometry_module initialization state when finalizing (#1165) Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_init_mod.F90 commit 3d6877fb2dbb81de5ae048f8995065b8ff0fc9e0 Author: WeiqunZhang Date: Tue Jul 21 15:56:05 2020 -0700 Remove Long version of Gatherv and reimplement AllGatherBoxes (#1161) Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_ParallelDescriptor.H commit a44b32f2d3aa92ddd33624361a60b85a2ae6f883 Author: WeiqunZhang Date: Tue Jul 21 15:16:15 2020 -0700 GatherLayoutDataToVector and DistributionMapping (#1159) Use int version of gatherv because the long version is not scalable. Use GatherLayoutDataToVector in DistributionMapping because it is faster than ReduceSum. Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelDescriptor.H commit e2da3ce40ab41cae399207e21e80df22584303c3 Author: Zach Jibben Date: Mon Jul 20 14:50:41 2020 -0600 Add interfaces for bottom solve Hypre configuration (#1150) * Add interfaces for bottom solve Hypre configuration * Remove preserve_hypre_solver flag This commit moves the Hypre and Petsc solver reset calls inside the needsUpdate if statement, removing the need for the flag. Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 27ac069c768ae5b90bbcdd6394d3070edb9b9c13 Author: WeiqunZhang Date: Mon Jul 20 13:02:35 2020 -0700 Optimization of TagBoxArray::collate (#1156) Use a new way to remove duplicated tags. Instead of removing duplicated from vector, we remove duplicates when tags are still stored in FabArray. Because they are in FabArray with a BoxArray that has no overlapped valid cells, we can use ParallelAdd to remove duplicates due to the overlap of valid cells with ghost cells. Assertion in AmrCore on blocking factor to make sure that there are no overlapped valid cells in TagBoxArray after coarsening. Use int version of Gatherv. The long version is not scalable. Broadcast pre-maxsized BoxList instead of tags. In most cases, this should reduce the amount of data to be broadcasted. Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 9a48873f0addaeeac3fff323c5feb3554bf3e260 Author: Andrew Myers Date: Sat Jul 18 14:16:36 2020 -0700 Combine two functions for periodically shifting particles into one and re-use (#1152) * combine periodic shifts into one and re-use * fix assertion Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H commit ba534dcd5f7b09285c95ed6bbcd18f49fe3922ea Author: Andrew Myers Date: Sat Jul 18 13:47:19 2020 -0700 remove the sumParticleMass function, which has been deprecated in favor of the generic reduction functions that also work on the GPU (#1153) Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d7de3d65aeea07683ecd698228925e505e2b8065 Author: jmsexton03 Date: Fri Jul 17 15:33:54 2020 -0400 Change hdf5 make syntax (#1151) Tools/GNUMake/packages/Make.hdf5 commit fedc596633f0f2c52f5b9de7349adf30873d0f04 Author: WeiqunZhang Date: Thu Jul 16 19:55:26 2020 -0700 add github action for 1D and 2D using configure (#1147) .github/workflows/linux.yml commit 62bee904a589df82e835da2a41a909955ff78db8 Author: WeiqunZhang Date: Thu Jul 16 16:54:26 2020 -0700 Error on implicit capture of this by extended lambda by default (#1148) Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 824b23f6b26b787d86d6c67a5b55be1d00b574f5 Author: Axel Huebl Date: Thu Jul 16 11:58:42 2020 -0700 CMake: More NVCC Controls (#1095) * CMake: More NVCC Controls Add control for more debug and warning flags with NVCC. - [x] ptx debug infos: performance neutral and good - [x] compilation timer: useful for interactions with Nvidia engineers - [x] keep files: good for inspecting generated PTX code - [x] warnings: accidental capture of this (CUDA11+) - [x] device LTO: awesome new feature to try (CUDA11+) - [x] unknown flags: just forward to host, make build more robust (CUDA10.2+) * Docs: New CMake CUDA Options Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_SetupCUDA.cmake commit 3efc8a9fe5aed2b82d5199dedf26baf772f40579 Author: WeiqunZhang Date: Thu Jul 16 09:31:53 2020 -0700 fix 1d compilation error in #1109 (#1144) Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 97ca27aa8a3b704309eaa92343ac8d99dedbad60 Author: Mu-Hua Chien Date: Wed Jul 15 19:15:18 2020 -0400 update semicoarsening for agglomeration (#1109) Co-authored-by: Kan Bok-Hua Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 878143a8cfb2e94fef4a769719c794e1c71314dd Author: Mark Meredith Date: Wed Jul 15 18:50:35 2020 -0400 Fix warnings (#1123) * nxm possibly uninitialized * psize possibly unused * m_runtime_r_ptrs.size() comparison of signed and unsigned types * Fix indentation Co-authored-by: Mark Meredith Src/EB/AMReX_EB2_3D_C.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleTile.H commit de3fa02f2e8415458ba11e8f0f409b44dbab779a Author: Andrew Myers Date: Wed Jul 15 15:49:25 2020 -0700 fix the redistribute test for single precision (#1141) Tests/Particles/Redistribute/main.cpp commit a3132f373219c14cc9637b3d9f28ff57f10d94a8 Author: Andrew Myers Date: Wed Jul 15 15:40:42 2020 -0700 fix clamping in enforcePeriodic (#1142) Src/Particle/AMReX_ParticleUtil.H commit e991cc91c4b5db6cd9d751f485f70c61c7626968 Author: Andrew Myers Date: Wed Jul 15 15:32:07 2020 -0700 Fix indexing error in initial conditions for EM PIC Tutorial (#1143) Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 4b182a4f608796beb37c07697599b7a0d6fc7925 Author: mic84 Date: Wed Jul 15 15:24:34 2020 -0700 Fix line lenght issues in fixed-form Fortran sources (#1139) Src/CMakeLists.txt Src/Extern/ProfParser/AMReX_AVGDOWN_2D.F Src/Extern/ProfParser/AMReX_AVGDOWN_3D.F Src/Extern/amrdata/AMReX_FABUTIL_2D.F Src/Extern/amrdata/AMReX_FABUTIL_3D.F Tools/CMake/AMReXFlagsTargets.cmake commit 7666b346859276821a0fddcc022cf014afea4e26 Author: mic84 Date: Wed Jul 15 13:51:42 2020 -0700 CMake: re-factor parallel backends setup (#1103) * CMake: start reordering parallel backends setup * CMake: forgot to add the parallel backend setup file * CMake: finalize re-organization of parallel backends setup * CMake: forgot to commit a comment Src/Base/CMakeLists.txt Src/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Tools/CMake/AMReXParallelBackends.cmake Tools/CMake/AMReX_Config.cmake commit 6f2e60118d757a374b8a8e93da195cfe244ee4cc Author: mic84 Date: Wed Jul 15 13:02:49 2020 -0700 CMake: fix missing PETSc setup in Config file (#1134) Tools/CMake/AMReXConfig.cmake.in commit bb17d53ada8c76203d8aedc90e3742d63a69b659 Author: Johannes Blaschke Date: Wed Jul 15 11:02:06 2020 -0700 work with ax3l: fail when fortran c interface could not be found -- and fail (#1140) Tools/CMake/AMReX_Defines.cmake commit 4bd7976676539d015ef1aeb6a82f45ee677fd5dd Author: mic84 Date: Tue Jul 14 15:14:06 2020 -0700 Add missing AMREX_D_DECL (#1138) Src/Extern/ProfParser/AMReX_CommProfStats.cpp commit d307624f8451a18da755a6cb1b5a3c31a42cdd48 Author: Axel Huebl Date: Mon Jul 13 19:16:17 2020 -0700 FORTLINK: Guess if Unknown (#1126) * FORTLINK: Guess of Unknown Guess the FORTLINK API convention is `UNDERSCORE` for unknown values, unless it's the classic (non-clang) IBM Fortran compiler, where it's `LOWERCASE`. * add edge case where FORTLINK couldn't be determined by CMake Co-authored-by: Johannes Blaschke Tools/CMake/AMReX_Defines.cmake commit a8ad3ad4dab830e5e425df064a8c2ca59d50ca74 Author: WeiqunZhang Date: Fri Jul 10 13:14:02 2020 -0700 remove ifdef AMREX_USE_GPU from nodal GpuBndryFunc so that it works for CPU build (#1133) Src/Base/AMReX_PhysBCFunct.H Tutorials/GPU/CNS/Source/CNS_bcfill.cpp commit cbbe896e9ab20375c8f1cc9b93f663d329fda3fb Author: mic84 Date: Thu Jul 9 17:22:59 2020 -0700 CMake: allow an application to use a different compiler than the one used to build AMReX (#1130) * CMake: an application to use a different compiler than the one used to build AMReX * CMake/mkconfig.py: more info in error message * mkconfig.py: change error message * Update mkconfig.py Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReXInstallHelpers.cmake Tools/CMake/AMReX_Config.H.in Tools/CMake/AMReX_Options.cmake Tools/libamrex/mkconfig.py commit 2be81a2ff2571fbed90a81741bb01c45748539b5 Author: WeiqunZhang Date: Thu Jul 9 15:26:39 2020 -0700 BndryFunc for nodal data (#1116) Src/Base/AMReX_FilND_C.H Src/Base/AMReX_FilND_C.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 1fd999f073b2a052732dc9bf4014895785e5b3c5 Author: Axel Huebl Date: Thu Jul 9 13:57:34 2020 -0700 AppleClang, MSVC: Avoid Malformed Config.H (#1127) * AppleClang, MSVC: Avoid Malformed Config.H Identify AppleClang as LLVM for AMReX compiler defines. Also add a fallback to avoid malforming the config header file on new/unknown/experimental compilers. * Update Tools/CMake/AMReXInstallHelpers.cmake Co-authored-by: mic84 Tools/CMake/AMReXInstallHelpers.cmake commit 03bfa214aa5fe0ea0f31968f935f8e128fd703ea Author: asalmgren Date: Thu Jul 9 13:08:46 2020 -0700 Update path for tutorials that were moved (#1128) Tutorials/FortranInterface/Advection_F/Exec/Make.Adv Tutorials/FortranInterface/Advection_octree_F/Exec/Make.Adv Tutorials/FortranInterface/Advection_octree_F2/Exec/Make.Adv commit c2a57a21bee0e80b16db46babbd3c723c2d2efa7 Author: Max Katz Date: Thu Jul 9 09:32:50 2020 -0700 Retain old timestep data during post-timestep regrid (#1122) Src/Amr/AMReX_Amr.cpp commit 0d45d8c407236d5e542b6a57e348def385f488a8 Author: WeiqunZhang Date: Thu Jul 9 09:04:56 2020 -0700 FaceLinear Interpolater for face data (#1118) It's linear in the nodal direction and constant in others. This preserves the divergence, but it's only first-order. Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp commit fd4e0d1078a489fe9f07f0d4aa9de77f1680ed2c Author: Andrew Myers Date: Wed Jul 8 21:23:02 2020 -0700 revert 1073, which introduces a subtle bug (#1121) Src/Particle/AMReX_ParticleContainerI.H commit d30a61ffbd5e0d0171242c0827ca2470c9a54d40 Author: asalmgren Date: Wed Jul 8 19:10:27 2020 -0700 Move several tutorials from Tutorials/Amr to Tutorials/FortranInterface (#1120) Tutorials/FortranInterface/Advection_F/CMakeLists.txt Tutorials/FortranInterface/Advection_F/Exec/Make.Adv Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/GNUmakefile Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Make.package Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Prob_2d.f90 Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/Prob_3d.f90 Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/face_velocity_3d.F90 Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/inputs Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/inputs.physbc Tutorials/FortranInterface/Advection_F/Exec/SingleVortex/inputs.rt Tutorials/FortranInterface/Advection_F/README Tutorials/FortranInterface/Advection_F/Source/Make.package Tutorials/FortranInterface/Advection_F/Source/Src_2d/Make.package Tutorials/FortranInterface/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/FortranInterface/Advection_F/Source/Src_2d/compute_flux_2d.f90 Tutorials/FortranInterface/Advection_F/Source/Src_2d/slope_2d.f90 Tutorials/FortranInterface/Advection_F/Source/Src_3d/Adv_3d.f90 Tutorials/FortranInterface/Advection_F/Source/Src_3d/Make.package Tutorials/FortranInterface/Advection_F/Source/Src_3d/compute_flux_3d.f90 Tutorials/FortranInterface/Advection_F/Source/Src_3d/slope_3d.f90 Tutorials/FortranInterface/Advection_F/Source/amr_data_mod.F90 Tutorials/FortranInterface/Advection_F/Source/averagedown_mod.F90 Tutorials/FortranInterface/Advection_F/Source/bc_mod.F90 Tutorials/FortranInterface/Advection_F/Source/compute_dt_mod.F90 Tutorials/FortranInterface/Advection_F/Source/evolve_mod.F90 Tutorials/FortranInterface/Advection_F/Source/fillpatch_mod.F90 Tutorials/FortranInterface/Advection_F/Source/fmain.F90 Tutorials/FortranInterface/Advection_F/Source/initdata.F90 Tutorials/FortranInterface/Advection_F/Source/my_amr_mod.F90 Tutorials/FortranInterface/Advection_F/Source/plotfile_mod.F90 Tutorials/FortranInterface/Advection_F/Source/tagging_mod.F90 Tutorials/FortranInterface/Advection_octree_F/CMakeLists.txt Tutorials/FortranInterface/Advection_octree_F/Exec/Make.Adv Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/GNUmakefile Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/Make.package Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/Prob.f90 Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/inputs Tutorials/FortranInterface/Advection_octree_F/Exec/SingleVortex/inputs.rt Tutorials/FortranInterface/Advection_octree_F/README Tutorials/FortranInterface/Advection_octree_F/Source/Make.package Tutorials/FortranInterface/Advection_octree_F/Source/Src_2d/Make.package Tutorials/FortranInterface/Advection_octree_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/FortranInterface/Advection_octree_F/Source/Src_2d/compute_flux_2d.f90 Tutorials/FortranInterface/Advection_octree_F/Source/Src_2d/slope_2d.f90 Tutorials/FortranInterface/Advection_octree_F/Source/amr_data_mod.F90 Tutorials/FortranInterface/Advection_octree_F/Source/averagedown_mod.F90 Tutorials/FortranInterface/Advection_octree_F/Source/bc_mod.F90 Tutorials/FortranInterface/Advection_octree_F/Source/compute_dt_mod.F90 Tutorials/FortranInterface/Advection_octree_F/Source/evolve_mod.F90 Tutorials/FortranInterface/Advection_octree_F/Source/fillpatch_mod.F90 Tutorials/FortranInterface/Advection_octree_F/Source/fmain.F90 Tutorials/FortranInterface/Advection_octree_F/Source/initdata.F90 Tutorials/FortranInterface/Advection_octree_F/Source/my_amr_mod.F90 Tutorials/FortranInterface/Advection_octree_F/Source/plotfile_mod.F90 Tutorials/FortranInterface/Advection_octree_F/Source/tagging_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Exec/Make.Adv Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/GNUmakefile Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/Make.package Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/Prob.f90 Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/FortranInterface/Advection_octree_F2/Exec/SingleVortex/inputs Tutorials/FortranInterface/Advection_octree_F2/README Tutorials/FortranInterface/Advection_octree_F2/Source/Make.package Tutorials/FortranInterface/Advection_octree_F2/Source/Src_2d/Make.package Tutorials/FortranInterface/Advection_octree_F2/Source/Src_2d/advect_2d_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/Src_2d/compute_flux_2d.f90 Tutorials/FortranInterface/Advection_octree_F2/Source/Src_2d/slope_2d.f90 Tutorials/FortranInterface/Advection_octree_F2/Source/amr_data_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/averagedown_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/bc_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/compute_dt_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/evolve_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/fillpatch_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/fmain.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/initdata.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/my_amr_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/plotfile_mod.F90 Tutorials/FortranInterface/Advection_octree_F2/Source/tagging_mod.F90 commit c4c271bc5468e9b0c0c49b6b05f07682e0dda312 Author: WeiqunZhang Date: Wed Jul 8 17:25:11 2020 -0700 fix BCRec vector in Fortran fillpatch thanks to @tpg2114. (#1117) Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp commit 5d82195e36511970b7a957cfafe9fb20d7576609 Author: Andrew Myers Date: Wed Jul 8 12:04:51 2020 -0700 remove another unused variable from the particle io routines (#1115) Src/Particle/AMReX_WriteBinaryParticleData.H commit 8ce63fbe9ff71287507d396dd38a85523aea8261 Author: Andrew Myers Date: Wed Jul 8 10:09:36 2020 -0700 remove unused variable (#1114) Src/Particle/AMReX_WriteBinaryParticleData.H commit 3af57db43e1c68a072903bd7068fab1e195978fc Author: WeiqunZhang Date: Tue Jul 7 23:33:43 2020 -0700 add AMREX_NO_INLINE attribute (#1111) Src/Base/AMReX_Extension.H commit 201f6e86fc95b2a7dccd328a59181544ed52dcad Author: Axel Huebl Date: Tue Jul 7 22:58:07 2020 -0700 Tutorials: Build System Race Condition (#1112) Fix a naming collision in generated Fortran modules: with enough build parallelism (N>1), a race condition could lead to sporadically failing builds. Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/SENSEI/Advection_AmrLevel/CMakeLists.txt commit c42df3e4ce635aec781dfb1a6a6a8bfcc188203d Author: mic84 Date: Tue Jul 7 17:05:22 2020 -0700 CMake: get rid of soon-to-be deprecated CUDA Fortran defines (#1110) Tools/CMake/AMReX_Defines.cmake commit de150caec585325aa540e95c36cfc01c6f7c48dc Author: asalmgren Date: Tue Jul 7 11:05:21 2020 -0700 Mlmg hypre fix (#1105) * When the operator is singular and we are solving with hypre, subtract off the average value of the solution -- hypre seems to want to add a very large constant to the solution for singular problems ... Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e354f1d2f9c2255ba5c332c528498b610cc09980 Author: WeiqunZhang Date: Mon Jul 6 22:12:53 2020 -0700 update DPC++ wishlist (#1106) Docs/Notes/DPCPPWishlist.md commit 6564cfa7c107e08bd8eb043eac71869dba6b38a9 Author: mic84 Date: Mon Jul 6 15:03:52 2020 -0700 CMake: HYPRE and PETSc support don't need Fortran anymore (#1102) Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit a5fe6eaee216cf42758612b04528d6fcdbec1afe Author: Axel Huebl Date: Mon Jul 6 15:00:20 2020 -0700 CMake: Fix CUDA Host Check (#1081) The check did only write a regular message due to a typo of the message type. Then checking the test, I realized it is not save: - false negatives are raised if e.g. CXX is set to g++ while CUDAHOSTCXX defaults to c++ - checking only env variables is not sufficient to validate user intent: setting explicitly off compilers with -DCMAKE_... variables slips through The only save check we can implement is checking compiler name and ID, but that one is blocked by a missing upstream feature: https://gitlab.kitware.com/cmake/cmake/-/issues/20901 All in all: fallback now to (flawed) env-logic but only throw a warning. Tools/CMake/AMReX_SetupCUDA.cmake commit e02489e5ed8044210a449550c96b7b838bc08d1f Author: mic84 Date: Mon Jul 6 13:39:24 2020 -0700 CMake: forgot to print option ENABLE_MPI_THREAD_MULTIPLE (#1101) Tools/CMake/AMReX_Options.cmake commit 579a0c4418e0025b5e781f4b209c9f2b0bd336b0 Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com> Date: Mon Jul 6 13:07:48 2020 -0700 Porting fortran files to cpp in Src/Extern/HYPRE (#1049) Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Habec_2D_K.H Src/Extern/HYPRE/AMReX_Habec_3D_K.H Src/Extern/HYPRE/AMReX_Habec_K.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/Extern/HYPRE/AMReX_Hypre_fort_mod.F90 Src/Extern/HYPRE/CMakeLists.txt Src/Extern/HYPRE/Make.package Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/Extern/PETSc/AMReX_PETSc_fort_mod.F90 Src/Extern/PETSc/CMakeLists.txt Src/Extern/PETSc/Make.package commit cc1f9d44fccd3e1dcdb921e24f52add3400a026e Author: Max Katz Date: Mon Jul 6 13:06:18 2020 -0700 Document GPUS_PER_SOCKET and GPUS_PER_NODE (#1097) * Document GPUS_PER_SOCKET and GPUS_PER_NODE * Update Docs/sphinx_documentation/source/GPU.rst Co-authored-by: WeiqunZhang Docs/sphinx_documentation/source/GPU.rst commit 454e55a94cb9bc85323a0f7497f9659b80ead1ed Author: WeiqunZhang Date: Mon Jul 6 13:05:46 2020 -0700 Clarify how load is measured in DistributionMapping generation. (#1100) Docs/sphinx_documentation/source/LoadBalancing.rst commit 6175b18620ede1f7a735306b3ef22133d273e4cd Author: WeiqunZhang Date: Fri Jul 3 23:49:39 2020 -0700 For nvcc >= 10.2, tell it to forward unknowns to host compiler, and we… (#1094) * For nvcc >= 10.2, tell it to forward unknowns to host compiler, and we no longer need to sanitize options for nvcc. * fix -pthread for using cuda and pgfortran Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 53bdc7c1d9109ba880874ea7539a5cbcc96b4935 Author: Andrew Myers Date: Thu Jul 2 21:43:02 2020 -0700 Add copy filter (#1089) * reimplement NumberOfParticlesInGrid * some works towards filter for add and copy * add option to filter particles when copying and adding them to the container * add trailing return type Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_Particles.H Tests/Particles/ParticleTransformations/main.cpp commit 115bdf23eed3499228508c696488126fb73fc047 Author: asalmgren Date: Thu Jul 2 21:41:30 2020 -0700 Nodal overset fix (#1091) * For nodal solves now -- test on whether we have an overset (masked) region with Dirichlet bc's -- and if so, don't set is_singular to true Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 9808be202fa3fddd724aa26b2309c3626be50e13 Author: asalmgren Date: Thu Jul 2 21:37:04 2020 -0700 Cc overset fix (#1090) * When we have an interior overset (masked) region with Dirichlet bc's, we don't set is_singular to true even if the domain bc's are all Neumann/periodic Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 33fecca07f1e8533eed7fea6daa3e3b99820041a Author: WeiqunZhang Date: Thu Jul 2 19:58:29 2020 -0700 fix rereflux at domain boundary: ghost cells outside non-periodic domain should not participate rereflux (#1088) Src/EB/AMReX_EBFluxRegister.cpp commit 37a7986b8ca114a183ec4d0ac05367a69f9c6cbc Author: Andrew Myers Date: Thu Jul 2 17:05:41 2020 -0700 Add back the levelDirectoriesCreated routine, which is used by Nyx (#1087) * add back the levelDirectoriesCreated routine, which is used by Nyx * missed async version Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleHDF5.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_WriteBinaryParticleData.H commit 78ceea62b6dfff644a335ae84b731b14693ea0be Author: Brandon Runnels Date: Thu Jul 2 16:43:18 2020 -0600 Fixed error in grownnodaltilebox (#1086) Src/Base/AMReX_MFIter.cpp commit 0e09a85064b04df316db9633ff3e95a69ced59de Author: Andrew Myers Date: Thu Jul 2 14:38:33 2020 -0700 GCC 81 workaround for Async IO (#1085) * Workaround for GCC 8.1 in particle async IO * ifdef this to only happen in 8.1 Src/Particle/AMReX_WriteBinaryParticleData.H commit a19fb05e6cb95d403e6609ffe4e1798ee6892635 Author: Mu-Hua Chien Date: Thu Jul 2 14:04:59 2020 -0400 Semicoarsening (#1072) Co-authored-by: Kan Bok-Hua Co-authored-by: Weiqun Zhang Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 1390da59e7992653390b1cd10b22fdfc1ea1c77b Author: asalmgren Date: Thu Jul 2 10:58:03 2020 -0700 Mlmg abort fix (#1083) * Abort the MLMG iterations if the residual becomes greater than 1e20 times the initial rhs (or initial resid) Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e33845666a19c0c11904bdf2e2a72fa48e30b7d3 Author: asalmgren Date: Thu Jul 2 09:43:01 2020 -0700 Nodal hypre fix (#1082) * Allow 2d nodal solver to use hypre at mglev > 0 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 600d31dd401b05326e7449d9b217d2d5e9712b4d Author: asalmgren Date: Thu Jul 2 08:44:29 2020 -0700 Mac projector fix (#1080) 1) Allow MAC projector to take overset mask 2) have MacProjector's setVerbose not just reset local variable but also reset LinOp's verbosity Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 0f1dfb3e12505a6912e7f7838a9e8b0ea0bedb8a Author: mic84 Date: Wed Jul 1 18:39:35 2020 -0700 CMake: add support for MPI multiple threads (#1079) Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.H.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 9d9d06a91ce3bb7d7b2411a63f1d5cd5ce54f477 Author: WeiqunZhang Date: Wed Jul 1 15:12:53 2020 -0700 class BackgroundThread and use it for AsyncOut (#1078) * add BackgroundThread class * use BackgroundThread in AsyncOut * fix for Windows Src/Base/AMReX_AsyncOut.H Src/Base/AMReX_AsyncOut.cpp Src/Base/AMReX_BackgroundThread.H Src/Base/AMReX_BackgroundThread.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit a5ba208b4a2c5aec85551ef1fd40e08263b0b7ce Author: Andrew Myers Date: Wed Jul 1 14:05:44 2020 -0700 reimplement NumberOfParticlesInGrid (#1077) Src/Particle/AMReX_ParticleContainerI.H commit 12190b20114393254b689e7456857e734a7b566a Author: Andrew Myers Date: Wed Jul 1 11:06:01 2020 -0700 reimplement NumParticlesAtLevel (#1073) * reimplement NumParticlesAtLevel * I guess this needs to be host / device Src/Particle/AMReX_ParticleContainerI.H commit 443fad731bd28291c3d03b58cb521a339b40852b Author: Andrew Myers Date: Wed Jul 1 11:01:31 2020 -0700 Async IO for Particles (#1058) Src/Base/AMReX_GpuAllocators.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleHDF5.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_WriteBinaryParticleData.H Src/Particle/CMakeLists.txt Src/Particle/Make.package Tests/Particles/AsyncIO/GNUmakefile Tests/Particles/AsyncIO/Make.package Tests/Particles/AsyncIO/inputs Tests/Particles/AsyncIO/main.cpp commit 2e188a7500bc84572d91410b92bbe9c1a1b6c7e5 Author: Andrew Myers Date: Wed Jul 1 10:34:22 2020 -0700 Restore nl tutorial (#1075) * add back in this tutorial * update for levels * use parallelfor instead of the macro for some reason * move this tutorial to Particles Src/Particle/AMReX_DenseBins.H Tutorials/Particles/NeighborList/CMakeLists.txt Tutorials/Particles/NeighborList/CheckPair.H Tutorials/Particles/NeighborList/Constants.H Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/MDParticleContainer.H Tutorials/Particles/NeighborList/MDParticleContainer.cpp Tutorials/Particles/NeighborList/Make.package Tutorials/Particles/NeighborList/README.md Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/script.sh commit ca12febf19571d51a4cb7f164f25ed2a17f194ca Author: WeiqunZhang Date: Wed Jul 1 09:18:49 2020 -0700 update CHANGES (#1076) CHANGES commit a2f432016158000b797d4a6b7f5c72879be505f1 Author: Andrew Myers Date: Tue Jun 30 15:54:43 2020 -0700 bugs in documenation pointed out by Mark Sussman (#1074) Docs/sphinx_documentation/source/Particle.rst commit 6558075e444749af7021ecda9abe7c1c25cc2e46 Author: OscarAntepara <52221614+OscarAntepara@users.noreply.github.com> Date: Tue Jun 30 11:12:41 2020 -0700 Updating external solvers doc (#1068) * Updating external solvers doc * Fixing couple of lines in the doc Docs/sphinx_documentation/source/LinearSolvers.rst commit 8117ed5e33f35b77de2b96396709c581ed59c1dc Author: asalmgren Date: Mon Jun 29 16:57:49 2020 -0700 Nodal hypre fix (#1069) Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d93db0a9500dda2d1964abac5e0f1d8a29f0d59c Author: WeiqunZhang Date: Sat Jun 27 13:42:20 2020 -0700 Manage memory (#1066) * add runtime parameter to not use managed memory for The_Arena * udpate documentation Docs/sphinx_documentation/source/GPU.rst Src/Base/AMReX_Arena.cpp commit ef8ac4a78d4ee45b50ffc7dcc7731163d8887cb3 Author: Max Katz Date: Sat Jun 27 13:41:55 2020 -0700 Set backtrace threadprivate exception for PGI (#1067) Src/Base/AMReX_BLBackTrace.H commit 38572ef1ff1da8fe89482183f66bf5ba6b91813d Author: WeiqunZhang Date: Fri Jun 26 17:36:25 2020 -0700 Gpu stream thread safety (#1064) * Make gpu streams omp cpu thread safe. Add OpenMP namespace for convenience. * use the new OpenMP:: functions * fix typo Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_OpenMP.H Src/Base/AMReX_Random.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 0f17d07b66aa1a80de8384f7b8b55316fef2f630 Author: kngott <30483578+kngott@users.noreply.github.com> Date: Fri Jun 26 13:23:47 2020 -0700 GPU + OMP documentation adjustment. (#1065) Docs/sphinx_documentation/source/GPU.rst commit d1ce22a7c19948363adb1d3af97b2a57ce6b688e Author: WeiqunZhang Date: Fri Jun 26 10:57:39 2020 -0700 Add mpi reduction to fix a bug in overset linear solver (#1061) Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 116ff2a98f40ac1b742b7d2bc6d930b312f1dc62 Author: Max Katz Date: Fri Jun 26 10:02:38 2020 -0700 MFIter reducer belongs only to AMREX_USE_GPU_PRAGMA (#1063) * MFIter reducer belongs only to AMREX_USE_GPU_PRAGMA * Simplify logic for operator++ Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 385a0a5c8881deabeb469f38d1a8399f39be0731 Author: Max Katz Date: Thu Jun 25 15:02:09 2020 -0700 Only add generic GNU flags to F compiler when appropriate (#1060) * Only add generic GNU flags to F compiler when appropriate * Remove redundant flags Tools/GNUMake/comps/gnu.mak commit 62619cc04a0795fdd8def9e94f3698b660e12a5b Author: WeiqunZhang Date: Thu Jun 25 14:24:38 2020 -0700 fix the version of tilebox that takes index type and grow cells (#1059) Src/Base/AMReX_MFIter.cpp commit 7e5c619d5ce21907e6f4dbcff17fef3c3a10d992 Author: WeiqunZhang Date: Thu Jun 25 13:39:01 2020 -0700 remove compile time BACKTRACE flag for simplicity (#1055) * remove compile time BACKTRACE flag for simplicity * update documentation on backtrace .github/workflows/linux.yml .github/workflows/macos.yml Docs/Notes/Readme.backtrace Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/BuildingAMReX.rst Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.H.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/GNUMake/Make.defs commit a3924af54d4ae1825d1d3a5462e614c4f547726c Author: Cyrus Harrison Date: Thu Jun 25 12:30:59 2020 -0700 fix const issue with blueprint particle wrapping (#1057) Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit 26d8bf04ef87c3090d8e68e63fbcfe776c4b3bc1 Author: Cyrus Harrison Date: Thu Jun 25 10:37:45 2020 -0700 blueprint: wrap amr nesting info for use in ascent (#1051) * this is the magic * populate nestset * get the nesting correct * cleanup * remove more debugging statements * restore file * make a uniform data set * only add nestsets to more than 1 level * don't add nestset unless there are children or parents * change the order of find packages for conduit * have ENABLE_ASCENT trigger the conduit path Co-authored-by: Matt Larsen Src/CMakeLists.txt Src/Extern/Conduit/AMReX_Conduit_Blueprint.H Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp Src/Extern/Conduit/CMakeLists.txt commit 87c998acd4004796090ffad5285345ef3f725d79 Author: WeiqunZhang Date: Wed Jun 24 17:15:02 2020 -0700 fix Abs for FabArray (#1004) Src/Base/AMReX_FabArrayUtility.H commit dc2a02a30555986af0f6825b490d18a59e39bd8d Author: mic84 Date: Wed Jun 24 17:04:08 2020 -0700 CMake: print out only the enabled configuration options (#1052) Tools/CMake/AMReX_Options.cmake commit 32d2e44041cc0cc113ea66a3cce4526b114b0a4c Author: mic84 Date: Wed Jun 24 15:57:16 2020 -0700 CMake: add HDF5 support (#1048) Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_Config.H.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit df3e65beac99290a0d9d1e0753b06e29f1002940 Author: WeiqunZhang Date: Wed Jun 24 06:52:55 2020 -0700 Fix Allocator comparison operator (#1050) * Remove allocator comparison operators, because they are too generic. * fix bug in PODVector * fix PloymorphicAllocator * fix cast in PODVector * fix return Src/Base/AMReX_GpuAllocators.H Src/Base/AMReX_PODVector.H commit a8b4d5c95b74e6e87fa8ddf119b246f58f76e718 Author: Andrew Myers Date: Tue Jun 23 18:21:37 2020 -0700 put USE_HDF5 in the GNUMake build system (#1047) Tests/HDF5Benchmark/GNUmakefile Tests/Slice/GNUmakefile Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.hdf5 commit 5ad4ae219e76730d009319b516de6a635f5d4164 Author: Marc Day Date: Tue Jun 23 08:34:52 2020 -0700 fix bug in arguments passed to derFuncFab in one of the derive functions (#1045) Src/Amr/AMReX_AmrLevel.cpp commit 9b2172017f8aa6aea00bda090e7c93e7919ff6eb Author: asalmgren Date: Sun Jun 21 16:19:47 2020 -0700 Fix for hypre (#1044) * When using hypre, limit number of possible multigrid levels by how much the EB can be coarsened * Remove assertion that hypre can only be called when number of mg levels = 1 now that we restrict the building of levels based on coarsening of the EB. Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit d6a28508104c2a22a6075c0e68c95d6efec35e37 Author: WeiqunZhang Date: Sat Jun 20 21:56:36 2020 -0700 dpc++: unless explicitly specified, use default standard, which is c+… (#1043) * dpc++: unless explicitly specified, use default standard, which is c++ 17 in beta 7 * CMake: enforce c++17 for dpc++ builds Co-authored-by: Michele Rosso Tools/CMake/AMReXSYCL.cmake Tools/GNUMake/comps/dpcpp.mak commit 82ec2dc54fd2a8bd21d79291d8bbf7ca91f8b8a8 Author: WeiqunZhang Date: Fri Jun 19 17:50:58 2020 -0700 fix 2d initializaton of linear solver tutorials (#1042) Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 commit 8be36ee57c5d4ab4ad810d0898dc79c2fa9f3d5b Author: WeiqunZhang Date: Fri Jun 19 17:46:54 2020 -0700 Initialize MPI_Wtime (#1041) Src/Base/AMReX_ParallelDescriptor.cpp commit 123970a7dd6a6a066121e3bacae365c47d0e1f73 Author: WeiqunZhang Date: Fri Jun 19 13:38:09 2020 -0700 Since DPC++ beta7, we can use link time flag -device-math-lib (#1040) Tools/GNUMake/comps/dpcpp.mak commit ca2138c3853e9232f1f8fa81afaa3edd17c00547 Author: mic84 Date: Fri Jun 19 12:31:54 2020 -0700 CMake: disable 'run' test when ENABLE_DPCPP=ON (#1039) Tutorials/Basic/HeatEquation_EX1_CF/CMakeLists.txt commit e16f97e878fefe544917caf5f0566048ad933d04 Author: WeiqunZhang Date: Fri Jun 19 11:36:31 2020 -0700 fix a tutorial for dpc++ (and cuda) (#1038) * fix a tutorial for dpc++ (and cuda) * Fix code block alignment Co-authored-by: Axel Huebl Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp commit cc65bd6f21d65e6d3183ebc8b875252b67b23a15 Author: Axel Huebl Date: Fri Jun 19 09:02:00 2020 -0700 CI: DPC++ (#943) Prepares Intel DPC++ CI builds. .github/workflows/cmake/dependencies_dpcpp.sh .github/workflows/linux.yml commit b3609f062ea6fb968be05ab7a2415d7e1e841a57 Author: Axel Huebl Date: Thu Jun 18 20:44:24 2020 -0700 CMake Summary: No Fortran (#1037) Disable Fortran summary details if Fortran is not used. Tools/CMake/AMReX_Config.cmake commit 4b4719ab7be2d5b7c8669df32e69b2226c66544c Author: Houjun Date: Thu Jun 18 15:53:05 2020 -0700 Update HDF5 particle write and benchmark codes (#1035) * Update HDF5 related code for better write performance * Update Makefile for HDF5Benchmark * Update GNUmakefile * Update inputs * Use correct MPI datatype from AMReX Co-authored-by: Houjun Tang Src/Base/AMReX_PlotFileUtil.cpp Src/Particle/AMReX_ParticleHDF5.H Tests/HDF5Benchmark/GNUmakefile Tests/HDF5Benchmark/inputs Tests/HDF5Benchmark/main.cpp commit dfa064a3547e643f3dbc1a6317794dc943e85ee2 Author: asalmgren Date: Thu Jun 18 14:55:44 2020 -0700 Remove CCSE-specific info from Tools/GNUMake. (#1036) Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.ccse commit 67a96b8b3f50633b9c8d00bdcf8bd40485d9f2f2 Author: Axel Huebl Date: Wed Jun 17 21:16:15 2020 -0700 Conduit: Work-Around Missing Const (#1032) This is a work-around for missing `const` qualifier overloads in Conduit's `node::set_external()`. Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit 1816b9cd1936ba737d438ee43edfd88ad01513d5 Author: mic84 Date: Wed Jun 17 13:45:43 2020 -0700 CMake: create SYCL target to handle dpcpp builds (#1034) * CMake: get rid of dpc++ flags -fsycl-unnamed-lambda at link time * CMake: create SYCL target to handle dpcpp builds * CMake: treat libsycl-glibc.o as link object rather than an interface source * Add SYCL AOT Comment Co-authored-by: Axel Huebl Src/CMakeLists.txt Tools/CMake/AMReXSYCL.cmake Tools/CMake/AMReX_Config.H.in Tools/CMake/AMReX_Config.cmake commit 6e99321e9a49c5a1899c8ca7b8034fd4b4dd79e8 Author: Andrew Myers Date: Wed Jun 17 10:20:12 2020 -0700 Allow customization of the allocator used for ParticleTile (#1026) * add ability to specify allocator for a particle tile * fix ifdef * missed a few places where the default allocator was used Src/Base/AMReX_GpuAllocators.H Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit a9a2e82e3972e991df03bd71578827b1f2344f20 Author: WeiqunZhang Date: Wed Jun 17 08:12:33 2020 -0700 remove reference to master branch. change terminology in StateDescriptor. (#1033) CONTRIBUTING.md Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/index.rst Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp commit 8f94577b219700a5117d0fd67c6e8a198c79ebf3 Author: WeiqunZhang Date: Tue Jun 16 20:38:59 2020 -0700 overset support for tensor solver (#1029) Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Tests/LinearSolvers/TensorOverset/GNUmakefile Tests/LinearSolvers/TensorOverset/Make.package Tests/LinearSolvers/TensorOverset/MyTest.H Tests/LinearSolvers/TensorOverset/MyTest.cpp Tests/LinearSolvers/TensorOverset/MyTest_K.H Tests/LinearSolvers/TensorOverset/main.cpp commit 5ed64778cdca5134248b3055db037a4f25a14a8d Author: mic84 Date: Tue Jun 16 17:42:10 2020 -0700 CMake: get rid of AMReX_Machines.cmake (#1028) * CMake: remove AMReX_Machines.cmake * CMake: get system info via native CMake tools rather than uname CMakeLists.txt Tools/CMake/AMReXBuildInfo.cmake Tools/CMake/AMReX_Machines.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake commit 99a008f7c094d177946f9a297568076051d767cc Author: Axel Huebl Date: Tue Jun 16 17:42:01 2020 -0700 Conduit: Fix CMake Target Typo (#1031) Add a missing : in the `conduit::conduit` target. Src/Extern/Conduit/CMakeLists.txt commit 467dc1cc53d5745bb2382afff001057da4cb5976 Author: Brian Friesen Date: Tue Jun 16 17:39:27 2020 -0700 Tools: remove Make.cscs since Piz Daint is not used anymore (#1027) Tools/GNUMake/sites/Make.cscs commit 747e5cf57faaf93b416998596b01968e529a2fc4 Author: asalmgren Date: Tue Jun 16 10:54:19 2020 -0700 Update how we write out EB data so it correctly handles problo !=0 (#1024) * Update how we write out EB data so it correctly handles the case when problo is not 0. * replace real(lo) and real(llc) by real(lo,amrex_real) and real(llc,amrex_real) Src/EB/AMReX_WriteEBSurface.cpp Src/EB/AMReX_WriteEB_F.H Src/EB/AMReX_eb_to_pvd.F90 commit df7729dc498e81cb366ed874a3cd613bd2a5e567 Author: WeiqunZhang Date: Mon Jun 15 18:13:23 2020 -0700 Support for overset in cell-centered MLABecLaplacian (#1023) * cell-centered ABecLaplacian linear solver for overset * At coarse MG levels, we rescale the b coefficient at the overset boundary so that the overset points are essentially at fixed location. This is important for convergence. * set overset region's rhs to zero inside the solver * clean up Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/CellOverset/GNUmakefile Tests/LinearSolvers/CellOverset/Make.package Tests/LinearSolvers/CellOverset/MyTest.H Tests/LinearSolvers/CellOverset/MyTest.cpp Tests/LinearSolvers/CellOverset/main.cpp commit bc6134dfdf464b40bef483c05c28644a1d540b2d Author: Andrew Myers Date: Mon Jun 15 17:27:54 2020 -0700 Fix conduit for changes to particles (#1010) Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H Src/Particle/AMReX_ArrayOfStructs.H commit 65d60c442e95498239f18d47fc64d0082124b774 Author: WeiqunZhang Date: Fri Jun 12 17:58:27 2020 -0700 add assertion on EB statck (#1020) Src/EB/AMReX_EB2.H commit c397ad30b72d7ce6af1045c4572984c297a729f8 Author: mic84 Date: Fri Jun 12 17:11:50 2020 -0700 CMake: add support for DPCPP (#1016) Co-authored-by: Axel Huebl CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 6a5131cbbae227f6af07e0efc93bd95df0ac81c7 Author: WeiqunZhang Date: Fri Jun 12 16:44:23 2020 -0700 These files need to be included even when Fortran is off. (#1019) Src/Base/CMakeLists.txt commit 9a40723c7846191aac6288db996a20450b6d2b5a Author: mic84 Date: Fri Jun 12 14:50:33 2020 -0700 CMake: set minimum C++ standard to 17 for Windows builds (#1017) * CMake: set minimum C++17 for Windows builds * CMake CI: no need to set C++ standard for windows CI .github/workflows/windows.yml Tools/CMake/AMReX_Config.cmake commit 1d75ba05f084cd3c1d91dacefdfedc6c2e85ab7f Author: Andrew Myers Date: Fri Jun 12 08:15:06 2020 -0700 fix typo introduced in #995 (#1013) Src/Particle/AMReX_NeighborParticlesI.H commit d59c1a8b8bdc58b435b9281072afc3ecf51c2a45 Author: Axel Huebl Date: Fri Jun 12 06:26:11 2020 -0700 Single Precision: INVALID_TIME Value OoR (#1011) * SinglePrecision: INVALID_TIME Value OoR AppleClang 11.0.3 in single precision build errors with on WarpX: ``` error: constexpr variable 'INVALID_TIME' must be initialized by a constant expression static constexpr Real INVALID_TIME = -1.0e200; ^ ~~~~~~~~ WarpX/build_sp/_deps/fetchedamrex-src/Src/Amr/AMReX_StateData.cpp:17:38: note: value -1.0E+200 is outside the range of representable values of type 'const amrex::Real' (aka 'const float') static constexpr Real INVALID_TIME = -1.0e200; ``` This changes the numeric value of this constant to the minimum in the supported range of the underlying data type. * INVALID_TIME: Only change for Float Src/Amr/AMReX_StateData.cpp commit ba9be262a0fa5d493e8193f253a5b219244536bb Author: Axel Huebl Date: Thu Jun 11 21:46:47 2020 -0700 CI: Verbose Make (#1012) Although we build with `-j2` to speed up CI on all available cores, this can improve understanding if things fail. .github/workflows/linux.yml .github/workflows/macos.yml .github/workflows/windows.yml commit 33a35a8ff4af38924c2c54fb53f8fdceab8f18e8 Author: mic84 Date: Thu Jun 11 17:09:54 2020 -0700 CMake: fix bug introduced in PR #996 (#1009) Tools/CMake/AMReXFlagsTargets.cmake commit c69e431ed9bfe71d13c2c00dd39ac9f75f420650 Author: WeiqunZhang Date: Thu Jun 11 14:32:21 2020 -0700 add -DNDEBUG for non-debug build (#1006) * add -DNDEBUG for non-debug build * Don't define NDEBUG if USE_ASSERTION is TRUE Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit d73c9d180b0e4e485473a121ddf0bda04103ab87 Author: WeiqunZhang Date: Thu Jun 11 13:50:43 2020 -0700 use launch function instead of macro so that we can have ifdef inside (#1008) Src/Base/AMReX_Scan.H commit 6cfdc9f634273953b5b6e9f51db2bfd2134d4431 Author: WeiqunZhang Date: Thu Jun 11 11:51:46 2020 -0700 use iso646 to provide alternative operator names for Windows (#1003) Src/Base/AMReX.H Src/Base/AMReX_Extension.H Tools/CMake/AMReXFlagsTargets.cmake commit cccc96a37de6098316069fb5ada5839d8e5526b4 Author: WeiqunZhang Date: Thu Jun 11 11:18:58 2020 -0700 update comments on abs function (#1005) Src/Base/AMReX_Math.H commit 607d36634d331425f0f433913af601b4cba7433d Author: WeiqunZhang Date: Thu Jun 11 11:03:56 2020 -0700 reduce duplication in indexFromValue (#1002) Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit 2d4ad87b5f30f33768c91a307151a54c111a2cfe Author: Andrew Myers Date: Thu Jun 11 08:55:46 2020 -0700 Particle parallel context (#995) Src/Base/AMReX_ParallelDescriptor.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleBufferMap.cpp Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleMPIUtil.cpp Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_ParticleUtil.cpp Src/Particle/AMReX_TracerParticles.cpp Tests/Particles/ParallelContext/GNUmakefile Tests/Particles/ParallelContext/Make.package Tests/Particles/ParallelContext/inputs.rt Tests/Particles/ParallelContext/main.cpp commit 2e15ac4b042b8154bb05733636824b3543a8266f Author: WeiqunZhang Date: Wed Jun 10 13:36:43 2020 -0700 Remove this OutOfMemory that is never defined. (#999) Src/Base/AMReX.H commit 9550f73aa21a04c243d3617b1cc1ece0acc1955d Author: WeiqunZhang Date: Wed Jun 10 13:35:55 2020 -0700 fix unused variable warning (#1000) Src/Base/AMReX_AsyncOut.cpp commit 231990f61bcde4946d1dae23080496e5fa5f632e Author: WeiqunZhang Date: Wed Jun 10 13:35:23 2020 -0700 No need to make subcommunicator if neither agglomeration nor consolidation is done (#998) Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit fd03d74ea9df3b081e667bb9b82773dec5391666 Author: WeiqunZhang Date: Wed Jun 10 13:17:10 2020 -0700 fix nvcc version for Cuda 11 (#997) Tools/GNUMake/comps/nvcc.mak commit 3bee52740bf4201a870e5b418f13e0613851686f Author: Robert Maynard Date: Wed Jun 10 16:07:24 2020 -0400 CMake: improve MSVC+CUDA support (#996) The primary issue now is that nvcc doesn't seem to be parsing with /Za enabled, so alternate tokens are causing compile failures. Tools/CMake/AMReXFlagsTargets.cmake Tools/CMake/AMReX_SetupCUDA.cmake commit 37224d307ab7baa32b6eea666a981a9758ab06f4 Author: Andrew Myers Date: Wed Jun 10 10:29:44 2020 -0700 Non const iterator neighbor list (#994) * build non-const iterator for neighbor lists * build non-const iterator for neighbor lists * implement non-const iterators for neighbor list * remove second access operator for Neighbors::iterator * const Co-authored-by: Johannes Blaschke Src/Particle/AMReX_NeighborList.H Tests/Particles/NeighborParticles/MDParticleContainer.cpp commit 399917f45ac0502ebf2247dd2ac182e1705e33ca Author: Andrew Myers Date: Tue Jun 9 07:34:29 2020 -0700 Make PrintToFile() and AllPrintToFile() work with ParallelContext (#991) Src/Base/AMReX_Print.H commit 1eff033385765a49110b9cea681bdaa619e4e298 Author: Andrew Myers Date: Mon Jun 8 22:13:21 2020 -0700 remove some testing code I checked in by mistake (#992) Tests/Particles/Redistribute/main.cpp commit db9e1d25230331869aed5abf0e4fb2b121718efe Author: mic84 Date: Mon Jun 8 22:11:12 2020 -0700 CMake: improve MSVC support (#989) * CMake: do not force 64bit CUDA builds on Windows CUDA only supports 64bit builds on windows ( 32bit builds are deprecated ). Thus the option "--machine 64", AKA "-m64" is set by the msbuild configuration automatically. * CMake: new interface library Flags_CXX_REQUIRED * CMake: always use C++ required flags in the build * CMake: remove wrong definition of compile options for MSVC. The new Flags_CXX_REQUIRED will take care of MSVC correctly. * CMake: pass required C++ flags to CUDA compiler. * CMake: fix bug in setting CXX required flags for CUDA target * CMake: update required MSVC flags * CMake: add comment * CMake: modify MSVC flags to account for compiler version * CMake CI: force verbosity during MS build * Revert "CMake CI: force verbosity during MS build" This reverts commit 8f6148ab70df1dac9627a9e4aae32fa9daed57bc. * CMake: make sure C++ compiler version for GNU and MSVC > minimum. CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReXFlagsTargets.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_SetupCUDA.cmake Tools/CMake/AMReX_Utils.cmake commit 3a1915e324ffcd170473ae690b1411703b76b42b Author: Andy Nonaka Date: Mon Jun 8 14:39:59 2020 -0700 Compare single-level plotfiles; diff and norms; all nodalities (#983) * new utility to compare plotfiles and take norms. goal is to work for any nodality * begin new functionality for ComparePlotfiles routine * ComparePlotfiles.cpp WIP * saving progress * periodicity fix * fix a bug in norm2 where there are overlaps * first draft of ComparePlotfiles, including PrintUsage * plotfile diff and norm utility * consolidated all cases into 1 loop * more comments * remove debugging statement * option to point to data directly, rather than plotfile base this is useful for warpx when using "plot_raw_fields"; where the nodal data is output to a non-standard directory * implement Weiqun's suggestions Co-authored-by: Weiqun Zhang Tools/C_util/Convergence/ComparePlotfiles.cpp Tools/C_util/Convergence/GNUmakefile commit a2961b1e2b91ad2bc9801ac85a655cb5915e5a9a Author: WeiqunZhang Date: Mon Jun 8 12:15:06 2020 -0700 use __CUDACC_VER_MAJOR__ instead of AMREX_NVCC_MAJOR_VERSION, which is gone (#988) Src/Base/AMReX_GpuDevice.cpp commit 8eb5b5e6859f4e0a0ff9cec75811cf871ed1a2b0 Author: kngott <30483578+kngott@users.noreply.github.com> Date: Mon Jun 8 10:51:16 2020 -0700 Modify HeatEquation dts to account for non-cubic cases. (#977) Src/Base/AMReX_SPACE.H Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_CF/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_F/Make.package Tutorials/Basic/HeatEquation_EX1_F/fmain.F90 Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_CF/Source/main.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp commit 86a361c8856bdda455e3fe7d2c01b4d7ce35261a Author: WeiqunZhang Date: Mon Jun 8 08:58:56 2020 -0700 Fix a missing semicolon (#986) Src/Base/AMReX_GpuLaunchFunctsG.H commit 70afa5a814a16fdeba7b18f03115f6ece5b8b5a2 Author: WeiqunZhang Date: Sat Jun 6 16:58:01 2020 -0700 fix a bug in norm2 where there are overlaps (#982) Src/Base/AMReX_MultiFab.cpp commit f52f7beeb1c47b30ebd15830c1f3c25e3a025c89 Author: WeiqunZhang Date: Sat Jun 6 15:48:42 2020 -0700 Make: use -M to generate dependencies (#980) * Make: use -M to generate dependencies * use > to save output because pgi does not support -o * remove redundant flag * comment out some cray flags that generate compile information we usually don't need * use -o for dpcpp because it does not put output of -M in stdout Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/cray.mak Tools/GNUMake/comps/nvcc.mak commit 6d76716ef6d108f2f66ae918e7d80976331cc4c5 Author: mic84 Date: Sat Jun 6 09:40:50 2020 -0700 Remove compiler version defines from compile definitions (#981) Tools/CMake/AMReX_Config.H.in Tools/CMake/AMReX_Config.cmake Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/llvm-flang.mak Tools/GNUMake/comps/llvm.mak Tools/GNUMake/comps/nag.mak Tools/GNUMake/comps/nvcc.mak commit f889ad3b6081e188ead46a14927517e26f08df5a Author: WeiqunZhang Date: Wed Jun 3 17:21:45 2020 -0700 add a macro so that it's easy to reproduce the issue (#976) Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 1132127817d4b5edfd6130853a16f4df44452624 Author: WeiqunZhang Date: Wed Jun 3 17:21:26 2020 -0700 This earlier stopgap for EB tensor solver with DPC++ is no longer needed. (#974) Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit c69e4409ae3fad6f285ab173a23ea6c79acfb092 Author: WeiqunZhang Date: Wed Jun 3 15:20:44 2020 -0700 Option to add extra CPPFLAGS from command line (#975) Tools/GNUMake/Make.defs commit 1841a87f9531e3c6f29887e1f79ee2d521ff97c0 Author: WeiqunZhang Date: Wed Jun 3 14:01:52 2020 -0700 fix DPC++ bug introduced in 8272ea8b84f3027f1d (#973) Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit befabe69319379658510d47896f4e79e27c28db0 Author: WeiqunZhang Date: Wed Jun 3 09:55:54 2020 -0700 update documentation for Windows (#972) Docs/sphinx_documentation/source/BuildingAMReX.rst commit d462130220d51d44ea406b7fd33ed246dd89acb3 Author: Axel Huebl Date: Wed Jun 3 09:05:33 2020 -0700 CI: Mainly Debug (#971) Enable debug builds for most CI builds. Easier to catch errors and enables more checks. .github/workflows/linux.yml .github/workflows/macos.yml .github/workflows/windows.yml commit a3a1e8fe5174dc84cc1f4e4e415fba085f7904aa Author: Andrew Myers Date: Tue Jun 2 17:03:59 2020 -0700 remove moveKick, which is not used any more (#970) Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 294066686c92f5a2d11687c188824c6fb8a5d808 Author: Axel Huebl Date: Tue Jun 2 12:52:13 2020 -0700 CMake CUDA: Cleanups & CCache (#964) * CMake CUDA: Cleanups & CCache - gencode: use no-space syntax; this confuses CCache<4.0 (all available releases today) and is complicating deduplication operations on lists - min CXX standard in CUDA: technically the right thing to set this as well for the CMake CUDA C++ language * Update AMReX_Config.cmake CUDA meta-features were introduced with CMake 3.17, see: [https://blog.kitware.com/cmake-3-17-0-rc3-is-ready-for-testing/](https://blog.kitware.com/cmake-3-17-0-rc3-is-ready-for-testing/). Co-authored-by: mic84 Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_SetupCUDA.cmake commit d74a1c95a41438ea77c2e3c320b567607fb1e562 Author: Andrew Myers Date: Tue Jun 2 12:29:15 2020 -0700 remove WriteCoarsenedAsciiFile method (#968) Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H commit 3aaa8b67f6bf18b291e0136db57c659da719d9d8 Author: Andrew Myers Date: Tue Jun 2 12:28:32 2020 -0700 fix new bug I just introduced (#969) Src/Particle/AMReX_ParticleInit.H commit 0950e22ac4433f98642f43afa25d4508d43e03c0 Author: Andrew Myers Date: Tue Jun 2 11:38:01 2020 -0700 Remove directly accessing the m_idata and m_rdata structs internally (#963) Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleHDF5.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 33d534b2c021355f4eaaf643cba97b2a3588c84a Author: Andrew Myers Date: Tue Jun 2 09:29:14 2020 -0700 make sure we enable particles in cmake CI (#966) .github/workflows/linux.yml .github/workflows/macos.yml commit bfdf479f1092ca75677f8431e812efa58178fc79 Author: WeiqunZhang Date: Tue Jun 2 09:21:50 2020 -0700 ifdef out htod_memcpy (#967) Src/EB/AMReX_EB2_IF_Polynomial.H commit 98663ccab011d20a5f0ec54359f4a2d262b8eab2 Author: Axel Huebl Date: Tue Jun 2 06:35:34 2020 -0700 ParticleIO: Update Arg Signature Usage (#965) Follow-up to new function signature. Src/Particle/AMReX_ParticleIO.H commit 8272ea8b84f3027f1d78746006c62f570f3cadb0 Author: WeiqunZhang Date: Mon Jun 1 22:41:55 2020 -0700 Windows (#947) * If it's Windows, use C++17 for files system operations, and avoid posix functions. * Avoid gcc extension that allows embedded prepressor directive in function macro. * Get around some MSVC template argument deduction issues. * Rename amrex::USleep to amrex:Sleep and use C++ thread for sleep. The reason for renaming is it would be very confusing that usleep in unistd sleeps for given microseconds whereas amrex::USleep sleep for given seconds. * Windows CI Co-authored-by: Axel Huebl .github/workflows/windows.yml Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX.cpp Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array4.H Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Extension.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FileSystem.H Src/Base/AMReX_FileSystem.cpp Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuMemory.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_SPACE.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Difference.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EB_utils.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/Particle/AMReX_ParticleIO.H Tests/AsyncOut/multifab/main.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/MKDir/MKDir.cpp Tools/AMRProfParser/TestCodes/AMRProfTest0.cpp Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp Tools/CMake/AMReXFlagsTargets.cmake Tools/CMake/AMReX_Config.cmake commit 2d2dbf423b2977460f19aac2f108b72932c4d875 Author: Andrew Myers Date: Mon Jun 1 22:40:07 2020 -0700 remove the RealDescriptor args, which aren't used anyway (#962) Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H commit baaed44ccff92c696503e800c3cb913cc65737ce Author: Andrew Myers Date: Mon Jun 1 15:33:30 2020 -0700 handle more unused variables (#961) Src/AmrCore/AMReX_Interpolater.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_PhysBCFunct.H commit dfa5023c9237476a4fb770740959f5ce6ea53fb6 Author: Andrew Myers Date: Mon Jun 1 15:03:37 2020 -0700 only define these functions if AMREX_USE_GPU is true (#960) Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_PODVector.H commit b6ea3e816af7a32709079ff695689d281506dc0a Author: WeiqunZhang Date: Mon Jun 1 15:03:17 2020 -0700 avoid embedded macro directive in macro function argument because it's not portable (#959) Src/Base/AMReX_Arena.cpp Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuElixir.cpp Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_Scan.H Tests/GPU/Locking/main.cpp commit 79d62bebd471442d8aa638f2ff38f28c26f6d4c7 Author: Shreyas Ananthan Date: Mon Jun 1 14:43:14 2020 -0600 DistributionMapping::makeSFC - distribute to user-defined procs (#957) Extends the makeSFC method to take an additional argument where the user can override the number of processes a BoxArray is distributed to. Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 6612258dcd4f4bfb1d1539539ed626ddc0a9eeff Author: Andrew Myers Date: Mon Jun 1 13:42:00 2020 -0700 remove unused variables from tutorials (#956) Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Basic/HeatEquation_EX1_CF/Source/advance.cpp Tutorials/Basic/HeatEquation_EX2_CF/Source/advance.cpp Tutorials/LinearSolvers/MultiComponent/main.cpp commit 54ea99efa50b9765979ace6541ca5ab7ea685de2 Author: Andrew Myers Date: Mon Jun 1 13:40:24 2020 -0700 fix a few unused / uninitialized variable warnings (#955) Src/Base/AMReX_FabArrayBase.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit 3a9341800b675c09f793229d618d960c400ea916 Author: Andrew Myers Date: Mon Jun 1 13:38:46 2020 -0700 add cuda test script from cuda to the repo (#954) Tools/RegressionTesting/AMReX-cuda-tests.ini commit 3e7366503edb5dcbabdf2b22d4c7417b22f52995 Author: WeiqunZhang Date: Mon Jun 1 13:37:29 2020 -0700 turn tiling off by default for gpu (#953) Src/Base/AMReX_FabArrayBase.cpp commit af68380aa4b23ce7f01223d696aafa82cfa5e06c Author: mic84 Date: Mon Jun 1 12:27:45 2020 -0700 CMake: improve handling of options (#946) * CMake: move general setup operations out of AMReX_Options.cmake * CMake: better handling of option inter-dependencies via cmake_dependent_option * CMake: refactor AMReX_Options.cmake * Update Tools/CMake/AMReX_Options.cmake Co-authored-by: Axel Huebl * Update CMakeLists.txt Co-authored-by: Axel Huebl * Update Tools/CMake/AMReX_Options.cmake Co-authored-by: Axel Huebl Co-authored-by: Axel Huebl CMakeLists.txt Src/Extern/SUNDIALS4/CMakeLists.txt Tools/CMake/AMReX_Options.cmake commit 227bf82812793dc942fa8472974bcdd3d3e60ad3 Author: Andrew Myers Date: Mon Jun 1 10:04:01 2020 -0700 use explicit casts to silence compiler warnings (#952) Src/Particle/AMReX_Particle_mod_K.H commit b83904febeb29df3901f9f46e94ca3204944ccf6 Author: WeiqunZhang Date: Sun May 31 22:04:16 2020 -0700 set up DPC++ regression test suite (#951) Tools/GNUMake/Make.defs Tools/RegressionTesting/AMReX-dpcpp-tests.ini commit e6a312fc09f534fbefaebf1d96e70165fc27cb49 Author: WeiqunZhang Date: Sun May 31 17:55:05 2020 -0700 update CHANGES (#950) CHANGES commit 1b30da66e7f7c9fe7b66905c9d6a9fb1e82fe574 Author: Axel Huebl Date: Fri May 29 15:38:43 2020 -0700 C++20 Compatibility: GCC 10.1 (#949) .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_gcc10.sh .github/workflows/dependencies/dependencies_mac.sh .github/workflows/linux.yml commit 4e051cdebf11fb8b31a4162e16e5040383180c7f Author: Axel Huebl Date: Fri May 29 14:06:16 2020 -0700 GH Action CI: Restructure (#948) Restructure the CI dirs and workflow names: split by OS. Preparation for Windows. .github/workflows/dependencies/dependencies.sh .github/workflows/dependencies/dependencies_mac.sh .github/workflows/dependencies/dependencies_nofortran.sh .github/workflows/dependencies/dependencies_nvcc.sh .github/workflows/linux.yml .github/workflows/macos.yml commit 5738a0a334d581473ea2986a8875e52da103496e Author: WeiqunZhang Date: Wed May 27 09:38:55 2020 -0700 remove const for compare_exchange_strong (#941) Src/Base/AMReX_GpuAtomic.H commit f96af7af7c11a1c29658464764f39fd2a69650af Author: Axel Huebl Date: Wed May 27 07:09:05 2020 -0700 Atomics: Constify Wrapper (#927) Src/Base/AMReX_GpuAtomic.H commit d4e2a30df8bb086b4583e991837c926083b1ba31 Author: Andrew Myers Date: Tue May 26 18:08:55 2020 -0700 Unused warnings (#940) * silence unused variable warnings in Src/Base * silence unused variable warnings in Src/Particle * silence unused variable warnings in Src/LinearSolvers Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_EArena.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_GpuUtility.cpp Src/Base/AMReX_Machine.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particle_mod_K.H commit f25de11b41cedcdbc25010c00e5b89211d7a8645 Author: Andrew Myers Date: Tue May 26 12:58:28 2020 -0700 add cstdlib header to AMReX_MATH.H (#939) Src/Base/AMReX_Math.H commit fadf58ef77be62e832b528e15e7c996af1791c55 Author: Axel Huebl Date: Tue May 26 11:38:45 2020 -0700 CMAKE_INSTALL_PREFX: Only Toplevel (#936) Set a non-default CMAKE_INSTALL_PREFIX only if AMReX is the top-level CMake project. Otherwise, the default of a downstream project using AMReX as subproject will be placed in a quite confusing, temporary directory. CMakeLists.txt commit 38f9ee12c68022eca233c79f219361537eb93cbf Author: WeiqunZhang Date: Mon May 25 11:45:14 2020 -0700 C order support for Array2D and Array3D (#934) Src/Base/AMReX_Array.H commit 6c877f0884d03d40e9b993cac5b39a591fbefaff Author: WeiqunZhang Date: Mon May 25 11:15:38 2020 -0700 disable unqualified abs function with amrex namespace (#938) Src/Base/AMReX.H Src/Base/AMReX_Math.H commit b055d9aa331f5498b21283235e5f208f69b022b9 Author: Burlen Loring Date: Mon May 25 09:54:16 2020 -0700 updates for SENSEI 3.2 release (#929) * updates for SENSEI 3.0 * The data adaptor for amrex::Amr is working with SENSEI 3.0. * The adaptor for amrex::AmrMesh has new SENSEI 3.0 API's in place and compiles but is not filling all metadata. * The bridge code has been updated for SENSEI 3.0 and is working * updates to the SENSEI tutorial * Added a Python example. * Added an ADIOS2 example. * Updated ParaView Catalyst scripts for use with PareView 5.7. * Added a README describing tutorial layout in the root dir. * Cleaned up the make files. * updates for SENSEI 3.2 * Adds per-array per-block range metadata calculations. For cell centered data, the cells covered by those in refined levels are skipped. This lets one be more precise about which blocks are needed for iso-surfacing. For other centerings ranges include all cells. * finish updates to AmrMesh data adaptor for SENSEI 3.2 * finish updates to Amr data adaptor for SENSEI 3.2 Src/Extern/SENSEI/AMReX_AmrDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrInSituBridge.cpp Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.cpp Src/Extern/SENSEI/AMReX_InSituBridge.cpp Src/Extern/SENSEI/AMReX_InSituUtils.H Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/histogram.py Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/histogram_python.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/SENSEI/Advection_AmrCore/README_SENSEI.md Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/histogram.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/histogram_python.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/iso_extract.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/read_adios2_bp4_default.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/read_adios2_sst_default.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_adios2_bp4.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_adios2_sst.xml Tutorials/SENSEI/README.md commit e3ad694e2fa924a6fc80bf84b6c99d521f9c39e6 Author: mic84 Date: Sun May 24 19:45:48 2020 -0700 CMake: link to OpenMP::Fortran only when needed (#935) Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake commit 019617c097a5aa35f7f1c03bf8b9ce6dff718cc7 Author: WeiqunZhang Date: Sat May 23 17:05:17 2020 -0700 DPC++: disable gpu launch for mlndlap because the compiler hangs (#932) Docs/Notes/DPCPPWishlist.md Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit cbd2effff3b228dfa60fa3db4df363fbe0bac4ca Author: WeiqunZhang Date: Sat May 23 17:04:34 2020 -0700 more kernel size reduction in MLEBABecLap (#933) Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 02b21fa0c28c0c345359065fc24fa9ad72b8a0a7 Author: WeiqunZhang Date: Sat May 23 16:39:07 2020 -0700 more on reducing dpc++ kernel parameter size (#917) * more on reducing dpc++ kernel parameter size * In order to reduce kernel parameter size, launch separate kernels with DPC++ * dpc++: disable launch region in tensor bc. reduce kernel size. Src/Base/AMReX_GpuLaunchFunctsG.H Src/EB/AMReX_EB2_Level.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit da9036d5f9fe23d48c37b8e4e5f627015e1c2654 Author: WeiqunZhang Date: Fri May 22 23:04:28 2020 -0700 add non-const data() to GpuArray (#931) Src/Base/AMReX_Array.H commit d425eb7668d231d1b114f9f54404172bd90486ab Author: WeiqunZhang Date: Fri May 22 10:40:55 2020 -0700 Hip/scan (#920) * hip version of scan * use ::exp for HIP Src/Base/AMReX_Scan.H Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H Tutorials/Basic/HeatEquation_EX2_C/Source/mykernel.H commit b759012b2c3bbbfa373f5b59c45907e35109734c Author: WeiqunZhang Date: Thu May 21 22:10:09 2020 -0700 Return immediately from memcpy if size is zero. (#928) Src/Base/AMReX_GpuDevice.H commit 528b74ab46b36ddae74791b2217903edb6e32b0a Author: asalmgren Date: Thu May 21 17:16:59 2020 -0700 Aa/more docs (#926) * Add EB stuff to Linear Solvers in addition to Linear Solvers stuff in EB * Update documentation to describe how to set homogeneous or inhomogeneous bc's on EB faces in a cell-centered solve Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/LinearSolvers.rst commit 9e4d718e579bca6be82be54b17a4c829e4bd40ee Author: WeiqunZhang Date: Thu May 21 16:45:32 2020 -0700 move operator<< for pair from neighbor particles test into amrex print so that dpcpp does not have ADL issue (#925) Src/Base/AMReX_Print.H Tests/Particles/NeighborParticles/main.cpp commit c5c9907b0c8c4c7cdca1a55db4719472167d867c Author: WeiqunZhang Date: Thu May 21 16:41:38 2020 -0700 typo (#923) CONTRIBUTING.md commit bede80010c37c0fb46e88704f4c59642b56992b1 Author: Andrew Myers Date: Thu May 21 16:01:45 2020 -0700 silence some unused parameter warnings (#921) Src/AmrCore/AMReX_AmrMesh.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabFactory.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_GpuUtility.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particles.H commit 7a1812da68bcb409afa48a48fba1ef7d30fd41c2 Author: asalmgren Date: Thu May 21 15:29:09 2020 -0700 Update the section about EB Linear solvers to reflect (#922) 1) what bc's on EB faces are supported, 2) how to set center vs centroid locations for solution variable and for face-based coefficients Docs/sphinx_documentation/source/EB.rst commit 2e2bb92415dac28552249e94886ca107cf3c6ca0 Author: mic84 Date: Thu May 21 13:48:53 2020 -0700 CMake: do not set Fortran properties when Fortran is disabled. (#919) In particular, do not specify Fortran module files path when Fortran is off, else superbuilds will fail. Src/CMakeLists.txt commit e2079f703fd483b54f7c07991a8bfdb287f25294 Author: WeiqunZhang Date: Thu May 21 09:30:02 2020 -0700 Fix new bug in mlebabeclap. Forgot about the change in index order when I switched from 2d C Array to Array2D. (#918) Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H commit 97b888bcfb9282e7b788e2c11a76f68e35e5979d Author: WeiqunZhang Date: Wed May 20 11:11:20 2020 -0700 document JIT fpe (#916) Docs/Notes/DPCPPWishlist.md commit f2940620f73a3373dbb605ec1c83f1ca4955f25e Author: WeiqunZhang Date: Wed May 20 10:58:11 2020 -0700 get around dpc++ kernel parameter size issue in EB build_cells (#914) Src/EB/AMReX_EB2_3D_C.cpp commit d4773e7585ae53292be8bf235736b5ef7d99ad37 Author: WeiqunZhang Date: Wed May 20 10:40:38 2020 -0700 fix new bug in 2675b0915d0b11d6e: Array2D does not have operator[] (#915) Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H commit f5cdf22b9251eba96b07cb3854d83818a55553ce Author: WeiqunZhang Date: Wed May 20 10:07:20 2020 -0700 add HIP issues we have (#913) Docs/Notes/HIPIssues.md commit 2283b88487ed2798e2fd3efbceb76a56dd624a33 Author: WeiqunZhang Date: Wed May 20 10:07:00 2020 -0700 reorganize DPC++ wishlist in terms of severity (#912) Docs/Notes/DPCPPWishlist.md commit 2675b0915d0b11d6e897db04bc77003e6c41674d Author: WeiqunZhang Date: Wed May 20 10:06:44 2020 -0700 Dpcpp/debug/mlmg (#911) * DPC++: manually copy ABecLapLacian gsrb kernel arguments to get around size limit * minor: remove unused capture * use GpuArray and initialization to get around DPC++ bug Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit 2e8aa8d90945611b7f10215336729cacb87d7b91 Author: Mark Meredith Date: Tue May 19 19:41:01 2020 -0400 Fix sign-compare warnings (#910) Co-authored-by: Mark Meredith Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleTile.H commit 4f11dbb113304bb119c07c1e657c3b6b5b9cfa5d Author: Andrew Myers Date: Tue May 19 10:47:07 2020 -0700 No longer fall back to the CPU when calling Redistribute with ngrow != 0 (#909) * no longer fall back on cpu implementation when ngrow != 0 * change the assert at the end of redistribute to account for nGrow * fix assertions * make sure we replicate exactly the behavior of the CPU locate * make sure we correctly search the gpu map structure for the boxes with ngrow Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_ParticleUtil.H commit 4809ebef8a417b2629cc36bfdff665eae7b5cdd9 Author: WeiqunZhang Date: Tue May 19 10:24:34 2020 -0700 make device version random compile with dpc++, though it doesn't work yet. (#906) Src/Base/AMReX_GpuQualifiers.H Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp commit 520f154e54a29a2b75a8371489340d9688322362 Author: Andrew Myers Date: Tue May 19 10:24:25 2020 -0700 add synchronize statements to UpdateNeighbors (#908) Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 1aa23e9a5334b01fe11fa0168bab9719bc621384 Author: WeiqunZhang Date: Tue May 19 10:06:47 2020 -0700 replace cuda specific code (#907) Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H commit d8fe45c4fae04663a90adc2924a2ef927ac6cdf0 Author: WeiqunZhang Date: Tue May 19 07:45:06 2020 -0700 Allow zero-length GpuArray. This fixes zero-length array, a gcc extension, in ParticleTile that is not allowed by the standard (#903) Src/Base/AMReX_Algorithm.H Src/Base/AMReX_Array.H Src/Base/AMReX_Dim3.H commit 31f46837f0af9e4a97f0fa4e71869533ecea8d93 Author: WeiqunZhang Date: Tue May 19 07:44:47 2020 -0700 directive inside macro argument is non-standard (#905) Src/Base/AMReX_MultiFabUtil.cpp commit 18d87ed313cf9a7c0806f1ee89cd3b8394f09023 Author: WeiqunZhang Date: Tue May 19 07:43:57 2020 -0700 fix data type (#904) Src/Base/AMReX_DistributionMapping.cpp commit ff4669b940fe5406fdee5fd1e0c5a62c0198f70b Author: WeiqunZhang Date: Mon May 18 17:30:36 2020 -0700 Avoid new line in ParmParse's Fortran namelist for PGI and IBM (#902) Src/Base/AMReX_ParmParse.cpp commit 43e281ae862c9e1cb3f27afc1ca05cfc137f8c8b Author: mic84 Date: Mon May 18 17:28:22 2020 -0700 CMake: add helper function setup_target_for_cuda_compilation() (#866) * CMake: add helper function setup_target_for_cuda_compilation() This function ensures that the CUDA compilation of a dependent target is consistent with amrex CUDA build. * Update Tools/CMake/AMReXTargetHelpers.cmake Co-authored-by: Axel Huebl * Leave default value for CUDA_RESOLVE_DEVICE_SYMBOLS Co-authored-by: Axel Huebl * CMake: deploy setup_target_for_cuda_compilation() Co-authored-by: Axel Huebl Src/CMakeLists.txt Tools/CMake/AMReXTargetHelpers.cmake Tools/CMake/AMReX_Config.cmake commit 7d88e64f656dc1b522eb4bef6412841d492cfa1d Author: WeiqunZhang Date: Mon May 18 16:40:44 2020 -0700 add BL_NO_FORT to hip makefile (#901) Tools/GNUMake/comps/hip.mak commit ce8e12f49ac6d15c0c38f082419805bdc677440c Author: WeiqunZhang Date: Mon May 18 16:23:08 2020 -0700 DPC++: add fortran support (#900) Tools/GNUMake/Make.defs Tools/GNUMake/comps/dpcpp.mak commit 0aadce3d0713de3ec87bb33bf16d86b1a76d4fbf Author: WeiqunZhang Date: Mon May 18 16:22:49 2020 -0700 ParticleMesh test: std::floor -> amrex::Math::floor for DPC++ (#899) Tests/Particles/ParticleMesh/main.cpp commit 9a1957ae1c273d53b283198ca3f497dc6a65b0d4 Author: WeiqunZhang Date: Mon May 18 13:55:06 2020 -0700 fix EB MacProj tutorial due to interface change (#898) Tutorials/EB/MacProj/main.cpp commit beb6beb76d830f3df01f802be1a6509b804c3555 Author: WeiqunZhang Date: Mon May 18 10:15:39 2020 -0700 fix the logic of setting USE_MPI when MPI_THREAD_MULTIPLE is defined (#896) Tools/GNUMake/Make.defs commit f836e77216d5573182ebcfe87da829dd2d46e3f0 Author: WeiqunZhang Date: Mon May 18 10:15:01 2020 -0700 tulip: add amdgpu-target only if USE_HIP=TRUE (#895) Tools/GNUMake/sites/Make.frontier-coe commit 197d77678fdad597883cb2052642d33a2a08aa8c Author: WeiqunZhang Date: Mon May 18 07:24:25 2020 -0700 fix bug in 16e256420f2e34c8d0d8 (#894) Src/Base/AMReX_FBI.H commit 72ef88ee6a1df083cbb32609cc417ce735a5fb5c Author: asalmgren Date: Sun May 17 09:51:53 2020 -0700 "single_vauled_bits" --> "single_valued_bits" (#893) Src/EB/AMReX_EBCellFlag.H commit 16e256420f2e34c8d0d8c3e56d18ab100c0f8a80 Author: WeiqunZhang Date: Sat May 16 22:48:08 2020 -0700 * add user defined constructors to Dim3 for hip (#892) * add amrex::Math::sqrt for hip * both heat equation and cns compile with hip, but crash at runtime Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Dim3.H Src/Base/AMReX_FBI.H Src/Base/AMReX_GpuComplex.H Src/Base/AMReX_Math.H Src/Base/AMReX_RealVect.H Src/Base/AMReX_iMultiFab.cpp Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H commit d040966d15540893563367f8769b68e3e0826e34 Author: WeiqunZhang Date: Sat May 16 21:02:52 2020 -0700 get HelloWorld to compile on tulip (#891) Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Math.H Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.frontier-coe commit 43bcd0cf01333e2638313bd98c16211f113e189c Author: Eloise Yang <55457939+eloisejyang@users.noreply.github.com> Date: Sat May 16 10:58:34 2020 -0700 Heat Equation 2 to GPU (#884) * Converting Heat Equation 2 to GPU * Putting HeatEquation2_CF Back Tutorials/Basic/HeatEquation_EX2_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs Tutorials/Basic/HeatEquation_EX2_C/Source/Make.package Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/mykernel.H Tutorials/Basic/HeatEquation_EX2_CF/CMakeLists.txt Tutorials/Basic/HeatEquation_EX2_CF/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX2_CF/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX2_CF/Exec/inputs_3d Tutorials/Basic/HeatEquation_EX2_CF/Source/Make.package Tutorials/Basic/HeatEquation_EX2_CF/Source/advance.cpp Tutorials/Basic/HeatEquation_EX2_CF/Source/advance_2d.f90 Tutorials/Basic/HeatEquation_EX2_CF/Source/advance_3d.f90 Tutorials/Basic/HeatEquation_EX2_CF/Source/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX2_CF/Source/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX2_CF/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_CF/Source/myfunc.H Tutorials/Basic/HeatEquation_EX2_CF/Source/myfunc_F.H commit d05946a9d30faf7f3a348dd8438bce89d9928495 Author: WeiqunZhang Date: Fri May 15 19:27:04 2020 -0700 fix division by zero (#890) Src/EB/AMReX_algoim_K.H commit af9dd8431835c6e83bc98731d7472be7d2a85879 Author: WeiqunZhang Date: Fri May 15 17:58:38 2020 -0700 increase the maximal depth of backtrace stack to 64 (#889) Src/Base/AMReX_BLBackTrace.cpp commit 78fad8e0b9a06204864a4af0608216da3b72326e Author: kngott <30483578+kngott@users.noreply.github.com> Date: Fri May 15 16:59:22 2020 -0700 The Invisible PR (#888) * Remove non-ASCII characters from the docs. * Remove non-ASCII characters from the doc tutorials. * Remove non-ASCII characters from paper.md * Remove non-ASCII characters from SWFFT. * Fix warning in docs of identically named tables. Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/AmrLevel.rst Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/Basics_Chapter.rst Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/CVODE.rst Docs/sphinx_documentation/source/CVODE_top.rst Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/External_Profiling_Tools.rst Docs/sphinx_documentation/source/Fortran.rst Docs/sphinx_documentation/source/Fortran_Chapter.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/GettingStarted_Chapter.rst Docs/sphinx_documentation/source/IO.rst Docs/sphinx_documentation/source/IO_Chapter.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/Particle.rst Docs/sphinx_documentation/source/SUNDIALS3.rst Docs/sphinx_documentation/source/Visualization.rst Docs/sphinx_documentation/source/Visualization_Chapter.rst Docs/sphinx_tutorials/source/CVODE_Tutorial.rst Src/Extern/SWFFT/AlignedAllocator.h Src/Extern/SWFFT/COPYING Src/Extern/SWFFT/CheckDecomposition.c Src/Extern/SWFFT/Dfft.H Src/Extern/SWFFT/DfftC.cpp Src/Extern/SWFFT/Distribution.H Src/Extern/SWFFT/DistributionC.cpp Src/Extern/SWFFT/Error.h Src/Extern/SWFFT/TimingStats.h Src/Extern/SWFFT/complex-type.h Src/Extern/SWFFT/distribution.c Src/Extern/SWFFT/distribution_c.h paper/paper.md commit a017d599f4d11898b43246f3ab6240a0e397d86b Author: WeiqunZhang Date: Thu May 14 17:46:25 2020 -0700 fix interp functions for single precison (#887) Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H commit e5d0c103cdbc6a1a8e53143f838bf7182ab453a4 Author: WeiqunZhang Date: Thu May 14 17:46:06 2020 -0700 update DPC++ wishlist (#886) Docs/Notes/DPCPPWishlist.md commit a595fc350b7c610799233b46f0f7aa0347d57404 Author: WeiqunZhang Date: Thu May 14 14:55:09 2020 -0700 valid_cells_only option in VisMF::AsyncWrite (#878) Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs commit aa9a2acefe565186ddac24985a998182725e2c39 Author: Brandon Runnels Date: Thu May 14 15:53:48 2020 -0600 Templating FillPatch and Interpolator (#883) * updated so that setdomainbndry does not create template issues * templating the nodebilin interpolator functions Src/AmrCore/AMReX_FillPatchUtil_I.H Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp commit 4d9c627d1d5ff8483c2f1207cf9d17ce457460dc Author: Andrew Myers Date: Thu May 14 10:51:27 2020 -0700 Fix bug I introduced in PR 882 and add an assertion Src/Particle/AMReX_NeighborList.H commit 780fd94cb7502118eeb28f187fb475ce81693a91 Author: WeiqunZhang Date: Wed May 13 15:40:11 2020 -0700 FillPatch: use factory only if FAB is FArrayBox (#879) Src/AmrCore/AMReX_FillPatchUtil_I.H commit 80631854f4dba8d9138f1c7e9f787715d1c1293c Author: WeiqunZhang Date: Wed May 13 15:23:26 2020 -0700 PhysBCFunct: no longer need to be virtual (#872) * PhysBCFunct: no longer need to be virtual * Fix typo in AmrCore.rst Co-authored-by: Andrew Myers Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/Basics.rst Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_FPhysBC.cpp commit 0c4606cf624aebe2ab6072ed91086281747f0a41 Author: WeiqunZhang Date: Wed May 13 12:58:39 2020 -0700 MLMG::apply: need to apply inhomogeneous Neumann BC (#875) Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 1eed01cedff56af6c38a388c152720d4f39d9fd3 Author: Andrew Myers Date: Wed May 13 12:28:50 2020 -0700 use explicit casts to silence warnings (#882) * use explicit casts to silence warnings Src/Particle/AMReX_NeighborList.H commit ac9cd4ca023c2df78bd8ecebc5dda568b999a927 Author: Andrew Myers Date: Wed May 13 08:46:41 2020 -0700 set the tiling options at runtime rather than hard-coding them (#880) * set the tiling options at runtime rather than hard-coding them Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 04725d6a5de3d0f3e72a73cd87d9e548678e8852 Author: Andrew Myers Date: Tue May 12 16:30:50 2020 -0700 Teach the gpu particle locators about lev_min, lev_max, and ngrow (#877) * teach the gpu particle locators about lev_min, lev_max, and ngrow * missed an nGrow Src/Particle/AMReX_ParticleLocator.H commit ce38af7239fd44d58755890dfbc52fe4c84204d5 Author: WeiqunZhang Date: Tue May 12 12:20:19 2020 -0700 Mpi thread multiple (#873) * MPI_MULTIPLE -> MPI_THREAD_MULTIPLE for clarity * check mpi thread support level too when we does not initialize mpi Src/Base/AMReX_AsyncOut.cpp Src/Base/AMReX_ParallelDescriptor.cpp Tests/AsyncOut/multifab/GNUmakefile Tools/GNUMake/Make.defs Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs commit 874b65e914751464418987982c1a04604c3fd6f3 Author: WeiqunZhang Date: Tue May 12 10:37:10 2020 -0700 remove profiler from WriteGenericPlotfileHeader because it's not async safe (#871) Src/Base/AMReX_PlotFileUtil.cpp commit d1484d49c1505d9883cbcb0f02b03efbc55102a2 Author: WeiqunZhang Date: Tue May 12 10:36:32 2020 -0700 Async cleanup (#863) * remove superseded functions * update test Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Tests/AsyncOut/multifab/GNUmakefile Tests/AsyncOut/multifab/Make.package Tests/AsyncOut/multifab/inputs Tests/AsyncOut/multifab/main.cpp Tests/VELOC/multifab/GNUmakefile Tests/VELOC/multifab/Make.package Tests/VELOC/multifab/Readme Tests/VELOC/multifab/inputs Tests/VELOC/multifab/main.cpp Tests/VELOC/multifab/veloc.cfg Tests/VELOC/pltfile_mpi/GNUmakefile Tests/VELOC/pltfile_mpi/Make.package Tests/VELOC/pltfile_mpi/inputs Tests/VELOC/pltfile_mpi/main.cpp commit c11bbc9bec2762299447402c6ca6f5aa4389a0c4 Author: MaxThevenet Date: Mon May 11 22:16:23 2020 -0700 Fix bug in GpuComplex substraction (#870) Src/Base/AMReX_GpuComplex.H commit 8d573c62bd4c95bde0853c65370e34d150806685 Author: WeiqunZhang Date: Mon May 11 19:21:35 2020 -0700 add inline namespace literals and use in CNS and Heat Equation tutorials (#869) Src/Base/AMReX_REAL.H Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/RT/cns_prob_parm.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob_parm.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_parm.H Tutorials/GPU/CNS/Source/CNS_parm.cpp Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/CNS/Source/main.cpp commit 6efe80c0c19dd0c11a6785a594250ad2dd871da9 Author: Brandon Runnels Date: Mon May 11 17:28:17 2020 -0600 Templating the PhysBCBase class (#867) * Added () operator to PhysBCFunctBase and templated the FillPatchUtil functions to take a BC functor Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil_I.H Src/Base/AMReX_PhysBCFunct.H commit 0a92755c0e43b29e1c8386cf454ed2eff6a4fc4e Author: mic84 Date: Mon May 11 15:46:29 2020 -0700 GNUMake: fix mispelled header name (#868) Src/EB/Make.package commit a15e9be68b1bb853a176cce013a42fa864443386 Author: Axel Huebl Date: Mon May 11 12:40:17 2020 -0700 DPCPP Makefile: Fix CC Typo (#865) Typo: treat C as C++ code for now. We can also use a shipped `clang` instead with DPC++ installs. Tools/GNUMake/comps/dpcpp.mak commit 57eccd045f9d7770dd86af04be7c4a36434cec3b Author: mic84 Date: Mon May 11 12:24:21 2020 -0700 CMake: add HeatEquation tutorials (#864) Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_F/CMakeLists.txt Tutorials/Basic/HeatEquation_EX2_C/CMakeLists.txt Tutorials/Basic/HeatEquation_EX3_C/CMakeLists.txt commit ef2a119c08d3cb52d631cdc0b340ff81978327b0 Author: WeiqunZhang Date: Mon May 11 09:34:32 2020 -0700 DPC++: add device api of rng to wishlist (#862) Docs/Notes/DPCPPWishlist.md commit 0547aa88bb0e3f13335ab5ef96691e3bd69dbcea Author: WeiqunZhang Date: Mon May 11 09:34:06 2020 -0700 use more relaxed memory order for BaseFab stats because we need them to be atomic but we do not require a specific synchronization order across threads (#860) Src/Base/AMReX_BaseFab.cpp commit 1a7f32f7cb8cd16691b45bf017ed9116aa33e8b2 Author: WeiqunZhang Date: Mon May 11 09:30:16 2020 -0700 restore tutorial of the traditional hybrid C++/Fortran way (#861) Tutorials/Basic/HeatEquation_EX1_CF/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_CF/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX1_CF/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX1_CF/Exec/inputs_3d Tutorials/Basic/HeatEquation_EX1_CF/Source/Make.package Tutorials/Basic/HeatEquation_EX1_CF/Source/advance.cpp Tutorials/Basic/HeatEquation_EX1_CF/Source/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_CF/Source/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_CF/Source/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX1_CF/Source/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX1_CF/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_CF/Source/myfunc.H Tutorials/Basic/HeatEquation_EX1_CF/Source/myfunc_F.H commit 390f32d233d7679bab460639a2189e058456aa4e Author: WeiqunZhang Date: Mon May 11 09:19:39 2020 -0700 HeatEquation_Ex1_C: add missing files (#859) Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/mykernel.H commit f9131627f9096b95a3ab6bf089230ab11fe7ef8b Author: WeiqunZhang Date: Sat May 9 09:06:43 2020 -0700 asyncout in AmrLevel::checkPoint() (#858) Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StateData.cpp Src/Boundary/AMReX_FabSet.cpp commit fa82c15ea6b5959bc59a058e8bc566e716a906eb Author: WeiqunZhang Date: Sat May 9 09:06:02 2020 -0700 extract common code in writePlotFile and writeSmallPlotfile into a private function (#857) Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp commit 3c115e68bea60f8567ab03b3516bb722ef7aed0d Author: WeiqunZhang Date: Fri May 8 17:08:28 2020 -0700 Update heat equation tutorial to our currently preferred style. (#853) * HeatEquation_EX1_C -> HeatEquation_EX1_CF and move gpu version of heat equation to basic * update documentation for the change in heat equation tutorial Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_tutorials/source/GPU_Tutorial.rst Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/Basic/HeatEquation_EX1_C/Source/Make.package Tutorials/Basic/HeatEquation_EX1_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/mykernel.F90 Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/mykernel.F90 Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/Exec/default/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/default/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d_hip Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.ascent Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.nocuda.script Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summit Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/Make.HEAT Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit be8104b25776036ac741da7c72d31bd1292ded13 Author: WeiqunZhang Date: Fri May 8 16:16:05 2020 -0700 DPC++: add max parameter size to device properties (#856) Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit e7b91ef94801aaf3afa7b9d7070526137830a937 Author: WeiqunZhang Date: Fri May 8 15:03:03 2020 -0700 DPC++: currently allocating too much memory might fail, so we set the initial arena size to 1GB. (#855) Src/Base/AMReX_Arena.cpp commit 01aaa928d4da6c9dc48aae758e41a942a21350ac Author: mic84 Date: Fri May 8 14:33:13 2020 -0700 CMake: link against OpenMP_Fortran only when Fortran is enabled (#851) * CMake: link against OpenMP_Fortran only when Fortran is enabled * CMake: fix if() statement Tools/CMake/AMReX_Config.cmake commit 52e11a11b8ee4d3a6b19f20ddef723a23fbe72f6 Author: Andrew Myers Date: Fri May 8 13:49:51 2020 -0700 Particle locator fix (#854) * fix logic for re-building the particle locator * if the entry isn't in the map, then the number of copies is 0 Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleLocator.H commit 8194c10004aae594e2d120d79c5e30aa7b2dce3e Author: WeiqunZhang Date: Thu May 7 18:20:37 2020 -0700 some updates on Chapter Basic of the documentaion (#849) * some updates on Chapter Basic of the documentaion * Minor proofreading changes to Basics.rst Co-authored-by: Andrew Myers Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst commit 72fe04903c6a67ce901c9350f58a9f565d9fa6a2 Author: asalmgren Date: Thu May 7 17:41:25 2020 -0700 Add nodal_proj.num_pre_smooth, nodal_proj.num_post_smooth, mac_proj.num_pre_smooth and (#850) mac_proj.num_post_smooth options -- these can be used to pass the parameters through to the MLMG. Src/LinearSolvers/Projections/AMReX_MacProjector.cpp Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 1c24f8a94c482ff79d401e1226502a98394e5ad2 Author: WeiqunZhang Date: Thu May 7 08:22:45 2020 -0700 Async out (#845) * AsyncOut using a background thread. This is based on our previous implementations of async output. In our first implementation, we use std::async to launch a thread for the output job. There are two issues with that first implementation. First, it does not scale to a large number of MPI processes. We do not want every MPI process to write to disk simultaneously. To avoid that, the first implementation writes a small file to the disk and uses that to coordinate. This way of message passing using file does not scale. The second issue is it is hard to manage multiple jobs. Ideally we would like the second job to start after the first job is finish to avoid launching too many threads writing to the disk. In our second implementation, MPI is initialized with support for multiple threads. This solves the first issue above. However, the second issue still exists. To write a plotfile with multiple MultiFabs like the functions in AMReX_PlotFileUtil, the second implementation has a new function to manually merge multiple MultiFabs' data into one contiguous chunk of memory for a std::async job. However this cannot be easily extended to AmrLevel's WritePlotfile function. In this third implementation, we launch a background thread specifically for async output. The thread persists during the run waiting on a C++ conditional variable. The thread is woke up when a job is submitted to the async job queue. As in the second implementation, MPI_THREAD_MULTIPLE is used. The use of a background thread and a job queue provides flexibility. For example, writing plotfile in AmrLevel requires only a few lines of changes. One can submit multiple jobs to the queue, as long as there is enough memory, without worrying about launching too many threads. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX.cpp Src/Base/AMReX_AsyncOut.H Src/Base/AMReX_AsyncOut.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Tests/VELOC/mf_mpi/inputs Tests/VELOC/multifab/main.cpp Tools/GNUMake/Make.defs commit a9d1c7649200f186419be0b1e07114ff3b5ddb56 Author: WeiqunZhang Date: Wed May 6 13:53:20 2020 -0700 fix a corner case in which the object is fully contained within a coarse cell without touching its surface. this could happen during the coarsening of fine geometry. (#847) Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H commit fc08afe8327f96d507cda7f9f9a6423787381b2b Author: Andrew Myers Date: Tue May 5 14:35:06 2020 -0700 For cuda > 10, use cudaLaunchHostFunc instead of cudaStreamAddCallback, which has been marked as deprecated (#844) Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuElixir.cpp commit d555fcad06bfc4e7d3fb076a819064664deb92a4 Author: WeiqunZhang Date: Tue May 5 12:46:33 2020 -0700 Move prefetch from AmrLevel WritePlotfile to VisMF::Write. Avoid unn… (#843) * Move prefetch from AmrLevel WritePlotfile to VisMF::Write. Avoid unnecessary work if no ghost cells. * If not manged memory, we do not need to start MFIter Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_VisMF.cpp Tutorials/GPU/EBCNS/Source/CNS_io.cpp commit 0dbb88eb067149d719fa1eaf2f46d0b38385b466 Author: WeiqunZhang Date: Mon May 4 20:30:54 2020 -0700 prefetch only if it's managed memory (#842) Src/Base/AMReX_BaseFab.H commit 46000d3312a926242b9dd328982dfe5be1ea836b Author: WeiqunZhang Date: Mon May 4 13:13:07 2020 -0700 User literals: add a space before _ to make gcc 4.8 happy (#841) Src/Base/AMReX_REAL.H commit a718d8f90da3299a686a7aab6f84ec9b88518b7a Author: mic84 Date: Mon May 4 13:11:32 2020 -0700 CMake: make AMReX_buildInfo.cpp always out of date (#835) * CMake: make AMReX_buildInfo.cpp always out of date. buildInfoGetBuildDate() will now return the date and time of the build. Before this change, it returned the date and time of the CMake configuration step. * CMake: allow user to set build date and time. This is meant to facilitate reproducible builds. Tools/CMake/AMReXBuildInfo.cmake Tools/CMake/AMReX_buildInfo.cpp.in commit cb069a03468a4d5e33a9a93cad087f3e9801c248 Author: Andrew Myers Date: Mon May 4 12:24:27 2020 -0700 Particle hdf5 move (#840) * fix some indentation * move all the HDF5 particle routines to a separate file Src/Particle/AMReX_ParticleHDF5.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 0d9dcf511355d59900b97eca468edb649e28d073 Author: Andrew Myers Date: Mon May 4 11:24:07 2020 -0700 Do not explicitly reset the device on finalize (#839) Src/Base/AMReX_GpuDevice.cpp commit cc04525912bd71264cb879780bb5fdc28e56236a Author: Andrew Myers Date: Sun May 3 19:45:44 2020 -0700 Add a short section to the docs about runtime particle components (#838) * Add a short section to the docs about runtime particle components * add some more detail about how and when to call DefineAndReturnParticleTile * add in some missing style markers Docs/sphinx_documentation/source/Particle.rst commit 53490404d74eb49e8a833cc5b1e0f7b84d78c166 Author: mic84 Date: Sat May 2 23:01:52 2020 -0700 CMake: do not install Fortran modules directory if Fortran is not enabled. (#833) Tools/CMake/AMReXInstallHelpers.cmake commit ad63449780e4d2a7c428937dfb0476624fefa569 Author: WeiqunZhang Date: Sat May 2 13:15:21 2020 -0700 DPC++ scan (#837) * DPC++ scan * ParallelScan tutorial: add std version and put thrust version unside ifdef AMREX_USE_CUDA Src/Base/AMReX_FBI.H Src/Base/AMReX_Scan.H Tutorials/GPU/ParallelScan/main.cpp commit d4970bb0db316234a93969a1564df275f64e6ea7 Author: WeiqunZhang Date: Sat May 2 12:09:16 2020 -0700 remove -g so that dpcpp beta6 doesn't generate warnings at runtime (#836) Tools/GNUMake/comps/dpcpp.mak commit 39d51cb631fd1916ac182a7f0e787eb3acf66a91 Author: Andrew Myers Date: Fri May 1 20:36:12 2020 -0700 InitFromAsciiFile Improvements (#831) * GPU-friendly init from ascii file * add test for InitFromAscii * make InitFromAscii handle SoA data Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/InitFromAscii/GNUmakefile Tests/Particles/InitFromAscii/Make.package Tests/Particles/InitFromAscii/inputs Tests/Particles/InitFromAscii/main.cpp Tests/Particles/InitFromAscii/particles.txt commit a9b8d6c16ff3b5eed92b0c0f0b79c2862fc0b393 Author: Andrew Myers Date: Fri May 1 17:30:44 2020 -0700 catch the case that the message size is too big. (#834) Src/Base/AMReX_FabArrayBase.cpp commit aa16f495770661ac14ca9d8b8865e720f150261e Author: kngott <30483578+kngott@users.noreply.github.com> Date: Fri May 1 15:10:09 2020 -0700 Async I/O (#808) Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Tests/VELOC/mf_mpi/GNUmakefile Tests/VELOC/mf_mpi/Make.package Tests/VELOC/mf_mpi/inputs Tests/VELOC/mf_mpi/main.cpp Tests/VELOC/pltfile_mpi/GNUmakefile Tests/VELOC/pltfile_mpi/Make.package Tests/VELOC/pltfile_mpi/inputs Tests/VELOC/pltfile_mpi/main.cpp Tools/GNUMake/Make.defs Tutorials/GPU/HeatEquation_EX1_C/Exec/default/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 2e66e12f94e2e9b0bcf09c3a423f47110004a892 Author: WeiqunZhang Date: Fri May 1 08:21:04 2020 -0700 update CHANGES (#829) CHANGES commit 47882ba850b9876c61943d5160df9fe7ee518958 Author: WeiqunZhang Date: Thu Apr 30 13:58:54 2020 -0700 Add a suggestion about not merging pr branch into development (#830) CONTRIBUTING.md commit 72b2ad1efce53d176da22b374c660b1bdcce12a4 Author: WeiqunZhang Date: Thu Apr 30 06:46:45 2020 -0700 fix VisMF::min and max when they are not in the header (#828) Src/Base/AMReX_VisMF.cpp commit dccaf5b22f1462a98aea8215a31e7b394b31f084 Author: WeiqunZhang Date: Wed Apr 29 20:05:04 2020 -0700 DPC++: add link to unsupported math functions (#827) Src/Base/AMReX_Math.H commit 6973ef43e6d21fbcff6fea27ea656c18b1e38d51 Author: WeiqunZhang Date: Wed Apr 29 17:06:09 2020 -0700 DPC++: replace order_queue, subgroup all and any that are deprecated in beta6 (#825) Src/Base/AMReX_FBI.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuTypes.H commit 013bfe6843f40a98c46ae8f83e10fa2a42c71715 Author: Andrew Myers Date: Wed Apr 29 16:23:13 2020 -0700 fix a new-ish bug I introduced with tiling + neighbor lists (#826) Src/Particle/AMReX_NeighborParticlesI.H commit f96a7bd6d445864d4dc2c2ac41425ae722562210 Author: WeiqunZhang Date: Wed Apr 29 13:50:26 2020 -0700 split sycl device code per kernel be default (#824) Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Tools/GNUMake/comps/dpcpp.mak commit ad3619d745727a814fdbfc74118387702cb520bc Author: Candace Gilet Date: Wed Apr 29 14:41:03 2020 -0400 Macproj fix eb set bcoeffs (#823) * Pass m_beta_loc in call to setBCoeffs * MacProjector:: Remove unneeded local copies of phi_loc and beta_loc Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 45f2c8f9a4ae6f6f977ed67623c516fedb0b0fa9 Author: Axel Huebl Date: Wed Apr 29 09:18:23 2020 -0700 CI: GitHub Checkout Action v2 (#822) Just updates to the latest stable release of the checkout action. I saw some problems with the old v1 version in other projects recently, so proactively migrating this. .github/workflows/cmake.yml commit bce44ba71508f8bd8bd0accfe8d8c6da6635938b Author: asalmgren Date: Tue Apr 28 21:25:57 2020 -0700 Move m_phi_loc from MLCellLinOP to MLABecLap and (#821) 1) set default to Location::CellCenter 2) create setPhiOnCentroids() 3) allow call to setPhiOnCentroids from AMREX_MacProjector Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 2f0c802e52c365a8e0273cd2f4961e9487764a6f Author: WeiqunZhang Date: Tue Apr 28 17:04:07 2020 -0700 add links to oneapi-spec issues (#817) Docs/Notes/DPCPPWishlist.md commit eff6aa113fef06786b9c74316ec13e4ed855950d Author: WeiqunZhang Date: Tue Apr 28 16:38:04 2020 -0700 add non-mpi github action (#819) .github/workflows/cmake.yml commit b77d1dfe45ff9d12330d2e87f6443395e308be04 Author: WeiqunZhang Date: Tue Apr 28 16:15:04 2020 -0700 remove extra explicit qualificaton (#820) Src/Base/AMReX_ParallelDescriptor.H commit bd1ed4ed8aa9046a82e3d2999cb6d3e6b1bcc976 Author: WeiqunZhang Date: Tue Apr 28 15:40:14 2020 -0700 add non-MPI version of GatherLayoutDatatoVector (#818) Src/Base/AMReX_ParallelDescriptor.H commit 587a39d54c83a5c0343220fdb1dc7c0cdb5dd496 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Tue Apr 28 12:29:18 2020 -0700 Add LayoutData overload for makeKnapSack and makeSFC (#805) Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelDescriptor.H commit 778ff85a222f248f62832784d4fd9cc2f0a70d57 Author: mic84 Date: Tue Apr 28 12:05:36 2020 -0700 CMake: fix some minor bugs in AMReX_Options.cmake (#812) Tools/CMake/AMReX_Options.cmake commit 37e0d28c074316717038b2bb0e0d4822991dc0e0 Author: asalmgren Date: Tue Apr 28 11:54:26 2020 -0700 Bug fix in AMReX_MacProjector.cpp (#816) Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 96a2dbab1f169d45f2bb69eed8ab0fcf5b9590c8 Author: asalmgren Date: Tue Apr 28 10:17:47 2020 -0700 EB Linear Solver Test/Tutorials fix (#815) Tests/LinearSolvers/EBTensor/MyTest.cpp Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit d04999c60f76c86a664bc60b1f98bc39bb3552d6 Author: asalmgren Date: Mon Apr 27 20:10:57 2020 -0700 Modify the EB-aware cell-centered solvers to distinguish between the coefficients on face centers vs face centroids; similarly distinguish between solution variable and RHS on cell centers vs cell centroids (#810) Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit d74624d7b800488590d23f7711cbdf7fab286286 Author: mic84 Date: Mon Apr 27 17:58:29 2020 -0700 CMake: must build source files erroneusly excluded from build when ENABLE_FORTRAN=OFF. (#813) Src/Base/CMakeLists.txt commit 445ca73ad93a7aac52a188ebf72de7de5d39e47a Author: WeiqunZhang Date: Sun Apr 26 19:49:43 2020 -0700 explicitly construct Array to avoid overload error (#811) Tutorials/ForkJoin/MLMG/main.cpp commit 17500c6090396367ac07857a0b3745d7930bafb0 Author: WeiqunZhang Date: Sun Apr 26 16:26:52 2020 -0700 EB_utils: add new interfaces and deprecate the old ones (#802) Co-authored-by: asalmgren Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp commit ee96dee9864a40624eeba43bd4c4c37e51ce7abd Author: Johannes Blaschke Date: Sun Apr 26 10:17:02 2020 -0700 neighbor lists are stored per level (#807) Tests/Particles/NeighborParticles/MDParticleContainer.cpp commit efae0bd0964e98753255e9dd90f1170cf91d1a94 Author: Andrew Myers Date: Sat Apr 25 16:47:02 2020 -0700 make sure these loops only go over the valid particles (#806) Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_TracerParticles.cpp commit f24bfd7805b80978fa4e6b9199eaa7774d5f32d7 Author: Andrew Myers Date: Fri Apr 24 15:07:05 2020 -0700 EnableIf for ParticleContainer plotfile methods (#803) Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H commit a56106e4855bab7df8691ca5b09caf0f8b1bb878 Author: Andrew Myers Date: Fri Apr 24 14:29:04 2020 -0700 Call the same code for building neighbor lists whether we are on the CPU or GPU (#799) * start to unify GPU and CPU versions of neighbor particle / neighbor list implementations * allow for checking > 1 neighboring bin in GPU implementation of NeighborList::build Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParIter.H Src/Particle/AMReX_ParticleContainerI.H Tutorials/GPU/NeighborList/CMakeLists.txt Tutorials/GPU/NeighborList/CheckPair.H Tutorials/GPU/NeighborList/Constants.H Tutorials/GPU/NeighborList/GNUmakefile Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/Make.package Tutorials/GPU/NeighborList/README.md Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp Tutorials/GPU/NeighborList/script.sh Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/Make.package Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/inputs.mr Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/neighbor_list_2d.f90 Tutorials/Particles/NeighborList/neighbor_list_3d.f90 Tutorials/Particles/NeighborList/neighbor_list_F.H commit df00a0bf2ef7217ae0f8d861d433058c93d07b97 Author: WeiqunZhang Date: Fri Apr 24 13:51:54 2020 -0700 make ParallelFor work for functors (#804) Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_TypeTraits.H commit a516406c25c5df90d7e4426394bfa2cb92e9acf7 Author: WeiqunZhang Date: Fri Apr 24 09:41:20 2020 -0700 For CPU, GpuArray is no longer an alias to std::array (#801) * For CPU, GpuArray is no longer an alias to std::array * fix Tutorials/LinearSolvers/MultiComponent Src/Base/AMReX_Array.H Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp commit 77a1b9b189a022e6390d06864a7a2f12795bedf0 Author: WeiqunZhang Date: Fri Apr 24 08:53:06 2020 -0700 add semicolon due to change in TinyProfiler macros (#800) Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_utils.cpp commit 445d25e26667ac96b71f59050930678726eb0cf5 Author: WeiqunZhang Date: Fri Apr 24 06:49:38 2020 -0700 use enableif in various parallel for functions (#790) Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_TypeTraits.H commit 0f2e7aae8713b697ce4679a2a1d2d1ba82558e6c Author: Abhishek Bagusetty <59661409+abagusetty@users.noreply.github.com> Date: Thu Apr 23 19:12:01 2020 -0500 Support for DPCPP USM prefetch and mem_advise (#793) * Support for DPCPP USM prefetch and mem_advise * addressing PR comments for prefetch and mem_advise Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 86dab656439481c20a1ffcfb1707afcbafc675f5 Author: WeiqunZhang Date: Thu Apr 23 09:42:50 2020 -0700 remove some semincolons in TinyProfiler macros to avoid warning about extra semicolons (#798) Src/Base/AMReX_BLProfiler.H commit 9c9699f7387709cea7baafba8129688deb3e75b5 Author: WeiqunZhang Date: Wed Apr 22 16:03:15 2020 -0700 add host device for functions (#789) Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H commit c02f8124c3a3bfbd24c03e69803dde079d7dceca Author: mic84 Date: Wed Apr 22 15:05:04 2020 -0700 CMake: get rid of zero size arrays in AMReX_buildInfo.cpp (#794) Tools/CMake/AMReXBuildInfo.cmake commit 285b06832e3a446ce6529f36a0e4574467c813ba Author: Andrew Myers Date: Wed Apr 22 14:33:21 2020 -0700 Fix a couple of minor typos in Contributing.md (#796) * replace ';' with '.' * fix capitalization CONTRIBUTING.md commit e0658315005f4521b73a530d53fc6c47fce93cba Author: Andrew Myers Date: Wed Apr 22 13:30:28 2020 -0700 Some long -> amrex::Long (#792) Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_ParticleTransformation.H commit 6e59367c8fad3005d1cebe28afe0ac7e728c4aab Author: asalmgren Date: Tue Apr 21 18:26:58 2020 -0700 Remove calls to std::min in eb_interp_centroid2facecent in Src/EB/AMReX_EBMultiFab_3D_C.H (#791) * Don't use std::min on the gpu! Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit e8cac4c8e754be4391c219ef4d3b584b85c04763 Author: WeiqunZhang Date: Tue Apr 21 11:54:15 2020 -0700 Make 1d launch macro consistent with 3d and 4d in terms of return and continue. That is continue will fail to compile and return will return from the lambda not the enclosed funciton. (#788) Src/Base/AMReX_GpuLaunchMacrosG.H commit 49fc0fed1cd3ce4648b1c66e2ca353b672e9f739 Author: mic84 Date: Tue Apr 21 10:57:13 2020 -0700 CMake: set CMake minimum required version in package config file. (#787) Tools/CMake/AMReXConfig.cmake.in commit 67e5c6d94bd7cedcade1dc9722ee22e07118fa31 Author: Andrew Myers Date: Tue Apr 21 10:01:58 2020 -0700 add note about deleting feature branches when they are done (#786) CONTRIBUTING.md commit 70e9b1cb70d08ebc445d4962de3b943fe87a272c Author: mic84 Date: Mon Apr 20 18:49:12 2020 -0700 CMake: generate AMReX_Config.H the CMake way (#785) * CMake: fix issue with installation of AMReX_Config.H Tools/CMake/AMReXInstallHelpers.cmake Tools/CMake/AMReX_Config.H.in commit f54a9f4f61ba3d129e82df5117d79dc8861f9004 Author: WeiqunZhang Date: Mon Apr 20 17:40:56 2020 -0700 CNS tutorial: make [GC]puBndryFuncFab local instead of static (#784) Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/bc_fill.H Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp commit a496d6aff094a50818a3c091fc25be2e5a7e6cc2 Author: mic84 Date: Mon Apr 20 17:13:35 2020 -0700 CMake: update defines list. (#783) Tools/CMake/AMReX_Defines.cmake commit a9c3122cd4528df5b34b193b0fc7d4bf5c1552cb Author: Andrew Myers Date: Mon Apr 20 14:43:50 2020 -0700 Bugfix after PR#780 (#782) * use return instead of continue to break out of AMREX_PARALLEL_FOR, which does not work now that PR#780 is merged. * avoid return altogether in these launch macros Src/Particle/AMReX_ParticleCommunication.H commit 319aa0e1f408781a314ac8125d47bd3cf851a782 Author: mic84 Date: Mon Apr 20 13:48:54 2020 -0700 CMake: make generation of AMReX_buildInfo.cpp more robust. (#781) This commit improves the handling of quotes escaping. Tools/CMake/AMReXBuildInfo.cmake commit 527094da45e54820f9ed583e5dea1ff058fb611c Author: WeiqunZhang Date: Mon Apr 20 13:34:37 2020 -0700 Simplify launch macros by calling launch functions (#780) Src/Base/AMReX_GpuLaunchMacrosG.H commit c23a44085bee6fa5acd79b1d9b7a54fae17feb0f Author: asalmgren Date: Mon Apr 20 11:26:09 2020 -0700 Remove print statements accidentally left in (#779) * Fix logic for 3D interpolation of cell centroids to face centroids * Remove print statement that I left in by accident Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit cb74aed183813f826d9571d402a8a73bb27ac9f7 Author: asalmgren Date: Mon Apr 20 09:56:04 2020 -0700 Fix logic for 3D interpolation of cell centroids to face centroids (#778) Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 82bd805ef145a2cfedd52e812680e694cdcd4cf2 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Sun Apr 19 22:00:58 2020 -0700 fixing minor typos (#777) Docs/Notes/DPCPPWishlist.md Docs/sphinx_documentation/source/GettingStarted.rst commit cc48e0e3e033275f7dc167f734126b4f65a1839d Author: WeiqunZhang Date: Sun Apr 19 20:50:39 2020 -0700 DPC++ kernel too big (#776) * This kernel's parameters are too big for DPCPP on Gen9 that has a limit of 1KB. * sqrt -> std::sqrt Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit 500e4e8cb0f3141a7aef1548d8b573dd95c4ce7b Author: Weiqun Zhang Date: Sun Apr 19 16:55:41 2020 -0700 add support for DPC++ Ahead of Time compilation Tools/GNUMake/comps/dpcpp.mak commit 87300a943d4967292eeda6c9791c370af8ae0ee7 Author: WeiqunZhang Date: Sun Apr 19 11:30:16 2020 -0700 fix instruction in CONTRIBUTING.md (#774) CONTRIBUTING.md commit c0c4b6293f7683dc9a633e20d6e6027d47f7e158 Author: Michael Zingale Date: Sun Apr 19 14:08:36 2020 -0400 fix Stony Brook spelling (#773) CONTRIBUTING.md commit 6ff71302e7e092e1b3fcf0aff23a54f27362b108 Author: WeiqunZhang Date: Sun Apr 19 10:58:41 2020 -0700 fix link to amrex github page (#771) CONTRIBUTING.md commit 571b72cb4b2b06c2aaa2aa3c6202ecbd4f9e2b55 Author: Andrew Myers Date: Sat Apr 18 21:24:07 2020 -0700 Add a CONTRIBUTING.md (#770) * add a CONTRIBUTING.md file explaining how to use forks and pull requests. * merge discussion of branch structure and core contributors into CONTRIBUTING.md * all caps * advise users to set their development branches to track the upstream one instead of their forks * use draft PRs instead of a [WIP] tag in the PR title. * add link to CONTRIBUTING.md from README.md * add a 'cd' and a 'fetch' to the instructions * also add note to set master to track upstream * instruct people to set the push url for upstream to their fork * add a note about re-forking CONTRIBUTING.md README.md commit ae38db0d088bf1978d149c16f0f885a717fc8e3c Merge: 95de5f025 8c07fd8c0 Author: Weiqun Zhang Date: Fri Apr 17 21:04:31 2020 -0700 Merge branch 'master' into development commit 95de5f0251c9b616ddfbfdead9fdf09f35bb0335 Author: WeiqunZhang Date: Fri Apr 17 21:00:09 2020 -0700 Merge master back to development for consitence (#769) * "maxorder" is an unused variable when doing the nodal projection. * remove large grids files (#763) * remove more grids files (#765) * remove timestramp files from Tools (#764) * Weiqun/rm eps pdf (#766) * remove large grids files * remove timestramp files from Tools * remove more grids files * remove unused eps and pdf files * remove these sensi files because there is already Tutorials/SENSEI (#768) Co-authored-by: Ann Almgren Docs/sphinx_documentation/source/Visualization/ParaView.png Docs/sphinx_documentation/source/Visualization/ParaView.png.REMOVED.git-id Docs/sphinx_documentation/source/Visualization/ParaView_particles.png Docs/sphinx_documentation/source/Visualization/ParaView_particles.png.REMOVED.git-id Docs/sphinx_documentation/source/Visualization/rt_2048_paraview_000500.png Docs/sphinx_documentation/source/Visualization/rt_2048_paraview_000500.png.REMOVED.git-id Docs/sphinx_documentation/source/Visualization/rt_2048_visit_000500.png Docs/sphinx_documentation/source/Visualization/rt_2048_visit_000500.png.REMOVED.git-id Docs/sphinx_documentation/source/_static/theme_overrides.css Docs/sphinx_tutorials/source/_static/theme_overrides.css Docs/sphinx_tutorials/source/figs/mf_remap_hires.png Docs/sphinx_tutorials/source/figs/mf_remap_hires.png.REMOVED.git-id Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 8c07fd8c0e36475b309f5cd365f0e20ccf856b78 Author: WeiqunZhang Date: Fri Apr 17 19:49:57 2020 -0700 remove these sensi files because there is already Tutorials/SENSEI (#768) Docs/sphinx_documentation/source/Visualization/ParaView.png Docs/sphinx_documentation/source/Visualization/ParaView.png.REMOVED.git-id Docs/sphinx_documentation/source/Visualization/ParaView_particles.png Docs/sphinx_documentation/source/Visualization/ParaView_particles.png.REMOVED.git-id Docs/sphinx_documentation/source/Visualization/rt_2048_paraview_000500.png 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Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/GPU/Advection_AmrCore/README_SENSEI.md commit ac0e50721b599f3311ec47d2eeed7a3e2658cb27 Author: WeiqunZhang Date: Fri Apr 17 17:50:26 2020 -0700 Weiqun/rm eps pdf (#766) * remove large grids files * remove timestramp files from Tools * remove more grids files * remove unused eps and pdf files Docs/sphinx_documentation/source/AmrCore/figs/Adv1.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv2.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv3.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv4.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv5.pdf Docs/sphinx_documentation/source/AmrCore/figs/flowchart.pdf Docs/sphinx_documentation/source/AmrCore/figs/subcycling.pdf Docs/sphinx_documentation/source/AmrLevel/figs/flowchart.pdf 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Docs/sphinx_documentation/source/Visualization/ParaView_particles.pdf Docs/sphinx_documentation/source/Visualization/VisIt_2D.eps Docs/sphinx_documentation/source/Visualization/VisIt_2D.pdf Docs/sphinx_documentation/source/Visualization/VisIt_3D.eps Docs/sphinx_documentation/source/Visualization/VisIt_3D.pdf commit 71623c0c255945c24bd7e07ba9fc2a5f49e97ee6 Author: WeiqunZhang Date: Fri Apr 17 17:50:06 2020 -0700 remove timestramp files from Tools (#764) Tools/Postprocessing/python/timestamp_00.REMOVED.git-id Tools/Postprocessing/python/timestamp_02.REMOVED.git-id commit dd60d07a9015ab0aabbc313c8baf8abf783ce208 Author: WeiqunZhang Date: Fri Apr 17 17:31:43 2020 -0700 remove more grids files (#765) Tests/C_BaseLib/ba.15456.REMOVED.git-id Tests/C_BaseLib/ba.15784.REMOVED.git-id Tests/C_BaseLib/ba.213 Tests/C_BaseLib/ba.23925.REMOVED.git-id Tests/C_BaseLib/ba.25600.REMOVED.git-id Tests/C_BaseLib/ba.3865 Tests/C_BaseLib/ba.5034 Tests/C_BaseLib/ba.60 Tests/C_BaseLib/ba.95860.REMOVED.git-id Tests/C_BaseLib/ba.mac.294 commit 3b3b27fba21c08135c6a99a46b55932644272cfe Author: WeiqunZhang Date: Fri Apr 17 17:29:29 2020 -0700 remove large grids files (#763) Tests/LinearSolvers/C_CellMG/grids/gr.2_19boxes Tests/LinearSolvers/C_CellMG/grids/gr.2_256squared Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/gr.2_3x2 Tests/LinearSolvers/C_CellMG/grids/gr.2_big Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/gr.2_small_a Tests/LinearSolvers/C_CellMG/grids/gr.2_small_b 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Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d Tests/LinearSolvers/C_CellMG/grids/in.2per_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed Tests/LinearSolvers/C_CellMG/grids/in.3_256cubed Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.3_512cubed Tests/LinearSolvers/C_CellMG/grids/in.3_big Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp Tests/LinearSolvers/C_CellMG/grids/in.3_small_a Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a Tests/LinearSolvers/C_CellMG/grids/in.3per_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.grids.15456 Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/grids/in.grids.25600 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Tests/LinearSolvers/MLMG/grids/grids.15456.REMOVED.git-id Tests/LinearSolvers/MLMG/grids/grids.213 Tests/LinearSolvers/MLMG/grids/grids.25600.REMOVED.git-id Tests/LinearSolvers/MLMG/grids/grids.5034 Tests/complementIn/grids/grids_1 Tests/complementIn/grids/grids_10.REMOVED.git-id Tests/complementIn/grids/grids_2 Tests/complementIn/grids/grids_3.REMOVED.git-id Tests/complementIn/grids/grids_4.REMOVED.git-id Tests/complementIn/grids/grids_5.REMOVED.git-id Tests/complementIn/grids/grids_6 Tests/complementIn/grids/grids_7 Tests/complementIn/grids/grids_8.REMOVED.git-id Tests/complementIn/grids/grids_9.REMOVED.git-id commit 86cf441f037a80ab6fa3ddd1933b7e06f556eef3 Author: WeiqunZhang Date: Fri Apr 17 19:49:57 2020 -0700 remove these sensi files because there is already Tutorials/SENSEI (#768) Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/GPU/Advection_AmrCore/README_SENSEI.md commit 3be8f0daaaba6c897f2e95eeefaae6214a0c0f93 Author: WeiqunZhang Date: Fri Apr 17 17:50:26 2020 -0700 Weiqun/rm eps pdf (#766) * remove large grids files * remove timestramp files from Tools * remove more grids files * remove unused eps and pdf files Docs/sphinx_documentation/source/AmrCore/figs/Adv1.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv2.pdf 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Docs/sphinx_documentation/source/Visualization/Amrvis_2d.pdf Docs/sphinx_documentation/source/Visualization/Amrvis_3d.eps Docs/sphinx_documentation/source/Visualization/Amrvis_3d.pdf Docs/sphinx_documentation/source/Visualization/ParaView.eps Docs/sphinx_documentation/source/Visualization/ParaView.pdf Docs/sphinx_documentation/source/Visualization/ParaView_particles.eps.REMOVED.git-id Docs/sphinx_documentation/source/Visualization/ParaView_particles.pdf Docs/sphinx_documentation/source/Visualization/VisIt_2D.eps Docs/sphinx_documentation/source/Visualization/VisIt_2D.pdf Docs/sphinx_documentation/source/Visualization/VisIt_3D.eps Docs/sphinx_documentation/source/Visualization/VisIt_3D.pdf commit 6a52f407bc6edbfdfe2498d64cddb7e37ea426d1 Author: WeiqunZhang Date: Fri Apr 17 17:50:06 2020 -0700 remove timestramp files from Tools (#764) Tools/Postprocessing/python/timestamp_00.REMOVED.git-id Tools/Postprocessing/python/timestamp_02.REMOVED.git-id commit 5710b81dec26ee1935ed9f4e8cfca9660792f490 Author: WeiqunZhang Date: Fri Apr 17 17:31:43 2020 -0700 remove more grids files (#765) Tests/C_BaseLib/ba.15456.REMOVED.git-id Tests/C_BaseLib/ba.15784.REMOVED.git-id Tests/C_BaseLib/ba.213 Tests/C_BaseLib/ba.23925.REMOVED.git-id Tests/C_BaseLib/ba.25600.REMOVED.git-id Tests/C_BaseLib/ba.3865 Tests/C_BaseLib/ba.5034 Tests/C_BaseLib/ba.60 Tests/C_BaseLib/ba.95860.REMOVED.git-id Tests/C_BaseLib/ba.mac.294 commit 1aba0fdb287760db3b4d6b4d7a2cd69cbd6f8dff Author: WeiqunZhang Date: Fri Apr 17 17:29:29 2020 -0700 remove large grids files (#763) Tests/LinearSolvers/C_CellMG/grids/gr.2_19boxes Tests/LinearSolvers/C_CellMG/grids/gr.2_256squared Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/gr.2_3x2 Tests/LinearSolvers/C_CellMG/grids/gr.2_big Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/gr.2_small_a Tests/LinearSolvers/C_CellMG/grids/gr.2_small_b Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_a Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_b Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_c Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_d Tests/LinearSolvers/C_CellMG/grids/gr.3_128cubed Tests/LinearSolvers/C_CellMG/grids/gr.3_256cubed Tests/LinearSolvers/C_CellMG/grids/gr.3_2boxes_a Tests/LinearSolvers/C_CellMG/grids/gr.3_2x3x4 Tests/LinearSolvers/C_CellMG/grids/gr.3_512cubed Tests/LinearSolvers/C_CellMG/grids/gr.3_big Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_a Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_b Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_c Tests/LinearSolvers/C_CellMG/grids/gr.3_mac_tst Tests/LinearSolvers/C_CellMG/grids/gr.3_shiftedUp Tests/LinearSolvers/C_CellMG/grids/gr.3_small_a Tests/LinearSolvers/C_CellMG/grids/gr.3_stack_a Tests/LinearSolvers/C_CellMG/grids/grids.15456.REMOVED.git-id Tests/LinearSolvers/C_CellMG/grids/grids.213 Tests/LinearSolvers/C_CellMG/grids/grids.25600.REMOVED.git-id Tests/LinearSolvers/C_CellMG/grids/grids.5034 Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes Tests/LinearSolvers/C_CellMG/grids/in.2_256squared Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/in.2_3x2 Tests/LinearSolvers/C_CellMG/grids/in.2_big Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/in.2_small_a Tests/LinearSolvers/C_CellMG/grids/in.2_small_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d Tests/LinearSolvers/C_CellMG/grids/in.2per_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed Tests/LinearSolvers/C_CellMG/grids/in.3_256cubed Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.3_512cubed Tests/LinearSolvers/C_CellMG/grids/in.3_big Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp Tests/LinearSolvers/C_CellMG/grids/in.3_small_a Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a Tests/LinearSolvers/C_CellMG/grids/in.3per_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.grids.15456 Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/grids/in.grids.25600 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 Tests/LinearSolvers/C_TensorMG/grids/gr.3_2x3x4 Tests/LinearSolvers/C_TensorMG/grids/gr16.dog Tests/LinearSolvers/C_TensorMG/grids/gr16x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr2D Tests/LinearSolvers/C_TensorMG/grids/gr32.dog Tests/LinearSolvers/C_TensorMG/grids/gr32x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr64.dog Tests/LinearSolvers/C_TensorMG/grids/gr8.dog Tests/LinearSolvers/MLMG/grids/gr.3_128cubed Tests/LinearSolvers/MLMG/grids/gr.3_256cubed Tests/LinearSolvers/MLMG/grids/gr.3_2boxes_a Tests/LinearSolvers/MLMG/grids/gr.3_2x3x4 Tests/LinearSolvers/MLMG/grids/gr.3_512cubed Tests/LinearSolvers/MLMG/grids/gr.3_big Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_a Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_b Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_c Tests/LinearSolvers/MLMG/grids/gr.3_mac_tst Tests/LinearSolvers/MLMG/grids/gr.3_shiftedUp Tests/LinearSolvers/MLMG/grids/gr.3_small_a Tests/LinearSolvers/MLMG/grids/gr.3_stack_a Tests/LinearSolvers/MLMG/grids/grids.15456.REMOVED.git-id Tests/LinearSolvers/MLMG/grids/grids.213 Tests/LinearSolvers/MLMG/grids/grids.25600.REMOVED.git-id Tests/LinearSolvers/MLMG/grids/grids.5034 Tests/complementIn/grids/grids_1 Tests/complementIn/grids/grids_10.REMOVED.git-id Tests/complementIn/grids/grids_2 Tests/complementIn/grids/grids_3.REMOVED.git-id Tests/complementIn/grids/grids_4.REMOVED.git-id Tests/complementIn/grids/grids_5.REMOVED.git-id Tests/complementIn/grids/grids_6 Tests/complementIn/grids/grids_7 Tests/complementIn/grids/grids_8.REMOVED.git-id Tests/complementIn/grids/grids_9.REMOVED.git-id commit 273b9d0c132f5259d71f7a564e143ff1feff0cf9 Author: Ann Almgren Date: Fri Apr 17 13:25:49 2020 -0700 Add EB_interp_CellCentroid_to_FaceCentroid routines in 2D and 3D... Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 64728fa54c01aa9307dd31ee129b15a7c4a62aed Merge: 8adea484f 2d2d0c02f Author: Andrew Myers Date: Fri Apr 17 12:50:49 2020 -0700 merging development into atmyers/mpi_datatype commit 2d2d0c02f6363820ac92cf596b15656a2660fbd0 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 16 19:12:46 2020 -0700 Add sort argument for makeKnapSack (#761) Co-authored-by: WeiqunZhang Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit a6e68d7731d35a55fd5d16a4bf0a602a236bd5ae Merge: 1cac20f21 61f751eb1 Author: Michele Rosso Date: Thu Apr 16 18:53:40 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1cac20f21344412c4b99cd09290a5020262be1eb Merge: 87e7f603e eda314ad8 Author: Michele Rosso Date: Thu Apr 16 18:53:21 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 61f751eb10fec682cc67e1f0f4d0e5a12753cc60 Author: Weiqun Zhang Date: Thu Apr 16 18:53:14 2020 -0700 replace pow with * Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 87e7f603ec9651b27952917fe051cb695fa7905f Author: Michele Rosso Date: Thu Apr 16 18:51:10 2020 -0700 CMake: use native CMake tools to generate AMReX_buildInfo.cpp. This commit removes the dependency on python to generate AMReX_buildInfo.cpp. AMReX_buildInfo.cpp is now generated from AMReX_buildInfo.cpp.in using CMake native configure_file(). Tools/CMake/AMReXBuildInfo.cmake Tools/CMake/AMReX_buildInfo.cpp.in commit eda314ad8a5c37e3f6f8c7a890bbb2858471b8db Merge: 92136adf2 8ee9bcad5 Author: Weiqun Zhang Date: Thu Apr 16 18:51:04 2020 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8ee9bcad53cac04d4625819096134cfe16cf6373 Merge: f4802fe5d 4f671cebd Author: mic84 Date: Thu Apr 16 18:43:55 2020 -0700 Merge pull request #762 from ax3l/topic-ciMacOS CI: macOS commit 4f671cebd64bff8a84ce16d72c60e4c2f3e6b03e Author: Axel Huebl Date: Thu Apr 16 17:58:16 2020 -0700 CI: macOS Since more than half of our developers use macOS for development, its time to check how well we support native compilers. .github/workflows/cmake.yml .github/workflows/cmake/dependencies_mac.sh commit 92136adf2791a92689702fc2321eb75356813571 Author: Weiqun Zhang Date: Thu Apr 16 17:13:17 2020 -0700 long -> amrex::Long in Tools Tools/Plotfile/AMReX_PPMUtil.cpp Tools/Plotfile/fboxinfo.cpp Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp commit 2667bfdec8537194fc219330b6fcaec57b4f7a65 Author: Weiqun Zhang Date: Thu Apr 16 17:04:21 2020 -0700 long -> amrex::Long in Tutorials Tutorials/Basic/PrefixSum_MultiFab/main.cpp Tutorials/GPU/Launch/main.cpp Tutorials/GPU/ParallelReduce/main.cpp Tutorials/GPU/ParallelScan/main.cpp Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp commit f71ca214f4700ee0c931c5398d5323a69eb76fb5 Author: Weiqun Zhang Date: Thu Apr 16 16:56:54 2020 -0700 long -> amrex::Long in Src/Extern Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/Extern/PETSc/AMReX_PETSc.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 19be07bb06ac55a7dfb101c053444853206cb5f3 Author: Weiqun Zhang Date: Thu Apr 16 10:00:46 2020 -0700 long -> amrex::Long in Particle/ and F_Interfaces Src/Base/AMReX_Utility.cpp Src/Base/AMReX_ccse-mpi.H Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_ParticleMPIUtil.H Src/Particle/AMReX_ParticleMPIUtil.cpp Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_SparseBins.H commit 80f30c5675e04fa2ec870bc8e3a0b972c4119354 Author: Weiqun Zhang Date: Thu Apr 16 09:46:24 2020 -0700 more long -> amrex::Long Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H commit 082e714c5d7fbf05f99f610ba54f522723e38bf2 Author: Weiqun Zhang Date: Wed Apr 15 17:34:04 2020 -0700 long -> amrex::Long in Base/ Docs/sphinx_documentation/source/BuildingAMReX.rst Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array4.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_GpuAtomic.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuMemory.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_INT.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MemProfiler.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_Scan.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Vector.H Src/Base/AMReX_VectorIO.H Src/Base/AMReX_VectorIO.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_ccse-mpi.H Src/Base/AMReX_fort_mod.F90 Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit f4802fe5d08f4473a0750d88ce43ae089804768c Author: Emmanuel Motheau Date: Wed Apr 15 16:41:49 2020 -0700 porting CompVelGrad to EB world to allow compilation of IAMR and PeleLM with EB=TRUE Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 23a8c3516f5dcb98df87155607c2b193661d0861 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Wed Apr 15 16:39:38 2020 -0700 Add profiling to makeSFC routines (#760) Src/Base/AMReX_DistributionMapping.cpp commit a95520e59aeabb730bc8858aef7dc93d15951504 Author: Weiqun Zhang Date: Wed Apr 15 16:19:57 2020 -0700 typo Docs/sphinx_documentation/source/BuildingAMReX.rst commit b48397202fb3458877f75b35958c35231ee42930 Author: Weiqun Zhang Date: Wed Apr 15 15:56:18 2020 -0700 update documentaion Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/Introduction.rst commit 26e07326c33254149039db52d2ffb373b3ef60fa Author: Weiqun Zhang Date: Wed Apr 15 15:50:23 2020 -0700 set DIM=3 by default for consistence with cmake Tools/GNUMake/Make.defs commit a66374e07ac48de468e7ab519c2d64721a9cf92b Author: Weiqun Zhang Date: Wed Apr 15 15:45:23 2020 -0700 no longer print arean usage for cpu build by default Src/Base/AMReX_Arena.cpp commit a877627493379151aacd52ebe6183ef35c81cb57 Author: Weiqun Zhang Date: Wed Apr 15 15:44:52 2020 -0700 add .hpp to vpath Tools/GNUMake/Make.rules commit 20f103825e33a39324d254797834c91d76acb922 Author: Weiqun Zhang Date: Wed Apr 15 15:44:30 2020 -0700 make DEBUG=FALSE the default to be consistent with cmake Tools/GNUMake/Make.defs commit b70dc0fffce1dfe733d3e88e475736a77005af41 Author: Ann Almgren Date: Wed Apr 15 12:35:26 2020 -0700 "maxorder" is an unused variable when doing the nodal projection. Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 3f2b4bf022fdedae4e67dd411ccf989e2263a4f5 Merge: 43e10a6c5 5ab5fd398 Author: Weiqun Zhang Date: Wed Apr 15 11:33:53 2020 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 43e10a6c5ce4cd50a0b5b186137c7273e871e836 Author: Weiqun Zhang Date: Wed Apr 15 10:19:54 2020 -0700 fix deprecated defeatures Src/EB/AMReX_EB2_GeometryShop.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/Particle/AMReX_ArrayOfStructs.H Tools/GNUMake/comps/gnu.mak Tutorials/EB/CNS/Source/CNS.cpp Tutorials/GPU/EBCNS/Source/CNS.cpp Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 5ab5fd39834a44e560d94becd961cd29ae07a873 Author: Michele Rosso Date: Wed Apr 15 10:10:48 2020 -0700 CMake: consider case of empty CMAKE_BUILD_TYPE in AMReXBuildInfo.cmake Tools/CMake/AMReXBuildInfo.cmake commit 3c341becd024cfc86b277003ffa402932e3d2b09 Author: Weiqun Zhang Date: Wed Apr 15 09:39:02 2020 -0700 option to add -Werror=deprecated Tools/GNUMake/comps/gnu.mak commit 8adea484f13b8faaa8c955832fe5466caee558aa Author: Andrew Myers Date: Tue Apr 14 20:24:38 2020 -0400 (more) use long to avoid overflow issues Src/Particle/AMReX_ParticleTile.H commit 16c28e6a09fe8f83ce00a764a42d24efca5e94cb Author: Andrew Myers Date: Tue Apr 14 20:24:07 2020 -0400 use long to avoid overflow issues Src/Particle/AMReX_ParticleCommunication.H commit cdbb701a5986ad32b00421027f95b7f8350d510a Author: Andrew Myers Date: Tue Apr 14 20:23:20 2020 -0400 make sure the host and device copies of the level offsets have the same size Src/Particle/AMReX_ParticleBufferMap.cpp commit c4252f5bbf535cac03075298421461c69da85540 Author: Weiqun Zhang Date: Tue Apr 14 15:07:04 2020 -0700 fix shadow warning in some cases Src/Base/AMReX_BLProfiler.H commit b7630cb2b70ebaa648664f8166281140d9171a25 Author: Weiqun Zhang Date: Tue Apr 14 14:33:39 2020 -0700 fix reorder Src/Base/AMReX_TinyProfiler.H commit ad8330be0fa0894b071ff9222941c217520a4d59 Author: Weiqun Zhang Date: Tue Apr 14 11:08:59 2020 -0700 minor optimization by avoiding copy Src/Base/AMReX_MultiFabUtil.cpp commit 479f5c0abd6ab2d12a88566dca0cd8c2f2f170da Merge: 0982acd9c f0822e8c4 Author: Weiqun Zhang Date: Mon Apr 13 20:25:29 2020 -0700 Merge branch 'dpcpp' into development commit 0982acd9c6bf7e613601a60efcadbb2cbd1745d7 Author: Weiqun Zhang Date: Mon Apr 13 19:29:41 2020 -0700 GpuBndryFunc: special cases for single box and cpu Src/Base/AMReX_PhysBCFunct.H commit 9cbd8a63ac276075968e3e3eb6d0da68a54404f4 Author: Weiqun Zhang Date: Mon Apr 13 17:13:05 2020 -0700 get rid of a bunch of ___ Src/Base/AMReX_BLProfiler.H Tutorials/Blueprint/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc_F.H Tutorials/SDC/MISDC_ADR_2d/Source/myfunc_F.H commit 938db17c0a61b7f40af4a1ddb17ab9aa77f512a4 Author: Weiqun Zhang Date: Mon Apr 13 16:48:01 2020 -0700 some cleanup of cputitrace Src/Base/AMReX.cpp Src/Base/AMReX_CuptiTrace.H Src/Base/AMReX_CuptiTrace.cpp commit cd24b951778e36f4051ee867f36f8fc911263724 Merge: 7d0b93a31 83c63f2ea Author: Michele Rosso Date: Mon Apr 13 19:17:54 2020 -0400 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 83c63f2eac8bbf63f3c215e35a9b46539f8679ce Author: Weiqun Zhang Date: Mon Apr 13 15:54:36 2020 -0700 fix for pgi on cori gpu Tools/GNUMake/sites/Make.nersc commit 7d0b93a31a43cd4a36c90b871a146d27b13d4427 Author: Michele Rosso Date: Mon Apr 13 18:42:42 2020 -0400 CMake: disable target run_HeatEquation_EX1_C.exe if ENABLE_CUDA=ON Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit e7ee45e4ca1805aaeebd4b98be21a05299c1b00b Merge: c336311bd 26fb102e1 Author: Michele Rosso Date: Mon Apr 13 18:10:03 2020 -0400 Merge branch 'development' into mr/cmake-bl-no-fort commit 26fb102e1c4d8ded5d1d384cef442329da44d517 Merge: cd8fd3314 2fb140db3 Author: Michele Rosso Date: Mon Apr 13 17:56:41 2020 -0400 Merge branch 'mr/cmake-cuda-tutorials' into development commit cd8fd331432fb10cef3ed1cb2777c20c477ddedb Merge: 8e84e8f97 3b1b92e36 Author: WeiqunZhang Date: Mon Apr 13 14:46:00 2020 -0700 Merge pull request #616 from mrowan137/mrowan/CUPTI_trace Add CUPTI trace feature for GPU kernel timing commit 2fb140db316c4f096b8ce54beda46b2ef0d95fe6 Author: Michele Rosso Date: Mon Apr 13 17:28:05 2020 -0400 CMake: set language of amrex sources via set_cpp_sources_to_cuda_language Src/CMakeLists.txt commit 8761f5018ecd83843617d6d2598ab9341994027a Author: Michele Rosso Date: Mon Apr 13 17:16:54 2020 -0400 CMake: CUDA-fy tutorials Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt Tutorials/LinearSolvers/ABecLaplacian_C/CMakeLists.txt Tutorials/LinearSolvers/MultiComponent/CMakeLists.txt Tutorials/LinearSolvers/NodalPoisson/CMakeLists.txt Tutorials/LinearSolvers/NodeTensorLap/CMakeLists.txt commit 702f293072cc86cf8b564769d418a903c1dc89fb Author: Michele Rosso Date: Mon Apr 13 17:16:27 2020 -0400 CMake: add helper function to mark C++ source files as CUDA Tools/CMake/AMReXTargetHelpers.cmake commit f0822e8c424ecc0de39836ab78dd78bd4614a5f5 Author: Weiqun Zhang Date: Mon Apr 13 13:17:25 2020 -0700 make Tutorials/GPU/CNS work with DPC++ by avoiding global variables Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp Tutorials/GPU/CNS/Exec/RT/cns_prob_parm.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/cns_prob_parm.H Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_derive.cpp Tutorials/GPU/CNS/Source/CNS_parm.H Tutorials/GPU/CNS/Source/CNS_parm.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit 0780ea0e8fb0ff7d92aad16facb9a09cf70d5785 Author: Weiqun Zhang Date: Mon Apr 13 12:05:07 2020 -0700 operator delete: for safety test the pointer first Src/Base/AMReX_GpuMemory.H commit 0af0f99a72777960e56a3666b692009745e03043 Author: Weiqun Zhang Date: Mon Apr 13 09:41:23 2020 -0700 reorganize various ParalleFor functions Src/Base/AMReX_GpuLaunchFunctsG.H commit cf0b059c96b0e307872d06b334a547d75a7734b3 Author: Weiqun Zhang Date: Mon Apr 13 09:10:34 2020 -0700 add amrex::IsHostDeviceLambda Src/Base/AMReX_TypeTraits.H commit 8e84e8f97ea8205214be04a7a205ed5b6f6cd3f5 Author: Weiqun Zhang Date: Sun Apr 12 20:15:06 2020 -0700 fix link to mpi on Cori gpu Tools/GNUMake/sites/Make.nersc commit 1699c94d4364fc3b09a0e8d82d6f2b986bf1a726 Author: Ann Almgren Date: Sun Apr 12 13:13:19 2020 -0700 Copy beta from host to GPU when beta is Vector not just Real -- in setEBDirichlet and setEBHomogDirichlet Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit fa6530436ba95b67313218a54f0204e27c2e089c Author: Ann Almgren Date: Sun Apr 12 12:00:00 2020 -0700 For setting the beta coefficients for a multicomponent CC solve in EB and non-EB versions, 1) we now allow the user to pass an array of scalars as an alternative to a single scalar 2) when a MultiFab is passed in, we assert that there is either 1 component or the same number of components as the solution so either copy component by component or just from the one component as appropriate. These changes are in the setBCoeffs, setEBDirichlet and setEBHomogDirichlet calls of AMReX_MLABecLaplacian.* and AMReX_MLEBABecLap.*. Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit ae9b193116606101ca9ebfd47447c12af1a53a1d Author: Weiqun Zhang Date: Fri Apr 10 14:02:07 2020 -0700 update wishlist Docs/Notes/DPCPPWishlist.md commit c336311bdb1407b43a4674f5027d2a2a8d91cd97 Author: Michele Rosso Date: Thu Apr 9 17:23:01 2020 -0700 CMake: don't build tutorials with Fortran sources if ENABLE_FORTRAN=OFF Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit a6b5acda22cb651ce76eb969b1a6ff7c9e565306 Author: Michele Rosso Date: Thu Apr 9 17:05:27 2020 -0700 CI: add make command to build tutorials .github/workflows/cmake.yml commit 96b1117e36d3c49495310bfd005391256a8e4e78 Merge: 15220b232 7c3b2698a Author: mic84 Date: Thu Apr 9 17:01:09 2020 -0700 Merge pull request #759 from ax3l/fix-cmakeVersionMatch CMake: Regex Version Validator commit 7c3b2698a13094d702a92820d2649a52c1da154b Author: Axel Huebl Date: Thu Apr 9 16:49:39 2020 -0700 CMake: Regex Version Validator If what we get from `git describe` does not match `.[.][-something]` then we treat that as not a proper version. CMakeLists.txt commit 15220b232aca637c27a644f70ecb72a3acf37d96 Author: jmsexton03 Date: Thu Apr 9 10:52:55 2020 -0700 Cori-gpu make update for testing USE_MPI=TRUE USE_CUDA=FALSE (#753) Building with USE_CUDA=TRUE on Cori login nodes is now disallowed; CUDA builds must be done from cgpu nodes. We now uniformly support OpenMPI, MVAPICH, and MPICH. The Make.nersc file is cleaned up a bit as a result. Src/Base/AMReX_Machine.cpp Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nersc commit 570844d3d2bc9bbf71392813f2a3afc555681f04 Merge: effc622d2 f918ae798 Author: Michele Rosso Date: Wed Apr 8 21:04:26 2020 -0700 Merge branch 'mr/cmake-bl-no-fort' of https://github.com/AMReX-Codes/amrex into mr/cmake-bl-no-fort commit effc622d2f89093c5f32414e507d3acff8e52469 Author: Michele Rosso Date: Wed Apr 8 21:04:08 2020 -0700 CMake: implement ENABLE_FORTRAN (BL_NO_FORT) option CMakeLists.txt Docs/sphinx_documentation/source/BuildingAMReX.rst Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/EB/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 30314de4f19256b7736dc7389771d335586fbf97 Author: Weiqun Zhang Date: Wed Apr 8 20:51:47 2020 -0700 loop on cpu instead Tools/Plotfile/fsnapshot.cpp commit f918ae7982cf1415abdf4f8eb25a47d0c489d35e Author: Axel Huebl Date: Wed Apr 8 19:13:28 2020 -0700 CI: Remove gfortran for No-Fortran Build .github/workflows/cmake.yml .github/workflows/cmake/dependencies_nofortran.sh commit 64edb83bbccfee00572b59de83dbf39cd2807a52 Author: Axel Huebl Date: Wed Apr 8 19:11:16 2020 -0700 CI: Add a Fortran-Free CMake Build .github/workflows/cmake.yml commit 206a3c9c816a7ca6fe2dab72a21aa4f533656e07 Author: Michele Rosso Date: Wed Apr 8 18:29:58 2020 -0700 No need to define Fortran functions if BL_NO_FORT is TRUE Src/Base/AMReX_BLFort.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Random.cpp commit 5fb3be52571d82d2252d2ca6e86bd42bf262737f Author: Michele Rosso Date: Wed Apr 8 17:16:06 2020 -0400 CMake: add CUDA-support to plotfile tools build. It fixes issue #748 Tools/Plotfile/CMakeLists.txt commit a82d6303a607ae6c372881e86184ec80e6a6bbff Author: Andrew Myers Date: Wed Apr 8 10:28:21 2020 -0700 add some missing AMREX_GPU_HOST_DEVICE Tools/Plotfile/fsnapshot.cpp commit 84265ea5db97cbee1342da22e957c6976a631530 Author: Weiqun Zhang Date: Tue Apr 7 20:01:47 2020 -0700 fix multiple exectuables build for CUDA Tools/GNUMake/Make.rules commit 09f9cb751a43e8d4c4163e59e2c84c69ba6f5c1c Merge: 53b056f40 524fd6e71 Author: Michele Rosso Date: Tue Apr 7 17:41:43 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/cmake-bl-no-fort commit 524fd6e7136517311dbd8f9a04d4628c21b8cd35 Author: Weiqun Zhang Date: Tue Apr 7 17:35:03 2020 -0700 No need to define BL_FORT_USE_ if BL_NO_FORT is TRUE Src/Base/AMReX_BLFort.H commit 53b056f4065daf70f2e8dafbb79ba6d225498270 Author: Michele Rosso Date: Tue Apr 7 11:36:34 2020 -0700 CMake: add native include guard to AMReX_Options.cmake Tools/CMake/AMReX_Options.cmake commit 7c77e104e653d1b1e29c4fab2ffe3ade98ce2f50 Author: Weiqun Zhang Date: Mon Apr 6 22:08:20 2020 -0700 fix some warnings Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_Utility.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_distFcnElement.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_TracerParticle_mod_K.H Tools/GNUMake/comps/gnu.mak Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit 9bf2d4be00eae70313480f5b72268c788d8cd515 Author: Weiqun Zhang Date: Mon Apr 6 20:12:13 2020 -0700 static_cast to avoid warning Src/Base/AMReX_MultiFabUtil_nd_C.H commit 49ea587bcab6e373062efd13ff8e0b9e4cb62120 Author: Weiqun Zhang Date: Mon Apr 6 18:22:42 2020 -0700 fcompare: always return Tools/Plotfile/fcompare.cpp commit 95375ec320b2250b6aef731ed3d131aff36487fb Merge: 0ec72262d 3fda5d099 Author: WeiqunZhang Date: Mon Apr 6 14:24:12 2020 -0700 Merge pull request #758 from MaxThevenet/ixtype add function IndexType::toIntVect commit 3fda5d0990aeccaf3df906df89c8b274baa52382 Author: MaxThevenet Date: Mon Apr 6 13:54:19 2020 -0700 add function IndexType::toIntVect Src/Base/AMReX_IndexType.H commit 0ec72262d86817ec06a9d61fa865f689adc70131 Author: Andrew Myers Date: Mon Apr 6 13:10:39 2020 -0700 allow evaluation of f on the gpu for particle filtering Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H commit ff2634d4ff0d97cd7cfaff54f38d438e96022d71 Author: Weiqun Zhang Date: Sat Apr 4 16:09:07 2020 -0700 fix namespace Src/Base/AMReX_Utility.H commit 810480b2b4bae1834b079885c68abfba426df479 Merge: 5aa5c3e45 2425a7894 Author: WeiqunZhang Date: Sat Apr 4 09:26:03 2020 -0700 Merge pull request #746 from AMReX-Codes/writeplotfile_eb Writeplotfile eb commit 5aa5c3e45aefb093b74ea5b41e047a93f05df500 Author: Weiqun Zhang Date: Fri Apr 3 21:51:17 2020 -0700 add trim and is_it function for string Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 2774693d0b43e710f2e5d02995aabe4cfabce98c Merge: ff4bc0009 4305a7677 Author: mic84 Date: Fri Apr 3 18:48:10 2020 -0700 Merge pull request #755 from ax3l/fix-cmakeInvalidGitVersions CMake: Discard Invalid Git Versions commit 4305a76772b720214752dc4238a4935d4b794c42 Author: Axel Huebl Date: Fri Apr 3 18:39:28 2020 -0700 CMake: Discard Invalid Git Versions In case a user only performed a shallow copy of the git repo, `git describe` will not find a latest tag and return only a hash. Hashes are not valid `VERSION` attributes in CMake and crash the configuration stage. This fix just discards invalid versions and tries the fallback of parsing the change log file. Fix #731 (continued) Ref.: https://github.com/AMReX-Codes/amrex/issues/731#issuecomment-596077396 CMakeLists.txt commit ff4bc0009cca362d4b9349787e38f735ceafcbc7 Merge: d13c2a662 14f0634ae Author: mic84 Date: Fri Apr 3 18:28:21 2020 -0700 Merge pull request #749 from ax3l/topic-cmakePropsCUDA Default CMake CXX Standard Control commit 14f0634ae7e6480f35cec5c0fb6ab902cc2b51c7 Author: Axel Huebl Date: Fri Apr 3 18:07:03 2020 -0700 Finalize Build: Docs & Labels .github/workflows/cmake.yml CMakeLists.txt Docs/sphinx_documentation/source/BuildingAMReX.rst commit 3a8c0402a2405e34e720ca1dc43960e69a3fe977 Author: Axel Huebl Date: Fri Apr 3 17:39:08 2020 -0700 Library CMake Build: C++17 .github/workflows/cmake.yml Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit d13c2a662c330b528d4bc5027f07defe05efa017 Merge: 597cf62af 89ff6e88c Author: WeiqunZhang Date: Fri Apr 3 17:38:01 2020 -0700 Merge pull request #754 from rporcu/development substitute RunOn::Device with RunOn::Host in copyTo function commit 507366d5b5b82a6ec8ab39be9e7ac66449739dc0 Author: Axel Huebl Date: Mon Mar 30 18:19:43 2020 -0700 Add CMAKE_C_COMPILER: gcc-4.8 Otherwise the system-wide 7.5.0 GCC is picked up for C sources (and potentially some linking). .github/workflows/cmake.yml commit 9adf70a3b80f9244915b434f2646bee76b6c85c5 Author: Axel Huebl Date: Fri Apr 3 17:09:13 2020 -0700 Skip CMake Install Is there some recent CMake laying around?? .github/workflows/cmake.yml .github/workflows/cmake/dependencies.sh .github/workflows/cmake/dependencies_nvcc.sh commit 2efd03550f49e65e957d97aeaf3ac28d26f6d963 Author: Axel Huebl Date: Mon Mar 30 17:20:35 2020 -0700 CMake: Std only via Compile Feature .github/workflows/cmake.yml Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 89ff6e88c5d78083a1eda1ece22a720af58dde02 Author: rporcu Date: Fri Apr 3 19:38:04 2020 -0400 substitute RunOn::Device with RunOn::Host in copyTo function Src/Base/AMReX_FabArrayCommI.H commit 1eb6f5334ae54c0e49011dd22530a71f5ceadd90 Merge: 3859780d8 597cf62af Author: Andrew Myers Date: Fri Apr 3 17:42:04 2020 -0400 Merge branch 'development' into atmyers/mpi_datatype commit 597cf62afa2d9f8b483eb19f7cfc97186dad363e Merge: 193adb277 b31826feb Author: Weiqun Zhang Date: Fri Apr 3 08:25:41 2020 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3b1b92e36306a070a8df846153a1cd3ac4bf23e8 Author: Michael Rowan Date: Thu Apr 2 10:41:37 2020 -0700 [WIP] Formatting Src/Base/AMReX_TinyProfiler.cpp Tests/GPU/CuptiTest/Source/main.cpp commit 8a6b318c7cf686ade56e8243cfa0a98f6ec7f646 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:23:25 2020 -0700 Update main.cpp Tests/GPU/CuptiTest/Source/main.cpp commit e219285438a724e7efc0796e32a380ed24f40678 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:22:31 2020 -0700 Update nvcc.mak commit 36d3435e5d70036464387807c5914cad3838eb03 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:21:51 2020 -0700 Update nvcc.mak commit 7d809db8de008ddf00963c63ecae600db1e6c2a5 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:21:19 2020 -0700 Update Make.defs commit 315890077cda14e849a3d5933ccb3317cd05b34a Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:20:43 2020 -0700 Update Make.package commit 2ac2a2d9cefc9b96bfaa905ac2bc484ce94cc8c9 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:20:08 2020 -0700 Update Make.CUPTI commit cf3e95cf2f3a0bc38eb3016e9f970ae49735eab0 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:19:36 2020 -0700 Update myfunc.cpp commit b949602b310524e6b1982e3115b7dfb71f210c90 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:19:00 2020 -0700 Update myfunc.H commit 427baec4c9cce5272438951a95fee86a5d1ecb51 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:18:32 2020 -0700 Update Make.package commit 8e424e71853f9df2adff16cf328bb433f5bdabf1 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:18:00 2020 -0700 Update GNUmakefile commit 2bceefda93480fe2ced6c037fb839c86768024c0 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:17:24 2020 -0700 Update Make.package Src/Base/Make.package commit ffbad9a336b2d3aa8301c092b9ce5b771004dc92 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:15:10 2020 -0700 Update AMReX_TinyProfiler.H commit 93e307f7c35e6374c2dc90889e77e6e9531c8803 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:14:44 2020 -0700 Update AMReX_CuptiTrace.cpp Src/Base/AMReX_CuptiTrace.cpp commit 32e94fa2f4ceb0339934604652d16567004f1156 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:13:48 2020 -0700 Update AMReX_CuptiTrace.H commit ebc22600d34c1422bf68691e7afa15f1750da0a1 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:13:22 2020 -0700 Update AMReX_BLProfiler.H commit d7954ce34f8299fda95350f555eed97c97188f34 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Thu Apr 2 10:05:30 2020 -0700 Update AMReX_CuptiTrace.cpp Src/Base/AMReX_CuptiTrace.cpp commit c40835214cbd88aaf3745777efdaaa37a084a7ba Author: Michael Rowan Date: Thu Apr 2 10:00:56 2020 -0700 [WIP] formatting mykernel.H Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H commit ecde67289e6935ab282db55e904bf670dc016280 Author: Michael Rowan Date: Thu Apr 2 02:31:19 2020 -0700 [WIP] Review fixes Src/Base/AMReX_CuptiTrace.H Src/Base/AMReX_CuptiTrace.cpp commit c7caac2b81d7a0c28ff6713e0cae803455adb3e5 Author: Michael Rowan Date: Thu Apr 2 02:20:30 2020 -0700 [WIP] Review fixes Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp commit 6a2d004ddb8324f18e66ab9831081da6128adb3a Author: Michael Rowan Date: Thu Apr 2 02:02:14 2020 -0700 [WIP] Review fixes Src/Base/AMReX_CuptiTrace.H Src/Base/AMReX_CuptiTrace.cpp Src/Base/AMReX_TinyProfiler.cpp Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp commit 5ee7327e76cabc781b5ccb16ac838a2524975323 Author: Michael Rowan Date: Wed Apr 1 20:06:33 2020 -0400 [WIP] review changes Src/Base/AMReX_CuptiTrace.H Src/Base/AMReX_CuptiTrace.cpp Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp commit b31826feb6b76b584d1f7c4a231abb17875a657f Merge: 6eac633c8 a782eba56 Author: Weiqun Zhang Date: Wed Apr 1 13:43:56 2020 -0700 Merge branch 'master' into development commit 193adb277cd44ff117a3e81f58454b0ac470a032 Merge: 7075f2575 6eac633c8 Author: Weiqun Zhang Date: Wed Apr 1 13:42:28 2020 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e4502c77de6d65ee75816eee565eed8dab86fe86 Merge: 0a813f20a 6eac633c8 Author: Michael Rowan Date: Wed Apr 1 15:36:38 2020 -0400 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace commit 6eac633c8c4388ccd31eac3acee9a85fefb169af Merge: 2fcea2a1d bef840955 Author: WeiqunZhang Date: Wed Apr 1 09:21:18 2020 -0700 Merge pull request #750 from mwm126/patch-1 Fix warning maybe-uninitialized for: the_send_data commit 7075f25758cd1e79a2bcc2db4ed98339b89e17c6 Merge: b7e78115e a782eba56 Author: Weiqun Zhang Date: Wed Apr 1 09:08:46 2020 -0700 Merge branch 'development' into dpcpp commit a782eba56e024d3c6743a0953302eac21d1a2d17 Author: Weiqun Zhang Date: Wed Apr 1 09:07:33 2020 -0700 update CHANGES CHANGES commit bef840955be84fe9ce2ca826e1af62c8708d31d4 Author: Mark Meredith Date: Wed Apr 1 10:43:45 2020 -0400 Fix warning maybe-uninitialized for: the_send_data Compiler warning with GCC 9.3: .../Src/Base/AMReX_FabArrayCommI.H: In member function 'void amrex::FabArray::ParallelCopy(const amrex::FabArray&, int, int, int, const amrex::IntVect&, const amrex::IntVect&, const amrex::Periodicity&, amrex::FabArrayBase::CpOp, const amrex::FabArrayBase::CPC*) [with FAB = amrex::FArrayBox]': .../Src/Base/AMReX_FabArrayCommI.H:611:40: error: 'the_send_data' may be used uninitialized in this function [-Werror=maybe-uninitialized] amrex::The_FA_Arena()->free(the_send_data); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ Src/Base/AMReX_FabArrayCommI.H commit b7e78115e8e1ed37ea66fd40e09b90225f81fee4 Merge: 7a8cbfcc2 2fcea2a1d Author: Weiqun Zhang Date: Sun Mar 29 21:50:11 2020 -0700 Merge branch 'development' into dpcpp commit 2fcea2a1d574031189416f86a056ed2760720663 Author: Weiqun Zhang Date: Sun Mar 29 21:49:49 2020 -0700 remove an ifdef AMREX_USE_CUDA meant for HIP Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H commit 7a8cbfcc2fc5442279e24f7f392c10ef74b4989b Author: Weiqun Zhang Date: Sun Mar 29 21:43:22 2020 +0000 update wishlist Docs/Notes/DPCPPWishlist.md commit 02d043ad38da27557340164ad74e05ad90ba6562 Author: Weiqun Zhang Date: Sun Mar 29 21:28:20 2020 +0000 add -fsycl Tools/GNUMake/comps/dpcpp.mak commit fd6219895658c835fb94bb8a379da195a248dbf9 Author: kngott Date: Sun Mar 29 12:59:01 2020 -0700 Missed a { Src/Base/AMReX_GpuLaunch.H commit 6df41cdd76cd6dbc07ee15a559a94ccf980d4659 Author: kngott Date: Sun Mar 29 12:36:00 2020 -0700 Few strays. Src/Base/AMReX_FArrayBox.cpp Src/Boundary/AMReX_Mask.H commit 44d9bc1486b35162712c36ad55f8f0072cef4f54 Author: Weiqun Zhang Date: Sun Mar 29 19:12:18 2020 +0000 udpate DPC++ wishlist Docs/Notes/DPCPPWishlist.md commit 7858e3b28c46e8fc9404738cad8c55bbc8e5642f Author: kngott Date: Sun Mar 29 12:11:55 2020 -0700 How'd I miss BaseFab? Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_BaseFab.H commit 2d69ab8cb932d3b9833fb5ec58fa3a9a7037b0b7 Author: kngott Date: Sun Mar 29 11:18:54 2020 -0700 Change FLAG based launches from bool to RunOn. Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_GpuLaunch.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBInterpolater.cpp commit ddcdbf99a17150c3d08ce7d1a7f6b02b94151bc3 Author: Weiqun Zhang Date: Sun Mar 29 17:35:11 2020 +0000 Revert "more amrex::Math for broken dpc++" Revert "fix sycl::pow so that it works for pow(double,int) like c++ standard does" Revert "use amrex::Math for dpc++" Revert "dpc++: use amrex::Math" Revert "some math functions are broken in dpc++ beta5" No longer needed after we link to libsycl-fp64. Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_GpuComplex.H Src/Base/AMReX_Math.H Src/Base/AMReX_RealVect.H Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_IF_Base.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Torus.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Tests/LinearSolvers/CellEB/MyEB.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB/initEB.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H commit b38324d6a544809b59c13bc1dcac294a7e41e57d Author: Weiqun Zhang Date: Sun Mar 29 17:33:24 2020 +0000 dpc++: we now have to link to libsycl-cmath-fp64 for double precision math Tools/GNUMake/comps/dpcpp.mak commit b93a02069cdf4b438c8ac43316df149e569bf162 Author: Weiqun Zhang Date: Sun Mar 29 07:45:13 2020 -0700 more amrex::Math for broken dpc++ Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_GpuComplex.H Src/Base/AMReX_RealVect.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H commit 49a92c2d412f576d654acd2c3b014daba5f33972 Author: Weiqun Zhang Date: Sun Mar 29 07:27:01 2020 -0700 fix sycl::pow so that it works for pow(double,int) like c++ standard does Src/Base/AMReX_Math.H commit 713d5d104f547dcb53cb32ebe1f80b7acb668f8c Author: Weiqun Zhang Date: Sun Mar 29 07:10:22 2020 -0700 use amrex::Math for dpc++ Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_IF_Base.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Torus.H Tests/LinearSolvers/CellEB/MyEB.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB/initEB.cpp commit 36185dcc018e5d3bb1a674f1373c3f524d44c853 Author: Weiqun Zhang Date: Sun Mar 29 06:57:27 2020 -0700 remove trivial dtor from a number of EB implicit functions so that they are trivially destructible and thus can work with DPC++ Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Difference.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/AMReX_EB2_IF_Spline.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H Tests/LinearSolvers/CellEB/MyEB.H Tests/LinearSolvers/CellEB2/MyEB.H Tests/LinearSolvers/EBConvergenceTest/MyEB.H Tests/LinearSolvers/EBflux_grad/MyEB.H commit 42f5cc87b35564b5b5cf0bcac89f494a187e05b7 Author: Weiqun Zhang Date: Sun Mar 29 06:47:30 2020 -0700 dpc++: use amrex::Math Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H commit 61dd1d04896675ceb04da08f99a870ea5e12da8c Author: Weiqun Zhang Date: Sun Mar 29 04:55:31 2020 +0000 dpc++: explicitly access id so that it works for beta4 too Src/Base/AMReX_GpuReduce.H commit 3424240b792fdadb06b6ade328ab28b943f675bd Author: Weiqun Zhang Date: Sun Mar 29 02:05:18 2020 +0000 some math functions are broken in dpc++ beta5 Src/Base/AMReX_Math.H commit 7d8be7c461454922365141c5e5ee0f6f23a6e68a Author: Weiqun Zhang Date: Sat Mar 28 21:10:50 2020 +0000 dpc++: use 16 as subgroup size because shuffle_down does not work otherwise Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuReduce.H commit 1bdc1d077489de6860f57f18a7e9c470f8fc4783 Author: Weiqun Zhang Date: Sat Mar 28 19:24:38 2020 +0000 dpc++ use sub_group methods to get land and warp id and comment out unsupported code Src/Base/AMReX_GpuReduce.H commit 33bd5149cb9a45dd073736a5069e459494b84082 Author: Weiqun Zhang Date: Sat Mar 28 18:11:55 2020 +0000 dppc++: use subgroup shuffle_down for reduction Src/Base/AMReX_GpuReduce.H commit 242cb2e23c7576b35f079c273ed37e901bb3fb33 Author: Weiqun Zhang Date: Sat Mar 28 17:31:57 2020 +0000 dpc++: allocate local memory for reduction Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_Reduce.H commit 492172f433dd7508c8427e2649564296b2d3add7 Author: Weiqun Zhang Date: Sat Mar 28 03:32:31 2020 +0000 add Gpu::Handler for DPC++ Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_GpuTypes.H Src/Base/AMReX_Reduce.H commit f396e29cfc8e20b71689b8c2cf8377cfca9b606b Author: Weiqun Zhang Date: Fri Mar 27 18:25:16 2020 -0700 turn on AMREX_REQUIRE_SUBGROUP_SIZE for dpc++ Src/Base/AMReX_GpuQualifiers.H commit 3eb820a7c5b7fee54882f2fa5a661a2c8f92b8fd Author: Weiqun Zhang Date: Fri Mar 27 17:02:53 2020 +0000 use sycl::isnan Src/Base/AMReX_GpuUtility.H commit daf78c4e33512f46e48da55123febda6725996a7 Author: Weiqun Zhang Date: Fri Mar 27 16:28:11 2020 +0000 update Make file for jlse Tools/GNUMake/Make.defs commit 26c22d5ca7b8fe95374ffc70835627c1cbd21e22 Merge: 73c70e4e4 9e9f7b8f6 Author: Andrew Myers Date: Fri Mar 27 11:15:54 2020 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 73c70e4e4ae48569b09dced609a73ac5053f05e1 Author: Andrew Myers Date: Fri Mar 27 11:15:13 2020 -0400 always sync at the end of redistribute Src/Particle/AMReX_ParticleContainerI.H commit 0a813f20af8c5530913132a27e11eead37e76a8a Author: Michael Rowan Date: Thu Mar 26 19:39:29 2020 -0400 Review changes Src/Base/AMReX_CuptiTrace.cpp commit 39f3553f07eb43b202b8fea572bec0fae1056b01 Merge: ab3930c6e 9e9f7b8f6 Author: Michael Rowan Date: Thu Mar 26 19:38:02 2020 -0400 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace commit f8619663ac2ab54fd6b73f42e19ab944596774ff Author: Weiqun Zhang Date: Thu Mar 26 16:21:16 2020 -0700 update wording Docs/Notes/DPCPPWishlist.md commit 232aa130b39f579fe9c512685f9a7cc891330414 Author: Weiqun Zhang Date: Thu Mar 26 16:18:29 2020 -0700 update format Docs/Notes/DPCPPWishlist.md commit ef3fc32850627f75eb5c3918abd067d6db24a832 Author: Weiqun Zhang Date: Thu Mar 26 16:12:44 2020 -0700 add DPC++ wishlish Docs/Notes/DPCPPWishlist.md Docs/Notes/Readme.dpcpp commit 2425a78944298cf18589b876901c854c856825f7 Author: atmyers Date: Thu Mar 26 15:12:45 2020 -0700 left out an important part of that Src/Amr/AMReX_AmrLevel.cpp commit 78426326fd55b13693f066166b8b5508f6b53205 Author: atmyers Date: Thu Mar 26 14:50:48 2020 -0700 add eb information to AMRLevel's writePlotFile routine Src/Amr/AMReX_AmrLevel.cpp Tutorials/EB/CNS/Source/CNS_io.cpp commit ab3930c6e46d01bb52cb3ec0adc771323a2dca6f Author: Michael Rowan Date: Wed Mar 25 21:48:12 2020 -0400 Remove unneeded ActivityTraceAsync file Src/Base/AMReX_ActivityTraceAsync.H Src/Base/AMReX_ActivityTraceAsync.cpp commit 8ff5b565ad49ddced6ae7c04b52f003d3d894983 Author: Michael Rowan Date: Wed Mar 25 18:44:12 2020 -0700 Review changes Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_CuptiTrace.H Src/Base/AMReX_CuptiTrace.cpp Src/Base/AMReX_TinyProfiler.H Tools/GNUMake/comps/nvcc.mak commit 8d1f6715212edaf9980d7934a7c6f7478accfbac Merge: 1ed6ec669 34c5d391e Author: Michael Rowan Date: Wed Mar 25 17:02:38 2020 -0700 Merge conflict commit 1ed6ec669f185ddd4aa304a653337bd248a037c9 Merge: 8432d8d24 e348a5f7b Author: Michael Rowan Date: Wed Mar 25 16:46:17 2020 -0700 Merge branch 'master' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace commit 9e9f7b8f63f1fdb7eb765a699d3a18fd2340fab0 Author: atmyers Date: Wed Mar 25 15:32:39 2020 -0700 make sure we are using the float version of abs in AMReX_EBMultiFabUtil_?D_C.H Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit d1affc0bfd0cfa9680c6a9a5bb292032feb7e2a3 Merge: 2c7c61fab 2f9e8b17f Author: Weiqun Zhang Date: Tue Mar 24 21:21:00 2020 -0700 Merge branch 'weiqun/bat' into development commit 2f9e8b17fece1fdec01ffed0fa995890bf0f1620 Author: Weiqun Zhang Date: Tue Mar 24 18:38:23 2020 -0400 BoxArray BATransformer: optimization Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit a5da328a37e12b4586b2a1889e6c01185004faf3 Author: Weiqun Zhang Date: Tue Mar 24 10:23:18 2020 -0700 fix a couple of new bugs Src/Base/AMReX_BoxArray.H commit 07ffa91b18b2048ae3b8d5666ed990699ba686c2 Author: Weiqun Zhang Date: Tue Mar 17 21:13:18 2020 -0700 get rid of virtual transformer in BoxArray Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_MultiMask.cpp commit 2c7c61fab9e9a91f737b44f138f1fff8d601fc39 Merge: 5369e707b e02e0a971 Author: WeiqunZhang Date: Sat Mar 21 17:19:55 2020 -0700 Merge pull request #744 from AMReX-Codes/setphysboundaryvalues_fab Use Fab interface in setPhysBoundaryValues if available commit e02e0a9719a3caa08a988d2daeb564cd77478630 Author: Max Katz Date: Fri Mar 20 22:01:56 2020 -0700 Use Fab interface in setPhysBoundaryValues if available Src/Amr/AMReX_AmrLevel.cpp commit 5369e707b4c57ffd06433752c51b02547077695f Author: Weiqun Zhang Date: Fri Mar 20 11:33:05 2020 -0700 add template keyword otherwise Clang does not like it Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit 7955ceb5a071b7bb19d94f51f30f167da34de39f Author: atmyers Date: Thu Mar 19 23:01:17 2020 -0700 fix several of the WritePlotFile methods for runtime components Src/Particle/AMReX_ParticleIO.H commit 123ba3aa2aec03e8e33faecfc135fe1bca5314df Author: Weiqun Zhang Date: Thu Mar 19 14:15:54 2020 -0700 fix pthread for nvcc by default in Make.unknown Tools/GNUMake/sites/Make.ccse Tools/GNUMake/sites/Make.unknown commit 87c6428bcbb599e0e1da988bf13fa0b71d5b59ec Author: Weiqun Zhang Date: Thu Mar 19 14:14:42 2020 -0700 make sure mpi_cxx is linked when nvcc is used for linking Tools/GNUMake/sites/Make.unknown commit 1f1351dcaa85a517d7da5fc16271e7c70c4c7293 Author: Weiqun Zhang Date: Thu Mar 19 10:54:07 2020 -0700 fix some BaseFab RunOn Src/Base/AMReX_BaseFab.H commit afddf068f1b4067d48878043551d2416ca75de6a Author: Weiqun Zhang Date: Thu Mar 19 10:22:11 2020 -0700 fix FabArray:copyTo RunOn Src/Base/AMReX_FabArrayCommI.H commit 0ffb4eb5852d9c0c19344cc44b4db0045cfdab4b Merge: cbd85536b 7edab7812 Author: WeiqunZhang Date: Wed Mar 18 11:01:14 2020 -0700 Merge pull request #741 from jrood-nrel/update_nrel_site Update makefiles for NREL site commit 7edab7812053047f3d0c842a8376026b8596752a Author: Jon Rood Date: Wed Mar 18 11:51:03 2020 -0600 Update makefiles for NREL site to remove Peregrine machine and allow building with CUDA. Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nrel commit cbd85536b64d887670984267ac16163d8c8ff6e5 Author: Michele Rosso Date: Tue Mar 17 15:55:22 2020 -0700 CMake: only install required subfolders within Tools directory Tools/CMake/AMReXInstallHelpers.cmake commit 3d0788c0fe27c0d4e840b5e2f9986951c4aaf000 Author: Michele Rosso Date: Tue Mar 17 15:07:34 2020 -0700 CMake: remove ENABLE_CUDA option duplicate Tools/CMake/AMReX_Options.cmake commit 7de60498d064ffaa2b67957343555fb0015ca483 Author: Weiqun Zhang Date: Tue Mar 17 14:24:12 2020 -0700 fix Arena test in FArrayBox and IArrayBox Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.cpp commit 38f25e08f7803c39b79da425362e509f6c040ba1 Merge: b938fad38 b99f08366 Author: Weiqun Zhang Date: Mon Mar 16 16:35:02 2020 -0700 Merge branch 'development' into weiqun/dev commit b99f08366d904df9f2adb22f329ddd75724a23bb Author: Weiqun Zhang Date: Mon Mar 16 15:38:17 2020 -0700 fix a new bug in FluxRegister::SumReg Src/AmrCore/AMReX_FluxRegister.cpp commit b938fad38ac7f26dc4b51878d684ce47a04bdedc Merge: c63c131bf 2db7bf32a Author: Weiqun Zhang Date: Mon Mar 16 10:19:00 2020 -0700 Merge branch 'development' into weiqun/dev commit 2db7bf32a5955fe7af8c977aff26adb23e227ab6 Author: Weiqun Zhang Date: Mon Mar 16 10:17:06 2020 -0700 remove some temporary variables Src/Base/AMReX_FilCC_3D_C.H commit 2724030e1628bf6370dabb450383ae32f293c375 Author: Weiqun Zhang Date: Mon Mar 16 09:20:29 2020 -0700 use DeviceVector instead of AsyncArray because it does not need to be async safe Src/EB/AMReX_EBMultiFabUtil.cpp commit b9f76a6a0beddf9aa7e3d1ac491a1db0d14439f7 Author: Weiqun Zhang Date: Mon Mar 16 09:10:27 2020 -0700 no need to be virtual Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H commit 81192d9d2417e844aefbfc91d629316bc2ded767 Merge: c6f8b693d ccd483e79 Author: Weiqun Zhang Date: Mon Mar 16 08:24:35 2020 -0700 Merge branch 'development' into dpcpp commit c63c131bf23705f34e42c136663b6d7972c4ba34 Merge: ccd483e79 c6f8b693d Author: Weiqun Zhang Date: Mon Mar 16 08:23:35 2020 -0700 Merge branch 'dpcpp' into weiqun/dev commit ccd483e791d456c9275c559742099fb919aee6f4 Merge: 3830a2435 69651f46d Author: Weiqun Zhang Date: Mon Mar 16 08:21:43 2020 -0700 Merge branch 'development' into basefab_runon commit 69651f46d9307acd5190583c44542838c91f0de7 Author: Weiqun Zhang Date: Sun Mar 15 17:03:15 2020 -0700 EB: optional to build coarse level from GeometryShop when coarsening fails. This could be used for hyperbolic system with EB resolved to the finest level Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IndexSpaceI.H commit 2b08d7a7901eb8ac927fc65b5a4a2e21971e8858 Author: Weiqun Zhang Date: Sun Mar 15 09:31:19 2020 -0700 fix warning when BL_NO_FORT is true Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 3d44d648c4c6e214b569a83e1ceee5a639e5c6a9 Author: atmyers Date: Fri Mar 13 15:21:14 2020 -0700 silence missing braces warning in clang, which is too aggressive Tools/GNUMake/comps/llvm.mak commit 3efe0e4887f0715fdcf07a0b8f1c948e11593037 Merge: 39e619cdd 755a332fd Author: atmyers Date: Fri Mar 13 15:13:29 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 39e619cdd5c26266ac6eb522e45fbc510e253f10 Author: atmyers Date: Fri Mar 13 15:12:25 2020 -0700 some casts to silence warnings when doing mixed precision Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particle_mod_K.H commit 755a332fde7f8b16358c33110ff89b83e5d33f18 Merge: df479eab6 0fdcc4969 Author: WeiqunZhang Date: Fri Mar 13 15:09:03 2020 -0700 Merge pull request #740 from AMReX-Codes/Emmanuel/velocity_gradients_for_LES Emmanuel/velocity gradients for les commit 1f8383f4f39891652ffb5c03e311746e6cb1c1ce Author: atmyers Date: Fri Mar 13 14:42:35 2020 -0700 fix 'default initialization of an object of const type without a user-provided default constructor' Src/Base/AMReX_GpuContainers.H commit c4152373c029739162040663d9547a55d47d82ec Author: atmyers Date: Fri Mar 13 14:38:31 2020 -0700 fix some narrowing conversion warnings in Particle_mod_K.H Src/Particle/AMReX_Particle_mod_K.H commit c6f8b693d1eb8077ad3e18749d764237074523c2 Author: Weiqun Zhang Date: Fri Mar 13 08:44:40 2020 -0700 update Advection_AmrCore tutorial for DPC++ Src/Base/AMReX_FBI.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H commit 5711bb6d122e3d0e66e38fd73eaa5d4d242053c2 Merge: f849352bb 3830a2435 Author: Weiqun Zhang Date: Thu Mar 12 20:17:03 2020 -0700 Merge branch 'basefab_runon' into dpcpp commit 3830a243592ddacb36108c19169c3eaa53e112be Merge: 25f87f90d df479eab6 Author: Weiqun Zhang Date: Thu Mar 12 20:14:10 2020 -0700 Merge branch 'development' into basefab_runon commit df479eab6f15e94b66e5f1da0155cd5456879929 Merge: ba8d2ec4f 4d8da23b0 Author: Weiqun Zhang Date: Thu Mar 12 20:12:24 2020 -0700 Merge branch 'weiqun/dev' into development commit f849352bb76d3c78f1d41de707cb5cd9eeb49af0 Author: Weiqun Zhang Date: Thu Mar 12 20:11:23 2020 -0700 implement DPC++ version of fab to fab op with mask in communcation Src/Base/AMReX_FBI.H commit 32758a85e7e66d159fcaec6fb5c955d0e9442978 Author: Weiqun Zhang Date: Thu Mar 12 20:08:17 2020 -0700 update GPU/Launch tutorial for basefab_runon Tutorials/GPU/Launch/CMakeLists.txt Tutorials/GPU/Launch/Make.package Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/Launch/main.cpp commit ba8d2ec4f070dbcb4564f89206eb87b7478c3b05 Author: Michele Rosso Date: Thu Mar 12 18:34:08 2020 -0700 CMake: add C++ 17 among valid options for AMREX_CXX_STANDARD Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_Options.cmake commit 76898f1ae14cfaa3219f5f03ce6ff5b0fcba9d59 Author: Michele Rosso Date: Thu Mar 12 17:36:00 2020 -0700 CMake: allow user to specify C++ standard .github/workflows/cmake.yml Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 6c96edb32bc6dd0087b420f2a97e09a95d7fca2b Author: Weiqun Zhang Date: Thu Mar 12 15:32:36 2020 -0700 cmake: change C++ standard target to 11 so that cuda build in github workflow works Tools/CMake/AMReX_Config.cmake commit fef0ebb0be99abc02a3e04ec76aa4b2fe1c4db9a Author: Weiqun Zhang Date: Thu Mar 12 13:15:11 2020 -0700 use gcc-4.8 for build build in github workflow .github/workflows/cmake.yml .github/workflows/cmake/dependencies.sh .github/workflows/cmake/dependencies_nvcc.sh commit 8eae0cd11bc65e5cb94d7fecdf30ff26da0d08c8 Merge: ab9704b1c 25f87f90d Author: Weiqun Zhang Date: Thu Mar 12 12:33:42 2020 -0700 Merge branch 'basefab_runon' into dpcpp commit 25f87f90dd0a253510f8b7499467dbdce38d1488 Merge: 5e26513bb 0153dc0af Author: Weiqun Zhang Date: Thu Mar 12 12:32:45 2020 -0700 Merge branch 'development' into basefab_runon commit 4d8da23b016eee8e27c1632fba20558f05154868 Author: Weiqun Zhang Date: Thu Mar 12 09:17:39 2020 -0700 template FillPatch* so that they can work on any FabArray Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_I.H Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package Src/Base/AMReX_MultiFab.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp commit 0fdcc4969dd7aabf5d515a7495a214ada636464f Merge: a5f80946d 0153dc0af Author: emotheau Date: Wed Mar 11 18:13:31 2020 -0700 Merge remote-tracking branch 'origin/development' into Emmanuel/velocity_gradients_for_LES commit 9a8c4c3a8736c14a07a4cd28eff2dadf81439957 Merge: 4c5a93a3c 0153dc0af Author: Weiqun Zhang Date: Wed Mar 11 17:02:43 2020 -0700 Merge branch 'development' into weiqun/dev commit a5f80946db73aa9bfa66fd80f61d291e7e9f6937 Author: Emmanuel Motheau Date: Wed Mar 11 16:02:15 2020 -0700 some cleaning Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 0153dc0afc19b48464321be1700e0d7939808044 Author: Weiqun Zhang Date: Wed Mar 11 15:25:48 2020 -0700 add option to set fixed number of iterations in the Fortran interface of linear solver Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 commit 2f52133decf2c0138fe26ae4997565275b20bbdd Author: Weiqun Zhang Date: Wed Mar 11 14:58:11 2020 -0700 Create alias Fab in FabArray using factory so that the EB information can be carried over Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_MultiCutFab.H commit 77f4264c2d72d56f8829de7122de94208773aa49 Author: Emmanuel Motheau Date: Wed Mar 11 14:41:11 2020 -0700 bug fix in 3D Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 2ae0257baebeb2d927ea6fbaac1062dc10f5f07f Author: Emmanuel Motheau Date: Wed Mar 11 14:23:29 2020 -0700 routines are now available in 3D Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 81ec27925d84a6f3393dcc6ce1ec9b84929d6ef8 Author: atmyers Date: Wed Mar 11 11:36:27 2020 -0700 add missing include guard Src/Particle/AMReX_ParIter.H commit 1b704499778d372b08687423f061d0acf2ed4be8 Author: atmyers Date: Wed Mar 11 11:34:41 2020 -0700 unused variable Src/Base/AMReX_Arena.cpp commit ab9704b1c3a6880a6e3fb6f4714972ad7d68d9d4 Author: Weiqun Zhang Date: Tue Mar 10 15:45:36 2020 -0700 add DPC++ flag to relax SYCL restriction Tools/GNUMake/comps/dpcpp.mak commit 3fdabfe9d432a6c3ece36b1505cc47bfddd3d82e Author: Weiqun Zhang Date: Tue Mar 10 11:07:39 2020 -0700 update GPU limitations Docs/sphinx_documentation/source/GPU.rst commit 3859780d834256225f5b489806830470dd47d3e9 Merge: 3075027b1 cd00f209b Author: Andrew Myers Date: Mon Mar 9 16:18:37 2020 -0700 Merge branch 'development' into atmyers/mpi_datatype commit 3075027b140364819f9676627d058dacf8a48ce6 Author: Andrew Myers Date: Mon Mar 9 15:52:23 2020 -0700 another fix for the corner case where we don't do any sends Src/Particle/AMReX_ParticleCommunication.H commit 9f108ab53882b49399769ffff07c430f55c617bf Author: Andrew Myers Date: Mon Mar 9 13:43:43 2020 -0700 add switch based on message size Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit cd00f209b4b482890561b985580bc91bb37d5fce Merge: d21cc21eb 1a01fda0a Author: WeiqunZhang Date: Mon Mar 9 12:40:35 2020 -0700 Merge pull request #736 from rporcu/development Implementation of operator *= (Real) was missing commit d21cc21ebf50c6048c70e60937a0c6c493cbe24d Author: Andrew Myers Date: Mon Mar 9 11:21:23 2020 -0700 fix index error in interpolate_cic Src/Particle/AMReX_Particle_mod_K.H commit 5e26513bb6783ab36c545ebe19cfd9b019317655 Author: Weiqun Zhang Date: Sat Mar 7 19:12:39 2020 -0800 fix FArrayBox and IArrayBox template function operator= Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Particle/AMReX_ParticleContainerI.H commit 0ec556a436236aedbb2e667c9ac1743c5997d5da Merge: 866654b34 bcd9ade9c Author: Weiqun Zhang Date: Sat Mar 7 18:20:41 2020 -0800 Merge branch 'development' into basefab_runon commit 1a01fda0ad182d984055bd3b6e5f6245c8f5330c Author: Roberto Porcu Date: Sat Mar 7 18:08:28 2020 -0800 Implementation of *=(Real) was missing Src/Base/AMReX_RealVect.H commit f4803821418b25f5a9962cbeb6f9dc25ea73c4b9 Merge: 0c7787b48 bcd9ade9c Author: emotheau Date: Sat Mar 7 16:00:16 2020 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/velocity_gradients_for_LES commit 0c7787b489741cef73b01d714f09a3f6bce3f3d5 Author: Emmanuel Motheau Date: Sat Mar 7 15:58:40 2020 -0800 new routine in TensorOP to compute gradients of velocity at each face. Only in 2d and no EB for now Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H commit bcd9ade9ca6e015ba7afa31e045c62e653b510de Author: Weiqun Zhang Date: Sat Mar 7 10:59:48 2020 -0800 fix some warnings Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp commit 4a11a0279fa7d744258c16673a175deae59f3187 Author: Weiqun Zhang Date: Fri Mar 6 23:02:27 2020 -0800 add AMREX_LOOP_3D and 4D Src/Base/AMReX_Loop.H commit 866654b3404eb4d3ebf89f4ca0e795aedcbcf955 Merge: 4e573e47d b93348cb3 Author: Weiqun Zhang Date: Fri Mar 6 22:26:06 2020 -0800 Merge branch 'basefab_runon_nodefault' into basefab_runon commit b93348cb31bd2a996abf6ad79e9a3d3051329e0a Author: Weiqun Zhang Date: Fri Mar 6 22:25:43 2020 -0800 fix makeFineMask_doit template Src/Base/AMReX_MultiFabUtil.cpp commit 4e573e47d3b6d539df7eef75d9d251fdafd44a9b Merge: b5db926d1 1e597b7fd Author: Weiqun Zhang Date: Fri Mar 6 21:37:32 2020 -0800 Merge branch 'basefab_runon_nodefault' into basefab_runon commit 1e597b7fde5eedb9b49a2155a57072d331ae99d2 Merge: ed99f7e7e d0b98e963 Author: Weiqun Zhang Date: Fri Mar 6 21:37:00 2020 -0800 Merge branch 'development' into basefab_runon_nodefault commit d0b98e9636337f67dd85e96d04288e6beb458420 Author: Weiqun Zhang Date: Fri Mar 6 21:34:20 2020 -0800 add a new makeFineMask function that returns MultiFab Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 92a025bd6bad1dfc3ebfba855360bee75545f3a6 Merge: 31f42022f 56b1ea5b7 Author: Andrew Myers Date: Fri Mar 6 16:47:50 2020 -0800 Merge pull request #734 from Alpine-DAV/task/2020_03_bp_particle_mesh_name_opt conduit blueprint: add topo name option to particle container wrapper commit 56b1ea5b76bdb8ed355eed18ecc307d640c9e09b Author: Cyrus Harrison Date: Fri Mar 6 15:55:02 2020 -0800 add comment about new topology_name arg Src/Extern/Conduit/AMReX_Conduit_Blueprint.H commit b5db926d1bf63dd9c4dc7380ab96092344d5bb2d Merge: bcd64e203 ed99f7e7e Author: Weiqun Zhang Date: Fri Mar 6 15:49:52 2020 -0800 Merge branch 'basefab_runon_nodefault' into basefab_runon commit ed99f7e7ea9fafd8092e269fc7d237a7763fc5cf Merge: 88a3a4000 31f42022f Author: Weiqun Zhang Date: Fri Mar 6 15:48:45 2020 -0800 Merge branch 'development' into basefab_runon_nodefault commit bcd64e203ba001a8034e3418ba5b2a225a8d88eb Merge: a8054fca4 88a3a4000 Author: Weiqun Zhang Date: Fri Mar 6 15:47:06 2020 -0800 Merge branch 'basefab_runon_nodefault' into basefab_runon commit 88a3a40002531442964e23e3481e3c3cd8d9e89f Author: Weiqun Zhang Date: Fri Mar 6 15:46:27 2020 -0800 fix the new DistributionMapping functions Src/Base/AMReX_DistributionMapping.cpp commit 0a2830d20868bb767b708fbeeead81eff417bfa0 Author: Andrew Myers Date: Fri Mar 6 15:44:09 2020 -0800 fix sign error in pad offset computation, add some useful assertions Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit a8054fca4ff924296005c528420f544d490534bf Merge: 51cd1dc3b 8dcbb083a Author: Weiqun Zhang Date: Fri Mar 6 15:29:05 2020 -0800 Merge branch 'basefab_runon_nodefault' into basefab_runon commit 8dcbb083a2553b29ac8a09e09a7c162e2d73dcb5 Author: Weiqun Zhang Date: Fri Mar 6 15:28:43 2020 -0800 remove device code from ~BaseFab Src/Base/AMReX_BaseFab.H commit 9254908d30993e0da79ca40fea0f818d6d16b32c Author: Andrew Myers Date: Fri Mar 6 13:53:17 2020 -0800 more debug code Src/Particle/AMReX_ParticleCommunication.H commit 99de5f9b8eb7ebfd032627729ce168adce96ae78 Author: Andrew Myers Date: Fri Mar 6 13:47:38 2020 -0800 remove debug prints Src/Particle/AMReX_ParticleCommunication.H commit 012e83223ab37abc2c02802e158388d871785a93 Author: Andrew Myers Date: Fri Mar 6 13:41:12 2020 -0800 add missing header Src/Base/AMReX_ParallelDescriptor.cpp commit 1ada983a94618490e08e9d8b182045417899cb52 Author: Andrew Myers Date: Fri Mar 6 13:39:06 2020 -0800 using unsigned long long as the datatype for particle mpi comms Src/Particle/AMReX_ParticleCommunication.H commit 76ecf6939ca20c1ecdbb74738e16ccc24cf8e210 Author: Andrew Myers Date: Fri Mar 6 13:29:40 2020 -0800 refactr the alignment / comm_type functions so they can be used outside of FabArra Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 083fbeb22006e0c611fe86fcb006b08d8455378b Author: Andrew Myers Date: Fri Mar 6 13:13:01 2020 -0800 remove some commented out code Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit f76e83861b380f3aa74e3f20221934a8e23a12be Author: Cyrus Harrison Date: Fri Mar 6 13:04:52 2020 -0800 allow explicit name for particle mesh topos Src/Extern/Conduit/AMReX_Conduit_Blueprint.H Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit 0532ce148829071dbf27081c9c20850c5c30258e Author: Andrew Myers Date: Fri Mar 6 12:46:18 2020 -0800 add ability to pad mpi messages by an alignment size Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 0d24b8aa157ed3d4e64041422c4b7bc640129361 Merge: 21ef1d8d6 31f42022f Author: Andrew Myers Date: Fri Mar 6 12:08:18 2020 -0800 Merge branch 'development' into atmyers/mpi_datatype commit 31f42022f8193aeb48fa9b415ad2c7341a9bbe0f Author: Andrew Myers Date: Fri Mar 6 12:07:43 2020 -0800 remove kdtree Src/Particle/AMReX_KDTree_1d.F90 Src/Particle/AMReX_KDTree_2d.F90 Src/Particle/AMReX_KDTree_3d.F90 Src/Particle/AMReX_KDTree_F.H Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/CMakeLists.txt Src/Particle/Make.package Tests/Particles/LoadBalance/GNUmakefile Tests/Particles/LoadBalance/Make.package Tests/Particles/LoadBalance/create_binary_particle_file.py Tests/Particles/LoadBalance/inputs Tests/Particles/LoadBalance/main.cpp Tests/Particles/LoadBalance/visualize_output.ipynb commit 51cd1dc3b8929ad35d4fb248b69089ddbada0e55 Merge: a87d84dfe f3e870010 Author: Weiqun Zhang Date: Fri Mar 6 11:34:09 2020 -0800 Merge branch 'basefab_runon_nodefault' into basefab_runon commit f3e870010bd1ab7430062e3d2d68091991902693 Merge: b63ba2ece ea755eb94 Author: Weiqun Zhang Date: Fri Mar 6 11:33:23 2020 -0800 Merge branch 'development' into basefab_runon_nodefault commit a87d84dfef1845d42f95cb868ef947961bfc8341 Author: Weiqun Zhang Date: Fri Mar 6 11:31:12 2020 -0800 add RunOn::Host as default when not using GPU Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Boundary/AMReX_Mask.H commit b63ba2eced14efa1c4bd95612ccfed439396118c Author: Weiqun Zhang Date: Fri Mar 6 11:04:46 2020 -0800 fix tutorial for RunOn Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H commit cc524566d15132b8ae3bbba937290330ed828c32 Author: Weiqun Zhang Date: Fri Mar 6 10:47:07 2020 -0800 rm old tests Tests/GPU/FusedLaunches/GNUmakefile Tests/GPU/FusedLaunches/Make.package Tests/GPU/FusedLaunches/inputs_3d Tests/GPU/FusedLaunches/main.cpp Tests/GPU/FusedLaunches/run.corigpu Tests/GPU/Particles/Redistribute/Constants.H Tests/GPU/Particles/Redistribute/GNUmakefile Tests/GPU/Particles/Redistribute/Make.package Tests/GPU/Particles/Redistribute/TestParticleContainer.H Tests/GPU/Particles/Redistribute/TestParticleContainer.cpp Tests/GPU/Particles/Redistribute/inputs Tests/GPU/Particles/Redistribute/main.cpp Tests/GPU/Particles/Redistribute/test_3d.F90 Tests/GPU/Particles/Redistribute/test_F.H Tests/GPU/Partition/GNUmakefile Tests/GPU/Partition/Make.package Tests/GPU/Partition/inputs Tests/GPU/Partition/main.cpp Tests/GPU/ScratchPad/GNUmakefile Tests/GPU/ScratchPad/Make.package Tests/GPU/ScratchPad/inputs_3d Tests/GPU/ScratchPad/main.cpp Tests/GPU/ScratchPad/run.script Tests/GPU/Test/GNUmakefile Tests/GPU/Test/Make.package Tests/GPU/Test/main.cpp Tests/GPU/Test/run.exitcode Tests/GPU/Test/run.script Tests/GPU/TestB/GNUmakefile Tests/GPU/TestB/Make.package Tests/GPU/TestB/main.cpp Tests/GPU/TestB/return_test.F90 Tests/GPU/TestC/GNUmakefile Tests/GPU/TestC/Make.package Tests/GPU/TestC/main.cpp Tests/GPU/TestC/run.summit Tests/GPU/TestC/run.summitdev Tests/GPU/buildHybrid/GNUmakefile Tests/GPU/buildHybrid/MyKernel.H Tests/GPU/buildHybrid/MyKernel.cpp Tests/GPU/buildHybrid/MyKernelB.H Tests/GPU/buildHybrid/MyKernelB.cpp Tests/GPU/buildHybrid/MyKernel_F.F90 Tests/GPU/buildHybrid/MyKernel_F.H Tests/GPU/buildHybrid/Readme Tests/GPU/buildHybrid/main.cpp Tests/GPU/buildHybrid/run.script Tests/GPU/buildNotused/Extern.H Tests/GPU/buildNotused/GNUmakefile Tests/GPU/buildNotused/MyKernel.H Tests/GPU/buildNotused/MyKernel.cpp Tests/GPU/buildNotused/MyKernelB.H Tests/GPU/buildNotused/MyKernelB.cpp Tests/GPU/buildNotused/Notused.H Tests/GPU/buildNotused/Notused.cpp Tests/GPU/buildNotused/Readme Tests/GPU/buildNotused/main.cpp Tests/GPU/buildTest/GNUmakefile Tests/GPU/buildTest/MyKernel.H Tests/GPU/buildTest/MyKernel.cpp Tests/GPU/buildTest/MyKernelB.H Tests/GPU/buildTest/MyKernelB.cpp Tests/GPU/buildTest/Readme Tests/GPU/buildTest/main.cpp Tests/GPU/buildTest/run.script commit 7165d47d896932ebbe3308f76849adb8332502cb Author: Weiqun Zhang Date: Fri Mar 6 09:42:18 2020 -0800 add more RunOns Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/PETSc/AMReX_PETSc.cpp Src/Particle/AMReX_ParticleContainerI.H Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp commit ea755eb94d4f6991995453faa59f7fd8a4614579 Merge: de3e8972b 7aeef1811 Author: Andrew Myers Date: Fri Mar 6 09:21:52 2020 -0800 Merge pull request #725 from mrowan137/mrowan/loadbalance Add efficiency argument to makeSFC, makeKnapSack commit 1eb7bbfdb946e763da1f4855bb39c8408392875e Merge: 32f74b8cb de3e8972b Author: Weiqun Zhang Date: Fri Mar 6 08:19:06 2020 -0800 Merge branch 'development' into basefab_runon commit 32f74b8cbb55017d61fb1584604b03c294853726 Author: Weiqun Zhang Date: Fri Mar 6 08:15:02 2020 -0800 add RunOn to a test Tutorials/Basic/PrefixSum_MultiFab/main.cpp commit cc0a00dfd8a735c65177865844cfd36666359307 Author: Weiqun Zhang Date: Thu Mar 5 21:06:42 2020 -0800 clean up Src/Base/AMReX_IArrayBox.cpp commit 21ef1d8d6ecc2f44a994a094e4d425a96d6e6edd Author: Andrew Myers Date: Thu Mar 5 16:44:16 2020 -0800 remove some variables I ended up not using Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 4f6a83f633478bb541c73d7b96005c51882fd55f Author: Andrew Myers Date: Thu Mar 5 16:36:22 2020 -0800 fix for one proc case Src/Particle/AMReX_ParticleCommunication.H commit c9e0e4778b70e558a0b0331f0ab37111b8fe47b8 Author: Andrew Myers Date: Thu Mar 5 16:22:33 2020 -0800 also adding the rcv padding Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 8bc6a7a05e7bfc0d7457973b12677b3c6da732d3 Author: Andrew Myers Date: Thu Mar 5 15:29:36 2020 -0800 also use the snd buffer functor in unpack Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleTile.H commit de3e8972b47e37b2b6c6cb9902ea5eea727c2c3f Author: Weiqun Zhang Date: Thu Mar 5 15:08:20 2020 -0800 allow nodal solver to coarsen more Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 188634614b2b3c2ac5cb6dc9f7da99e39bf043ef Author: Andrew Myers Date: Thu Mar 5 14:59:21 2020 -0800 forgot to copy to device Src/Particle/AMReX_ParticleCommunication.H commit 450637088236fa8f0a8a6f6d2e06093acd0f76d4 Author: Andrew Myers Date: Thu Mar 5 14:54:52 2020 -0800 also compute rcv pad Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit eae6110e4df027a3059f091c094fbc6143c6bca7 Author: Andrew Myers Date: Thu Mar 5 14:18:53 2020 -0800 combine send buffer offset calculation into single functor Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit e2e9c4741f8ad23953f8452e0bee8d740c10f06d Author: Andrew Myers Date: Thu Mar 5 13:37:57 2020 -0800 change pack to work in terms of address Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleTile.H commit ac984c0208a18566d634b3f0c25ce0e04978c949 Author: Andrew Myers Date: Thu Mar 5 13:33:19 2020 -0800 need to include self in neighbor procs for this to work Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleUtil.cpp commit a2b5b13e5fabd99962825a11d0524b74a614cc05 Author: Weiqun Zhang Date: Thu Mar 5 11:48:07 2020 -0800 remove old tutorials INSTALL OldTutorials/.gitignore OldTutorials/MeshRefinement/GNUmakefile OldTutorials/MeshRefinement/Make.package OldTutorials/MeshRefinement/MyAmr.H OldTutorials/MeshRefinement/MyAmr.cpp OldTutorials/MeshRefinement/main.cpp OldTutorials/MultiColor_C/GNUmakefile OldTutorials/MultiColor_C/Make.package OldTutorials/MultiColor_C/ff.f90 OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp OldTutorials/MultiFabTests_C/GNUmakefile OldTutorials/MultiFabTests_C/Make.package OldTutorials/MultiFabTests_C/MultiFabFillBoundary.cpp OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp OldTutorials/PIC_C/GNUmakefile OldTutorials/PIC_C/Make.package OldTutorials/PIC_C/README OldTutorials/PIC_C/inputs OldTutorials/PIC_C/main.cpp OldTutorials/PIC_C/single_level.cpp OldTutorials/PIC_C/solve_for_accel.cpp OldTutorials/PIC_C/solve_with_mlmg.cpp OldTutorials/PIC_C/two_level.cpp OldTutorials/README_C OldTutorials/Tiling_C/GNUmakefile OldTutorials/Tiling_C/Make.package OldTutorials/Tiling_C/main.cpp OldTutorials/Tiling_C/work.f90 OldTutorials/Tiling_Heat_C/GNUmakefile OldTutorials/Tiling_Heat_C/Make.package OldTutorials/Tiling_Heat_C/advance_3d.f90 OldTutorials/Tiling_Heat_C/init_phi_3d.f90 OldTutorials/Tiling_Heat_C/inputs_3d OldTutorials/Tiling_Heat_C/main.cpp OldTutorials/Tiling_Heat_C/results/results.org OldTutorials/Tiling_Heat_C/results/run-babbage.sh OldTutorials/Tiling_Heat_C/results/run-edison.sh OldTutorials/Tiling_Heat_C/writePlotFile.H OldTutorials/Tiling_Heat_C/writePlotFile.cpp OldTutorials/TwoGrid_PIC_C/GNUmakefile OldTutorials/TwoGrid_PIC_C/Make.package OldTutorials/TwoGrid_PIC_C/main.cpp OldTutorials/TwoGrid_PIC_C/solve_for_accel.cpp OldTutorials/TwoGrid_PIC_C/solve_with_mlmg.cpp OldTutorials/TwoGrid_PIC_C/split_boxes.cpp OldTutorials/WaveEquation_C/GNUmakefile OldTutorials/WaveEquation_C/Make.package OldTutorials/WaveEquation_C/advance_2d.f90 OldTutorials/WaveEquation_C/advance_3d.f90 OldTutorials/WaveEquation_C/init_data_2d.f90 OldTutorials/WaveEquation_C/init_data_3d.f90 OldTutorials/WaveEquation_C/inputs_2d OldTutorials/WaveEquation_C/inputs_3d OldTutorials/WaveEquation_C/main.cpp OldTutorials/WaveEquation_C/writePlotFile.H OldTutorials/WaveEquation_C/writePlotFile.cpp Tools/CompileTesting/compiletesting.py Tutorials/Basic/Build_with_libamrex/GNUmakefile commit 99cdacd7c6e4c0d6b878a059319497db3334b4e5 Author: Andrew Myers Date: Thu Mar 5 11:39:25 2020 -0800 refactor slightly to compute and reuse snd sizes and offsets Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit eef7ea4bfdf5a5de840c8a9e8e9b1743c73f89ed Author: Weiqun Zhang Date: Thu Mar 5 11:15:36 2020 -0800 update Mask for RunOn Src/Boundary/AMReX_Mask.H commit c54388b16811745feaf5a30eb5db6e395155124b Author: Michele Rosso Date: Thu Mar 5 10:24:48 2020 -0800 CMake: use CMAKE_CURRENT_LIST_DIR instead of CMAKE_SOURCE_DIR when retrieving version info. This fixes issue #731. CMakeLists.txt commit 2179dc8dfbc18d51eb148a227cfebc188585b0a0 Author: Weiqun Zhang Date: Thu Mar 5 10:20:29 2020 -0800 update IArrayBox for RunOn Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.cpp Src/EB/AMReX_EB_LSCoreBase.cpp commit 07f0c6151263efbfaeb1c5c9f2765791aaad339f Author: Weiqun Zhang Date: Thu Mar 5 10:10:32 2020 -0800 update FArrayBox for RunOn Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_GpuLaunch.H commit 6a69bf762b0def4905d394f927597f4055cd05ea Author: Weiqun Zhang Date: Wed Mar 4 20:02:07 2020 -0800 fix for gpu Src/Base/AMReX_BaseFab.H commit 7aeef181117102fa54bcc64e074e086f47e13011 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Wed Mar 4 20:48:56 2020 -0800 Remove tab Src/Base/AMReX_DistributionMapping.cpp commit 111ac9d60c2e7530347d5dba57471b03ea827d93 Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Wed Mar 4 20:45:29 2020 -0800 Remove print statement Src/Base/AMReX_DistributionMapping.cpp commit c1196da64a04fc36a5be3f87a6fbc49ac3b4e52b Author: Weiqun Zhang Date: Wed Mar 4 19:53:53 2020 -0800 prepare for default parameter Src/Base/AMReX_BaseFab.H commit 83edb3cf65eeed2abced0c7594ff7477122d511b Author: Weiqun Zhang Date: Wed Mar 4 19:25:56 2020 -0800 add a number of Src/Base/AMReX_FabArray.H Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleMesh.H Tests/C_BaseLib/tUMap.cpp Tests/IOBenchmark/IOTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 0ab577a9c29686916f0253eddc85f9fa9b83ec0f Merge: dd5f85f81 abbc81dee Author: Marc Day Date: Wed Mar 4 17:30:16 2020 -0800 Merge pull request #733 from AMReX-Codes/fix_EB_setCoveredFace Fix EB_set_covered_face: now use the input value. Also duplicate commit abbc81deecb505a32b5770a6294e5eaa690e2904 Author: Lucas Esclapez Date: Wed Mar 4 16:39:14 2020 -0800 Fix EB_set_covered_face: now use the input value. Also duplicate function to set a range of the MF component. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 7b602fe8b628a53ec0f7acb90f740e0441920e83 Author: Weiqun Zhang Date: Wed Mar 4 16:20:22 2020 -0800 template more BaseFab functions with RunOn Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_PCI.H Tutorials/EB/CNS/Source/CNS_advance.cpp commit dd5f85f81b580efe6efde233f16825ff10bb56cb Merge: ace0e084e f75989fdf Author: Andrew Myers Date: Wed Mar 4 15:57:33 2020 -0800 Merge pull request #732 from AMReX-Codes/jmsexton/particle_bounds Fix for single-precision RedistributeCPU PeriodicShift particle loss commit ace0e084e42b57963e2d46f5138f7919e4824232 Merge: 5907f0f85 522ae3d2b Author: Andrew Myers Date: Wed Mar 4 15:53:44 2020 -0800 Merge pull request #724 from Alpine-DAV/task/2020_03_bp_fix_particle_type Conduit Blueprint: fix case needed for single prec particles commit f75989fdf1e33924f6f259c108d6bf14e04afe6e Author: Jean M. Sexton Date: Wed Mar 4 15:06:16 2020 -0800 Update fix for case where ProbLo is not 0 Src/Particle/AMReX_ParticleContainerI.H commit 82c03f5e4cb6a90e6550f51a80aebc4433bf4015 Author: Jean M. Sexton Date: Wed Feb 12 15:03:39 2020 -0800 Fix for single precision mis-match by testing using particle typename Src/Particle/AMReX_ParticleContainerI.H commit 5907f0f85e9a6cfa31b76bfb6e377ecae467d02a Author: Weiqun Zhang Date: Wed Mar 4 12:56:41 2020 -0800 In computing RHS, we always double at Neumann boundary as before. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e7e2b05976528a9d18caeccbbf309d9ee1f14e3f Author: Michael Rowan Date: Tue Mar 3 18:01:31 2020 -0500 Add efficiency argument to makeSFC, makeKnapSack Additional variant of FlashFluxRegister load method (untested) 1. Add another variant of load method, amrex_flash_fluxregister_load_1_area, Since we will frequently use this for FLASH. This is for when we have area factors, but do not use an additional (cflux) input as in amrex_flash_fluxregister_load_2_area. It turns out we never need a separate scalar scaling factor in this case, so I also removed that. 2. Rename previous amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area and amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area 3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple amrex_fi_flash_fluxregister_load_foo calls, as apparently intended. fix for amrex_flash_fluxregister_load_FOO procedure names fix typo fixed comment now random() returns numbers in [0.0,1.0) for both CPU and GPU Fix minor typo Tools/libamrex/configure.py Add efficiency argument to makeSFC, makeKnapSack Cleanup Cleanup Minor Logic fix Add efficiency argument to makeSFC, makeKnapSack Additional variant of FlashFluxRegister load method (untested) 1. Add another variant of load method, amrex_flash_fluxregister_load_1_area, Since we will frequently use this for FLASH. This is for when we have area factors, but do not use an additional (cflux) input as in amrex_flash_fluxregister_load_2_area. It turns out we never need a separate scalar scaling factor in this case, so I also removed that. 2. Rename previous amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area and amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area 3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple amrex_fi_flash_fluxregister_load_foo calls, as apparently intended. fix for amrex_flash_fluxregister_load_FOO procedure names fix typo fixed comment now random() returns numbers in [0.0,1.0) for both CPU and GPU Fix minor typo Tools/libamrex/configure.py Add efficiency argument to makeSFC, makeKnapSack Cleanup Cleanup Minor Logic fix Add efficiency argument to makeSFC, makeKnapSack Additional variant of FlashFluxRegister load method (untested) 1. Add another variant of load method, amrex_flash_fluxregister_load_1_area, Since we will frequently use this for FLASH. This is for when we have area factors, but do not use an additional (cflux) input as in amrex_flash_fluxregister_load_2_area. It turns out we never need a separate scalar scaling factor in this case, so I also removed that. 2. Rename previous amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area and amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area 3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple amrex_fi_flash_fluxregister_load_foo calls, as apparently intended. fix for amrex_flash_fluxregister_load_FOO procedure names fix typo fixed comment now random() returns numbers in [0.0,1.0) for both CPU and GPU Fix minor typo Tools/libamrex/configure.py Add efficiency argument to makeSFC, makeKnapSack Cleanup Cleanup Minor Logic fix Add efficiency argument to makeSFC, makeKnapSack Additional variant of FlashFluxRegister load method (untested) 1. Add another variant of load method, amrex_flash_fluxregister_load_1_area, Since we will frequently use this for FLASH. This is for when we have area factors, but do not use an additional (cflux) input as in amrex_flash_fluxregister_load_2_area. It turns out we never need a separate scalar scaling factor in this case, so I also removed that. 2. Rename previous amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area and amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area 3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple amrex_fi_flash_fluxregister_load_foo calls, as apparently intended. fix for amrex_flash_fluxregister_load_FOO procedure names fix typo fixed comment now random() returns numbers in [0.0,1.0) for both CPU and GPU Fix minor typo Tools/libamrex/configure.py Add efficiency argument to makeSFC, makeKnapSack Cleanup Cleanup Minor Logic fix Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 542bde669824916da6d51c8ad4085d52bbdadedc Merge: f2cbed89f 284618dc1 Author: Michael Rowan Date: Wed Mar 4 13:36:41 2020 -0500 Merge branch 'development' of https://github.com/AMReX-Codes/amrex commit 284618dc1a33a00a38af11558b15fcec4de8e408 Merge: db1d028bd ff75afc26 Author: WeiqunZhang Date: Wed Mar 4 10:36:23 2020 -0800 Merge pull request #729 from cselab/fabian/pullreq Fix minor typo Tools/libamrex/configure.py commit db1d028bd03204120b3f624f49648d78e26e3112 Merge: ee6dde591 0c2574f50 Author: Weiqun Zhang Date: Wed Mar 4 10:34:49 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ee6dde591ab9a0a4c4ddd96168a5435ca78f2d81 Merge: 1604c0262 e137ef417 Author: Weiqun Zhang Date: Wed Mar 4 10:31:07 2020 -0800 Merge branch 'development' into FlashFluxRegister commit 0c2574f500a3e911a59ad9893e35c1e6b6b83c80 Merge: e137ef417 575af1b7c Author: Andrew Myers Date: Wed Mar 4 10:31:06 2020 -0800 Merge pull request #726 from lucafedeli88/fix_doc_random Make amrex::Random() return numbers in the same interval for both CPU and GPU: [0:1) commit e137ef41706e81143bb59aa24dfc6900124714dc Author: Weiqun Zhang Date: Wed Mar 4 10:30:28 2020 -0800 fix typo Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 1604c0262f87953d1c5f404d76d734fbb1c879b6 Merge: e97431df1 54be23e8e Author: WeiqunZhang Date: Wed Mar 4 10:29:50 2020 -0800 Merge pull request #728 from kweide/FlashFluxRegister Additional variant of FlashFluxRegister load method (untested) commit ff75afc2603aff502dce5e1b08bb81f380166605 Author: Fabian Wermelinger Date: Wed Mar 4 10:16:00 2020 -0800 Fix minor typo Tools/libamrex/configure.py Tools/libamrex/configure.py commit f2cbed89f6b15dc377fd701e3b22044539d685f7 Merge: 332ae3119 1bd08c21b Author: Michael Rowan Date: Wed Mar 4 13:16:13 2020 -0500 Merge branch 'master' of https://github.com/mrowan137/amrex commit 332ae3119f6ffd7db5d3c2e6bc9d37b7300aaf4f Author: Weiqun Zhang Date: Wed Mar 4 09:31:59 2020 -0800 fix Neumann for divu too Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 54be23e8e677ce6481f5282372a13c0169bb484f Author: Klaus Weide Date: Wed Mar 4 11:52:22 2020 -0600 fix for amrex_flash_fluxregister_load_FOO procedure names Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit e96e5da37fdbfe7684aa479fa8c07664572ffa16 Author: Klaus Weide Date: Wed Mar 4 09:36:55 2020 -0600 Additional variant of FlashFluxRegister load method (untested) 1. Add another variant of load method, amrex_flash_fluxregister_load_1_area, Since we will frequently use this for FLASH. This is for when we have area factors, but do not use an additional (cflux) input as in amrex_flash_fluxregister_load_2_area. It turns out we never need a separate scalar scaling factor in this case, so I also removed that. 2. Rename previous amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area and amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area 3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple amrex_fi_flash_fluxregister_load_foo calls, as apparently intended. Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit 575af1b7c68964afed9ea013a004b8e3c8fe9505 Author: Luca Fedeli Date: Wed Mar 4 16:06:02 2020 +0100 now random() returns numbers in [0.0,1.0) for both CPU and GPU Src/Base/AMReX_Random.cpp commit 6cbd0cb6e46081bacac754565c6f32617d5ad990 Author: Luca Fedeli Date: Wed Mar 4 16:05:20 2020 +0100 fixed comment Src/Base/AMReX_Random.H commit 1bd08c21b93438ba1473425e6e19325b9bea8061 Merge: dcea782fb 59ea39584 Author: Michael Rowan Date: Tue Mar 3 20:19:04 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex commit 59ea39584d84764da76ef49bd6583d6f7c08559e Merge: 8a2378ef8 6268db578 Author: Weiqun Zhang Date: Tue Mar 3 19:25:16 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8a2378ef8bc1039e78878e9c9efe0639f42561b6 Author: Weiqun Zhang Date: Tue Mar 3 19:25:09 2020 -0800 should not multiple by 2 at Neumann BC when using RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit dcea782fbb2307b585da9bc5e2bca7d11808e7a6 Merge: 6268db578 c275ccc2f Author: Michael Rowan Date: Tue Mar 3 16:25:01 2020 -0800 Merge branch 'mrowan/loadbalance' of https://github.com/mrowan137/amrex commit 6268db5787b3c631c796b5e5938b62dcae487204 Author: Andrew Myers Date: Tue Mar 3 15:43:15 2020 -0800 decrease max buffer size Src/Particle/AMReX_ParticleUtil.H commit 6659bcf4849f0283c4dfe5f77e9589840e708056 Author: Andrew Myers Date: Tue Mar 3 15:42:35 2020 -0800 can exit early from the no particle case Src/Particle/AMReX_ParticleUtil.H commit d33b926f241f0a25e89a662bf49815185cf43258 Author: Andrew Myers Date: Tue Mar 3 15:42:11 2020 -0800 make sure to handle the invalid particle case here Src/Particle/AMReX_ParticleContainerI.H commit c275ccc2ff6e7f3ee3496b0dbb417b5e5114a928 Author: Michael Rowan Date: Tue Mar 3 18:01:31 2020 -0500 Add efficiency argument to makeSFC, makeKnapSack Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 522ae3d2b5cf310a5fecd1dbb4736d44c65df394 Author: Cyrus Harrison Date: Tue Mar 3 12:44:43 2020 -0800 fix particle case where ParticleReal is needed Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit f7d989ca12c0a1dcfae0897c12d5e2e842d51b00 Author: Andrew Myers Date: Tue Mar 3 11:54:20 2020 -0800 prevent overflow error Src/Particle/AMReX_ParticleUtil.H commit dc915e981a702818a6439485b82df22a4ad02d54 Author: Weiqun Zhang Date: Mon Mar 2 16:22:36 2020 -0800 disable cl::intel_reqd_sub_group_size for now because it causes CL_INVALID_KERNEL_NAME failure Src/Base/AMReX_GpuQualifiers.H commit fd522194c913a043102d252c64e7883312aafce2 Merge: f521886e7 495c398dc Author: Andrew Myers Date: Mon Mar 2 15:52:08 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f521886e767e4ff831a7ab75a267001eff57127f Author: Andrew Myers Date: Mon Mar 2 15:51:57 2020 -0800 another tweak to particle_compare Tools/Postprocessing/C_Src/particle_compare.cpp commit 495c398dc816eb8e30cbba55ff0daeddde882b8f Merge: a2b6859ba 35e0b44bc Author: Weiqun Zhang Date: Mon Mar 2 14:25:12 2020 -0800 Merge branch 'development' into dpcpp commit a2b6859baabb2452f741db440ddbbf4429bdb5b9 Author: Weiqun Zhang Date: Mon Mar 2 14:22:18 2020 -0800 add cl::intel_reqd_sub_group_size and get rid of compiler warnings Src/Base/AMReX_FBI.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuQualifiers.H Src/Base/AMReX_Machine.cpp Src/Base/AMReX_Reduce.H commit 35e0b44bc929fc7dbbf15952be9fdedec0578797 Author: Weiqun Zhang Date: Mon Mar 2 14:11:53 2020 -0800 update DPC++ notes Docs/Notes/Readme.dpcpp commit 6c6c9df46ad02737539c2cb7e7a75dacefbcb0d9 Merge: ccc4b5c66 50595a480 Author: Weiqun Zhang Date: Mon Mar 2 14:05:41 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 50595a480ef53880aa83d7376ec36c4578fa01ea Author: Andrew Myers Date: Mon Mar 2 13:38:36 2020 -0800 need to do this at run time instead of compile time Tools/Postprocessing/C_Src/particle_compare.cpp commit a9b771f3ecbf48909ec9ba5a81ef1993b0381a24 Author: Andrew Myers Date: Mon Mar 2 13:16:43 2020 -0800 make particle_compare respect single precision Tools/Postprocessing/C_Src/particle_compare.cpp commit ccc4b5c66e7021d943c3142b5407b6f5fedf9183 Merge: e348a5f7b 6a4f8d868 Author: Weiqun Zhang Date: Mon Mar 2 10:23:32 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6a4f8d868d51e3fd5ffeb7c5e3c2af5a63c5645e Merge: 645e5cc9e f5fc91130 Author: Andrew Myers Date: Mon Mar 2 10:19:49 2020 -0800 Merge branch 'atmyers/memopt' into development commit e348a5f7b6f036b3ed9f7bcc55ebbc64d4cc1fb4 Author: Weiqun Zhang Date: Mon Mar 2 09:12:22 2020 -0800 update CHANGES CHANGES commit 2a31c2a6a5d7fde098790bb25e6cd2025b33517b Author: Weiqun Zhang Date: Sun Mar 1 18:30:45 2020 -0800 fix typo Src/Base/AMReX_BaseFab.H commit 29ae52325be9f8ee5b83f9dfe7a26984d89abbaa Author: Weiqun Zhang Date: Sun Mar 1 14:31:38 2020 -0800 template BaseFab::sum with RunOn Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_DistributionMapping.cpp commit b8cd05f729a5e5f7a4c6292c998417b224995e75 Author: Weiqun Zhang Date: Sun Mar 1 13:50:50 2020 -0800 remove device code from BaseFab::minIndex and maxIndex Src/Base/AMReX_BaseFab.H commit 756ea9312cfbb5043620cc858648a27583b4d9cb Author: Weiqun Zhang Date: Sun Mar 1 13:40:24 2020 -0800 rm BaseFab::indexFromValue Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit 2ad2f906f0b6ee8b5104c5ff4ce371ae58fbccdd Author: Weiqun Zhang Date: Sun Mar 1 13:09:34 2020 -0800 template BaseFab::min, max and norm with RunOn Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Src/EB/AMReX_EB_LSCoreBase.cpp commit 96dd9739562626361ee49d556be34da96397b7be Author: Weiqun Zhang Date: Sat Feb 29 20:18:13 2020 -0800 template BaseFab::copyToMem, copyFromMem and addFromMem with RunOn Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FBI.H Src/EB/AMReX_MultiCutFab.H commit 8380ebf4b815887c15a0a83d20b92b1c2871cbcc Author: Weiqun Zhang Date: Sat Feb 29 20:06:42 2020 -0800 template BaseFab::copy with RunOn Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FBI.H Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PCI.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_MultiCutFab.H commit 25a293d08b91ba4220cf1b03cdcfa613953501dd Author: Weiqun Zhang Date: Sat Feb 29 19:14:19 2020 -0800 setVal: pass by const& Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H commit a26cca5b5c7c136dcc725217d9fe70f384e5ce46 Author: Weiqun Zhang Date: Sat Feb 29 19:08:26 2020 -0800 template setVal with RunOn Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_Loop.H Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_VisMF.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EB_levelset.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit f5fc911308d2dc386a5001475aac3888cc8377e9 Author: Andrew Myers Date: Sat Feb 29 16:22:43 2020 -0800 ability to do a 'chunked' partition Src/Particle/AMReX_ParticleUtil.H commit 0a5da0d2e9197651e9baf3ce3c40720a0ca76596 Author: Andrew Myers Date: Sat Feb 29 16:22:28 2020 -0800 swap particle routine Src/Particle/AMReX_ParticleTransformation.H commit 34c5d391e85ec79bf64b472416353e2412eaa444 Author: Michael Rowan Date: Sat Feb 29 14:22:21 2020 -0500 CUDAPATH --> SYSTEM_CUDA_PATH Tools/GNUMake/comps/nvcc.mak commit 8f2fba619699c842a0b55d15bc29dbf360e4fb17 Author: Weiqun Zhang Date: Sat Feb 29 10:51:42 2020 -0800 move ~T() calls to a function Src/Base/AMReX_BaseFab.H commit 98d1d279450e5e93651a3c911cdc927409f4ed80 Author: Weiqun Zhang Date: Sat Feb 29 10:39:57 2020 -0800 add RunOn to operator= and change the parameter to const& Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.cpp commit 8d8f8b1b8f20ac0b533c8130a229cd2cebd61a05 Author: Weiqun Zhang Date: Sat Feb 29 08:47:27 2020 -0800 remove AMREX_GPU_HOST_DEVICE qualifier from BaseFab functions Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H Src/Boundary/AMReX_Mask.H commit 8b612f61d27d2e1cd05ba2a32f9f6b8370cc57e7 Merge: 4c5a93a3c 645e5cc9e Author: Weiqun Zhang Date: Fri Feb 28 21:34:34 2020 -0800 Merge branch 'development' into weiqun/dev commit 645e5cc9e2e60e29b9acb9729caa983bebc6a29f Author: Michele Rosso Date: Fri Feb 28 17:38:55 2020 -0800 CMake: set versioning variables before project() CMakeLists.txt Tools/CMake/AMReXInstallHelpers.cmake commit f0467fdcc44775b47ce7ef68059d6fdc30f11417 Merge: 44ceea24c 26fbe3874 Author: mic84 Date: Fri Feb 28 14:44:40 2020 -0800 Merge pull request #721 from ax3l/topic-ciTutorials CI: Make Tutorials commit 26fbe387440ca1fc0b1be408b34d73f61ae11130 Author: Axel Huebl Date: Fri Feb 28 14:33:07 2020 -0800 CI: Make Tutorials Remove demonstrator `CMakeLists.txt` files from tutorials as they confuse the tutorial superbuild. Build tutorials with and without CUDA. .github/workflows/cmake.yml .github/workflows/cmake/dependencies_nvcc.sh Tutorials/Basic/HelloWorld_C/CMakeLists.txt Tutorials/Particles/CellSortedParticles/CMakeLists.txt commit 44ceea24cb6dd6ea90940e0944c78bd4b7a9e5bf Author: Michele Rosso Date: Fri Feb 28 12:49:13 2020 -0800 CMake: add defines for Clang version Tools/CMake/AMReX_Config.cmake commit 64cb1fc7e9435daff9a19a34c88afb2683e14056 Author: Michele Rosso Date: Fri Feb 28 12:47:15 2020 -0800 CMake: allow building with Cray compiler Partially fixes issue #719 Tools/CMake/AMReX_Config.cmake commit 5d5b8d33b4f7cf4fdcc7663939638d8d8b31d486 Author: Michele Rosso Date: Fri Feb 28 12:45:49 2020 -0800 CMake: update flags target + add Clang flags Tools/CMake/AMReXFlagsTargets.cmake commit 092d417cf35a96790d64ce7e0faa3358443b01c1 Author: Andrew Myers Date: Fri Feb 28 12:31:53 2020 -0800 ifdef out function if no GPU Src/Particle/AMReX_ParticleUtil.H commit de5a297a66a4eb8797b72879b3726ab849c499b2 Author: Andrew Myers Date: Fri Feb 28 15:20:08 2020 -0500 add missing header Src/Particle/AMReX_ParticleUtil.H commit 8031fbd79466ebdffd247f5c8fde487a0a08c1ce Author: Andrew Myers Date: Fri Feb 28 15:13:17 2020 -0500 move partition step into its own function Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_ParticleUtil.H commit 59b27bae370c573b8a34ed9273874bbde1cea041 Author: Andrew Myers Date: Fri Feb 28 14:10:59 2020 -0500 move lev, grid calculations to be on-the-fly Src/Particle/AMReX_ParticleContainerI.H commit 4c5a93a3c151466630452e2de0234c2cea4ac349 Author: Weiqun Zhang Date: Fri Feb 28 10:47:37 2020 -0800 set ghost cells to zero to avoid fpe Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e4091e882d79dc339d77520258c4bb01fc13153f Author: Michael E Rowan <38045958+mrowan137@users.noreply.github.com> Date: Fri Feb 28 10:42:22 2020 -0800 Formatting Src/Base/AMReX_TinyProfiler.cpp commit 88ee09c2e4ad55294fb53a02202f8306327b402f Author: Michael Rowan Date: Fri Nov 8 12:30:38 2019 -0800 Add CUPTI trace feature for GPU kernel timing Cleanup CUPTI GPU timer Save more kernel stats to activity record Cleanup; eliminate unneeded functions Cleanup Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_CuptiTrace.H Src/Base/AMReX_CuptiTrace.cpp Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/Make.package Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile Tests/GPU/CuptiTest/Exec/CUDA/Make.package Tests/GPU/CuptiTest/Exec/CUDA/myfunc.H Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H Tests/GPU/CuptiTest/Make.CUPTI Tests/GPU/CuptiTest/Source/Make.package Tests/GPU/CuptiTest/Source/main.cpp Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 7943502fe23ed86b0e986f51a5d4f37ae1d7f820 Merge: 787f0de5e a2ce2acee Author: Weiqun Zhang Date: Fri Feb 28 09:48:20 2020 -0800 Merge branch 'dpcpp' into weiqun/dev commit a2ce2aceef149ced0aac7cc7114a0d05f056335d Author: Weiqun Zhang Date: Fri Feb 28 09:40:23 2020 -0800 fix gpu race conditions in YAFluxRegister::FineAdd Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H commit 787f0de5edcf0b4ea6a67f1671b70f38fc49668f Author: Weiqun Zhang Date: Thu Feb 27 22:00:45 2020 -0800 IntVect::coarsen optimization Src/Base/AMReX_IntVect.H commit 737b607a0462d6157b0e87603d18b95bd4e96861 Merge: f42684ca7 4e3aa38c0 Author: Andrew Myers Date: Thu Feb 27 21:41:41 2020 -0800 Merge pull request #718 from AMReX-Codes/empic-offset Initialize the particles in the first cell of each tile for EM PIC tutorial commit f42684ca71b8a0dcfd0186b71ad4b4b1c52ec08b Merge: 8c5dbb6a4 599ccf16a Author: Michele Rosso Date: Thu Feb 27 21:29:36 2020 -0500 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8c5dbb6a4ac930390cd66738c400a1592bc3c0fa Author: Michele Rosso Date: Thu Feb 27 21:26:12 2020 -0500 CMake: do not enable CUDA via AMReX_SetupCUDA. From now on, application codes will need to enable CUDA directly instead of relying on AMReX_SetupCUDA. However, AMReX_SetupCUDA must still be included by application codes to setup the CUDA build environment for linking to AMReX. CMakeLists.txt Tools/CMake/AMReX_SetupCUDA.cmake commit 4e3aa38c00542e3f5d96e7abdb93079234c0b247 Author: Donald E. Willcox Date: Thu Feb 27 17:41:50 2020 -0800 Subtract the number of particles in the first cell of each tile to get the offset index for the first particle in each cell. Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 599ccf16a721a09091a02d43154844cbb41348fd Merge: d9b1fffa8 7627071b9 Author: Axel Huebl Date: Thu Feb 27 13:42:29 2020 -0800 Merge pull request #705 from ax3l/fix-warnExpansionToDefined Fix Warning in AMREX_DEVICE_COMPILE commit 7627071b99be332c27c6d8ad36e4d8e714420229 Author: Axel Huebl Date: Wed Feb 26 14:12:31 2020 -0800 Remove defines in AMREX_DEVICE_COMPILE Adding `defined()` in a macro is raising warnings of undefined behavior (clang) or non-portable behavior (gcc). This patch seems to work on for CUDA, DPC++ and non-gpu. (HIP untested.) Co-authored-by: Weiqun Zhang Src/Base/AMReX_GpuQualifiers.H commit 49666bba776bb1cf242756353c0385cc067bbd55 Author: Axel Huebl Date: Tue Feb 25 23:36:36 2020 -0800 Fix Warning in AMREX_DEVICE_COMPILE Calling the macro `AMREX_DEVICE_COMPILE` with `()` in pre-processor calls seams to be an alternative, non-portable way of checking `defined()`. Modern versions of GCC issue a `-Wexpansion-to-defined` warning on this. Remove the `()` from `AMREX_DEVICE_COMPILE()` calls since they should not be needed. Src/Base/AMReX.H Src/Base/AMReX_Array4.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuAtomic.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuRange.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Polynomial.H commit d9b1fffa8b78b23ca800e65da60181593605ad1d Merge: 529a74151 fd4a5b6af Author: mic84 Date: Thu Feb 27 12:38:21 2020 -0800 Merge pull request #716 from ax3l/fix-enableFortranCmake CMake: CXX Downstream Transitive Fortran commit fd4a5b6af482ce9b02f18023207f265c902aa62d Author: Axel Huebl Date: Thu Feb 27 10:45:11 2020 -0800 CMake: Fix Transtive Fortran Libs CMake currently has the bug that some transitive, implicit language dependencies as not commuted downstream if the downstream project does not `enable_language` the same lang. as upstream. This is mostly visible in missing `-lgfortran` links. This adds a useful work-around by just exposing these implicit Fortran "standard" libraries as explicit link dependencies. Src/CMakeLists.txt commit 529a74151350da4f7fa6d5ae48917a761ada97e2 Merge: 288c14646 989ee2242 Author: Andrew Myers Date: Thu Feb 27 10:39:04 2020 -0800 Merge pull request #713 from ax3l/topic-ciBadges Readme: Add CI Badges commit 1249afd1e9a499192dce96302da0b2a17380796d Author: Axel Huebl Date: Thu Feb 27 10:37:39 2020 -0800 CMake: CXX Downstream Transtive Fortran CMake currently has the bug that some transitive, implicit language dependencies as not commuted downstream if the downstream project does not `enable_language` the same lang. as upstream. This is mostly visible in missing `-lgfortran` links. This triggers this bug. Tutorials/Basic/HelloWorld_C/CMakeLists.txt commit 288c14646bced8e90247f02645030f51833104ca Merge: e6aa32068 742ecd37c Author: mic84 Date: Thu Feb 27 10:29:14 2020 -0800 Merge pull request #714 from ax3l/fix-offWarningClangGfortran CMake Tools: Fix CXX Host Compiler Check commit 742ecd37cb020e17a2ebeb85ac7f2eb40513b9a4 Author: Axel Huebl Date: Wed Feb 26 23:38:10 2020 -0800 CMake Tools: Fix CXX Host Compiler Check False Warning with Clang+Gfortran builds. Tools/CMake/AMReX_Config.cmake commit 989ee2242c351d770c18ee978d23d8cc704396e9 Author: Axel Huebl Date: Wed Feb 26 22:28:58 2020 -0800 Readme: Add CI Badges Add Travis-CI and GitHub Action status badges for the `development` branch. README.md commit e6aa32068caa8cb45c714b446ab8b7f3c00d5665 Merge: 1425839ff 563b7242a Author: Andrew Myers Date: Wed Feb 26 19:33:33 2020 -0800 Merge pull request #712 from ax3l/topic-ghActionCMake CI: Add GitHub Workflow for CMake commit 563b7242af14ddfc6c0ec3d63652ad15383f7e15 Author: Axel Huebl Date: Wed Feb 26 16:12:40 2020 -0800 CI: Add GitHub Workflow for CMake Add a CI job via GitHub actions to ensure CMake builds are not breaking. .github/workflows/cmake.yml .github/workflows/cmake/dependencies.sh Tutorials/Basic/HelloWorld_C/CMakeLists.txt Tutorials/Particles/CellSortedParticles/CMakeLists.txt commit 1425839ffb5d7c2f215571445f45b41d5b87c923 Merge: d57f56875 f9e9fc33b Author: mic84 Date: Wed Feb 26 17:27:48 2020 -0800 Merge pull request #711 from ax3l/fix-newFortranInterfaceFile CMake: New Fortran Interface File commit d57f568754fe5f32c903058e68c6d0478d395ccc Merge: 415a09e22 cc4330cd7 Author: mic84 Date: Wed Feb 26 17:24:29 2020 -0800 Merge pull request #710 from ax3l/topic-cmakeAlias CMake: AMReX::amrex Alias commit f9e9fc33bdfc0a0efa1d73d79d0b9033ffd888d4 Author: Axel Huebl Date: Wed Feb 26 16:06:02 2020 -0800 CMake: New Fortran Interface File Add a new Fortran file to the F_Interface sources. Fixes a compile issue. Src/F_Interfaces/CMakeLists.txt commit cc4330cd771fe848cfcfc064a2199a1efbf47939 Author: Axel Huebl Date: Wed Feb 26 14:44:47 2020 -0800 CMake Targets: More Namespace Aliases Add installed namespace alias to all public AMReX targets. Tools/CMake/AMReXFlagsTargets.cmake commit 1f05c40dfe5897afd5cf4938ee9862666e233464 Author: Axel Huebl Date: Wed Feb 26 14:41:10 2020 -0800 CMake: AMReX::amrex Alias Adding a project alias on `CMakeLists.txt` level that is identical to the installed CMake namespace. This is a community-convention in CMake and makes sure that both `add_subdirectory(AMReX_DIR)` as well as `find_package(AMReX)` targets can just be accessed as `AMReX::amrex` in all cases in user code. Src/CMakeLists.txt commit 415a09e22df63723587aa5a3ed290f64736d622c Merge: f3958d151 f68c92290 Author: WeiqunZhang Date: Wed Feb 26 12:14:13 2020 -0800 Merge pull request #709 from AMReX-Codes/load_balance_api Load balance api commit f3958d151830a1a6a01a3a33fa3aad253b696c12 Author: Weiqun Zhang Date: Wed Feb 26 12:04:39 2020 -0800 make Tools/GNUMake/comps/gnu.mak commit f68c92290f7d90f09795cd5e0f66f697e5efd688 Author: Andrew Myers Date: Wed Feb 26 12:01:23 2020 -0800 Add rcost version of makeSFC Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 5373dabb441de43f253ab6f803f96bfd847fe37c Author: Andrew Myers Date: Wed Feb 26 11:46:55 2020 -0800 add nmax argument to rcost version of makeKnapSack Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit dcb3da2a63f77360428d1986e04ff3453f2e41f8 Author: Weiqun Zhang Date: Wed Feb 26 09:12:14 2020 -0800 fix USE_CUDA=TRUE BL_NO_FORT=TRUE Tools/GNUMake/sites/Make.unknown commit 9e5adaac2b8f67330a339f2354f672c28e07c794 Merge: e883ebf89 334d2b7ba Author: Michael Zingale Date: Tue Feb 25 21:13:40 2020 -0500 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit e883ebf8916016c628255f6a026fdf16e19bad24 Author: Michael Zingale Date: Tue Feb 25 21:13:27 2020 -0500 strings should not be gpu managed Tools/F_scripts/write_probin.py commit 334d2b7ba63c954414a7da04435f7b88ecb207b5 Author: Weiqun Zhang Date: Tue Feb 25 11:39:03 2020 -0800 make some Macs even more happier with make Tools/GNUMake/sites/Make.unknown commit f125809d61f36d1da2336648cfc55d1258bf6ca5 Author: Weiqun Zhang Date: Tue Feb 25 11:13:14 2020 -0800 make some Macs happy with make Tools/GNUMake/sites/Make.unknown commit 63f4e2248ed3181319a757c200924fc20759dd64 Author: Weiqun Zhang Date: Tue Feb 25 08:53:19 2020 -0800 fix for hip Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak commit 1ba6c22f27058b02ac056b19b3a293480cb49e34 Merge: f45019991 be5232a9c Author: Andrew Myers Date: Tue Feb 25 01:47:08 2020 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f45019991709df63f9bba670c184d26464e8e40a Author: Andrew Myers Date: Tue Feb 25 01:46:49 2020 -0500 use Send instead of Asend in particle communication Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit be5232a9c51ab4641c75e2373aeb767aa28eb029 Author: Weiqun Zhang Date: Mon Feb 24 16:08:06 2020 -0800 If one compiles with NVCC_CCBIN=gcc-x, it will be used as the nvcc host compiler Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/nvcc.mak commit a8b60a3b0a6a12059cc89753a53bb013778949d2 Merge: 7d1eb6004 f9c81ed9b Author: Andrew Myers Date: Mon Feb 24 16:37:22 2020 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7d1eb600495e816a8ab00701c4dde73cd13ac1f0 Author: Andrew Myers Date: Mon Feb 24 16:23:39 2020 -0500 make these temporary instead of member data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 15ccf23ea44027e9c10b73a7658cb63d78d1a822 Author: Andrew Myers Date: Mon Feb 24 16:23:04 2020 -0500 shrink to fit and capacity methods for ParticleTile Src/Particle/AMReX_ParticleTile.H commit f9c81ed9b1b08b5e76f617b7b2c817cbef1519b2 Merge: 487366bed b1c8ce10b Author: Weiqun Zhang Date: Mon Feb 24 12:36:45 2020 -0800 Merge branch 'dpcpp' into development commit 487366bed987a7c2478562e33bc2a3bda0ca09d7 Author: Weiqun Zhang Date: Mon Feb 24 11:26:16 2020 -0800 add CArena::heap_space_actually_used Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit 7f1bf0a7a1afec98ed1959169d53d5e2ee0ca7c2 Merge: f5d8735ad 771e143d3 Author: WeiqunZhang Date: Mon Feb 24 10:24:51 2020 -0800 Merge pull request #701 from AMReX-Codes/cgilet_dev Cgilet dev commit f5d8735ad032b8a772270c7e76845da66c8dfda1 Author: Weiqun Zhang Date: Mon Feb 24 10:17:25 2020 -0800 add CArena::sizeOf to return the size of momory held by a pointer Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit b1c8ce10b852b646040397321b179dd2ba462860 Author: Weiqun Zhang Date: Mon Feb 24 09:45:37 2020 -0800 cannot use sycl::abs directly because it returns unsigned int given int. Src/Base/AMReX_Math.H commit 55a396c4d72217599b28d19b49426c8fdf64703f Author: Weiqun Zhang Date: Mon Feb 24 09:37:14 2020 -0800 FBI: we can assume thread safety if not using OpenMP. Src/Base/AMReX_FabArrayBase.cpp commit 771e143d3b48abd77d0520dd85b52cb37ab332ba Author: cgilet Date: Mon Feb 24 08:16:57 2020 -0500 Allow EBFabFactories with Basic EB support to use boxArray() and DistributionMap() Src/EB/AMReX_EBFabFactory.cpp commit f1d2244bcea147128790efbc7e20d101e5f8445b Merge: b11160ac8 185b2d4cd Author: cgilet Date: Mon Feb 24 08:13:25 2020 -0500 Merge remote-tracking branch 'origin/development' into cgilet_dev commit 135c9ea682a2b101579c25d4d2cf3706185e55c5 Author: Weiqun Zhang Date: Sun Feb 23 13:29:49 2020 -0800 make the heat equation problem bigger and there is no need to create plotmf Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 185b2d4cd61969379a629092e7ef7cf1da07a816 Merge: db72de3d0 0b512f363 Author: Michael Zingale Date: Sun Feb 23 16:06:59 2020 -0500 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit db72de3d04afa17bb027ba6412e520ab6932e4a8 Author: Michael Zingale Date: Sun Feb 23 16:04:19 2020 -0500 add character support Tools/F_scripts/write_probin.py commit d28a52e37fead82a1974cc3c8cf2f54853d1383e Author: Weiqun Zhang Date: Sun Feb 23 09:35:57 2020 -0800 set USE_CUDA=FALSE when USE_HIP=TRUE Tools/GNUMake/Make.defs commit 7f002a20184705ad23496f4d2e6571968b751a58 Author: Weiqun Zhang Date: Sun Feb 23 09:33:43 2020 -0800 Heat equation tutorial: merge CUDA and HIP Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/mykernel.H Tutorials/GPU/HeatEquation_EX1_C/Exec/default/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/default/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d_hip Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.ascent Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.nocuda.script Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summit Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summitdev commit 8c929d513c9ad75464ca03b724ded617e1b1ca00 Author: Weiqun Zhang Date: Sun Feb 23 09:12:30 2020 -0800 remove enable_if for non-DPC++ Src/Base/AMReX_Reduce.H commit 2d70f51fc09bac602efc8c89e1ac572646f40621 Merge: 75cc8040e 0b512f363 Author: Weiqun Zhang Date: Sun Feb 23 09:08:02 2020 -0800 Merge branch 'development' into dpcpp commit 0b512f3630779f632f18d001d9a47f904064fc86 Author: Weiqun Zhang Date: Sat Feb 22 22:38:38 2020 -0800 one more int -> long Src/Base/AMReX_FabArrayBase.H commit 75cc8040ea9b158aea089dcec098ace139dce4a5 Author: Weiqun Zhang Date: Sat Feb 22 21:28:20 2020 -0800 update DPC++ notes Docs/Notes/Readme.dpcpp commit 872a3a677cb52b70410948dc52bc4414a49c2773 Author: Weiqun Zhang Date: Sat Feb 22 20:59:11 2020 -0800 get around DPC++ bug? Src/Base/AMReX_Reduce.H commit 738ca166f23f93ecae5dafbacd44d4b697dfd202 Author: Weiqun Zhang Date: Sat Feb 22 19:52:53 2020 -0800 make GpuTuple's default ctor host device function Src/Base/AMReX_Tuple.H commit a5d3676c74e3e8ad7ffddcdb1eae53afe34c9255 Author: Weiqun Zhang Date: Sat Feb 22 18:13:39 2020 -0800 update ParallelReduce tutorial Tutorials/GPU/ParallelReduce/main.cpp commit 98524153e355c97cdc59ffbf903ff4ff37de008a Author: Weiqun Zhang Date: Sat Feb 22 18:13:12 2020 -0800 fix a typo Src/Base/AMReX_GpuLaunchFunctsG.H commit b736f2ea84215a9494f1613c4b4fe673f03916e5 Author: Weiqun Zhang Date: Sat Feb 22 18:12:12 2020 -0800 avoid capture GpuTuple by value in reduction because dpc++ does like it's not standard layout Src/Base/AMReX_Reduce.H commit 312bd157995f4ada0fb00a264aa1b7772996e129 Merge: 784a199aa 560e11ff2 Author: Weiqun Zhang Date: Sat Feb 22 17:30:23 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 784a199aa0560ebaddf8e73cb1dccf46644bf4e7 Author: Weiqun Zhang Date: Sat Feb 22 17:30:03 2020 -0800 int -> long to avoid overflow Src/Base/AMReX_FabArrayBase.H commit 560e11ff292f5b7c303dbe76adb0c40a8d1fa878 Author: Andrew Myers Date: Sat Feb 22 19:17:02 2020 -0500 ManagedVector -> DeviceVector throughout ParticleContainer Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H commit 715face89aaaa6b89dc5a5b8a291a6ffa480abdb Merge: f63d9af67 04ac0df52 Author: Weiqun Zhang Date: Fri Feb 21 21:32:35 2020 -0800 Merge branch 'dpcpp' into development commit 04ac0df524c922fda5d057bc96c6524901e3d8fe Author: Weiqun Zhang Date: Fri Feb 21 21:32:11 2020 -0800 note to GpuTuple and DPC++ Docs/Notes/Readme.dpcpp commit f63d9af676b6c261ba6b75cef3fdb7ff3266cd17 Author: Max Katz Date: Fri Feb 21 20:40:33 2020 -0800 Deal with the case where extern is in a subdirectory Tools/F_scripts/write_probin.py commit 87686a7ee1bd07087172d8b1d9ab4f7394d98b19 Author: Weiqun Zhang Date: Fri Feb 21 16:04:51 2020 -0800 fix DPCPP launch macros Src/Base/AMReX_GpuLaunchMacrosG.H Tutorials/GPU/Launch/Make.package commit 319385afff27bceea60e48d6cf6b9df84a127cf3 Author: Weiqun Zhang Date: Fri Feb 21 14:59:03 2020 -0800 DPCPP: abort in amrex::launch if shared memory is asked Src/Base/AMReX_GpuLaunchFunctsG.H commit b54644026d649070dd0180762d253e919c0417d0 Merge: a54971835 2d6772c93 Author: WeiqunZhang Date: Fri Feb 21 14:12:46 2020 -0800 Merge pull request #700 from ax3l/fix-FBIConstr FAB: Fix Constructor Calls commit 2d6772c930120385ecb791557fd4df0a3a84b366 Author: Axel Huebl Date: Fri Feb 21 13:38:53 2020 -0800 FAB: Fix Constructor Calls This fixes a bug in `Array4CopyTag` construction while pushing back to a vector. The current call does not what one expects to do, as hinted by the nvcc warning: ``` Src/Base/AMReX_FBI.H(920): warning: variable "zero" was set but never used detected during: instantiation of "void amrex::FabArray::FBEP_nowait(int, int, const amrex::IntVect &, const amrex::Periodicity &, __nv_bool, __nv_bool) [with FAB=amrex::FArrayBox, F=amrex::FArrayBox, =void]" Src/Base/AMReX_FabArray.H(1993): here instantiation of "void amrex::FabArray::FillBoundary_nowait(int, int, const amrex::IntVect &, const amrex::Periodicity &, __nv_bool) [with FAB=amrex::FArrayBox]" Src/Base/AMReX_FabArray.H(1870): here instantiation of "void amrex::FabArray::FillBoundary(const amrex::Periodicity &, __nv_bool) [with FAB=amrex::FArrayBox]" Src/Base/AMReX_FBI.H(955): warning: variable "zero" was set but never used detected during: instantiation of "void amrex::FabArray::FillBoundary_finish() [with FAB=amrex::FArrayBox, F=amrex::FArrayBox, =void]" Src/Base/AMReX_FabArray.H(1871): here instantiation of "void amrex::FabArray::FillBoundary(const amrex::Periodicity &, __nv_bool) [with FAB=amrex::FArrayBox]" ``` Basically the last arguments were not passed to object construction of `amrex::Array4CopyTag`. Further fixes: - add missing includes - move created r-values in (`emplace_back`) Src/Base/AMReX_FBI.H commit a5497183578cd5d6c2b77910c12e06fbb1a72dc1 Merge: 5b535ee5c 556438f6d Author: Weiqun Zhang Date: Fri Feb 21 13:21:57 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 556438f6d4e72d0460748d7fa61cf0af75f5105e Merge: e13001f2c 052c5cc6a Author: Weiqun Zhang Date: Fri Feb 21 13:21:44 2020 -0800 Merge branch 'dpcpp' into development commit 052c5cc6a260466ba0be47460a000b403faec7e5 Author: Weiqun Zhang Date: Fri Feb 21 13:21:19 2020 -0800 notes on DPC++ Docs/Notes/Readme.dpcpp commit 5b535ee5c8e59425ab410686becf7fb5f6d330d9 Merge: e13001f2c 1a3fc7cbf Author: Weiqun Zhang Date: Fri Feb 21 13:19:45 2020 -0800 Merge branch 'dpcpp' into development commit 1a3fc7cbf78848f006ab9ea2e76b8da094771f20 Author: Weiqun Zhang Date: Fri Feb 21 13:08:49 2020 -0800 wait and throw Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuReduce.H commit ddfcd77d3b83166de8d9f6b1f689d9943bc9118a Author: Weiqun Zhang Date: Fri Feb 21 12:52:32 2020 -0800 update comments Src/Base/AMReX_GpuDevice.cpp commit e13001f2c92d5fdfac8dff6c107251d85f5d392e Author: Michele Rosso Date: Fri Feb 21 15:29:20 2020 -0500 CMake+CUDA: no need to specify libcuda manually Tools/CMake/AMReX_Config.cmake commit 8266379fa4b4cfe42077b525bdc41cb084b0909e Author: Michele Rosso Date: Fri Feb 21 15:13:07 2020 -0500 CMake:add missing sources from Extern/ProfParser Src/Extern/ProfParser/CMakeLists.txt commit 3d976f4c33859a8993df596ad390efa0eb6cecc6 Author: Weiqun Zhang Date: Fri Feb 21 09:48:44 2020 -0800 do not define dim3 for non-dpcpp Src/Base/AMReX_GpuTypes.H commit 3237a58d1edd575645e4c0b1d99c89d063cefa1f Author: Weiqun Zhang Date: Fri Feb 21 09:40:41 2020 -0800 remove shared_mem_bytes option from FabReduce and VecReduce Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_Reduce.H commit e1fa142531608ffdd5b4c437f18c339ed999bd3a Merge: 73ac4da6d cb0f385fa Author: Weiqun Zhang Date: Fri Feb 21 09:18:18 2020 -0800 Merge branch 'development' into dpcpp commit 73ac4da6d61f50c17936ba1239f513f1de1f4f8a Author: Weiqun Zhang Date: Thu Feb 20 21:55:33 2020 -0800 DPC++: implement AnyOf Src/Base/AMReX_Reduce.H commit 10db5b5993d6db903b4233a34c324a0f7986f2e2 Author: Weiqun Zhang Date: Thu Feb 20 21:42:19 2020 -0800 DPC++: implement some functions used by FillBoundary Src/Base/AMReX_FBI.H commit 5d0429f0f605febedfb3e3cda1cb5bd3991da75a Author: Weiqun Zhang Date: Thu Feb 20 21:11:47 2020 -0800 fix a number of cmath functions with hack Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealVect.H Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H Src/EB/AMReX_algoim_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_TracerParticle_mod_K.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit ecceecffb5bb06187bd0a3079c9034a253263d6d Author: Weiqun Zhang Date: Thu Feb 20 18:50:57 2020 -0800 update dpcpp todo comments Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuMemory.H Src/Base/AMReX_GpuUtility.H commit b4d40eaf6d2ddf98281cfd2777b5731c4b204ef3 Merge: e9d333ee4 1b17c9671 Author: Weiqun Zhang Date: Thu Feb 20 18:39:59 2020 -0800 Merge branch 'development' into dpcpp commit e9d333ee4b6f9606e4109f5bb0c468cbc7c8f97c Merge: 6dd56834d 102e00216 Author: Weiqun Zhang Date: Thu Feb 20 18:39:51 2020 -0800 Merge branch 'dpcpp2' into dpcpp commit cb0f385fac872f6023432aafd10790853621c6a8 Merge: 90201e7af 1b17c9671 Author: Michele Rosso Date: Thu Feb 20 18:28:22 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 90201e7afec3ba02e3044d4291b9bc27222e8037 Author: Michele Rosso Date: Thu Feb 20 18:28:08 2020 -0800 CMake: fix how ProfParser is built Src/CMakeLists.txt Src/Extern/ProfParser/CMakeLists.txt commit 102e0021642b13e6c1fce4d08613cc3ea9623ba3 Author: Weiqun Zhang Date: Thu Feb 20 17:35:03 2020 -0800 link to libsycl-cmath Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_GpuComplex.H Src/Base/AMReX_Math.H Src/Base/AMReX_MultiFabUtil_nd_C.H Tools/GNUMake/Make.defs Tools/GNUMake/comps/dpcpp.mak commit fb95fdb0465866252c15f42e10888cd1575eaf0e Author: Weiqun Zhang Date: Thu Feb 20 16:47:23 2020 -0800 link to libsycl-glibc Tools/GNUMake/Make.defs Tools/GNUMake/comps/dpcpp.mak commit 1b17c9671fdf0d50c9a7226b073f781791a35484 Merge: ce9419a88 e97431df1 Author: Weiqun Zhang Date: Thu Feb 20 15:43:36 2020 -0800 Merge branch 'FlashFluxRegister' into development commit ce9419a8848d8f56950703cdd9fbe77c2a63ad3f Author: Michele Rosso Date: Thu Feb 20 15:15:03 2020 -0800 CMake+CUDA: link to nvToolsExt when ENABLE_BASE_PROFILE is on Tools/CMake/AMReX_Config.cmake commit e97431df18279c182186a8f3cfc89708cb98da56 Author: Weiqun Zhang Date: Thu Feb 20 09:12:41 2020 -0800 Optimization thanks to Klaus's suggestion Src/AmrCore/AMReX_AmrCore.cpp commit 730cd6a58aa0e6e5688f29a7fdf3aa2dbb1bd146 Author: Weiqun Zhang Date: Wed Feb 19 15:52:44 2020 -0800 NodalOverset test: use sigma strategy Tests/LinearSolvers/NodalOverset/MyTest.cpp commit 20b4130ef13ee8917d38b4733d709de670c7fb93 Author: Weiqun Zhang Date: Wed Feb 19 15:22:38 2020 -0800 AmrCore::regrid: if coarse level changes, we need to remake fine level so that flux register can be updated Src/AmrCore/AMReX_AmrCore.cpp commit 098de322f613c8b9e9ba0aba89a70d195671ff6f Merge: cf83828e2 3b3a210e6 Author: Weiqun Zhang Date: Wed Feb 19 14:17:26 2020 -0800 Merge branch 'weiqun/dev' into development commit 3b3a210e604bcee88e2bde8964dbbc998a510b00 Author: Weiqun Zhang Date: Wed Feb 19 13:34:10 2020 -0800 missing Make.package Tests/LinearSolvers/NodalOverset/Make.package commit 4872d803030a7b8e76956704db64ebecdc1682c0 Author: Weiqun Zhang Date: Wed Feb 19 13:32:24 2020 -0800 let user set nodal solver Dirichlet mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 1afcf8bc06ed4a9a54750eff1f5d7f079367b2b2 Author: Weiqun Zhang Date: Wed Feb 19 13:30:44 2020 -0800 template average_down_nodes Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H commit e73d62fb72521249c31e99b96aaa7833889bb59a Author: Weiqun Zhang Date: Wed Feb 19 13:28:43 2020 -0800 move is_nodal and is_cell_centered from MultiFab to FabArrayBase Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit f578bf9747038bc58fd92f14b65bb04feff16cec Author: Weiqun Zhang Date: Wed Feb 19 13:27:21 2020 -0800 add new test NodalOverset Tests/LinearSolvers/NodalOverset/GNUmakefile Tests/LinearSolvers/NodalOverset/MyTest.H Tests/LinearSolvers/NodalOverset/MyTest.cpp Tests/LinearSolvers/NodalOverset/main.cpp commit cf83828e2bde3114e3bb8b03f1e6cd72d4cd935c Merge: c7a1ff788 d02402f4e Author: Andrew Myers Date: Wed Feb 19 10:19:25 2020 -0800 Merge branch 'development' into sort_particles_bin commit c7ae49a5195fa16277f418f48564adfd0e83af66 Author: Weiqun Zhang Date: Wed Feb 19 09:15:43 2020 -0800 FlashFluxRegister: isFluxDensity Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit 987148a246030ee10efb44016c050c6118128f2c Merge: aaf960090 d02402f4e Author: Weiqun Zhang Date: Tue Feb 18 14:00:20 2020 -0800 Merge branch 'development' into FlashFluxRegister commit d02402f4e2d239f2c98c6880fda2bd70a8371405 Author: Andrew Myers Date: Tue Feb 18 09:46:03 2020 -0800 fix index error in mac tracer advection Src/Particle/AMReX_TracerParticle_mod_K.H commit 88372ce588c7cbdf1858e3dc09ea32b3741cf754 Merge: d5d0404fe a7dd3eeea Author: Andrew Myers Date: Tue Feb 18 09:31:34 2020 -0800 Merge branch 'particle_io_filter' into development commit c7a1ff78823f55a4bb79091b414fcd457ee8a87f Author: atmyers Date: Mon Feb 17 14:44:28 2020 -0800 bugfix Src/Particle/AMReX_ParticleContainerI.H commit f9aab1755ad13d0295b647dddcc29fdd1dda3598 Author: atmyers Date: Mon Feb 17 14:26:51 2020 -0800 Add SortParticlesByBin Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit a7dd3eeeadc249a562f5716f5c2b7475734d0c2a Author: atmyers Date: Mon Feb 17 13:38:47 2020 -0800 fix the io filter Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H commit 9eb898d60921fef103b9b53ed1a2fb97822f9b0a Author: Weiqun Zhang Date: Sun Feb 16 18:59:09 2020 -0800 more detail in abort message Src/Base/AMReX_FBI.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_Reduce.H commit 6dd56834d2f494fa64898409b6f67828beb213be Author: Weiqun Zhang Date: Sun Feb 16 13:20:31 2020 -0800 remove abort in DPC++ reduce Src/Base/AMReX_GpuReduce.H commit 2a81f457608a4faeb81bc4351118485ae982f771 Author: Weiqun Zhang Date: Sun Feb 16 13:20:31 2020 -0800 remove abort in DPC++ reduce Src/Base/AMReX_GpuReduce.H commit 883f1a8d312e4ee8f315dad7609046ed1744b36a Author: Weiqun Zhang Date: Sun Feb 16 11:35:19 2020 -0800 clean up Tools/GNUMake/comps/dpcpp.mak commit 35d1932dfbd73ae0bdde9ae036d94f3af6fdabc0 Author: Weiqun Zhang Date: Sun Feb 16 10:03:36 2020 -0800 amrex::Math Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_GpuComplex.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Math.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_RealVect.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H commit dccd99da140b3319693d92c7e801bc7f156afb15 Author: Weiqun Zhang Date: Sun Feb 16 08:43:48 2020 -0800 Revert "use scyl::abs and sycl::copysign. This commit should be reverted once they are in std:: in future version of DPC++" This reverts commit fe39b7a09ab4089c3f48953bd708e4a555d8356d. Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_BaseFab.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H commit 720d281c234f2e9f3b50f6baeb74d232e8020501 Author: Weiqun Zhang Date: Sun Feb 16 08:43:19 2020 -0800 Revert "missing using sycl::abs. This should be reverted too eventually." This reverts commit b182bd57042761dcab6aac1f2300772ca309d027. Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit f6d6a3c899113f10b833365b05ce84d8f16d40d6 Author: Weiqun Zhang Date: Sun Feb 16 08:42:04 2020 -0800 always add -DNDEBUG to get around compiler bug Tools/GNUMake/Make.defs commit 0feb4e34fa68aef6354c595e4a82a27a35067745 Author: Weiqun Zhang Date: Sat Feb 15 21:29:54 2020 -0800 avoid NDEBUG Src/Base/AMReX_Machine.cpp commit b219a3d57902bb95d200f6076e08f39a0dfc4aa8 Author: Weiqun Zhang Date: Sat Feb 15 21:21:42 2020 -0800 use amrex::Abort and ASSERT Src/Base/AMReX.H Src/Base/AMReX_Machine.cpp commit 47454df66dc3279b429b12a54f872063ac86c8e9 Author: Weiqun Zhang Date: Sat Feb 15 20:41:56 2020 -0800 more detail in abort message Src/Base/AMReX_GpuAssert.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H commit d5d0404fe1860fe653b66b375276545db3a45a0d Merge: 88c5e3186 1803fa5c6 Author: WeiqunZhang Date: Sat Feb 15 15:30:34 2020 -0800 Merge pull request #696 from AMReX-Codes/stream Add stream benchmark commit a7a27ab3cb3669e4ae69d1007604b8a136f4e096 Author: Weiqun Zhang Date: Sat Feb 15 15:13:15 2020 -0800 wait and throw Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 1803fa5c668dd90207986129686653a655b8e16d Author: Max Katz Date: Sat Feb 15 13:32:38 2020 -0800 Add stream benchmark Tests/Stream/GNUmakefile Tests/Stream/Make.package Tests/Stream/inputs Tests/Stream/main.cpp commit 1747d8936095282354a7f816d0dc6e5ace793bb5 Author: atmyers Date: Fri Feb 14 23:31:39 2020 -0800 particle type -> superparticletype Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H commit 3376fe9989d7d5d1cef988e7aa16c9f2472c2c9a Author: Weiqun Zhang Date: Fri Feb 14 19:56:29 2020 -0800 add placeholders for deviceReduce Src/Base/AMReX_GpuReduce.H commit 0782fda17ebe2a3c7c1f1676f463bffc23e51774 Author: Weiqun Zhang Date: Fri Feb 14 19:19:15 2020 -0800 use abort() instead of assert(0) Src/Base/AMReX_GpuAssert.H commit 5e79c491fefbbfc038dcfdacd145abc168e5633e Author: Weiqun Zhang Date: Fri Feb 14 16:38:08 2020 -0800 no need for __SYCL_DEVICE_ONLY__ Src/Base/AMReX_BaseFab.H commit 23cc995636bb2a98bf0a2fcb7d966c180b0d61be Author: Weiqun Zhang Date: Thu Feb 13 21:54:34 2020 -0800 remove shared memory from paralle for because it may be unsafe Src/Base/AMReX_GpuLaunchFunctsG.H commit a7be1bc354cb4a982349099878602a420f5c1369 Author: Weiqun Zhang Date: Thu Feb 13 19:42:08 2020 -0800 DPC++: start reduction Src/Base/AMReX_BlockMutex.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_Reduce.H commit b182bd57042761dcab6aac1f2300772ca309d027 Author: Weiqun Zhang Date: Thu Feb 13 19:41:06 2020 -0800 missing using sycl::abs. This should be reverted too eventually. Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit fe39b7a09ab4089c3f48953bd708e4a555d8356d Author: Weiqun Zhang Date: Thu Feb 13 15:13:50 2020 -0800 use scyl::abs and sycl::copysign. This commit should be reverted once they are in std:: in future version of DPC++ Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_BaseFab.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H commit f4cf306c1ece8321702cfc5ce4a1620c2c75e1e0 Merge: f3fce75e1 88c5e3186 Author: atmyers Date: Thu Feb 13 15:10:25 2020 -0800 Merge branch 'development' into particle_io_filter commit 5442903068d33a472e0f6980c35e8128f25c3dc5 Author: Weiqun Zhang Date: Thu Feb 13 15:09:20 2020 -0800 fix some issue in launch macros Src/Base/AMReX_GpuLaunchMacrosG.H commit 0df9e1075926a6ec5f020aaaf1339989467a0faf Author: Weiqun Zhang Date: Thu Feb 13 15:09:02 2020 -0800 add override Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H commit f3fce75e10e534b8fe4506805d51a75b4d88dfc2 Author: atmyers Date: Thu Feb 13 14:56:26 2020 -0800 add a filter to control which particles get written out Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H commit 88c5e318674a79096df9ad43c089159ac5acce36 Merge: 1ba9b1e05 075602eda Author: WeiqunZhang Date: Thu Feb 13 14:29:55 2020 -0800 Merge pull request #695 from maikel/feature/VirtualMakeBaseGrids Feature/virtual make base grids commit 53fec0ca63f47b551d8e81c103ed073c9cc70488 Author: Weiqun Zhang Date: Thu Feb 13 14:04:31 2020 -0800 fix launch macros Src/Base/AMReX_GpuLaunchMacrosG.H commit 075602eda011f8e27bc4066249c118d21249b1a8 Author: Maikel Nadolski Date: Thu Feb 13 22:24:59 2020 +0100 Add const qualifier to PostProcessBaseGrids Src/AmrCore/AMReX_AmrMesh.H commit 250a6e8981ef90a75f69c7df3ab7a8a3de173211 Author: Weiqun Zhang Date: Thu Feb 13 13:19:16 2020 -0800 DPC++: for now streamSynchronize in Elixir and AsyncArray clear() Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuElixir.cpp commit 4e5dee69716a08f0176d46ce1bea14fb88e7d383 Author: Maikel Nadolski Date: Thu Feb 13 22:16:10 2020 +0100 Add a virtual member function to AmrMesh This commit adds a PostProcessBaseGrids member function. This makes it possible to alter the box array for the coarsest level before it is being used. Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit e1ff734fdc632b196a4d0e6ef8ee3f075c3d3895 Author: Weiqun Zhang Date: Thu Feb 13 12:38:19 2020 -0800 Gpu::Atomic: add missing features and cleanup Src/Base/AMReX_GpuAtomic.H commit 8f1b48f4c89dc3ea2ef21602a03b9cb11a9ebb0d Author: Weiqun Zhang Date: Thu Feb 13 05:18:31 2020 -0800 put Gpu::Atomic in a new file Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAtomic.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_GpuUtility.H Src/Base/CMakeLists.txt Src/Base/Make.package commit bd47346656c109731b48e2b47c46420bb3271289 Author: Weiqun Zhang Date: Wed Feb 12 20:02:47 2020 -0800 DPC++: Gpu::Atomic::Add Src/Base/AMReX_GpuUtility.H commit b32c81e370148ebdc4b402991545525c557786ce Author: Weiqun Zhang Date: Wed Feb 12 16:31:09 2020 -0800 DPC++ add async error handler Src/Base/AMReX_GpuDevice.cpp commit a6c0fed6f4c471348e78bce61853700ba650f7a9 Author: Weiqun Zhang Date: Wed Feb 12 16:11:50 2020 -0800 some minor changes Src/Base/AMReX_BaseFab.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Polynomial.H commit a0ee6756ad8430eb568d41b0e4a9f07b17b37d96 Author: Weiqun Zhang Date: Wed Feb 12 15:01:04 2020 -0800 DPC++: always wait after memcpy Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuLaunchFunctsG.H commit ddbc17c824b5dffa735fea9b00474fdf62ae6097 Author: Weiqun Zhang Date: Wed Feb 12 14:28:11 2020 -0800 redefined AMREX_DEVICE_COMPILE as a macro Src/Base/AMReX.H Src/Base/AMReX_Array4.H Src/Base/AMReX_GpuAssert.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuPrint.H Src/Base/AMReX_GpuQualifiers.H Src/Base/AMReX_GpuRange.H commit 80cbc3587811509ee5adde3013151c30efe24a8d Author: Weiqun Zhang Date: Wed Feb 12 13:40:58 2020 -0800 DPC++: assert Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Array4.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAssert.H Src/Base/AMReX_GpuPrint.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_TypeTraits.H Src/Base/CMakeLists.txt Src/Base/Make.package commit aa630dbe1b5c28296710a74a61a189562d1b6bef Author: Weiqun Zhang Date: Wed Feb 12 12:33:26 2020 -0800 DPC++: printf Src/Base/AMReX_Array4.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuPrint.H Src/Base/CMakeLists.txt Src/Base/Make.package commit b1969f3ec6f739856891fea1ae53a3f984bd0650 Merge: 98707e1d2 6d947f3e7 Author: Weiqun Zhang Date: Wed Feb 12 12:03:43 2020 -0800 Merge branch 'dpcpp' of https://github.com/AMReX-Codes/amrex into dpcpp commit 6d947f3e73418936a311054c61e4e7728dae54d0 Author: Weiqun Zhang Date: Wed Feb 12 12:03:15 2020 -0800 have to use sycl::floor Src/Base/AMReX_MultiFabUtil_nd_C.H commit 98707e1d269edd62103919d29c719fe41f86d063 Merge: 9434b3573 0ad0a706d Author: Weiqun Zhang Date: Wed Feb 12 11:47:05 2020 -0800 Merge branch 'dpcpp' of https://github.com/AMReX-Codes/amrex into dpcpp commit 0ad0a706da151991509dddd26e6c034b9ddf3ef7 Author: Weiqun Zhang Date: Wed Feb 12 11:46:40 2020 -0800 make sure sycl doesn't see virtual funcitons Src/Base/AMReX.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_ParmParse.H commit a4a0d3029df21bc1a7a9a34660db3436a2488d9c Author: Weiqun Zhang Date: Wed Feb 12 05:59:18 2020 -0800 launch macros in DPC++ Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosC.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_PODVector.H Src/Base/AMReX_Random.cpp commit f949fed83d29080cc4e71ab21d15d2e59c4fde85 Author: Weiqun Zhang Date: Tue Feb 11 13:04:28 2020 -0800 launch functions in DPC++ Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuRange.H commit 6bafe7679bbb11328dbe8296ae69d22293bcb7de Merge: c94a089be 1ba9b1e05 Author: Weiqun Zhang Date: Tue Feb 11 10:31:39 2020 -0800 Merge branch 'development' into dpcpp commit 1ba9b1e05fcdd83162ce03ce1d4318b29096ebf6 Author: Weiqun Zhang Date: Tue Feb 11 10:31:08 2020 -0800 add Gpu::synchronize Src/EB/AMReX_EBMultiFabUtil.cpp commit 9434b3573641f2055e03479f9d95effe812705b3 Author: Weiqun Zhang Date: Tue Feb 11 10:29:05 2020 -0800 IsDeviceLambda always return true for DPC++ Src/Base/AMReX_FabArray.H Src/Base/AMReX_TypeTraits.H commit c94a089beb350b7eca24a158ae8048c8b133eb94 Merge: 81ad9c561 a427c460d Author: Weiqun Zhang Date: Tue Feb 11 08:54:35 2020 -0800 Merge branch 'dpcpp' of https://github.com/AMReX-Codes/amrex into dpcpp commit 81ad9c561c6ab53a3a50ce4d1425d7a8e2bcde3e Author: Weiqun Zhang Date: Tue Feb 11 08:54:28 2020 -0800 more place holders Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Random.H commit a427c460d0345ca5e9db38e15ec14c7413e46069 Merge: 6a833ce49 8a4093562 Author: Weiqun Zhang Date: Tue Feb 11 08:53:06 2020 -0800 Merge branch 'development' into dpcpp commit 8a40935623817e52ed0714bcfa9516bb3e3f94d2 Author: Weiqun Zhang Date: Tue Feb 11 08:50:08 2020 -0800 use __CUDA_ARCH__ and __HIP_DEVICE_COMPILE__ directly in preparation for DPC++ Src/Base/AMReX.cpp Src/Base/AMReX_Array4.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Random.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Polynomial.H commit f6b892db407122d89ab6113cf9a04ac42d9fd2dc Author: Andrew Myers Date: Mon Feb 10 22:36:55 2020 -0800 need to skip the size-0 entries in this loop, if we are going to do this in the one-box case Src/Particle/AMReX_ParticleCommunication.H commit d000aaa3ec2c84770b729a19e50e99e8dc06a5cb Author: Andrew Myers Date: Mon Feb 10 18:49:54 2020 -0800 remove these early exits from the particle communication code Src/Particle/AMReX_ParticleCommunication.H commit d040ef87f8c7f4e170238721a2943e79b9f6ace2 Author: Weiqun Zhang Date: Mon Feb 10 10:43:32 2020 -0800 add variadic version of std::is_same Src/Base/AMReX_TypeTraits.H commit 08562ec0240554a7dfeffdd75d77182401b799c9 Author: Weiqun Zhang Date: Sun Feb 9 07:12:08 2020 -0800 implicit conversion for 1d Src/Base/AMReX_Box.H commit fc9c503744ad2ed3aec78193b382e7fd545bcbc7 Author: Weiqun Zhang Date: Sat Feb 8 20:13:16 2020 -0800 move some RealVect functions from cpp to H file Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 77ef0f95f68f5e9991289311bc18e2ef0d3411d4 Merge: 1e29dfcba 1e47b1f2b Author: WeiqunZhang Date: Sat Feb 8 20:14:33 2020 -0800 Merge pull request #690 from AMReX-Codes/write_probin simplify write_probin + add C++ parameter support commit 1e47b1f2b17d54d2149a4e2e89b03e68bc523bd3 Author: Max Katz Date: Sat Feb 8 19:54:27 2020 -0800 Add __managed__ attribute to extern parameters Tools/F_scripts/write_probin.py commit 45abae9ac500cecc34dc198e040522aa1870b92e Merge: b292551bf 1e29dfcba Author: Max Katz Date: Sat Feb 8 19:19:07 2020 -0800 Merge branch 'development' into write_probin commit 6a833ce49c59d7371db729cfa652673c58e6b609 Author: Weiqun Zhang Date: Sat Feb 8 16:36:29 2020 -0800 make sure all queues use the same context with an empty async handler Src/Base/AMReX_GpuDevice.cpp commit 1e29dfcbae2180ecf270abad4b79ef3810614854 Author: Max Katz Date: Sat Feb 8 10:30:11 2020 -0800 Add AMREX_GPU_CONSTANT and AMREX_GPU_MANAGED Src/Base/AMReX_GpuQualifiers.H commit f1ed2b4c6590d983a435fee9b739f6e4bf8600c4 Author: Weiqun Zhang Date: Sat Feb 8 06:56:01 2020 -0800 placeholder in Array4 assert Src/Base/AMReX_Array4.H Src/Base/AMReX_GpuUtility.H commit b3cb68507249c714042eb04c1843066766fab7f2 Author: Weiqun Zhang Date: Fri Feb 7 16:30:44 2020 -0800 store subgroup size Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunchFunctsG.H commit e9d4577e6a2ddbe34a67e06b4735adbe0c668fb0 Author: Weiqun Zhang Date: Fri Feb 7 15:00:41 2020 -0800 fix some ifdefs Src/Base/AMReX_GpuDevice.H commit 2f68f73b1e18696285dd0dc9c4b42b16512a8c62 Author: Weiqun Zhang Date: Fri Feb 7 14:54:38 2020 -0800 minor change to make Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/dpcpp.mak commit 5af4b7785c0533ce31f1f68a63a1addf286ceabc Author: Weiqun Zhang Date: Fri Feb 7 13:33:47 2020 -0800 ParalleFor inside MFIter works Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuTypes.H Tools/GNUMake/Make.defs commit 2d75132396dcb86e67dd80161c774b9308c1c6c9 Author: Weiqun Zhang Date: Fri Feb 7 12:59:32 2020 -0800 ParallelFor works for a simple example Src/Base/AMReX_Array4.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunchFunctsG.H Tools/GNUMake/Make.rules Tools/GNUMake/comps/dpcpp.mak commit f4bb2905278deb4d535b3095feba0e54505c7097 Author: Weiqun Zhang Date: Fri Feb 7 10:24:31 2020 -0800 update Arena Src/Base/AMReX_Arena.cpp Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit ef075785130a4aded995048167d47c2c7e47239d Author: Weiqun Zhang Date: Thu Feb 6 21:38:49 2020 -0800 place holders and device properties Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BlockMutex.H Src/Base/AMReX_BlockMutex.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuElixir.cpp Src/Base/AMReX_GpuError.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuMemory.H Src/Base/AMReX_GpuQualifiers.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_Reduce.H Src/Base/AMReX_Scan.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/GNUMake/Make.defs commit 13f6b479f07875826d934dd6048a3651b21b6213 Author: Weiqun Zhang Date: Thu Feb 6 16:24:35 2020 -0800 compile with dpcpp Src/Base/AMReX_GpuTypes.H commit e39a8c15236ccb6ee8133eae9f0c13f46d581928 Merge: 0e71c1e5b 79360ad04 Author: Weiqun Zhang Date: Thu Feb 6 11:52:41 2020 -0800 Merge branch 'development' into dpcpp commit aaf960090453d2b4a11ec299664975d4370b1a5c Author: Weiqun Zhang Date: Thu Feb 6 11:24:20 2020 -0800 FlashFluxRegister: add addition load/store with area argument Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit 6d3cf34cee07b60edf6e7a6cf38abdf80d5d0f31 Author: Weiqun Zhang Date: Thu Feb 6 10:55:36 2020 -0800 FlashFluxRegister: add addition load Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit 79360ad04143dc06d1ac14ad28b79a1ab15861f0 Merge: 8744e4ab3 2cd152353 Author: WeiqunZhang Date: Thu Feb 6 09:20:01 2020 -0800 Merge pull request #684 from lucafedeli88/add_poisson_random_distribution Add Poisson random distribution commit 8744e4ab303afcd1b1663a8aa3a0e9db6c85c3bf Merge: fec9bc974 73637768c Author: WeiqunZhang Date: Thu Feb 6 08:53:25 2020 -0800 Merge pull request #687 from Alpine-DAV/task/2020_02_blueprint_multi_topo Conduit Blueprint Update to support Multiple Topologies commit fec9bc9742265ff858dc9ba7fd97c27b384f05e6 Author: Weiqun Zhang Date: Wed Feb 5 14:31:04 2020 -0800 fix bug in nodal solver bc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit 73637768cbf34e4a897e898c5a764a66a0e1f78c Author: Cyrus Harrison Date: Wed Feb 5 15:23:59 2020 -0600 blueprint: dont reset output node when wrapping data Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit c9fd1ef4d02ee4cd024c0b512875aabe794f23ca Merge: cb90c0a31 2e675c7b2 Author: Andrew Myers Date: Wed Feb 5 10:08:39 2020 -0800 Merge pull request #686 from AMReX-Codes/jmsexton/hdf5 Fix for USE_CUDA=TRUE case commit 2e675c7b22f5a7ed4b051b3e83f9406c467dffe1 Author: Jean M. Sexton Date: Wed Feb 5 12:58:03 2020 -0500 Fix for USE_CUDA=TRUE case Tests/HDF5Benchmark/GNUmakefile commit 2cd1523531db6f39194cfd3ee22d6e80f2745980 Author: Luca Fedeli Date: Wed Feb 5 02:10:41 2020 +0100 add Poisson random distribution Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp commit cb90c0a31969b33062bc583c890fee089ad28459 Author: Andrew Myers Date: Wed Feb 5 03:09:02 2020 -0500 remove some timers I don't need anymore Src/Particle/AMReX_ParticleCommunication.cpp commit 498823e15dbc528d48a8cb35814d210b87e553cd Author: Andrew Myers Date: Wed Feb 5 02:54:10 2020 -0500 an optmization for ParticleCopyPlan::buildMPI start in the local case Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 11f456f7b41c3abd64193460d8a0b309fb3b3307 Merge: d58c8adfd 86b29ea71 Author: WeiqunZhang Date: Tue Feb 4 16:16:28 2020 -0800 Merge pull request #656 from AMReX-Codes/kngott/hip [WIP] First draft of Changes for HIP commit 86b29ea71d7cce6518f88c6f43e68eaa4080be08 Author: Weiqun Zhang Date: Tue Feb 4 16:15:49 2020 -0800 fix typo Tests/GPU/RandomNumberGeneration/GNUmakefile commit c26406b24e6633f24b52047287cffe290ce53d4c Author: Weiqun Zhang Date: Tue Feb 4 15:32:28 2020 -0800 change DEBUG Tutorials/GPU/ParallelReduce/GNUmakefile commit 5a20b0e3d819ee9cd913e75b915dd82f32da4537 Author: Weiqun Zhang Date: Tue Feb 4 15:24:49 2020 -0800 restore USE_CUDA=TRUE Tests/GPU/RandomNumberGeneration/GNUmakefile commit 5dfff1935f1f32abf4e1002858403f6710c6b2cf Author: Weiqun Zhang Date: Tue Feb 4 14:58:07 2020 -0800 add amrex:: because macros doesn't know namespace Src/Base/AMReX_GpuLaunch.H commit 112e26a1cb3c5df4cf86f1f4e39ef8f7930b77b5 Author: Weiqun Zhang Date: Tue Feb 4 14:44:18 2020 -0800 fix for USE_MPI and CUDA >= 10 Src/Base/AMReX_GpuDevice.cpp commit 26a272419990e07ef21864f9b78f57c5432bf19e Author: Weiqun Zhang Date: Tue Feb 4 13:32:35 2020 -0800 use gcc in HelloWorld Tutorials/Basic/HelloWorld_C/GNUmakefile commit 6c90e33162763ed5861a6e6d47fe5191b2d173bb Author: Weiqun Zhang Date: Tue Feb 4 13:31:27 2020 -0800 disable USE_HIP in tutorials by default Tutorials/Basic/HelloWorld_C/GNUmakefile Tutorials/GPU/Launch/GNUmakefile Tutorials/GPU/ParallelReduce/GNUmakefile commit 1b1cd65154736bfd83a50954c5c90b57629e11d1 Merge: dcade0429 d58c8adfd Author: Weiqun Zhang Date: Tue Feb 4 13:27:06 2020 -0800 Merge branch 'development' into kngott/hip commit d58c8adfd46c9acab809a2a13f3774328c28a689 Author: Weiqun Zhang Date: Tue Feb 4 13:08:08 2020 -0800 fix setBndry for 1d and 2d. update setDomainBndry Src/Base/AMReX_FabArray.H commit 886c4e240283325310d332b05ae9bbc9fade975c Merge: 46c807c7e 87461f3db Author: WeiqunZhang Date: Tue Feb 4 12:54:31 2020 -0800 Merge pull request #673 from AMReX-Codes/kngott/newBndry New version of setBndry for GPUs. commit 46c807c7ebb2c2e507915af6d96226fc480ceacb Merge: cdca9338e 998c6d79e Author: WeiqunZhang Date: Tue Feb 4 12:27:56 2020 -0800 Merge pull request #653 from AMReX-Codes/ebtensor_flux Ebtensor flux commit cdca9338e2f6d0c2e285939905777bb640d32a69 Author: Weiqun Zhang Date: Tue Feb 4 11:55:50 2020 -0800 Tutorials/Amr: remove duplicated code Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_octree_F/Source/Src_2d/advect_2d_mod.F90 commit 1fada34e00d22ffd3f89582b6b93bdfe249e7078 Merge: 5f3e48732 0aadeb423 Author: Weiqun Zhang Date: Tue Feb 4 11:54:44 2020 -0800 Merge branch 'FlashFluxRegister' into development commit 5f3e487329b3def0300d2980836949da208e2e80 Author: Weiqun Zhang Date: Tue Feb 4 11:50:14 2020 -0800 FillPatch: no need to do interpolation of the time is exact Src/AmrCore/AMReX_FillPatchUtil.cpp commit a67d5fb68f3311e7dd1a259a8d13561f9c330c2f Author: Weiqun Zhang Date: Tue Feb 4 11:49:36 2020 -0800 if Cluster::new_chop fails, switch to Cluster::chop Src/AmrCore/AMReX_Cluster.cpp commit b1abf0be45d0b4064f3e9a709608711cd88b86f0 Author: Weiqun Zhang Date: Mon Feb 3 15:18:44 2020 -0800 Option to specify number of ghost cells in fill coarse patch Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit d0efe05ac7a235d58a9d4b3d0435074c1ab4fb42 Author: Andy Nonaka Date: Mon Feb 3 18:44:21 2020 -0800 update caption of advection tutorial figs Docs/sphinx_documentation/source/AmrCore.rst commit 90445ea2a13b24fa99ba075926b705a675dada9e Author: Andrew Myers Date: Mon Feb 3 15:49:40 2020 -0800 fix docstrings Src/Particle/AMReX_ParticleTransformation.H commit 2ed901095b8455c20760e4555640180f684abb36 Merge: bbca1d6ed a26d08210 Author: WeiqunZhang Date: Mon Feb 3 09:30:07 2020 -0800 Merge pull request #657 from kcdodd/development Change cell bilinear to work with odd refinement ratio commit bbca1d6ed839e73368f89af03fba8bdc661376cc Merge: 0650a0779 334c134ae Author: WeiqunZhang Date: Mon Feb 3 09:27:51 2020 -0800 Merge pull request #674 from ax3l/fix-shadowVisMF VisMF: Remove Shadow Warning commit 0650a077998e3242e185a3e8b6083a4da250e24f Author: Weiqun Zhang Date: Mon Feb 3 09:20:40 2020 -0800 update CHANGES CHANGES commit e96621d7f73fd707c88782d84f6dfe2734d01472 Merge: 26a67533b 4093c8dbc Author: Weiqun Zhang Date: Mon Feb 3 09:17:33 2020 -0800 Merge branch 'weiqun/AmrInfo' into development commit 26a67533b00e5aebe4b050c169c1b92afcc4ce80 Merge: e149db520 8e744786c Author: Weiqun Zhang Date: Mon Feb 3 09:17:05 2020 -0800 Merge branch 'weiqun/bl_no_fort' into development commit e149db520688a2f532ff82343c5ab1408dc581af Merge: 6ca35b031 5d36be589 Author: Weiqun Zhang Date: Mon Feb 3 09:16:16 2020 -0800 Merge branch 'weiqun/mfiter' into development commit 6ca35b031a421b2960245d071be6a88f87003731 Merge: b84aecdfa 41a552fb8 Author: Weiqun Zhang Date: Mon Feb 3 09:13:53 2020 -0800 Merge branch 'master' into development commit 41a552fb8429f637c1396818057b359284813c5d Author: Weiqun Zhang Date: Mon Feb 3 09:12:48 2020 -0800 update CHANGES CHANGES commit b84aecdfa5106c7a9bbf805b2adbb7b376879a40 Merge: 71dd0ddd3 bd470e49d Author: WeiqunZhang Date: Sat Feb 1 21:57:05 2020 -0800 Merge pull request #683 from ax3l/fix-floatBuild Fix Build With Single Precision commit b292551bf8832d69e02bb388cff24051ab30dd33 Author: Michael Zingale Date: Sat Feb 1 20:55:18 2020 -0500 add to the C++ header Tools/F_scripts/write_probin.py commit 031696034ee3c220b7cbce8aab2c803f972c1bd5 Author: Michael Zingale Date: Sat Feb 1 20:13:32 2020 -0500 fix python Tools/F_scripts/write_probin.py commit 2785e150bc4b08f4e04d6808197547d65229df65 Author: Michael Zingale Date: Sat Feb 1 20:08:45 2020 -0500 revert parameter name: Tools/F_scripts/write_probin.py commit b50bfd4cb0481dd844d8327d7837955363da8cb6 Author: Michael Zingale Date: Sat Feb 1 19:50:41 2020 -0500 fix comment Tools/F_scripts/write_probin.py commit f09b3a83c926c263426f22ac58658e9ea2308fa6 Merge: bb0550b18 4ae6d4962 Author: Michael Zingale Date: Sat Feb 1 19:47:35 2020 -0500 Merge branch 'write_probin' of ssh://github.com/AMReX-Codes/AMReX into write_probin commit bb0550b188ee5c4ecd1c2e33d0a3376f7c50d0ab Author: Michael Zingale Date: Sat Feb 1 19:47:20 2020 -0500 get rid of the option of 2 different parameter lists Tools/F_scripts/write_probin.py commit 4ae6d496240149cbf2fddb7344271e91c9e454c9 Author: Michael Zingale Date: Sat Feb 1 19:46:49 2020 -0500 add the C++ code Tools/F_scripts/write_probin.py commit 9559307bfe4ef5fa7b27f15f479bd7f95363cfa3 Author: Michael Zingale Date: Sat Feb 1 19:09:26 2020 -0500 add the Fortran -> C++ headers Tools/F_scripts/write_probin.py commit 2566433edf5dda20e5a6c96d721b727bbc39ea59 Author: Michael Zingale Date: Sat Feb 1 18:43:29 2020 -0500 automagically write the functions that will send F90 to C++ Tools/F_scripts/write_probin.py commit abf1056ae8969b8faca9716be2edc5b409f8fc3e Author: Michael Zingale Date: Sat Feb 1 18:07:52 2020 -0500 some cleaning / linting Tools/F_scripts/write_probin.py commit bd470e49d5c565e18b49b9a954137de5aad3bb5b Author: Axel Huebl Date: Sat Feb 1 14:03:15 2020 -0800 Fix Build With Single Precision With float builds (mismatched types in `max()`). Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 0e71c1e5b0c4b590e06b16b8fc33ae528e1471a7 Author: Weiqun Zhang Date: Fri Jan 31 12:35:26 2020 -0800 add dpcpp.mak Tools/GNUMake/Make.defs Tools/GNUMake/comps/dpcpp.mak commit 2460a719e270413e2f2e126e933b4925568cc37a Merge: 71dd0ddd3 8e744786c Author: Weiqun Zhang Date: Fri Jan 31 11:07:20 2020 -0800 Merge branch 'weiqun/bl_no_fort' into dpcpp commit 0aadeb4234db0d4442c7291d6ad30cf4d70a0c4a Author: Weiqun Zhang Date: Fri Jan 31 10:20:53 2020 -0800 BoxArray: this is probably better than the previous fix because it is more backward compatible Src/Base/AMReX_BoxArray.cpp commit 71dd0ddd357896d7a0c54fab73152ea1ad942aaf Author: Weiqun Zhang Date: Fri Jan 31 09:22:52 2020 -0800 create a local device copy of BCRec vector before using it on GPU Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 00f4d824b4a0586c9e18f01d97aaae8651873d82 Author: Weiqun Zhang Date: Thu Jan 30 21:33:33 2020 -0800 FlashFluxRegister tutorial: communicate only for fine levels Tutorials/Amr/Advection_octree_F2/Source/evolve_mod.F90 commit cb5edf1c52d2b1f016495622c5ed238725911797 Author: Weiqun Zhang Date: Thu Jan 30 21:23:29 2020 -0800 fix a corner case in building BoxArray hash map Src/Base/AMReX_BoxArray.cpp commit 7cf662696f16333c829b2c1471ca6f16eb40d202 Author: Weiqun Zhang Date: Thu Jan 30 21:22:10 2020 -0800 FlashFluxRegister: bugs fixed Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 Tutorials/Amr/Advection_octree_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/evolve_mod.F90 commit 264c194db809e27fb7d541de9c80cd90fb2bac14 Author: Weiqun Zhang Date: Thu Jan 30 15:07:52 2020 -0800 Tutorial using FlashFluxRegister Tutorials/Amr/Advection_octree_F2/Exec/Make.Adv Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/inputs Tutorials/Amr/Advection_octree_F2/README Tutorials/Amr/Advection_octree_F2/Source/Make.package Tutorials/Amr/Advection_octree_F2/Source/Src_2d/Make.package Tutorials/Amr/Advection_octree_F2/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_octree_F2/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_octree_F2/Source/amr_data_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/averagedown_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/bc_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/evolve_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/fillpatch_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/fmain.F90 Tutorials/Amr/Advection_octree_F2/Source/initdata.F90 Tutorials/Amr/Advection_octree_F2/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/plotfile_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/tagging_mod.F90 commit f1479f8db81b6478ccb29b68c3b3aef144e0ab77 Merge: 724d88e4f 33aa5ccd1 Author: Andrew Myers Date: Thu Jan 30 14:51:56 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 724d88e4f92d489194ebe01c5614696e0d3ff613 Author: Andrew Myers Date: Thu Jan 30 14:51:45 2020 -0800 fix circular dependency Src/Particle/AMReX_ParticleLocator.H commit b85a8ed9961814f01d28bb788561ddaf22301655 Author: Weiqun Zhang Date: Thu Jan 30 14:23:56 2020 -0800 FlashFluxRegister: fix BoxList index type Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp commit faaf49ec62f8ab92c9dbe1535b93e3c0e580eb14 Author: Weiqun Zhang Date: Thu Jan 30 14:18:40 2020 -0800 octree iterator for a given level Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 70bd030767650008a6c3e7da810e2dd007e6d14b Author: Weiqun Zhang Date: Thu Jan 30 13:43:23 2020 -0800 pass boxarray and distributionmap when building amrex_flash_fluxregister Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 Src/F_Interfaces/AmrCore/Make.package Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Src/F_Interfaces/Octree/Make.package commit 2119a99191bdc07e6d17d78306c7c6aec2fbedf9 Author: Weiqun Zhang Date: Thu Jan 30 13:18:05 2020 -0800 amrex_flash_fluxregister Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.H Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/Octree/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/Octree/AMReX_flash_fluxregister_mod.F90 Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Src/F_Interfaces/Octree/Make.package commit 998c6d79e3a97ee8815a0dae7395bbd8beeb9b97 Author: cgilet Date: Thu Jan 30 12:28:14 2020 -0800 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit a81396306020655ff0e184e028169d1d96d46142 Merge: e71750713 33aa5ccd1 Author: cgilet Date: Thu Jan 30 12:20:43 2020 -0800 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit e71750713b97a39109e03d6dcbc7f051ebf2d516 Author: cgilet Date: Thu Jan 30 12:20:37 2020 -0800 Clean up. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit bb32431fc5ff26fa0220a6e615a2033a405e816e Author: Weiqun Zhang Date: Thu Jan 30 11:25:37 2020 -0800 FlashFluxRegister Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.H Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/Octree/Make.package commit 4093c8dbcd27706765eca2b70585fc7d462a4632 Merge: aa7dbf181 cd68ff50d Author: WeiqunZhang Date: Thu Jan 30 09:45:11 2020 -0800 Merge pull request #680 from maikel/weiqun/AmrInfo Make AmrMesh destructor default commit cd68ff50d580f42633e16fefac16ebf96db1d3b4 Author: Maikel Nadolski Date: Thu Jan 30 18:32:56 2020 +0100 Make AmrMesh destructor default Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit aa7dbf1810accf9b64e54b1fa36f5154d1a53cff Author: Weiqun Zhang Date: Thu Jan 30 09:01:20 2020 -0800 remove Initialize and Finalize from AmrCore and AmrMesh Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit aa8bf562aac19590eeb152471ef4c1ace5c89067 Author: Weiqun Zhang Date: Thu Jan 30 08:58:59 2020 -0800 AmrMesh: protect AmrInfo and friend operator<< Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 33aa5ccd17bce31a7429d7d8394f88e0dc491579 Author: Weiqun Zhang Date: Wed Jan 29 21:28:09 2020 -0800 fix periodic bug in tensor solver Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit f025a39445aac82027ef030155c1ba078e10c30e Merge: f2723677f 9322c69e3 Author: Andrew Myers Date: Wed Jan 29 20:01:21 2020 -0800 Merge pull request #679 from houjun/development Add support to restart from HDF5 particle checkpoint file commit 1e6af4d3a729e5d0db9367e9e575a333ac89d4f5 Author: cgilet Date: Wed Jan 29 18:50:48 2020 -0800 WIP debugging corner fill issue Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 05c8af14f1912e0a1bd1c6d64fb9858cc9fb5ee4 Merge: 2b303c3c1 f2723677f Author: cgilet Date: Wed Jan 29 14:59:05 2020 -0800 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 8432d8d2424e8d3f97a7a7f790c2d2cd8bb5de60 Merge: 50a5fbe68 3ffe33d38 Author: Michael Rowan Date: Wed Jan 29 13:05:46 2020 -0800 Merge branch 'mrowan/CUPTI_trace' of https://github.com/mrowan137/amrex into mrowan/CUPTI_trace commit 9322c69e3bd20d9f68e056324d99df8d8a86cd2c Merge: 054c1758c f2723677f Author: Houjun Tang Date: Wed Jan 29 13:04:38 2020 -0800 Merge remote-tracking branch 'upstream/development' into development commit 054c1758cbec88d8b93b6387b8053110f6eca90d Author: Houjun Tang Date: Wed Jan 29 13:02:20 2020 -0800 Add support to restart from checkpointed HDF5 particle file Src/Base/AMReX_PlotFileUtil.cpp Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H Tests/HDF5Benchmark/main.cpp commit 50a5fbe68f099cc23dc81ac62a3eb9d630e25c61 Merge: 3b97486ee f2723677f Author: Michael Rowan Date: Wed Jan 29 12:58:01 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace commit eaffc15cf63523bb51ce3061cddf46b25e085a72 Merge: cc71abae5 f2723677f Author: Weiqun Zhang Date: Wed Jan 29 09:29:29 2020 -0800 Merge branch 'development' into weiqun/AmrInfo commit cc71abae5b784e2fee7424d4ee65462bee6a3b5b Author: Weiqun Zhang Date: Wed Jan 29 09:28:55 2020 -0800 New constructor for AmrMesh and AmrCore that does not use ParmParse Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit f2723677f35398f863c3c2d245c1312a892c3d67 Author: cgilet Date: Wed Jan 29 11:12:44 2020 -0500 Some clean up. Src/EB/AMReX_EB_utils.cpp commit b11160ac81dea11c06bc64dd5717b569f801a0a9 Author: cgilet Date: Wed Jan 29 10:55:00 2020 -0500 Some clean up. Src/EB/AMReX_EB_utils.cpp commit a09659e435bd23f2ea052b4e1dbbc0c3772be4b6 Merge: 3fbf12606 af7c69380 Author: WeiqunZhang Date: Wed Jan 29 07:46:15 2020 -0800 Merge pull request #678 from AMReX-Codes/cgilet_dev Fix apply_eb_redistrubution() to work in 3D. commit af7c69380d826c13afa53db80a8358b26ec51e9d Author: cgilet Date: Wed Jan 29 09:56:01 2020 -0500 Fix apply_eb_redistrubution() to work in 3D. Src/EB/AMReX_EB_utils.cpp commit 3fbf126063c19cfc4500aaac7a1e006efa80bd2b Author: Emmanuel Motheau Date: Tue Jan 28 16:05:58 2020 -0800 Some changes in eb_redistribution to avoid evaluating the redistribution near physical boundaries with data outside of the domain Src/EB/AMReX_EB_utils.cpp commit 459c725e12d10b071335100f6ea77edb6cd4d18a Author: Jean M. Sexton Date: Tue Jan 28 18:45:40 2020 -0500 Update summit MPS command -- is now a bsub command Tutorials/GPU/run.summit commit 8e744786c36f13d5e7719072768a991ce38c995a Merge: 563e61899 2e871a1b9 Author: Weiqun Zhang Date: Tue Jan 28 15:30:48 2020 -0800 Merge branch 'development' into weiqun/bl_no_fort commit 2e871a1b9f5e551d8046d9cd3a70d1c57d52f692 Merge: e4bb42235 41d775e65 Author: Weiqun Zhang Date: Tue Jan 28 13:25:47 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 563e61899cf8b9535baf86380480bf45274915c2 Author: Weiqun Zhang Date: Tue Jan 28 12:59:27 2020 -0800 no need to link to libgfortran Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/llvm.mak commit 41d775e6569dc258b29104d1308b8e7f5050c24c Merge: 4f2a7d1f9 14b8c797b Author: Andrew Myers Date: Tue Jan 28 12:52:52 2020 -0800 Merge pull request #676 from AMReX-Codes/jmsexton/particle Added check for RedistributeCPU edge case commit e4bb42235ed116c7e4600b13a67d65778b6e0fbb Merge: d44dfdbff 4f2a7d1f9 Author: Weiqun Zhang Date: Tue Jan 28 11:55:07 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9b1e83cdc880898649088c05fd7243be9cabf8ea Author: Weiqun Zhang Date: Tue Jan 28 11:45:33 2020 -0800 update configure for BL_NO_FORT Tools/libamrex/configure.py commit 4a22ce45f46ed3f02d19652325bd1774619edd3b Author: Weiqun Zhang Date: Tue Jan 28 11:22:10 2020 -0800 BL_NO_FORT: EB Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp Src/EB/Make.package commit 96d83f3f3eacbe6a6fd8c580c8a916b97ed51b8b Author: Weiqun Zhang Date: Tue Jan 28 10:40:52 2020 -0800 BL_NO_FORT in Amr Src/Amr/Make.package Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv Tutorials/GPU/CNS/Exec/Make.CNS commit edb32eb669d4101fb3a0b947ce342aae1776e5e4 Author: Weiqun Zhang Date: Tue Jan 28 10:21:51 2020 -0800 BL_NO_FORT in AmrCore Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile commit f544c44da602766422066a2076f3703a595b0ae6 Author: Weiqun Zhang Date: Tue Jan 28 09:49:39 2020 -0800 BL_NO_FORT in Particle Src/Particle/Make.package commit 7a2f3d33ad971f321def54d3cdd518d77c892013 Author: Weiqun Zhang Date: Tue Jan 28 09:41:35 2020 -0800 BL_NO_FORT in MLMG Src/Boundary/Make.package Src/Boundary/OpenSource.txt Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/Make.package Tests/NoFort/GNUmakefile Tools/GNUMake/Make.defs Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile commit 0a425059e053666f9e29ead7f2169a1db0bb5b52 Author: Weiqun Zhang Date: Mon Jan 27 20:25:18 2020 -0800 port fab_filcc to C++ Src/Base/AMReX_Box.H Src/Base/AMReX_FilCC_C.H Src/Base/AMReX_FilCC_C.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 22984d214f378fb3aa460ab1e72592f8ce77250d Author: Weiqun Zhang Date: Mon Jan 27 20:01:15 2020 -0800 add more fortran free files to BL_NO_FORT build Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/Make.package commit 5d36be5893712a475960e97ed43478839d18140e Author: Weiqun Zhang Date: Mon Jan 27 09:10:39 2020 -0800 make MFIter(BoxArray const&, DistributionMapping,...) omp safe Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 2b303c3c1b6f42913798dd40fd09d497ea43be6f Merge: 5517a2e2b 4f2a7d1f9 Author: cgilet Date: Mon Jan 27 07:31:05 2020 -0800 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 334c134ae4a4d2be03313abe36dca92ec119395b Author: Axel Huebl Date: Fri Jan 24 17:19:01 2020 -0800 VisMF: Remove Shadow Warning Change a private static interface to use the only-usage, same-class static control variable it passes to avoid variable name shadowing. Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 4f2a7d1f94cfd3bfcac61322fbccd0ee67fdfb80 Merge: 7a0f6f1f3 4babed47c Author: Andrew Myers Date: Fri Jan 24 16:41:18 2020 -0800 Merge pull request #672 from ax3l/fix-shadowTilingPC ParticleContainer: Fix Warnings commit 7a0f6f1f3426f9c71485af7acb9808791626a1d5 Merge: efabff7b6 c701bd89b Author: Andrew Myers Date: Fri Jan 24 16:42:21 2020 -0800 Merge branch 'development' into atmyers/sparse_bins commit c701bd89bfd1865d2e43301acbc48d4941f5567f Author: Andrew Myers Date: Fri Jan 24 16:26:21 2020 -0800 add missing include Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 87461f3db39bb769c9590d980aa63d37aa596bf9 Author: Kevin Gott Date: Fri Jan 24 19:25:18 2020 -0500 New version of setBndry. Src/Base/AMReX_FabArray.H commit 4babed47cefed437aeed9fe88b4dc0b9c2901ed1 Author: Axel Huebl Date: Fri Jan 24 15:38:06 2020 -0800 ParticleContainer: Fix Warnings Remove shadowed variable and unused local variable warnings. Src/Particle/AMReX_ParticleContainerI.H commit efabff7b61089f8a94512f69ad9dae9c96747e32 Author: Andrew Myers Date: Fri Jan 24 15:19:55 2020 -0800 reset default to the 'dense' binning strategy for now Src/Particle/AMReX_Particles.H commit e95ba6bdb50a64cf762523557a577a1a7c5fb6e0 Merge: 5d9ad8845 ce0fc37e3 Author: Andrew Myers Date: Fri Jan 24 15:19:07 2020 -0800 Merge branch 'development' into atmyers/sparse_bins commit 132672b0c12684d351997209d3814fff873f25c9 Author: Michele Rosso Date: Fri Jan 24 15:02:56 2020 -0800 NodalProjector: some minor cleaning/tweaks Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 823126a2752ebc20536dcb9bd4a21f60ba97f936 Author: Michele Rosso Date: Fri Jan 24 15:00:48 2020 -0800 NodalProjector: print norm0(RHS) after projection Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 26ca00a613f2538dbbc4fe234b35eb10730ef9f7 Author: Michele Rosso Date: Fri Jan 24 14:57:55 2020 -0800 NodalProjector: add code to handle fine->coarse averaging of velocity and fluxes Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 5d9ad88452276763ef3a42ba3e7ff2bd60c0ad1a Author: Andrew Myers Date: Fri Jan 24 12:03:41 2020 -0800 typo Src/Particle/AMReX_SparseBins.H commit 39cb0f1122ec981ced9bdc3ac42e3cea96ffb993 Author: Andrew Myers Date: Fri Jan 24 12:01:58 2020 -0800 getIndex needs to handle the corner case where there is only 1 bin Src/Particle/AMReX_SparseBins.H commit d44dfdbff17e14f81800e3a3acb7fa8d8f2af10f Author: Weiqun Zhang Date: Fri Jan 24 08:49:42 2020 -0800 simply using amrex_long = int64_t Src/Base/AMReX_INT.H commit ce0fc37e3541473194af571f18bb20bd25b2267a Author: Weiqun Zhang Date: Fri Jan 24 08:42:28 2020 -0800 long -> unsigned int Src/AmrCore/AMReX_AmrMesh.H commit 273e1feff1feee7f7bac32f2a9c3776fe4f6c328 Author: Weiqun Zhang Date: Fri Jan 24 08:22:55 2020 -0800 fix compilation Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 60d1c72b71fe33e9dd94efea5806f431d7d7bad1 Author: Weiqun Zhang Date: Fri Jan 24 05:59:05 2020 -0800 LinOp: use m_factory because a_factory might be empty Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 6085a6f2c0e92fcfb3080fc046ecebcfd635f385 Author: Weiqun Zhang Date: Thu Jan 23 18:59:21 2020 -0800 more robust way of detecting if SetDistributionMapping has been called Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit a5ed6ec58ff3d7d90fc8b941b612c4f150c900d6 Author: Weiqun Zhang Date: Thu Jan 23 18:37:23 2020 -0800 fix my recent mistake Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.cpp commit efc2de046df58d0e1ba25289fe18ee585b7c8f6d Author: Weiqun Zhang Date: Thu Jan 23 16:47:36 2020 -0800 Nodal sovler sigma: use EB_average_down Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit fa7d503d9d3aba68fbe297623d1fd6636dbaaed4 Author: Andrew Myers Date: Thu Jan 23 15:05:13 2020 -0800 forgot to set m_items Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_SparseBins.H commit 3a331a9595c50a3fe791f6e745290f7bac2fb519 Author: Andrew Myers Date: Thu Jan 23 14:48:29 2020 -0800 fix potential overflow Src/Particle/AMReX_BinIterator.H commit 156377ef58dd9d25fa72fb73bf66957cb9140df0 Author: Andrew Myers Date: Thu Jan 23 14:46:27 2020 -0800 fix CPU compile Src/Particle/AMReX_BinIterator.H Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_SparseBins.H commit baa486268d8c2b49f3d2bd1d1116e466d9f0cc2e Author: Andrew Myers Date: Thu Jan 23 14:24:06 2020 -0800 attempting to use SparseBins in the particle locator Src/Particle/AMReX_BinIterator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_SparseBins.H commit 488cd61291ce4552f9c01029ae8f27c48a99bb8c Author: Andrew Myers Date: Thu Jan 23 14:10:19 2020 -0800 a convenient typedef Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_SparseBins.H commit 5ec2f016ba91f9190a7ff0ccf06606637c7b5a8d Author: Andrew Myers Date: Thu Jan 23 14:06:36 2020 -0800 implement sparse bins search Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_SparseBins.H commit 5e8bc61503e7372e6e396f21ba9c1dc45d463098 Author: Andrew Myers Date: Thu Jan 23 13:07:43 2020 -0800 Within a bin, DenseBins and SparseBins can use the same iterator type Src/Particle/AMReX_BinIterator.H Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_SparseBins.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 2401ce8f978fb0fa01672be7dde5b320a25a8fea Author: Andrew Myers Date: Thu Jan 23 13:00:27 2020 -0800 adding SparseBinIteratorFactory Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_SparseBins.H commit db6f8489cae17150c4b648a838aed26c9f46343d Author: Andrew Myers Date: Thu Jan 23 12:52:18 2020 -0800 forgot to check in SparseBins Src/Particle/AMReX_SparseBins.H commit 23577ec7910a869c7963a672a7e78319ba7fc509 Author: Andrew Myers Date: Thu Jan 23 12:52:00 2020 -0800 some useful typedefs Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H commit 6998a7d95602e80834156ef107313699cf562773 Author: Weiqun Zhang Date: Thu Jan 23 11:16:30 2020 -0800 AmrCore: allow MakeNewLevelFromScratch to ignore DistribitionMapping provided Src/AmrCore/AMReX_AmrMesh.cpp commit 3dd3cf18c9bc70857fa8f58f3153dac07d6478c2 Author: Weiqun Zhang Date: Thu Jan 23 10:13:22 2020 -0800 AmrCore: allow users to ignore the DistributionMapping provided Src/AmrCore/AMReX_AmrCore.cpp commit dfb28ffe035a8fd283629484a662369a0058b19d Author: Weiqun Zhang Date: Wed Jan 22 20:10:44 2020 -0800 FillPatchTwoLevels: option to specify number of ghost cells Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 961c3479ea5ae1cefd8fd8f26d48a58f6e6daed2 Author: Andrew Myers Date: Wed Jan 22 16:15:44 2020 -0800 refactor dense bins to make it easier to incorporate sparse Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Tests/Particles/SparseBins/main.cpp commit 2142c1b2bd78c037f494137451b9c24ab7838a7e Author: Andrew Myers Date: Wed Jan 22 14:21:11 2020 -0800 code to compute a sparse binning structure Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/CMakeLists.txt Src/Particle/Make.package Tests/Particles/SparseBins/GNUmakefile Tests/Particles/SparseBins/Make.package Tests/Particles/SparseBins/inputs Tests/Particles/SparseBins/main.cpp commit cf1f2083ed8a6f1ae2e973898753c0a21026e77e Author: Weiqun Zhang Date: Wed Jan 22 09:54:37 2020 -0800 no need to use D_TERM Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit a6e519d0c712880ade4d6a2714f80e254d85264b Author: Weiqun Zhang Date: Wed Jan 22 09:49:59 2020 -0800 D_DECL -> AMREX_D_DECL Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 57e381f6094f49e7607daace4c45f10ad5b496eb Author: Weiqun Zhang Date: Wed Jan 22 09:10:02 2020 -0800 fix warning Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit a74381db392566d4e8f855ce121e8fc365e1be73 Author: Emmanuel Motheau Date: Wed Jan 22 09:02:50 2020 -0800 minor cosmetic cleaning Src/EB/AMReX_EBMultiFabUtil.cpp commit 5e332397d6a53a84938eb227c23244dfdd7bdc83 Merge: 79a6365f6 8f0ab38fd Author: emotheau Date: Wed Jan 22 09:01:15 2020 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit 8f0ab38fd70497ba5ef545a91f6be64e9d6ee282 Author: Weiqun Zhang Date: Tue Jan 21 20:43:39 2020 -0800 MacProjector: no ghost cells needed if mac velocity is already on centroid Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 3ffe33d382d2f63df73c7a6837633a652efc200e Merge: 3897a3f53 c55b4f48d Author: Michael Rowan Date: Tue Jan 21 17:29:54 2020 -0500 Get most recent. Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mrowan/CUPTI_trace commit 79a6365f612ac78a72e3ed4ec9ef0bf4936d46b7 Author: emotheau Date: Tue Jan 21 12:47:47 2020 -0800 Revert "fix to fill the ghost cells" This reverts commit 37c60739ede6399f9e523eae722d4c78a610af61. Src/EB/AMReX_EBMultiFabUtil.cpp commit 654fc82ce5d54bd80bde2e2cd7ad9d4fce0b74db Merge: 37c60739e c55b4f48d Author: emotheau Date: Tue Jan 21 12:47:26 2020 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit c55b4f48d0219d96b5b9d09bf248cccf93165408 Author: Jean M. Sexton Date: Tue Jan 21 12:39:33 2020 -0800 Fix run script comment to use absolute path Tutorials/GPU/run.corigpu commit ae5f600b1268a4d532ff7f9dcbaa15b89b5607d8 Merge: e800f66d3 4f86c5a59 Author: Andrew Myers Date: Tue Jan 21 12:23:19 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e800f66d32f264e6e6831d8af4c9da53bf8d64a3 Author: Andrew Myers Date: Tue Jan 21 12:23:10 2020 -0800 make USE_CUDA=FALSE on this test by default Tests/GPU/Vector/GNUmakefile commit 4f86c5a5902e6878695526b2e0d7c102e32f6594 Merge: 2e62c191c fb14dd295 Author: Andrew Myers Date: Tue Jan 21 14:24:21 2020 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2e62c191c3be1ec519d8768d30602047008f655f Author: Andrew Myers Date: Tue Jan 21 14:23:46 2020 -0500 this IO proc check is redundant and also wrong Tests/Particles/Redistribute/main.cpp commit fb14dd29591640f71e415485336a37e29881f5b5 Author: Andrew Myers Date: Tue Jan 21 11:08:52 2020 -0800 tweak test Tests/GPU/Vector/main.cpp commit fc3f1f0d273ec40023f77ca0fa0b59ce345573d5 Merge: 46c137a17 87dcbc4d7 Author: Andrew Myers Date: Tue Jan 21 11:06:50 2020 -0800 Merge branch 'device_vector_refactor' into development commit 87dcbc4d76dd5186eaf13286232967cd3cd17617 Author: Andrew Myers Date: Tue Jan 21 10:58:19 2020 -0800 adding tests of the various host / device vectors Tests/GPU/Vector/GNUmakefile Tests/GPU/Vector/Make.package Tests/GPU/Vector/inputs Tests/GPU/Vector/main.cpp commit 3d90bb9ca4c1b5be8e0ccc1020cbc2404f7b4169 Author: Andrew Myers Date: Tue Jan 21 10:48:54 2020 -0800 add missing const_cast Src/Base/AMReX_PODVector.H commit 6387d30064fed30698faf932db0271efc3f62cbf Author: Andrew Myers Date: Fri Jan 17 20:01:06 2020 -0800 these function signatures need to be consistent Src/Base/AMReX_PODVector.H commit df4763e2cc84c58ccc3842361056e2c5952327fc Author: Andrew Myers Date: Fri Jan 17 17:18:51 2020 -0800 do memmove Src/Base/AMReX_PODVector.H commit 965c98649e30dbeac3cbeea85fca4f6de9da249b Author: Andrew Myers Date: Fri Jan 17 16:32:32 2020 -0800 add missing streamSync here Src/Base/AMReX_PODVector.H commit 1a012c621eda3af616e6fe59ba61919522ce8767 Author: Andrew Myers Date: Fri Jan 17 16:13:07 2020 -0800 fixing a couple of bugs Src/Base/AMReX_PODVector.H commit 6e9ac4d9fd57c0238b38f21f58f837da875d40c5 Author: Andrew Myers Date: Fri Jan 17 15:17:20 2020 -0800 handling initializer list Src/Base/AMReX_PODVector.H Tests/Particles/Redistribute/main.cpp commit b83894deaf462a70fc974700dd702201771043dd Author: Andrew Myers Date: Fri Jan 17 14:57:55 2020 -0800 also do memcpy Src/Base/AMReX_PODVector.H commit 46c137a171c00576a5e17265ec3d2310930c98c6 Author: Weiqun Zhang Date: Fri Jan 17 14:52:51 2020 -0800 ParmParse: private -> protected Src/Base/AMReX_ParmParse.H commit 0a6c0bcbe5d051b978209cb4f2e9bcc07774f0d8 Author: Andrew Myers Date: Fri Jan 17 13:54:22 2020 -0800 adding uninitializedFillNImpl Src/Base/AMReX_GpuAllocators.H Src/Base/AMReX_PODVector.H commit 78932f81c1450073a0aa31fccfdf3cba659268eb Author: Weiqun Zhang Date: Fri Jan 17 12:29:27 2020 -0800 fix typo Src/Base/AMReX_GpuLaunchFunctsG.H commit e5511d3e4b71049580b3b6b432009e17f4219472 Author: Andrew Myers Date: Fri Jan 17 12:14:16 2020 -0800 some indentation fixes Src/Base/AMReX_PODVector.H commit 6904104e24423b50b56e92c436e175ec01b78957 Merge: 2a971c636 57e644e66 Author: Weiqun Zhang Date: Thu Jan 16 18:25:51 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2a971c636db67a873c9ea574f1f9a43d95f5b5b6 Author: Weiqun Zhang Date: Thu Jan 16 18:25:42 2020 -0800 fix constexpr Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 57e644e6627e5ef3dba45b3e3eb6d53cfb3f7372 Author: Jean M. Sexton Date: Thu Jan 16 15:38:56 2020 -0800 Updating job scripts Tutorials/GPU/run.corigpu Tutorials/GPU/run.summit commit dcade0429a5a4b743ef6bbdc037cd9483ae7fb65 Author: Kevin Gott Date: Thu Jan 16 12:33:27 2020 -0800 Forgot about those pesky non-GPU cases. Src/Base/AMReX_Random.cpp commit 71fa5bddb950229db05e87cd56bfed9a566a691e Merge: b1e25fd24 4f2b90adb Author: Andrew Myers Date: Thu Jan 16 12:30:39 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b1e25fd24accf3a43e681c6d5a79f6f4b3f971ca Author: Andrew Myers Date: Thu Jan 16 12:30:29 2020 -0800 docstrings for amrex::Partition and amrex::StablePartition Src/Base/AMReX_Partition.H commit 7eb05de1d60d3cd3a358f16f9c9c22262a33c7ba Author: Andrew Myers Date: Thu Jan 16 12:16:00 2020 -0800 remove call to deprecated function Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 4a1a72cd46796f181286ed7f67eba3fd37e6ccf3 Author: Andrew Myers Date: Thu Jan 16 12:15:50 2020 -0800 change default compiler for Cuda version to gcc Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/GNUmakefile commit 2b2d09f88b44a6fb1c5fa3da415e80a3b53bc43c Author: Andrew Myers Date: Thu Jan 16 12:15:22 2020 -0800 docstrings for GpuComplex Src/Base/AMReX_GpuComplex.H commit 4f2b90adbf5fd9cf00875c91cc7dd0c6f61f2fde Merge: 51110e91e dc6afb510 Author: Weiqun Zhang Date: Thu Jan 16 09:48:19 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 51110e91e914c477ac17437b21f8a8f745392af1 Author: Weiqun Zhang Date: Thu Jan 16 09:48:13 2020 -0800 fix launch region test Tests/GPU/CudaGraphs/GraphBoundary/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H commit dc6afb510247358d28fd5c580e67683385a8d151 Merge: 1e3fac6a4 bf430fdce Author: Andrew Myers Date: Thu Jan 16 09:47:42 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bf430fdce902f679eebec6d0995c8450130087bc Merge: 8a6dc6412 567e83f98 Author: WeiqunZhang Date: Thu Jan 16 08:46:19 2020 -0800 Merge pull request #661 from rporcu/development Added 'TheZeroVector', 'TheUnitVector' and 'floor' functions to class RealVect commit 8a6dc6412030a5cf25906725a0b52af409f4e66d Author: Weiqun Zhang Date: Wed Jan 15 21:20:53 2020 -0800 add explicit Src/Base/AMReX_Box.H commit 5517a2e2b87092a1955d0324e3c9eb254ad8c150 Author: cgilet Date: Wed Jan 15 18:43:10 2020 -0800 Fix const qualifier so compiles with CUDA Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 5ab66d52057430eb249eafe44097ea8cdf826ef6 Author: cgilet Date: Wed Jan 15 18:42:03 2020 -0800 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 37c60739ede6399f9e523eae722d4c78a610af61 Author: Emmanuel Motheau Date: Wed Jan 15 17:53:34 2020 -0800 fix to fill the ghost cells Src/EB/AMReX_EBMultiFabUtil.cpp commit 6215e492ac2bac2bea8aca3d3a2946ea2fd0b7f0 Author: cgilet Date: Wed Jan 15 17:53:44 2020 -0500 In MLTensorOp::compFlux(), surroundingnodes -> nodaltilebox Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 121e683978466d04be16583ca9af9b470a4c311b Author: cgilet Date: Wed Jan 15 17:52:02 2020 -0500 Create MLEBTensorOp::compCrossTerms() for use in apply() and compFlux(). This fixes a bug in compFlux. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 3304459a97075257626abc386e5a6ccd26cc4225 Author: kngott Date: Wed Jan 15 12:32:07 2020 -0800 Fix the portable Random. Src/Base/AMReX_BlockMutex.cpp Src/Base/AMReX_Random.cpp commit 567e83f98be91dc5c4f12434a9e102adaf1e5316 Author: Roberto Porcu Date: Wed Jan 15 11:51:06 2020 -0800 Add constructor from Real pointer for class RealVect Src/Base/AMReX_RealVect.H commit 4d5eaf6a1e6bbc7354ebc7e53fbc32d69368bf91 Merge: ebd002093 d10f51425 Author: cgilet Date: Wed Jan 15 09:28:57 2020 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit d29da0478da3ecaa069cb9ffee347a95c90e427e Author: Roberto Porcu Date: Tue Jan 14 18:12:56 2020 -0800 Added functions 'ceil' and 'round' to class RealVect Src/Base/AMReX_RealVect.H commit 0f591d744ddf85a3a81dc5a5b9217f3f875a5537 Merge: 30d0ce285 d10f51425 Author: Roberto Porcu Date: Tue Jan 14 17:59:53 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 507a087c6649fc92c2575323ba71e72cacd7d621 Merge: 610b468c1 d10f51425 Author: emotheau Date: Tue Jan 14 10:33:48 2020 -0800 Merge remote-tracking branch 'origin/mr/projections' into Emmanuel/new_EB_interpolation_routines commit 1e3fac6a4bd980c61dffa797e55fbb91685791f5 Merge: 4056d41fa d10f51425 Author: Andrew Myers Date: Mon Jan 13 17:06:54 2020 -0800 Merge branch 'development' into atmyers/no_thrust commit 4056d41fa28ae62e80ccf1f32bd0fde67f5a8442 Author: Andrew Myers Date: Mon Jan 13 16:55:29 2020 -0800 fix typo Src/Base/AMReX_Partition.H commit d10f514255a535ed149c5c614e647753b9a8f7fe Author: Michele Rosso Date: Mon Jan 13 15:41:25 2020 -0800 CMake: add all tutorials in Tutorials/LinearSolvers Tutorials/LinearSolvers/ABecLaplacian_F/CMakeLists.txt Tutorials/LinearSolvers/MAC_Projection_EB/CMakeLists.txt Tutorials/LinearSolvers/MultiComponent/CMakeLists.txt Tutorials/LinearSolvers/NodalPoisson/CMakeLists.txt Tutorials/LinearSolvers/Nodal_Projection_EB/CMakeLists.txt Tutorials/LinearSolvers/NodeTensorLap/CMakeLists.txt commit 30d0ce285484bcea9697952dff2a0b5bc0a440e8 Author: Roberto Porcu Date: Mon Jan 13 14:32:39 2020 -0800 Fix a bug in 'floor' function of class RealVect Src/Base/AMReX_RealVect.H commit dd9ac8e367172f1e439aadfa625f44230bb0604e Author: Roberto Porcu Date: Mon Jan 13 14:05:37 2020 -0800 Added 'TheZeroVector', 'TheUnitVector' and 'floor' functions to class RealVect Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 49fcc4d19617de43a4a617572ab8f5766ff91a33 Merge: 497387e09 593d2fa8a Author: Michele Rosso Date: Mon Jan 13 13:57:31 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit 593d2fa8aae135e02ef4141824c30d5787b45d60 Merge: 069fbc974 14efdb227 Author: WeiqunZhang Date: Mon Jan 13 11:18:37 2020 -0800 Merge pull request #660 from rporcu/development Fix a bug which can give errors when compiling commit 14efdb2275a2dd0a0ca8d4efafe9fda48a7d8a2d Author: Roberto Porcu Date: Mon Jan 13 10:56:29 2020 -0800 Fix a bug which can give errors when compiling Src/Particle/AMReX_Particle.H commit 019047e19e2c7d7093f11aa901c4325db5b567f3 Merge: 55d15b766 069fbc974 Author: Andrew Myers Date: Mon Jan 13 10:14:46 2020 -0800 Merge branch 'development' into atmyers/no_thrust commit 610b468c1fc6329836d62b5f1c9eeaa900bb2fef Merge: ac47ee1ab 069fbc974 Author: emotheau Date: Sun Jan 12 09:46:16 2020 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit 497387e098d840871d2b622e67e71ff9ac6daa22 Author: Michele Rosso Date: Sat Jan 11 16:54:22 2020 -0800 NodalProjector: some bug fixes and some improvements Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 84e09da9110e06bbca1b06eaeb7905cb9b660b2f Merge: 2c61161e0 069fbc974 Author: Michele Rosso Date: Sat Jan 11 16:04:19 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit 069fbc9749f99d7c0feacd664215977443d67ef7 Author: Ann Almgren Date: Sat Jan 11 14:11:33 2020 -0800 Rename amrex_compute ... rather than just compute... Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H commit 9528e5c59698dd2b8ccc3b688938cc37a18d2ae3 Author: Ann Almgren Date: Sat Jan 11 14:10:28 2020 -0800 Add routines to take convective differences -- analogous to the amrex_compute_divergence routine but doing convective not conservative differencing Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H commit 2c61161e008804fc9eb41f54e5615795e7b21b8f Merge: fdaa790d4 0bfb8bdcf Author: Michele Rosso Date: Fri Jan 10 14:37:28 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit 914a146a09ff67fc919b54bc4d19a85f74ff411d Author: kngott Date: Fri Jan 10 14:13:33 2020 -0800 Small changes for compatibility when running CUDA. Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Random.cpp commit ef64631b19a8cc0f401380743f62e930a8c65ec5 Author: Kevin Gott Date: Fri Jan 10 14:04:48 2020 -0800 Avoid std::uninitialized_fill for hip. Tests/GPU/Locking/main.cpp commit 0bfb8bdcf4dfd4a9a42ad121b657e0cbac08bed5 Merge: 76866b44c 191d4db72 Author: WeiqunZhang Date: Fri Jan 10 13:07:23 2020 -0800 Merge pull request #659 from rporcu/development Prevent rvalue component assignment for RealVect class commit 55d15b76668d804f5d1255d786c502c845faea84 Author: Andrew Myers Date: Fri Jan 10 13:06:00 2020 -0800 fix 'divide real by complex' operator Src/Base/AMReX_GpuComplex.H commit ead7bb6672947df56a18cd795562a772badd7779 Author: Andrew Myers Date: Fri Jan 10 12:55:58 2020 -0800 implement << operator for GpuComplex Src/Base/AMReX_GpuComplex.H commit 537c9778428276d354510e096b9f3aa4cb351071 Merge: 138d05211 76866b44c Author: Andrew Myers Date: Fri Jan 10 12:28:51 2020 -0800 Merge branch 'development' into atmyers/no_thrust commit 203ec5f6b0b859b94f2ddaa6513784daf096e112 Author: Kevin Gott Date: Thu Jan 9 21:13:16 2020 -0800 Add mutex to manual MemcpyToSymbol. Src/Base/AMReX_Random.cpp commit 191d4db72e4fe64235e44b1e1a3b30b885ca2fd9 Author: Roberto Porcu Date: Thu Jan 9 16:09:30 2020 -0800 Prevent rvalue component assignment for RealVect class Src/Base/AMReX_RealVect.H commit fdaa790d4485f2721e5cb6a418edb28381839a35 Author: Michele Rosso Date: Thu Jan 9 15:44:57 2020 -0800 NodalProjector: re-write code and add support for multilevel projection Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 76866b44c3f5b919cb36207d2d102e5d7392f58c Merge: bfb385865 6edea258c Author: Andrew Myers Date: Thu Jan 9 15:08:29 2020 -0800 Merge pull request #658 from rporcu/development Fix compilation bug for latest functions added in AMReX_Particle.H commit 6edea258c90c5db1f38df9817c7ba36485e3ea72 Author: Roberto Porcu Date: Thu Jan 9 14:56:57 2020 -0800 Fixed compilation bug for latest functions added i AMReX_Particle.H when AMREX_SPACEDIM == 1 Src/Particle/AMReX_Particle.H commit 988e4eaa582380523cd762992638e1a61bcd0830 Merge: e8836979b bfb385865 Author: Roberto Porcu Date: Thu Jan 9 14:55:38 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 138d0521156d01cc881dde48dc4f5570c82ff98b Merge: 90b43f7ee 0151136fd Author: Andrew Myers Date: Thu Jan 9 13:48:03 2020 -0800 Merge branch 'development' into atmyers/no_thrust commit bfb385865516e2f52bc476ae06e1619d5653d558 Merge: a024d1919 0151136fd Author: Weiqun Zhang Date: Thu Jan 9 13:31:11 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a024d191997f1055b1e7d69864cdc6db9dcdd3e9 Author: Weiqun Zhang Date: Thu Jan 9 13:31:07 2020 -0800 MLMG: functions to set constant coefficients Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit dff8c37db64ea47f2bbd8fd5d1bbaaac802cb2d3 Merge: 57a21b5d0 0151136fd Author: Michele Rosso Date: Thu Jan 9 10:35:19 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit 0151136fd0dc6ce3146e1b3ba62b5f4ce193a28d Author: Ann Almgren Date: Thu Jan 9 06:53:24 2020 -0800 fix some spelling typos Docs/sphinx_documentation/source/LinearSolvers.rst commit d99d890150f8db80c86584357637d8afc41b05be Author: Ann Almgren Date: Thu Jan 9 06:34:03 2020 -0800 More spelling corrections (thanks ispell!) Docs/sphinx_documentation/source/GPU.rst commit 11a9e63392c96b5a3c43a050016c38dcab9c8516 Author: Ann Almgren Date: Thu Jan 9 06:30:00 2020 -0800 Fix typo Docs/sphinx_documentation/source/GPU.rst commit e8836979bc9ef7e02706b08668c8a008ec71bb0a Merge: 8602c6fda f5e133129 Author: Roberto Porcu Date: Wed Jan 8 16:29:59 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8602c6fda9735a84ad8a64924367578fac05c4ab Author: Roberto Porcu Date: Wed Jan 8 15:18:51 2020 -0800 Revert "Add functions norm and norm_sqr to class RealVect" This reverts commit 5e7c9996426eaf77cbb5b65aeb85c53caae71730. Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit e4ca3fd4a8a7cc500d98cab48db6079552ca99bb Author: Kevin Gott Date: Wed Jan 8 15:00:52 2020 -0800 Add a Fix comment. Src/Base/AMReX_RealVect.H commit a26d0821064911d85f8d1eabcdf0bb9a3aafaa7d Author: Carter Dodd Date: Wed Jan 8 17:00:07 2020 -0600 Change cell bilinear to work with odd refinement ratio Src/AmrCore/AMReX_INTERP_3D.F90 commit 3d8da37480b628c2bd3d73cd655e235778774837 Author: Kevin Gott Date: Wed Jan 8 14:27:23 2020 -0800 Adjusting for HIP. Currently blows up at PODVector.H, line 82 due to std::uninitialized_fill_n. Tests/GPU/Locking/main.cpp commit 5e7c9996426eaf77cbb5b65aeb85c53caae71730 Author: Roberto Porcu Date: Wed Jan 8 14:09:12 2020 -0800 Add functions norm and norm_sqr to class RealVect Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit f5e13312968c279bd4f819dfdf608aa45b7be55b Merge: bbb294ace c523155db Author: Andrew Myers Date: Wed Jan 8 13:38:42 2020 -0800 Merge pull request #654 from rporcu/development Added functionality of extract a RealVect from Particle class commit 846356ef4a3443777c1771d57ba2f16bb00cfe5e Author: Kevin Gott Date: Wed Jan 8 13:31:35 2020 -0800 Make sure HIP-nvcc is off for now. Tools/GNUMake/Make.defs commit c523155dbf245efd09ad4cbf176b9ddeb7c6043f Author: Roberto Porcu Date: Wed Jan 8 13:24:37 2020 -0800 Added functionality of extract a RealVect from Particle class Src/Particle/AMReX_Particle.H commit 9f3cd5a370b49e2267ef1693d65f1e0055783359 Author: Kevin Gott Date: Wed Jan 8 13:23:05 2020 -0800 std::sqrt and HIP don't mix. Src/Base/AMReX_RealVect.H commit 9193e6f5529d942b9f95765da0d627ff0ca7a5ac Author: Kevin Gott Date: Wed Jan 8 13:22:47 2020 -0800 Adjust for state of HIP Random. Tutorials/GPU/ParallelReduce/main.cpp commit 842250ce6db17561d29f6d4b231edcde3e81e7e3 Merge: 76c9647d6 bbb294ace Author: Kevin Gott Date: Wed Jan 8 12:50:59 2020 -0800 Merge branch 'development' into kngott/hip commit ebd0020931f922f60d3eb6e9488cc9564c480e61 Merge: 8edd0b40a bbb294ace Author: cgilet Date: Wed Jan 8 11:23:40 2020 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit bbb294ace62ad1ca92ddc9da4e94188cf6c37695 Author: Weiqun Zhang Date: Tue Jan 7 20:22:36 2020 -0800 assert -> AMREX_ASSERT, std::min -> amrex::min and std::max -> amrex::max Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit d208eee2c5f00e61a1b710d199746b737c196203 Merge: 092887062 8e26b786b Author: Andrew Myers Date: Tue Jan 7 17:25:41 2020 -0800 Merge pull request #652 from rporcu/development Adding AMREX_GPU_HOST_DEVICE to functions and members of class RealVect commit 8e26b786bd2a3a8bb15ff82cdefdf20ed0dcc04d Merge: 8ec3f78d9 092887062 Author: Roberto Porcu Date: Tue Jan 7 17:11:10 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8ec3f78d914ad2d4769f833daab9e1ce09e7f14d Author: Roberto Porcu Date: Tue Jan 7 17:02:15 2020 -0800 Added function crossProduct to class RealVect Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 2ac2adc03aaaea91188b52976be02133b0380bd2 Author: Roberto Porcu Date: Tue Jan 7 16:50:28 2020 -0800 Adding AMREX_GPU_HOST_DEVICE attribute to functions and members of class RealVect Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 09288706217d6535783e8c701feeaf91aacf6e77 Author: Andrew Myers Date: Tue Jan 7 15:39:24 2020 -0800 add correctness testing for checkpoint / restart in HDF5Benchmark test Tests/HDF5Benchmark/inputs Tests/HDF5Benchmark/main.cpp commit 3ee6b26a7882e9bf566f39277d2b54582511ab98 Author: Andrew Myers Date: Tue Jan 7 10:46:19 2020 -0800 fix spaces Src/Particle/AMReX_ParticleTransformation.H commit e6f1606fb5985d4a76c5360bfb8fec91a9ce5187 Merge: 81ad9683f a043d311d Author: WeiqunZhang Date: Tue Jan 7 08:25:54 2020 -0800 Merge pull request #650 from eschnett/patch-2 Convert comment to English commit a043d311dc557112884d1c33b57942397edab0c4 Author: Erik Schnetter Date: Tue Jan 7 10:10:39 2020 -0500 Convert comment to English Tools/CMake/AMReX_Defines.cmake commit 81ad9683faaf735181e0cd943507d398d91cadbc Author: Andrew Myers Date: Mon Jan 6 16:48:47 2020 -0800 ignore unused return value Src/Particle/AMReX_ParticleIO.H commit ac47ee1abab0c6dca2b5890d010353aff31523f1 Author: Emmanuel Motheau Date: Mon Jan 6 15:52:04 2020 -0800 bug fix missing copy for regular cells Src/EB/AMReX_EBMultiFabUtil.cpp commit ba206b9fec0ee47b41cb7b5e75872966bcf84c4f Merge: f4c6158ad 6b88dd706 Author: Emmanuel Motheau Date: Mon Jan 6 14:18:21 2020 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit 6b88dd706527ad432af52fb0e1970315e143209c Author: Andrew Myers Date: Mon Jan 6 12:34:32 2020 -0800 docstrings for the particle reduction functions Src/Particle/AMReX_ParticleReduce.H commit 43b570f9729bc64b4ecd35f0ccd31875941e435e Merge: 6e25131f0 b26186db6 Author: Andrew Myers Date: Mon Jan 6 10:40:27 2020 -0800 Merge pull request #646 from houjun/development Add support to write particle data in HDF5 format commit 6e25131f057a41ebd521f6f08462ad2bfa2566e8 Merge: b4eb21dd4 511879d90 Author: Weiqun Zhang Date: Mon Jan 6 09:45:30 2020 -0800 Merge branch 'development' into weiqun/dev commit 511879d90371c2d465d57a21f8d0364d64e39c2b Merge: 9cf68e868 00179bba0 Author: WeiqunZhang Date: Mon Jan 6 09:26:17 2020 -0800 Merge pull request #649 from sudormroot/master The defition of single_level() should be 'void' rather 'int', otherwise compilers will report errors. commit 9cf68e8687a213bca3351b3d5a93cd3c9225becc Author: Weiqun Zhang Date: Mon Jan 6 09:17:53 2020 -0800 fix the pull-request just merged Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EB2_Level.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a16b4a53757fce07d1edb66018dcdef6876bfac6 Merge: b6be55026 ff793aba5 Author: WeiqunZhang Date: Mon Jan 6 08:57:53 2020 -0800 Merge pull request #639 from rporcu/development Added begin and end methods to IntVect and RealVect classes commit 00179bba07dca9f320d80995f5770e7c6c1b4b4d Author: sudormroot Date: Sun Jan 5 11:34:47 2020 +0800 The defition of single_level() should be 'void' rather 'int', otherwise, in some cases, the comiplers will report errors. OldTutorials/PIC_C/single_level.cpp commit b6be5502640fd4e7e3b60854ff60d6fc9fdbd6ed Author: Weiqun Zhang Date: Sat Jan 4 19:23:02 2020 -0800 constexpr void -> void so that it works with C++11 Src/Base/AMReX_Utility.H commit b26186db61ac87549d62dbead93e11d788161dd5 Author: Houjun Tang Date: Fri Jan 3 13:20:34 2020 -0800 Remove particle write in ascii format Tests/HDF5Benchmark/main.cpp commit e7f86d65bd58b3c50b4730d588f2298d93eb8864 Author: Houjun Tang Date: Fri Jan 3 13:12:58 2020 -0800 Add environmental var option to set Lustre stripe parameters Src/Particle/AMReX_ParticleIO.H commit 444189954e1387926422184af032dce3c4b0223b Author: Houjun Tang Date: Fri Jan 3 10:47:10 2020 -0800 Fix an attribute write error with multiple levels Src/Particle/AMReX_ParticleIO.H commit d23822256019c3e45ceeaeec0827603912327241 Merge: 5d0b6ce8b 0afe2b6e7 Author: Houjun Tang Date: Fri Jan 3 10:20:33 2020 -0800 Solve conflicts with merge commit 5d0b6ce8b23dbee5b9eeeeb71bb7fe415b0726c8 Author: Houjun Tang Date: Fri Jan 3 10:04:47 2020 -0800 Add particle data write in HDF5 format Src/Base/AMReX_PlotFileUtil.cpp Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H Tests/HDF5Benchmark/main.cpp commit ff793aba5c451db118bcbd06150116070493c486 Author: Roberto Porcu Date: Thu Jan 2 10:49:29 2020 -0800 Removed comment for variable that is needed in 1D or 2D simulations Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp commit b4eb21dd4c4e63a114a119c2ea3c5f76e208224d Author: Weiqun Zhang Date: Wed Jan 1 21:12:33 2020 -0800 need to inline TopIndexSpace Src/EB/AMReX_EB2.H commit 9f6a51c87d18ba47d5b0ce562056d8f8f81b6c55 Merge: 1dd582017 0afe2b6e7 Author: Weiqun Zhang Date: Wed Jan 1 21:07:53 2020 -0800 Merge branch 'development' into weiqun/dev commit 0afe2b6e7cfcbafe8db8fbdc4e9e2047707b86c9 Merge: d3de6a9d6 9ec47d3ec Author: Weiqun Zhang Date: Wed Jan 1 08:57:36 2020 -0800 Merge branch 'weiqun/comm' into development commit d3de6a9d69e0d4f2bac07469ff155fa0a6688d31 Merge: fd64303ae e45bd82f3 Author: Weiqun Zhang Date: Wed Jan 1 08:57:19 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e45bd82f36b6b5249226707275455a8b09b6cebc Author: Weiqun Zhang Date: Wed Jan 1 08:46:57 2020 -0800 update CHANGES CHANGES commit 9ec47d3eca334ddfc8bb9fd3840eb367701a9b93 Author: Weiqun Zhang Date: Wed Jan 1 08:13:53 2020 -0800 ignore_unuesd: variadic and gpu host device Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Utility.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H commit 1da10a4706271ad10315a2ad83ec0cbe139779c2 Author: Weiqun Zhang Date: Tue Dec 31 23:11:54 2019 -0800 clean up and avoid potential OMP issues Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 5b12e4701f214b87b90fc9793ec9e9d473c09b42 Author: Weiqun Zhang Date: Tue Dec 31 22:56:07 2019 -0800 fix assertion Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit 1a0cfece62d185494f649a1cfa0744687130b386 Author: Weiqun Zhang Date: Tue Dec 31 22:30:54 2019 -0800 support up to 128 GB of communication data for FabArray Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ccse-mpi.H commit 1a90ec90a8ad797d892cd749d67d58d93ab07529 Author: Weiqun Zhang Date: Tue Dec 31 21:30:36 2019 -0800 two new FabArray functions are for USE_MPI only Src/Base/AMReX_FabArrayCommI.H commit fd64303aecf2df0cad2be0a6b656b8e44a8f5652 Author: Weiqun Zhang Date: Tue Dec 31 21:18:14 2019 -0800 support up to 16 GB of communication data for FabArray Src/Base/AMReX_Arena.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 7e0fd8581a46ace7de87852fead9c24357e3768e Author: Weiqun Zhang Date: Tue Dec 31 16:48:48 2019 -0800 add amrex::aligned_size Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp commit f71cef8258c61aac1b320ee533057d97ee53317a Merge: 58e8b4d61 ff3264fed Author: WeiqunZhang Date: Tue Dec 31 11:39:45 2019 -0800 Merge pull request #643 from eschnett/patch-1 Always check MPI buffer size for overflow commit 1dd582017a5223620f605c5853fc2ad2b008fa8e Author: Weiqun Zhang Date: Tue Dec 31 11:28:18 2019 -0800 minor Src/EB/AMReX_EB2.H commit ff3264fedcf334bcd8bcdf63cabfd24edb2f603e Author: Erik Schnetter Date: Tue Dec 31 11:45:00 2019 -0500 Always check MPI buffer size for overflow Always check MPI buffer size for overflow. This check is very fast compared to the overall communication time. Src/Base/AMReX_FabArrayCommI.H commit 58e8b4d61e7cf9b99b190a3d6d0d5499bbbd7544 Merge: 14448043a 30f84f3e2 Author: WeiqunZhang Date: Mon Dec 30 20:01:51 2019 -0800 Merge pull request #640 from AMReX-Codes/block_reduce_fix Handle an edge case where the block size is less than a warp commit 30f84f3e26d2fc466c96ecc998828ac3266f4944 Author: Weiqun Zhang Date: Mon Dec 30 11:58:08 2019 -0800 avoid std::max because in C++11 it doesn't work on GPU and because blockDim.x and warpSize are not the same integer type (one is unsinged whereas the other is signed) Src/Base/AMReX_GpuReduce.H commit 14448043a8b453112365f72c1a0383b3eb1ecf95 Author: Max Katz Date: Sat Dec 28 03:45:09 2019 -0800 Use a 1D block/thread layout for most loops Src/Base/AMReX_GpuDevice.cpp Tools/F_scripts/write_cuda_headers.py commit 133b27a6d00e1ad903c4490b37894a76e6cbc465 Author: Max Katz Date: Sat Dec 28 00:57:53 2019 -0800 Select a better block layout for 1D and 2D Src/Base/AMReX_GpuDevice.cpp commit bf29d2b0141c9d3ce7c47cb408a1f9b1394eab43 Author: Max Katz Date: Fri Dec 27 00:17:34 2019 -0800 Add GPU pragma option for a device sync Tools/F_scripts/write_cuda_headers.py commit 4c77d7acec90e8427e67c17fafa66999cb174a72 Author: Max Katz Date: Wed Dec 25 01:27:00 2019 -0800 Handle an edge case where the block size is less than a warp Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_fort_mod.F90 commit f4c6158adcd730d17fc58ca2fe1d6a03194db265 Author: Marc Day Date: Mon Dec 23 13:14:35 2019 -0800 Only setVal result components that will be filled. Src/EB/AMReX_EBMultiFabUtil.cpp commit 5cd5133b13b66899f633028a9f2d26f607f23316 Author: Roberto Porcu Date: Mon Dec 23 11:42:01 2019 -0800 Fix some warning messages Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EB2_Level.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 2d89d44dea03ae182e99d43313296b6e1e55d597 Author: Roberto Porcu Date: Sun Dec 22 15:23:47 2019 -0800 Added begin and end methods to IntVect and RealVect classes Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealVect.H commit b137b42cff06eba95dc933befc1ab3aac2ea8377 Author: Marc Day Date: Fri Dec 20 21:06:27 2019 -0800 Use consistent stencil to move cell-centered data to cell and face centroids. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 90b43f7ee60dbc2c088dec91c15bee0cf26c5e73 Author: Andrew Myers Date: Fri Dec 20 11:26:51 2019 -0800 that is not how complex numbers work Src/Base/AMReX_GpuComplex.H commit f3a9410dc912bf709f16b055d8910b2afb636e0e Author: Emmanuel Motheau Date: Thu Dec 19 15:43:38 2019 -0800 Revert "WIP fixing interplation" This reverts commit 81549df93c7a04af1fc61b031695bba139bdb0c0. Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit 0d62ebfd08139b944071a6538d32d6a804210e6b Author: Weiqun Zhang Date: Thu Dec 19 15:40:48 2019 -0800 MacProjector: no need for FillBoundary if already on centroid Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 68ee2a36c798a41f20e9fd4ec64380166f7eab67 Merge: 3cc3f2f85 93c4658b0 Author: Andrew Myers Date: Thu Dec 19 15:23:59 2019 -0800 Merge branch 'development' into atmyers/no_thrust commit 3cc3f2f8556aa4e8b4c991ee4ecd74e1d2d27cfd Author: Andrew Myers Date: Thu Dec 19 14:55:31 2019 -0800 fix typo Src/Base/AMReX_Partition.H commit 81549df93c7a04af1fc61b031695bba139bdb0c0 Author: Emmanuel Motheau Date: Thu Dec 19 14:30:10 2019 -0800 WIP fixing interplation Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit f53fb5e34ef242b296657a3c234c13c91e1d4d62 Author: Weiqun Zhang Date: Thu Dec 19 13:52:34 2019 -0800 add GetVecOfArrOfConstPtrs Src/Base/AMReX_Vector.H commit 4cc8226018c0e51758a54a8ba062b39d06d8ef77 Author: Weiqun Zhang Date: Thu Dec 19 13:52:20 2019 -0800 skip ccmask if already on centroids Src/EB/AMReX_EBMultiFabUtil.cpp commit 93c4658b0c100ffff7a1fb81336db530a731fbc7 Merge: 5a6811ae4 b26e9df72 Author: Andrew Myers Date: Thu Dec 19 13:33:18 2019 -0800 Merge pull request #638 from AMReX-Codes/dw/pmesh In ParticleToMesh, apply SumBoundary & finalize MultiFab for both GPU and CPU commit 051923a7ee99cf0836ed3c3c64fa68bcf473caca Author: Weiqun Zhang Date: Thu Dec 19 13:23:23 2019 -0800 NodalProjector: simga may not have ghost cells. No need to call FillBoundary. Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 4318157a3600ac79946bfd56df04365c557731d9 Author: Weiqun Zhang Date: Thu Dec 19 13:21:38 2019 -0800 EBCellFlag::setCovered: simply assign covered value Src/EB/AMReX_EBCellFlag.H commit b26e9df7217498d342bd0712e98fa500793149f8 Author: Donald E. Willcox Date: Thu Dec 19 13:08:09 2019 -0800 Move SumBoundary and MultiFab copy & cleanup outside the not-in-launch-region scope. Src/Particle/AMReX_ParticleMesh.H commit 5a6811ae41ec46b3c6ddd2fd795fd1019ff84a09 Author: Oscar Antepara Date: Thu Dec 19 13:06:46 2019 -0800 [Docs] Adding addtional comments on Paraview section Docs/sphinx_documentation/source/Visualization.rst commit 21449b7586306fec59f6b030252e375043ac5507 Merge: adfd9f3b7 0717f6206 Author: Andrew Myers Date: Thu Dec 19 12:50:02 2019 -0800 merging development into atmyers/no_thrust commit 0717f6206e86eaff776e6506e2e3e0774ca8b8da Merge: 1735dfa9a 00abe5b34 Author: Andrew Myers Date: Thu Dec 19 12:48:35 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1735dfa9aa54e06a6e71c898a3f1649933ff71f8 Author: Andrew Myers Date: Thu Dec 19 12:48:20 2019 -0800 a host / device version of swap Src/Base/AMReX_Algorithm.H Src/Base/AMReX_PODVector.H Src/Base/AMReX_Partition.H commit 32ea5942719735b894fa0558c3757e43a5d13ae3 Author: Marc Day Date: Wed Dec 18 18:31:52 2019 -0800 Fix cc2cent interp stencil in 2D Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit adfd9f3b73bea1ac6b4dde43ef5e82f510ba3c58 Author: Andrew Myers Date: Wed Dec 18 15:54:02 2019 -0800 more code reuse in amrex::Partition and amrex::StablePartition Src/Base/AMReX_Partition.H commit 5f15e0f20834cf64922ae04bc1660816ccfac205 Author: Andrew Myers Date: Wed Dec 18 15:07:57 2019 -0800 fix spaces Src/Particle/AMReX_ParticleTransformation.H commit 0ab02eab4c449147b8c12aa2a126c8d1d7510e4c Author: Andrew Myers Date: Wed Dec 18 15:07:46 2019 -0800 reorder these functions Src/Base/AMReX_Partition.H commit 48345f66146622dc8efa117e4b7e80c474066326 Merge: b55f911de 00abe5b34 Author: Weiqun Zhang Date: Wed Dec 18 14:17:08 2019 -0800 Merge branch 'development' into weiqun/dev commit 00abe5b3435c584e53aa134a7373d488f63e2f66 Merge: 130b3c2b8 cdb57360c Author: Weiqun Zhang Date: Wed Dec 18 14:14:32 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b55f911de9368aa432fc76077529ff5ce4bb193a Author: Weiqun Zhang Date: Wed Dec 18 13:05:17 2019 -0800 Make FillPatchSingleLevel safe when the destination is the same as source. Change the interface of virtual PhysBCFunctBase::FillBoundary that unfortunately breaks backward compatibility. Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_FPhysBC.cpp commit 8edd0b40a5843f162e794d05049a342740d71815 Author: cgilet Date: Wed Dec 18 17:00:36 2019 -0500 Fix testing for regular cells in compFluxes and compGrad. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit cb4d4d5f3c95ecc6a4e19dd69f7b5229ff9b73bd Author: Andrew Myers Date: Wed Dec 18 13:35:37 2019 -0800 ensure that the Partition and ParallelScan Tests still work Tests/GPU/Partition/main.cpp Tutorials/GPU/ParallelScan/main.cpp commit 8288ef114b01ccbd05324f6707948db947b0b7e7 Author: Andrew Myers Date: Wed Dec 18 13:35:11 2019 -0800 move implementation of inclusive_scan and exclusive_scan to get around circular dependency issue Src/Base/AMReX_GpuContainers.H Src/Base/AMReX_Scan.H commit 47f77cb5db3ab3851899fd7c6003d78134c389b6 Author: Andrew Myers Date: Wed Dec 18 13:34:23 2019 -0800 add alternate versions of Parition and StablePartition Src/Base/AMReX_Partition.H commit a5e47bd8708a24004339cc09daf805db0ad31acb Author: cgilet Date: Wed Dec 18 16:27:28 2019 -0500 Add MLEBTensorOp::compFlux at face centroids Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 130b3c2b8c912fa4b9f603f76b09f7911ee585da Author: Weiqun Zhang Date: Wed Dec 18 09:49:56 2019 -0800 OrientationIter: ok -> isValid for consistence with MFIter Src/Base/AMReX_Orientation.H commit 94d4a81239396cbeb6eb6277c28f74b0ecec49fc Merge: 89c82ab45 cdb57360c Author: cgilet Date: Wed Dec 18 09:38:10 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 76c9647d6c9d58708a65e2ba8aa7336d60fc2b0f Merge: 8e76d22ab cdb57360c Author: Kevin Gott Date: Wed Dec 18 04:08:03 2019 -0800 Merge branch 'development' into kngott/hip commit c9ad3c03bfb5bdc063e27be0986984202a10458c Merge: 2c870195f cdb57360c Author: Andrew Myers Date: Tue Dec 17 17:21:31 2019 -0800 Merge branch 'development' into atmyers/no_thrust commit 2c870195f84219e57199ec7fac6112565be2e24e Merge: b9d1a0f97 378fac897 Author: Andrew Myers Date: Tue Dec 17 17:18:41 2019 -0800 Merge branch 'development' into atmyers/no_thrust commit b9d1a0f9775bf36b6c3dbb3d07b315fc0de11c53 Author: Andrew Myers Date: Tue Dec 17 17:18:14 2019 -0800 less confusing implementation of complex int pow Src/Base/AMReX_GpuComplex.H commit cdb57360cf7663e5fd77196ae11439498f83fb52 Merge: 378fac897 149997448 Author: Andrew Myers Date: Tue Dec 17 17:17:58 2019 -0800 Merge pull request #637 from eschnett/development Avoid compiler warnings commit 54d02704886c4ae03c22d7a01829759fb6c6db73 Author: Marc Day Date: Tue Dec 17 15:26:49 2019 -0800 Add destComp to EB_interp_CC_to_Centroid Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 378fac8979817a172a73c83519a2ba02013c8586 Author: Michele Rosso Date: Tue Dec 17 15:10:21 2019 -0800 CMake: fix problems with PETSc support Src/CMakeLists.txt Src/Extern/HYPRE/CMakeLists.txt Src/Extern/PETSc/CMakeLists.txt Tools/CMake/AMReX_Options.cmake commit af1c9406ab4926857ea0f402c82eecd0466e272d Merge: e37e0672b 29f1fd37a Author: mic84 Date: Tue Dec 17 15:00:09 2019 -0800 Merge pull request #636 from petsc/add-petsc Add support for CMake to handle PETSc commit fcdb382c2b824c4998d149794b734b6530f5e8a0 Author: Andrew Myers Date: Tue Dec 17 14:42:54 2019 -0800 COMPLEX -> GPUCOMPLEX Src/Base/AMReX_GpuComplex.H commit f9abb676e6f90278c5abeee86a18120604b0cc61 Author: Andrew Myers Date: Tue Dec 17 14:21:05 2019 -0800 add amrex::GpuComplex Src/Base/AMReX_GpuComplex.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 149997448dddf4ee4e31debe85a298df0b4cf700 Author: Erik Schnetter Date: Tue Dec 17 15:57:52 2019 -0500 Avoid compiler warnings Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_StructOfArrays.H commit e13a8054c6b20ceb1a31174463ee3c45ab4869d1 Merge: e03ee8390 e37e0672b Author: Andrew Myers Date: Tue Dec 17 10:58:59 2019 -0800 Merge branch 'development' into atmyers/no_thrust commit e37e0672bb6ec39156eff9bbc1c39e05ba0b5592 Author: Max Katz Date: Mon Dec 16 22:49:23 2019 -0800 Move some NVCC options to be included for C source files Tools/GNUMake/comps/nvcc.mak commit c2b60f26da030a11f1d2ad9df93fdeb7892a1a63 Author: Max Katz Date: Mon Dec 16 22:48:54 2019 -0800 Include C sources in the CUDA preprocessing Tools/GNUMake/Make.rules commit c1bafe5e85ee9536f576c7c6765a22d2c6ddb7c4 Merge: e7ade72e2 0a490f82d Author: Emmanuel Motheau Date: Mon Dec 16 16:39:57 2019 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit e7ade72e24a222111b15b640316cc1f84ceda74c Author: Emmanuel Motheau Date: Mon Dec 16 16:39:41 2019 -0800 CC2Face and CC2FaceCentroid in 3D now Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 89c82ab45bebcfc430632d51041c7b9d4e5857fb Merge: c8af77e99 0a490f82d Author: cgilet Date: Mon Dec 16 19:13:13 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 3897a3f534cc36d957d8ee6e129b62d985646b38 Author: Michael Rowan Date: Mon Dec 16 11:45:13 2019 -0800 Save more kernel stats to activity record Src/Base/AMReX_ActivityTraceAsync.H Src/Base/AMReX_ActivityTraceAsync.cpp commit 0a490f82d7ed91f1aba44f7a5e82d91906d306fa Author: Weiqun Zhang Date: Mon Dec 16 10:32:16 2019 -0800 add std:: Src/Base/AMReX_PODVector.H commit 85ab455d0a3e06d8c9a05dbd6af6a065fe3e261b Author: Weiqun Zhang Date: Mon Dec 16 10:32:05 2019 -0800 fix typo CHANGES commit c8af77e990cae92e46ffc1c536edecbcc6b2ca9f Merge: 2998db0c4 4274ca7fd Author: cgilet Date: Mon Dec 16 10:25:59 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 29f1fd37a2d1a363a90a29ef4542b9e60045f518 Author: Barry Smith Date: Sun Dec 15 21:10:58 2019 -0600 Add support for CMake to handle PETSc Add missing include files to Src/EB/CMakeLists.txt Src/CMakeLists.txt Src/EB/CMakeLists.txt Src/Extern/PETSc/CMakeLists.txt Tools/CMake/FindPETSc.cmake commit 4274ca7fd551a7ca9af7e11e73d261475cf493c1 Author: Weiqun Zhang Date: Sat Dec 14 18:27:15 2019 -0800 FabArray ReduceMin and ReduceMax that can take three FabArrays Src/Base/AMReX_FabArrayUtility.H commit 6883a8a74788cf31cee7f627c0163308411095e9 Author: Weiqun Zhang Date: Sat Dec 14 18:25:28 2019 -0800 add FabArray::isAllRegular Src/Base/AMReX_FabArray.H commit 38401028ca6c672a495a45ec173a182203251057 Author: Weiqun Zhang Date: Sat Dec 14 10:05:10 2019 -0800 only need to fill one ghost cell Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 523078d81dbf3508bc7233f1b5b9e8e9f76f39c9 Author: Weiqun Zhang Date: Sat Dec 14 10:04:03 2019 -0800 new Orientation constructor Src/Base/AMReX_Orientation.H commit 3facd4e3972faef06fb0e3fa5147d50225560d2e Author: Weiqun Zhang Date: Sat Dec 14 10:03:24 2019 -0800 make it safe to construct zero-component Fab Src/Base/AMReX_BaseFab.H commit 4393a178724392ae4a018aa7c30797b3403986fe Author: Weiqun Zhang Date: Sat Dec 14 10:02:29 2019 -0800 add new funcitons to AmrMesh to return vector of Geometry, BoxArray and DistributionMapping on a range of levels Src/AmrCore/AMReX_AmrMesh.H commit 1484aacc8a222c08075be1c9e2bd4360fcfc165c Author: Marc Day Date: Fri Dec 13 19:23:12 2019 -0800 Add scomp/dcomp to functions for face centroid Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit e6efc1f5b4534e0eee842379d9faa0dcb636ee53 Author: Marc Day Date: Fri Dec 13 18:51:52 2019 -0800 Remove grow op on interp function..remnant of where orig code was stolen from Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit d2c69d10647901e98dd519f8b028ab96593be2cc Merge: f620b4311 9dd79f66a Author: Emmanuel Motheau Date: Fri Dec 13 16:04:00 2019 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit f620b4311054512f1b7f2af24f0bb8b89ce046e7 Author: Emmanuel Motheau Date: Fri Dec 13 16:03:40 2019 -0800 some cleaning note that CC2FaceCentroid is missing in 3D Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 646a16fabb07d27b2eb8de72e6b0c7196aab27ad Author: Emmanuel Motheau Date: Fri Dec 13 15:58:23 2019 -0800 new design of CC2Centroid to get the correct cells without using a normal new routine to interpolate cc to face centroid Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 14b8c797ba16cac9702ed91493ec977ac39e1299 Author: Jean M. Sexton Date: Fri Dec 13 11:56:02 2019 -0800 Added check for RedistributeCPU edge case where particle gets reset to lo boundary, but is not contained in the Box it came from Src/Particle/AMReX_ParticleContainerI.H commit c0b505244e3208bf4af4e02d9836f264a7e7ac9e Author: Emmanuel Motheau Date: Fri Dec 13 11:09:49 2019 -0800 3Putting 3D version Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 2998db0c4ab94c5e18a8e28ea0f03b27d1483f07 Merge: eeaadfe17 9dd79f66a Author: cgilet Date: Fri Dec 13 10:19:05 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 73a226eccdbf86a05ffa69797875664c8801fbed Author: Emmanuel Motheau Date: Thu Dec 12 15:18:56 2019 -0800 Some cleaning Src/EB/AMReX_EBMultiFabUtil.cpp commit e03ee83909e1e1122feb06c98cfbd3a0fcb6d27f Merge: dfa7a7834 9dd79f66a Author: Andrew Myers Date: Thu Dec 12 17:37:32 2019 -0500 Merge branch 'development' into atmyers/no_thrust commit 9dd79f66adf56bf253ebeb7f3935a5e3eeae5681 Author: Andrew Myers Date: Thu Dec 12 17:37:02 2019 -0500 fix global parameter shadowing Src/Particle/AMReX_ParticleBufferMap.cpp commit 57a21b5d0bdeed9adf6b6a3ff088031f0b26b214 Merge: 2e3b3a308 cc9950f1c Author: Michele Rosso Date: Thu Dec 12 14:30:44 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit dfa7a7834494d1175af532eaca531731bbb2ef52 Author: Andrew Myers Date: Thu Dec 12 16:52:11 2019 -0500 remove old file from make system, restore some missing , Src/Base/AMReX_GpuContainers.H Src/Base/AMReX_PODVector.H Src/Base/Make.package commit cd3b6c97fd5a86e3a2434131a761f2ae5e3375da Author: Andrew Myers Date: Thu Dec 12 16:40:10 2019 -0500 removing all thrust calls from amrex Docs/sphinx_documentation/source/GPU.rst Src/Base/AMReX_GpuAllocators.H Src/Base/AMReX_GpuAllocators.cpp Src/Base/AMReX_GpuContainers.H Src/Base/AMReX_PODVector.H Src/Base/CMakeLists.txt commit 04128e437bcb6c5b4b105cbca8242d48935efb19 Author: Andrew Myers Date: Thu Dec 12 16:31:08 2019 -0500 fix cpu versions of exclusive and inclusive scan Src/Base/AMReX_GpuContainers.H commit c26ae799b35fe6282c0e26ade55a4a3dc6ca958c Merge: 68c764a86 cc9950f1c Author: Andrew Myers Date: Thu Dec 12 15:40:35 2019 -0500 Merge branch 'development' into atmyers/scan_compare commit facfabe423b7f77a3b232829979113a88ffbcd27 Author: Emmanuel Motheau Date: Wed Dec 11 21:05:34 2019 -0800 cleaning of the 2D routine Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit 6cc934e5e85c6a0d5ac02ef04b8069d4d398aa39 Merge: c86c20555 cc9950f1c Author: emotheau Date: Wed Dec 11 20:44:40 2019 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit c86c2055563c5bdbe8465fb38f135ae14c72577f Author: Emmanuel Motheau Date: Wed Dec 11 20:42:31 2019 -0800 WIP : create a new routine to interpolate Cell Center values to Centroid Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit cc9950f1c6514451d109f71a5a0c4c126c7c2b63 Merge: c2948a786 60fbfd426 Author: Ann Almgren Date: Wed Dec 11 15:34:30 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit c2948a78628a9bc549f0eb8de018091b56f17d82 Author: Ann Almgren Date: Wed Dec 11 15:33:47 2019 -0800 Update MAC_Projection_EB tutorial so that when regtest = 1 we don't plot zvel (used for regression testing with GPUs) Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 3b97486eebdcc9788eac70455f6874773271ee26 Author: Michael Rowan Date: Wed Dec 11 14:22:01 2019 -0800 Cleanup CUPTI GPU timer Src/Base/AMReX_ActivityTraceAsync.H Src/Base/AMReX_ActivityTraceAsync.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/Make.package Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile Tests/GPU/CuptiTest/Exec/CUDA/myfunc.H Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H Tests/GPU/CuptiTest/Source/main.cpp Tools/GNUMake/Make.defs commit 8e76d22abd8c8acbf94cf06cce2792d01796ce04 Author: Kevin Gott Date: Wed Dec 11 14:07:51 2019 -0800 Clean up hip make system. Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 60fbfd4263d5030e52abc6c7af1e315f2186396e Author: Weiqun Zhang Date: Wed Dec 11 13:45:06 2019 -0800 Need to set coverd cells in rhs_cc Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2ed977fe070c8feda6475a1813e07620f2581bd3 Author: Ann Almgren Date: Wed Dec 11 13:27:02 2019 -0800 Set default maxorder to 3 not 2 Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 382c619b5766ec2c7962da721d5cdf39cc8251d9 Merge: 9bf74235f bfbee79af Author: Kevin Gott Date: Wed Dec 11 12:55:13 2019 -0800 Merge branch 'development' into kngott/hip commit bfbee79af429d55c0b90acf17c5bc25ace50ab13 Author: Kevin Gott Date: Wed Dec 11 15:51:54 2019 -0500 __CUDA_ARCH__ inside functions instead of defining separate functions (hip-clang error) Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp commit 9bf74235f95e2d0419e4b8527efea8e67e64b974 Author: Kevin Gott Date: Wed Dec 11 12:29:46 2019 -0800 More function marking for hip-clang. Src/Base/AMReX_BaseFab.H commit eeaadfe17987c1d9a164b5905a2fe3f8028d1ae1 Merge: 7065a340c e129ae8e4 Author: cgilet Date: Wed Dec 11 14:43:32 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 2e3b3a308c8dd4f2ff6434285c479ab28481edc8 Author: Michele Rosso Date: Wed Dec 11 11:14:50 2019 -0800 NodalProjector: rename m_solver m_mlmg Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit bc172f3d29458d2b8ca9b9f375b9b546aaa6fa4c Author: Michele Rosso Date: Wed Dec 11 11:09:40 2019 -0800 NodalProjector: rename m_matrix m_linop Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit e129ae8e421226b31925747a993adb22452db77a Author: Weiqun Zhang Date: Wed Dec 11 09:59:43 2019 -0800 fix communicator bug when there is only one multigrid level and the solvability needs to be fixed Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 7065a340c910ca1bda5786b9702430117dda00ba Merge: 6153c3374 5070a127b Author: cgilet Date: Wed Dec 11 12:22:43 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 5070a127b8b1a56b42951e2cc8f829ec1daf62c3 Author: Michele Rosso Date: Tue Dec 10 17:37:14 2019 -0800 MacProjector: remove debug statement Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit e61c71fc52d6d678f871ff0d4214e71fdcb16785 Author: Michele Rosso Date: Tue Dec 10 17:36:13 2019 -0800 Update MAC_Projection_EB test Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 4ce674f60e269a7d58037d89c30e5d94998498ad Merge: 3f5a8f7d9 6f907ebbb Author: Michele Rosso Date: Tue Dec 10 17:30:23 2019 -0800 Merge branch 'mr/projections' into development commit 68c764a86a86e4d1fb2d1d14cc727df7f6330d83 Author: Andrew Myers Date: Tue Dec 10 20:08:59 2019 -0500 use amrex scan instead of thrust Src/Base/AMReX_GpuContainers.H commit 6f907ebbbd1b463be276bc6a9ba844e28cd0ba81 Author: Michele Rosso Date: Tue Dec 10 16:54:41 2019 -0800 MacProjector: give user access to linear operator and MLMG. Remove setters which now are superfluous. Create MLMG and set options from input file in constructor. Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 3f5a8f7d94fc092e3e5cdf0e48145fad2b2b4001 Author: Andrew Myers Date: Tue Dec 10 14:59:28 2019 -0800 fix incorrect table description in documentation Docs/sphinx_documentation/source/InputsPlotFiles.rst commit e6b287860b5aeeef0e86b527b56367fe31689a98 Author: Weiqun Zhang Date: Tue Dec 10 11:38:01 2019 -0800 fix a warning Src/EB/AMReX_EB2_GeometryShop.H commit bdb717baffec81bc69a4934a64989906920f088e Author: Oscar Antepara Date: Tue Dec 10 10:22:46 2019 -0800 Fixing MAC solver options Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 28dbe05b35b644eb2c91a11084ce645bc53c225c Merge: e3a86b0b3 c949c3895 Author: Michele Rosso Date: Mon Dec 9 14:39:52 2019 -0800 Merge branch 'mr/projections' into development commit c949c38958ca86c68c5b19e4164f1acd272396e9 Merge: e39567741 f33a41000 Author: Michele Rosso Date: Mon Dec 9 14:39:32 2019 -0800 Merge branch 'development' into mr/projections commit e3a86b0b3d1711ba661c77fa45c13ed71744d294 Author: Andrew Myers Date: Mon Dec 9 12:20:44 2019 -0800 more BL_ -> AMREX_ Src/Base/AMReX_REAL.H Src/Base/AMReX_fort_mod.F90 Src/Particle/AMReX_Particles.H commit 1c7b79e02b725ebc4926cde127788f66bd4b4292 Author: Andrew Myers Date: Mon Dec 9 12:16:39 2019 -0800 more BL_ -> AMREX_ Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_TracerParticles.H commit e13efe8ac0090424b17575d2e7519b27fc948ba8 Author: Andrew Myers Date: Mon Dec 9 12:14:04 2019 -0800 more BL_ -> AMREX_ Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H commit 4ce1b306a5302d8cd63e64188720618b29765f67 Author: Andrew Myers Date: Mon Dec 9 12:12:45 2019 -0800 BL_LAZY -> AMREX_LAZY Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 2f0310dc4e0ae6ebc58cc510ad02942a7c579cfb Author: Andrew Myers Date: Mon Dec 9 12:09:15 2019 -0800 BL_USE_MPI -> AMREX_USE_MPI Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleMPIUtil.H Src/Particle/AMReX_ParticleMPIUtil.cpp commit 195f9279fedf4b709adc57175f2a34d15cdfff63 Author: Andrew Myers Date: Mon Dec 9 11:56:57 2019 -0800 rename AMReX_ParIterI.H -> AMReX_ParIter.H Src/Particle/AMReX_ParIter.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 331839046fc68a544ca20cc7c1e019bdc5ca0ead Author: Andrew Myers Date: Mon Dec 9 11:55:45 2019 -0800 move implementation of ParIter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 6153c3374ccbf1481aeafe477b39688596e511cf Merge: 1fe275876 fd90437e6 Author: cgilet Date: Mon Dec 9 14:22:06 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit fd90437e6b58e102022edc03dcc4fdf8e6f73bb9 Author: Weiqun Zhang Date: Mon Dec 9 09:41:10 2019 -0800 add MLMG::getEBFluxes Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 1fe2758766fe08ce7034fae3e9a664e1927f87b8 Merge: a3cd10182 820e0e4ff Author: cgilet Date: Mon Dec 9 11:29:52 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 820e0e4ffbdf6546a91bb20f886812358d95d0f6 Author: Weiqun Zhang Date: Mon Dec 9 08:15:11 2019 -0800 fix 2d EB computeDivergence and computeGradient Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_2D_C.H commit a3cd10182024b260cd19aae4f0d6437a2c3c39bd Merge: afb28f3d9 d7e23ba08 Author: cgilet Date: Sat Dec 7 19:23:14 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit d7e23ba089c201004b56228293fe1683da92e599 Author: Max Katz Date: Sat Dec 7 10:13:22 2019 -0800 Specify in suffix if using OpenMP offload Tools/GNUMake/Make.defs commit 25f1130e936b91d030b7ce5e898fa890e96bcca6 Author: Kevin Gott Date: Fri Dec 6 18:34:43 2019 -0800 Nearly fixed. Likely managed isn't appropriately covered. Src/Base/AMReX_BlockMutex.cpp Src/Base/AMReX_Random.cpp commit 92a791ba38c3c8296f35e9c3d0bba1ef167164d1 Merge: 36f26a8d7 cc7db21bc Author: Kevin Gott Date: Fri Dec 6 18:31:06 2019 -0800 Merge branch 'development' into kngott/hip commit 961ca2189da600a80485049ea148cec788315715 Merge: a47703550 9c5e67fd5 Author: Andrew Myers Date: Fri Dec 6 17:23:29 2019 -0800 Merge pull request #632 from AMReX-Codes/twoway_transform Two-way particle transforms commit a47703550cc94d28e4464fa682b39432c35dbfe1 Author: Andrew Myers Date: Fri Dec 6 17:14:39 2019 -0800 further tweaks to locking test Tests/GPU/Locking/inputs Tests/GPU/Locking/main.cpp commit e181cadca8391ab886e6479acfb46bfc4b7a7db4 Author: Andrew Myers Date: Fri Dec 6 17:05:11 2019 -0800 tweak output of Locking test Tests/GPU/Locking/main.cpp commit 9c5e67fd55041cea89227bdb7d77757fc7ce7996 Merge: 6718b8310 a9e75a7db Author: Andrew Myers Date: Fri Dec 6 16:59:06 2019 -0800 Merge branch 'development' into twoway_transform commit 6718b8310168c83da8564c85391f2ae501b54833 Author: Andrew Myers Date: Fri Dec 6 16:53:31 2019 -0800 implement and test two-way filter and transform Src/Particle/AMReX_ParticleTransformation.H Tests/Particles/ParticleTransformations/main.cpp commit f33a41000b988921e7c3569ab3709ba8e9e9a74a Merge: 8c2f74ea9 bd82c0bd9 Author: Michele Rosso Date: Fri Dec 6 16:27:09 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8c2f74ea95d6162d2fd0c74b3c23ea201de0371f Author: Michele Rosso Date: Fri Dec 6 16:26:59 2019 -0800 computeGradient(): add support for RZ geometry Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_2D_C.H commit a9e75a7dbc241b25c7bf447aa9e68edcc8710c92 Merge: cba0db3bb ea18e035d Author: Weiqun Zhang Date: Fri Dec 6 16:26:54 2019 -0800 Merge branch 'development' into weiqun/dev commit ea18e035de757788ac5e6cc450cacc4903ec9082 Author: Weiqun Zhang Date: Fri Dec 6 16:24:00 2019 -0800 fix CXXSTD for nvcc with gcc > 5 Tools/GNUMake/comps/nvcc.mak commit ec1e8c9c5c0de64058fdd8eb2c525aee8d1d952d Author: Michele Rosso Date: Fri Dec 6 16:21:25 2019 -0800 computeDivergence(): add support for RZ geometry Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_2D_C.H commit bd82c0bd9343b749572da079a1bc2db067eaa293 Author: Weiqun Zhang Date: Fri Dec 6 16:06:29 2019 -0800 for nvcc we have to make sure CXXSTD is defined Tools/GNUMake/comps/nvcc.mak commit e1aa3c306b0a6eb32f49e1ea4f5b478dabc9dc61 Author: Andrew Myers Date: Fri Dec 6 15:59:46 2019 -0800 remove extraneous word from comment Src/Particle/AMReX_ParticleTransformation.H commit 5d0f2110ae1a6624c4032cc69d26bd3757732df4 Author: Andrew Myers Date: Fri Dec 6 15:58:01 2019 -0800 allow the Src and Dst particle tile types to be different for the transform functions Src/Particle/AMReX_ParticleTransformation.H commit 489a02f22d45a807137b09958307451845a7e049 Author: Andrew Myers Date: Fri Dec 6 15:41:45 2019 -0800 implement and test two-way transforms Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_Particles.H Tests/Particles/ParticleTransformations/main.cpp commit cc7db21bcd9bc41d471b857606b451d746758056 Merge: 69f67bf33 b5b9cc90b Author: WeiqunZhang Date: Fri Dec 6 15:18:53 2019 -0800 Merge pull request #631 from AMReX-Codes/lock_reimplement Lock reimplement commit 69f67bf33a1c7384c0905a12c184a14130ef5a54 Merge: 4ec5a952e 08530bf64 Author: WeiqunZhang Date: Fri Dec 6 15:14:36 2019 -0800 Merge pull request #630 from ax3l/topic-cxxStdControl CXXSTD: Project Control of C++ Std commit b5b9cc90b5300d66306bd9e66744e4f6952756f8 Author: Andrew Myers Date: Fri Dec 6 15:09:50 2019 -0800 fix order of namespace and #ifdef Src/Base/AMReX_BlockMutex.cpp commit 08530bf645a7ecc793e72e2a640e7796ef76b75d Author: Axel Huebl Date: Thu Dec 5 11:16:06 2019 -0800 CXXSTD: Project Control of C++ Std Add a new option, defaulting to C++11, to give projects control over the required C++ standard of a project. This improves the current logic, which does not cleanly fail if a compiler does not support e.g. C++14 but instead gave hard-to-read error messages such as "hm, dunno what std::make_unique is" :) Now the compiler will fail with messages such as: "gcc: error: unrecognized command line option ‘-std=c++14’" which is better and safes us from re-implementing a ton of logic that CMake provides out-of-the-box. Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/GNUMake/comps/cray.mak Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/hip.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/intel.mak Tools/GNUMake/comps/llvm-flang.mak Tools/GNUMake/comps/llvm.mak Tools/GNUMake/comps/nag.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 5b9486a148cae82c4552c0aad295685a5ab2bc26 Author: Andrew Myers Date: Fri Dec 6 15:04:40 2019 -0800 put these implementations in namespace amrex Src/Base/AMReX_BlockMutex.cpp commit c27de5cb21184d3fe078f8796f9823cecd339e33 Author: Andrew Myers Date: Fri Dec 6 15:04:21 2019 -0800 add __threadfence() Tests/GPU/Locking/main.cpp commit e7fa758f3d3f3e64c3f4d49aa5aec941a42bfe6e Author: Michele Rosso Date: Fri Dec 6 14:28:00 2019 -0800 computeDivergence(): fix assertions to work with any AMREX_SPACEDIM Src/Base/AMReX_MultiFabUtil.cpp commit 7338a22eab1c9f5610a3017742a1958ef5889ee5 Author: Andrew Myers Date: Fri Dec 6 14:00:15 2019 -0800 actually add file Src/Base/AMReX_BlockMutex.cpp commit 7954bba09f2730a34f736f31d76146f3917c1509 Author: Andrew Myers Date: Fri Dec 6 13:58:35 2019 -0800 split up the declaration and definition for BlockMutex Src/Base/AMReX_BlockMutex.H Src/Base/CMakeLists.txt Src/Base/Make.package commit d8fcba3a5967c5decff78a88e9775095ec567666 Author: Andrew Myers Date: Fri Dec 6 13:42:31 2019 -0800 no need to duplicate this static_assert Src/Base/AMReX_Random.cpp commit b6f1d650b4633b5fde8987ea9584b11a4bfabbe6 Author: Andrew Myers Date: Fri Dec 6 13:39:43 2019 -0800 add block counting to the locking test Tests/GPU/Locking/main.cpp commit 36f26a8d7fc501f358387a833e69b2195d75bed2 Merge: a08d0de0d 96879dd69 Author: Kevin Gott Date: Fri Dec 6 13:36:21 2019 -0800 Merge branch 'development' into kngott/hip commit 4419aa94e34eb0562570ba179a00876f4edf2cb3 Author: Andrew Myers Date: Fri Dec 6 13:29:58 2019 -0800 forgot to add new file Src/Base/AMReX_BlockMutex.H commit 7dd940245c7b90446b287983890180d145e304ca Author: Andrew Myers Date: Fri Dec 6 13:20:31 2019 -0800 impose a naming convention on the global random state and lock variables Src/Base/AMReX_Random.cpp commit 4a570f14d63bb0681bea0857ecb8c4c046e30a4e Author: Andrew Myers Date: Fri Dec 6 13:15:28 2019 -0800 package the locking together in a BlockMutex class. Src/Base/AMReX_Random.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/Locking/main.cpp commit cba0db3bb7b963e82a4e25b41558798cbe67ada9 Author: Weiqun Zhang Date: Fri Dec 6 09:42:27 2019 -0800 nodal solver on gpu: need to call nodal sync if there are more than one Jacobi sweeps Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5e660e16e063bc6e497b3fb8add5de7147843ab1 Author: Weiqun Zhang Date: Fri Dec 6 09:36:47 2019 -0800 tweak nodal solver smoother for gpu Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 4ec5a952ee00e3c1a4f393f163fad66befbc1887 Author: Andrew Myers Date: Thu Dec 5 16:49:41 2019 -0800 update the section of the documentation about Particles on GPUs Docs/sphinx_documentation/source/GPU.rst commit 092eee2cdcabcd9f0a8ebb65b3e26c98c49cbc6f Author: Kevin Gott Date: Thu Dec 5 16:31:40 2019 -0800 Add documentation performance comment about thrust execution policies. Docs/sphinx_documentation/source/GPU.rst commit 959227d1bd9835a06f786687d4b5af667f73d5b2 Author: Andrew Myers Date: Thu Dec 5 16:12:13 2019 -0800 modify this test to execute 100 times in a loop Tests/GPU/Locking/main.cpp commit 5711a37969bf2e35801035010a3fec70d1dfda0c Author: Andrew Myers Date: Thu Dec 5 11:11:17 2019 -0800 move print statement Tests/GPU/RandomNumberGeneration/main.cpp commit 8d27e3cb22f2c536ed76174d0d329a25e2a086ed Author: Andrew Myers Date: Thu Dec 5 11:06:06 2019 -0800 clean up random number test a little bit Tests/GPU/RandomNumberGeneration/main.cpp commit 6736ac30c02f80845975c21ea367f18f33c26464 Author: Andrew Myers Date: Thu Dec 5 10:50:33 2019 -0800 reimplement lock using 64-bit CAS to simultaneously update the block and the counts. Src/Base/AMReX_Random.cpp Tests/GPU/Locking/main.cpp commit e3956774189309355a322a4829cf6971d3ad9796 Author: Michele Rosso Date: Wed Dec 4 15:13:26 2019 -0800 MacProjector: streamline handling of solver options Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit d8cd3dcbb80eadbf76405f484667711b3fb6a8a1 Author: Michele Rosso Date: Wed Dec 4 14:41:05 2019 -0800 NodalProjector: streamline handling of solver options Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit e61f2273ec2bcb5919bf4dd7447ca1a0ba70a720 Merge: f1879e73c 359c10924 Author: Weiqun Zhang Date: Wed Dec 4 13:09:53 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 359c10924998d5605270b412878644fc77277c7d Merge: 022775ef7 016edb791 Author: Andrew Myers Date: Wed Dec 4 12:07:25 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 022775ef766499b37c8ee04c14bcadd90a1d34d0 Author: Andrew Myers Date: Wed Dec 4 12:07:07 2019 -0800 change the way this buffer is unpacked to work around potential alignment issues Src/Particle/AMReX_ParticleContainerI.H commit f1879e73ca322f3c72a23c359be561c5017ea522 Author: Weiqun Zhang Date: Wed Dec 4 11:47:01 2019 -0800 fix template parameter for std::uninitialized_fill Src/Base/AMReX_PODVector.H commit 016edb79182f3981597724c563dd6b311ca84f19 Author: Weiqun Zhang Date: Wed Dec 4 09:51:51 2019 -0800 missed return type Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 8acf1d3b97baf4f2dee3fedafae7b0ed153761d4 Author: Weiqun Zhang Date: Wed Dec 4 09:47:52 2019 -0800 linear solver on gpu: change the default grid size for agglomeration and consolidation Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.H commit afb28f3d902ae16e15c922cfe53db314fb694158 Merge: 0c3cfbb4c e86805bee Author: cgilet Date: Wed Dec 4 09:39:32 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit e86805beea3e1d09bc2e93ccb06c7b37028eced3 Author: Weiqun Zhang Date: Tue Dec 3 17:04:15 2019 -0800 NodeEB test: agglomeration and consolidation parameters Tests/LinearSolvers/NodeEB/MyTest.cpp commit 2880de7cb2482709c59a0a674e335e70bdb95f60 Author: Weiqun Zhang Date: Tue Dec 3 16:54:46 2019 -0800 mod NodeEB test for scaling test Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp Tests/LinearSolvers/NodeEB/main.cpp commit ed9c740342bff69954e79e050a0c9bf2f04f42db Author: Andrew Myers Date: Tue Dec 3 16:30:18 2019 -0800 this method needs to return an iterator Src/Base/AMReX_PODVector.H commit 92c737c94bb230e852fb8293c26eb142d7887c91 Author: Andrew Myers Date: Tue Dec 3 16:17:32 2019 -0800 fix indentation Src/Base/AMReX_PODVector.H commit d76e2a71c45e4478bd4d35d9083d69f1fa80d62b Merge: ab20bff27 aec1ba070 Author: Andrew Myers Date: Tue Dec 3 16:13:28 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ab20bff273cbd1d28b2717f3884d530d80e6eedd Author: Andrew Myers Date: Tue Dec 3 16:13:18 2019 -0800 handle some shadowing and unused variable warnings Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_ParticleUtil.H commit 17de1cea0c18fdc836c69f63ac5adf3b3ff9d0eb Author: Andrew Myers Date: Tue Dec 3 16:12:42 2019 -0800 handle some edge cases involving inserting into empty PODVectors Src/Base/AMReX_PODVector.H commit aec1ba070375a801590ab029eff6fbbbf8871729 Author: Weiqun Zhang Date: Tue Dec 3 18:16:38 2019 -0500 CellEB2 test: parameters for agglomeration and consolidation Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp commit 3d53df8c07b084418bad586db497c2499b3c0e49 Author: Andrew Myers Date: Tue Dec 3 15:15:58 2019 -0800 remove unused variable Src/Particle/AMReX_DenseBins.H commit 43239eea1ad23cac7e96b491b858ef8b71884ba2 Author: Kevin Gott Date: Tue Dec 3 14:42:42 2019 -0800 Remove the CPU version of AMREX_GPU_LAUNCH_HOST_DEVICE_LAMBDA_ASYNC. GPU version was previously removed. Src/Base/AMReX_GpuLaunchMacrosC.H commit 04f34c95324645378ec1ad0c6c7634bf0edfc584 Author: Weiqun Zhang Date: Tue Dec 3 13:43:52 2019 -0800 fix pragma omp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a08d0de0d26a1125e1ee8fe3196e77cc4c773bfa Author: Kevin Gott Date: Tue Dec 3 13:44:05 2019 -0800 Adjust inputs to allow HeatEquation to run without managed memory. Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/inputs_3d commit 96879dd6924d49d3bf38580830cf1a6ac5f8f580 Author: Weiqun Zhang Date: Tue Dec 3 13:43:52 2019 -0800 fix pragma omp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f4ea453d505f8ae278c67f006b408d5a453871e7 Author: Weiqun Zhang Date: Tue Dec 3 13:10:54 2019 -0800 missed amrex:: Tests/LinearSolvers/CellEB2/main.cpp commit 8ef4edafd450638a41bdeaa4fb42bb0f672fe08b Author: Weiqun Zhang Date: Tue Dec 3 13:08:41 2019 -0800 CellEB2: don't write plotfile if doing scaling test Tests/LinearSolvers/CellEB2/main.cpp commit df1b9893928903863c5a2959f7d227c8e6c82908 Author: Weiqun Zhang Date: Tue Dec 3 11:25:27 2019 -0800 add some functions to MLMG for querying residuals, number of iterations, etc. after solve() is called. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit b1858334d1ded409995878aa74067360ab8b393d Author: Weiqun Zhang Date: Tue Dec 3 08:00:32 2019 -0800 FArrayBox::initVal: do it on gpu for non-NaN too Src/Base/AMReX_FArrayBox.cpp commit 32c796d6dce214a141c407cc9a58b508ff0710c0 Author: Weiqun Zhang Date: Mon Dec 2 21:23:40 2019 -0800 FArrayBox: use = to initialize snan on gpu Src/Base/AMReX_FArrayBox.cpp commit e0114f2ee62e63054f4aad68a6092c68492205c8 Author: Weiqun Zhang Date: Mon Dec 2 21:22:30 2019 -0800 add init_snan support for float Src/Base/AMReX_MemPool.cpp commit d27fe673248e8d44416d67733bb9b33be238cf01 Author: Weiqun Zhang Date: Mon Dec 2 21:21:19 2019 -0800 fix for single precision Src/Base/AMReX_MultiFab.cpp commit fb5c48a69968e5d578cf773996ee6c28e9f3f57f Merge: 671c35810 cbf027fdc Author: Weiqun Zhang Date: Mon Dec 2 16:03:30 2019 -0800 Merge branch 'weiqun/dev' into development commit 671c3581078c2912ce8f301e00c7f8cbab4ffaad Author: Max Katz Date: Mon Dec 2 13:38:02 2019 -0800 Move OMP offload flags into ibm.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/sites/Make.olcf commit cbf027fdcc005b7945aa137c6af4d14a93e66138 Merge: 076e8636d d6236fefb Author: Weiqun Zhang Date: Mon Dec 2 12:30:46 2019 -0800 Merge branch 'development' into weiqun/dev commit 0c3cfbb4c992b514d1b95a1727c1498b954e617e Merge: 3807d29e8 8c7b00219 Author: cgilet Date: Mon Dec 2 15:12:32 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit d6236fefb76f1ac6b84e4f8fd6c741ac9701f45a Merge: df66cfa92 8c7b00219 Author: Weiqun Zhang Date: Mon Dec 2 12:08:22 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 076e8636d96d96dd85648466d320bd1f709fc0f1 Author: Weiqun Zhang Date: Mon Dec 2 11:52:10 2019 -0800 CellEB2 test on gpu Tests/LinearSolvers/CellEB2/Make.package Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/MyTest_F.H Tests/LinearSolvers/CellEB2/MyTest_K.H Tests/LinearSolvers/CellEB2/mytest_f.F90 commit 8c7b00219eb14639f713ab9b95e48178d93363b5 Author: cgilet Date: Mon Dec 2 14:50:53 2019 -0500 Minor changes in single_level_weighted_redistribute(): add assert, be consistent about not filling ghost cells for div_out Src/EB/AMReX_EB_utils.cpp commit 8d31d5656dd6400514e05f1b3c612939f29d1d32 Merge: ba991ed65 df66cfa92 Author: Weiqun Zhang Date: Mon Dec 2 11:21:54 2019 -0800 Merge branch 'development' into weiqun/dev commit df66cfa92fcb4c0246bccc744d0a8307ee1d4b2a Author: Weiqun Zhang Date: Mon Dec 2 10:03:21 2019 -0800 move some functions used by EBLSCore into its own file Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtilI.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 3807d29e818628187abb7a5cd66d5f5438abf1a3 Author: cgilet Date: Mon Dec 2 11:45:09 2019 -0500 Update single_level_weighted_redistribute() Src/EB/AMReX_EB_utils.cpp commit ca5c7f27ed03785c010b068c877678e3b2a1a494 Merge: 9d741714b a367b50a1 Author: Weiqun Zhang Date: Mon Dec 2 08:41:55 2019 -0800 Merge branch 'master' into development commit a367b50a1b4c7006fd7d49c52ee38eddf51a2713 Author: Weiqun Zhang Date: Mon Dec 2 08:41:05 2019 -0800 update CHANGES CHANGES commit 7ec0e16e461804775fc0fb58c7e43ad1e7bf7101 Merge: 3966a58e8 9d741714b Author: cgilet Date: Mon Dec 2 08:37:05 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 9d741714b7ec5fedca995bfebb33594be899e188 Author: Johannes Blaschke Date: Sat Nov 30 17:37:08 2019 +0100 remove amrex submodule, wrong repo .gitmodules amrex commit 3bf5c62eb4e520c169302d29c944fa24e4e0fccc Author: Johannes Blaschke Date: Sat Nov 30 17:22:53 2019 +0100 add amrex .gitmodules amrex commit 0d099047335dff4000b23ababfca8a3c1bb0b36c Author: Kevin Gott Date: Fri Nov 29 13:31:29 2019 -0800 ParallelScan working, but extremely slow. Src/Base/AMReX_Scan.H Tutorials/GPU/ParallelScan/main.cpp commit 85d04cc4aef7958e5239b2162c45004c674ee103 Merge: 7f7352a48 bbdf4cbf8 Author: Weiqun Zhang Date: Wed Nov 27 21:05:32 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7f7352a4879cc5b6fb565899fd4d820c52687982 Author: Weiqun Zhang Date: Wed Nov 27 21:04:47 2019 -0800 BndryFunc: make RunOnGpu() and hasFabVersion() virtual Src/Amr/AMReX_StateDescriptor.H commit 3966a58e8f8e0d743e224debaffe0d04e4cf64fb Merge: cb6ecf4d3 bbdf4cbf8 Author: cgilet Date: Wed Nov 27 21:54:33 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit bbdf4cbf8c2bec0a8afa610cfd3523a5ee60c6fb Author: atmyers Date: Wed Nov 27 14:29:02 2019 -0800 add missing header Src/Base/AMReX_PODVector.H commit b79af2bbc46cfc7db512381a04e68c750bc6782e Merge: 284bf23b2 402a18d82 Author: atmyers Date: Wed Nov 27 12:06:57 2019 -0800 Merge branch 'development' into amrex_mutex commit cb6ecf4d3832fabec81ab45919987bdfafad5cb0 Merge: cf166df9c 402a18d82 Author: cgilet Date: Wed Nov 27 05:28:07 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 284bf23b2531c6b6cfdcf2ab090af193efbdebb7 Author: Andrew Myers Date: Tue Nov 26 14:48:25 2019 -0800 move the position of the __threadfence() to after the random states are updated Src/Base/AMReX_Random.cpp commit cfd809eaea06702cfe1f40488b0e0c463534a93b Author: Andrew Myers Date: Tue Nov 26 14:09:24 2019 -0800 change the way that get_state and free_state are implemented Src/Base/AMReX_Random.cpp commit a2270d2abc178f3cc516f2d2ac729e5ceb1fa479 Author: Andrew Myers Date: Tue Nov 26 14:09:07 2019 -0800 make the Test for random number generation harder to pass Tests/GPU/RandomNumberGeneration/main.cpp commit ba991ed659611ab11f97661674f6b05c622905d8 Author: Weiqun Zhang Date: Tue Nov 26 13:45:05 2019 -0800 use BuildMask function Src/EB/AMReX_EBMultiFabUtil.cpp commit 23cde1ae45f48f57a6ae7062105ff5aab1476160 Author: Andrew Myers Date: Tue Nov 26 13:38:01 2019 -0800 fix spaces Src/Base/AMReX_Random.cpp commit 402a18d82b7b6ab65a1c674a1689d0eea0d96001 Author: Weiqun Zhang Date: Tue Nov 26 13:26:21 2019 -0800 to not break MCNodalLinOP Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit c2244597d9c7548e6fbdfb784f5bec5d5c86d884 Author: Weiqun Zhang Date: Tue Nov 26 10:16:41 2019 -0800 remove duplicated codes Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 5be2ac0233bb5a7753786b5dcb914dd317e08f77 Author: Weiqun Zhang Date: Tue Nov 26 09:48:50 2019 -0800 rework on nodal dirichlet mask Src/Base/AMReX_FabArray.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 6ce3058684677eeeb6d82cfd1601eb9a45d47b94 Author: Weiqun Zhang Date: Tue Nov 26 09:25:42 2019 -0800 YAFluxRegister: use the new RecvLayoutMask Src/Boundary/AMReX_YAFluxRegister.cpp commit 5a57b6ed9719d6d030abda0e25d23f2ba2f8caf4 Merge: 8460a3415 12cfab736 Author: Weiqun Zhang Date: Tue Nov 26 08:48:27 2019 -0800 Merge branch 'development' into weiqun/dev commit 12cfab7369296acf4af36179c7345f75ba6b8ed7 Merge: 19ba2a8d0 73d2b9401 Author: WeiqunZhang Date: Tue Nov 26 08:46:55 2019 -0800 Merge pull request #628 from AMReX-Codes/statedata_arena Explicitly specify which Arena StateData uses commit 19ba2a8d08321c63c6e7fd534f3439d718092854 Merge: 47746185e 9251c9d97 Author: WeiqunZhang Date: Tue Nov 26 08:45:52 2019 -0800 Merge pull request #627 from AMReX-Codes/multifab_swap Add a MultiFab operation that explicitly swaps dst/src data commit 9251c9d97a375965d6beccf012fd416aacc0ff6c Author: Max Katz Date: Tue Nov 26 00:04:39 2019 -0800 Fix the ghost cell check Src/Base/AMReX_MultiFab.cpp commit 8678ba3d1bcbe0c6fc2d20a8d25aa280cd71415d Merge: d074714ae 47746185e Author: Max Katz Date: Mon Nov 25 23:52:25 2019 -0800 Merge branch 'development' into multifab_swap commit d074714ae6aea791ca692522a5f8df7e822fd214 Author: Max Katz Date: Mon Nov 25 23:44:51 2019 -0800 Take a shortcut in MultiFab::Swap() when we can Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_MultiFab.cpp commit fb7e38cbdb9e02908e40501f8623647d74376a11 Merge: b34875dc2 0981258a5 Author: Kevin Gott Date: Mon Nov 25 17:55:19 2019 -0800 Merge branch 'kngott/hip' of https://github.com/AMReX-Codes/amrex into kngott/hip commit b34875dc252d7226bbc29e6d95029824271bf664 Author: Kevin Gott Date: Mon Nov 25 17:54:58 2019 -0800 Add the complex MPI support to HIP in Device::Initialize and cleanup Device::Finalize. Src/Base/AMReX_GpuDevice.cpp commit 8460a3415916f0f6366e394871534acec2f9afaa Author: Weiqun Zhang Date: Mon Nov 25 16:30:03 2019 -0800 nodal solver: reimplement cc mask Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 47746185e3f595f344e63a461e8420a8e6f21ab4 Author: Andrew Myers Date: Mon Nov 25 16:02:12 2019 -0800 BL_ASSERT -> AMREX_ASSERT Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_ParticleMPIUtil.cpp Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 06688de331e483f243c952c8ffdbd76b1e73dc39 Merge: 51bc72cca e05ad5ce8 Author: Andrew Myers Date: Mon Nov 25 13:06:55 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 51bc72cca2bcd3a3b9e23b221c0636c4f1beb8b0 Author: Andrew Myers Date: Mon Nov 25 13:06:46 2019 -0800 an All-To-All communication pattern for comparison Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit fb398c02b770d4e35d4477f0d9bd79eb2f43b7f9 Author: Weiqun Zhang Date: Mon Nov 25 12:20:31 2019 -0800 MLEBABecLap: build mask using existing function in FabArray Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit e05ad5ce882366bf84f08b6d421b2c75724efd2d Merge: f564b616a a20981d9b Author: Andrew Myers Date: Mon Nov 25 14:56:41 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f564b616a9979cbe34216c02f03298ce673b365f Author: Andrew Myers Date: Mon Nov 25 14:56:25 2019 -0500 pp.get -> pp.query Tests/Particles/Redistribute/main.cpp commit 9d4771d6eb5178193bafa7db8154a48986509dd2 Author: Weiqun Zhang Date: Mon Nov 25 10:48:29 2019 -0800 return Arena* instead of const Arena* so that it can be used Src/Base/AMReX_FabArray.H commit a20981d9b8e726d5cfcf3f49a88ede1a405c5938 Merge: 703d08002 44ef24b73 Author: Weiqun Zhang Date: Mon Nov 25 10:43:24 2019 -0800 Merge branch 'weiqun/dev' into development commit 703d08002c7bf01bd6ff0c73680155dccaac2c97 Merge: 40d92017e adbdbbea7 Author: Weiqun Zhang Date: Mon Nov 25 10:43:19 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 44ef24b7332bf84db4eb5bf52bfd982e27082f61 Author: Weiqun Zhang Date: Mon Nov 25 10:20:20 2019 -0800 remove an incorrect assertion Src/Base/AMReX_FBI.H commit cf166df9c85034938c76d535a65d9d39f8a63b92 Merge: 7153bbab5 adbdbbea7 Author: cgilet Date: Mon Nov 25 13:16:31 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit adbdbbea7b5e003e9c1e3b6416aea57e49796a3c Author: cgilet Date: Mon Nov 25 13:12:11 2019 -0500 MLNodeLaplacian::compSyncResidualCoarse() - crse_cc_mask only needs 1 ghost cell; fix tests on the mask. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7153bbab5b090762807c9882a5c4b4d76e651801 Merge: 7fe7afd06 85c887fd0 Author: cgilet Date: Mon Nov 25 09:33:03 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 85c887fd05af26ac5ddc07d1bdf2c8313ac9ff1c Author: cgilet Date: Mon Nov 25 09:30:27 2019 -0500 MLNodeLaplacian::compSyncResidualCoarse() - crse_cc_mask needs 2 ghost cells. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7fe7afd06092d136c4f88a85f804ad93f7f1b8fc Merge: d4b128271 c31722024 Author: cgilet Date: Mon Nov 25 09:08:25 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 73d2b940110dbf983ff4d43c3b3272dc512cf6c6 Author: Max Katz Date: Sun Nov 24 14:18:03 2019 -0500 Explicitly specify which Arena StateData uses Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit 7c896638f6ba8dca4bf64bafb1e7cb7238ec3c83 Author: Max Katz Date: Sun Nov 24 14:14:59 2019 -0500 Add a MultiFab operation that explicitly swaps dst/src data Also add this as an option for StateData Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 40d92017e9cdea0ebf50373ae8f81ec726777ce9 Author: Weiqun Zhang Date: Sat Nov 23 07:41:02 2019 -0800 fix new bug in 835565 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit c9e087e7d948cbfca05405a0db3a54c0d3830f7b Author: Weiqun Zhang Date: Sat Nov 23 07:25:36 2019 -0800 remove unused variable Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7a34007f5d7f3a1326a28b175cc10eae2679c006 Author: Weiqun Zhang Date: Fri Nov 22 19:18:01 2019 -0800 around gcc bug Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c31722024951c63a877ff5abf327ff0e38d12546 Author: Andrew Myers Date: Fri Nov 22 17:20:35 2019 -0800 include lower offset Src/Particle/AMReX_ParticleLocator.H commit effb8018b516f95a3244dd4f312127bf7bc317a1 Author: Weiqun Zhang Date: Fri Nov 22 16:11:28 2019 -0800 redo some box intersection stuff in MLMG Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit deae44d187790bdde6cd58c402a45287ca78e04e Author: Weiqun Zhang Date: Fri Nov 22 15:45:58 2019 -0800 fix gpu compilation Src/Boundary/AMReX_YAFluxRegister.cpp commit 03f1edb987b26983f23d2ba48b11ef47aaea66c0 Author: Weiqun Zhang Date: Fri Nov 22 15:36:09 2019 -0800 reimplement YAFluxRegister part 2 Src/Base/AMReX_MultiFabUtil.cpp Src/Boundary/AMReX_YAFluxRegister.cpp commit d0fd8cd7b5c01018a350bc3ca1905d09de34b1a0 Author: Weiqun Zhang Date: Fri Nov 22 15:20:39 2019 -0800 use Reduce::AnyOf in nodal solver Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b0218a665ae1f413a0a7993c8826ed2b60dcad4f Author: Weiqun Zhang Date: Fri Nov 22 15:14:14 2019 -0800 reimplement YAFluxRegister part 1 Src/Boundary/AMReX_YAFluxRegister.cpp commit c59189f93c9d8ce913458299624981234f9ba048 Author: Weiqun Zhang Date: Fri Nov 22 15:13:38 2019 -0800 add Reduce::AnyOf Src/Base/AMReX_Reduce.H commit 3b56da9399822ec4d8712e08370ec0f21df8db44 Merge: 14b0943f3 8b91900c6 Author: Andrew Myers Date: Fri Nov 22 14:52:40 2019 -0800 Merge branch 'development' into dense_bins_locator commit 8b91900c6b15083fd11a0180496809a34cbdb6a9 Author: Andrew Myers Date: Fri Nov 22 14:05:46 2019 -0800 change the function to return a bool instead of Aborting Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp commit d8c2be65721b269c0c68c49bfc997c516a1610eb Author: Andrew Myers Date: Fri Nov 22 13:36:45 2019 -0800 add a function to abort if there are unused ParmParse entries Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp commit 14b0943f3bd3487bb021dd926a1025f637f42237 Author: Andrew Myers Date: Fri Nov 22 11:52:20 2019 -0800 resuse DenseBins in the ParticleLocator Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H commit db6fb71b044796e14a8be193d435fa964b509abe Author: Weiqun Zhang Date: Fri Nov 22 11:07:15 2019 -0800 around gcc bug Src/Base/AMReX_iMultiFab.cpp commit 7696d7a5edba38eb1c7120f2fcf488409568f23e Author: Weiqun Zhang Date: Fri Nov 22 10:25:15 2019 -0800 reimplement MultiMask define Src/Boundary/AMReX_MultiMask.cpp commit 517ec96b5238252aae266d908103b5ccedb36b91 Author: Weiqun Zhang Date: Fri Nov 22 10:24:51 2019 -0800 minor change in Vector to use size_type Src/Base/AMReX_Vector.H commit 5133637c13b974137fc12bfb0c869a6cc2725431 Author: Andrew Myers Date: Fri Nov 22 09:41:26 2019 -0800 don't use amrex:: namespace explicitly here for conciseness. Src/Particle/AMReX_ParticleMesh.H Src/Particle/AMReX_ParticleUtil.H commit d66759dee059ac9c2d654b55b16adf3bfccc14aa Author: Weiqun Zhang Date: Fri Nov 22 09:37:36 2019 -0800 reimplement owner mask Src/Base/AMReX_iMultiFab.cpp commit d4b1282716ff02e0a0f828f7a55043741b672e1e Merge: 556a6e733 9ce943f14 Author: cgilet Date: Fri Nov 22 10:23:57 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 9ce943f14108e599d74e98ad21f51c90c6535844 Author: Weiqun Zhang Date: Thu Nov 21 16:06:56 2019 -0800 fix a new typo in launch macro Src/Base/AMReX_GpuLaunchMacrosG.H commit 1d9f80fb50aeb4244ae88fa1180e26e17d82a1fa Author: Weiqun Zhang Date: Thu Nov 21 10:21:14 2019 -0800 nodal solver: sync residual for RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 0dd61542dfddad31c012ec8e5f3f817f10109a97 Author: Weiqun Zhang Date: Thu Nov 21 09:51:16 2019 -0800 nodal solver: build grid stencil in case we need it for sync solve. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ca4cacb1108095f66cdc4a1fb38b53861736b73d Author: Andrew Myers Date: Thu Nov 21 14:37:02 2019 -0800 enable these functions only for PC Src/Base/AMReX_TypeTraits.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleMesh.H Src/Particle/AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_Particles.H commit 60ea2c4abf6aaa48cbc8840caea0dacf8aa8ecb4 Author: Andrew Myers Date: Thu Nov 21 13:01:51 2019 -0800 automatically set USE_PARTICLES=TRUE in Src/Particles/Make.package Src/Particle/Make.package commit 0b3ad546116dbbdf44809c4410280ec8be7de0b8 Author: Andrew Myers Date: Thu Nov 21 13:01:27 2019 -0800 add is_particle_iterator and is_particle_container type traits Src/Base/AMReX_TypeTraits.H commit 020c29ada3a102c38a076466e37bc197e9621f3a Author: Andrew Myers Date: Thu Nov 21 13:01:02 2019 -0800 a version of numParticlesOutOfRange that operates only a single tile Src/Particle/AMReX_ParticleUtil.H commit 8f45dbed21480e2956779537f760f710e7243980 Author: Andrew Myers Date: Thu Nov 21 13:00:39 2019 -0800 fix spaces Src/Particle/AMReX_ParticleContainerI.H commit 74d85764b83abc15d40b7e06ea1907ca5034980b Author: Andrew Myers Date: Thu Nov 21 13:00:21 2019 -0800 move getTileIndex to .H file for inline Src/Particle/AMReX_ParticleUtil.cpp commit b743901c0ec9742fccdf3d6dba153e48a28731d8 Author: Andrew Myers Date: Thu Nov 21 12:59:55 2019 -0800 add a method allowing users to get a Geom from a ParIter Src/Particle/AMReX_Particles.H commit b4105608cd68b52ee47a09a2aa6a4ab6041e979b Author: Andrew Myers Date: Thu Nov 21 12:59:23 2019 -0800 have the particle iterator store a reference to the parent particle container Src/Particle/AMReX_ParIterI.H commit e042dd9121d16ef984c57533d07c2a9377a987f3 Author: Andrew Myers Date: Wed Nov 20 17:03:03 2019 -0800 been doing my briefs wrong for Doxygen... Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_Particles.H commit f09ade54d24468c8618d011a083d68fed7fd9a1d Merge: 794fd6764 46f8540f5 Author: Andrew Myers Date: Wed Nov 20 16:53:15 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 794fd6764ee61f6815a7f01f13541b9b0c2f3529 Author: Andrew Myers Date: Wed Nov 20 16:53:06 2019 -0800 docstrings for numOutOfRange Src/Particle/AMReX_ParticleUtil.H commit 46f8540f58f6a9edd74b62b69b301bad92d537b7 Author: Michele Rosso Date: Wed Nov 20 16:48:15 2019 -0800 EB redistribution: enable 2D support Src/EB/AMReX_EB_utils.cpp commit 556a6e73395781ca23711cb80e0e04e7d9ec5be5 Author: Michele Rosso Date: Wed Nov 20 16:48:15 2019 -0800 EB redistribution: enable 2D support Src/EB/AMReX_EB_utils.cpp commit c208e59906f8dd77a291c57c3249bfb271b3740c Author: Ann Almgren Date: Wed Nov 20 16:35:44 2019 -0800 Add CITATION file for AMReX CITATION commit 66866e84696ba318e11eecaee2d70a1c6b12f5b1 Merge: c8cd756b9 69544d386 Author: Weiqun Zhang Date: Wed Nov 20 16:25:55 2019 -0800 Merge branch 'weiqun/dev' into development commit 69544d386895ace27698f3b9a1ea3868243ea474 Author: Weiqun Zhang Date: Wed Nov 20 16:25:40 2019 -0800 nodal solver sync residual: WIP for RAP Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c8cd756b95a1bab5a2a5410952e61de4c8486108 Author: Andrew Myers Date: Wed Nov 20 15:55:44 2019 -0800 remove faulty assertion Src/Particle/AMReX_DenseBins.H commit 0981258a533748d3dd2486b8e87a94b07f5cb198 Author: Kevin Gott Date: Wed Nov 20 16:03:34 2019 -0700 Fix HIP FIX comments Src/Base/AMReX_Extension.H Src/Base/AMReX_FBI.H commit 6e69ab50e5bf404ae58d157a2bb315b6c28d2090 Author: Weiqun Zhang Date: Wed Nov 20 14:45:54 2019 -0800 SumBoundary: avoid self copy Src/Base/AMReX_MultiFab.cpp commit e9dcabb44a244db6d1fb80a9aa3bffb7aee320fa Merge: e9171a15b 35ccdcbee Author: Weiqun Zhang Date: Wed Nov 20 12:52:53 2019 -0800 Merge branch 'weiqun/dev' into development commit 35ccdcbee0572d11575e9ecd12d01de1e63d8cea Author: Weiqun Zhang Date: Wed Nov 20 12:52:21 2019 -0800 FArrayBox::initVal is back on gpu now Src/Base/AMReX_FArrayBox.cpp commit 5a8a07cfbcaf8eb1bd5be24324ced6fa3bea3de8 Author: Weiqun Zhang Date: Wed Nov 20 12:46:56 2019 -0800 make launch macros more robust Src/Base/AMReX_GpuLaunchMacrosG.H commit e9171a15b3dcdda56ca603a34d5071f864409a5b Author: Andrew Myers Date: Wed Nov 20 10:58:29 2019 -0800 make aborting if not all found an option Tools/Plotfile/fcompare.cpp commit a26ae5d5fcbb258b2d324c2f89495b456f3c9efd Author: Andrew Myers Date: Wed Nov 20 10:32:55 2019 -0800 have fcompare and particle_compare fail if the same variables are not present in the two plotfiles Tools/Plotfile/fcompare.cpp Tools/Postprocessing/C_Src/particle_compare.cpp commit ffacacb1885af4798768289fcfecb7870030332c Author: Andrew Myers Date: Wed Nov 20 10:24:45 2019 -0800 go back to using lower-case phi for the advection tutorials Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit 804cf006a44ed5f5177c89e815abe591d761726b Author: Weiqun Zhang Date: Wed Nov 20 09:55:09 2019 -0800 fix function name that has changed Src/Base/AMReX_FabArray.H commit 200f7fe053fa4bb490a97c03be7a9d77e754c374 Merge: b1ef82f57 eca997a7a Author: Weiqun Zhang Date: Wed Nov 20 09:47:36 2019 -0800 Merge branch 'development' into weiqun/dev commit b1ef82f5784b073ca1f6dc162a374081c1128165 Author: Weiqun Zhang Date: Wed Nov 20 09:47:03 2019 -0800 new makeFineMask that reuses parallel copy meta data Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit eca997a7a9aba57ba58c3ef14b5254b4f34d6d5a Merge: c300b8b62 3e4b549d1 Author: WeiqunZhang Date: Wed Nov 20 08:53:09 2019 -0800 Merge pull request #584 from shashankNREL/SY/FixSplineIF Fixes to the spline IF routines commit 3e4b549d14fb0717acd404d4803d34a7f3e6f990 Author: ShashankNREL Date: Wed Nov 20 08:28:11 2019 -0700 Made changes to solve thomas based on Weiqun suggestions on PR Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp commit c300b8b627e0953438b2f94f07a7948bbbe397e4 Author: Weiqun Zhang Date: Tue Nov 19 16:33:56 2019 -0800 comment out buggy code Src/Base/AMReX_FArrayBox.cpp commit 59d3a7172b4f0e30e934c152caf44776c8fc681f Author: Weiqun Zhang Date: Tue Nov 19 16:33:56 2019 -0800 comment out buggy code Src/Base/AMReX_FArrayBox.cpp commit 6213a6a1d14e828707e2faad8dfdea78bea9ce7f Merge: a4a80eea4 17a5e28d8 Author: Andrew Myers Date: Tue Nov 19 14:16:09 2019 -0800 Merge pull request #624 from ax3l/doc-exposeParticleTemplates Particles: Expose Template Arguments commit 17a5e28d844d96d55b141191fefd7f9b776139ca Author: Axel Huebl Date: Tue Nov 19 14:45:34 2019 -0700 Particles: Expose Template Arguments In order to code more generically downstream in WarpX, let's expose the template arguments that make up a particle and particle container as public constexpr. Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particles.H commit 291c3d02bb77f3698f6f62c1aab88e7018e18be2 Merge: 34bd51eaa 426a9a102 Author: Weiqun Zhang Date: Tue Nov 19 12:45:10 2019 -0800 Merge branch 'development' into weiqun/dev commit a4a80eea4a0d09f11dedfed4e08699f27ae0f145 Merge: 172e9817f 617df7a81 Author: Andrew Myers Date: Tue Nov 19 12:15:42 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 172e9817f485bcbbf28f3d8f87fad71bd9e78d14 Author: Andrew Myers Date: Tue Nov 19 12:15:31 2019 -0800 implement add / copy for particle container in a GPU friendly way Src/Particle/AMReX_ParticleContainerI.H commit 309778b59c32b1e8fef0bae7a14f2b58699031a1 Author: Andrew Myers Date: Tue Nov 19 12:15:10 2019 -0800 add copyParticles form of transformation Src/Particle/AMReX_ParticleTransformation.H commit 617df7a81fd6e3c0010b8bacab639b8bbe2b937b Author: Brandon Runnels Date: Tue Nov 19 13:10:26 2019 -0700 added option in libamrex configure script to specify cuda-arch (#623) * added option in libamrex configure script to specify cuda-arch * fixed strip() incompatibility Tools/libamrex/configure.py commit f91d915598ac97eb82d379998c42675c4121d9ff Author: Andrew Myers Date: Tue Nov 19 11:43:01 2019 -0800 fix some more spaces Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_DenseBins.H commit 426a9a1020ee553f7eae496bea6475f062182bfc Merge: 2804fe608 f91d91559 Author: Weiqun Zhang Date: Tue Nov 19 11:41:44 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 40bea036c0b378de45e0366e4aaa9d9a6bc427b1 Author: Andrew Myers Date: Tue Nov 19 11:41:41 2019 -0800 fix some spaces Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 2804fe608216f848a0c419aa5498bb44e45d6523 Author: Weiqun Zhang Date: Tue Nov 19 11:41:34 2019 -0800 update assertion Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 3d286b3a185b33b0260b04bb31d6a7789964b967 Author: Andrew Myers Date: Tue Nov 19 11:41:08 2019 -0800 use rvalue references in MeshToParticle, ParticleToMesh Src/Particle/AMReX_ParticleMesh.H commit 565b78636c2ae279d3227f592f0b36cf1dfa3fb2 Author: Andrew Myers Date: Tue Nov 19 11:36:51 2019 -0800 also change the non-Gpu version of these typedefs Src/Base/AMReX_GpuContainers.H commit 3f9b95265cb5d05952e595a38824c6389a6100d3 Author: Andrew Myers Date: Tue Nov 19 11:32:27 2019 -0800 remove CUDA ifdef Src/Particle/AMReX_ParticleContainerI.H commit 8e1f943de6c0d0e1043b033468a9259debcd7113 Author: Andrew Myers Date: Tue Nov 19 11:32:07 2019 -0800 EnforcePeriodicGPU -> EnforcePeriodic Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 7c08bfdbc2c7666b375860af0d929dbc19a932e3 Merge: 3fea03401 8cf5e3e55 Author: Andrew Myers Date: Tue Nov 19 11:23:23 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3fea034012a49f5adf76312a211f0c44c8c65e1c Author: Andrew Myers Date: Tue Nov 19 11:23:12 2019 -0800 update the docs re: thrust vectors Docs/sphinx_documentation/source/GPU.rst commit 34bd51eaa5f94be9f6342fd85980c53d1cf98a83 Author: Weiqun Zhang Date: Tue Nov 19 11:17:10 2019 -0800 reimplement gpu version of overlap mask Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp commit d33d65f0ca359d6df7024590f311ecbd7a5d1e6f Author: Andrew Myers Date: Tue Nov 19 11:05:17 2019 -0800 add some docstrings to the GpuContainers Src/Base/AMReX_GpuContainers.H commit 7b466a86a92361d5b3a3f0700175a047e4d79782 Author: Andrew Myers Date: Tue Nov 19 10:58:22 2019 -0800 ManagedDeviceVector -> ManagedVector Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 5b81e97f901fc483134de46b73565f21f0ad22be Author: Andrew Myers Date: Tue Nov 19 10:54:59 2019 -0800 PinnedDeviceVector -> PinnedVector, same for Polymorphic Src/Base/AMReX_GpuContainers.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_Particles.H commit 8cf5e3e551c0b96465e4cd2477942e36fbc87dc5 Merge: 2329449c3 1f8510edc Author: Weiqun Zhang Date: Tue Nov 19 10:48:58 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2329449c304eac2ccc1bc82f017d52f9dbe16d8e Author: Weiqun Zhang Date: Tue Nov 19 10:35:02 2019 -0800 init signaling nan on gpu in FArrayBox::initVal Src/Base/AMReX_FArrayBox.cpp commit 51d58914be6f47c029b406e340db355b912a33b1 Author: Andrew Myers Date: Tue Nov 19 10:32:39 2019 -0800 remove old thrust test Tests/Particles/StructOfArrays/CudaManagedAllocator.H Tests/Particles/StructOfArrays/GNUmakefile Tests/Particles/StructOfArrays/Make.package Tests/Particles/StructOfArrays/StructOfArrays.H Tests/Particles/StructOfArrays/main.cpp commit 1f8510edc1f548f9f1f3da23329548b13f393ae6 Author: Weiqun Zhang Date: Tue Nov 19 10:29:06 2019 -0800 fix typo Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit c0aa96225927e5332ab2b3ee4f1eb16a38007760 Author: Andrew Myers Date: Tue Nov 19 10:24:09 2019 -0800 remove unneeded thrust includes Src/Base/AMReX_Vector.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H commit 35b5788a2ab20a8b47b04b4b642fc3fea8ad6873 Author: Weiqun Zhang Date: Tue Nov 19 10:24:01 2019 -0800 fix typo Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 4682052e4646f2a8c233d8a0903906d61d728a28 Author: Andrew Myers Date: Tue Nov 19 10:16:54 2019 -0800 remove unused file / function Src/Particle/AMReX_Functors.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 7b3ea980af0d2af1fb7be14d447a12ad70a7afa0 Merge: bd188d90e ad70bc1a3 Author: Andrew Myers Date: Tue Nov 19 10:13:42 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bd188d90e29e6b538b40e2359fdb16d08c044675 Author: Andrew Myers Date: Tue Nov 19 10:13:35 2019 -0800 reuse copyParticle function in Redistribute Src/Particle/AMReX_ParticleContainerI.H commit ad70bc1a373dac10d8360c5ea7d7109f5f83608f Author: Weiqun Zhang Date: Tue Nov 19 09:44:48 2019 -0800 rename myArena to arena Src/Base/AMReX_FabArray.H commit cd47aead73238c36c72dd3ebecc9b135411ed8b4 Author: Weiqun Zhang Date: Tue Nov 19 09:22:05 2019 -0800 fix a couple issues with tiling and gpu Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Src/EB/AMReX_MultiCutFab.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 0f04f7571fbbb58598ebfefd1fc408549eee31d2 Merge: 545f19e6f 7c052f50a Author: Andrew Myers Date: Mon Nov 18 16:42:27 2019 -0800 Merge branch 'development' into particle_transformation commit 545f19e6f60d623cc06427a3d5772f23da8b5158 Author: Andrew Myers Date: Mon Nov 18 16:41:58 2019 -0800 add some enable_if and decltype for maximum obfuscation Src/Particle/AMReX_ParticleTransformation.H commit 7c052f50a12213e47632c37ab91f5c3afa4fe885 Merge: eadec9400 9833b1491 Author: Weiqun Zhang Date: Mon Nov 18 15:58:39 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit eadec9400d496891c6624ee8853c1b3807f0181e Author: Weiqun Zhang Date: Mon Nov 18 15:58:29 2019 -0800 fix corner case for EB tensor solver Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit faaf0492d96f111509f0bf472c83bbeede684a14 Merge: f7b7619a4 9833b1491 Author: Andrew Myers Date: Mon Nov 18 15:35:51 2019 -0800 Merge branch 'development' into particle_transformation commit 9833b14910984e7347471bf893b9a01a4fdac40c Author: Andrew Myers Date: Mon Nov 18 15:35:25 2019 -0800 use forwarding references in AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleReduce.H commit e9c4690512ee797f6b5ec4329eb4b08fb80dc379 Author: Weiqun Zhang Date: Mon Nov 18 13:14:25 2019 -0800 add some LaunchSafeGuards Src/AmrCore/AMReX_TagBox.cpp commit f7b7619a4bbdc8e1342fd4c3c60d32f91ef0a4e2 Author: Andrew Myers Date: Mon Nov 18 15:25:36 2019 -0800 use std::forward Src/Particle/AMReX_ParticleTransformation.H Tests/Particles/ParticleTransformations/main.cpp commit 2db29c377c9bf695dc6381274012b08ec120266d Author: Andrew Myers Date: Mon Nov 18 14:50:15 2019 -0800 move all the transformation stuff to a separate file Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 6f4a7b18a00766f301f06c6efae2e54c55d1edd1 Author: Andrew Myers Date: Mon Nov 18 10:40:31 2019 -0800 fix spaces Src/Particle/AMReX_Particles.H commit 103d46d04ce3b3de0885e8344393aedbcb9924b6 Author: Andrew Myers Date: Mon Nov 18 13:47:10 2019 -0800 fix and test filterAndTransform Src/Particle/AMReX_ParticleUtil.H Tests/Particles/ParticleTransformations/main.cpp commit 42efed5618bdca62a6587cfb1a00f811ec5b5beb Merge: fc90f3435 ebdfecc07 Author: Andrew Myers Date: Mon Nov 18 13:25:53 2019 -0800 Merge branch 'development' into particle_transformation commit fc90f3435cb942c246f2157f221462e3952d6219 Author: Andrew Myers Date: Mon Nov 18 13:25:27 2019 -0800 make filter tests more strict Tests/Particles/ParticleTransformations/main.cpp commit 0aa3d2b5cf720d904b19d742e26a91659fa34c5e Author: Andrew Myers Date: Mon Nov 18 13:15:49 2019 -0800 add assertion Tests/Particles/ParticleTransformations/main.cpp commit ced10b74d7f397878c2fe0e291f0193db4eba0cc Author: Andrew Myers Date: Mon Nov 18 13:13:24 2019 -0800 fix name Tests/Particles/ParticleTransformations/main.cpp commit 15fb3b0b254574643abc998f75313882d811e811 Author: Andrew Myers Date: Mon Nov 18 13:11:52 2019 -0800 fixes for filter Src/Particle/AMReX_ParticleUtil.H Tests/Particles/ParticleTransformations/main.cpp commit 1f9ccd094ef7d0092f29e639f149d51b0588cefb Author: Andrew Myers Date: Mon Nov 18 12:52:42 2019 -0800 some fixes for filter Src/Particle/AMReX_ParticleUtil.H Tests/Particles/ParticleTransformations/main.cpp commit ebdfecc07100dcd2b4e4ff5121850781a9d79c50 Author: Weiqun Zhang Date: Mon Nov 18 12:08:32 2019 -0800 add single precision compile test Tests/SinglePrecision/GNUmakefile Tests/SinglePrecision/Make.package Tests/SinglePrecision/main.cpp Tools/CompileTesting/compiletesting.py commit e27ae203f37a91ca98bb129bd17f3810ae613b3a Author: Weiqun Zhang Date: Mon Nov 18 11:10:38 2019 -0800 remove BaseFab RunOn because it doesn't work and there is no nice ways to fix it Src/Base/AMReX_BaseFab.H commit 5772132bc7adff6ae31e5303fd06a0c551ed4f5e Author: Andrew Myers Date: Mon Nov 18 11:07:01 2019 -0800 some refactoring of the transform test Tests/Particles/ParticleTransformations/main.cpp commit cceb8bc8528789c784f5084bdf85d5f6898f92a5 Author: Weiqun Zhang Date: Mon Nov 18 10:59:07 2019 -0800 rm BaseFab::ForEach Src/Base/AMReX_BaseFab.H Tests/ThirdPartyLib/foo.cpp commit 26ffdd176d181a1d281796157c17c2f68c57e3f2 Merge: 2ee205374 199c471ec Author: cgilet Date: Mon Nov 18 13:50:20 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 4082fd24c8c5ef9038bf11410d68fc08580dd50f Author: Andrew Myers Date: Mon Nov 18 10:41:06 2019 -0800 Stronger test of transformations Tests/Particles/ParticleTransformations/main.cpp commit 54ba9996aeb53e071dec6741d45926123f52e8f0 Author: Andrew Myers Date: Mon Nov 18 10:40:31 2019 -0800 fix spaces Src/Particle/AMReX_Particles.H commit f82ae3af6574beaa5df255e3638855c0dd7ee79a Merge: 963e315f8 199c471ec Author: Andrew Myers Date: Mon Nov 18 10:09:26 2019 -0800 Merge branch 'development' into particle_transformation commit 199c471ecdf0b6462944e964a8bf6d378ae67616 Merge: d1a5612db 6741c4fef Author: WeiqunZhang Date: Mon Nov 18 08:32:48 2019 -0800 Merge pull request #621 from ax3l/fix-warningFinal PhysBCFunct: Final Warning commit 6741c4fef234f02cf2ae357bc63261e691b8b5db Author: Axel Huebl Date: Mon Nov 18 00:34:27 2019 -0700 PhysBCFunct: Final Warning Warning with Clang: ``` ../amrex/Src/Base/AMReX_PhysBCFunct.H:112:42: warning: class with destructor marked 'final' cannot be inherited from [-Wfinal-dtor-non-final-class] virtual ~PhysBCFunctNoOp () override final {} ^ ../amrex/Src/Base/AMReX_PhysBCFunct.H:106:7: note: mark 'amrex::PhysBCFunctNoOp' as 'final' to silence this warning class PhysBCFunctNoOp ``` Src/Base/AMReX_PhysBCFunct.H commit d1a5612db842d5fe359f1c927b9d7a14e1c2bbfc Author: Weiqun Zhang Date: Sun Nov 17 18:37:36 2019 -0800 rm deprecated Fortran files Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H commit bffa678da6142242707c8e4c0ce032d3f155fe19 Merge: aef2ba848 9b8c9bda4 Author: Weiqun Zhang Date: Sun Nov 17 17:06:40 2019 -0800 Merge branch 'development' into weiqun/dev commit aef2ba8482c9d372c4d9958dd1a50b95e9cb071e Author: Weiqun Zhang Date: Sun Nov 17 17:04:28 2019 -0800 nodal solver on gpu: reflux Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit 5d351fc12a6217fb56c27e2834e0eaf4458b21c2 Merge: 6802ac494 9b8c9bda4 Author: Kevin Gott Date: Fri Nov 15 16:27:29 2019 -0800 Merge branch 'development' into kngott/hip commit 9b8c9bda4aad606eb88eccb7efa2fa5a6ff75592 Author: Kevin Gott Date: Fri Nov 15 16:26:13 2019 -0800 Add access to the Arena used to build a FabArray through a BaseFab::DataAllocator. Src/Base/AMReX_FabArray.H commit f015477d515f51e6df0007840e8215d125c83a65 Author: Weiqun Zhang Date: Fri Nov 15 16:20:15 2019 -0800 fix warning Src/Base/AMReX_GpuContainers.H commit eaeacfc09ffb664be2234db62371493294a37997 Author: Weiqun Zhang Date: Fri Nov 15 16:20:15 2019 -0800 fix warning Src/Base/AMReX_GpuContainers.H commit af346a31507b3d52b3b6f5368ddd65cc01d16ba6 Author: Weiqun Zhang Date: Fri Nov 15 15:25:57 2019 -0800 nodal solver on gpu: coarse sync residual Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c2d0484d369a59670c8b67a503b4d71ac527af70 Author: Weiqun Zhang Date: Fri Nov 15 15:24:11 2019 -0800 some very important spaces to me Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp commit 2898dbae3b8a526590b783c24b5a0a226c841e32 Author: Kevin Gott Date: Fri Nov 15 14:06:19 2019 -0800 Use Pinned Arena for plotting. Avoids unneeded memory movement. Src/Base/AMReX_PlotFileUtil.cpp commit da98b660f0fd911b80571aa2837c944d1158cddd Author: Andrew Myers Date: Fri Nov 15 13:48:49 2019 -0800 need to include Base in makefile Tools/Postprocessing/C_Src/GNUmakefile commit dddbfa083e081c37c40a5be77666c819364cae92 Author: Andrew Myers Date: Fri Nov 15 13:46:33 2019 -0800 remove debug print Tools/Postprocessing/C_Src/particle_compare.cpp commit 0c31231d00d4ee3283d48372ef229bc3a430ee15 Author: Andrew Myers Date: Fri Nov 15 13:45:05 2019 -0800 fix some typos in fcompare.cpp Tools/Plotfile/fcompare.cpp commit 311a08be3c12be880f73ca3683cc49c66134963a Author: Andrew Myers Date: Fri Nov 15 13:44:41 2019 -0800 make particle_compare respect a relative tolerance Tools/Postprocessing/C_Src/particle_compare.cpp commit 4e88756be2589fb75b85733a24c97b070544a8bc Author: Andrew Myers Date: Fri Nov 15 13:14:06 2019 -0800 sort particle data by id and cpu before comparing Tools/Postprocessing/C_Src/particle_compare.cpp commit 6bc284af828f7621a0aa906e03aa3a3a3021e623 Author: Weiqun Zhang Date: Fri Nov 15 09:33:42 2019 -0800 fix the number of components Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp commit 92201d5b002283d2cff1b0133306ecd2b7808304 Author: Weiqun Zhang Date: Fri Nov 15 09:24:55 2019 -0800 fix variable names Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp commit da7daaa8abe563d4fe898796233652b90308884b Author: Weiqun Zhang Date: Fri Nov 15 08:52:01 2019 -0800 remove some variables from plotfile for gpu regression test Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp commit 6802ac494856033c7815d316d658d7253c47c069 Author: Kevin Gott Date: Thu Nov 14 16:53:36 2019 -0800 First draft for Pinned copy I/O HeatEquation. Need to store Arena and use same one throughout before it will work. Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 963e315f8428e6877b847707c731e2f711e16e46 Author: Andrew Myers Date: Thu Nov 14 16:38:16 2019 -0800 AMREX_FOR_1D -> AMREX_HOST_DEVICE_FOR_1D, to respect launch region flag Src/Particle/AMReX_ParticleUtil.H commit df4306c313233fe13072558f46ca7299c58cc8f7 Merge: 9b7513829 83a2d3c71 Author: Weiqun Zhang Date: Thu Nov 14 16:31:11 2019 -0800 Merge branch 'weiqun/dev' into development commit dc3da0a8fd7adc622cc5fd3a809532d131dca7e6 Author: Andrew Myers Date: Thu Nov 14 16:31:09 2019 -0800 make the test abort on error Tests/Particles/ParticleTransformations/main.cpp commit 9b75138291d331af62f4dcf8e856d6e1ffbed562 Merge: 2d71d64bc 9eaf3876e Author: Weiqun Zhang Date: Thu Nov 14 16:31:04 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f5ffd51ba6c4d3cf054edb8265f002b84667d2ee Author: Andrew Myers Date: Thu Nov 14 16:29:33 2019 -0800 use forwarding references for function objects Src/Particle/AMReX_ParticleUtil.H commit 3d4a8f82ce4dbeb1e2a60875870a1f374b1668d3 Author: Andrew Myers Date: Thu Nov 14 16:22:37 2019 -0800 fix comment Src/Particle/AMReX_ParticleUtil.H commit 83a2d3c719eee984a9eae6279025329748859aeb Author: Weiqun Zhang Date: Thu Nov 14 15:54:07 2019 -0800 fix index type Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5323bd10ef988730194978e7157102b85150734e Merge: 7b27ab9e4 9eaf3876e Author: Andrew Myers Date: Thu Nov 14 15:22:47 2019 -0800 Merge branch 'development' into particle_transformation commit 9eaf3876ebfef72c8899756a5db47e9002c4d30a Author: Andrew Myers Date: Thu Nov 14 15:20:04 2019 -0800 add an additional debug assert Src/Particle/AMReX_DenseBins.H commit dabc585e676fc9da3e8daaff30f21c86a066328f Author: Andrew Myers Date: Thu Nov 14 15:19:28 2019 -0800 use Gpu::copy instead of dtod_memcpy, which is a no-op on the CPU Src/Particle/AMReX_DenseBins.H commit 8ae492cd8a780d6bcfd1e9ea315b02a91a89c491 Author: Weiqun Zhang Date: Thu Nov 14 15:17:28 2019 -0800 fix a warning on calling host function from host device function Src/Base/AMReX_MultiFabUtil.cpp commit 0702c0a73e5df3c51241c5669bbcfb4e9175e8c7 Author: Weiqun Zhang Date: Thu Nov 14 15:17:05 2019 -0800 make Array4::operator bool host and device Src/Base/AMReX_Array4.H commit 2d71d64bcf37650ba57732c678dfdaf2fac93e5d Merge: 81bedd553 4654a2f51 Author: Weiqun Zhang Date: Thu Nov 14 15:10:04 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 81bedd55327aec139cf697bd07abe4c312c007fd Author: Weiqun Zhang Date: Thu Nov 14 15:09:37 2019 -0800 nodal solver on gpu: coarse residual Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8cd0375fd9c4ba1a15e31db9776c9ab9bd84109e Author: Weiqun Zhang Date: Thu Nov 14 14:11:42 2019 -0800 refactor makeFineMask for gpu Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 7b27ab9e40c11081b432b9473797ca2ff7e041c2 Merge: 49dd7cf53 4654a2f51 Author: Andrew Myers Date: Thu Nov 14 13:54:49 2019 -0800 Merge branch 'development' into particle_transformation commit 4654a2f51c4fc6f61c2cfce0da122f0b9283ef89 Merge: dd3bb608a 5fd80b1d4 Author: Andrew Myers Date: Thu Nov 14 13:51:09 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit dd3bb608a30d97b5a5ad4f198950559ac6cfbf04 Author: Andrew Myers Date: Thu Nov 14 13:51:01 2019 -0800 need to handle the cpu-only case in these functions Src/Base/AMReX_GpuContainers.H commit 49dd7cf53bc5618e54d4ff08a366c2672ba06d9a Author: Andrew Myers Date: Thu Nov 14 13:45:47 2019 -0800 initial test for particle transformations Src/Particle/AMReX_Particles.H Tests/Particles/ParticleTransformations/GNUmakefile Tests/Particles/ParticleTransformations/Make.package Tests/Particles/ParticleTransformations/inputs Tests/Particles/ParticleTransformations/main.cpp commit 3e2dfdb8df7762d6be564ec6cf195e9f73741826 Author: Andrew Myers Date: Thu Nov 14 11:33:00 2019 -0800 start adding some general particle transformation and filtering routines Src/Particle/AMReX_ParticleUtil.H commit 5fd80b1d4b702af2cd9edb53f52aba6467069eee Merge: b4cb612c2 8e7f439da Author: Weiqun Zhang Date: Thu Nov 14 11:06:00 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b4cb612c21ba44b12278c29083212c5bfffcba30 Author: Weiqun Zhang Date: Thu Nov 14 11:05:20 2019 -0800 nodal solver on gpu: coarse contribution to divu Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit e6c2f2fec970924e8458c1ef10beb1b75f374c5b Author: Weiqun Zhang Date: Thu Nov 14 11:04:23 2019 -0800 add operator bool to Array4 Src/Base/AMReX_Array4.H commit 8e7f439daaf18fecab63fcfb9181a9dd335402f8 Merge: 41e3b3a1e c9e098c04 Author: Andrew Myers Date: Thu Nov 14 10:34:25 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 41e3b3a1eb69ea16a4286e4ac3b339830f5b3368 Author: Andrew Myers Date: Thu Nov 14 10:34:16 2019 -0800 remove over-zealous assertion Src/Particle/AMReX_StructOfArrays.H commit c9e098c04161b3c4046960616f61124b8b3f3482 Merge: f9042b21f fd1a6f393 Author: WeiqunZhang Date: Thu Nov 14 10:22:26 2019 -0800 Merge pull request #619 from AMReX-Codes/amrex_copy Amrex copy commit fd1a6f3931f10370903c5801dcdd364376be05ec Author: Andrew Myers Date: Thu Nov 14 10:13:48 2019 -0800 add static_assert for trivial copyability Src/Base/AMReX_GpuContainers.H commit 4f9538fdc97a0cb2e2d80b548e4763905a303c6d Author: Andrew Myers Date: Thu Nov 14 10:03:17 2019 -0800 fix copy/paste error in docstring Src/Base/AMReX_GpuContainers.H commit ed5bdd6fb8a9f16ba2252a2ce91a81926c2a11b9 Merge: 5ba6091e6 f9042b21f Author: Andrew Myers Date: Thu Nov 14 10:01:44 2019 -0800 Merge branch 'development' into amrex_copy commit f9042b21f361ac8b84483503f2c286582ed1c92d Author: Andrew Myers Date: Thu Nov 14 09:59:45 2019 -0800 the number of bins is actually m_offsets.size()-1 Src/Particle/AMReX_DenseBins.H commit fa9c0a0505b295b3997b75ebdea441f89ac6c667 Author: Weiqun Zhang Date: Thu Nov 14 09:24:47 2019 -0800 nodal solver on gpu: fine contribution to rhs Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 877c7550c0eafdc7a6e1ef5144aaf36a61d054db Author: Kevin Gott Date: Wed Nov 13 16:10:57 2019 -0800 qFix AMREX_HIP_OR_CUDA in MemPool init. Src/Base/AMReX_MemPool.cpp commit 9978dbbe924ed95c37fe2b13254d6768242f4e91 Author: Kevin Gott Date: Tue Nov 12 23:38:41 2019 -0800 First MPI HIP adjustments (MPI is WIP -- Pretty much just turned on at this point). Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Tools/GNUMake/Make.defs commit adbcbe66fa6b5b0c8765de5ede7cfe8932c22151 Author: Weiqun Zhang Date: Wed Nov 13 15:11:41 2019 -0800 fix xsdk Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_distFcnElement.cpp commit 1a0aa3a1be60275839ad23e2bfb3ae88108325fa Author: Andrew Myers Date: Wed Nov 13 14:36:45 2019 -0800 same for the DenseBins structure Src/Particle/AMReX_Particles.H commit f342cf32506ff7a62ddf222db99678bb68e6b6a5 Author: Andrew Myers Date: Wed Nov 13 14:35:42 2019 -0800 need m_ptile_r whether compiling for GPU or not Src/Particle/AMReX_Particles.H commit 7510d847594d7640b4d5a362e05fb0b2d9ced3e9 Merge: b1e108950 645254833 Author: Andrew Myers Date: Wed Nov 13 14:27:05 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b1e1089505000596d17c0addca005641479e1c68 Author: Andrew Myers Date: Wed Nov 13 14:26:56 2019 -0800 don't need this AMREX_USE_CUDA guard Src/Particle/AMReX_ParticleContainerI.H commit 02ad00e727c896d9f1889b6bdad5a03f1f61980a Author: Andrew Myers Date: Wed Nov 13 14:26:25 2019 -0800 add inputs for test that bins particles by cell Tests/Particles/Redistribute/inputs.rt.cuda.sort commit 2ee20537459a679aada4606c4fc21a17100a683f Merge: 4a7b3e28a 2bdf4365c Author: Michele Rosso Date: Wed Nov 13 14:25:16 2019 -0800 Merge branch 'ebtensor_flux' of https://github.com/AMReX-Codes/amrex into ebtensor_flux commit 4a7b3e28ae359996ca04a04cc27c243a77adfc9c Author: Michele Rosso Date: Wed Nov 13 14:24:18 2019 -0800 Fix comp index when calling EB_set_covered in redistribution Src/EB/AMReX_EB_utils.cpp commit 6452548339e57052c1b17872aaba263a2b3c834a Author: Michele Rosso Date: Wed Nov 13 14:24:18 2019 -0800 Fix comp index when calling EB_set_covered in redistribution Src/EB/AMReX_EB_utils.cpp commit add72a8c1c8fd383b035fdde7e60b962333bf083 Author: Andrew Myers Date: Wed Nov 13 14:07:09 2019 -0800 replace runtime_real with runtime_int here Src/Particle/AMReX_ParticleUtil.H commit 0abd1e5f73cc1eb0eae2ea4bf9249adb860ff1f1 Author: Andrew Myers Date: Wed Nov 13 14:01:09 2019 -0800 add some docstrings for copyParticle, gather, and scatter Src/Particle/AMReX_ParticleUtil.H commit 5ba6091e67694b9fd3a123958f2d253664d78c5c Author: Andrew Myers Date: Wed Nov 13 13:50:46 2019 -0800 docstrings Src/Base/AMReX_GpuContainers.H commit 26e35d967ffb8e1e6f7196000961b5af731b46d3 Merge: 8ddbfbb5b 0014c0f3b Author: Andrew Myers Date: Wed Nov 13 13:31:07 2019 -0800 Merge branch 'development' into amrex_copy commit 8ddbfbb5b88cb622693687845cdc825747a97da2 Author: Andrew Myers Date: Wed Nov 13 13:29:40 2019 -0800 fix silly mistake uncovered by this PR Tests/Particles/Redistribute/main.cpp commit 0014c0f3b38c71f174035ac6477c7e8d81c80b05 Author: Andrew Myers Date: Wed Nov 13 16:27:57 2019 -0500 use new swap method of ParticleTile Src/Particle/AMReX_ParticleContainerI.H commit 2bdf4365c9dc80f30c61a9b589981e2331d11d6a Author: cgilet Date: Wed Nov 13 16:06:07 2019 -0500 MLEBTensorOp::compFlux abort if Location!=FaceCenter. Clean up. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 292956d4060fd287f4ca33819d8b717ffcf95b5d Author: Andrew Myers Date: Wed Nov 13 12:50:13 2019 -0800 add async versions Src/Base/AMReX_GpuContainers.H commit 96e14cc4d3841348cd19ce82e8a5dcbd17ce4f27 Author: Andrew Myers Date: Wed Nov 13 12:48:53 2019 -0800 replace thrust_copy with amrex_copy Docs/sphinx_documentation/source/GPU.rst Src/Base/AMReX_GpuContainers.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleBufferMap.cpp Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_ParticleLocator.H Tests/Particles/Intersection/main.cpp Tests/Particles/NeighborParticles/MDParticleContainer.cpp Tests/Particles/ParticleReduce/main.cpp Tests/Particles/Redistribute/main.cpp Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit e142267ca0b551d14963e5e287d0578a96ebb0f6 Author: Andrew Myers Date: Wed Nov 13 10:22:26 2019 -0800 thrust_copy is in the Gpu:: namespace Tests/Particles/NeighborParticles/MDParticleContainer.cpp commit d1b41388a9a857bf8ab1af801cd34cb660fe41f5 Author: Weiqun Zhang Date: Wed Nov 13 10:12:17 2019 -0800 for eb nodal on gpu, do a Jacobi sweep before Gauss Seidel Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8d083fcd65099663e387948dd662c8173becfcd1 Merge: 869fa0fac d6aa3a3a0 Author: Andrew Myers Date: Tue Nov 12 17:24:07 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 869fa0fac0485b874c3f2072844f50994aaf9e35 Author: Andrew Myers Date: Tue Nov 12 17:23:18 2019 -0800 clean up building this neighbor copy op and add a missing stream sync Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit cd00e125ce440408b62449d844495388f58f32ca Author: Andrew Myers Date: Tue Nov 12 17:22:38 2019 -0800 adjust size of counts so we don't have a weird +1 Src/Particle/AMReX_ParticleCommunication.H commit 9749c7d3cb0e1d0fe8a6fe27b2e5c097191de1a8 Author: Andrew Myers Date: Tue Nov 12 17:21:31 2019 -0800 use 'size' here so these assertions will work when neighbor particles are in play Src/Particle/AMReX_ParticleTile.H commit 1ab692d865b4d56ce66580ad5144ca0e939acbfb Author: Kevin Gott Date: Tue Nov 12 16:56:20 2019 -0800 More no-GPU fixes. Src/Base/AMReX_IntVect.H Src/Base/AMReX_Random.cpp commit d6aa3a3a05debf5257c5b2ac1d54b621225ddeac Author: Andrew Myers Date: Tue Nov 12 19:10:08 2019 -0500 fix typo Src/Particle/AMReX_ParticleUtil.H commit c9d9831bf6e7fff10f3b7565fb7977c1c4dfd589 Author: Kevin Gott Date: Tue Nov 12 15:15:50 2019 -0800 Adjustments for no GPU builds. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_Random.cpp commit f7aa3d44821d513284209a278d8db618ce3e436f Merge: 873b9569f 1354f8369 Author: Andrew Myers Date: Tue Nov 12 18:09:43 2019 -0500 fix merge conflict commit 873b9569fa7ed24e52f1a5f115a41ffc5ac356a2 Author: Andrew Myers Date: Tue Nov 12 18:06:58 2019 -0500 update test Tests/Particles/Redistribute/main.cpp commit 361d6593646135dfee87cea509d88a49976490c6 Author: Andrew Myers Date: Tue Nov 12 18:06:36 2019 -0500 go ahead and implement scatter too, why not Src/Particle/AMReX_ParticleUtil.H commit 82e725e9932a54261d42a483fd959c3e9c0c9e60 Author: Andrew Myers Date: Tue Nov 12 18:02:07 2019 -0500 implement gather in terms of a general copyParticle host / device function Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_ParticleUtil.H commit 42739fd37259444cbd65e32059a64f6a67d7621f Author: Andrew Myers Date: Tue Nov 12 17:02:26 2019 -0500 a few missing helper routines for ParticleTile Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit 19f16695d337cd9fab1a69db7a6a522ca9026f41 Author: Andrew Myers Date: Tue Nov 12 16:49:19 2019 -0500 implement our own gather particles routine, remove calls to the thrust one Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_ParticleUtil.H commit 1354f83699e4b8c5ec3872dd524078dbced3359f Author: Weiqun Zhang Date: Tue Nov 12 12:54:53 2019 -0800 add IntVect n_filled to FabArray to help users to keep track of how many ghost cells have been updated by FillBoundary ParallelCopy Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit eb7f6e98443a88259e7a8390c8c94eeb934c6b5c Author: Andrew Myers Date: Tue Nov 12 15:54:43 2019 -0500 remove unused variables Src/Particle/AMReX_ParticleContainerI.H commit 8531b90fbba00dafeb136b29b6d23bac56143d67 Author: Andrew Myers Date: Tue Nov 12 15:48:57 2019 -0500 reuse m_ptile_r for temp storage Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ad519247fe0d19d7e0a52122f603ef1e52b265ff Author: Weiqun Zhang Date: Tue Nov 12 12:26:52 2019 -0800 nodal solver: smooth on gpu and do it twice Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d6c97ff79435b6316d00d0fcf5f74d93740db626 Author: Weiqun Zhang Date: Tue Nov 12 10:17:00 2019 -0800 nodal solver: build stencil on gpu Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 24f4f16d1f6176f8f8976f70140648cab655b54a Author: Weiqun Zhang Date: Tue Nov 12 09:38:54 2019 -0800 removed more LaunchSafeGuards from nodal solver Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 262de7ff1db5a5fc8c07b6f2a7b25368cf9538de Author: Kevin Gott Date: Tue Nov 12 11:06:42 2019 -0800 Revert to using long through __shfl_down overload. Src/Base/AMReX_iMultiFab.cpp commit 39395656f6b8a65d1bfb695dd6cc1d568decbde1 Author: Kevin Gott Date: Tue Nov 12 11:06:16 2019 -0800 Hipify thrust::cuda::par function. Src/Base/AMReX_GpuAllocators.H commit a5ad28c7c7c43d19721444956c3daf5d92fa51b8 Author: Kevin Gott Date: Tue Nov 12 11:05:51 2019 -0800 Turn <<<>>> into GPU safe macro. Src/Base/AMReX_FBI.H commit 1614d0d855474e3c7726d6f7fc649eb2f34103e9 Merge: d0535f0e9 6546855fc Author: Andrew Myers Date: Tue Nov 12 10:01:07 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d0535f0e9bfdb63624be835dd6e907b03c0e545c Author: Andrew Myers Date: Tue Nov 12 10:00:53 2019 -0800 call should be to the free function, not to a member here Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 14ae49524fc5fa919c45ec8102ff561b1320b56e Merge: 90d32fd9f 6546855fc Author: Kevin Gott Date: Mon Nov 11 21:10:52 2019 -0800 Merge branch 'development' into kngott/hip commit 6546855fcddf3b9919c9a2b8e3f0a3448bc6b319 Author: Weiqun Zhang Date: Mon Nov 11 20:44:20 2019 -0800 fix using namespace Cuda Src/Base/AMReX_Gpu.H commit 83444e82b5bbe8525d970dd1faa34a4c7fe544d8 Author: Weiqun Zhang Date: Mon Nov 11 20:38:59 2019 -0800 add array and const_array functions taking starting component to FabArray and BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit 90d32fd9f73475dbbc4bc3ba6f90072abb1ce74b Merge: 1f0c76859 d0b1f05c7 Author: Kevin Gott Date: Mon Nov 11 17:57:46 2019 -0800 Merge branch 'development' into kngott/hip commit d0b1f05c7827feb1d32f243128491e9e3c51e567 Author: Kevin Gott Date: Mon Nov 11 20:56:22 2019 -0500 Change Cuda->Gpu in filenames and thrust/container/allocator calls throughout. Docs/sphinx_documentation/source/GPU.rst Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAllocators.H Src/Base/AMReX_GpuAllocators.cpp Src/Base/AMReX_GpuContainers.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Tests/GPU/Locking/main.cpp Tests/GPU/Partition/main.cpp Tests/GPU/RandomNumberGeneration/main.cpp Tests/Particles/NeighborParticles/MDParticleContainer.cpp Tests/Particles/ParticleReduce/main.cpp Tests/Particles/Redistribute/main.cpp Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 5304b59edf6f9fd2e3f0a14747a4531f83026646 Author: Kevin Gott Date: Mon Nov 11 20:24:08 2019 -0500 Convert CudaContainers and CudaAllocators to Gpu. Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_ParticleContainerI.H Tests/GPU/Partition/main.cpp Tutorials/GPU/ParallelScan/main.cpp commit 1f0c768594d161920278a6fd0be7bb1bb8431d3c Merge: 83aad7d15 fd7eebec8 Author: Kevin Gott Date: Mon Nov 11 17:19:20 2019 -0800 Merge branch 'development' into kngott/hip commit 8d0d202b121c288b9f0b6e880227fa97385e96c4 Author: Andrew Myers Date: Mon Nov 11 19:43:49 2019 -0500 optionally make this test do an extra particle sort step Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit fd7eebec8cea6bcfac770671cf2ccfefa13fb209 Author: Andrew Myers Date: Mon Nov 11 16:37:34 2019 -0800 add an additional out-of-range check to neighbor list construction Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit feaf146272f1fbf5274c3f3c31644a82054aea32 Author: Weiqun Zhang Date: Mon Nov 11 16:27:48 2019 -0800 removed some LaunchSafeGuards in MLNodeLaplacian Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e6d7f48a40410eeaefde731c87edbe56c367e014 Author: Andrew Myers Date: Mon Nov 11 19:23:18 2019 -0500 implement Sort in terms of DeviceBins Src/Particle/AMReX_ParticleContainerI.H commit 3849ff24f46e28f4a6654d8d86e910a164032202 Author: Andrew Myers Date: Mon Nov 11 19:22:48 2019 -0500 remove some unused temporaries Src/Particle/AMReX_Particles.H commit 302fac0e453ea3cff83ffc08f99adeef6d89f976 Author: Andrew Myers Date: Mon Nov 11 19:22:25 2019 -0500 thrust_copy -> dtod_memcpy Src/Particle/AMReX_DenseBins.H commit 1bb984f7e1505b28d54c310e4a9d44bfbea08626 Author: Andrew Myers Date: Mon Nov 11 19:21:34 2019 -0500 have this resize run on the device when compiling with GPUs Src/Base/AMReX_PODVector.H commit 83aad7d1595dbae681f2fa2568611a0c19d0e641 Author: Kevin Gott Date: Mon Nov 11 16:02:38 2019 -0800 Couple small HIP things. Src/Base/AMReX_Random.cpp Src/Base/AMReX_Scan.H commit 4abc1a4336364507da63ce29059b1ec9435de2ca Author: Kevin Gott Date: Mon Nov 11 16:02:05 2019 -0800 Add long wrapper for shfl_down and label old HIP FIX problems. Src/Base/AMReX_GpuUtility.H commit 4ad5db250b6acb034343998310fc9cf0fc81c341 Author: Kevin Gott Date: Mon Nov 11 16:01:27 2019 -0800 Turn on all reductions and adjust for noexcept. Tutorials/GPU/ParallelReduce/main.cpp commit 4257c1119317179cada34e219a41efe466d14ffe Author: Weiqun Zhang Date: Mon Nov 11 15:45:00 2019 -0800 forgot ifdef AMREX_USE_GPU Src/Base/AMReX_FBI.H commit 0f12b50c983a2c772a733da40b81eac69e86013d Author: Weiqun Zhang Date: Mon Nov 11 15:09:37 2019 -0800 FabArray::BuildMask on gpu Src/Amr/AMReX_Extrapolater.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp commit ca8b5f51ae8a68eb7cd6aa3315e318aac9f9639e Author: Max Katz Date: Mon Nov 11 16:39:42 2019 -0500 Allow code to compile for either old or no-host builds Src/Base/AMReX_filcc_mod.F90 commit def7c8df405e81fe35ff3d6d38c43649bc891382 Author: Andrew Myers Date: Mon Nov 11 15:33:20 2019 -0500 begin refactor of SortParticlesByCell Src/Particle/AMReX_ParticleContainerI.H commit 9b67a19234ee686109a677b8f65701c09527d26f Author: Andrew Myers Date: Mon Nov 11 15:11:09 2019 -0500 remove unnecessary thrust::reduce call in NeighborList::build Src/Particle/AMReX_NeighborList.H commit bdb04196fc0d140b9e48f9064436fbfd66ad54ec Merge: c3736efdb d0463208a Author: Andrew Myers Date: Mon Nov 11 14:25:58 2019 -0500 Merge branch 'runtime_soa' into development commit c3736efdbabd2cd2623c4c62eb7c88191832e691 Author: Weiqun Zhang Date: Mon Nov 11 09:12:51 2019 -0800 Fortran: add a new parallel copy routine that takes array for the number of ghost cells Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 7759efad45eefcd62e1e08d84bb55de840800fa0 Merge: 0cc07bb72 3b7e7bd6a Author: WeiqunZhang Date: Mon Nov 11 08:37:45 2019 -0800 Merge pull request #617 from AMReX-Codes/update_default_cuda_arch Update the default CUDA architecture to cc70 (Volta V100) commit 0cc07bb72ce31345d44588ae759482b7ed302adb Author: Max Katz Date: Sun Nov 10 21:36:03 2019 -0800 ifdef out CPU boundary fill functions for device-only pragma build Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_filcc_mod.F90 Src/Base/Make.package commit 56bd6ee8c2a41bfe76e7bb0e2a5f32077df2593f Author: Max Katz Date: Sun Nov 10 21:28:41 2019 -0800 Define a default value for a new make variable Tools/GNUMake/Make.defs commit 864ee51c1fbdd7f2f03ba9c0d04647132351eb3f Author: Max Katz Date: Sun Nov 10 21:03:15 2019 -0800 Add a define if we're using the no-host version Tools/GNUMake/Make.defs commit e76f21dd82b201c2e6a765653bce38fe9acedf8f Author: Max Katz Date: Sun Nov 10 20:27:02 2019 -0800 Add option for GPU pragmas to generate only a device version Tools/F_scripts/gpu_fortran.py Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 1729979c383d82e2bf90924ad5e7de770145734d Author: Max Katz Date: Sun Nov 10 19:13:33 2019 -0800 Implement amrex_fab_filcc without amrex_get_loop_bounds Src/Base/AMReX_filcc_mod.F90 commit a4844541b6d5dd1125f33dd2c5ca913b7b44e2bd Author: Weiqun Zhang Date: Sat Nov 9 16:50:32 2019 -0800 add IntVect ghost cells version of some MultiFab functions including Saxpy Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit c46d782a93a93243e5b4f9e4d9cbbc92d5df3ac7 Author: Weiqun Zhang Date: Sat Nov 9 07:25:00 2019 -0800 Node solver: remove some LaunchSafeGuards Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 3b7e7bd6aacdaa9275b1f04891364b201cef11a2 Author: Max Katz Date: Sat Nov 9 10:03:10 2019 -0500 Update the default CUDA architecture to cc70 (Volta V100) Tools/GNUMake/Make.defs commit 23d8121760c7fdc0351c8ad35df0f5f65754c52c Merge: d038f4814 adc2abd12 Author: Weiqun Zhang Date: Fri Nov 8 18:41:57 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d038f481493e587ca18b4b8bbf542591b301a4e4 Author: Weiqun Zhang Date: Fri Nov 8 18:41:45 2019 -0800 fix unused variables Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit cf3d5b580180ec69c2b05eae518bd2354f35a6fc Author: Weiqun Zhang Date: Fri Nov 8 16:21:40 2019 -0800 nodal eb on gpu: 2d intergral Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d0463208af26554155935bded24d090a925f3389 Merge: 1d15fc974 adc2abd12 Author: Andrew Myers Date: Fri Nov 8 19:17:06 2019 -0500 Merge branch 'development' into runtime_soa commit adc2abd1254141795e6fca6d150927ddbfa2b63b Author: Andrew Myers Date: Fri Nov 8 19:16:44 2019 -0500 remove this execution policy for now Src/Base/AMReX_CudaContainers.H commit 1d15fc97493cc4f97ea790b4a117d353df86bada Merge: 6eb85a13f f65e6c372 Author: Andrew Myers Date: Fri Nov 8 19:05:35 2019 -0500 Merge branch 'development' into runtime_soa commit 6eb85a13f6af31a557329d4008edd47da7c3714e Author: Andrew Myers Date: Fri Nov 8 19:05:00 2019 -0500 add some AMREX_RESTRICT Src/Particle/AMReX_ParticleTile.H commit 5b02532a92ef19ac96b4ac317be68da074ad7bb5 Author: Andrew Myers Date: Fri Nov 8 18:51:44 2019 -0500 need to include these changes to ParticleTile as well Src/Particle/AMReX_ParticleTile.H commit 17c86a7e6735b391aef59a1143988a9bf7eb1a42 Author: Andrew Myers Date: Fri Nov 8 18:50:48 2019 -0500 account for optional components in RedistributeGPU Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_Particles.H commit 700b0d4a6c8d95b9ab01d6a966ae193ef6971350 Author: Weiqun Zhang Date: Fri Nov 8 15:32:38 2019 -0800 eb nodal on gpu: rhcc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 3de668cb03ad3004a506ee7ccc6a4cc8af45a4a0 Author: Weiqun Zhang Date: Fri Nov 8 15:02:31 2019 -0800 fix new bug in eb nodal Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit 266a9b691574bac1f5e30717853d34edad96f467 Author: cgilet Date: Fri Nov 8 18:09:12 2019 -0500 For MLEBTensorOp::compFlux, fix cut cell flux bogus value for 2D Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H commit 91fe4c26b86c132a9022950a77d77006d3d4897c Author: cgilet Date: Fri Nov 8 18:05:47 2019 -0500 Fix MLEBTensorOp::compFlux Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit e3cd43b576135e357c6ba7c603b236a1768897d8 Author: Weiqun Zhang Date: Fri Nov 8 14:57:33 2019 -0800 eb nodal on gpu: mknewu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 17c537d0856ed5a4e1e168a23640f5b18c5bbe05 Author: Weiqun Zhang Date: Fri Nov 8 13:49:02 2019 -0800 eb nodal on gpu: divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c20d672b1f743469e713b794d80575f61462119b Author: Michael Rowan Date: Fri Nov 8 12:30:38 2019 -0800 Add CUPTI trace feature for GPU kernel timing Src/Base/AMReX_ActivityTraceAsync.H Src/Base/AMReX_ActivityTraceAsync.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/Make.package Tests/GPU/CuptiTest/Exec/CUDA/GNUmakefile Tests/GPU/CuptiTest/Exec/CUDA/Make.package Tests/GPU/CuptiTest/Exec/CUDA/myfunc.H Tests/GPU/CuptiTest/Exec/CUDA/myfunc.cpp Tests/GPU/CuptiTest/Exec/CUDA/mykernel.H Tests/GPU/CuptiTest/Make.CUPTI Tests/GPU/CuptiTest/Source/Make.package Tests/GPU/CuptiTest/Source/main.cpp Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit a4beddd9b453702f3699d51293fbdb8fe65a4511 Author: Kevin Gott Date: Fri Nov 8 13:37:59 2019 -0800 Additional cleanup. Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_iMultiFab.cpp commit 71381ed2735f86c68fb70e322a66fe8877e047ed Author: Kevin Gott Date: Fri Nov 8 13:37:19 2019 -0800 Clean up tests. Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/main.cpp Tutorials/GPU/ParallelReduce/main.cpp commit 44da881124ebf57cc4fb683714398e342a65d557 Author: Kevin Gott Date: Fri Nov 8 13:12:45 2019 -0800 Remove unneeded ifdef. Src/Base/AMReX_CudaAllocators.H commit 457925f1bdccae314ef9e6ea452671a456c18ce8 Merge: 3dd8e07fa f65e6c372 Author: Kevin Gott Date: Fri Nov 8 13:08:42 2019 -0800 Merge branch 'development' into kngott/hip commit f65e6c3722840593384a144cee29b452d61ec714 Author: Andrew Myers Date: Fri Nov 8 13:08:54 2019 -0800 remove unused CudaManagedAllocator Src/Base/AMReX_CudaAllocators.H commit 2d5b48b8f5a9e70f5122df068fcc6770275220fd Author: Weiqun Zhang Date: Fri Nov 8 13:08:19 2019 -0800 eb nodal on gpu: set stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 3dd8e07faf40598abc099ceffb63ad1f06058860 Author: Kevin Gott Date: Fri Nov 8 12:59:36 2019 -0800 Turn ThrustAllocator on for HIP. Src/Base/AMReX_CudaAllocators.H commit 75a83db0f2a6365034eef6f509b3ea980f70bbb9 Merge: 25cd8720e e67e8531c Author: Andrew Myers Date: Fri Nov 8 12:51:23 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 25cd8720e5f84e4bc17788034ad265a8a8e24998 Author: Andrew Myers Date: Fri Nov 8 12:51:09 2019 -0800 remove unused functors Src/Particle/AMReX_Functors.H commit 2764a17d510a7abb0c9257077c232f94119e8fcd Author: Andrew Myers Date: Fri Nov 8 12:47:14 2019 -0800 be explicit about thrust::device execution policy Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Tutorials/GPU/ParallelReduce/main.cpp commit c89b4558d74a795a99d03a4a4ce43b560965d0bb Author: Weiqun Zhang Date: Fri Nov 8 11:35:52 2019 -0800 eb nodal on gpu: set_connection Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d7eb46ea9cd1e4dfb53e38a5cbb0c1e4605014f8 Merge: 65269c411 e67e8531c Author: Kevin Gott Date: Fri Nov 8 11:33:25 2019 -0800 Merge branch 'development' into kngott/hip commit 951fcba866968e50de209312de006e8172b68ae2 Merge: debc51c90 84804b9fe Author: cgilet Date: Fri Nov 8 13:40:08 2019 -0500 Merge branch 'ebtensor_flux' of https://github.com/AMReX-Codes/amrex into ebtensor_flux commit debc51c909c09d17a410042f8ede20fa46ba99ef Merge: 30fdf7aa6 e67e8531c Author: cgilet Date: Fri Nov 8 13:34:27 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit e67e8531ceaedfb9dde05bef9a5c83278046bbe4 Author: Weiqun Zhang Date: Fri Nov 8 09:55:34 2019 -0800 remove deprecated Fortran functions Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H commit ec4aadad976d49af023a52a3806e291f53f267fc Merge: 1967f01c5 4e1e6585e Author: Weiqun Zhang Date: Fri Nov 8 09:50:00 2019 -0800 Merge branch 'development' into weiqun/dev commit 1967f01c50f8e48d878d9e3781e004f6240a3c0a Author: Weiqun Zhang Date: Thu Nov 7 13:48:27 2019 -0800 mlndlap_stencil_rap on gpu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit efc1eae6b722bea2a98642787118733725d9744d Author: Weiqun Zhang Date: Thu Nov 7 13:48:09 2019 -0800 add Array1D, Array2D and Array3D Src/Base/AMReX_Array.H commit 4e1e6585e70fc713cd0143cbd3f5947a85544290 Author: Max Katz Date: Thu Nov 7 16:35:17 2019 -0500 Report numerical CUDA error Src/Base/AMReX_GpuError.H commit 28c7b7bd2c33f9b348dd74f44fa82496119820ab Merge: c67b962e4 9cf789af8 Author: Andrew Myers Date: Thu Nov 7 11:56:02 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c67b962e4b526485e818887c4e2ef9851ca65456 Author: Andrew Myers Date: Thu Nov 7 11:55:53 2019 -0800 const versions of offsetsPtr and permutationPtr Src/Particle/AMReX_DenseBins.H commit 84804b9fe69ce20a15059e76569e7d525cde9518 Author: Michele Rosso Date: Thu Nov 7 11:35:15 2019 -0800 MacProjector: allow to set BCs on a per-level basis Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 7a9540c7d83317f98ac8d6981b50d085b6fb1bbe Author: Michele Rosso Date: Wed Nov 6 15:51:17 2019 -0800 NodalProjector: fix bug in definition of nodal grids Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 9cf789af8d7884a8fafe69bc4a32a0528f7e469d Merge: 3654520c5 0836a3c30 Author: Michele Rosso Date: Thu Nov 7 11:35:21 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3654520c5a2ae59a65d14e6751b76500daa41fa7 Author: Michele Rosso Date: Thu Nov 7 11:35:15 2019 -0800 MacProjector: allow to set BCs on a per-level basis Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 0836a3c30997b7b01b0627dc75605a9d79f28abd Merge: d7d52cded 9019a3f46 Author: Andrew Myers Date: Wed Nov 6 16:46:26 2019 -0800 Merge pull request #614 from AMReX-Codes/dense_bins Expose "dense bins" data structure so that WarpX can use it to implement binary collisions commit 9019a3f467d71ec6a1b4e70cbdf9afcdf49a72f0 Author: Andrew Myers Date: Wed Nov 6 16:40:33 2019 -0800 add an extra entry to counts to avoid having +1/-1 below Src/Particle/AMReX_DenseBins.H commit 13e077fa6652e1dc3cdda80e0d6d8edffe6c0637 Author: Andrew Myers Date: Wed Nov 6 15:58:42 2019 -0800 streamSynchronize at the end of DenseBins Src/Particle/AMReX_DenseBins.H commit dad8775c253104eea56b46fa2a93498a157835b8 Author: Andrew Myers Date: Wed Nov 6 15:57:16 2019 -0800 use AMREX_D_DECL for 2D Src/Particle/AMReX_NeighborList.H commit b6c88342ae4ec8216a94f96e82e509a40d6c5bb0 Author: Andrew Myers Date: Wed Nov 6 15:56:12 2019 -0800 add AMReX_BLProfiler.H Src/Particle/AMReX_DenseBins.H commit 643229d353b227a46d7b22ed76a9322401589023 Author: Andrew Myers Date: Wed Nov 6 15:55:12 2019 -0800 make these types public Src/Particle/AMReX_DenseBins.H commit f253c166d5a18b4ec4bfc4a665a658f188ef62cc Author: Andrew Myers Date: Wed Nov 6 15:54:44 2019 -0800 fix comment Src/Particle/AMReX_DenseBins.H commit 3b13a6d504c9dd08e4e8f960a394c03665074edd Merge: 0c022635f d7d52cded Author: Andrew Myers Date: Wed Nov 6 15:54:03 2019 -0800 Merge branch 'development' into dense_bins commit d7d52cded85ba1c0633da6c239741e85b53571bb Author: Michele Rosso Date: Wed Nov 6 15:51:17 2019 -0800 NodalProjector: fix bug in definition of nodal grids Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit f0a34d5b0335cedfe6d9e72e5438f72243d623b9 Merge: 0ef69cbe4 d7d52cded Author: Andrew Myers Date: Wed Nov 6 18:49:53 2019 -0500 Merge branch 'development' into runtime_soa commit 5de720f3901ca3732558994e84318a75df096c48 Merge: 9d5783807 64e56deba Author: Weiqun Zhang Date: Wed Nov 6 15:40:08 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9d57838074c1d8eafbcd1b3d5eba59f0eff25bee Author: Weiqun Zhang Date: Wed Nov 6 15:00:00 2019 -0800 MLNodeTensorLap tutorial: use cg and increase bottom max iters Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Tutorials/LinearSolvers/NodeTensorLap/MyTest.cpp commit 65269c4113dbd6533c99afa266e7ea2d4e74d2d5 Merge: 3d130037e 64e56deba Author: Kevin Gott Date: Wed Nov 6 14:30:12 2019 -0800 Merge branch 'development' into kngott/hip commit 3d130037ea0f5c2db9100703cb625e9ba79d791b Author: Kevin Gott Date: Wed Nov 6 14:29:49 2019 -0800 Add rocprim and rocthrust header-only libraries. Tools/GNUMake/comps/hip.mak commit f878f382ae9eb5e7525919c5287f7d457e389be5 Merge: ad77d18a5 618a63e7b Author: Kevin Gott Date: Wed Nov 6 14:29:01 2019 -0800 Merge branch 'development' into kngott/hip commit 64e56deba10cf91603108bdbf4c5cf386f217f70 Merge: 536d8c9ad 576c3ea11 Author: Andrew Myers Date: Wed Nov 6 16:16:00 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 536d8c9ad88923d9fee22f46e90c9ed4d9a3951b Author: Andrew Myers Date: Wed Nov 6 16:15:35 2019 -0500 add missing device synchronize after packing buffer but before copying to pinned memory. Src/Particle/AMReX_ParticleContainerI.H commit 576c3ea11ebe184b7f9331bde23e766e815accbb Merge: 180086142 18cb858b6 Author: Weiqun Zhang Date: Wed Nov 6 10:58:35 2019 -0800 Merge branch 'nodal_tensor_poisson' into development commit 18cb858b65e70ff3efc3ec6c93f1df30a0417e15 Author: Weiqun Zhang Date: Tue Nov 5 16:14:42 2019 -0800 MLNodeTensorLaplacian: hypre Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Tutorials/LinearSolvers/NodeTensorLap/GNUmakefile Tutorials/LinearSolvers/NodeTensorLap/MyTest.H Tutorials/LinearSolvers/NodeTensorLap/MyTest.cpp commit 30fdf7aa686d34740395c22e10c6a1d8a3278398 Merge: 35c06bf03 180086142 Author: cgilet Date: Wed Nov 6 12:03:05 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 1800861420b66bf933ec3a78f603c07445f576ef Author: Ann Almgren Date: Tue Nov 5 15:40:45 2019 -0800 fix oops Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 34bcab5abe9c24ff5631248c00746b655b554453 Author: Ann Almgren Date: Tue Nov 5 15:33:44 2019 -0800 Need to call normalize on the tilebox not the full box.Z Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 0c022635f82a3704e4f29e5585c0d1b51e2d2856 Author: Andrew Myers Date: Tue Nov 5 15:30:57 2019 -0800 Revert "start to implement particle locator in terms of DenseBins" This reverts commit e458866dee5e14b4c8033b50551f86d688c2561c. Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H commit 170cf62b8bf8bd1ec0299a9a3adb91c9586557d7 Author: Andrew Myers Date: Tue Nov 5 14:59:39 2019 -0800 make sure we re-calculate the comm_size when enableInverse is toggled Src/Particle/AMReX_NeighborParticles.H commit e458866dee5e14b4c8033b50551f86d688c2561c Author: Andrew Myers Date: Tue Nov 5 14:26:11 2019 -0800 start to implement particle locator in terms of DenseBins Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H commit 45e243e2cfed6ee9ad03157034004f7cac3f2fa2 Author: Andrew Myers Date: Tue Nov 5 13:49:19 2019 -0800 expose dense bins data structure so it can be used to implement binary collisions in WarpX Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_NeighborList.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 36a55adb2dc5ab3bb1acbe3205287f44b113966e Author: Weiqun Zhang Date: Tue Nov 5 13:35:56 2019 -0800 tutorial for Nodal Tenosr Laplacian solver Tutorials/LinearSolvers/NodeTensorLap/GNUmakefile Tutorials/LinearSolvers/NodeTensorLap/Make.package Tutorials/LinearSolvers/NodeTensorLap/MyTest.H Tutorials/LinearSolvers/NodeTensorLap/MyTest.cpp Tutorials/LinearSolvers/NodeTensorLap/MyTestPlotfile.cpp Tutorials/LinearSolvers/NodeTensorLap/main.cpp commit e66b3c6eb820e50b3367dc2487299e9b6cd47b48 Author: Weiqun Zhang Date: Tue Nov 5 13:02:49 2019 -0800 MLNodeTensorLaplacian: 3d Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H commit 0ef69cbe4459cb2c44f306f3911e2469a871be63 Author: Andrew Myers Date: Tue Nov 5 14:20:28 2019 -0500 add some runtime components to the redistribute tests Tests/Particles/Redistribute/inputs.rt.cuda Tests/Particles/Redistribute/inputs.rt.cuda.mr Tests/Particles/Redistribute/inputs.rt.cuda.nonperiodic commit ca6b81f134f79d434bc7158b8a3d28cfb901a2cb Author: Andrew Myers Date: Tue Nov 5 14:13:56 2019 -0500 also update the type of the snd/rcv buffers in neighbor particles Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit b71d3d07a52cb33520d3a2c163489d3c67371821 Author: Andrew Myers Date: Tue Nov 5 14:03:30 2019 -0500 restore get/set superparticle, which is used in the reductions Src/Particle/AMReX_ParticleTile.H commit e24a99ef74844cf968d53e753b52660ed6a3aadf Merge: a16f13b50 a0131d234 Author: WeiqunZhang Date: Tue Nov 5 10:52:19 2019 -0800 Merge pull request #613 from dpgrote/fix_xlinker Mini PR: Fix XLinker option to allow spaces in directory names commit 2f8c6417f8e45c3f93feaaea32bf58a8597db75c Author: Andrew Myers Date: Tue Nov 5 13:40:45 2019 -0500 add runtime components setting in the inputs files Tests/Particles/Redistribute/inputs.rt Tests/Particles/Redistribute/inputs.rt.cuda Tests/Particles/Redistribute/inputs.rt.cuda.mr Tests/Particles/Redistribute/inputs.rt.cuda.nonperiodic commit 32f2dee4c42ee8c504d52262982b3ec39ce2a5ce Author: Houjun Tang Date: Mon Nov 4 15:55:04 2019 -0800 Change the HDF5 benchmark to use the new HDF5 write plot file implementation, fix a memory access issue for 1 level data. Src/Base/AMReX_PlotFileUtil.cpp Tests/HDF5Benchmark/GNUmakefile Tests/HDF5Benchmark/Make.package Tests/HDF5Benchmark/WritePlotfileHDF5.H Tests/HDF5Benchmark/WritePlotfileHDF5.cpp Tests/HDF5Benchmark/main.cpp commit 527f997ccd7582f7d68fe204cd71b5e153b7d8ee Author: Andrew Myers Date: Mon Nov 4 16:18:29 2019 -0500 make the runtime comps 0 by default Tests/Particles/Redistribute/inputs commit a25a053f35355990bb1050f47f2214e9129fceb2 Author: Andrew Myers Date: Mon Nov 4 16:17:40 2019 -0500 parmparse the runtime components Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit 97ab3d810f24d26f1637345b7a6791b226f9502b Author: Andrew Myers Date: Mon Nov 4 16:09:34 2019 -0500 setup redistribute test to use runtime components Tests/Particles/Redistribute/main.cpp commit ee5b013cf8743218a0c7749c9885bacf6a5bd6cf Author: Andrew Myers Date: Mon Nov 4 16:07:54 2019 -0500 set up particle tile data with runtime information on the fly Src/Particle/AMReX_ParticleTile.H commit d2352564a089eb74ce55ff72129f564d703bc0dd Author: Andrew Myers Date: Mon Nov 4 16:07:28 2019 -0500 use ptile for temp storage in partition Src/Particle/AMReX_ParticleContainerI.H commit ed9189edaffed50f4153b505d7a3ce8c55312cec Author: Andrew Myers Date: Mon Nov 4 16:05:57 2019 -0500 also define and return in the local unpack Src/Particle/AMReX_ParticleCommunication.H commit 2c8301aa49132242fb5b274ab63704f1a00f32a7 Author: Andrew Myers Date: Mon Nov 4 16:04:31 2019 -0500 make sure we set up the runtime components in the non-local unpack Src/Particle/AMReX_ParticleCommunication.H commit a16f13b50e2192effbed3646b52b9b1437233dc5 Author: Ann Almgren Date: Mon Nov 4 12:52:22 2019 -0800 If we leave in the Gpuable line, the garuda compiler complains (error) when DEBUG=TRUE Src/EB/AMReX_EB2_IF_Polynomial.H commit 87888a5b972e6aa7bc843cb9329f4aea35673cd8 Author: Andrew Myers Date: Mon Nov 4 15:41:00 2019 -0500 formatting fix Src/Particle/AMReX_StructOfArrays.H commit bd1bfe2132cd4cb4327220ac162a02c4fe799aff Author: Weiqun Zhang Date: Mon Nov 4 11:00:55 2019 -0800 MLNodeTensorLaplacian: set sigma Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp commit 70c545c5bc726f374e41f4498a9808cf0b7393d8 Author: Weiqun Zhang Date: Mon Nov 4 10:48:56 2019 -0800 MLNodeTensorLaplacian: 2d normalize Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp commit 98edd9dece2df1c9d0bb00577a10dfc1ea5d5d91 Author: Weiqun Zhang Date: Mon Nov 4 10:41:08 2019 -0800 MLNodeTensorLaplacian: 2d Gauss Seidel Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp commit bb338a6ac8b51fc39c8e885f2939325c08868356 Author: Weiqun Zhang Date: Mon Nov 4 10:31:13 2019 -0800 MLNodeTensorLaplacian: 2d A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp commit a0131d234043ae24d2a0faf74a5441b18174d8af Author: Dave Grote Date: Mon Nov 4 10:13:48 2019 -0800 Fix XLinker option to allow spaces in direector names Tools/GNUMake/Make.defs commit 9f0d75505839daf8e83cdb38f14b2ad424a2829d Author: Weiqun Zhang Date: Mon Nov 4 08:52:55 2019 -0800 MLNodeTensorLaplacian: move applyBC to MLNodeLinOp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 27c5bba4373e1b26e4d8cef002037cb81a8c3fb4 Author: Weiqun Zhang Date: Fri Nov 1 16:00:42 2019 -0700 MLNodeTensorLaplacian: WIP Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit 35c06bf0332fb6c64086b9e854ec71f6a1dab4d3 Merge: 1ef6fca59 578198f9a Author: cgilet Date: Mon Nov 4 10:39:17 2019 -0500 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 578198f9a4bbfdea7ec4aadf22a488d95e184b3a Merge: 49499fb36 cb5eb80e1 Author: WeiqunZhang Date: Fri Nov 1 14:08:57 2019 -0700 Merge pull request #612 from AMReX-Codes/prefixsum-tutorial In PrefixSum tutorial, update exclusive sum using sorted grid IDs. commit cb5eb80e1fcf2f5bee1ac03ff27348ecd0dde5e2 Author: Donald E. Willcox Date: Fri Nov 1 14:00:10 2019 -0700 In PrefixSum tutorial, update exclusive sum using the previous sorted grid ID. Test with different values in each cell. Tutorials/Basic/PrefixSum_MultiFab/Parallel-Prefix-Sum.ipynb Tutorials/Basic/PrefixSum_MultiFab/main.cpp commit d437f294345099f3878256a49153ae16ec511eea Author: Weiqun Zhang Date: Mon Oct 21 16:15:42 2019 -0700 skeleton of MLNodeTensorLaplacian Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit 1f4dd92ee47ff60cf8cb86860040538fb0b93e2b Author: Andrew Myers Date: Fri Nov 1 14:20:51 2019 -0400 make this member protected Src/Particle/AMReX_Particles.H commit f97b5150f01c0903ba80e370282b52c5ebe87820 Author: Andrew Myers Date: Fri Nov 1 13:38:57 2019 -0400 remove setStream call included by mistake Src/Particle/AMReX_ParticleCommunication.H commit 9bf766c8b4401ae250b0579a6719972f4b4fa21a Author: Andrew Myers Date: Fri Nov 1 13:37:42 2019 -0400 include the runtime components in the initial partition Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 49499fb36839461460e53278a1d299a20d726c30 Author: Weiqun Zhang Date: Fri Nov 1 07:54:09 2019 -0700 update CHANGES CHANGES commit c08fd84d175e732fad855ead63a8a26c62b8b06c Author: Weiqun Zhang Date: Thu Oct 31 20:30:15 2019 -0700 AmrCore::regrid: return if the base level is already the max level. Src/AmrCore/AMReX_AmrCore.cpp commit 69053281246a1a7a7b8c29865ab3eb02181541f5 Author: Andrew Myers Date: Thu Oct 31 19:51:06 2019 -0400 fix cpu compilation Src/Particle/AMReX_ParticleTile.H commit a29b64d78266cf06f973f389405d3d1d249ac4fd Author: Andrew Myers Date: Thu Oct 31 19:43:04 2019 -0400 make the snd / rcv buffers char Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particles.H commit 6791f57da69f78c5e47126914ecfb81af34e427a Author: Michele Rosso Date: Thu Oct 31 15:37:30 2019 -0700 NodalProjector: remove unused member variable Src/LinearSolvers/Projections/AMReX_NodalProjector.H commit ad77d18a5327b4b4e9e228ebf678c5f6d2776f3d Author: Kevin Gott Date: Thu Oct 31 15:19:23 2019 -0700 Add libraries. cuRand and hipRand working! Src/Base/AMReX_Random.cpp commit a292fbc9fa2228e673c63fabfa50fe4c2ff7d3a0 Author: Kevin Gott Date: Thu Oct 31 15:17:03 2019 -0700 More noexcepts. Src/Base/AMReX_BaseFabUtility.H commit cc0ae5a832e46febbf450963aed9ecd327802e8a Author: Kevin Gott Date: Thu Oct 31 15:16:42 2019 -0700 Another failed initialization list. Good reproducer option? Src/Base/AMReX_BaseFab.H commit 17903fe1ea9208b0064fabc4c7e77751b76ead34 Author: Kevin Gott Date: Thu Oct 31 17:55:45 2019 -0400 Generalize HIP path names. Tools/GNUMake/comps/hip.mak commit 425eaab9f76147489b4b62499d3fdd65f39a53d9 Author: Kevin Gott Date: Thu Oct 31 17:49:33 2019 -0400 Features needed for HIPrand run on CUDA. Need to test on dogora. Src/Base/AMReX.cpp Src/Base/AMReX_Random.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit 618a63e7b5632217153cb36e1a41037fb00b9735 Author: Michele Rosso Date: Thu Oct 31 14:14:05 2019 -0700 NodalProjector: add option to pass LPInfo to constructor Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 1418f8ff9bd4715f25620734bfa52207d277944a Merge: bcab86cfd f3918ed0a Author: Kevin Gott Date: Thu Oct 31 14:55:47 2019 -0400 Merge branch 'development' into kngott/hip Conflicts: Src/Base/AMReX_BaseFab.H commit f3918ed0ab51a9b028f881c125be16b2bf59a89a Author: Michele Rosso Date: Wed Oct 30 12:46:51 2019 -0700 NodalProjector: fix bug introduced with 2D support Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit b3d16f1e7180f24a460bd45b31d754a842d61910 Merge: db3e5c354 6c398fa50 Author: WeiqunZhang Date: Wed Oct 30 10:48:02 2019 -0700 Merge pull request #607 from AMReX-Codes/mf-prefix-sum Add MultiFab parallel prefix sum tutorial example. commit db3e5c3544bcca8550505694997dd0d682fe3cec Author: MaxThevenet Date: Wed Oct 30 10:34:39 2019 -0700 Add one version of FillBoundary (#609) * FabArray::FillBoundary takes argument nghost, with default loop on comps * typo Src/Base/AMReX_FabArray.H commit c7410205e17b58b6f5143644d44f83d8fd036fb6 Author: Weiqun Zhang Date: Wed Oct 30 09:27:35 2019 -0700 add EBFArrayBoxFactory::isAllRegular Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp commit 1ef6fca59582021ec4a56d301936f9c904d6b6f1 Merge: 322c0eb2d da1008a45 Author: cgilet Date: Wed Oct 30 10:32:23 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit da1008a45489268a96fb6258b6f3de90cbe1b93a Author: Max Katz Date: Wed Oct 30 02:23:12 2019 -0400 Set OpenACC stream to be the same as the CUDA stream Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_acc_mod.F90 commit e225ebd553eb468e0e005024029d90d7ea69631e Author: Max Katz Date: Wed Oct 30 02:22:46 2019 -0400 For OpenACC where CCOMP is not pgc++, still include openacc.h Tools/GNUMake/comps/pgi.mak commit f18c7ab911843b0c88f9268b5bda3ca084972516 Author: Weiqun Zhang Date: Tue Oct 29 20:17:49 2019 -0700 fix a typo Src/Base/AMReX_FabArrayUtility.H commit 4f9fa55cc57fe2dea44dd966845a5f96483309a8 Merge: 304eea13d 076c54c88 Author: WeiqunZhang Date: Tue Oct 29 15:22:18 2019 -0700 Merge pull request #610 from michaeljbrazell/mjb/reducesum_bug small bug fix for a three MultiFab ReduceSum commit 304eea13dfca9d9861a41cde3ad8f3bae31553fc Author: Weiqun Zhang Date: Tue Oct 29 15:15:23 2019 -0700 remove stray #define thanks to Christoph Behrens Src/Base/AMReX_REAL.H commit 076c54c88f8558b27f7a0e3aad9948837dcd3f71 Author: michael brazell Date: Tue Oct 29 15:11:52 2019 -0700 small bug fix for a three MultiFab ReduceSum Src/Base/AMReX_FabArrayUtility.H commit 0c19db118f07a13837a89f803cdd8993aaceef8e Author: Max Katz Date: Tue Oct 29 17:23:19 2019 -0400 Add peak at OLCF Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.olcf commit 24b3bfc82c524540c3d06d966c5d33a037929d73 Author: Michele Rosso Date: Mon Oct 28 18:06:00 2019 -0700 NodalProjector: print diagnostics only if verbosity is enabled Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 43a2a5fbdbf2d1b1c3544f196a1fdd97133605e5 Author: Michele Rosso Date: Mon Oct 28 18:02:41 2019 -0700 NodalProjector: replace unique_ptr with standard pointers Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 8d32cab030fd0e75679d2325ea245f18ade9ae03 Author: cgilet Date: Mon Oct 28 13:24:00 2019 -0400 Make NodalProjector::define 2D compatable. Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 3da080f072bdf2c370f4beb4defd2c188a14662c Author: Max Katz Date: Mon Oct 28 09:49:21 2019 -0700 Remove debugging print Src/AmrCore/AMReX_AmrMesh.cpp commit 322c0eb2d89f1d08dd62588fbaa8a1c08b76807a Merge: 83485022b ceceb9a50 Author: cgilet Date: Mon Oct 28 09:44:42 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit ceceb9a502b471531169628bcdd284a53dbb6eb0 Author: Max Katz Date: Sun Oct 27 19:13:21 2019 -0700 Only include PTX output from PGI if verbose Tools/GNUMake/comps/pgi.mak commit d0f236faf3b401512273a1baf4564e79d6220393 Author: Max Katz Date: Sun Oct 27 01:12:13 2019 -0700 Revert "Only define __device__, etc. if using CUDA or HIP" This reverts commit 6a4ac2da0486642432cb0962e972b6e00ac82ec7. Src/Base/AMReX_GpuQualifiers.H commit 6a4ac2da0486642432cb0962e972b6e00ac82ec7 Author: Max Katz Date: Sun Oct 27 00:34:55 2019 -0700 Only define __device__, etc. if using CUDA or HIP Src/Base/AMReX_GpuQualifiers.H commit 9b83f379cc4eed9bbde51a303b50b9035c65b517 Author: Weiqun Zhang Date: Sat Oct 26 07:08:34 2019 -0700 put NodalProjector into namespace amrex Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 0b31494d14e3cefb02144847dbed8b07cad65d92 Author: Weiqun Zhang Date: Fri Oct 25 21:22:55 2019 -0700 In error message, tell people how to get around blocking_factor not power of 2 error. Src/AmrCore/AMReX_AmrMesh.cpp commit 83485022b270c0f38eab5f938fbc6c8a3e5ecde3 Merge: 0db095b07 eceb952c2 Author: cgilet Date: Fri Oct 25 22:10:28 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit eceb952c25975a301e39d8ec04b578f2fd046570 Author: Ann Almgren Date: Fri Oct 25 18:45:47 2019 -0700 Add documentation about: 1) blocking_factor must be power of 2 2) using n_error_buf to make larger grids. Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/InputsLoadBalancing.rst commit c0e7ef80d8c23f402086a42ba7e2520b977e45a9 Merge: 640d5f2ff c93afa00f Author: Ann Almgren Date: Fri Oct 25 18:22:19 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 640d5f2ff9cd81531683c07db46157434c2a632b Author: Ann Almgren Date: Fri Oct 25 18:20:09 2019 -0700 Enforce in AmrCore (as in Amr) that blocking_factor must be a multiple of 2. Src/AmrCore/AMReX_AmrMesh.cpp commit bcab86cfdca1ec4623d8553908de074dc0dc98ae Author: Kevin Gott Date: Fri Oct 25 16:56:13 2019 -0700 Go back to managed Vector. Src/Base/AMReX_CudaContainers.H commit fed10ea40913b4a1f2a1f5b0e7525a25cc9be8fa Author: Kevin Gott Date: Fri Oct 25 16:15:38 2019 -0700 More Random Number Generator Updates Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_Random.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit 6c398fa5053147d00e6ef780f99cb5934a6ced22 Author: Donald E. Willcox Date: Fri Oct 25 16:09:04 2019 -0700 Add MultiFab parallel prefix sum tutorial example. Tutorials/Basic/PrefixSum_MultiFab/GNUmakefile Tutorials/Basic/PrefixSum_MultiFab/Make.package Tutorials/Basic/PrefixSum_MultiFab/Parallel-Prefix-Sum.ipynb Tutorials/Basic/PrefixSum_MultiFab/README.md Tutorials/Basic/PrefixSum_MultiFab/inputs Tutorials/Basic/PrefixSum_MultiFab/main.cpp commit c93afa00fc5f738a947797f76b10827a571ffcdb Author: Michele Rosso Date: Fri Oct 25 15:35:39 2019 -0700 NodalProjector: check grid type of arguments of computeRHS Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit fe5c740b7e36276eaf44c9b4415f5dcc86b531c1 Author: Kevin Gott Date: Fri Oct 25 14:31:09 2019 -0700 1st attempt: Random without MemcpyToSymbol Src/Base/AMReX_Random.cpp commit 9ed64c6f80c6046b3edd6efbe7d84058c362e523 Merge: 8e3065264 d450ed75b Author: Michele Rosso Date: Fri Oct 25 13:06:13 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8e30652644b4da0d13a4c46346f6d1b5bbb0d785 Author: Michele Rosso Date: Fri Oct 25 13:06:06 2019 -0700 NodalProjector: pass arguments to compRHS in correct order Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit d450ed75b321c1eb5864d9f66cb8fdf3651e9766 Author: Weiqun Zhang Date: Fri Oct 25 12:40:52 2019 -0700 add AmrMesh function to return level number given domain box Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 17d46c51cab330fb509b24e91ad71978343b99d0 Merge: 1a0eccc45 b3e3634b6 Author: Michele Rosso Date: Fri Oct 25 12:36:11 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1a0eccc45183d3a9ede2ba338f1169e1b5cd75c4 Author: Michele Rosso Date: Fri Oct 25 12:36:04 2019 -0700 NodalProjector: add non-EB version Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit b3e3634b6923f4b73fff22aa34f3fb75f06be74f Merge: 1f29ec3e7 d6c4da885 Author: Andrew Myers Date: Fri Oct 25 12:29:56 2019 -0700 Merge pull request #606 from houjun/development Add support to write plotfile in HDF5 format commit 0db095b075e89782cb1bcb2c5e0f36218c6b1e4b Author: cgilet Date: Fri Oct 25 14:57:45 2019 -0400 WIP - add EBTensorOp::compFlux() with restriction that cut cell fluxes are not set to a bogus value Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 389d3bc747ed08f5b77c4a7c037c9952ab7e0a29 Merge: cfa446f16 3166d72cd Author: cgilet Date: Fri Oct 25 14:45:36 2019 -0400 Merge branch 'TensorFluxes' of https://github.com/cgilet/amrex into TensorFluxes commit 3166d72cda824f3e71c92c1960a3bd45a8036be2 Merge: bbc4f7a9c 1f29ec3e7 Author: cgilet Date: Fri Oct 25 14:42:00 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit d6c4da88594762386a9dec1b146ed864887760a6 Author: Houjun Tang Date: Fri Oct 25 09:40:29 2019 -0700 Add support to write plotfile in HDF5 format Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit 1f29ec3e72ad70e8419ad313deb9aee89e18f83f Author: Ann Almgren Date: Thu Oct 24 22:30:00 2019 -0700 Add NodalProjector class to amrex/Src/LinearSolvers/Projections Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp Src/LinearSolvers/Projections/Make.package commit 947a8184ba9bc2940b622f9ef6ec617b1dc31886 Author: Kevin Gott Date: Thu Oct 24 17:18:19 2019 -0700 Simplify the abort fix. Src/Base/AMReX_Machine.cpp commit f35c6dcbecb5ed4a00abd30b7a49822fc40d79cf Author: Weiqun Zhang Date: Thu Oct 24 12:24:53 2019 -0700 Reduce* for FabArray can now take lambda working on Array4. bug fix and optimization in the new EB functions added to MulitFab. tidy. Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_REAL.H commit 11bc438ee0d020f4bc192ee85d63a301ca7d6df4 Author: Weiqun Zhang Date: Thu Oct 24 11:00:45 2019 -0700 add AMREX_REAL_MIN, AMREX_REAL_MAX and AMREX_REAL_LOWEST for convenice. Src/Base/AMReX_REAL.H commit cd6766f5e19d3d8cd1cfe8eb0792903b4ab4466d Author: Weiqun Zhang Date: Wed Oct 23 15:54:19 2019 -0700 rm AMREX_PRAGMA_SIMD for reduce loops Src/Base/AMReX_Reduce.H commit 7ad5295c98efb6129696c3fcf7c3005f0db1a95d Author: Weiqun Zhang Date: Wed Oct 23 15:53:02 2019 -0700 make launch functions macros safe with empty boxes Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuRange.H commit 1225ca4501ae6661450f6d025fa907a1fd9f987e Author: atmyers Date: Thu Oct 24 04:44:39 2019 -0700 make sure dummy_mf gets updated Src/Particle/AMReX_ParticleContainerI.H commit 1c78b9e29505e3b0a7de9ef667f3ce6ecd883e95 Author: Kevin Gott Date: Wed Oct 23 16:45:47 2019 -0700 Fix make system and get rpath working. Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 34730233cc485025db069b569a133290843f6522 Author: Kevin Gott Date: Wed Oct 23 16:45:02 2019 -0700 More NOEXCEPTs Src/Base/AMReX_GpuLaunch.H commit 0afd4913bec953469430da049f16e76a3ea1e059 Author: Kevin Gott Date: Wed Oct 23 16:44:50 2019 -0700 Get rid of memcpy_to_symbol. Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_Random.cpp commit c9e8e93580b00e53c1e1e44ce9c327787bb1d025 Author: Kevin Gott Date: Wed Oct 23 16:44:26 2019 -0700 AMREX_NOEXCEPT and additional initialization lists. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Extension.H commit 08dabb4520ec581b8ce8ad0f6c3433243505c8a0 Author: Andrew Myers Date: Wed Oct 23 19:19:23 2019 -0400 nghsot -> nghost Src/Base/AMReX_FabArray.H commit b83c2ba6a3475d33771dd6e2a8d7f63205e72ec5 Merge: 4b6ed005c 3f5686191 Author: Andrew Myers Date: Wed Oct 23 18:17:17 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4b6ed005cbb5e4f82e7ae57effda1699efceda79 Author: Andrew Myers Date: Wed Oct 23 18:16:42 2019 -0400 add missing Gpu::Device::synchronize() to InitFromBinaryFile Src/Particle/AMReX_ParticleInit.H commit 3f5686191a34292eb54dd4d01acd078f094d02d6 Author: Weiqun Zhang Date: Wed Oct 23 14:47:09 2019 -0700 remove FabView from BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFabUtility.H Src/Boundary/AMReX_Mask.H Src/EB/AMReX_EB2_GeometryShop.H Tests/Vectorization/kc.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit 0112718e1335cbd9d62b57c6f63b36fceb2d37fe Merge: 2720d6166 78141f059 Author: Andrew Myers Date: Wed Oct 23 16:13:44 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2720d616673fcef38a8e32429e053df27f706b49 Author: Andrew Myers Date: Wed Oct 23 16:13:23 2019 -0400 when deciding if a particle stays or not, we must also consider the case that particles have been added to the correct grids, not NOT on the correct procs Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleBufferMap.cpp Src/Particle/AMReX_ParticleContainerI.H commit 78141f05958a4da13cf4c2b8a37f2fdd1701ab5d Author: Weiqun Zhang Date: Wed Oct 23 12:24:30 2019 -0700 fix some warnings Src/Base/AMReX_GpuLaunch.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/EBTensor/MyTest.cpp Tests/LinearSolvers/EBTensor/MyTest_K.H commit fba7ef82b36ccb9f23d11c554fe89173425b2174 Author: Weiqun Zhang Date: Wed Oct 23 11:19:46 2019 -0700 rm unused file Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H Src/LinearSolvers/MLMG/Make.package commit 699d0ad4b2d5e9f5cfe8acd9a51067a028cea70d Merge: a21a523ff f84a3d070 Author: WeiqunZhang Date: Wed Oct 23 12:09:09 2019 -0700 Merge pull request #604 from kcdodd/development Change MPI_Frotran to MPI_Fortran commit f84a3d0703e03e4f1b3871cac747fff2dcf2d1a2 Author: Carter Dodd Date: Wed Oct 23 13:44:03 2019 -0500 Change MPI_Frotran to MPI_Fortran Src/F_Interfaces/CMakeLists.txt commit d9f6d38f83e6117d2732be24f069945c13a048bc Merge: 3185f92a0 a21a523ff Author: Kevin Gott Date: Wed Oct 23 11:43:35 2019 -0700 Merge branch 'development' into kngott/hip commit a21a523ffe01852445d53a130b2996f8d2abf9da Author: Weiqun Zhang Date: Wed Oct 23 11:01:26 2019 -0700 Replace AMREX_IS_D_LAMBDA with armex::IsDeviceLambda. This will fix a template parameter deduction issue. Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_TypeTraits.H commit aa5a26b0835c89432b5189baa54b8e062b822e86 Author: Weiqun Zhang Date: Wed Oct 23 10:23:23 2019 -0700 missed a return Src/Base/AMReX_FabArrayUtility.H commit 787bbca0b38d8243ace4f7e5f7f3f1c2c7a976fd Author: Max Katz Date: Wed Oct 23 07:18:56 2019 -0700 Avoid race conditions in reduction code called multiple times cuda-memcheck --tool racecheck reported race conditions in this code if we called the block reduction multiple times in a kernel, since some warps in the first reduction could be reading from shared memory at the same time as other warps in the second reduction were writing to it. By inserting a syncthreads prior to the first write to shared memory, we avoid this (at some performance cost for the cases where we only call the reduction once in a kernel). Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_fort_mod.F90 commit cfa446f16f480ae896eacfeefc68a41d84b6218b Merge: bb7c600ad 14af20e6e Author: cgilet Date: Wed Oct 23 09:48:50 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 3185f92a09f2e5eda84344f84ca885077a7f3326 Author: Kevin Gott Date: Tue Oct 22 15:31:42 2019 -0700 Label std::abort() HIP FIX. Src/Base/AMReX_Machine.cpp commit 931b56945f602c0561b2d9b2233e322ee9b98391 Author: Kevin Gott Date: Tue Oct 22 15:30:37 2019 -0700 Saving before noexcept attempt. Src/Base/AMReX_GpuQualifiers.H Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 14af20e6e2d581168dd0ac3633cc2b8c7f75285b Author: Max Katz Date: Tue Oct 22 12:32:31 2019 -0400 Reorder to work around XL compiler bug Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 27e948b3857e197c7286e994562dc479415624f3 Merge: 7efd37fe1 11ba3b2f0 Author: Kevin Gott Date: Tue Oct 22 09:17:45 2019 -0700 Merge branch 'development' into kngott/hip commit 11ba3b2f03b5984d59e96190252e6dec8f932893 Author: Kevin Gott Date: Tue Oct 22 12:14:43 2019 -0400 Temporary fix for std::abort in HIP. This allows AMReX to compile with HIP on Summit. Src/Base/AMReX_Machine.cpp commit fb0e97e05671be9bbc97d383b54a0c29112d6247 Author: Kevin Gott Date: Tue Oct 22 12:14:06 2019 -0400 Fix HIP error messages in cudaGraphs. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuError.H Src/Base/AMReX_GpuQualifiers.H Tools/GNUMake/Make.defs commit 6d9b602b95eb7bea13ef4403bf9b285f3b46a2d7 Author: Kevin Gott Date: Tue Oct 22 12:10:59 2019 -0400 Update HIP calls. Src/Base/AMReX_Arena.cpp commit 91231d76804febc09430c84a3d32da8c84193757 Author: Ann Almgren Date: Mon Oct 21 18:14:31 2019 -0700 Fix redistribute so it doesn't assume we start at component 0. Src/EB/AMReX_EB_utils.cpp commit 650c786783d4dc6f35a2915b218c37c84e2a0c44 Author: Ann Almgren Date: Mon Oct 21 17:29:40 2019 -0700 Fix compilation of AMReX_EB_utils.cpp in 2D. Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp commit 8a684e0e778dbcea17bade2ec2b90cede32c856d Merge: 676372b6b 444110075 Author: Ann Almgren Date: Mon Oct 21 16:18:29 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 676372b6b87c257da5612110eba592ea1a253841 Author: Ann Almgren Date: Mon Oct 21 16:18:16 2019 -0700 Oops -- accidentally committed the un-weighted version. Src/EB/AMReX_EB_utils.cpp commit 4441100757ca8c4ad73e78e2ab39b9ab580e8f4f Author: Weiqun Zhang Date: Mon Oct 21 16:17:06 2019 -0700 BaseFab::linComb missed default template parameter Src/Base/AMReX_BaseFab.H commit f6bf1ed8dd9f0f08a7fd6df675ab960472327a9b Merge: 4707fe9c0 90cc50bf5 Author: Ann Almgren Date: Mon Oct 21 15:43:20 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 4707fe9c0d6c045e855196326e120526a7735c00 Author: Ann Almgren Date: Mon Oct 21 15:43:02 2019 -0700 Move single-level redistribution code from incflo to amrex/Src/EB. Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp commit 7efd37fe14407bd7f0158eddd61a344f0dcb5e92 Merge: d9e066238 90cc50bf5 Author: Kevin Gott Date: Mon Oct 21 12:09:25 2019 -0700 qMerge branch 'development' into kngott/hip commit d9e06623821b6f62516635fedfa7ad9c2483fe47 Merge: 7395fe32d 7910f2c0d Author: Kevin Gott Date: Mon Oct 21 12:08:50 2019 -0700 Merge branch 'development' into kngott/hip commit 90cc50bf5ddaf09913399afb08a0e8a0dc6f3589 Author: Weiqun Zhang Date: Mon Oct 21 10:01:55 2019 -0700 InterpBndryData: make sure index is within bound for 2d refratio=4 case Src/Boundary/AMReX_InterpBndryData_2D_K.H commit bb7c600ad0ef478b94987107c4d5f270676da0dd Merge: cd2e17c69 aa7d9ab55 Author: cgilet Date: Mon Oct 21 10:59:48 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit cd2e17c69b98554c28202c061696174608e3edf6 Merge: c50605a08 b8062c23f Author: cgilet Date: Mon Oct 21 10:56:53 2019 -0400 Merge branch 'development' into TensorFluxes commit aa7d9ab55e6c22ae763473a3f3f55e63d72a74de Author: Weiqun Zhang Date: Sun Oct 20 18:31:08 2019 -0700 add std:: Src/AmrCore/AMReX_Cluster.cpp Src/Base/AMReX_RealBox.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp commit 1809d8e4b01465fc772bd1bacb1bab89c2a4220f Merge: 1561d1bef 897c23cf4 Author: Weiqun Zhang Date: Sun Oct 20 17:17:23 2019 -0700 Merge branch 'fix_tensor_corner' into development commit 897c23cf481fde33c475c7ce6d1f099c82b69019 Author: Weiqun Zhang Date: Sun Oct 20 15:38:11 2019 -0700 Merge branch 'development' into fix_tensor_corner Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_ParmParse.cpp Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_Particles.H Tutorials/Basic/HelloWorld_C/main.cpp commit 1561d1bef30b61efb67cf0e117bc55d8fd368d51 Author: Weiqun Zhang Date: Sun Oct 20 15:24:55 2019 -0700 make set_eb_data gpu host device function Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H commit 72b3b3c49df895bd9c88b0fe5908e4e1831c1051 Author: Weiqun Zhang Date: Sun Oct 20 15:13:47 2019 -0700 MLMG tensor: cleanup Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit d3d340418751e4104718721e10a92afeb4a225e8 Author: Weiqun Zhang Date: Sun Oct 20 14:19:49 2019 -0700 MLMG: fill corners for 3d tensor Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit e52b6ac455a67d25b301a16fe43a0647df9f86d6 Author: Weiqun Zhang Date: Sun Oct 20 12:09:56 2019 -0700 MLMG: fill edges for 3d tensor Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit f5b6c6684e54a1524822d670a5a54b0c74ee6783 Author: Ann Almgren Date: Sat Oct 19 19:49:30 2019 -0700 We had "abs" rather than "std::abs" in two lines in one of the RAP interpolation routines -- turns out that plain abs turns 5.1 into 5 and 0.51 into 0 ... not what was intended! Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit 5d87b172c806f67f00bb33da7262c2a6b65579a8 Author: Ann Almgren Date: Sat Oct 19 15:18:14 2019 -0700 When we set cells to covered because vfrac < small_volfrac, we must also make sure that any originally Regular cells touching them get relabeled to SingleValued and their EB-related data must be set correctly. Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H commit 72d868566cf69ddc681336f3d6166b0759147d0f Merge: 88c271ccb e7f3bc7a2 Author: Emmanuel Motheau Date: Fri Oct 18 15:24:31 2019 -0700 Merge pull request #600 from AMReX-Codes/feature_nd_Pele Feature nd pele/IAMR commit 4ac343d99ecfc7b9edd04efba7b3667b9c2677f3 Author: Weiqun Zhang Date: Fri Oct 18 14:37:29 2019 -0700 WIP: MLMGBndry/InterpBndry in 2d fills corners too Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H commit 88c271ccbbe8cf7d2cba4930b57162579682d015 Merge: 7910f2c0d da3d8a7a7 Author: WeiqunZhang Date: Fri Oct 18 10:11:46 2019 -0700 Merge pull request #601 from AMReX-Codes/abort_on_unused_inputs Abort on unused inputs commit da3d8a7a7c0d1a26f3d6ce96642d2b1abd4ccb21 Author: Andrew Myers Date: Fri Oct 18 09:51:12 2019 -0700 Add option to abort at the end of the run if unused variables are in the ParmParse table, instead of exiting cleanly. Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_ParmParse.cpp commit e7f3bc7a2234c2626045276ac18c22be56dd0820 Merge: 8afad8778 7910f2c0d Author: Lucas Esclapez Date: Thu Oct 17 18:49:04 2019 -0700 Merge branch 'development' into feature_nd_Pele commit 8afad8778e06905620b48837fdf7387136a7a57b Author: Lucas Esclapez Date: Thu Oct 17 18:47:46 2019 -0700 [Feature_nd_Pele] Missing change for 3D bc function in some amr level derive call. Src/Amr/AMReX_AmrLevel.cpp commit 7910f2c0d91599637e288a9df7a72bc34a8e3711 Merge: 6084bfdf5 cf0e26e47 Author: Weiqun Zhang Date: Thu Oct 17 16:24:59 2019 -0700 Merge branch 'weiqun/dev' into development commit 6084bfdf5534ea6299f0f91cb56c801eb9d66100 Author: Andrew Myers Date: Thu Oct 17 15:38:29 2019 -0700 fix typo Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 67d827661ce297f0add206f2ef1767c8df3376c6 Author: Weiqun Zhang Date: Thu Oct 17 15:33:51 2019 -0700 tensor 2d: test for true corner Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit aee576ce33a91ee0170ec4f6282679d697fdf8d1 Author: Weiqun Zhang Date: Thu Oct 17 14:16:39 2019 -0700 use amrex::coarsen for int coarsening Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit 0d7695c7797317c7a7946e787f51271787816b38 Author: Weiqun Zhang Date: Thu Oct 17 14:03:42 2019 -0700 replace hardwired numbers with enum Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit ab49a459eba522753ef8d00615c34ca56a6c37ea Author: Weiqun Zhang Date: Thu Oct 17 13:52:44 2019 -0700 add new file to gnu make and cmake systems Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/Make.package commit aadb6b06c7d1c2563c93232eeacd5b22bae2bc14 Merge: 4c13f8451 db48d4a2a Author: Andrew Myers Date: Thu Oct 17 12:36:57 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4c13f84516fe403d99767beff9c9d1ffe3ce8350 Author: Andrew Myers Date: Thu Oct 17 12:36:34 2019 -0700 fix typo Src/Particle/AMReX_Particles.H commit 9cc63d98accb1a123c0ee330151f21713d3412b9 Author: Andrew Myers Date: Thu Oct 17 12:35:02 2019 -0700 ba -> BoxArray Src/Particle/AMReX_Particles.H commit 6ed6abac847c77ab8d73edc85ee444f120f31897 Author: Andrew Myers Date: Thu Oct 17 12:34:29 2019 -0700 fix typo Src/Particle/AMReX_Particles.H commit 386361c0c5a6cfa901eba2d4edab05f1d6ca76a0 Merge: dc847f5c9 b662a3537 Author: Weiqun Zhang Date: Thu Oct 17 12:20:27 2019 -0700 Merge branch 'development' into pr-598 commit db48d4a2a233525c920b2888c9055d215555d16c Merge: b662a3537 c0772b10c Author: WeiqunZhang Date: Thu Oct 17 12:16:44 2019 -0700 Merge pull request #599 from lucafedeli88/enable_range_based_loops_for_GpuArray added begin() and end() to GpuArray commit cf0e26e47dcd1c967aa273ce9d27a84915f6f140 Merge: c95915afc b662a3537 Author: Weiqun Zhang Date: Thu Oct 17 12:15:51 2019 -0700 Merge branch 'development' into weiqun/dev commit b662a35372753507aa91ed5145852b82a60cbef1 Author: Weiqun Zhang Date: Thu Oct 17 12:15:30 2019 -0700 fix some makefiles for the MacProjector change GNUmakefile.in Tutorials/EB/MacProj/GNUmakefile Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile commit c95915afcdc9bf942d93d05e11e62c7ef9d10d84 Merge: 31c12f445 bf9de17e3 Author: Weiqun Zhang Date: Thu Oct 17 11:25:08 2019 -0700 Merge branch 'development' into weiqun/dev commit 31c12f445a4c628be38453d1fcc090767ba55e3a Author: Weiqun Zhang Date: Wed Oct 16 14:47:25 2019 -0700 add RunOn to more BaseFab functions Src/Base/AMReX_BaseFab.H commit bf9de17e399625b99c0b42fe4dfdd9943dd697e2 Author: Ann Almgren Date: Thu Oct 17 10:06:57 2019 -0700 Move MacProjector* out of LinearSolvers/MLMG into LinearSolvers/Projections. Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/Make.package Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp Src/LinearSolvers/Projections/Make.package commit c0772b10cf74fca5166e522c1a1d8a81cd65b4a4 Author: Luca Fedeli Date: Thu Oct 17 10:06:06 2019 +0200 added begin() and end() to GpuArray Src/Base/AMReX_Array.H commit dc847f5c977396fe340f95bf54ebfcdc261f5bc9 Author: cgilet Date: Thu Oct 17 00:27:59 2019 -0400 Add updated mltensor_fill_corners(). Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 98c52f8fb69699c15daf5bcfff44883b72b8c820 Merge: 5fa313e45 9690689fa Author: Andrew Myers Date: Wed Oct 16 16:23:32 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5fa313e453baa76f08f60268f82cafa0e73f9d28 Author: Andrew Myers Date: Wed Oct 16 16:23:23 2019 -0700 fix compilation of electrostatic pic tutorial Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H commit 9690689fa4532a67c26792c1c4d512150846e6eb Merge: 086630371 57996077a Author: Andrew Myers Date: Wed Oct 16 14:18:24 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 086630371c606429a2f8d9dbfe0068397ec86e3d Author: Andrew Myers Date: Wed Oct 16 14:18:03 2019 -0400 fix intersection test Tests/Particles/Intersection/main.cpp commit c50605a08e5d4ab0e1d9219bc1ff091c2fa20f52 Merge: bbc4f7a9c afcd33c5c Author: cgilet Date: Wed Oct 16 13:29:25 2019 -0400 Merge remote-tracking branch 'origin/mltensor_corner_fill_fix' into TensorFluxes commit afcd33c5c9b12a5d77a3ef38d6b8f7f740ead614 Author: cgilet Date: Wed Oct 16 13:11:10 2019 -0400 More clean up. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit d00e12dadb33cf71bf298b5c2e48ee3a41bcf838 Author: cgilet Date: Wed Oct 16 12:58:37 2019 -0400 Clean up. Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit 67e73856f94a38f64007abad335223041f98593b Author: cgilet Date: Wed Oct 16 11:37:29 2019 -0400 Add missing colon. Remove debugging Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 2641dbffd358ccbf0397901d5ce893474135a594 Merge: 327e78007 57996077a Author: cgilet Date: Wed Oct 16 10:28:55 2019 -0400 Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix commit 57996077ac4bbb3a92ecd9f55aba904bcb8337cd Merge: a67269b23 8ed96c134 Author: WeiqunZhang Date: Tue Oct 15 16:07:41 2019 -0700 Merge pull request #595 from AMReX-Codes/doc_Paraview [Docs] Update Paraview section with new implementations of Paraview 5.7. commit a67269b2320d5f15e99a5484c852f7868405a832 Merge: 0e3326b74 239ad64e8 Author: Andrew Myers Date: Tue Oct 15 14:41:44 2019 -0700 Merge pull request #594 from AMReX-Codes/jmsexton/particle host_device enforcePeriodic matching cpu version, fab setVal -> multifab setVal commit 0e3326b744d62cfccdab29421ff6e54004c6fe67 Author: Max Katz Date: Tue Oct 15 14:18:43 2019 -0700 Fix grammar Src/Base/AMReX_GpuDevice.cpp commit 8ed96c1341ecef220290ff43cffd203936cdca70 Author: Lucas Esclapez Date: Tue Oct 15 12:33:07 2019 -0700 [Docs] Update Paraview section with new implementations of Paraview 5.7. Docs/sphinx_documentation/source/Visualization.rst commit 0868f803c6899b654a1d62c8f56609fd72f90344 Author: Weiqun Zhang Date: Tue Oct 15 09:41:59 2019 -0700 use abspath for rpath Tools/GNUMake/Make.defs commit 32af3a7fcc0504c2a6bdd8c8ffe00eeeef55f4b4 Author: Weiqun Zhang Date: Tue Oct 15 09:30:33 2019 -0700 add -L when USE_RPATH Tools/GNUMake/Make.defs commit 9d6279e524fe8dd8d697da529d03f33e7b894662 Merge: e7e4c2035 d87808595 Author: Lucas Esclapez Date: Mon Oct 14 17:52:40 2019 -0700 Merge branch 'development' into feature_nd_Pele commit d87808595694873f23e06b5c8eba9105b22c7c1c Merge: 3406baeab 2aa0af167 Author: WeiqunZhang Date: Mon Oct 14 16:03:59 2019 -0700 Merge pull request #592 from DUGKS/dugks-dev add mathematical boundary types : HOEXTRAPLI commit 3406baeab81829224af2eea4117ebc5911b70469 Merge: b52b03c3b cba673a69 Author: WeiqunZhang Date: Mon Oct 14 15:39:58 2019 -0700 Merge pull request #593 from AMReX-Codes/convergence_tool Convergence tool commit b52b03c3bf3b23f5cba7fb622965e702f289ae11 Merge: 048060feb 8056fe61a Author: WeiqunZhang Date: Mon Oct 14 15:33:11 2019 -0700 Merge pull request #590 from ax3l/topic-rpathSupport Linker: Use RPath commit 8056fe61af8dc3c9cae558e7b1f022f26bfa7b8f Author: Axel Huebl Date: Thu Oct 10 11:13:55 2019 -0400 USE_RPATH: Do not yet enable by default Let's test this for a period of time on volunteering downstream projects (WarpX, Castro, ...?). Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/GNUMake/Make.defs commit 048060febe0f2377032ee7debc23d3153f3f9d1e Author: Weiqun Zhang Date: Mon Oct 14 14:53:16 2019 -0700 More Reduce functions can now take a device lambda. Src/Base/AMReX_FabArrayUtility.H Tutorials/GPU/EBCNS/Source/CNS.cpp commit 7395fe32dcb13fe1a6b8cc9ad95409731af658ea Merge: 0c39c4431 cfa6d098e Author: Kevin N Gott Date: Mon Oct 14 11:54:07 2019 -0700 Merge branch 'development' into kngott/hip commit cfa6d098e713bb3c0cd343de7a3f0e4a0cf0293c Author: Weiqun Zhang Date: Mon Oct 14 11:26:08 2019 -0700 ReduceMin can now take a device lambda. However if the lambda is a device lambda and the launch region is off, a runtime error will occur. Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_TypeTraits.H Tutorials/GPU/CNS/Source/CNS.cpp commit 338e6569ff4903dec324207f4bc911141d802cca Author: Weiqun Zhang Date: Mon Oct 14 09:26:28 2019 -0700 print out the total number of gpus used only if nvcc >= 10 Src/Base/AMReX_GpuDevice.cpp commit b425b67d490179c6ef759f9727b581d342ff9e22 Author: Andrew Myers Date: Mon Oct 14 10:52:47 2019 -0700 docstrings for the Particle IO routines Src/Particle/AMReX_Particles.H commit 69e057c6bd05ae60faa560a730cc8c8f88d63f85 Author: Andrew Myers Date: Mon Oct 14 10:27:52 2019 -0700 docstring formatting changes Src/Particle/AMReX_Particles.H commit e3c2e5758f0fb7aa080398c7570477d701d359f0 Author: Andrew Myers Date: Mon Oct 14 10:09:43 2019 -0700 more docstrings for ParticleContainer Src/Particle/AMReX_Particles.H commit 544f9db9b4a3f6e50a81f134e1425ca69d3f8981 Author: Andrew Myers Date: Mon Oct 14 09:52:42 2019 -0700 remove unused function Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 2d83e26d81dedb4639ce81ec7b360d11433ac7a4 Author: Andrew Myers Date: Mon Oct 14 09:51:59 2019 -0700 add some docstrings to the ParticleContainer constructors / define methods Src/Particle/AMReX_Particles.H commit fbae0870c68718fb3c0aec316fe5f969acb41bae Author: Weiqun Zhang Date: Sat Oct 12 16:20:11 2019 -0700 add RunOn to BaseFab functions Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFabUtil.cpp Tutorials/Basic/HelloWorld_C/main.cpp commit cba673a69fa6f060e5a1b371320a8048fc7b2221 Author: Michael Zingale Date: Sat Oct 12 13:13:39 2019 -0400 make the output more readable, disable latex by default Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit a95e783d1412fa9724a80816e7c8a23f69447e60 Merge: 76f34eee4 f9205c16d Author: Michael Zingale Date: Sat Oct 12 12:27:27 2019 -0400 Merge branch 'development' into convergence_tool commit 2aa0af167febd918e3d591ae6608bcbc45c5c353 Author: DUGKS Date: Sat Oct 12 21:17:39 2019 +0800 add HOEXTRAPCC boundary type Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_bc_types.fi Src/Base/AMReX_bc_types_mod.F90 Src/Base/AMReX_filcc_mod.F90 commit 7345753f592a73e5b475ae015e15651e63ae4c3e Author: Michele Rosso Date: Fri Oct 11 16:09:01 2019 -0700 Fix args order in call to MultiFab constructor when computing EB-norm0 Src/Base/AMReX_MultiFab.cpp commit 2c083fd630e86c58dce0e4eeb9c946486ed9180d Author: atmyers Date: Fri Oct 11 13:15:00 2019 -0700 expand the particle reduction tests Tests/Particles/ParticleReduce/main.cpp commit bcb621303830f2e39ef4796e3902b3831cdcf6e3 Author: atmyers Date: Fri Oct 11 13:14:43 2019 -0700 update the particle reduction functions to work with SoA data Src/Particle/AMReX_ParticleReduce.H commit 4fb0e3f7831b7bbf21dba0d9a6a9a3cc3e0e40f6 Author: atmyers Date: Fri Oct 11 13:14:19 2019 -0700 do some bounds checking for the particle components if DEBUG=TRUE Src/Particle/AMReX_Particle.H commit fa8c932e77b67d5d4b78a649a9eae9ea8fe1da4a Author: atmyers Date: Fri Oct 11 13:14:01 2019 -0700 fix some order of initialization issues Src/Particle/AMReX_ParticleLocator.H commit 239ad64e8c73d95b5fcea6fc00fecbe96df533fd Author: Jean M. Sexton Date: Fri Oct 11 13:33:22 2019 -0400 Make one setVal a multifab setVal, make enforcePeriodic match cpu version to fix losing particles in single precision Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H commit 327e780078a056743a5120950646d2e07f74e889 Author: cgilet Date: Fri Oct 11 13:23:28 2019 -0400 give accurate error message Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit b6231668cf9a5a23c68f89bccbf294630cfec36d Author: cgilet Date: Fri Oct 11 12:11:16 2019 -0400 Fix applyBCTensor: Must take StateMode into account. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 8e26d6a6d64e7f5d12416455988dfa880334ec0a Merge: 7785e7e77 ee47967c3 Author: WeiqunZhang Date: Fri Oct 11 08:51:00 2019 -0700 Merge pull request #589 from eschnett/development Avoid compiler warnings commit 99f5c9a0590b0622b75c464d9465693bb8479e93 Merge: 207d4a98c 7785e7e77 Author: cgilet Date: Fri Oct 11 10:23:23 2019 -0400 Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix commit 7785e7e77ef24ed09342e7ed689be521c7ba8833 Author: Kevin Gott Date: Fri Oct 11 07:07:09 2019 -0400 Clean up CudaGraphs and Tests. Only preferred method remains. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp Tests/GPU/CudaGraphs/CrazyGraphs/GNUmakefile Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp Tests/GPU/CudaGraphs/Readme.txt commit f91e3ed71cc80ebbf0a5562869d39e782dba3710 Author: DUGKS Date: Fri Oct 11 16:23:59 2019 +0800 add mathematical boundary types : HOEXTRAPLI Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_bc_types_mod.F90 Src/Base/AMReX_filcc_mod.F90 commit 1ff6d684d59d2da3844021dd6f49c51cc2ca6a17 Merge: cf7bb47e6 838561d07 Author: Andrew Myers Date: Fri Oct 11 00:31:27 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cf7bb47e642ece3d2833723b4510e80a2eab135b Author: Andrew Myers Date: Fri Oct 11 00:24:38 2019 -0400 calculate the early exit properly for local=false Src/Particle/AMReX_ParticleCommunication.cpp commit 0fb914ee1c9ec3282d1ea2f98986c4205dbfd967 Author: Andrew Myers Date: Fri Oct 11 00:23:40 2019 -0400 make sure the local option gets passed through correctly Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H commit 0c39c443176125eb62d94acbb27eebfdccf30def Author: Kevin Gott Date: Thu Oct 10 13:24:34 2019 -0400 Turn Random back on in ParallelReduce tests. Tutorials/GPU/ParallelReduce/main.cpp commit e4aab89e9f834170430e79502c365840c2be83d2 Author: Kevin Gott Date: Thu Oct 10 13:22:48 2019 -0400 Mark {{ Initialization lists for now. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_PlotFileDataImpl.H commit 3478d66a2bbc21c390cad2188db8f09a7b04958b Author: Kevin Gott Date: Thu Oct 10 11:33:35 2019 -0400 Fix and use the memcpy_to_symbol wrapper. Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_Random.cpp commit f3591f47f4ee29ebda8c4d1fcca296b8afbaa8d6 Author: Kevin Gott Date: Thu Oct 10 10:44:35 2019 -0400 Strip managed variable out of Random for HIP compatibility. Src/Base/AMReX_Random.cpp commit 6601c6263903c031a8b0b27bb06da87329a384a7 Author: Axel Huebl Date: Thu Oct 10 10:03:43 2019 -0400 Linker: Use RPath Although AMReX does not come with much dependencies besides runtimes, the build system allows to add various libraries for downstream application dependencies. In the case of WarpX, we link auxiliary libraries for I/O among others. When linking against shared libraries, these dependent libraries (think: `.so`|`.dylib`|`.dll` files) must be present and accessible at runtime again. Usually, one sets their paths in `export LD_LIBRARY_PATH` hints which is both cumbersome for users as well as bad for file-systems which will be heavily loaded with meta-data operations while searching for the corresponding dependencies, especially at scale. Luckily, all modern Unix systems support RPath hints, which embed the location of a dependent shared library at link time into the generated binary. https://en.wikipedia.org/wiki/Rpath We now enable this feature by default. The linker flag is implemented in a generic way that works with the most common compilers: - clang :heavy_check_mark: - gcc :heavy_check_mark: - nvcc :heavy_check_mark: - icc :heavy_check_mark: - pgcc :heavy_check_mark: - xlC :heavy_check_mark: - crayc++ "classic" :heavy_multiplication_x: - crayc++ 9.0+ "LLVM": :heavy_check_mark: In case there are any regressions or the intentional wish to not use RPaths, users can just set `USE_RPATH=FALSE` as `make` option. Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/GNUMake/Make.defs commit 838561d07a1052d2d8d7de93d0f37eb2ae737a2f Merge: 40f110b36 5172271fe Author: Andy Nonaka Date: Wed Oct 9 14:47:25 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 40f110b3611795681f521245d81643ba67b87f49 Author: Andy Nonaka Date: Wed Oct 9 14:46:02 2019 -0700 get the NeighborList particle tutorial running again. instead of crashing right away, it now crashes after 15 time steps for unknown reason Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/inputs.mr Tutorials/Particles/NeighborList/main.cpp commit 5172271fe17ea01274f5871f26335e7b9a216977 Author: cgilet Date: Wed Oct 9 16:51:02 2019 -0400 Minor fix in EB_computeDivergence: Only assert on 3rd dimension if AMREX_SPACEDIM==3 Src/EB/AMReX_EBMultiFabUtil.cpp commit 207d4a98c0746ca6e9e8f2e30ccda6fd522ce3a3 Author: cgilet Date: Wed Oct 9 16:17:49 2019 -0400 Update MLEBTensor::applyBCTensor Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit d54f4bfb5b49b59207cbe431d0a821bf797b3dd9 Author: cgilet Date: Wed Oct 9 16:15:32 2019 -0400 Force inline Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit 8bb4601c3eb2f936d05f359882cff0a780e7f798 Merge: 6268af922 42f7964e0 Author: Kevin Gott Date: Wed Oct 9 14:26:58 2019 -0400 Merge branch 'development' into kngott/hip commit 6268af922c9d2f3d00f97f43488230a65c93d62d Author: Kevin Gott Date: Wed Oct 9 10:38:15 2019 -0700 Wrap libraries and includes for HIP. Tests/GPU/RandomNumberGeneration/GNUmakefile commit 442af0f3fc2c081a2b041984465d2b7109c57662 Author: Kevin Gott Date: Wed Oct 9 10:35:08 2019 -0700 First draft of HIP for random. Need to fix memcpytoSymbol wrapper and make gpu_nstates non-managed. Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp commit b506ebf241482cf12b69ecc3e7942670d07e42a0 Author: Kevin Gott Date: Wed Oct 9 10:33:49 2019 -0700 memcpytoSymbol wrapper. [WIP] Doesn't seem to be working in Random.cpp Src/Base/AMReX_GpuDevice.H commit 7c3fdfc370ad78f078a5d879105a826b394ec08f Author: Kevin Gott Date: Wed Oct 9 10:32:59 2019 -0700 Initialize Random after Arenas to allow Arena use in Random Initiatlize. Src/Base/AMReX.cpp commit 33281c34d1239c6d962dab16efd8b171c8d2fe71 Author: Kevin Gott Date: Wed Oct 9 10:31:52 2019 -0700 Add HIPrand librarys and includes to the GNUmakefile for RandomNumberGenerator. Tests/GPU/RandomNumberGeneration/GNUmakefile commit bf476542fa048506a36db85515591caa402693b1 Author: Kevin Gott Date: Wed Oct 9 10:27:57 2019 -0700 Is this library needed? Src/Base/AMReX_GpuUtility.H commit 27919c362fa724ff5220ae3d23341161160ee1d6 Author: cgilet Date: Wed Oct 9 12:28:44 2019 -0400 Bug fix for case BCMode::Homogeneous Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit e916a48420bcffe6f33741a6d9d3bb4d4255631a Merge: dfd00f033 42f7964e0 Author: cgilet Date: Wed Oct 9 11:31:43 2019 -0400 Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix commit dfd00f033b1f10b197ed149ef31e9ecbacf3a0f0 Author: cgilet Date: Wed Oct 9 11:31:23 2019 -0400 WIP - MLMG not converging. Corner/edge cells fill appears reasonable Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 42f7964e040a2f8e7edfef5dbe384539b844142a Merge: 12c228e90 5cdb3461f Author: Andrew Myers Date: Wed Oct 9 06:48:13 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 12c228e90254231d0d754c500b6bb741513aa976 Author: Andrew Myers Date: Wed Oct 9 06:47:49 2019 -0700 allow thrust::complex in PODVector, even though it doesn't strictly meet the requirements of std::is_trivially_copyable Src/Base/AMReX_PODVector.H commit 9555c24d360bfda5615466e75ce37598441fa477 Merge: df2d572cd 5cdb3461f Author: Kevin Gott Date: Tue Oct 8 17:38:03 2019 -0700 Merge branch 'development' into kngott/hip commit 5cdb3461feed09530720cd03536e422b2067161b Author: Michele Rosso Date: Tue Oct 8 15:58:05 2019 -0700 CMake: add AMReX_Random.H and AMReX_Random.cpp to CMakeLists Src/Base/CMakeLists.txt commit 2631250d436da31a56fbd00c20e09628f3f4cfa0 Merge: 213f34516 a1b7a9f88 Author: Kevin Gott Date: Tue Oct 8 16:40:50 2019 -0400 Merge branch 'kngott/random' into development commit a1b7a9f881ff1833efddfa7ce29bfb174debbc69 Author: Kevin Gott Date: Tue Oct 8 16:40:01 2019 -0400 Fixing Random libraries. Src/Base/AMReX_Random.H Src/Base/AMReX_Utility.H commit c80035112676ab23727d765681da97d566f0d667 Author: Kevin Gott Date: Tue Oct 8 12:35:28 2019 -0700 Move Random functionality to separate file. Src/Base/AMReX.cpp Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/Make.package commit df2d572cde6c1a4f2aa5e6e4060155ee5aea0937 Author: Kevin Gott Date: Tue Oct 8 12:05:54 2019 -0700 1st version of HIP HeatEquation. No output. Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/mykernel.H commit 2eca21b79844c813400052b1bfb5911467c5b762 Author: Kevin Gott Date: Tue Oct 8 12:04:47 2019 -0700 Setup testing of ParallelReduce tutorial. Tutorials/GPU/ParallelReduce/GNUmakefile Tutorials/GPU/ParallelReduce/main.cpp commit 0d46d02d4afe0e23dafabb1772e9f3f17d104fe3 Author: Kevin Gott Date: Tue Oct 8 12:03:39 2019 -0700 Updated makefiles for testing. Tutorials/Basic/HelloWorld_C/GNUmakefile Tutorials/GPU/Launch/GNUmakefile commit 4b173b830b707964233f8a79dfb972c47b129ede Author: Kevin Gott Date: Tue Oct 8 11:59:47 2019 -0700 HelloWorld Work around for HIP shuffle intrinsics. Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_iMultiFab.cpp commit 213f3451658b3982ebfa888e8ec23e117a104de1 Merge: a3754a39f aefa1644a Author: Andrew Myers Date: Tue Oct 8 10:28:12 2019 -0700 Merge branch 'development' into atmyers/vector_memory_usage commit aefa1644ae399e651a42f512fe520a7147095e87 Merge: cad3614cf 58c293670 Author: Andrew Myers Date: Tue Oct 8 10:27:41 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cad3614cfe956cc3458229b3ccf10f4931e192c5 Author: Andrew Myers Date: Tue Oct 8 10:27:24 2019 -0700 fix ParticleMesh test Tests/Particles/ParticleMesh/main.cpp commit a3754a39feeba9a741e0dd49e10929ac3c7a3d07 Author: Andrew Myers Date: Tue Oct 8 12:57:00 2019 -0400 offload 'assign' in PODVector Src/Base/AMReX_PODVector.H commit b2918e2e698664e5654a9dfb81fcc46759055e0a Author: Andrew Myers Date: Tue Oct 8 12:31:01 2019 -0400 templated implementation of == and != for the Allocators Src/Base/AMReX_CudaAllocators.H commit ccd57a89551460dd0be2ca15e7290d7bb9b25611 Author: Andrew Myers Date: Tue Oct 8 08:39:53 2019 -0700 fix cpu compilation Src/Base/AMReX_CudaContainers.H commit ee47967c3773fdc4ea8a26dc63fbc32af083b681 Author: Erik Schnetter Date: Tue Oct 8 11:31:58 2019 -0400 Avoid compiler warnings Avoid warnings about signed/unsigned comparisons and about unused variables. Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArrayCommI.H commit 81707603e6008ca83c20cc2a5556e4742f02885d Author: Andrew Myers Date: Tue Oct 8 08:26:12 2019 -0700 some refactoring and simplication of the gpu allocators Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H commit 58c293670d728b2547dbc69e15b13a3796102202 Merge: d91052fc3 605b65eb3 Author: WeiqunZhang Date: Tue Oct 8 08:08:01 2019 -0700 Merge pull request #588 from ax3l/fix-printfWarnings GCC 7.4.0 Warnings in Prints commit d91052fc38ab7cb529245f52342310ba319a6174 Merge: 17b84c095 964666d92 Author: WeiqunZhang Date: Tue Oct 8 08:07:10 2019 -0700 Merge pull request #586 from AMReX-Codes/bugfix-install add a missing D in the Make.package file for MLNodeLap commit 70a641d27b621f98a279eb6caf101e819535c661 Merge: ac59fe275 17b84c095 Author: Andrew Myers Date: Tue Oct 8 07:00:04 2019 -0700 merging development into amrex/vector_memory_usage commit 17b84c095e380469455a3c43d4e8415cb8a8958f Merge: 60ea95ce6 382d6ce6b Author: Andrew Myers Date: Tue Oct 8 06:40:31 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 60ea95ce6674304211bbf38d33363948f8a5ae71 Author: Andrew Myers Date: Tue Oct 8 06:40:08 2019 -0700 iterate over map directly when early exiting from RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 605b65eb33909239f4b00c93711a121b7d17bb29 Author: Axel Huebl Date: Tue Oct 8 09:24:01 2019 -0400 GCC 7.4.0 Warnings in Prints Fix warnings of the type ``` In file included from /usr/include/stdio.h:862, from /usr/include/c++/8/cstdio:42, from ../amrex/Src/Base/AMReX_ParallelDescriptor.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:64:35: note: ‘__builtin___snprintf_chk’ output between 105 and 617 bytes into a destination of size 512 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../amrex/Src/Base/AMReX_ParallelDescriptor.cpp: In function ‘void amrex::ParallelDescriptor::Barrier(const string&)’: ../amrex/Src/Base/AMReX_ParallelDescriptor.cpp:198:23: warning: ‘%s’ directive output may be truncated writing up to 512 bytes into a region of size 383 [-Wformat-truncation=] snprintf(buf, N, "AMReX MPI Error: File %s, line %d, %s: %s", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``` when compiling with WarpX. Src/Base/AMReX_ParallelDescriptor.cpp commit 964666d92dcf606e817eb4888c9ce20524198c2e Author: Brandon Runnels Date: Mon Oct 7 15:30:05 2019 -0600 add a missing D in the Make.package file Src/LinearSolvers/MLMG/Make.package commit 382d6ce6bfea2186cd4c1d11024d17900aec094c Author: Ann Almgren Date: Sat Oct 5 15:07:36 2019 -0700 The point of passing in "loc" is to use it! Replace "MLMG::Location::FaceCenter" by loc in call to get Fluxes. Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 4c2c93062c787416ec6686ad640231b67c2c9052 Merge: 6b60f2aa5 1d422cb24 Author: WeiqunZhang Date: Sat Oct 5 14:56:42 2019 -0700 Merge pull request #585 from AMReX-Codes/max_gpu_streams Reduce number of CUDA streams to 4 commit 1d422cb24ed4d306d6fd2a1ec5adb9a7cc6b73cb Author: Max Katz Date: Sat Oct 5 16:27:47 2019 -0400 Reduce number of CUDA streams to 4 Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_MFIter.cpp commit 6b60f2aa54ac12daf48bedcd3d297ab4db10d2cd Author: Weiqun Zhang Date: Fri Oct 4 20:23:31 2019 -0700 for gpu regression tests, avoid saving errors in plotfiles Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTestPlotfile.cpp commit 6970468f530a61fb31f053f2d63894382f741e92 Author: Weiqun Zhang Date: Fri Oct 4 17:58:22 2019 -0700 add inputs for Nodal Poisson regression test Tutorials/Basic/HelloWorld_C/main.cpp Tutorials/LinearSolvers/NodalPoisson/inputs-rt commit 0e0a04c3482c0520a814775997b9f2bf1d337fba Author: cgilet Date: Fri Oct 4 16:50:28 2019 -0400 WIP - bug fix in mltensor_fill_edges(). some clean-up Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit 33e2c60c6b2bd5deba524b3052ac473aea53a358 Author: Emmanuel Motheau Date: Fri Oct 4 13:26:43 2019 -0700 update EB/MacProj tutorial to match last version of AMReX Tutorials/EB/MacProj/main.cpp commit 58b510ae290ea34c5e02d6f65fa01c0b1dee69a6 Author: Weiqun Zhang Date: Fri Oct 4 13:17:17 2019 -0700 add a new function for removing duplicates using hash Src/Base/AMReX_Vector.H commit 5f0b2fc8cf8a0090d484b495772808963ade5090 Author: Kevin Gott Date: Fri Oct 4 12:54:14 2019 -0700 Add fortran to hip builds. Straight copy from llvm using gfortran. Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 0d0d9d4ce923c0a898a3923ee2c079c542ac982c Author: Kevin Gott Date: Fri Oct 4 12:53:47 2019 -0700 shfl note. Src/Base/AMReX_GpuReduce.H commit b8062c23fe3b07299c669dd80777beda0ac27f28 Merge: c4a56aa02 b5d4fa0b1 Author: cgilet Date: Fri Oct 4 15:05:06 2019 -0400 Merge remote-tracking branch 'upstream/development' into development commit 8bf0b146d98a220988fadfda6f9444fdbea9398d Author: Kevin Gott Date: Thu Oct 3 13:21:35 2019 -0700 Cleanup. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Geometry.H commit b5d4fa0b1991a0ec2757d142d5c427d12b236be7 Merge: 8bb904a80 a9c393f0c Author: Andrew Myers Date: Thu Oct 3 12:19:02 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8bb904a80d42c551f546d6d0fee905e207e33c41 Author: Andrew Myers Date: Thu Oct 3 12:18:54 2019 -0700 fix corner case bug in ParticleCopyPlan::build Src/Particle/AMReX_ParticleCommunication.H commit e24875addb9ccc3940a2858d16a70376c36eabc0 Author: Kevin Gott Date: Thu Oct 3 11:50:28 2019 -0700 Callback on HIP. Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuElixir.cpp commit 58fd40e73fd31dd4f0f69d315f7f7bd51fb9ef92 Author: Kevin Gott Date: Wed Oct 2 17:45:02 2019 -0700 Covert to AMREX_HIP_TO_CUDA. Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MultiFabUtil_nd_C.H commit bd9d27667a113677192c07b0ca06c95c879ab63e Merge: 6c373053e a9c393f0c Author: Kevin Gott Date: Wed Oct 2 16:36:07 2019 -0700 Merge branch 'development' into kngott/hip commit 6c373053e7aba3835407e158f132fd39dcaa3cef Author: Kevin Gott Date: Wed Oct 2 16:34:59 2019 -0700 Add label to update Random to HIP. Src/Base/AMReX_Utility.cpp commit 1178281d2c0c2f6ff4230f2172d47637484733cf Author: Kevin Gott Date: Wed Oct 2 15:56:32 2019 -0700 Label FabView HIP changes. Src/Base/AMReX_BaseFab.H commit 6e231f96400a192f4b6ca7a79167ea23215aef89 Author: Kevin Gott Date: Wed Oct 2 15:55:05 2019 -0700 Add labels to HIP FIX comments. Src/Base/AMReX.cpp Src/Base/AMReX_Array4.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuElixir.cpp Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_Utility.cpp commit 5bd0eb17196b4413b9fbe0b1c741bdc03551df8d Author: Kevin Gott Date: Wed Oct 2 15:54:19 2019 -0700 std function wrappings for HIP. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil_nd_C.H commit 2fd4a8e5745377ec07f25ade462f7f14ef1e2a66 Author: Kevin Gott Date: Wed Oct 2 15:52:18 2019 -0700 Add iMultiFab destructor for HIP. Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit f44ce46a5c628bb0eb0a98ee78fa2267262166f8 Author: Kevin Gott Date: Wed Oct 2 15:51:10 2019 -0700 __all_sync and __any_sync for HIP Src/Base/AMReX_FBI.H commit 19b74aa1522f615eea7c287fdf36e3bc0a1e0cfa Author: Kevin Gott Date: Wed Oct 2 15:22:25 2019 -0700 Add a CPU CArena option for HIP. Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_MemPool.cpp commit a9c393f0c12150412f3d141d47b66d91ae551923 Author: Weiqun Zhang Date: Wed Oct 2 14:00:13 2019 -0700 readBoxArray: make the special flag optional Src/Base/AMReX_BoxArray.H commit 74a575af8d54c724a48533f7b9e6f4ea27601d53 Author: Andrew Myers Date: Wed Oct 2 16:51:59 2019 -0400 add another specialization for placementNew that explicitly does nothing for arithmetic types Src/Base/AMReX_BaseFab.H commit ab2a34edaf62b95e264ef416c41e388a6d4c5226 Author: Weiqun Zhang Date: Wed Oct 2 13:11:10 2019 -0700 make gnu make NVCC_HOST_COMP more robust Tools/GNUMake/Make.defs commit e7e4c20354846c6db141349130a64a9672fc256d Author: Lucas Esclapez Date: Wed Oct 2 11:59:01 2019 -0700 [feature_nd_Pele] Add a 3D version of bc in Derive for dim. agnostic codes. Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp commit 1e4702a19ba60adbe8fae823866e7a303b28da4b Author: shashankNREL Date: Fri Sep 6 10:18:07 2019 -0600 Fixes to the spline IF routines Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp Tutorials/EB/GeometryGeneration/main.cpp commit d59c4b01f0c879af99bf7a08e783fe1efa4f2b29 Merge: 8af435766 159461a47 Author: Ann Almgren Date: Wed Oct 2 07:17:54 2019 -0700 Merge branch 'development' into mr/multicomp-div commit 90ee8c6ffa90a17f297c14d7e46e6a36da9c6c38 Author: Kevin Gott Date: Tue Oct 1 17:07:48 2019 -0700 manual memset. alloc doesn't seem to be working. Src/Base/AMReX_MemPool.cpp commit 38a95751797c5ce73b2b68528733d6b9748dd965 Author: Kevin Gott Date: Tue Oct 1 17:07:22 2019 -0700 FabView Constructor wrappers for DEBUG and USE_HIP=FALSE. Src/Base/AMReX_BaseFab.H commit a6867be24b8e516721c13c14e6fc2ff0190b3a5c Author: Kevin Gott Date: Tue Oct 1 16:30:15 2019 -0700 HIP doesn't like memset? HelloWorld is running with HIP. Src/Base/AMReX_MemPool.cpp commit c4a7c8791d5c3dadd266c32916428ebf5f123617 Author: Kevin Gott Date: Tue Oct 1 16:20:50 2019 -0700 Remove the C++14 flag. Tools/GNUMake/comps/hip.mak commit fed441acaae7f0ae2ed83bdc18b5c794a81e272a Author: Kevin Gott Date: Tue Oct 1 15:40:51 2019 -0700 Comment out virtual destructor. Conflict with LLVM 'key function'? Src/Base/AMReX_iMultiFab.H commit 01bc7276af77ccb5529d5358e83e16fcc38b8ae7 Author: Kevin Gott Date: Tue Oct 1 15:40:12 2019 -0700 Comment out std distribution functions. Src/Base/AMReX_Utility.cpp commit 71353837735b499bb61d5600f50d84b8aa50b237 Author: Kevin Gott Date: Tue Oct 1 15:39:46 2019 -0700 More launch macros. Src/Base/AMReX_Reduce.H commit 6544a7700375a98a5f641aa1ee3189ebebcec761 Author: Kevin Gott Date: Tue Oct 1 15:39:34 2019 -0700 std::floor to floor. Src/Base/AMReX_MultiFabUtil_nd_C.H commit acca5523457b921148fa7f671a450853ba0dcd15 Author: Kevin Gott Date: Tue Oct 1 15:39:23 2019 -0700 std::abs to abs. Src/Base/AMReX_IntVect.H commit dab8b5b82dbbfa2a69dcd8845aa51de750783559 Author: Kevin Gott Date: Tue Oct 1 15:39:07 2019 -0700 Comment out _shfl_down_sync. Src/Base/AMReX_GpuReduce.H commit 999866bbfc2f00a64b0966fcb22e6b91c9a706e1 Author: Kevin Gott Date: Tue Oct 1 15:38:39 2019 -0700 Comment out callback functions. Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuElixir.cpp commit e4955b69e83e9b3df4c71df754b51dae6e6c4965 Author: Kevin Gott Date: Tue Oct 1 15:38:14 2019 -0700 Comment out _any_sync and _all_sync. Src/Base/AMReX_FBI.H commit 91ab0cef38c7b85e6ac20621d891e4018011c456 Author: Kevin Gott Date: Tue Oct 1 15:37:53 2019 -0700 Getting around failing initalization lists. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Geometry.H commit 9e544faa38e29a9043a1e302154cc657ecac3af6 Author: Kevin Gott Date: Tue Oct 1 15:37:12 2019 -0700 Comment out printf on device. Src/Base/AMReX.cpp Src/Base/AMReX_Array4.H commit b4a332f0a7190eaa084deaf4920d1b26110b1475 Author: Kevin Gott Date: Tue Oct 1 15:36:48 2019 -0700 Launch Macro. Switch between (<<< >>>) and hipLaunchKernelGGL. Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H commit ce8e8f5ca0501fd61374ea596d281ff345931fd4 Author: Kevin Gott Date: Tue Oct 1 15:34:54 2019 -0700 hipHostAlloc -> hipHostMalloc & hipFreeHost -> hipHostFree Src/Base/AMReX_Arena.cpp commit caee68dc7e6001197058fb0a0858ae0778915828 Author: Kevin Gott Date: Tue Oct 1 15:22:47 2019 -0700 DEBUG=FALSE and NO_FORT build. Tutorials/Basic/HelloWorld_C/GNUmakefile commit 446197fbfec24c8c9ed5323fc140f1ab6a210610 Author: Kevin Gott Date: Tue Oct 1 15:22:15 2019 -0700 lineinfo unknown and start tracking down -std=c++11 flags. Tools/GNUMake/comps/hip.mak commit 159461a47f0be4054b2022baa01e2a84b5a00558 Author: Andrew Myers Date: Tue Oct 1 15:18:05 2019 -0700 update success string Tests/Particles/ParticleReduce/main.cpp commit 5b1ebf3582a1c8fbe7c65268062fc34eaacd941b Merge: 908b639ec 9c00149ca Author: Andrew Myers Date: Tue Oct 1 15:14:03 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 908b639ecf497e928c7b8030414184f4a99e0e10 Author: Andrew Myers Date: Tue Oct 1 15:13:54 2019 -0700 rewrite particle reductions in the new style Src/Particle/AMReX_ParticleReduce.H commit 5ec826cdf45d10b3f95fbd83f48e9acae4c9c590 Author: Andrew Myers Date: Tue Oct 1 15:13:31 2019 -0700 update ParticleReduce test Tests/Particles/ParticleReduce/main.cpp commit 9c00149ca01b5a027058ac570f14790c461c63ee Merge: 1990d7c02 f4cbb17e9 Author: Andrew Myers Date: Tue Oct 1 14:45:07 2019 -0700 Merge pull request #583 from AMReX-Codes/single_precision_random Single precision random commit f4cbb17e9c5070d42e4e414932a20bea31954acf Merge: e4e7c3fc7 1990d7c02 Author: Andrew Myers Date: Tue Oct 1 14:24:08 2019 -0700 Merge branch 'development' into single_precision_random commit e4e7c3fc7007b4582ff5abd91c5802fdac430df5 Author: Andrew Myers Date: Tue Oct 1 14:19:32 2019 -0700 Real -> amrex::Real Src/Base/AMReX_Utility.cpp commit 3435f967f01a1c39870a6a793735dcb9910b684e Author: Andrew Myers Date: Tue Oct 1 14:15:41 2019 -0700 Random and RandomNormal for single and double precision Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 1990d7c027d53d6141695999345858c8f5432bce Merge: 3db90209c 317bd6ea6 Author: Andrew Myers Date: Tue Oct 1 13:57:48 2019 -0700 Merge pull request #581 from ax3l/fix-tracerNarrowingFloat Tracer Particles: Fix Narrow Warnings commit 317bd6ea6ffec96a1a4ff7f34dfa821e2794af5a Author: Axel Huebl Date: Tue Oct 1 13:48:04 2019 -0700 Tracer Particles: Narrow Warnings Mitigate some narrowing warnings in tracer particles when compiling in single precision: ``` Src/Particle/AMReX_TracerParticle_mod_K.H:86:27: warning: narrowing conversion of ‘(1.0e+0 - ((double)xint))’ from ‘double’ to ‘amrex::Real {aka float}’ inside { } [-Wnarrowing] ``` Src/Particle/AMReX_TracerParticle_mod_K.H commit 8af4357663e3b8917cfe5d3642bf76821ff3b835 Author: Michele Rosso Date: Tue Oct 1 12:25:14 2019 -0700 Make EB_computeDivergence components-aware Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit dbb5fd73a5a01e8d4e1d68157ea4166eb5c5a44d Merge: 89b55703e 3db90209c Author: Michele Rosso Date: Tue Oct 1 10:43:19 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/mf-eb-methods commit 3db90209c6df3e343f03881116263d7790cd6708 Merge: b7c1e4fc6 d97ba204a Author: Weiqun Zhang Date: Tue Oct 1 06:48:43 2019 -0700 Merge branch 'weiqun/dev' into development commit b7c1e4fc6d38ee9340331ce30a24dd84f79b9ee2 Author: Weiqun Zhang Date: Tue Oct 1 06:47:12 2019 -0700 update CHANGES CHANGES commit 5bca4b65e00c6b4763136f3794a91eef823dd18d Merge: 346882f3a ccefb4dfc Author: Weiqun Zhang Date: Tue Oct 1 06:31:17 2019 -0700 Merge branch 'development' commit d97ba204a2df9f50337784da01ff84cb1c6304a6 Author: Weiqun Zhang Date: Mon Sep 30 19:58:28 2019 -0700 gpu nodal rap: restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ccefb4dfcca14933b0a463d8df54e2f9e24ef2c6 Author: Weiqun Zhang Date: Mon Sep 30 20:07:45 2019 -0700 fix dangling pointer Src/Base/AMReX.cpp commit 679e091c6e7971fc8176a128c79a1c40d0e63d49 Author: Max Katz Date: Mon Sep 30 18:06:37 2019 -0700 Add flag for enabling ptxas verbosity Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 968d074df7620485ff3f78adad0dfb73a8f3afba Author: Max Katz Date: Mon Sep 30 18:06:09 2019 -0700 Do not use device_prop.uuid for CUDA < 10 Src/Base/AMReX_GpuDevice.cpp commit cfb2817033240c42a1c25fc2dddf4ad9177e3a0e Author: Max Katz Date: Mon Sep 30 16:39:46 2019 -0700 Add Device method for returning GPU model name Src/Base/AMReX_GpuDevice.H commit bb56d80bc85b1a436449ff80f3499498ebf1ccfa Author: Weiqun Zhang Date: Mon Sep 30 12:51:34 2019 -0700 gpu nodal rap: interpadd Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 45d6080a4b004de4449915a5db161af5d95fe7d1 Author: Andrew Myers Date: Mon Sep 30 12:32:43 2019 -0700 tweak these prints as well Tests/Particles/NeighborParticles/MDParticleContainer.cpp commit 7f9ba81b98affaff8ffb96dfb4c84f03d6e6f4d0 Author: Andrew Myers Date: Mon Sep 30 12:29:54 2019 -0700 tweak this test to diff a plain txt file Tests/Particles/NeighborParticles/MDParticleContainer.cpp Tests/Particles/NeighborParticles/main.cpp commit 603da943db0b94ddb4e02d8f0dab455322b7c9f6 Merge: e010cde46 c6ed9686a Author: cgilet Date: Mon Sep 30 14:15:46 2019 -0400 Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix Conflicts: Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit bdce7ca29924ec4ac1dbb16ce47d1532a18b9d18 Author: Andrew Myers Date: Mon Sep 30 11:05:37 2019 -0700 add more inputs scripts to the redistribute test for regression testing Tests/Particles/Redistribute/inputs.rt.cuda Tests/Particles/Redistribute/inputs.rt.cuda.mr Tests/Particles/Redistribute/inputs.rt.cuda.nonperiodic commit e010cde461a44c3e1bf241d30555ea01ca4cb799 Author: cgilet Date: Mon Sep 30 12:04:34 2019 -0400 Updates for 3D. Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 1fa9cb09e6a681d37c9e3ff8b22df98b9bc21ddf Author: Weiqun Zhang Date: Sun Sep 29 21:37:49 2019 -0700 gpu nodal: jacobi stencil version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 3d2dd8911f861e4c12415a01dd44fca75367b9e7 Author: Weiqun Zhang Date: Sun Sep 29 21:27:38 2019 -0700 gpu nodal: gauss seidel stencil version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7ad21d9284af2b335bfe1b6a8ad41e9ab4ebf8e4 Author: Weiqun Zhang Date: Sun Sep 29 21:07:21 2019 -0700 gpu nodal: normalize stencil version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5022ad28c4d8831fd912b5c67cd8267b1dded990 Author: Weiqun Zhang Date: Sun Sep 29 20:47:05 2019 -0700 gpu nodal: A dot x stencil version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e2ac5e6b63dbcef081a5d4c23cc2e3e9666a34a9 Author: Weiqun Zhang Date: Sun Sep 29 20:29:01 2019 -0700 nodal gpu: set stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e7233b0b2a52825bf8b1df76ecf9cfbb8f224aa1 Author: Weiqun Zhang Date: Sun Sep 29 17:02:20 2019 -0700 gpu nodal: fill bc for nodal phi Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp commit 4dca4be57a17e555f5079ffaa6fda8300fd3e3a7 Author: Weiqun Zhang Date: Sun Sep 29 15:56:33 2019 -0700 gpu nodal: fix bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 0f556e08f1adc8f04fee7f26c782bb085fed5bba Author: Weiqun Zhang Date: Sun Sep 29 15:24:39 2019 -0700 2d compiles Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H commit ac425b02dd167ae298b92730b013f1573b6eb035 Author: Weiqun Zhang Date: Sun Sep 29 15:04:37 2019 -0700 gpu nodal: fill bc for sigma Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp commit dd7213c381cdb9cc31ebdbe8783b3dd3ddb422d4 Merge: 5a2ecbe3c 7c6663bf7 Author: Weiqun Zhang Date: Sun Sep 29 07:24:20 2019 -0700 Merge branch 'development' into weiqun/dev commit c6ed9686a12c188f0fb0dc962b73fab719a40634 Author: Ann Almgren Date: Sat Sep 28 17:26:10 2019 -0700 Update MAC projector documentation to reflect that, when USE_EB=TRUE, we must now specify whether the incoming (and outgoing) face velocities are defined on face centers or centroids Docs/sphinx_documentation/source/LinearSolvers.rst commit 2383c180dc82388b25d2db3c2c2ad85e8df57352 Author: Ann Almgren Date: Sat Sep 28 17:21:13 2019 -0700 Create interface in the absence of EB that does not require the specification of FaceCenter vs FaceCentroid. Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit 813ec8248fcd2fc4ff246d927c9f3bef9f25f5c1 Merge: 08c620df0 fd4a60fec Author: Ann Almgren Date: Sat Sep 28 17:12:03 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 08c620df0718ceac3353ef51b0a2de243dae4c35 Author: Ann Almgren Date: Sat Sep 28 17:11:11 2019 -0700 We must now specify whether the MAC projection is being given normal velocities at face centers or at face centroids. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit fd4a60fec3f572d492c013abc53f0409b840cfd2 Author: Weiqun Zhang Date: Sat Sep 28 12:58:30 2019 -0700 fix the inputs for gpu regression test Tutorials/GPU/CNS/Exec/RT/inputs-rt commit 6c497073d9338f039d3805d7056ef198eef009c1 Author: Weiqun Zhang Date: Sat Sep 28 12:45:23 2019 -0700 add inputs for gpu regression tests Tutorials/GPU/CNS/Exec/RT/inputs-rt Tutorials/GPU/CNS/Exec/Sod/inputs-rt commit 78f5603d53a36bc605271cda7b03ba9cca87dd9b Author: Weiqun Zhang Date: Fri Sep 27 22:51:18 2019 -0700 add garuda Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.ccse commit a45432f5656a26b81ce06f20f7c3bca5c99eca5a Author: Kevin Gott Date: Fri Sep 27 17:01:08 2019 -0700 BaseFab host device. Src/Base/AMReX_BaseFab.H commit b0caab9be65256e85f7069d20224442688e87161 Author: Kevin Gott Date: Fri Sep 27 16:40:18 2019 -0700 __host__ __device__ on declarations and functions test. Src/Base/AMReX_IntVect.H commit d3479e03aca9929a434255dcb4dd2a804902ea2d Author: Kevin Gott Date: Fri Sep 27 16:36:06 2019 -0700 Corresponding HIP makefile for the build system. Tutorials/Basic/HelloWorld_C/GNUmakefile commit 1abfab0afd784f00d59dbab6c6758a1a98524f08 Author: Kevin Gott Date: Fri Sep 27 16:35:35 2019 -0700 Add hip library. Why is this needed? It's in AMReX_Gpu.H Src/Base/AMReX_GpuQualifiers.H commit 7e9d63c434b2440b3e61f3b886139ee8f3e6220b Author: Kevin Gott Date: Fri Sep 27 16:35:06 2019 -0700 Quick first hack-y build system update for HIP. Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 7c6663bf78479a7bcee95052c652d27bbb307201 Author: Michele Rosso Date: Fri Sep 27 12:32:23 2019 -0700 CMake: fix typo Src/Extern/Conduit/CMakeLists.txt commit 4ce8cd8bd8b4a640f54f011315849b03223e57ac Author: Max Katz Date: Fri Sep 27 09:44:22 2019 -0700 Count number of GPUs used in total Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 5a428d2b057fe5f7ace811fbe95125131bd23bc0 Merge: e37deefd3 4b6fd5c4a Author: WeiqunZhang Date: Thu Sep 26 17:11:36 2019 -0700 Merge pull request #578 from ax3l/topic-userLiteralForParticleReal C++ User Literal for amrex::ParticleReal (_prt) commit 4b6fd5c4afdc1a8852a498de1bd91b2fe2c0ba17 Author: Axel Huebl Date: Thu Sep 26 17:05:40 2019 -0700 Typo & Doxygen Src/Base/AMReX_REAL.H commit 39dd95d103d7391a7146cd809a2dce877e2d0306 Author: Axel Huebl Date: Thu Sep 26 16:33:08 2019 -0700 C++ User Literal for amrex::ParticleReal (_prt) Same as the literal for `amrex::Real`. Src/Base/AMReX_REAL.H commit e37deefd3808ed3bf673c1cbe06aa03210d2b167 Merge: 773aa759d 9465815d7 Author: WeiqunZhang Date: Thu Sep 26 16:17:04 2019 -0700 Merge pull request #577 from ax3l/topic-userLiteralForReal C++ User Literal for amrex::Real (_rt) commit 9465815d7dc0420731801ef6173b7ea87b7d330d Author: Axel Huebl Date: Thu Sep 26 15:30:57 2019 -0700 Use new Real literal in code base Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_AmrCore.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_FArrayBox.cpp Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleContainerI.H commit 47a3c40d53d47e84ddc224d48c7f4e8b651a0ab3 Author: Axel Huebl Date: Thu Sep 26 15:32:16 2019 -0700 C++ User Literal for amrex::Real (_rt) This adds a user literal for `amrex::Real`. This is a C++11 feature and allows to type constants properly instead of relying on implicit conversation. A typical fallacy is the following user code: ```C++ auto const mypi = 3.14; Real const sphere_volume = 4/3 * mypi * pow(r,3); ``` The first term `4/3` makes the whole expression an `int` until the result is casted to `amrex::Real`. Urgh! We can do better, with `amrex::Real(4)/::amrex:Real(3)` but who wants to write such verbose code, right? So C++11 user literals to the rescue! ```C++ auto const mypi = 3.14_rt; // that's a real, too! Real const sphere_volume 4_rt / 3_rt * mypi * pow(r,3); ``` Src/Base/AMReX_REAL.H commit 773aa759d5eb46afdae00219261c75c8028fa9e0 Merge: a8fa098c7 0a1623d07 Author: Andrew Myers Date: Thu Sep 26 17:55:41 2019 -0400 Merge branch 'development' into multilevel_gpu_redistribute commit 0a1623d077fe752e6d168077e50c347ebd14a220 Author: Weiqun Zhang Date: Thu Sep 26 14:51:14 2019 -0700 add int8_t support in typecheck Tools/typechecker/typechecker.py commit 70b03eb5215e1cbe1a9b29c1630f1f9f9e69f62b Author: Weiqun Zhang Date: Thu Sep 26 14:49:29 2019 -0700 add amrex::Long Src/Base/AMReX_BLFort.H Src/Base/AMReX_INT.H Src/Base/AMReX_IntVect.H Src/Base/CMakeLists.txt Src/Base/Make.package commit a8fa098c742befef3f088a886700bd445389e289 Author: Andrew Myers Date: Thu Sep 26 17:46:34 2019 -0400 handle case that people have added particles on grids that aren't owned by the proc in question Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit f9205c16dde74b9cac4307050be8bfdc0b6f7553 Merge: 366cef4a8 70894ced0 Author: Andrew Myers Date: Thu Sep 26 13:37:50 2019 -0700 Merge pull request #576 from AMReX-Codes/single_precision various fixes for single precision and particle real commit 70894ced00e6e8fe9ca48b12fcf89becb4224288 Author: Weiqun Zhang Date: Thu Sep 26 13:30:13 2019 -0700 various fixes for single precision and particle real Src/Base/AMReX_REAL.H Src/Base/AMReX_VectorIO.H Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Src/Particle/AMReX_TracerParticle_mod_K.H commit d4217e695f5fa969c51db2c02f3953d834c0bde9 Author: Andrew Myers Date: Thu Sep 26 15:37:05 2019 -0400 remove m_need_handshake, which isn't used any more Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 818cc4cb15dee256db901062860528fb3050505e Author: Andrew Myers Date: Thu Sep 26 15:36:50 2019 -0400 update neighbor_copy_op with level information Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 12dc799cdb6b3f5cf9dbda5c699c4559698be631 Author: Andrew Myers Date: Thu Sep 26 15:11:26 2019 -0400 also remove the redistribute mask from enforce periodic Src/Particle/AMReX_ParticleContainerI.H commit ab3fa5e6a9aa3d32adbc4db79818fd0b209d8cb2 Author: Andrew Myers Date: Thu Sep 26 14:38:01 2019 -0400 don't need mask in RedistributeGPU any more Src/Particle/AMReX_ParticleContainerI.H commit 5a2ecbe3ca0fe394caa4f2b5e5974eba7c3268fe Author: Weiqun Zhang Date: Wed Sep 25 21:23:37 2019 -0700 gpu nodal: interpadd Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f0e701856f48053141871543859a527a90c3e99a Merge: 3a8e6660c 366cef4a8 Author: Andrew Myers Date: Wed Sep 25 17:50:57 2019 -0700 Merge branch 'development' into multilevel_gpu_redistribute commit 3a8e6660c02c118477496efd99973c71ae1bf952 Author: Andrew Myers Date: Wed Sep 25 17:29:02 2019 -0700 skip invalid particles in numOutOfRange Src/Particle/AMReX_ParticleUtil.H commit 366cef4a8c3af171b43fc4256ee7f3758f2b2dc1 Author: Ann Almgren Date: Wed Sep 25 17:25:52 2019 -0700 fix formatting? Docs/sphinx_documentation/source/BuildingAMReX.rst commit 2c90e756a15494960ffb950c140e8305d8ecf62b Author: Ann Almgren Date: Wed Sep 25 16:54:15 2019 -0700 Add comments about AMReX on Windows (per Weiqun) Docs/sphinx_documentation/source/BuildingAMReX.rst commit 842c4f1b02767ff68b4259da6eae453bdaf6d5e6 Author: Andrew Myers Date: Wed Sep 25 15:00:19 2019 -0700 update test for 1 and 2D Tests/Particles/Redistribute/main.cpp commit a9bdb4ee6b109767e0ff46c444eab5c49238c6db Author: Andrew Myers Date: Wed Sep 25 14:35:20 2019 -0700 add methods for changing the geometry object of particle locator Src/Particle/AMReX_ParticleLocator.H commit d8bd500c35b13cdab329674aa75815c4d345c7ac Author: Andrew Myers Date: Wed Sep 25 14:34:25 2019 -0700 need to set lev_max here Src/Particle/AMReX_ParticleContainerI.H commit 070c75d4eaa0b1ab8f18fc306c74d1bdfc616581 Author: Andrew Myers Date: Wed Sep 25 13:21:47 2019 -0700 need to clamp these quantities in 2D Src/Particle/AMReX_ParticleLocator.H commit 3f4d348366c649928fa0937c0402de7d1af5d2a8 Merge: 7e7b66aab d54cbc5bb Author: Weiqun Zhang Date: Wed Sep 25 12:37:01 2019 -0700 Merge branch 'development' into weiqun/dev commit d54cbc5bb7a25dcc51335019ce8d5b37ca8809ea Merge: cde68b826 5939f8dc2 Author: WeiqunZhang Date: Wed Sep 25 09:14:57 2019 -0700 Merge pull request #574 from awehrfritz/UNSW Tools/GNUMake - Add Australian machines commit cde68b826e18e4f8d50b331afa63f290430e1648 Merge: cb416f0a1 f3cd2ebd6 Author: Andy Nonaka Date: Wed Sep 25 08:07:28 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit cb416f0a1acbe2bf154c4f426624553bf75b2970 Author: Andy Nonaka Date: Wed Sep 25 08:07:09 2019 -0700 note about subset -> levels in VisIt Docs/sphinx_documentation/source/Visualization.rst commit f3cd2ebd658dfa8612eadd6a206e7a13648cc79a Author: Ann Almgren Date: Tue Sep 24 18:02:57 2019 -0700 slight clean-up of tensor solve section Docs/sphinx_documentation/source/LinearSolvers.rst commit 7e7b66aab4049477309cef48218924a4943a9b4a Author: Weiqun Zhang Date: Tue Sep 24 16:57:12 2019 -0700 gpu nodal: restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 02a2563eb04ddf6610edbcdf9e67f941d54e86a6 Author: Ann Almgren Date: Tue Sep 24 16:38:19 2019 -0700 Add code snippet for calling the tensor solve explicitly Docs/sphinx_documentation/source/LinearSolvers.rst commit 5920bc2c4c67d69e550ef26eaa8156802963fbab Author: Ann Almgren Date: Tue Sep 24 16:26:29 2019 -0700 update tensor stencil Docs/sphinx_documentation/source/LinearSolvers.rst commit 4046734b740b549af593e9e7db30b6162dbc4455 Author: Andrew Myers Date: Tue Sep 24 19:22:29 2019 -0400 fix new bug in ParticleBufferMap Src/Particle/AMReX_ParticleBufferMap.cpp commit 00e5ca8f014ff6ccc1c2a09fb2205e31ba3258b8 Merge: 69f49f55f 576183c00 Author: Ann Almgren Date: Tue Sep 24 15:37:19 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 69f49f55feb0b70d1227ce64d8264aed4eb88a31 Author: Ann Almgren Date: Tue Sep 24 15:35:48 2019 -0700 Update formulat in tensor solve documentation Docs/sphinx_documentation/source/LinearSolvers.rst commit c496e2cbafe4697c75a0a398678d9f9bcc15f351 Author: Andrew Myers Date: Tue Sep 24 18:23:35 2019 -0400 fix assertion Src/Particle/AMReX_ParticleCommunication.H commit f95f0da5909d8906607d023ee152e173e5ae260a Merge: 411a3f53d 576183c00 Author: Andrew Myers Date: Tue Sep 24 14:51:04 2019 -0700 Merge branch 'development' into multilevel_gpu_redistribute commit 576183c00d937f93b57d5eac83f6c64a475afbbe Merge: 086ca71d8 48172595b Author: Andrew Myers Date: Tue Sep 24 14:50:22 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 086ca71d8a70351e5c9b74a1161e67f9448dfdec Author: Andrew Myers Date: Tue Sep 24 14:50:02 2019 -0700 make the return type of this function template match the function body Src/Base/AMReX_Tuple.H commit 411a3f53d33478559957590766b1ecc7d14dcee8 Author: Andrew Myers Date: Tue Sep 24 14:49:26 2019 -0700 don't need to use std::forward here any more Src/Particle/AMReX_ParticleLocator.H commit cde37bdaa1798d4d11177613ca495b6a3fe1a9c3 Author: Andrew Myers Date: Tue Sep 24 14:44:52 2019 -0700 need temporaries for the lev Src/Particle/AMReX_Particles.H commit d621ca869a70731ee091ba837ffb7c17fa6ff0ce Author: Andrew Myers Date: Tue Sep 24 14:39:01 2019 -0700 missed a factor of the level offset in building the buffer map Src/Particle/AMReX_ParticleBufferMap.cpp commit 636a530b458c61d11360e749178dec9cbf36f8b8 Author: Andrew Myers Date: Tue Sep 24 12:28:47 2019 -0700 use tuple in the grid assignor Src/Particle/AMReX_ParticleLocator.H commit 861181e8c72032d9e2278fef6e69fb25b25ff4ec Author: Andrew Myers Date: Tue Sep 24 12:28:22 2019 -0700 computing dst lev Src/Particle/AMReX_ParticleContainerI.H commit 5a0f18050bb73d381c9a23ac5b5b79faef4fffbe Author: Andrew Myers Date: Tue Sep 24 12:27:56 2019 -0700 lev -> dst_lev Src/Particle/AMReX_ParticleCommunication.H commit 3b8ae464dc8167c1d94167aeb06d90e079de8167 Author: Andrew Myers Date: Tue Sep 24 10:39:32 2019 -0700 more flexible construction for AmrParticleLocator Src/Particle/AMReX_ParticleLocator.H commit 2880164f6759eafb823077d128caa4e33e6815b2 Author: Andrew Myers Date: Tue Sep 24 10:27:26 2019 -0700 another form of () for the particle locator Src/Particle/AMReX_ParticleLocator.H commit 4453c565dee6852589186b115a4e9a6afa29907a Author: Andrew Myers Date: Tue Sep 24 10:26:49 2019 -0700 move this call to outside the loop over levels Src/Particle/AMReX_ParticleContainerI.H commit 48172595b3b1d20e6b828678b05bbe77ddbdd618 Author: Weiqun Zhang Date: Tue Sep 24 09:49:31 2019 -0700 EB Tensor solver: enforce periodic boundary Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 77188fab8e931006e591790d21e4385f6032f8c4 Author: Weiqun Zhang Date: Mon Sep 23 21:28:00 2019 -0700 Tensor solver: enforce periodic boundary Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 8315dd8251ae7265da8b5217439f6bb1c44a64df Author: Andrew Myers Date: Mon Sep 23 20:32:53 2019 -0400 move the loop over levels to inside the particle locator Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H commit 8bbc18b3e1753e631dc8b9592eacb15d34371863 Author: Ann Almgren Date: Mon Sep 23 16:58:24 2019 -0700 update tensor stuff Docs/sphinx_documentation/source/LinearSolvers.rst commit 89b55703e08898573ea5984c1bddd60da72a7f84 Author: Michele Rosso Date: Mon Sep 23 16:56:53 2019 -0700 MultiFab: add EB-aware implementation of norm0, max and min Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit aa013f8e6fde9679fe76081d77d4d1039ca52112 Author: Andrew Myers Date: Mon Sep 23 19:56:48 2019 -0400 fix some (new) bugs in the particle locator Src/Particle/AMReX_ParticleLocator.H commit 046794674ace1336cd5e84aad3e3cafa748e779e Author: Ann Almgren Date: Mon Sep 23 16:50:51 2019 -0700 Fix math Docs/sphinx_documentation/source/LinearSolvers.rst commit 6f0fe63c6d711571c9b93a48b9ac174905e684e5 Merge: e7ec1ac10 072eb00a1 Author: Ann Almgren Date: Mon Sep 23 16:27:37 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit e7ec1ac102ba64ea8f9dbf9fe23469a0c01130b5 Author: Ann Almgren Date: Mon Sep 23 16:27:05 2019 -0700 intro to tensor solve Docs/sphinx_documentation/source/LinearSolvers.rst commit 072eb00a11611fa093fe6280a297d8f265994789 Author: Weiqun Zhang Date: Mon Sep 23 16:20:29 2019 -0700 fix tensor solver's domain bc corners Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit bbc4f7a9cae8aa2fe4f82d294cafb362348f79f9 Author: cgilet Date: Mon Sep 23 12:23:35 2019 -0400 A little clean-up Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 25dcf56b675960d51dcec6238cb14f2839de124a Author: Ann Almgren Date: Mon Sep 23 08:44:02 2019 -0700 Fix 1 --> ncomp in AssignDensity; we were a bit mix-n-match before. Src/AmrCore/AMReX_AmrParticles.H commit 89c5cd28dc8e2008555227920c432ec0c9a0e5ba Merge: c3a3422a9 6cea2c32b Author: cgilet Date: Mon Sep 23 09:41:18 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 6cea2c32bdb3145d12c8b8ffb0909d171e5c60da Author: Weiqun Zhang Date: Sun Sep 22 18:09:40 2019 -0700 avoid gcc bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit 1bcaf5e915d52f16e510aa2826733b74b06a5ce6 Author: Weiqun Zhang Date: Sun Sep 22 17:36:38 2019 -0700 gpu nodal: gauss seidel Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 386899b30f721fdb0df3c5910515e7fb5e139f9d Author: Weiqun Zhang Date: Sun Sep 22 17:00:01 2019 -0700 gpu nodal: jacobi Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f413b255a11953919edd63e94d18b4e41db8d96a Author: Weiqun Zhang Date: Sun Sep 22 16:25:04 2019 -0700 gpu nodal: normalize Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 82007b85ba2a0fe5c8574c15993d84170e8538ec Author: Weiqun Zhang Date: Sun Sep 22 13:45:44 2019 -0700 fix 1d Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H commit d973f3f8a8877f0ac5f5c4367f4d759895a822a4 Merge: 84d3f615a 3959dbc87 Author: Weiqun Zhang Date: Sun Sep 22 12:56:14 2019 -0700 Merge branch 'development' into weiqun/dev commit 84d3f615a376985636d3c76940978f25349848d7 Author: Weiqun Zhang Date: Sun Sep 22 12:55:06 2019 -0700 gpu nodal: adotx aa version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 815fcbc82dbefa19979f461d3d5d4c3afc954d44 Author: Weiqun Zhang Date: Sun Sep 22 12:34:23 2019 -0700 gpu nodal: adotx ha version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d74b8a6e5102a210bf881300172e3d80fbe23915 Author: Weiqun Zhang Date: Sun Sep 22 10:26:58 2019 -0700 nodal gpu: average down sigma Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 3959dbc87e4d32956f3917d04a7311b7c300fc67 Author: Weiqun Zhang Date: Sat Sep 21 21:08:57 2019 -0700 fix nodal mc test Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp commit 60196629596146d8d99358f07ceafaa969ee3a12 Author: Weiqun Zhang Date: Sat Sep 21 19:56:51 2019 -0700 gpu nodal: dot mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f5ba7c11694f17884f1357f8638321622579188d Author: Weiqun Zhang Date: Sat Sep 21 19:12:08 2019 -0700 gpu nodal: res mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit be58649c603820df87ac236c3a52832952ec9c0f Author: Weiqun Zhang Date: Sat Sep 21 19:05:32 2019 -0700 gpu nodal: dirichlet mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7d47fce43cac1130386fe11c7516d0747e7693d5 Author: Weiqun Zhang Date: Sat Sep 21 17:55:50 2019 -0700 gpu nodal: nodal mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 05b4b562107e272952becc2f6651bd32c51737d7 Author: Weiqun Zhang Date: Sat Sep 21 16:58:45 2019 -0700 gpu nodal: fix sign Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit a0256388cb16a9f2c035810d465da5e562d5ede6 Author: Weiqun Zhang Date: Sat Sep 21 09:19:32 2019 -0700 gpu nodal: pass the correct mask to divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b86eaa57fce73827f27d2008d221ec897ee87f88 Author: Weiqun Zhang Date: Sat Sep 21 09:19:32 2019 -0700 gpu nodal: fix bug in the new Neumann BC Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H commit 49f4f517d23d53b0259d2620f09a9d69b73b7933 Author: Weiqun Zhang Date: Sat Sep 21 08:13:20 2019 -0700 gpu nodal: mknewu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 784dbf994f9643ed2642faac51b028429a36a8ce Author: Weiqun Zhang Date: Sat Sep 21 07:43:24 2019 -0700 gpu nodal: rhcc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 25e2368d80edcf14af795d7c6b1903943f7bbda1 Author: Weiqun Zhang Date: Fri Sep 20 22:22:57 2019 -0700 gpu nodal: divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 08d60c2f00fc74a8b84d1482c7b2fa7380c8910b Author: Weiqun Zhang Date: Fri Sep 20 21:36:54 2019 -0700 gpu nodal: impose neumann bc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 1510fcf86c2de2c791c4ce9cc56ae18d6c3339e2 Author: Weiqun Zhang Date: Fri Sep 20 18:50:00 2019 -0700 add AMREX_HOST_DEVICE_PARALLEL_FOR_?D Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchMacrosC.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit bb259585c9d0194e8b5448ce15764a8a4b051620 Author: Weiqun Zhang Date: Fri Sep 20 16:55:38 2019 -0700 gpu nodal: ported some anyd functions Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_ND_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit 08183e99f118a491f8e55bc809a806397dfd7fe2 Author: Andrew Myers Date: Fri Sep 20 19:52:02 2019 -0400 update Redistribute test for multiple levels Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/inputs.rt Tests/Particles/Redistribute/main.cpp commit 8aaf9b415ac6e5a068bc96add28b8354c1bd813a Author: Andrew Myers Date: Fri Sep 20 19:51:36 2019 -0400 fix error in level offset calculation in ParticleBufferMap Src/Particle/AMReX_ParticleBufferMap.cpp commit b7f081b396d243d3919d2bc3269f7bdde1c88afb Author: Weiqun Zhang Date: Fri Sep 20 16:24:20 2019 -0700 add some empty files in preparation for rewriting nodal solver kernels Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_ND_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit b113f15627f8bf4a864bd5d1df61c04fe2d8e075 Author: Andrew Myers Date: Fri Sep 20 19:14:47 2019 -0400 particle locator seems to be accounting for multiple levels correctly Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H commit d5898231901e1399b57a8fa62ad4b1422aa8f777 Author: Weiqun Zhang Date: Fri Sep 20 16:12:55 2019 -0700 add a missing if(Gpu::notInLaunchRegion()) Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit e3492a2130cf139a646844645c312c490cbde5e2 Author: Weiqun Zhang Date: Fri Sep 20 15:52:34 2019 -0700 MLMG: nodal interp on gpu Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H Src/LinearSolvers/MLMG/AMReX_MLMG_K.H Src/LinearSolvers/MLMG/Make.package commit e8441c494f158af4acdadf23feb8c8cb5b471d94 Author: Andrew Myers Date: Fri Sep 20 18:35:01 2019 -0400 Amr version of ParticleLocator Src/Particle/AMReX_ParticleLocator.H commit 0fdd50d5d8a964331239d4880302726e7886ba0f Author: Weiqun Zhang Date: Fri Sep 20 14:37:55 2019 -0700 MLMG: eb_cc_interp on gpu Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H commit 14828da6b11e94eed1c4ad52bb3579e9986b9758 Author: Andrew Myers Date: Fri Sep 20 16:52:08 2019 -0400 do loop over levels throughout particle communication code Src/Particle/AMReX_ParticleCommunication.H commit 56e9301833cbe72cb6da052c26bdf28755883165 Author: Andrew Myers Date: Fri Sep 20 16:30:31 2019 -0400 add loop over levels to pack and build Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_Particles.H commit 974ec17c64c68dece11dd839f2ea773acf8a6afa Author: Andrew Myers Date: Fri Sep 20 16:30:05 2019 -0400 methods for computing the neighbor procs on the fly, without as mask Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_ParticleUtil.cpp commit c9304aa0adc2881a439f4dfa7426ec9245740979 Author: Andrew Myers Date: Fri Sep 20 16:29:17 2019 -0400 a few more methods for particle buffer map Src/Particle/AMReX_ParticleBufferMap.H commit 1aedb81fe3fd7888641f170ce90c1d057fcd4ddb Author: Weiqun Zhang Date: Fri Sep 20 12:53:31 2019 -0700 add regression test inputs for EBTensor Tests/LinearSolvers/EBTensor/inputs.rt.3d commit c3a3422a9da9d5255b135e954a4fe81520c6b8a4 Merge: 32efff60c 76c1d7759 Author: cgilet Date: Fri Sep 20 15:35:37 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit c4a56aa028ee8ef3d757b011abce2398d2907bc7 Merge: e86d462a6 76c1d7759 Author: cgilet Date: Fri Sep 20 15:34:50 2019 -0400 Merge remote-tracking branch 'upstream/development' into development commit e86d462a6b2b55c87ee82dd40ab3bfe86fbec5e0 Merge: f07671bcc 251c59b1d Author: cgilet Date: Fri Sep 20 15:27:58 2019 -0400 Merge remote-tracking branch 'upstream/development' into development commit 32efff60ce0334c1c0df3c094776460017c180e2 Merge: fbc90e19a 251c59b1d Author: cgilet Date: Fri Sep 20 15:26:03 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit fbc90e19ab069f90fe6faf095b54c8364a9622ad Merge: c19740dd6 9efd66178 Author: cgilet Date: Fri Sep 20 15:10:09 2019 -0400 Merge branch 'TensorFluxes' of https://github.com/cgilet/amrex into TensorFluxes Conflicts: Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit c19740dd6b859f175735831f4293bd15a07daba4 Author: cgilet Date: Fri Sep 20 14:10:31 2019 -0400 WIP - 2D now compiles 2D not tested further. Cut cell fluxes not yet defined correctly. Set to bogus val to know if they're being used. 3D not done yet. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H commit 76c1d77595e20b41ff2eef3f7b3602110dc2338c Author: Weiqun Zhang Date: Fri Sep 20 09:47:02 2019 -0700 rm Gpu::LaunchSafeGuard from MLEBTensorOp::apply Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 68cd9150ebf7c42103b68ee72ab1a5cec567b53d Author: Weiqun Zhang Date: Thu Sep 19 17:16:17 2019 -0700 fix habec Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 6495db56c6d1edd8564299f0934ac31db26a1d67 Author: Weiqun Zhang Date: Thu Sep 19 15:48:10 2019 -0700 MLEBABecLap::interpolation on gpu and rm deprecated files Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MG_K.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/Make.package commit 4aef19ffe81df1ac413820eabbc461c06d514f8e Author: Andrew Myers Date: Thu Sep 19 18:54:06 2019 -0400 generalize the ParticleCopyOp for multi-level Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit 346882f3ae96ac8f71dd8d7862b2452199bf01ad Merge: 2d905c33b b4f79407f Author: Weiqun Zhang Date: Thu Sep 19 13:35:40 2019 -0700 Merge branch 'master' of github.com:AMReX-Codes/amrex commit 43b8d7fe6908094faeb68e040f867b120534ce1e Author: Weiqun Zhang Date: Thu Sep 19 13:27:09 2019 -0700 MLEBABecLap::normalize on gpu Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit 25b9f0919a6fbde0ea45f3c4fd051c1a134df502 Author: Andrew Myers Date: Thu Sep 19 14:55:24 2019 -0400 extending the particle buffer map to work with multiple levels Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleBufferMap.cpp Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit 13f49232e1eac955a1df4079db75a6f75ec73b95 Author: Weiqun Zhang Date: Thu Sep 19 09:48:13 2019 -0700 clean up Src/Base/AMReX.cpp Src/Base/AMReX_FabArray.H commit 5939f8dc221b7aa775afc9d0298d153a2bd8a396 Author: Armin Wehrfritz Date: Thu Sep 19 03:47:11 2019 +1000 Tools/GNUMake - Add Australian machines Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nci Tools/GNUMake/sites/Make.pawsey commit 7a45a5040af6add69be3192155b4575f8c324a74 Merge: f746e2833 89cece487 Author: Weiqun Zhang Date: Wed Sep 18 18:31:16 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f746e28336a65e8cbb7b8e8cdb937a4a44af6bc2 Author: Weiqun Zhang Date: Wed Sep 18 18:28:37 2019 -0700 cleanup Src/Base/AMReX_GpuLaunchFunctsG.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit 89cece4872369dfde6565195924d3dd643879946 Author: Stefan Vater Date: Thu Sep 19 03:28:14 2019 +0200 some modifications for the Nodal poisson tutorial program (#563) * - fixed exact solution for 2d - added plotting routine * added averaging from nodal to cell values for plotting Tutorials/LinearSolvers/NodalPoisson/Make.package Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp Tutorials/LinearSolvers/NodalPoisson/main.cpp commit 89566964a9efe3da62bc7bb5df2d40dfa2efd7f7 Author: Weiqun Zhang Date: Wed Sep 18 15:32:02 2019 -0700 MLEBABecLap::compGrad on gpu Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit 2329b4e11004690d26acb9942709891c2b505e77 Author: Weiqun Zhang Date: Wed Sep 18 12:51:56 2019 -0700 MLEBABecLap::FFlux on gpu Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 7042203361fe74efb0efb3f2adb6b319e753772c Author: Weiqun Zhang Date: Tue Sep 17 17:24:58 2019 -0700 cleanup Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit 554a5b25b58076d306c25bfcdd3844d772ac0854 Merge: a42467b44 4da4fe3d0 Author: Andrew Myers Date: Tue Sep 17 15:28:56 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a42467b4482721cbe588aec95833473b8cbc28c1 Author: Andrew Myers Date: Tue Sep 17 15:28:39 2019 -0700 remove incorrect assertion(s) Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 4da4fe3d03a821e3d1432df812c61751cb5f53f8 Author: Weiqun Zhang Date: Tue Sep 17 15:26:38 2019 -0700 manually write out the loops so that gcc 8 does not crash Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit f88e9a6a8f87084bbdf29582ff26ea078109dbe6 Author: Weiqun Zhang Date: Tue Sep 17 15:06:24 2019 -0700 fix new bug: have to rebuild array4 because fab has been shifted Src/Boundary/AMReX_MultiMask.cpp commit 46f955b5233f6e89d849fbe0316509dc33dfaafd Author: Weiqun Zhang Date: Tue Sep 17 14:55:00 2019 -0700 fix typo Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit 1af1e8bfc077ebbc3289324df5fd78b2abe9ac08 Author: Weiqun Zhang Date: Tue Sep 17 13:42:11 2019 -0700 fix a new bug I merged into development this morning. The original beta has only one component. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 8234f20a4b91f4f75e9175d920778f34e64da2b9 Author: Ann Almgren Date: Tue Sep 17 12:27:02 2019 -0700 Update nodal projection code snippet Docs/sphinx_documentation/source/LinearSolvers.rst commit a11de4851a9a804f164fae5b14c2144d3f62be8a Author: Ann Almgren Date: Tue Sep 17 11:46:16 2019 -0700 Update formatting slightly and README. Tutorials/LinearSolvers/MAC_Projection_EB/README Tutorials/LinearSolvers/Nodal_Projection_EB/README Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp commit 739c3d6d68f0d4a4537e8e8be8591f57dce1c2ba Merge: 4f7e53aa8 87d4b8290 Author: Weiqun Zhang Date: Tue Sep 17 11:40:11 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4f7e53aa875297241fa83aa3d1e95ef5ecbb2b84 Author: Weiqun Zhang Date: Tue Sep 17 11:39:53 2019 -0700 fix Nodal_Project_EB tutorial Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp commit 87d4b829056b2ce82a74b2042a663125b0eb44c5 Merge: 724ea5efb b1575042d Author: asalmgren Date: Tue Sep 17 11:11:49 2019 -0700 Merge pull request #569 from AMReX-Codes/fi_lincomb_fix Fix indexing in fortran interface for MultiFab::LinComb commit b1575042dfc28a8e8388cbb0299c09dd01a9add9 Author: Donald E. Willcox Date: Tue Sep 17 11:06:04 2019 -0700 Decrement source component for multifab 2 in amrex_multifab_lincomb for the Fortran interface. Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit f436dcb0b0fbabda05b130f604bb6a9ef7f9bfba Merge: 724ea5efb 134547c30 Author: Weiqun Zhang Date: Tue Sep 17 11:02:28 2019 -0700 Merge branch 'weiqun/dev' into development commit 724ea5efb70ea29c63ead0336a57e61af3a35e8d Author: Ann Almgren Date: Tue Sep 17 10:37:40 2019 -0700 Update documentation about tutorials. Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst commit 3f682a0cc4364b5936e07b4b59f12e5f1476eb7c Author: Ann Almgren Date: Tue Sep 17 10:08:12 2019 -0700 Add example of nodal projection with EB analogous to the example in MAC_Projection_EB. Current commit does not compile. Tutorials/LinearSolvers/Nodal_Projection_EB/GNUmakefile Tutorials/LinearSolvers/Nodal_Projection_EB/Make.package Tutorials/LinearSolvers/Nodal_Projection_EB/README Tutorials/LinearSolvers/Nodal_Projection_EB/inputs_3d Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp commit 9d2784bdb6c4f0d24a69660d91b9d9937c25b603 Author: Ann Almgren Date: Tue Sep 17 08:11:32 2019 -0700 Simplify the EB MAC projection tutorial so it just sets nine obstacles rather than reading in the IDs from the inputs Tutorials/LinearSolvers/MAC_Projection_EB/README Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 7468387650aa78663e52e171254b3e6f6c95f478 Author: Andrew Myers Date: Mon Sep 16 19:22:40 2019 -0400 slight optimization(s) Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit ab21a5714209f1d41476c065774fb868cadae912 Merge: 3fbb1bff1 0a831349e Author: Michele Rosso Date: Mon Sep 16 14:32:35 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3fbb1bff10e5be33c8dcb6e08871485e84ffbfc3 Author: Michele Rosso Date: Mon Sep 16 14:32:22 2019 -0700 Update doc on nodal projection Docs/sphinx_documentation/source/LinearSolvers.rst commit ec9e0b574df10396ed6f40838276ac984e2c56a6 Author: cgilet Date: Mon Sep 16 16:37:59 2019 -0400 WIP - make sure coarse-fine boundary corner cells get filled for AllPeriodic case. fix const qualifier in relation to m_bndry_sol in applyBCTensor. 2D seems to work 3D not finished yet Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 0a831349e03e6065589d7131e41213eaeed31772 Author: Andy Nonaka Date: Mon Sep 16 12:21:40 2019 -0700 small update to docs Docs/sphinx_documentation/source/AmrLevel_Chapter.rst commit f6f35a89e1362de34a2398e77f0632e71724837c Author: cgilet Date: Mon Sep 16 15:10:58 2019 -0400 WIP - Add MLEBTensorOp::compFluxes(). Needs testing. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 134547c30311c5dbcfbcb88da9b488676686e279 Author: Weiqun Zhang Date: Sun Sep 15 13:09:22 2019 -0700 WIP: MLEBABecLap: gsrb on gpu Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H commit ea806a44f01c8b9fc34948f96795e443bd28032f Author: Weiqun Zhang Date: Sun Sep 15 15:26:35 2019 -0700 EB nodal solver: average cell-centered rhs to node Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8572bcde16be61775c8cfd48798c3a7f8c26f53c Author: Ann Almgren Date: Sun Sep 15 07:03:34 2019 -0700 update documentation re bc's for linear solvers Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 2f2a270e461ec182e5c8cdb2e6a7e0884cea0684 Author: Ann Almgren Date: Sun Sep 15 07:03:18 2019 -0700 Add more detail re bc's for linear solvers Docs/sphinx_documentation/source/LinearSolvers.rst commit 1b754697a9b4e39ec684ec7faae0686e7d51a6bb Author: Ann Almgren Date: Sat Sep 14 19:15:30 2019 -0700 Update to section on Linear Solvers: Boundary Conditions Docs/sphinx_documentation/source/LinearSolvers.rst commit 58a1cc07b63ee66bcb0a863f34110989deef7f79 Author: Weiqun Zhang Date: Sat Sep 14 16:47:22 2019 -0700 MLEBABecLap: adotx on gpu Src/Base/AMReX_Array4.H Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H Src/LinearSolvers/MLMG/Make.package commit 64e4fac347463871fe0a267234a2ae683645b61d Merge: 10f77a210 1b1d6c934 Author: Michele Rosso Date: Sat Sep 14 16:53:01 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 10f77a210aff7d79bf20a6a2b573713dc74fc340 Author: Michele Rosso Date: Sat Sep 14 16:52:48 2019 -0700 CMake: add missing include statement Tools/CMake/AMReXTargetHelpers.cmake commit 1b1d6c934c441110b5a3350f4f081d85c7fba874 Author: Ann Almgren Date: Sat Sep 14 16:43:12 2019 -0700 Update the solver bc stuff and the MacProjection section. Docs/sphinx_documentation/source/LinearSolvers.rst commit b8a35448acb73edcc055f1ec66fbce535caf59ef Author: Ann Almgren Date: Sat Sep 14 15:31:18 2019 -0700 Update section about boundary conditions for linear solvers Docs/sphinx_documentation/source/LinearSolvers.rst commit d21523b562071d1c244f05fa58e4789aae01c7ed Author: Ann Almgren Date: Fri Sep 13 20:15:49 2019 -0700 fix typos Docs/sphinx_documentation/source/LinearSolvers.rst commit 705078d1572b854b6dd0777fe2e3b94b81b007ad Author: Weiqun Zhang Date: Fri Sep 13 18:30:41 2019 -0700 more gpu support in MLEBABecLap Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 00aa7bd9ef17f22a1bbc31fdde566c4951ff9a95 Author: Weiqun Zhang Date: Fri Sep 13 17:44:37 2019 -0700 update FlowerIF Tests/LinearSolvers/CellEB/MyEB.H Tests/LinearSolvers/CellEB2/MyEB.H Tests/LinearSolvers/EBConvergenceTest/MyEB.H Tests/LinearSolvers/EBflux_grad/MyEB.H commit 251c59b1d99cf2a895d71d36f6bd23f27e523e74 Merge: 8a8e7d994 9b64ea375 Author: Michele Rosso Date: Fri Sep 13 17:40:12 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8a8e7d9948a6c167b9554d3070b24ac3914db5ec Author: Michele Rosso Date: Fri Sep 13 17:39:58 2019 -0700 Doc: add snippet for nodal projection Docs/sphinx_documentation/source/LinearSolvers.rst commit af9b08897e842e1626eaab028f02d7e1bb51f8ce Merge: 78ecbff7d 9b64ea375 Author: Weiqun Zhang Date: Fri Sep 13 11:58:59 2019 -0700 Merge branch 'development' into weiqun/dev commit 9b64ea375586d032b65ff64f8d1d8ab3b7bb5208 Merge: ad1e3fe1b fc72b7d4c Author: WeiqunZhang Date: Fri Sep 13 11:16:23 2019 -0700 Merge pull request #560 from bcfriesen/bcf/cce9 Tools: update compiler flags for Cray compiler v9 commit 4a3ecd6d7b1155d41147ffd3f18c47890682ddad Merge: 5d757ec97 ad1e3fe1b Author: cgilet Date: Fri Sep 13 10:41:01 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 3676d6ab94e20d9b4506f72955c5dc0c573f896f Author: cgilet Date: Fri Sep 13 10:28:02 2019 -0400 WIP - 2D appears to work for MLTensorOp not fully tested yet Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit ad1e3fe1bcb9dc04d8efde837dc0db75f268d530 Merge: 93a3d048b ceb2251bb Author: Michele Rosso Date: Thu Sep 12 16:41:29 2019 -0700 Merge branch 'mr/cmake' into development commit ceb2251bba23af7de3d2cc5f8254e9bdb614dd7b Author: Michele Rosso Date: Thu Sep 12 16:07:02 2019 -0700 Revert "CMake: improve handling of arguments passed to makebuildinfo.py" This reverts commit ca09eddd5d5e2f82c6f84641ed1101b47a27ec30. Tools/CMake/AMReXBuildInfo.cmake commit ca09eddd5d5e2f82c6f84641ed1101b47a27ec30 Author: Michele Rosso Date: Thu Sep 12 14:42:51 2019 -0700 CMake: improve handling of arguments passed to makebuildinfo.py Tools/CMake/AMReXBuildInfo.cmake commit 92a1cce9032baa046cf37a9f12a7bd09d7dfcd42 Author: Michele Rosso Date: Thu Sep 12 13:34:27 2019 -0700 CMake: add quotes to arguments when invoking build info script Tools/CMake/AMReXBuildInfo.cmake commit 93a3d048b051601b32b49d191f7f9dc564aaf1dd Author: Ann Almgren Date: Thu Sep 12 12:50:52 2019 -0700 Add first text about nodal approximate projection. Docs/sphinx_documentation/source/LinearSolvers.rst commit 154679833f37b007c440da4cd87d089dab92cfef Author: Ann Almgren Date: Thu Sep 12 11:34:31 2019 -0700 Update to reflect we can't do level solves with this functionality yet. Docs/sphinx_documentation/source/LinearSolvers.rst commit 404567294e8e4122795d844133447c42da9af022 Author: Michele Rosso Date: Thu Sep 12 10:55:07 2019 -0700 CMake: use verbatim mode to issue command to makebuildinfo python script Tools/CMake/AMReXBuildInfo.cmake commit 06320a01d5c8a8663579b00b0e2575c31d9629ed Author: Ann Almgren Date: Thu Sep 12 02:57:18 2019 -0700 add inhomog Neumann as boundary type Docs/sphinx_documentation/source/LinearSolvers.rst commit 78ecbff7d3add7861ecb50b981e716b71edc1065 Author: Weiqun Zhang Date: Wed Sep 11 16:54:28 2019 -0700 prepare some linear solver tests for gpu Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/EBflux_grad/MyTest.H Tests/LinearSolvers/EBflux_grad/MyTest.cpp Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp commit ec945bdaeaa231decde6ff7f1ba278e6388d5598 Author: Weiqun Zhang Date: Wed Sep 11 15:34:28 2019 -0700 gpu for Mask Src/Boundary/AMReX_MultiMask.cpp commit ad668b8d7acafc8570304a6c8d31ff28f3806822 Author: Weiqun Zhang Date: Wed Sep 11 15:12:50 2019 -0700 add inhomogNeumann to opeartor<< and minor clean up Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_LO_BCTYPES.cpp commit c9923e9be3e1592ea8ebe76c89a40db572db1dbd Author: Weiqun Zhang Date: Wed Sep 11 15:12:24 2019 -0700 minor changes to get NodalPoisson test compile with cuda Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp commit e16a4b9d5703e17b64ab963597e9ab1d14661ee7 Merge: 71f8baa3a 603b3624f Author: Andrew Myers Date: Wed Sep 11 17:57:47 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 71f8baa3a928e047e193dc908c0938cec9df7c74 Author: Andrew Myers Date: Wed Sep 11 17:48:30 2019 -0400 always get the list of neighbor ranks from the redistribute mask Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_Particles.H commit 6bf8f68ce7d9efff4748f37ab9c30c9990721299 Author: Andrew Myers Date: Wed Sep 11 17:47:53 2019 -0400 these memcopies need to be synchronous Src/Particle/AMReX_ParticleContainerI.H commit 603b3624ffcda70b73a1dfebfb03e87ae2cc2cf1 Merge: 2a7d2e537 7b77f05e5 Author: WeiqunZhang Date: Wed Sep 11 14:32:53 2019 -0700 Merge pull request #561 from ax3l/topic-constCorrectness FabConv: Little Const-Correctness Params commit 2a7d2e537af6bbe03113cf578663d46428b167c2 Merge: 9a0c93ced 811ac1534 Author: WeiqunZhang Date: Wed Sep 11 14:31:14 2019 -0700 Merge pull request #562 from ax3l/doc-mpiCUDA Docs: Intro (+MPI/CUDA) commit 811ac1534e5c68da72f0616ed033267d2aef93ab Author: Axel Huebl Date: Wed Sep 11 14:21:23 2019 -0700 Docs: Intro (+MPI/CUDA) Update the introduction in the docs: AMReX also supports MPI/CUDA these days :) Docs/sphinx_documentation/source/Introduction.rst commit 7b77f05e54dacd5f7e341f6c509892b77a4f5897 Author: Axel Huebl Date: Wed Sep 11 14:15:13 2019 -0700 Little Const-Correctness Params Just two little places found when compiling WarpX with clang tidy and: https://clang.llvm.org/extra/clang-tidy/checks/readability-non-const-parameter.html Src/Base/AMReX_FabConv.cpp commit fc72b7d4c3aafd708a493edc19ebd094023a7b42 Author: Brian Friesen Date: Wed Sep 11 10:48:47 2019 -0700 Tools: update compiler flags for Cray compiler v9 In CCE 9, Cray overhauled their C/C++ compilers and moved to clang/LLVM, so the flags for C/C++ compilers are totally different than in previous versions of CCE. Confusingly, the Fortran compiler was *not* changed significantly in CCE 9, so its flags are the same as before. As a result, we need some more complex logic to get the right flags for the right version of CCE. Tools/GNUMake/comps/cray.mak commit 9a0c93cedb61828ae635796723674c9766506442 Author: cgilet Date: Wed Sep 11 13:43:10 2019 -0400 Fix typo, n-> icomp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit bbb3575d31ce6b3e1c29e6361c9280ccf8000000 Author: Weiqun Zhang Date: Wed Sep 11 10:22:16 2019 -0700 need to update the multi-component version of setDomainBC Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit b4f5caa8d028bc273892a39004dcfb10cba61da4 Author: Candace Gilet Date: Wed Sep 11 12:18:41 2019 -0400 Make sure Vector bounds check catches negative indices. (#559) * Make sure Vector bounds check catches negative indices. * Cleaner way to check Vector bounds Src/Base/AMReX_Vector.H commit f07671bccbf91bc83e83a3a2d0f63a8a10b4f704 Merge: 82d9bb7c8 1db1b179f Author: cgilet Date: Wed Sep 11 12:15:19 2019 -0400 Merge remote-tracking branch 'upstream/development' into development commit 82d9bb7c82aca2a0e623a5b65bd624518b843851 Author: cgilet Date: Wed Sep 11 12:14:36 2019 -0400 Cleaner way to check Vector bounds Src/Base/AMReX_Vector.H commit 1db1b179f9129efb383c417dbbf79f04069f1752 Author: Weiqun Zhang Date: Tue Sep 10 21:04:39 2019 -0700 inhomogeneous Neummann in curvilinear coordinates Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a2a31c2a0dbda45f46a90fcb29ef7c80662019e3 Author: cgilet Date: Tue Sep 10 20:55:03 2019 -0400 Make sure Vector bounds check catches negative indices. Src/Base/AMReX_Vector.H commit adfb00b8c430761514350c8f4aa03c9dc569c069 Merge: c0fd94d09 431f5ad1c Author: Andrew Myers Date: Tue Sep 10 16:31:18 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c0fd94d0941b7f7a66cbd5084b2fcd1dea864742 Author: Andrew Myers Date: Tue Sep 10 16:30:37 2019 -0400 need to add a Barrier at the start of communicateParticles Src/Particle/AMReX_ParticleCommunication.H commit 431f5ad1c31d0a100f527c8fe07b6d61d8bba91e Author: Weiqun Zhang Date: Tue Sep 10 10:33:12 2019 -0700 minor optimization Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit d1a3eb16769e26ca0c4ef600486d20aba824f9b4 Author: Weiqun Zhang Date: Tue Sep 10 09:56:54 2019 -0700 fix test problem boundary Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H commit f599e85af1e33ac7c9731416db92a77efbeea8ef Author: Weiqun Zhang Date: Mon Sep 9 22:15:45 2019 -0700 MLMG: inhomogeneous Neumann Src/Boundary/AMReX_LO_BCTYPES.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTestPlotfile.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/LinearSolvers/ABecLaplacian_C/inputs-inhomNeumann commit 6ea36dd251f0ff346ef364138c96fa4bafc1a37e Author: Weiqun Zhang Date: Sun Sep 8 16:12:05 2019 -0700 fix order of initialization Src/Particle/AMReX_ParticleLocator.H commit 7c89abac3b2245ff8856b9bd8b80f576c3264bb1 Author: Weiqun Zhang Date: Sun Sep 8 14:38:27 2019 -0700 fix some bugs in BaseFab Src/Base/AMReX_BaseFab.H commit 3c9f647938caa1ac4d5535f47d04352db8150984 Merge: 12825e658 9746b6a06 Author: Weiqun Zhang Date: Sat Sep 7 18:28:41 2019 -0700 Merge branch 'weiqun/dev' into development commit 9746b6a06d88bc5524a2143f2fbd4853c8e5040a Author: Weiqun Zhang Date: Sat Sep 7 21:25:13 2019 -0400 fix type Src/Base/AMReX_GpuReduce.H commit 3d1c9a51e023a2054dc37ca5cf31e88eefccfb09 Author: Weiqun Zhang Date: Sat Sep 7 18:14:32 2019 -0700 fix new bug Src/Base/AMReX_GpuReduce.H commit 195a2e3797463aba63c39ab6220edbe639647b36 Author: Weiqun Zhang Date: Sat Sep 7 18:03:18 2019 -0700 minor Src/Base/AMReX_Reduce.H commit 22992d0fc02dee1349d5062526dc283d7217772d Author: Weiqun Zhang Date: Sat Sep 7 16:14:42 2019 -0700 optimization of iMultiFab::sum Src/Base/AMReX_iMultiFab.cpp commit e09715044c21bc5030e6e65cb4a6feb11bb2167c Author: Weiqun Zhang Date: Sat Sep 7 15:56:16 2019 -0700 reimplement FabArray Reduce Src/Base/AMReX_FabArrayUtility.H commit e5816d9eaf47d9cbf9f4e6b21f63922ecbc98b5f Author: Weiqun Zhang Date: Sat Sep 7 15:55:34 2019 -0700 add ReduceOpLogicalAnd and Or Src/Base/AMReX_Reduce.H commit 0003da79d74e6c4cecb76dddb2a7d04b9e1538d8 Author: Weiqun Zhang Date: Sat Sep 7 14:53:00 2019 -0700 add deviceReduceLogicalAnd and Or Src/Base/AMReX_Functional.H Src/Base/AMReX_GpuReduce.H commit 12825e658fdaf12a61a9b9a47fc20962ba580c2b Merge: 7017e21e9 14c29ab92 Author: asalmgren Date: Sat Sep 7 13:08:12 2019 -0700 Merge pull request #558 from cgilet/development Development commit 7017e21e9addc3486d93105ba3d2af68b968f4d4 Author: Weiqun Zhang Date: Sat Sep 7 12:22:36 2019 -0700 ReduceOps now takes lambda on Box Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Reduce.H Src/Base/AMReX_Utility.H Tutorials/GPU/ParallelReduce/main.cpp commit dc7b72e372550e01f111b439b14e5284762d90a6 Merge: 3a1afb7be 5c0c14bdc Author: Michele Rosso Date: Fri Sep 6 16:44:55 2019 -0700 Merge branch 'mr/cmake' into development commit 5c0c14bdcbdd8daf22042453cb8bfc60183b4adb Author: Michele Rosso Date: Fri Sep 6 16:41:45 2019 -0700 CMake: improve build summary printout Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake commit 4f279e5975195ecf77f4a0061fa9ad95cdb366e0 Author: Michele Rosso Date: Fri Sep 6 15:19:24 2019 -0700 CMake: add comments to document new modules Tools/CMake/AMReXBuildInfo.cmake Tools/CMake/AMReXTargetHelpers.cmake commit 1ada310f6909ebebe14ace16516ee8751b248d36 Author: Michele Rosso Date: Fri Sep 6 14:39:21 2019 -0700 CMake: add GIT info in BuildInfo Tools/CMake/AMReXBuildInfo.cmake commit 3a1afb7be0e22b306870c521b4020ce2f9ff6c47 Author: Weiqun Zhang Date: Fri Sep 6 12:41:41 2019 -0700 move -> forward because we have recently changed the parameters from r-value to forwarding reference Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H commit c95776aa0c31d95f432ca9adce2e5fb633e14728 Author: Michele Rosso Date: Fri Sep 6 11:30:05 2019 -0700 CMake: make OpenMP imported targets GLOBAL Tools/CMake/AMReX_Config.cmake commit b629b1135cc806f447cbbdcfb6a4146acfd266c1 Author: Michele Rosso Date: Fri Sep 6 11:20:17 2019 -0700 CMake: make imported targets GLOBAL Src/Base/CMakeLists.txt Src/Extern/Conduit/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Tools/CMake/FindHYPRE.cmake Tools/CMake/FindSUNDIALS.cmake commit da30684a6d2dc79a008cb4d3f86f1778f80ab41d Author: Weiqun Zhang Date: Fri Sep 6 09:47:27 2019 -0700 added PETSc to linear solver doc Docs/sphinx_documentation/source/LinearSolvers.rst commit 14c29ab92a0e78c67c39a8fb4eaa2021a59c7ab8 Author: cgilet Date: Fri Sep 6 11:21:53 2019 -0400 update MACProjector documentation and tutorial Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst commit aa1bf886d64c7f038211557d120e75b2aa78c916 Author: cgilet Date: Fri Sep 6 11:09:26 2019 -0400 Update so commented examples will work if uncommented. Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 0e73f21c8f074ee8025984a2e1e0a118aa41a387 Author: cgilet Date: Fri Sep 6 11:02:44 2019 -0400 Update comments to reflect what code actually does Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d commit 008d037ed5ebc4ea9e8e8322f6e18f6b69d217a2 Author: Ann Almgren Date: Fri Sep 6 02:08:38 2019 -0700 Add comment that Dirichlet bc's are assumed to be homogeneous Docs/sphinx_documentation/source/LinearSolvers.rst commit bf646f521bd953e9072ce0514bc8269b6913d523 Author: Ann Almgren Date: Fri Sep 6 02:04:44 2019 -0700 Merge the description of non-zero S with the rest of the text. Docs/sphinx_documentation/source/LinearSolvers.rst commit e0aeea779499807c5f61c67f470628909ba88335 Author: Michele Rosso Date: Thu Sep 5 18:32:11 2019 -0700 CMake: handle amrex path when generating build info Tools/CMake/AMReXBuildInfo.cmake commit 8a6d5bb7793540982664a5215d5754068cbbd794 Author: Michele Rosso Date: Thu Sep 5 18:27:39 2019 -0700 CMake: make get_target_prop_recursive() more robust Tools/CMake/AMReXTargetHelpers.cmake commit cc59803e110dbd0711567a6ad9c2dbc5a0b32080 Author: Michele Rosso Date: Thu Sep 5 16:08:56 2019 -0700 CMake: fix typo Tools/CMake/AMReXBuildInfo.cmake commit 7aba0f9d281bf422717cd54a5f00ed3f67e8d9e4 Author: Michele Rosso Date: Thu Sep 5 16:07:46 2019 -0700 CMake: make BuildInfo module more robust Tools/CMake/AMReXBuildInfo.cmake commit 20bebfc52f7271aa219a710454369884059a7138 Author: Andy Nonaka Date: Thu Sep 5 15:49:12 2019 -0700 note on how to specific non-zero divergence for MAC projection tutorial Docs/sphinx_documentation/source/LinearSolvers.rst commit 1a654edab85ac8359ce737b87257f4e9e7cb5d0a Merge: 78e55950d 011bcacbf Author: Ann Almgren Date: Thu Sep 5 15:26:46 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 78e55950d20495f0e8f8710a595f80f6368f3eb5 Author: Ann Almgren Date: Thu Sep 5 15:10:48 2019 -0700 Fix typo Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit 011bcacbf754356f3a420c9079e3d0a5093ba768 Author: Weiqun Zhang Date: Thu Sep 5 15:03:23 2019 -0700 latest AMReX regression test script Tools/RegressionTesting/AMReX-tests.ini commit bbd5330b88e3806ca21ddf21afa044df63d2865d Author: Ann Almgren Date: Thu Sep 5 14:52:38 2019 -0700 hypre --> External Solvers (still needs petsc info) Docs/sphinx_documentation/source/LinearSolvers.rst commit a442c46cda17bccfb27bf5a884b64303b1719058 Author: Ann Almgren Date: Thu Sep 5 14:49:55 2019 -0700 Swap B <--> beta in linear solver notation Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit 78738496d4600b7988567d45102b6c2a930902cb Author: Weiqun Zhang Date: Thu Sep 5 14:35:56 2019 -0700 minor change and make it work for C++11 Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit db01dbe8d490729c6c8604ebc6aac1aa4bf21aa6 Author: Andy Nonaka Date: Thu Sep 5 13:37:44 2019 -0700 updated mac projection tutorial documentation + comments Docs/sphinx_documentation/source/LinearSolvers.rst Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit f3fa7be8f06a86a4f2a8811342ecd8ddddfeadcf Author: Michele Rosso Date: Thu Sep 5 10:36:20 2019 -0700 CMake: update some modules to reflect new changes Tools/CMake/AMReXTypecheck.cmake Tools/CMake/AMReX_Config.cmake commit b4f79407f07989fc4a63317c5e69715277af0e86 Author: Ann Almgren Date: Thu Sep 5 06:39:21 2019 -0700 Update docs Docs/sphinx_documentation/source/LinearSolvers.rst commit 7236800c920b661dafd47fdee46c601a60728fae Author: Ann Almgren Date: Thu Sep 5 06:32:42 2019 -0700 Update MACProjector documentation and tutorial. Docs/sphinx_documentation/source/LinearSolvers.rst Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 54db3a97d86cd5b87ccb9618c3b6bf003cc131db Author: Ann Almgren Date: Thu Sep 5 04:10:00 2019 -0700 Fix formatting Docs/sphinx_documentation/source/LinearSolvers.rst commit 7e3b7651fe49529ef4b7aa851e469661d432416e Author: Ann Almgren Date: Thu Sep 5 04:10:00 2019 -0700 Fix formatting Docs/sphinx_documentation/source/LinearSolvers.rst commit 04b6967657355481b593f8cc16cd4ad49b18f67f Author: Ann Almgren Date: Thu Sep 5 03:55:26 2019 -0700 Update with code snippet for MAC Projection. Docs/sphinx_documentation/source/LinearSolvers.rst commit 3772272cd221dae3b15d8668235031dfea80d218 Author: Ann Almgren Date: Thu Sep 5 03:55:26 2019 -0700 Update with code snippet for MAC Projection. Docs/sphinx_documentation/source/LinearSolvers.rst commit 404cd3f46b54a27c233a786eeebf47ead319ee7c Author: Ann Almgren Date: Thu Sep 5 03:23:30 2019 -0700 change default Tutorials/LinearSolvers/MAC_Projection_EB/Backtrace.0 Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile commit a6cf6104f24d78b793fdcb3c22507bf0758e91f3 Author: Ann Almgren Date: Thu Sep 5 03:22:27 2019 -0700 Oops -- didn't want to commit the plotfile Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Header Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_D_00000.REMOVED.git-id Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_H commit 2752fabf1b9354d9363bf4fa42ac422b2c457a1e Author: Ann Almgren Date: Thu Sep 5 03:21:37 2019 -0700 Add new tutorial demonstrating MACProjection with EB obstacles. Tutorials/LinearSolvers/MAC_Projection_EB/Backtrace.0 Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile Tutorials/LinearSolvers/MAC_Projection_EB/Make.package Tutorials/LinearSolvers/MAC_Projection_EB/README Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Header Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_D_00000.REMOVED.git-id Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_H commit 3f43eb2d8ce294d6fcfb1f7f34105b7bd50f7999 Author: Ann Almgren Date: Thu Sep 5 02:13:40 2019 -0700 Update linear solver section of documentation Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit a9b5ac54059109bd96eebf608c8b00c2fda6d07f Author: Ann Almgren Date: Thu Sep 5 02:13:40 2019 -0700 Update linear solver section of documentation Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit 08500484ac27cbc40eed92d458c6493e193f6150 Author: Michele Rosso Date: Wed Sep 4 17:51:18 2019 -0700 CMake: change paradigm to include build info into app code. * Create a dedicated CMake module * Let application code to drive the inclusion of build info into consuming target. Src/CMakeLists.txt Tools/CMake/AMReXBuildInfo.cmake commit a39926c9dfbb44da0de621c1471599900b9a8ec2 Author: Michele Rosso Date: Wed Sep 4 17:49:53 2019 -0700 CMake: add a module to collect helpers to handle targets Tools/CMake/AMReXTargetHelpers.cmake commit 6bc7af4fb202adef92193df793fa1f6222d5c99e Author: Michele Rosso Date: Wed Sep 4 17:38:24 2019 -0700 CMake: improve GENEX handling. * Group genex-related macros/functions in a dedicated module file * evaluate_genex: add support for NOT operation * evaluate_genex: improve handling of COMPILE_LANGUAGE genex Tools/CMake/AMReXGenexHelpers.cmake Tools/CMake/AMReX_Utils.cmake commit 71699c5bfee86e48c1f6a0ff33dd9c12f0d4adf5 Merge: 138b1a3cf 9cbb98ad2 Author: Andrew Myers Date: Wed Sep 4 19:02:55 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 138b1a3cfceeab4e185a22671a37e9264140d4ef Author: Andrew Myers Date: Wed Sep 4 19:02:33 2019 -0400 optimization - reduce number of messages sent in communicateParticles Src/Particle/AMReX_ParticleCommunication.cpp commit 5d757ec976cc9d71fd2494536d638bcb88c92f1a Merge: 8e5f6dbe6 9cbb98ad2 Author: cgilet Date: Wed Sep 4 16:49:24 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 9cbb98ad29d657ae8aa7ac6f3e567ff8ebde5b98 Author: Andrew Myers Date: Wed Sep 4 13:03:56 2019 -0700 a fix for the local + CPU + single precision particles Src/Particle/AMReX_ParticleContainerI.H commit 5b76d34eab080a20c34f13c53af6697748c369b4 Merge: 17929af07 4f7b4a43d Author: Andrew Myers Date: Wed Sep 4 10:59:22 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 17929af0709fe005f90de1ea81366490afd64206 Author: Andrew Myers Date: Wed Sep 4 10:59:11 2019 -0700 convert image to png (docs) (travis) Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.png commit 053d18b01f8a755b3184a347ebdbab5ab5d97789 Author: Andrew Myers Date: Wed Sep 4 10:51:19 2019 -0700 (travis) remove this package .travis.yml commit 4f7b4a43deebb015ee7d44436e3baf6a3dbf9fa8 Author: Weiqun Zhang Date: Wed Sep 4 10:21:14 2019 -0700 fcompare: option to set a relative tolerance Tools/Plotfile/fcompare.cpp commit 4a5deef8003d6cc1b50c6cd20c8e92ac4f5fe566 Author: Andrew Myers Date: Tue Sep 3 17:01:32 2019 -0700 add svg package to travis build .travis.yml commit 9229d21d926e4cf2d5c6f04bca373fad93d7f290 Merge: c56f8af2a 3c5529e9c Author: Andrew Myers Date: Tue Sep 3 16:50:24 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c56f8af2ae8c26f11477dfb403251badf464fca4 Author: Andrew Myers Date: Tue Sep 3 16:50:09 2019 -0700 seems that we need travis_wait again .travis.yml commit 3c5529e9cdcaa0369e0e9a96bd1f065b818562c9 Author: Weiqun Zhang Date: Tue Sep 3 16:25:53 2019 -0700 remove noexcept so that Intel 18 is happy Src/EB/AMReX_EBCellFlag.H commit 2d905c33b2b5e678222b8b7db90af2e8b98c25f9 Author: Weiqun Zhang Date: Tue Sep 3 16:25:53 2019 -0700 remove noexcept so that Intel 18 is happy Src/EB/AMReX_EBCellFlag.H commit 2663b515bdbf9f6009f262e82ccf21cfe26172a8 Author: Andrew Myers Date: Tue Sep 3 16:24:30 2019 -0700 move assignment and constructor for ParticleContainer Src/Particle/AMReX_Particles.H commit d1915ec18412141becf8a1f1c93e4e215bf1061e Merge: cba6b99ca 08e8856e6 Author: Andrew Myers Date: Tue Sep 3 18:39:25 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cba6b99caee19a559584a92999301015ae99f566 Author: Andrew Myers Date: Tue Sep 3 18:38:50 2019 -0400 need to reset the m_need_handshake flag when calling fillNeighbors Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit db496c41d1b1f7ab62b8bce31407a1624c0d4fbf Author: Michele Rosso Date: Tue Sep 3 15:29:06 2019 -0700 Add missing include guards. CMake: do no process installed headers with name ending in "*I.H" since they are meant to always be included by host headers which are properly processed after installation. Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Tools/CMake/modify_installed_headers.cmake commit 08e8856e6b6f24336a044b6a08d449d737f7705a Author: Weiqun Zhang Date: Tue Sep 3 13:12:22 2019 -0700 MultiComponent tutorial: call Finalize() Tutorials/LinearSolvers/MultiComponent/main.cpp commit beccdce9df0ce4aff04674f243eb4b0447246e3f Merge: efc8c2eea 4810b679f Author: WeiqunZhang Date: Tue Sep 3 12:09:45 2019 -0700 Merge pull request #556 from AMReX-Codes/mcmlmg-test Mcmlmg test commit 4810b679fe82d1b5fbd65e37b1b0078cdad69313 Author: Brandon Runnels Date: Tue Sep 3 12:21:53 2019 -0600 added sphinx documentation Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.pdf Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.svg Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst commit efc8c2eea13397c9e5af854af7bd091d9c79e631 Author: Andrew Myers Date: Tue Sep 3 10:26:32 2019 -0700 add missing parameter to inputs.rt Tests/Particles/Redistribute/inputs.rt commit 5e5953426fa1e620e344eebda36f19c65c348c48 Author: Andrew Myers Date: Tue Sep 3 10:25:00 2019 -0700 change test name Tests/Particles/Intersection/main.cpp commit ac507c8f89ef340afcc850e04651099a6d6b5eda Merge: 4179e74be 841b39215 Author: Andrew Myers Date: Tue Sep 3 10:24:17 2019 -0700 Merge branch 'global_redistribute_gpu' into development commit 016898f4e017c8045b2ad3cff08130d21d80ec4f Author: Brandon Runnels Date: Tue Sep 3 11:17:16 2019 -0600 added documentation to tutorial Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tutorials/LinearSolvers/MultiComponent/inputs Tutorials/LinearSolvers/MultiComponent/main.cpp commit 4179e74be5f865dea412787ae120aa1f4f8c254e Author: Weiqun Zhang Date: Tue Sep 3 09:07:09 2019 -0700 update CHANGES CHANGES commit 5de4d3a2487c3d261adb760aa2c6068c74d6e844 Merge: 68d0036bb 32a5f97b3 Author: Brandon Runnels Date: Tue Sep 3 09:47:15 2019 -0600 Merge branch 'development' into mcmlmg-test commit 68d0036bb9fce5af504207ddb5b68defe610dde5 Author: Brandon Runnels Date: Tue Sep 3 09:46:40 2019 -0600 moved to tutorials Tutorials/LinearSolvers/MultiComponent/GNUmakefile Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tutorials/LinearSolvers/MultiComponent/Make.package Tutorials/LinearSolvers/MultiComponent/inputs Tutorials/LinearSolvers/MultiComponent/main.cpp commit 32a5f97b31c5fe04caf925f50f2dbfabfb535458 Author: Jean Sexton Date: Sat Aug 31 14:22:15 2019 -0400 Fix typo Src/Particle/AMReX_NeighborParticlesI.H commit 59c01ff2a4e78df937ec14731e032dee12964b25 Merge: 0c28d4ae5 c1729131b Author: Weiqun Zhang Date: Fri Aug 30 16:56:31 2019 -0700 Merge branch 'weiqun/dev' into development commit c1729131b8fa27b020d1bf7b8b6e98f68d1cd7d0 Author: Weiqun Zhang Date: Fri Aug 30 16:43:36 2019 -0700 add explicit host dtors so that host device versions are not generated Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Difference.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H commit 3f0c1f375bfd23b5442d34d78c8f8fc53fbd1a2c Author: Weiqun Zhang Date: Fri Aug 30 13:29:48 2019 -0700 PolynomialIF on GPU Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuMemory.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H commit 841b392159ce95e803bcf8347be792288a4f2ed2 Merge: 952ddecdc 709261bf9 Author: Andrew Myers Date: Fri Aug 30 13:47:22 2019 -0700 Merge branch 'global_redistribute_gpu' of github.com:AMReX-Codes/amrex into global_redistribute_gpu commit 952ddecdc7ebdf4fa6926bc0ba0b7a8e4c1d32ed Merge: ed272f30f 0c28d4ae5 Author: Andrew Myers Date: Fri Aug 30 13:47:03 2019 -0700 Merge branch 'development' into global_redistribute_gpu commit 0c28d4ae5fe50b228ce10dbabaac1a359e3bc2d1 Author: Andrew Myers Date: Fri Aug 30 13:45:37 2019 -0700 fix typos Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit 241dbb88e0c0dab69fb6d6f51f19965c16156364 Author: Andrew Myers Date: Fri Aug 30 13:44:22 2019 -0700 call base fab setVal instead of fab array one in threaded region (avoids race condition) Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit 709261bf93827dab0afb3f0809384d07bfadf056 Author: Andrew Myers Date: Fri Aug 30 15:20:32 2019 -0400 fix typo in test Tests/Particles/Redistribute/main.cpp commit 9606c8cd72339346a9df6ecd1a4ece30878f1ca1 Merge: 941ea6f49 19d52da90 Author: Andrew Myers Date: Fri Aug 30 15:08:56 2019 -0400 Merge branch 'development' into global_redistribute_gpu commit 19d52da90959d833abf4c15f008bff32b25d03dd Author: Andrew Myers Date: Fri Aug 30 11:27:14 2019 -0700 use an ifdef for MPI in these particle comm routines Src/Particle/AMReX_ParticleCommunication.cpp commit 1a3f65100ed48f518c264bdaf88eb27fbdd8ea7a Author: Andrew Myers Date: Fri Aug 30 11:08:55 2019 -0700 workaround for gcc 8.2 bug Src/Particle/AMReX_ParticleLocator.H commit 941ea6f49640843c2f428424dd688d687af0ad0b Author: Andrew Myers Date: Thu Aug 29 21:17:19 2019 -0400 some more error checking Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H commit 3e6e41469c7ddb9c95eaf553eeae5ecf6b52703d Author: Andrew Myers Date: Thu Aug 29 21:15:02 2019 -0400 set this size so it can be used in error checking Src/Particle/AMReX_ParticleTile.H commit bce8ae8073485aebed33d9f99c0d6e6e594b8778 Author: Weiqun Zhang Date: Thu Aug 29 17:51:46 2019 -0700 rm deprecated functions Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H commit ed272f30fc88fdcfedec0b71a8a73856cbfa087c Author: Andrew Myers Date: Thu Aug 29 17:35:51 2019 -0700 make sure we rebuild the particle locator even if not local Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H commit fdafac6ce0cea7a79090664296ca6faed79bd18d Merge: 9b3512a64 6b4b8dda2 Author: Weiqun Zhang Date: Thu Aug 29 17:34:16 2019 -0700 Merge branch 'development' into weiqun/dev commit 6b4b8dda2cc65d8abe78296a71f819d8d0d4c040 Author: Andrew Myers Date: Thu Aug 29 19:47:35 2019 -0400 fix particle locator for 2D Src/Particle/AMReX_ParticleLocator.H commit 5b42f4ed282bcc017579a2085fef6901cd0f1611 Author: Andrew Myers Date: Thu Aug 29 19:48:55 2019 -0400 fix dmap in test Tests/Particles/Redistribute/main.cpp commit effee01844a74590ca74cece44f39c2752280821 Author: Andrew Myers Date: Thu Aug 29 19:48:31 2019 -0400 update Intersection test for multiple levels Tests/Particles/Intersection/inputs Tests/Particles/Intersection/main.cpp commit 13028965d20144a4f8e50ca4707fbccba3e53068 Author: Andrew Myers Date: Thu Aug 29 19:47:35 2019 -0400 fix particle locator for 2D Src/Particle/AMReX_ParticleLocator.H commit 4fefe62968f6fbb4e191c0e8e8beee694a1e7e37 Author: Andrew Myers Date: Thu Aug 29 19:47:11 2019 -0400 add timer Src/Particle/AMReX_ParticleBufferMap.cpp commit 9b3512a64a51a8ddd7f6f83f6270f3efaf491450 Author: Weiqun Zhang Date: Thu Aug 29 16:25:29 2019 -0700 should not include old header Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit edb0d51af6f8d4ab381ffe2dc04c23e8cfcce9ef Author: Weiqun Zhang Date: Thu Aug 29 16:17:28 2019 -0700 rm deprecated Fortran files Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/CMakeLists.txt Src/EB/Make.package commit a54a2b1a6ec2d2155322b72e20567280fa1aaac2 Author: Weiqun Zhang Date: Thu Aug 29 16:03:48 2019 -0700 EBMultiFabUtil on GPU Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 6a422fae1c09ed26eeb91d4b15ab7b2c0bb804ad Author: Andrew Myers Date: Thu Aug 29 15:54:12 2019 -0400 add test for global gpu redistribute Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit b89f02a3fcdbd2ba658743497048b6a84816b06b Author: Andrew Myers Date: Thu Aug 29 15:53:46 2019 -0400 allow non-local redistribute to be dispatched to the GPU Src/Particle/AMReX_ParticleContainerI.H commit 668e753641d9dff0388792cfeefe022ceb3b5ba8 Author: Andrew Myers Date: Thu Aug 29 15:26:41 2019 -0400 implement non-local mpi communication pattern for gpu redistribute Src/Particle/AMReX_ParticleCommunication.cpp commit 1db0a894dc6f289fdaf31d0cbd7585e594cf58e3 Merge: 8e42f03a7 ed60ddbf5 Author: Andrew Myers Date: Thu Aug 29 14:39:33 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ed60ddbf5c59cd580d23b1e1438a7c29d2af7d42 Merge: 6a8450425 fd4b944b1 Author: Weiqun Zhang Date: Thu Aug 29 10:33:16 2019 -0700 Merge branch 'weiqun/dev' into development commit 6a8450425ddf02c2ba4f219a53d55e29598357a5 Author: Weiqun Zhang Date: Thu Aug 29 10:33:10 2019 -0700 add an assertion Src/Base/AMReX_FabArray.H commit fd4b944b12cbf1ec3fb893e2e3d26d62881435f1 Merge: 9b39b9a19 1a21a0aec Author: Weiqun Zhang Date: Thu Aug 29 10:07:23 2019 -0700 Merge branch 'development' into weiqun/dev commit 9b39b9a19e8be135c00e912539e4a29f4106fc59 Author: Weiqun Zhang Date: Thu Aug 29 10:06:59 2019 -0700 tidy Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_GpuLaunch.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBInterpolater.cpp commit 1a21a0aecce23e8b593138ee67bc4fd988dc0d19 Author: Weiqun Zhang Date: Thu Aug 29 09:09:15 2019 -0700 fix knapsack when nmax is very small Src/Base/AMReX_DistributionMapping.cpp commit 0c80f47cfb37ecb20dc4c8e36ad9394cca845891 Author: Weiqun Zhang Date: Thu Aug 29 04:42:45 2019 -0700 EBFluxRegister: rm Fortran Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_1d.F90 Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3D_C.H Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Src/EB/CMakeLists.txt Src/EB/Make.package commit e78b43df62ce3870dd9b255c571532c7e41096c2 Author: Weiqun Zhang Date: Wed Aug 28 22:09:38 2019 -0700 avoid name conflicts Src/Base/AMReX_GpuLaunchMacrosG.H commit b2d1baae7723e6f9df4b4f98786eaa296d693401 Author: Weiqun Zhang Date: Wed Aug 28 21:58:06 2019 -0700 EBFluxRegister: rereflux Src/Base/AMReX_GpuLaunchMacrosG.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H commit e2a62d8646b14f1f48b41b55061363895b73d0e7 Author: Weiqun Zhang Date: Wed Aug 28 18:05:17 2019 -0700 EBFluxRegister: fine add dm Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H Src/EB/AMReX_EBFluxRegister_nd.F90 commit e6434bc851a35b1a49eb57ad15e6c85ad2d1b616 Author: Weiqun Zhang Date: Wed Aug 28 17:05:00 2019 -0700 EBFluxRegister fine_add: rm a temporary array Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H commit 8e42f03a7244e8c8e9a09ca8f10e98cd0200c0f3 Author: Andrew Myers Date: Wed Aug 28 19:53:22 2019 -0400 some more code reuse Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H commit 2eeac2a3ea157afb0825a5f5a97eed9ad1b15b98 Author: Andrew Myers Date: Wed Aug 28 19:47:00 2019 -0400 some code reuse Src/Particle/AMReX_ParticleUtil.H commit 6e61fe0fbfb30f65f115a23b89c65dc51f1c935d Author: Andrew Myers Date: Wed Aug 28 19:37:12 2019 -0400 fix cpu compile Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H commit 81ef27d0b246ccc3012e0ea76f00191ec15d63d0 Author: Andrew Myers Date: Wed Aug 28 19:18:24 2019 -0400 use the new non-local distributor in the gpu redistribute Src/Particle/AMReX_ParticleContainerI.H commit 55bf3deaf076e7ff4c1611ca2096839aaef8cc93 Author: Weiqun Zhang Date: Wed Aug 28 16:15:52 2019 -0700 EBFluxRegister: fineadd Src/Base/AMReX_Array4.H Src/Base/AMReX_GpuLaunch.H Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H commit 4a4069255cc745785ae45acd9d4b947e8b7fc27f Author: Andrew Myers Date: Wed Aug 28 18:06:56 2019 -0400 a particle locator to the ParticleContainer class Src/Particle/AMReX_Particles.H commit 34e0b7c24e8da15f047cbd9e0a41101908149474 Author: Andrew Myers Date: Wed Aug 28 18:06:28 2019 -0400 a get particle cell function Src/Particle/AMReX_ParticleUtil.H commit b56b964b7e1b98b31d667e5a9ae0168604d6eda6 Author: Andrew Myers Date: Wed Aug 28 17:29:47 2019 -0400 test for the GPU boxarray intersection class Tests/Particles/Intersection/GNUmakefile Tests/Particles/Intersection/Make.package Tests/Particles/Intersection/inputs Tests/Particles/Intersection/main.cpp Tests/Particles/Intersection/script.sh commit 2a20abfbbd6217c0429b7c9cdd0100b6f50ba9ba Author: Andrew Myers Date: Wed Aug 28 17:28:00 2019 -0400 add class for locating particles on the gpu with no assumption of locality Src/Particle/AMReX_ParticleLocator.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 9aaa81afd68f4e8a02ba768a4616f13613c9e419 Author: Andrew Myers Date: Wed Aug 28 17:27:23 2019 -0400 add early exit for size 0 messages Src/Particle/AMReX_ParticleCommunication.cpp commit 5dcde5172ab116057f9b35e821addd51f7013d4d Author: Weiqun Zhang Date: Wed Aug 28 08:31:34 2019 -0700 EBFluxRegister: crseadd Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H Src/EB/AMReX_EBFluxRegister_C.H Src/EB/CMakeLists.txt Src/EB/Make.package commit 98f36e58fb83ca6ac0ce306cadb7c61947cc3292 Merge: 2d92aef2b 9e13c3db4 Author: Weiqun Zhang Date: Tue Aug 27 21:04:49 2019 -0700 Merge branch 'weiqun/dev' into development commit 9e13c3db4679fc3ee62e21246b6f9ef69f771576 Author: Weiqun Zhang Date: Tue Aug 27 20:26:27 2019 -0700 prefer const_array() to implicit conversion of the result of array() Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 3e523ca0f18264670991cb5bd1e4e73ba9008ee1 Author: Weiqun Zhang Date: Tue Aug 27 17:26:29 2019 -0700 make sure no race condition in LaunchSafeGuard even in omp parallel region Docs/sphinx_documentation/source/Basics.rst Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBInterpolater.cpp commit 37e44b49e3626c828b12662810f1f5469e5cdd38 Author: Weiqun Zhang Date: Tue Aug 27 15:49:19 2019 -0700 GPU: EBInterpolater Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBInterp_F.H Src/EB/AMReX_EBInterpolater.cpp Src/EB/AMReX_ebinterp_1d.F90 Src/EB/AMReX_ebinterp_2d.F90 Src/EB/AMReX_ebinterp_3d.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit e1772106cd142460e86b26b4055100e5f8c0a4d9 Author: Weiqun Zhang Date: Tue Aug 27 15:07:50 2019 -0700 EBCellFlag: rm region Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBFArrayBox.cpp commit d2c208b25422708975d15ec52a11c3d559ec4ee0 Author: Weiqun Zhang Date: Tue Aug 27 14:10:23 2019 -0700 add MultiCutFab::const_array Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 3f5c3313301db744b11f50df666d46b612d1781e Author: Weiqun Zhang Date: Tue Aug 27 13:39:02 2019 -0700 EB2_Level: more gpu Src/EB/AMReX_EB2_Level.cpp commit 2d92aef2b629592953be22859c391a205d1b0b15 Author: Andrew Myers Date: Tue Aug 27 13:28:46 2019 -0700 rewrite the buffer_size calculation to be more idiomatic Src/Particle/AMReX_ParticleContainerI.H commit 1c2a4ca949978bc5c982b7b32c4ca817d289bc71 Merge: 8bcd76342 2909827f1 Author: Andrew Myers Date: Tue Aug 27 13:15:23 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8bcd76342967ce02ae5af2a4ddf1432b24c4dbd3 Author: Andrew Myers Date: Tue Aug 27 13:15:14 2019 -0700 tweak particle mesh test Tests/Particles/ParticleMesh/main.cpp commit 72842755a6650a6548271e881bcf312e1748f4b1 Author: Weiqun Zhang Date: Tue Aug 27 13:13:18 2019 -0700 minor Src/EB/AMReX_EB2_Level.cpp commit 96998b2cab7863dd82888b61d22f63cd1d10e48e Author: Weiqun Zhang Date: Tue Aug 27 12:52:56 2019 -0700 fix a bug Src/EB/AMReX_EB2_IF_Box.H commit 24fd63ad3401e36fd225497770dd8a1ea3651d89 Author: Weiqun Zhang Date: Tue Aug 27 12:42:23 2019 -0700 EB: rm deprecated parameter Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp commit 41a93bd71dc61f0c1058ac68aa6c88a849bb72f6 Author: Weiqun Zhang Date: Tue Aug 27 12:32:38 2019 -0700 GeometryShop: getBoxType on gpu Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp commit 2909827f16e6684325cf9543d4c46c6f85338068 Merge: d4359e238 d4fb03f29 Author: Andrew Myers Date: Tue Aug 27 15:29:58 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d4359e2381fd54999f93fb2613d991e4b9f4a2f0 Author: Andrew Myers Date: Tue Aug 27 15:29:42 2019 -0400 don't use int for total number of particles in this test Tests/Particles/Redistribute/main.cpp commit d4fb03f2976c62d2e97c7f436457b7a98e577b57 Author: Andrew Myers Date: Tue Aug 27 12:28:36 2019 -0700 tweak test Tests/Particles/ParticleMesh/main.cpp Tools/RegressionTesting/AMReX-tests.ini commit 54ba44cffe33d47637d9735c36610a1382b95049 Author: Andrew Myers Date: Tue Aug 27 12:19:54 2019 -0700 add an automated test for particle-mesh operations Tools/RegressionTesting/AMReX-tests.ini commit af8b36de1b0478877c952b359cbd509b420b4de6 Merge: 9a1312fc2 ca05839a4 Author: Andrew Myers Date: Tue Aug 27 11:36:10 2019 -0700 Merge branch 'mpi_datatype' into development commit 9a1312fc25acb8c827909440325a3343c5452f8e Merge: 9fbab69c7 95cf27676 Author: Andrew Myers Date: Tue Aug 27 13:53:58 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9fbab69c7cdc3e7c98095e4690f72dff30685297 Author: Andrew Myers Date: Tue Aug 27 13:53:37 2019 -0400 early exit from these MPI routines when we only have 1 process Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 95cf276760fdbde48e406576968b5d81eec60b01 Author: Weiqun Zhang Date: Tue Aug 27 10:42:30 2019 -0700 Option to use default stream in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 0797f8900d9639b5dec7b25217b7c913564a753e Merge: 1d4b4d235 85d740674 Author: Weiqun Zhang Date: Mon Aug 26 20:55:52 2019 -0700 Merge branch 'weiqun/dev' into development commit 85d7406743d537562659f57fb0958f448405fd1a Author: Weiqun Zhang Date: Mon Aug 26 20:55:26 2019 -0700 fix new bug in eb_set_covered_nodes Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit ca05839a4ca63155f6365600d0233410528dc933 Author: Andrew Myers Date: Mon Aug 26 18:10:47 2019 -0700 use an mpi data type other than char to up the limit on the number of particles that can be communicated (cpu-only) Src/Particle/AMReX_ParticleContainerI.H commit d09598b94417bd0164e582d718b7c3dab4c3ee7e Author: Weiqun Zhang Date: Mon Aug 26 16:11:18 2019 -0700 EBCellFlag: fix new OMP issue Src/EB/AMReX_EBCellFlag.cpp commit 2ffabefbe703694e8276fbf4243772d315564737 Author: Andrew Myers Date: Mon Aug 26 15:33:42 2019 -0700 add a MPI data type for unsigned long long Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ccse-mpi.H commit 6f24f0cd8dd4738fdfdf0ff32fc0e18a05405ced Author: Weiqun Zhang Date: Mon Aug 26 13:44:14 2019 -0700 EB: fix a new 2d bug Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_Level.cpp commit 64e04d72d7f0e41a058c546edeccdc7f05e9bebd Author: Weiqun Zhang Date: Mon Aug 26 13:24:32 2019 -0700 EBCellFlagFab: getType on GPU Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBCellFlag_F.H Src/EB/AMReX_distFcnElement.cpp Src/EB/AMReX_ebcellflag_mod.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit 5c52537cdaee7201378147eaf607c6660c2a9a8e Author: Weiqun Zhang Date: Sun Aug 25 21:23:23 2019 -0700 wip Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBFArrayBox.cpp commit 1d4b4d2357433cdf93a408e24350aefc09f58ea8 Author: Weiqun Zhang Date: Sun Aug 25 20:41:52 2019 -0700 distFcnElement: pass x by reference Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp commit 5372993ea3063e3fac6c127630496c49bd4c9310 Author: Weiqun Zhang Date: Sun Aug 25 20:38:25 2019 -0700 GPU: compute integrals Src/EB/AMReX_algoim.cpp commit 3e1ce784000fa59c7f81a8cd33857f8ad5b5f25c Author: Weiqun Zhang Date: Sun Aug 25 19:13:18 2019 -0700 GPU: eb_set_covered Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H commit 0c00090fb0ceb61c889f9b2383b11f28d9c62877 Merge: c0ed5b5b2 f7e07743a Author: Weiqun Zhang Date: Sun Aug 25 15:40:12 2019 -0700 Merge branch 'weiqun/dev' into development commit f7e07743adec11e13d81bc5d5b1115440bc081a4 Author: Weiqun Zhang Date: Sun Aug 25 15:35:53 2019 -0700 EB 3d: For uncovered cell, set self-connection Src/EB/AMReX_EB2_3D_C.H commit 544f9def38d5f8dcf9ba5cca64dfda86d105845d Author: Weiqun Zhang Date: Sun Aug 25 08:52:24 2019 -0700 EB GPU: fix bugs in the new coarsen_from_fine function Src/EB/AMReX_EB2_3D_C.H commit f38bea2ae3a65e142bebda32356fe70461f4f0cb Author: Weiqun Zhang Date: Sat Aug 24 22:11:36 2019 -0700 GPU: build_cellflags_from_ap Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit 19077b0554afdda4e65022cbb9e9246640b6ca67 Author: Weiqun Zhang Date: Sat Aug 24 18:07:53 2019 -0700 switch to use C++ coarsen_from_fine Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 commit 2994307de5b4d55204ba734adfaacbf53fc531b7 Author: Weiqun Zhang Date: Sat Aug 24 17:06:15 2019 -0700 GPU: coarsen from fine Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_Level.cpp commit c0ed5b5b205a7efab1266a4ab91068eee012a539 Author: Andrew Myers Date: Fri Aug 23 17:49:36 2019 -0700 tweak test Tests/Particles/Redistribute/inputs.rt Tests/Particles/Redistribute/main.cpp Tools/RegressionTesting/AMReX-tests.ini commit 88c639e0a40dcbde361552f41e8b8e4e52cdc144 Author: Andrew Myers Date: Fri Aug 23 17:30:51 2019 -0700 turn off CUDA by default Tests/Particles/Redistribute/GNUmakefile commit 67064de677e5d8188f8e3bc7f937ae0ea09d29fc Author: Andrew Myers Date: Fri Aug 23 17:30:25 2019 -0700 config entry for redistribute test Tools/RegressionTesting/AMReX-tests.ini commit cd00cd0ada50665248c11ec791dc56503a4e34f6 Author: Andrew Myers Date: Fri Aug 23 17:29:59 2019 -0700 configure this as a self-test Tests/Particles/Redistribute/main.cpp commit ff72c353f4d462869d8f3d595c8bcb653dea9293 Author: Andrew Myers Date: Fri Aug 23 17:29:46 2019 -0700 regtest inputs for Redistribute Tests/Particles/Redistribute/inputs.rt commit e2ea5e2d7884001d26b6b85b4edb9af93c7d49f9 Author: Andrew Myers Date: Fri Aug 23 17:04:52 2019 -0700 enable omp in numParticlesOutOfRange Src/Particle/AMReX_ParticleUtil.H commit 615079f975817a412ae5b8a6e4eeeb16816ef373 Author: Andrew Myers Date: Fri Aug 23 17:04:29 2019 -0700 combine two forms of OK() Src/Particle/AMReX_ParticleContainerI.H commit 3c0d78ff1c5eb5141a96e7da32d91a1c66b35f1b Author: Andrew Myers Date: Fri Aug 23 19:50:19 2019 -0400 tweak RedistributeTest inputs and script Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/script.sh commit cc7697f2c5e73683c1a00a9d819b3840cd166aaa Author: Andrew Myers Date: Fri Aug 23 19:45:40 2019 -0400 reimplement OKGPU in terms of numParticlesOutOfRange Src/Particle/AMReX_ParticleContainerI.H commit 5a2741baabab0d541e4c4f1423640709c4aa337d Author: Andrew Myers Date: Fri Aug 23 19:45:12 2019 -0400 add overload for numParticlesOutOfRange that lets you set the levels Src/Particle/AMReX_ParticleUtil.H commit 44508f93c8d54283da5d2cfb06b166e0dae9fbde Author: Andrew Myers Date: Fri Aug 23 17:24:08 2019 -0400 small world bug (gpu, newish) - need to apply periodic boundary conditions to particles that cross a periodic domain BUT stay on the same grid Src/Particle/AMReX_ParticleContainerI.H commit 48902a815926fa4915930a9b14ce12ce5b5e197a Author: Andrew Myers Date: Fri Aug 23 13:53:03 2019 -0400 function to validate that the particles are in range of the local redistribute function Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H commit 8e5f6dbe6e787614e361b136a04d1ab6924d42cd Merge: 75e1effbc 0ca353f7c Author: cgilet Date: Fri Aug 23 10:55:24 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit accccec58dbe5661b4a2311b88796a36fdde2448 Author: Weiqun Zhang Date: Thu Aug 22 11:58:14 2019 -0700 switch to use C++ check_mvmc Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 commit 0ca353f7c78ec22ce4655eebcc9b9889b9f0f2a4 Merge: 1b2827c67 99c49340a Author: Weiqun Zhang Date: Thu Aug 22 09:33:52 2019 -0700 Merge branch 'weiqun/dev' into development commit 99c49340a2c4fe1178526764be41a7439d601332 Author: Weiqun Zhang Date: Thu Aug 22 09:32:12 2019 -0700 add Gpu::synchronize after fabs are allocated in case kernesl are launched to do placement new Src/Base/AMReX_FabArray.H commit 56811204f341b1351a2f24c4bccc28a328a5be62 Author: Weiqun Zhang Date: Wed Aug 21 15:31:23 2019 -0700 wip Src/Base/AMReX_FabArray.H Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBMultiFabUtil.cpp commit 1b2827c67624e0115f8ecd0d22e0cf828a49c925 Author: kngott Date: Wed Aug 21 14:19:54 2019 -0700 Add number of streams to MFIter Info options. Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 5a70c78493376b1e0f58fe8201745dfc3a20fa90 Author: kngott Date: Wed Aug 21 14:15:36 2019 -0700 Make numGpuStreams available when USE_GPU=FALSE. Src/Base/AMReX_GpuDevice.H commit 3e42848f9f9f04a6cc9f8663ad01bf790b2534bc Merge: ab6d76a69 dd45b69b0 Author: Andrew Myers Date: Wed Aug 21 12:48:17 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ab6d76a69a86458dbd5e6688996f30597900829d Author: Andrew Myers Date: Wed Aug 21 12:48:06 2019 -0700 add a couple of convenience functions to ParIter Src/Particle/AMReX_Particles.H commit dd45b69b06142d3ca874a899ff6be241367960ce Author: kngott Date: Wed Aug 21 12:30:19 2019 -0700 Update CoriGPU example run script. Tutorials/GPU/run.corigpu commit b0547ae90a21f69e55172ac1b61d7aad0bae580f Merge: 38f941c1f f62675f54 Author: Weiqun Zhang Date: Wed Aug 21 06:15:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f62675f54c147cf3861819b7861baa0a19247386 Author: kngott Date: Tue Aug 20 18:35:39 2019 -0700 Thread multiple test and results on linear solver. Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/inputs.test Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-1.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-16.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-2.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-32.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-4.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-64.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-8.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-1.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-16.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-2.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-32.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-4.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-64.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-8.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/main.diff Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/results.org commit ae6af3b0923b4ee6726becd57d9d20d33fa2d96b Author: Andrew Myers Date: Tue Aug 20 17:30:19 2019 -0700 always do handshake in fillNeighbors Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 38f941c1f68c167e67c07be294e4ef2e3ae7e535 Author: Weiqun Zhang Date: Tue Aug 20 15:39:27 2019 -0700 ParallelFor taking multiple Boxes and lambdas Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Tools/CompileTesting/compiletesting.py commit 2ff96e509c1fbf3aab57d630fe9aefdd617044da Author: Weiqun Zhang Date: Tue Aug 20 14:02:53 2019 -0700 EB integral: add integral of x*y*z Src/EB/AMReX_algoim.H Src/EB/AMReX_algoim.cpp Src/EB/AMReX_algoim_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 95342996354fbdfe21c5025cd308e5a8c2a058b8 Merge: e08783249 db4d88120 Author: Andrew Myers Date: Tue Aug 20 13:21:42 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e08783249cf15cf52a0761b78820cabf0dd089f0 Author: Andrew Myers Date: Tue Aug 20 13:21:15 2019 -0400 only need to call doHandShake after regrid, not every Redistribute Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit db4d8812065d138044b1cea07bda87f52f250673 Author: Weiqun Zhang Date: Mon Aug 19 17:06:25 2019 -0700 comments on pinned arena. simplify an Array4 ctor. Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array4.H commit b299b41d021058344740fbf127064352feb2eaba Author: Andrew Myers Date: Mon Aug 19 17:05:42 2019 -0700 2D bugfix Src/Particle/AMReX_ParticleContainerI.H commit 6123abdbe82dd2a80f8f4e2c87af1ba93c005aef Author: Andrew Myers Date: Mon Aug 19 16:37:24 2019 -0700 move all the particle IO routines into a separate file Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit cd6a7a6d8f880633c4765c2eb426e67342c2ccfc Author: Weiqun Zhang Date: Mon Aug 19 13:04:45 2019 -0700 HostDevice::Atomic::Add that does OMP atomic for host code Src/Base/AMReX_GpuUtility.H commit 093fbdcaa53e0eb945c496b6fbda396fc305c974 Merge: c6b8da79d 6a09bb617 Author: WeiqunZhang Date: Sun Aug 18 18:12:02 2019 -0700 Merge pull request #550 from AMReX-Codes/convergence_cleanup Convergence cleanup commit 6a09bb617042162ca52d052628723e2b6f31b58b Author: Michael Zingale Date: Sun Aug 18 19:51:51 2019 -0400 remove unused files + fix 1-d compilation Src/Extern/ProfParser/AMReX_AVGDOWN_1D.F Tools/C_util/Convergence/AVGDOWN_1D.F Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile.temp Tools/C_util/Convergence/Make.package.SAVE Tools/C_util/Convergence/Make.package.temp commit 76f34eee415f28daf017470816cc1bf0ca234878 Author: Michael Zingale Date: Sun Aug 18 19:41:14 2019 -0400 some work on making a no-Latex version Tools/C_util/Convergence/AVGDOWN_1D.F Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit c6b8da79dd38b0e525dd67370a6131b1c3b22180 Merge: 654336784 1fa9a90c4 Author: Andrew Myers Date: Fri Aug 16 11:44:28 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6543367843f51b097d50058d0afd446ffb4ef7a2 Author: Andrew Myers Date: Fri Aug 16 11:44:17 2019 -0700 a test for the multilevel redistribute mask Tests/Particles/AssignMultiLevelDensity/main.cpp Tests/Particles/ParticleReduce/main.cpp commit 1fa9a90c42a02acb510b3c82d992e7ceb64826f5 Author: Weiqun Zhang Date: Fri Aug 16 11:32:11 2019 -0700 option to add extra flags from command line Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 8bddef09a1f5ead66398a4d6e51c06bd2aebd51f Author: Kevin Gott Date: Fri Aug 16 13:42:17 2019 -0400 Thread Multiple time Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/results.org commit 466d2afdf16c185bf244299d9ba1490875d10e4a Merge: 9235f2c27 a5f555ab4 Author: Weiqun Zhang Date: Fri Aug 16 09:59:05 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9235f2c279a9cf7cb39e23f5f94b54a09e8aeb2d Author: Weiqun Zhang Date: Fri Aug 16 09:58:49 2019 -0700 add new constructors for alias Fab to avoid implicit conversion Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit a5f555ab4e355af1d3052fda2cbbb737ad11d7d6 Author: Kevin Gott Date: Thu Aug 15 20:08:31 2019 -0400 Make all scaling tests gcc. Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-16.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-32.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-8.sh commit d2fab1bca2b9ceecb61483a59925797686eecd6e Author: Andrew Myers Date: Thu Aug 15 11:43:06 2019 -0700 add test for particle reduce Src/Particle/AMReX_ParticleReduce.H Tests/Particles/ParticleReduce/GNUmakefile Tests/Particles/ParticleReduce/Make.package Tests/Particles/ParticleReduce/inputs Tests/Particles/ParticleReduce/main.cpp Tests/Particles/Redistribute/main.cpp commit e98696a4ea40c045fe8578df0f311d1d4e1db1b8 Author: Andrew Myers Date: Thu Aug 15 11:04:19 2019 -0700 also use the ParIter in AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleReduce.H commit 267499cc8e3013655186be306a1791775427d606 Author: Andrew Myers Date: Thu Aug 15 10:50:22 2019 -0700 make code shorter using ParIter Src/Particle/AMReX_ParticleMesh.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 184ec762af808d29190d176dd0988311581418f2 Author: Andrew Myers Date: Thu Aug 15 10:34:14 2019 -0700 fix some things in MeshToParticle Src/Particle/AMReX_ParticleMesh.H Tests/Particles/ParticleMesh/main.cpp commit 9e1bb58a7488425cc258c4058c22f0582230b4b9 Author: Andrew Myers Date: Thu Aug 15 09:59:07 2019 -0700 implement lambda MeshToParticle Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleMesh.H Tests/Particles/ParticleMesh/main.cpp commit e22b559ce8f40d6b2b1fccfba39d29761e08986d Author: Weiqun Zhang Date: Thu Aug 15 07:07:25 2019 -0700 fix compFlux for 1d Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit f75737aec148488007d0b7eaf0f6c2cc4ed6048b Author: Weiqun Zhang Date: Wed Aug 14 19:11:22 2019 -0700 periodicShift MultiFab Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 31c995eca78e11b099b493c776ee5607d8e21ed8 Author: Andrew Myers Date: Wed Aug 14 16:41:33 2019 -0700 fix off-by-one error Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 90092d180fb4233e9bebcd3520efeae67d85ccce Author: Andrew Myers Date: Wed Aug 14 16:36:54 2019 -0700 add timer Src/Particle/AMReX_ParticleMesh.H commit 47c4c0544c4b67c0ede831ba8436bf37bc8aa83c Author: Andrew Myers Date: Wed Aug 14 16:30:30 2019 -0700 this pointer should not be unique Src/Particle/AMReX_ParticleMesh.H commit 99c0cbaba4a03ac65bad7ea27b2c9bc2757f3013 Author: Andrew Myers Date: Wed Aug 14 16:30:12 2019 -0700 tweak inputs Tests/Particles/ParticleMesh/inputs commit c55d27a7e6919ca2ee9ecfe0e680b1e7f2c4f01d Author: Andrew Myers Date: Wed Aug 14 16:18:35 2019 -0700 add particle mesh lambda test Tests/Particles/ParticleMesh/GNUmakefile Tests/Particles/ParticleMesh/Make.package Tests/Particles/ParticleMesh/inputs Tests/Particles/ParticleMesh/main.cpp commit b1f61e1895075199d984593df2afcc471b7614a2 Author: Andrew Myers Date: Wed Aug 14 13:58:56 2019 -0700 implementing a general particle-to-mesh function with lambdas Src/Particle/AMReX_ParticleMesh.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 07bc03f5991057c494fa22413ad47302c48c9a16 Author: Andrew Myers Date: Wed Aug 14 13:55:05 2019 -0700 And, Or -> LogicalAnd, LogicalOr Src/Particle/AMReX_ParticleReduce.H commit c1c962dab209142b9bc7c867c2026da0b934227f Merge: 11fea0772 6ae4a428d Author: Andrew Myers Date: Wed Aug 14 13:46:20 2019 -0700 Fixing merge conflict commit 6ae4a428daef681de7a35e89f89c475718c75f5d Author: Andrew Myers Date: Wed Aug 14 13:41:34 2019 -0700 need to reset m_nrcvs when doing early exit Src/Particle/AMReX_ParticleCommunication.cpp commit 34391250c1e65465e1868a2b13cb530b811754b5 Author: Weiqun Zhang Date: Wed Aug 14 13:26:59 2019 -0700 forgot a new file Src/Boundary/AMReX_LO_BCTYPES.cpp commit b9ecb0f40cc5e372d9e28aa81f44ee0ce78a1891 Author: Weiqun Zhang Date: Wed Aug 14 13:05:09 2019 -0700 operator<< for LinOpBCType Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/CMakeLists.txt Src/Boundary/Make.package commit 449b589b183ff681dd2436bf9066bb2ff1ef1198 Author: Weiqun Zhang Date: Wed Aug 14 12:52:29 2019 -0700 MLMG: coarsen geometry correctly without using any system defaults in case special geometry is passed in Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit b4cc6a25d865602eb4a316c31a222bfdd259be7d Merge: fdf9d55a2 89e1fcefe Author: Weiqun Zhang Date: Wed Aug 14 12:06:50 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fdf9d55a278a6d756a9c0216188628228e3d5da8 Author: Weiqun Zhang Date: Wed Aug 14 12:06:25 2019 -0700 Atomic::And -> Atomic::LogicalAnd, Atomic::Or -> Atomic::LogicalOr Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuUtility.H Src/Particle/AMReX_ParticleUtil.H commit 11fea077235cf715f1fd9f3ac418ab6a331c31c1 Author: Andrew Myers Date: Wed Aug 14 10:58:44 2019 -0700 move the particle reduction functions into their own file. Src/Particle/AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 89e1fcefed84b32d2f3807083a3cbe12e8c9c74c Merge: f99c2d29f 240f922f7 Author: Andrew Myers Date: Wed Aug 14 10:37:47 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f99c2d29f2a03782f66d64ed9310a8fd2ee03de5 Author: Andrew Myers Date: Wed Aug 14 10:37:25 2019 -0700 add additional overloads for particle reduction operations Src/Particle/AMReX_ParticleUtil.H commit 240f922f752861bb5d01120d810a1f206a0b6ecd Author: Ann Almgren Date: Wed Aug 14 10:35:32 2019 -0700 Move DataServicesTest0 from OldTutorials into Tests Tests/DataServicesTest0/DataServicesTest0.cpp Tests/DataServicesTest0/GNUmakefile commit 5593825a36f7784beacd58572b9abbe65930f7c1 Merge: 0e81dff10 befa8b29b Author: Andrew Myers Date: Wed Aug 14 10:23:37 2019 -0700 Merge branch 'development' into redistribute_opt commit befa8b29bcd85c3ea2b0dfb39573c8ce17552965 Merge: a84b43f1b ce5a9c51a Author: Weiqun Zhang Date: Wed Aug 14 09:55:27 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a84b43f1b638e4454abe9a9f38135fb04ef99788 Author: Weiqun Zhang Date: Wed Aug 14 09:54:30 2019 -0700 makeFineMask: add optional arguments specifying coarse and fine flag values Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit ce5a9c51aae0f0415d285ceb7e549e1cb9864e3d Author: Michele Rosso Date: Wed Aug 14 09:49:55 2019 -0700 CMake: remove C_CellMG Src/LinearSolvers/CMakeLists.txt commit f0fb80ad394d50a125b78f656802d68d2747cb96 Author: Weiqun Zhang Date: Wed Aug 14 09:04:33 2019 -0700 rename for consistence Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_Reduce.H commit d936961fa5dc66608b6b4e720c5e9cade845d8b6 Merge: 20d758c89 9d1a667b4 Author: WeiqunZhang Date: Wed Aug 14 08:46:34 2019 -0700 Merge pull request #547 from cgilet/development Development commit 9d1a667b4d8b5bf9423ce2552e92e697612b8fee Author: cgilet Date: Wed Aug 14 10:38:00 2019 -0400 Clean up MLTensorOp::compFluxes(). Remove unnecessary variable. Fix comments. Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 20d758c89e55a7c6b0c5b85f42a6839a0786682e Author: Weiqun Zhang Date: Wed Aug 14 07:23:21 2019 -0700 rm C_CellMG from many makefile because MLMG no longer uses files in C_CellMG GNUmakefile.in Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/ComparisonTest/COEF_1D.F Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_1d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_3d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord2 Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord3 Tests/LinearSolvers/ComparisonTest/inputs-rt-Neu Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBTensor/GNUmakefile Tests/LinearSolvers/EBflux_grad/GNUmakefile Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/NodeEB/GNUmakefile Tools/CompileTesting/compiletesting.py Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile Tutorials/EB/MacProj/GNUmakefile Tutorials/EB/Poisson/GNUmakefile Tutorials/ForkJoin/MLMG/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile Tutorials/LinearSolvers/NodalPoisson/GNUmakefile Tutorials/SDC/MISDC_ADR_2d/Exec/GNUmakefile commit 0207252bf54aed79d5c819ffc4948d65299f8872 Author: Weiqun Zhang Date: Wed Aug 14 06:38:11 2019 -0700 remove old regression tests Tools/RegressionTesting/AMReX-tests.ini commit d47532b86e8ebf98a12653209bd6af967cd17f4c Author: Weiqun Zhang Date: Wed Aug 14 06:32:23 2019 -0700 fix 2d EB Src/EB/AMReX_EBFluxRegister_2d.F90 commit 96922c0cd86226bfc5eb64e0497a3ad44ee959bc Merge: d22835e70 d40b43e8b Author: Tan Nguyen Date: Wed Aug 14 01:47:27 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d22835e7029a8e0fc30e46d1cc52737c3ad78e55 Author: Tan Nguyen Date: Wed Aug 14 01:47:14 2019 -0700 update the make system of AmrTask tutorials Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.omp Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.pthreads Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.upcxx Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Backtrace.0 Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Advection_AmrLevel/CMakeLists.txt Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/Make.Adv Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Prob.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/probin Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probin Tutorials/AmrTask/MiniApps/Advection_AmrLevel/README Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Adv_F.H Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/LevelBldAdv.cpp Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/main.cpp Tutorials/AmrTask/MiniApps/HeatEquation/GNUmakefile Tutorials/AmrTask/MiniApps/HeatEquation/Make.package Tutorials/AmrTask/MiniApps/HeatEquation/advance.cpp Tutorials/AmrTask/MiniApps/HeatEquation/advance_2d.f90 Tutorials/AmrTask/MiniApps/HeatEquation/advance_3d.f90 Tutorials/AmrTask/MiniApps/HeatEquation/init_phi_2d.f90 Tutorials/AmrTask/MiniApps/HeatEquation/init_phi_3d.f90 Tutorials/AmrTask/MiniApps/HeatEquation/inputs_2d Tutorials/AmrTask/MiniApps/HeatEquation/inputs_3d Tutorials/AmrTask/MiniApps/HeatEquation/main.cpp Tutorials/AmrTask/MiniApps/HeatEquation/myfunc.H Tutorials/AmrTask/MiniApps/HeatEquation/myfunc_F.H Tutorials/AmrTask/MiniApps/HeatEquation/physbc.cpp Tutorials/AmrTask/MiniApps/SMC_fixed_dt/GNUmakefile Tutorials/AmrTask/MiniApps/SMC_fixed_dt/LiDryer.c 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Tutorials/AmrTask/UnitTests/003_Jacobi_DynamicGraph.C Tutorials/AmrTask/UnitTests/Makefile commit d40b43e8be91fab038bdf068ac7f904e98b5d5d8 Author: Weiqun Zhang Date: Tue Aug 13 21:31:24 2019 -0700 make some changes for xSDK Src/EB/AMReX_WriteEBSurface.H Src/EB/AMReX_WriteEBSurface.cpp Src/EB/AMReX_WriteEB_F.H Src/EB/AMReX_eb_to_pvd.F90 commit 92f761d926f26eb580b13eb76ba4f51c70970af2 Merge: 7c08f66fe 05f0ee606 Author: Weiqun Zhang Date: Tue Aug 13 21:15:07 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 05f0ee606e8c84abf8927cd516a838088e2a227d Author: Ann Almgren Date: Tue Aug 13 17:18:42 2019 -0700 Remove old multigrid tutorial OldTutorials/MultiGrid_C/CMakeLists.txt OldTutorials/MultiGrid_C/COEF_2D.F90 OldTutorials/MultiGrid_C/COEF_3D.F90 OldTutorials/MultiGrid_C/COEF_F.H OldTutorials/MultiGrid_C/GNUmakefile OldTutorials/MultiGrid_C/Make.package OldTutorials/MultiGrid_C/README OldTutorials/MultiGrid_C/RHS_2D.F90 OldTutorials/MultiGrid_C/RHS_3D.F90 OldTutorials/MultiGrid_C/RHS_F.H OldTutorials/MultiGrid_C/inputs OldTutorials/MultiGrid_C/inputs-rt-c-neu OldTutorials/MultiGrid_C/inputs-rt-c-ord2 OldTutorials/MultiGrid_C/inputs-rt-c-ord3 OldTutorials/MultiGrid_C/main.cpp OldTutorials/MultiGrid_C/writePlotFile.H OldTutorials/MultiGrid_C/writePlotFile.cpp OldTutorials/README_C commit e5db7530909a510defcf29d086c0d49e2a7adc6d Author: Ann Almgren Date: Tue Aug 13 17:17:03 2019 -0700 Add new tutorial OldTutorials/libamrex_C/MyAmr.H OldTutorials/libamrex_C/MyAmr.cpp OldTutorials/libamrex_C/main.cpp OldTutorials/libamrex_C/myf.f90 Tutorials/Basic/Build_with_libamrex/GNUmakefile Tutorials/Basic/Build_with_libamrex/MyParams.H Tutorials/Basic/Build_with_libamrex/main.cpp Tutorials/Basic/Build_with_libamrex/my_func.f90 Tutorials/Basic/Build_with_libamrex/test_parameters.cpp commit 4401eeceaae6494a19094064558802f79808b7f4 Author: Ann Almgren Date: Tue Aug 13 17:16:49 2019 -0700 Add new tutorial Docs/sphinx_tutorials/source/Basic_Tutorial.rst commit 0e81dff10ff2e7ebcefe7a2a677c872bdd8e7833 Merge: dd7906262 077321cea Author: Andrew Myers Date: Tue Aug 13 16:48:26 2019 -0700 Merge branch 'development' into redistribute_opt commit dd790626261182249ff2abb660112b157c320518 Author: Andrew Myers Date: Tue Aug 13 16:47:30 2019 -0700 handle non-gpu aware mpi in a better in the particle communication routines Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit a5205b72a1f2ad2b54a67547aa07137c7ed7067e Author: Andrew Myers Date: Tue Aug 13 16:05:35 2019 -0700 restore use_gpu_aware_mpi flag to false by default Tests/Particles/Redistribute/inputs commit d990668f1f5d93e723286d769219d4c058a85f44 Author: Andrew Myers Date: Tue Aug 13 15:39:07 2019 -0700 fix indentation Src/Particle/AMReX_TracerParticle_mod_K.H commit 077321cea6f8055486cab2dd22664e5b8c58152d Author: Ann Almgren Date: Tue Aug 13 13:47:19 2019 -0700 Move the EB writing files into Src/EB instead of Tutorials and/or mfix code. Src/EB/AMReX_WriteEBSurface.H Src/EB/AMReX_WriteEBSurface.cpp Src/EB/AMReX_WriteEB_F.H Src/EB/AMReX_eb_to_pvd.F90 Src/EB/CMakeLists.txt Src/EB/Make.package Src/Extern/ProfParser/AMReX_AVGDOWN_1D.F Tutorials/EB/Donut/Src/EB_F.H Tutorials/EB/Donut/Src/Make.package Tutorials/EB/Donut/Src/main.cpp commit 5be5217a11ee49b4ef12d1dd5841df4477392398 Author: Ann Almgren Date: Tue Aug 13 13:22:50 2019 -0700 Fix comments only in interpolation routines Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_Interpolater.cpp Src/EB/AMReX_WriteEBSurface.cpp Src/EB/CMakeLists.txt Src/EB/Make.package commit cd4ff66fa15a02537546364a131d6e4348d68ef8 Author: Ann Almgren Date: Tue Aug 13 12:39:17 2019 -0700 1) remove Racetrack -- that was committed by accident 2) move Src/AmrTask/tutorials to Tutorials/AmrTask Src/EB/AMReX_EB2_IF_Racetrack.H Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.omp Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.pthreads 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Tutorials/AmrTask/MiniApps/SMC_fixed_dt/kernels.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/main.cpp Tutorials/AmrTask/MiniApps/SMC_fixed_dt/make_plot.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/transport_properties.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/variables.f90 Tutorials/AmrTask/UnitTests/001_TokenRing.C Tutorials/AmrTask/UnitTests/002_Jacobi_StaticGraph.C Tutorials/AmrTask/UnitTests/003_Jacobi_DynamicGraph.C Tutorials/AmrTask/UnitTests/Makefile commit 7c08f66fe12eb97fdbaae1bbc1954ab9fe3dd1d2 Merge: 0152499cf edc55d6d2 Author: Weiqun Zhang Date: Tue Aug 13 12:32:00 2019 -0700 Merge branch 'newcomm' into development commit 0152499cf4e35d591e7375b4cb35a68e9ba13736 Merge: 259e7cde9 a537ea19e Author: Weiqun Zhang Date: Tue Aug 13 12:31:49 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9c78c3d9a3c0b323e60122307e8f817895c1c45e Author: Ann Almgren Date: Tue Aug 13 12:30:05 2019 -0700 1) get rid of "dble" in Src code 2) get rid of hard-wired single- or double-precision constants (use,e.g one/half/zero instead) Src/AmrCore/AMReX_INTERP_1D.F90 Src/EB/AMReX_EB2_IF_Racetrack.H Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset_F.F90 Src/EB/AMReX_compute_normals.F90 commit edc55d6d20448a60d1fe5d163c88df09053c317f Author: Weiqun Zhang Date: Tue Aug 13 11:10:01 2019 -0700 revert accidental changes Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit a537ea19ee7ffb3494df21f68c5e995317c8ba9f Merge: 907c0ad03 21e818fd4 Author: WeiqunZhang Date: Tue Aug 13 10:48:10 2019 -0700 Merge pull request #548 from rhouim/development Development commit 131994686086fb2796272a6ccd2f0e55f779e027 Author: Weiqun Zhang Date: Tue Aug 13 10:26:12 2019 -0700 clean up the vector version of FillBoundary Src/Base/AMReX_FabArrayCommI.H commit 5ae2e79636a43331cb67a2e6b49104698e7d5a0d Author: Weiqun Zhang Date: Tue Aug 13 12:26:54 2019 -0400 add the latest linear solver scaling test result Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/results.org commit 8345b1ffad622f9a98508a962647b72d4f852979 Merge: 0ee95e7f9 259e7cde9 Author: Weiqun Zhang Date: Tue Aug 13 00:12:53 2019 -0400 Merge branch 'newcomm' of github.com:AMReX-Codes/amrex into newcomm commit 0ee95e7f975e7f3d980c801bdb27fdb0619aa0b8 Author: Weiqun Zhang Date: Tue Aug 13 00:12:27 2019 -0400 add linear solver scaling test stuff Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/inputs.test Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/main.diff Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/results.org Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-1.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-1024.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-128.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-16.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-2.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-2048.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-256.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-32.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-4.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-512.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-64.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-8.sh commit 0ad4378246a7147536bee9b1f4adb944b7e5e685 Merge: fe9e2074e 907c0ad03 Author: Andrew Myers Date: Mon Aug 12 20:25:42 2019 -0400 Merge branch 'development' into redistribute_opt commit fe9e2074e866cddaf96ffd0926fefd5a2472196a Author: Andrew Myers Date: Mon Aug 12 20:25:32 2019 -0400 powers of 6 for summit Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/script.sh commit 510d9a71b85f902faac2d6bfe83317e24c9d7571 Author: Andrew Myers Date: Mon Aug 12 20:24:56 2019 -0400 remove commented out code Src/Particle/AMReX_ParticleContainerI.H commit e7c7b676caa94902cf5c592a3594395d64712ffe Author: Andrew Myers Date: Mon Aug 12 20:00:52 2019 -0400 fix Redistribute test to be more sensitive to soa errors Tests/Particles/Redistribute/main.cpp commit 2abb0af7170212d8097c8a8eb973956074a5ff8e Author: Andrew Myers Date: Mon Aug 12 20:00:20 2019 -0400 fix new bug Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 907c0ad039c2c7769dfdb3d7cf2997d4f2a03651 Author: Andrew Myers Date: Mon Aug 12 19:46:35 2019 -0400 remove un-needed synchronization points Src/Base/AMReX_Utility.cpp commit 762982a91a37fe35f797905357a65651077ea7ff Author: Andrew Myers Date: Mon Aug 12 19:45:56 2019 -0400 use volatile in this test Tests/GPU/Locking/main.cpp commit 259e7cde9ff2d8caa50e45bef39a758f0e9b49a3 Merge: 1e515dc08 e45396c2e Author: Weiqun Zhang Date: Mon Aug 12 16:09:06 2019 -0700 Merge branch 'development' into newcomm commit 21e818fd419bce977c43b10cd07d8dcd3e397e0b Author: Ryan Houim Date: Mon Aug 12 17:41:04 2019 -0400 Fixed some bugs with the interpolation routines. Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 commit 1e515dc08fe12c307595755069ea08db553e707c Author: Weiqun Zhang Date: Mon Aug 12 12:58:59 2019 -0700 fuse kernels in ParallelCopy Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_PCI.H commit 878ab66268cb17a33e32982bf182eb892d53c02a Author: Ryan Houim Date: Mon Aug 12 15:52:36 2019 -0400 This commit fixes a strange issue with AMReX cell bilinear interp. We setup a 1D simulation (planar flame) on a 2D grid. After some time steps there would be significant transverse velocities (which should be zero) that affected the flame. This only occured with the Intel compiler with DEBUG=False and with the cell_bilinear interpolation. Compiling with GNU orIntel with DEBUG=True did not produce this behavior. Rearranging the interpolation procedure to the method typically done by students when interpolating tables by hand seems to work fine where the data is first interpolated long x-lines, then the x-line interpolated data is interpolated in the y-direction, and finally the y-interpolated data is interpolated in the z-direction to give the final value. Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 commit c09e25930811f8351733594974a8e724730ba700 Author: Weiqun Zhang Date: Mon Aug 12 11:01:58 2019 -0700 reorganize ParallelCopy's local copy Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_PCI.H commit 6478a525d60e2730e3cbc66fb1c83cfcf6f1c3d6 Author: Weiqun Zhang Date: Mon Aug 12 10:34:05 2019 -0700 fix new bugs Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArrayCommI.H commit a7dad87f43f84aea1ac9fd1d325e99456c348895 Author: cgilet Date: Mon Aug 12 12:48:21 2019 -0400 Add MLTensorOp::compFluxes() Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit a23c327cc5e74abb619678db87c1c483e399c3a4 Author: cgilet Date: Mon Aug 12 12:45:39 2019 -0400 Fix typo in error message Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H commit 75e1effbccbcf72e2e666cd557e7c757341f7b26 Author: cgilet Date: Mon Aug 12 11:18:47 2019 -0400 In MLCellLinOp::compFlux(), make sure temporary flux is sized to hold all components. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit bc4d9777a3f912b6f4cff07e403dc13f3d4c044a Author: cgilet Date: Fri Aug 9 16:14:58 2019 -0400 WIP Add MLTensorOp::getFluxes(). Compiles, but no further testing. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit c7e0bd0894aab679be042bae8d4c86f14c10307a Author: cgilet Date: Fri Aug 9 16:13:14 2019 -0400 Fix typo in error message Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H commit 81a28e7190948288c3c64e9f1187003853466313 Author: Weiqun Zhang Date: Sun Aug 11 22:04:15 2019 -0700 fix index for maskfabs Src/Base/AMReX_FBI.H commit 1c803c5461477bb431d75cfde3a359d9150860ef Author: Weiqun Zhang Date: Sun Aug 11 21:11:13 2019 -0700 tidy Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArrayCommI.H commit 9aa3c8bfd1e8c773e5a6406cbbe6542cc4f191ac Author: Weiqun Zhang Date: Sun Aug 11 23:26:38 2019 -0400 minor Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H commit a2a2fd97252ce6fc8f5bedf3605365eb47e4f0c0 Author: Weiqun Zhang Date: Sun Aug 11 18:59:47 2019 -0700 fuse gpu kernels in fillboundary and reorganization Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_PCI.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 54718eba6bee6dce4e82a8a05ff411191fb99d18 Author: Weiqun Zhang Date: Sat Aug 10 20:15:15 2019 -0700 remove deprecated PreAllocatable and isCopyOMPSafe Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 5cb1b27391ab5afdced145a7cdc2da785f735630 Author: Weiqun Zhang Date: Sat Aug 10 18:10:35 2019 -0700 fix omp for StreamIter Src/Base/AMReX_GpuUtility.cpp commit 1a885fc54c9edf5bb716b0b15afb5d5b3381f8fa Author: Weiqun Zhang Date: Sat Aug 10 17:56:12 2019 -0700 fuse local copy part of parallel copy Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_TypeTraits.H Src/EB/AMReX_EBCellFlag.H commit 22197ba45e7e095fc9ec0d1df8a6b0ca07579c98 Author: Weiqun Zhang Date: Sat Aug 10 11:29:15 2019 -0700 generalize fab_to_fab function and operator interfaces Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_TypeTraits.H Src/EB/AMReX_EBCellFlag.H commit e45396c2e38294e7ef3aa77c4247bf90508ab1a9 Author: Ann Almgren Date: Sat Aug 10 06:53:44 2019 -0700 Replace 1.e-14 by "small" and 1.e-15 by "tiny" to be consistent with 2d Src/EB/AMReX_EB2_3D_C.cpp commit 6d86900a76692edd0d271c212a352f64488849ba Author: Weiqun Zhang Date: Fri Aug 9 22:01:52 2019 -0700 amrex::HasAtomicAdd Src/Base/AMReX_TypeTraits.H commit 42f76ae585b39a5dcaf02eb18d02e821a260b1b2 Author: Weiqun Zhang Date: Fri Aug 9 21:51:46 2019 -0700 amrex::IsCopyAtomicSafe Src/Base/AMReX_TypeTraits.H Src/EB/AMReX_EBCellFlag.H commit ce137f0865ea612a5e97719fc1ecc228a7958837 Author: Weiqun Zhang Date: Fri Aug 9 21:08:28 2019 -0700 fix compilation for cuda < 10 Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_GpuDevice.cpp commit 08072fbb439dbfa10799b674882ee19939cb0a2c Author: Weiqun Zhang Date: Fri Aug 9 19:23:03 2019 -0700 add eb2.small_volfrac Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_Level.H commit 54ce2700fb88d2ac0e74dff8fb66010700b26376 Merge: 8e95ff523 f8f2426fb Author: Weiqun Zhang Date: Fri Aug 9 17:14:52 2019 -0700 Merge branch 'kngott/cudaGraphs' into weiqun/fuse commit 8e95ff523167901c057850ab990e17f3a3414737 Author: Weiqun Zhang Date: Fri Aug 9 17:05:32 2019 -0700 fused local copy Src/Base/AMReX_FabArrayCommI.H commit 36526b4f2d759f23be22e661a97d976fee50799a Merge: bbbb5f88a 729f9bc67 Author: Andrew Myers Date: Fri Aug 9 13:44:47 2019 -0700 Merge pull request #544 from ChrisDeGrendele/rng2 RNGs are now assigned a block instead of a thread + a test problem to test locking commit 69c1514d90aa85ee84720b1c317d3f9da3530b4c Author: Andrew Myers Date: Fri Aug 9 16:43:15 2019 -0400 fix debug build error Src/Particle/AMReX_ParticleCommunication.cpp commit 729f9bc676dce0f3813885ae8e7fd1250c64636d Author: Chris DeGrendele Date: Fri Aug 9 13:31:30 2019 -0700 Added threadfence to ensure global memory write is complete Src/Base/AMReX_Utility.cpp Tests/GPU/Locking/main.cpp commit 9efd66178131f0f7840307783431a52bbad650b3 Author: cgilet Date: Fri Aug 9 16:14:58 2019 -0400 WIP Add MLTensorOp::getFluxes(). Compiles, but no further testing. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit fc680f466e69d033d652cdc307dc2b2079842c67 Author: cgilet Date: Fri Aug 9 16:13:14 2019 -0400 Fix typo in error message Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H commit 36c7d5de2874c23eeede2a2d96a74ced1757f1c7 Merge: ed74d53a0 bbbb5f88a Author: Andrew Myers Date: Fri Aug 9 14:45:28 2019 -0400 Merge branch 'development' into redistribute_opt commit ed74d53a09e1301f638eca823d1acbfa91729a00 Author: Andrew Myers Date: Fri Aug 9 14:35:59 2019 -0400 replace redistribute with the new version Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H Tests/Particles/Redistribute/main.cpp commit 6c7fc8ee1b8bf953e0314db9ec21cf12a73f9070 Author: Andrew Myers Date: Fri Aug 9 14:08:12 2019 -0400 some AMREX_RESTRICT Src/Particle/AMReX_ParticleTile.H commit 2e8ce3de4fffd93b146f0aabfa175c0f9638920e Author: Andrew Myers Date: Fri Aug 9 14:05:22 2019 -0400 remove print Src/Particle/AMReX_ParticleContainerI.H commit 6bb799f613fafc0e4082728b67bf0d2bbae1ea94 Author: Andrew Myers Date: Fri Aug 9 14:04:06 2019 -0400 assert that the soa / aos data is correct Tests/Particles/Redistribute/main.cpp commit 2f1ec1cae88ebcd3c081d94c24a64c1f9a3632d2 Author: Andrew Myers Date: Fri Aug 9 13:35:27 2019 -0400 update inputs Tests/Particles/Redistribute/inputs commit b7a343c6f99b11d24578d464412170dc25804475 Author: Andrew Myers Date: Fri Aug 9 13:35:02 2019 -0400 add some soa data to the test Tests/Particles/Redistribute/main.cpp commit 366e063b200fa5d00f4f15a92d93494016280e98 Author: Andrew Myers Date: Fri Aug 9 13:34:39 2019 -0400 handling soa data Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particles.H commit bbbb5f88a21913c30c23ac5c2eac4224ed67ba75 Author: Ann Almgren Date: Fri Aug 9 06:27:39 2019 -0700 update to VisIt caveat Docs/sphinx_documentation/source/Visualization.rst commit e36fe4520088e35511a795ffe7411972aa40550f Author: Weiqun Zhang Date: Thu Aug 8 20:08:19 2019 -0700 fix bug in fixing small EB cell faces Src/EB/AMReX_EB2_3D_C.cpp commit f8f2426fb3d5a1c7873f060a9a9f158e54655d0e Merge: 6a937e97e f23dfe57a Author: Kevin Gott Date: Thu Aug 8 19:18:29 2019 -0400 Merge branch 'development' into kngott/cudaGraphs Conflicts: Src/Base/AMReX_GpuDevice.cpp commit f23dfe57a8700dfc1b0be1f5102577dd78154277 Author: Ann Almgren Date: Thu Aug 8 11:09:14 2019 -0700 Add comments about how VisIt reads "Cycle" from plotfile names Docs/sphinx_documentation/source/Visualization.rst commit 4c901fcbe8d158c5de13fcc690cd593833e8d51e Author: Chris DeGrendele Date: Thu Aug 8 10:43:49 2019 -0700 Modify test problem to actually test Tests/GPU/Locking/main.cpp commit cd263a5c377460504cdc41073c33a1b7d27e3030 Merge: 351cbaf64 876bde340 Author: Andrew Myers Date: Thu Aug 8 13:09:59 2019 -0400 Merge branch 'development' into redistribute_opt commit 6a937e97e715a5cc8963d4b4e03e5a57175f3b5f Author: Kevin Gott Date: Wed Aug 7 20:35:59 2019 -0400 Move graph building inside (N_recv > 0) check. Src/Base/AMReX_FabArrayCommI.H commit 876bde340261076fe0d068ab86b1561bcf6e2ab8 Author: Weiqun Zhang Date: Wed Aug 7 17:11:12 2019 -0700 change GpuTuple::operator= to match std Src/Base/AMReX_Tuple.H commit 94549baea05f48fa855d800913a35c70d13eaab9 Author: Weiqun Zhang Date: Wed Aug 7 16:56:54 2019 -0700 ForwardAsTuple Src/Base/AMReX_Tuple.H commit 351cbaf64fe9e70de7d908ef0cae25c7dff5c9a3 Merge: 4a81697d9 ffe45566f Author: Andrew Myers Date: Wed Aug 7 19:49:50 2019 -0400 Merge branch 'development' into redistribute_opt commit ffe45566f511784db478625d6dc0c6a0d0098a81 Author: Weiqun Zhang Date: Wed Aug 7 16:48:56 2019 -0700 missed a move Src/Base/AMReX_Tuple.H commit 4a81697d9cba3d39acc9aba07deff66d57818f26 Merge: 7a5078b2b f9cfdf555 Author: Andrew Myers Date: Wed Aug 7 19:44:34 2019 -0400 Merge branch 'development' into redistribute_opt commit 7a5078b2bb92af6adf86ff8561b6cbee8b8f445a Author: Andrew Myers Date: Wed Aug 7 19:44:03 2019 -0400 use gpu-aware mpi in this test Tests/Particles/Redistribute/inputs commit 953a7ba4cd6b0ce4412d4377a5389720ba1104a9 Author: Andrew Myers Date: Wed Aug 7 19:43:39 2019 -0400 use the ParticleTileData in pack/unpack Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit f9cfdf5550cfc5582845de125a1b11c55c086875 Author: Weiqun Zhang Date: Wed Aug 7 16:43:02 2019 -0700 GpuTuple: Tie and operator= Src/Base/AMReX_Tuple.H commit 7aed05f22402f281b174194a3ab0fa64a60193f9 Author: Chris DeGrendele Date: Tue Aug 6 12:31:24 2019 -0700 RNGs are now assigned a block instead of a thread Other random function as well Safer locking mechanism by thread block for older GPUs Now test problem actually uses locking Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/GPU/Locking/GNUmakefile Tests/GPU/Locking/Make.package Tests/GPU/Locking/main.cpp commit e0cd2b7a90e187436244423854208e01211e1455 Author: Andrew Myers Date: Wed Aug 7 15:51:23 2019 -0400 method for accessing all particle data on the GPU (whether AoS or SoA) Src/Particle/AMReX_ParticleTile.H commit e5b39837ae266e78d182dfe05bb4f9043440075c Author: Andrew Myers Date: Wed Aug 7 15:50:37 2019 -0400 respect the use_gpu_aware_mpi flag Src/Particle/AMReX_Particles.H commit 2af026eb173b14d708fe6c654027cc6a91d3cea8 Author: Weiqun Zhang Date: Wed Aug 7 12:39:51 2019 -0700 GpuTuple: allow conversion Src/Base/AMReX_Tuple.H commit 09e1f852344ec95e9338550ac7893b579bb712f3 Author: Kevin Gott Date: Wed Aug 7 13:49:41 2019 -0400 Fix GraphInit test. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit 6a92c2b78ad03b6aebd99798fa90c1c817ed2545 Author: Weiqun Zhang Date: Wed Aug 7 09:46:35 2019 -0700 Apply Src/Base/AMReX_Tuple.H commit 7d81e4f48895b74fd5d9160e19ab885bfc320e37 Author: Kevin Gott Date: Wed Aug 7 12:27:44 2019 -0400 Add working InitGraph. Src/Base/AMReX_GpuDevice.cpp commit 532313acdd41f339f721be49e52a2dd543982293 Merge: 071712bc2 225f3b520 Author: Andrew Myers Date: Tue Aug 6 23:58:04 2019 -0400 Merge branch 'development' into redistribute_opt commit 071712bc2e95140f2ab4a2fe2b74b2d0ee93f14d Author: Andrew Myers Date: Tue Aug 6 23:51:01 2019 -0400 allow overlapping communication / computation when building the mpi copy plan Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit 225f3b5205a8089dc705730649f57ec5ed529787 Author: Weiqun Zhang Date: Tue Aug 6 19:51:19 2019 -0700 TupleCat Src/Base/AMReX_Tuple.H commit dd1beaff2733a29e5a5905c604417d8fc9228bb7 Author: Kevin Gott Date: Tue Aug 6 20:13:06 2019 -0400 Simplified init function. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit def6e293f4d4007ed49fd9b71c192901e6105cff Author: Kevin Gott Date: Tue Aug 6 19:16:57 2019 -0400 Minimized graph init. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit 2652fc4615b747953c7f225613d580f6b674dae7 Author: Kevin Gott Date: Tue Aug 6 17:38:32 2019 -0400 Working version of graph init: events. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit a7e1d8a033754a016c4eb24f8d186558624eae16 Author: Brandon Runnels Date: Tue Aug 6 15:13:48 2019 -0600 fixed the problem! it was that the boundary conditions were not getting set properly Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/main.cpp commit 3cb282fcd31649087952abfdeba213a7c7821a86 Author: Tan Nguyen Date: Tue Aug 6 14:00:33 2019 -0700 review lock-free sync points in the MPI backend Src/AmrTask/rts_impls/mpi/Perilla.cpp commit fa1f252e9a456ddf65eacb1ed66c9144f61cfead Author: Brandon Runnels Date: Tue Aug 6 13:06:58 2019 -0600 added makefile Tests/LinearSolvers/MultiComponent/GNUmakefile commit 5f269004a854a763a9d8e82350e7ecc1fb364f26 Author: Brandon Runnels Date: Tue Aug 6 09:51:52 2019 -0600 updated BC update Tests/LinearSolvers/MultiComponent/main.cpp commit c841f6c642f92fd890b6e2608bb2f058c8b3091a Merge: 31d3a96b2 5753344c8 Author: Brandon Runnels Date: Tue Aug 6 09:42:45 2019 -0600 Merge branch 'development' into mcmlmg-test commit 31d3a96b2e3f7262e2c89eb1ef828f089261cf90 Author: Brandon Runnels Date: Tue Aug 6 09:42:11 2019 -0600 Generally working but bottom solver still failing Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit 958aecb023a4dbe205a64ea3dfae511acbf3f597 Merge: b16306860 5753344c8 Author: Andrew Myers Date: Mon Aug 5 23:31:46 2019 -0400 Merge branch 'development' into redistribute_opt commit b1630686009ae9456f47d933b109d8c2e41a44b5 Author: Andrew Myers Date: Mon Aug 5 23:30:51 2019 -0400 use amrex::Scan instead of thrust::partition in the particle redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 5753344c82170dc274fbf7b8ee64767ad40b68f9 Merge: a28493088 1d02043ab Author: WeiqunZhang Date: Mon Aug 5 11:49:14 2019 -0700 Merge pull request #539 from rporcu/rporcu Roberto Porcu commit 1d02043abc2bd36a9ffe90bd4c969fc740ee84ed Author: Roberto Porcu Date: Mon Aug 5 11:14:31 2019 -0700 Remove Warnings for getFluxes method which is only partially overwritten in MLCellABecLap and MLNodeLaplacian classes Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit a2d16061c2db0ef4ff8f4b85d0c5f39fcebbb248 Author: Roberto Porcu Date: Mon Aug 5 11:01:27 2019 -0700 Add missing header files Src/Particle/AMReX_Particle.H commit 783411b143cabb55cae6b6b51de404bfee3feb36 Author: Roberto Porcu Date: Mon Aug 5 11:00:52 2019 -0700 Add getter of Gpu shared memory size in Device properties Src/Base/AMReX_GpuDevice.H commit d7bab483e3e288bbc5dfc560cd1d1e5bebdca610 Author: Roberto Porcu Date: Mon Aug 5 10:59:29 2019 -0700 Add dataPtr() and size() methods to struct Array4 Src/Base/AMReX_Array4.H commit a284930885879f652fd493d321ea5bc4a2c7354a Author: Weiqun Zhang Date: Sat Aug 3 20:25:53 2019 -0700 ignore command line argument after -- Docs/sphinx_documentation/source/Basics.rst Src/Base/AMReX.cpp commit bdf3c72f61a6f0410f62caaa8c4ca1d46ff1d66b Author: Weiqun Zhang Date: Sat Aug 3 18:46:24 2019 -0700 put omp pragma inside ifdef Src/Base/AMReX_GpuReduce.H commit 329ded74a9714dd5b99ef495fabdf78680893b1c Author: Ann Almgren Date: Sat Aug 3 16:08:28 2019 -0700 re-try formatting Docs/sphinx_documentation/source/Basics.rst commit 7e376ebfd0f03c7a55e7671506604b65e5f04830 Author: Ann Almgren Date: Sat Aug 3 15:52:44 2019 -0700 Fix formatting Docs/sphinx_documentation/source/Basics.rst commit 85362b1643a519e15a45ca1579efb902a496824c Merge: 230debd2e 046d484e9 Author: Ann Almgren Date: Sat Aug 3 15:38:00 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 230debd2e077d9340075125b1ff9ea89b3c3d001 Author: Ann Almgren Date: Sat Aug 3 15:18:46 2019 -0700 Add section about setting argc=2 so amrex doesn't try to read past the inputs file name on the command line Docs/sphinx_documentation/source/Basics.rst commit 6c3e7cebaec75cf55a5446f339820c682aa5145d Merge: 1abd2425e 046d484e9 Author: Andrew Myers Date: Sat Aug 3 17:21:44 2019 -0400 Merge branch 'development' into redistribute_opt commit 046d484e9a657d786c5d1c4a83ae9afbf9823990 Merge: 1a844b04a df17dd684 Author: Andrew Myers Date: Sat Aug 3 17:20:19 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1a844b04a149fa80a4c98f2f3b2bc752217264e8 Author: Andrew Myers Date: Sat Aug 3 17:20:08 2019 -0400 GPU version of Random_int Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit df17dd6844ee159df39cdfa7206d942d09a77f07 Author: Weiqun Zhang Date: Sat Aug 3 10:23:16 2019 -0700 amrex::StablePartition Src/Base/AMReX_Partition.H Tests/GPU/Partition/main.cpp commit 0a25f4ef418ad54bd8ed6147a16f1fce2336435f Author: Weiqun Zhang Date: Sat Aug 3 09:27:49 2019 -0700 partition: return number of trues Src/Base/AMReX_Partition.H Src/Base/AMReX_Scan.H Tests/GPU/Partition/main.cpp commit 331539d7746831995adb933be60390ab1d059c22 Author: Weiqun Zhang Date: Fri Aug 2 21:22:32 2019 -0700 update Partition test Tests/GPU/Partition/main.cpp commit 688bee6d81d4d72ad9e8fbf8d0c0784e3e70014a Author: Weiqun Zhang Date: Fri Aug 2 21:19:36 2019 -0700 amrex::Partition Src/Base/AMReX_Partition.H Src/Base/AMReX_Scan.H commit 32f2d5033d3542838c4ddbaf893c6df27e3edb20 Author: Weiqun Zhang Date: Fri Aug 2 19:18:08 2019 -0700 generailize scan to take functions Src/Base/AMReX_Partition.H Src/Base/AMReX_Scan.H commit e9f5b4676b12e6bf7e6f38cda481059c7e45d488 Author: Weiqun Zhang Date: Fri Aug 2 18:57:33 2019 -0700 fix some typos Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_Partition.H commit af9935fb8d0b5308b67d60ddb20603023ef327f6 Author: Weiqun Zhang Date: Fri Aug 2 18:50:03 2019 -0700 #ifdef put gpu scan code Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_Partition.H Src/Base/AMReX_Scan.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 9724998ce624e390989ff4d12b4d4e1450f418e7 Author: Kevin Gott Date: Fri Aug 2 20:15:04 2019 -0400 Current Graph Init test. Tests/GPU/CudaGraphs/GraphInitTest/inputs_3d Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit 6a24b8dea297f3055c1f3f859ff40c51591eb6ed Merge: f6cb577f0 c5ad3d5a4 Author: Weiqun Zhang Date: Fri Aug 2 16:17:54 2019 -0700 Merge branch 'weiqun/reduce' into development commit f6cb577f02f221760ec416735ada522d3551a203 Author: Andrew Myers Date: Fri Aug 2 18:52:07 2019 -0400 an indepedent test of the particle partition Tests/GPU/Partition/GNUmakefile Tests/GPU/Partition/Make.package Tests/GPU/Partition/inputs Tests/GPU/Partition/main.cpp commit c5ad3d5a46ae15f3f5dcd49375c2d2a713085b3f Author: Weiqun Zhang Date: Fri Aug 2 13:59:40 2019 -0700 scan: use volatile Src/Base/AMReX_Scan.H commit 1abd2425e526c1fcbdf70e5baa7d6e3cffd28bad Author: Andrew Myers Date: Fri Aug 2 16:55:45 2019 -0400 thrust::device_vector -> Gpu::DeviceVector Src/Particle/AMReX_ParticleContainerI.H commit e8d008bbd1fc12f3b687d4471e4998dd59ebc8f8 Merge: d929f3897 22c2f61c0 Author: Andrew Myers Date: Fri Aug 2 16:31:42 2019 -0400 Merge branch 'development' into redistribute_opt commit d929f3897dc31a5cd64726a4bb200e0c82c48312 Author: Andrew Myers Date: Fri Aug 2 16:30:50 2019 -0400 use point-to-point communication to determine the number of bytes to rcv when the communication pattern is local Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d1e8bfa6106107a2ec0cdf708b0a59dd83cac5e0 Author: Weiqun Zhang Date: Fri Aug 2 10:20:23 2019 -0700 scan: use __threadfence for reliability Src/Base/AMReX_Scan.H commit 585caf1a15654265f3454192c95d51783de6e75f Author: Weiqun Zhang Date: Thu Aug 1 22:52:49 2019 -0400 scan: avoid asyncarray and devicescalar Src/Base/AMReX_Scan.H commit 22c2f61c0054815e17500797a0cf67a8db159516 Author: Ann Almgren Date: Thu Aug 1 18:18:09 2019 -0700 "gird" --> "grid" Tutorials/EB/Donut/Src/eb_to_pvf.F90 commit 8a2cfdc96de4cb8d3aaecbe95e0b52c6f90c5e5d Author: Weiqun Zhang Date: Thu Aug 1 20:49:57 2019 -0400 scan test: add synchronize just in case Tutorials/GPU/ParallelScan/main.cpp commit 9c755e2134b43dbc4ad7214923cfaa12f8dfb29a Author: Weiqun Zhang Date: Thu Aug 1 18:09:32 2019 -0400 scan: optimization Src/Base/AMReX_Scan.H commit e2cdad01cbfc0ea1cddb64a73afcc989e12e98b3 Author: Weiqun Zhang Date: Thu Aug 1 14:35:43 2019 -0400 scan: tweak # of chunks Src/Base/AMReX_Scan.H commit f0f219631d6d9b87cc32a2066ffefd30b38cfd22 Author: Andrew Myers Date: Thu Aug 1 14:21:08 2019 -0400 use non-blocking sends in the communicateParticles and ParticleCopyPlan::buildMPI routines Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit f4df94a485268c67d4a34cdfe9720ee55c751535 Author: Weiqun Zhang Date: Thu Aug 1 11:04:46 2019 -0700 scan: parallel lookback Src/Base/AMReX_Scan.H commit 38567bd4e90f60da8d1b196c9b0083e3fa02dc5f Author: Weiqun Zhang Date: Thu Aug 1 08:59:24 2019 -0700 update CHANGES CHANGES commit 26c7610ab2409e6bc9901875b691c424cd5ea53c Author: Weiqun Zhang Date: Wed Jul 31 21:37:43 2019 -0700 scan: memory fence optimization Src/Base/AMReX_Scan.H Tutorials/GPU/ParallelScan/main.cpp commit e29b6fc20267a888491377619c97ee1a823161d2 Merge: 88eff5e61 ab82b1607 Author: Andrew Myers Date: Wed Jul 31 20:55:44 2019 -0400 Merge branch 'development' into redistribute_opt commit afe4c9cedd181053093d8567bae66ac5fa79b331 Author: Weiqun Zhang Date: Wed Jul 31 20:52:19 2019 -0400 scan: tweak the number of chunks Src/Base/AMReX_Scan.H Tutorials/GPU/ParallelScan/main.cpp commit 88eff5e613d796f16acb420e4bbf4f5ad36ad44d Author: Andrew Myers Date: Wed Jul 31 20:13:03 2019 -0400 fix typo affecting debug mode Src/Particle/AMReX_ParticleCommunication.H commit ab82b1607657f17e3e020b72b7c1393359291fa8 Author: Andrew Myers Date: Wed Jul 31 17:06:17 2019 -0700 fix omp in tracer particles Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 3ef91646f9923e7635ee729a3d53275932a7cdda Author: Weiqun Zhang Date: Wed Jul 31 17:04:26 2019 -0700 add ParallelScan test Tutorials/GPU/ParallelScan/GNUmakefile Tutorials/GPU/ParallelScan/Make.package Tutorials/GPU/ParallelScan/main.cpp commit 99376182044997220707f20fa571c8b14c00795d Author: Weiqun Zhang Date: Wed Jul 31 16:38:01 2019 -0700 first version of scan Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Scan.H Src/Base/CMakeLists.txt Src/Base/Make.package commit d06af3cf4257b6fb6976510ec3d181ee6d56748e Author: Andrew Myers Date: Wed Jul 31 16:53:22 2019 -0700 continue should be return here Src/Particle/AMReX_TracerParticles.cpp commit e92e70abeb8df157c57ea0cac0aaf4df246905bb Author: Andrew Myers Date: Wed Jul 31 16:38:40 2019 -0700 a little bit of reorganization Src/Particle/AMReX_TracerParticles.cpp commit f7fb25f9bf1e644d67015be083ce898700e37ab8 Author: Andrew Myers Date: Wed Jul 31 14:44:21 2019 -0700 fix mac advection for tracer particles Src/Particle/AMReX_TracerParticle_mod_K.H commit e6c58d8d68716809a1bf74715aa5a9caf2db29ba Author: Andrew Myers Date: Wed Jul 31 17:26:40 2019 -0400 overlap communication with computation in Redistribute Src/Particle/AMReX_ParticleContainerI.H commit ce022323a806c62f7918d03b79594b5bd4c52c84 Author: Andrew Myers Date: Wed Jul 31 16:14:34 2019 -0400 split up start and finish in the MPI communicateParticles so it can be overlapped Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit def25a9c0d43c4d35e21f306b91496aa41e409a2 Merge: 653963060 c312d3dd1 Author: Ann Almgren Date: Wed Jul 31 13:07:02 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 65396306062dd34884e6bd4b3b67ed770d5f2943 Author: Ann Almgren Date: Wed Jul 31 13:02:31 2019 -0700 Fix bug in mac_interpolate used in advection of tracer particles. Src/Particle/AMReX_TracerParticle_mod_K.H commit 1d5ffd609dd02f44baff8600dae6ae6fd9f0e033 Author: Andrew Myers Date: Wed Jul 31 15:17:48 2019 -0400 fix resize error Src/Particle/AMReX_ParticleCommunication.cpp commit e904e93cbfff7d4181e8213c48c047db743e271d Author: Andrew Myers Date: Wed Jul 31 15:06:53 2019 -0400 remove commented out code Src/Particle/AMReX_ParticleCommunication.H commit 10c4b72877e3167a18b32c23f35a43fac833a541 Author: Andrew Myers Date: Wed Jul 31 15:05:26 2019 -0400 remove redundant all-to-all in communicateParticles Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 3b03d04bef5f601ada7feba31bd6773ca6ec8694 Merge: 2e8eaaea9 c312d3dd1 Author: Weiqun Zhang Date: Wed Jul 31 11:39:57 2019 -0700 Merge branch 'development' into weiqun/reduce commit c312d3dd1b20a654cf49d19dc18193759ce0797b Author: Donald E. Willcox Date: Tue Jul 30 21:04:45 2019 -0700 Fix case-sensitive bug in gpu_fortran.py preprocessor script. (#522) Tools/F_scripts/gpu_fortran.py commit 46c35ca2822b7e30c47425ab3c7b3b9a818a433d Merge: 4e64649a1 ab4829c71 Author: Marc Day Date: Tue Jul 30 17:10:43 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4e64649a190920d10921c6ab549534a1b6c334d8 Author: Marc Day Date: Tue Jul 30 17:10:38 2019 -0700 Add tool to generate turbulence files from plotfiles Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/PlotfileToTurb.cpp Tools/Postprocessing/C_Src/PlotfileToTurb_nd.f90 commit 115ba6267047c8237bc78d14e59fa5991bd7895b Author: Andrew Myers Date: Tue Jul 30 20:09:27 2019 -0400 missed a couple Src/Particle/AMReX_ParticleCommunication.cpp commit fe5f48873a9006354f2c79ff1e650caeae1ab4c0 Author: Kevin Gott Date: Tue Jul 30 20:09:15 2019 -0400 Basic init test running. Need to add graphs to it. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit 964be86a385a2cf884450eb0642dc3c604b0db90 Author: Andrew Myers Date: Tue Jul 30 20:00:26 2019 -0400 fix CPU compilation Src/Particle/AMReX_ParticleCommunication.H commit b5aa1f2af2b3a6c9756766f06fb876af62aee3b6 Author: Andrew Myers Date: Tue Jul 30 19:55:18 2019 -0400 add timer around the partition Src/Particle/AMReX_ParticleContainerI.H commit 70545eef4e928c2576d300f707fb775cfc6fbe6d Merge: b90ac56a7 ab4829c71 Author: Andrew Myers Date: Tue Jul 30 19:25:20 2019 -0400 Merge branch 'development' into redistribute_opt commit b90ac56a7d8ad002e5e77568b9fb78028fe5a3ed Author: Andrew Myers Date: Tue Jul 30 19:24:37 2019 -0400 perform an initial partition to keep the size of the redistribute copy operation down Src/Particle/AMReX_ParticleContainerI.H commit 6389d767740ab9c42b464b77e7ce4948e96fb27b Merge: af92d8721 ab4829c71 Author: Kevin Gott Date: Tue Jul 30 18:58:21 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit ab4829c71d8f33f1c6eca87d8e674ed73631787b Author: Kevin Gott Date: Tue Jul 30 18:56:28 2019 -0400 Set initial stream after device setup to the default stream. Src/Base/AMReX_GpuDevice.cpp commit cf0bdc4216020d8833a389313e76d353a74b03a9 Author: Tan Nguyen Date: Tue Jul 30 12:28:09 2019 -0700 fix a small error in the AMFIter Src/AmrTask/rts_impls/runtime_common/RGIter.cpp Src/AmrTask/rts_impls/runtime_common/WorkerThread.H Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_advance.cpp commit 2e8eaaea93bb5e6646aeb435fa0a1f1cd4756773 Author: Weiqun Zhang Date: Tue Jul 30 11:57:51 2019 -0700 reduce tutorial: use long for sum of iMultiFab for consistence with iMultiFab::sum function Tutorials/GPU/ParallelReduce/main.cpp commit 50d1b453c97da23463067b8bfa88a0590d5c0c3c Author: Weiqun Zhang Date: Tue Jul 30 11:50:25 2019 -0700 fix type in reduce Src/Base/AMReX_GpuReduce.H commit af92d8721ffe55be93cf623c54b72aebb0a93735 Author: Kevin Gott Date: Tue Jul 30 14:50:17 2019 -0400 Start of GraphInitTest. Tests/GPU/CudaGraphs/GraphInitTest/GNUmakefile Tests/GPU/CudaGraphs/GraphInitTest/Make.package Tests/GPU/CudaGraphs/GraphInitTest/inputs_3d Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit f75b096b497bcf784b6faa3f5d9e7db521124067 Author: Weiqun Zhang Date: Tue Jul 30 11:18:11 2019 -0700 finish simplification of reduce interface Src/Base/AMReX_Reduce.H Src/Base/AMReX_Tuple.H Tutorials/GPU/ParallelReduce/main.cpp commit 8708a7060bca492fdd032cc388d8d888f153cb5f Merge: b08fdf902 b5cb86b26 Author: Kevin Gott Date: Tue Jul 30 13:51:18 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit b5cb86b265bfce903f5cf1838385ecc83c6e0d1e Author: Andrew Myers Date: Tue Jul 30 10:18:19 2019 -0700 id_rsa_travis -> deploy_key build_and_deploy.sh commit 01dc3e2a78600d02cdf0e027af72d4b6079d52b1 Author: Andrew Myers Date: Tue Jul 30 13:17:55 2019 -0400 don't actually need to clear the copy op and plan here Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H commit 458804755f33a4d5b4f4f8c65751b7e97f08dc33 Author: Andrew Myers Date: Tue Jul 30 13:14:40 2019 -0400 parmparse nsteps in redistribute test Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit e668e7d5aee5735c19a19dc03f4fab31519698cc Author: Andrew Myers Date: Tue Jul 30 10:07:10 2019 -0700 update deploy key used by Travis CI build_and_deploy.sh deploy_key.enc id_rsa_travis.enc commit f7cfdbd3491da93b4fd14a99eea22e0af9d1efaf Author: Weiqun Zhang Date: Tue Jul 30 07:20:28 2019 -0700 simplify the interface for reduce Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_Reduce.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/ParallelReduce/main.cpp commit 80202711a5f5f5729e7a41d2cc3854d63b34dc0e Author: Andrew Myers Date: Mon Jul 29 17:09:21 2019 -0700 more 1D compilation errors Src/Particle/AMReX_TracerParticle_mod_K.H commit c47046e3b2727ae65938e505f913ff7c9d78dbb3 Merge: d76fbe0b3 ae05bd9e1 Author: Andrew Myers Date: Mon Jul 29 17:07:06 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d76fbe0b34e33ef6b600e09d57448d4df3cbccbd Author: Andrew Myers Date: Mon Jul 29 17:06:53 2019 -0700 fix 1D tracer particles Src/Particle/AMReX_TracerParticle_mod_K.H commit 274c1eb4e96e9ccc2cc8946df1763809f2768d9a Author: Andrew Myers Date: Mon Jul 29 15:59:34 2019 -0400 keep around the redistribute copy plan and op so it doesn't need to do any reallocation Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 9f796c1b8f1a9cc87ee533b8c1b14f4148f994ed Author: Andrew Myers Date: Mon Jul 29 15:53:14 2019 -0400 avoid pushing back onto device vector in particle communication Src/Particle/AMReX_ParticleCommunication.cpp commit ae05bd9e1fe9138cf49bb203c4b6e36f60adb35e Author: Ann Almgren Date: Mon Jul 29 12:44:15 2019 -0700 two *.H files were missing from Make.package Src/Particle/Make.package commit 1bb462984e5f87f3033e005ea6d511680f591e5b Author: Andrew Myers Date: Mon Jul 29 15:25:18 2019 -0400 fix routine name in profile region Src/Particle/AMReX_ParticleCommunication.H commit fdd03aafa488ac7154fd3f6a030b6aa3940c71fb Author: Andrew Myers Date: Mon Jul 29 15:04:01 2019 -0400 move early exit Src/Particle/AMReX_ParticleContainerI.H commit 467a446c82bf6847777bc30508fb18a370102739 Author: Andrew Myers Date: Mon Jul 29 15:03:21 2019 -0400 actually used the parmparsed values of move_dir and do_random Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit f91036ac5255b4da55c52181627a25aa82fd738c Author: Andrew Myers Date: Mon Jul 29 14:27:16 2019 -0400 change repo in submission script Tests/Particles/NeighborParticles/script.sh Tests/Particles/Redistribute/script.sh commit f5eea1453a29360c0c587873de6d63349b01de1a Author: Andrew Myers Date: Mon Jul 29 14:26:59 2019 -0400 add random move option for redistribute test Tests/Particles/Redistribute/main.cpp commit f2cc07c1db936224e0eb7d4d17bef2af9b89edb0 Author: Andrew Myers Date: Mon Jul 29 14:06:52 2019 -0400 update script Tests/Particles/NeighborParticles/script.sh commit c992577cf0fde3cce1399889e886c06d29e26cc8 Author: Andrew Myers Date: Mon Jul 29 14:06:13 2019 -0400 properly handle particles that leave the domain in non-periodic directions. Src/Particle/AMReX_ParticleCommunication.H commit bc5c3461753d676f985cd60343aaafdbdd64359f Author: Andrew Myers Date: Mon Jul 29 13:58:54 2019 -0400 fix typo in script Tests/Particles/Redistribute/script.sh commit 2966f1efd118e0fe520f68de3f9b36b6b567273c Merge: 61c0e7e15 3fd33a22b Author: Andrew Myers Date: Mon Jul 29 13:38:14 2019 -0400 Merge branch 'development' into redistribute_opt commit c47b0eb46ab2a548444f7f89199df190e7999152 Author: Weiqun Zhang Date: Sun Jul 28 19:28:19 2019 -0400 Reduce::Min, Reduce::Max and Reduce::MinMax Src/Base/AMReX_Functional.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Tutorials/GPU/ParallelReduce/main.cpp commit 93d136ec5350ed46f1c64ba30fcab23c5c832af8 Author: Weiqun Zhang Date: Sun Jul 28 15:12:22 2019 -0400 ParallelForReduce -> FabReduce and VecReduce. add Reduce::Sum Src/Base/AMReX_Functional.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuReduce.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/ParallelReduce/main.cpp commit 3fd33a22b9feb93a9aad1bd06c11fc99526d6189 Author: Ann Almgren Date: Sun Jul 28 10:27:33 2019 -0700 Remove setMaxCoarseningLevel since it wasn't working anyway Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit ca26d772abf344d6fb9ace16ed6a201c4712342c Author: Ann Almgren Date: Sun Jul 28 10:14:13 2019 -0700 Add a new MacProjector constructor that takes an lp_info so that we can pass m_max_coarsening_level in Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 4c4b042ec147fdb27f1cc68744ab825a6542f304 Author: Weiqun Zhang Date: Sat Jul 27 12:39:44 2019 -0400 ParallelForReduce: more overloads Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuMemory.H Src/Base/AMReX_GpuReduce.H Tutorials/GPU/ParallelReduce/main.cpp commit 80073a4358fc85dd4ac191bcc2b5429005b0e315 Author: Weiqun Zhang Date: Sat Jul 27 11:03:58 2019 -0400 ParallelForReduce Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuReduce.H Tests/GPU/ParallelReduce/main.cpp Tutorials/GPU/ParallelReduce/GNUmakefile Tutorials/GPU/ParallelReduce/Make.package Tutorials/GPU/ParallelReduce/main.cpp commit 0d7325fb817146a5098a1357b635980d7b643485 Merge: 5b7dfb5c9 627a429f3 Author: Weiqun Zhang Date: Sat Jul 27 00:03:17 2019 -0400 Merge branch 'development' into weiqun/reduce commit 61c0e7e1546c47f9cea673e2bc215f3886865e38 Author: Andrew Myers Date: Fri Jul 26 17:57:56 2019 -0400 checking particle redistribute test Tests/Particles/Redistribute/GNUmakefile Tests/Particles/Redistribute/Make.package Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp Tests/Particles/Redistribute/script.sh commit cfb0447e281eff877297abf7a51c2144288d17eb Author: Andrew Myers Date: Fri Jul 26 17:38:41 2019 -0400 forgot to put * Src/Particle/AMReX_ParticleContainerI.H commit e911bd4a2eb90bf754031028b5fd49e0a0d7ca83 Author: Andrew Myers Date: Fri Jul 26 17:32:34 2019 -0400 implement unpack policies so that the same communication routines can handle both redistribute and neighbor unpacking patterns Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H commit 07b6e67fb102fe1de4bb588ad9a04e7abbf8e5c1 Author: Andrew Myers Date: Fri Jul 26 16:11:40 2019 -0400 do the same for communicateParticles Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H commit 5b7dfb5c9bf1c2f4a19158adf62f1641f8a8825e Author: Weiqun Zhang Date: Fri Jul 26 12:35:42 2019 -0700 reducesum using __shfl_down_sync Src/Base/AMReX_GpuReduce.H Tests/GPU/ParallelReduce/GNUmakefile Tests/GPU/ParallelReduce/Make.package Tests/GPU/ParallelReduce/main.cpp commit 6048e8d360e25dc2a3718ae28e0674b072bd5688 Author: Andrew Myers Date: Fri Jul 26 15:28:16 2019 -0400 move pack and unpack buffers out of neighbor particle container so they can be reused. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 1d4e8e8a060dfd8a696cb93d93d831f75b56d643 Author: Brandon Runnels Date: Fri Jul 26 13:06:32 2019 -0600 works with multilevel and multigrid, but bottom solve is still failing Tests/LinearSolvers/MultiComponent/inputs commit ccbe827ffa07aedf545b326c1cfb65ab682f4a12 Author: Brandon Runnels Date: Fri Jul 26 13:03:37 2019 -0600 variable inputs working, but bottom solver is still failing for mglev>0 Tests/LinearSolvers/MultiComponent/MCNodalLinOp.H Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit e744e141eecd6921ad65dc9377d7f8262da39151 Author: Andrew Myers Date: Fri Jul 26 14:48:44 2019 -0400 remove extra clearNeighbors calls Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit dfd69e7053f399e7cff10d8e8deb62500914b3df Author: Andrew Myers Date: Fri Jul 26 14:42:42 2019 -0400 also build the parallel portion of the copy plan Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 509aab86e4f58e090ccc54910d0c549939f70ae5 Author: Andrew Myers Date: Fri Jul 26 14:29:28 2019 -0400 build method for ParticleCopyPlan Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_Particles.H commit cd14b40b95b47dc523d1add5e27f724f0cb5da29 Author: Andrew Myers Date: Fri Jul 26 14:01:52 2019 -0400 seperate the op and the plan Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 627a429f34d0ae91ff2284e71f33462dfae89ec4 Author: Kevin Gott Date: Fri Jul 26 13:49:46 2019 -0400 if (Gpu::notInLaunchRegion()) Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit 55bf0535b93d2ba4197b76d146be05f49044e9b8 Author: Kevin Gott Date: Fri Jul 26 12:41:03 2019 -0400 OwnerMask -> GPU. Src/Base/AMReX_iMultiFab.cpp commit 39a4905c7d4af5fddecd9a08f0d2d16aca65541f Author: Andrew Myers Date: Fri Jul 26 13:45:55 2019 -0400 create structs for particle copy ops and plans Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 847775accce0719dd4fdd125f429acd576e1d2be Merge: edef7f121 abaf6cae4 Author: Andrew Myers Date: Fri Jul 26 13:09:37 2019 -0400 Merge branch 'development' into redistribute_opt commit abaf6cae41c62820116f528171172059ffe22e2b Author: Andrew Myers Date: Fri Jul 26 13:09:09 2019 -0400 add an explanatory comment about the default number of cuda random states. Src/Base/AMReX_Utility.cpp commit 02158a53931fba8f712745cce24ccea77e619ca5 Author: Andrew Myers Date: Fri Jul 26 13:07:42 2019 -0400 make it so that users no longer need to call InitRandomSeedOnDevice explicitly Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit edef7f1214d062194d0155f530e6d8aeaaa027e8 Merge: d8acb0b48 4b66a19f0 Author: Andrew Myers Date: Fri Jul 26 12:54:30 2019 -0400 Merge branch 'development' into redistribute_opt commit 4b66a19f0ecae3a7a75331dc23ae2f09d6bd8acc Author: Andrew Myers Date: Fri Jul 26 12:52:49 2019 -0400 use std namespace for floor, don't use line continuation symbols Src/Particle/AMReX_TracerParticle_mod_K.H commit d8acb0b48304c80f5f0e93b686f9a50581b640a3 Merge: c232b0d08 6ca05c162 Author: Andrew Myers Date: Fri Jul 26 12:47:25 2019 -0400 Merge branch 'development' into redistribute_opt commit 6ca05c162914678bc52a5e7582ddb9606e8fd11f Merge: cf954e5c3 0bfcbaeec Author: Andrew Myers Date: Fri Jul 26 09:42:25 2019 -0700 Merge pull request #534 from ChrisDeGrendele/tracerparticles_2 This adds gpu support to tracer particles commit cf954e5c37b308828e66bb746f10c83135cf45d6 Author: Weiqun Zhang Date: Fri Jul 26 12:21:47 2019 -0400 value_type -> Real Src/Base/AMReX_VisMF.cpp commit 0bfcbaeecebfe9f4b2af2247ee90941b87224896 Author: Chris DeGrendele Date: Fri Jul 26 02:01:44 2019 -0400 Fixed segfault error Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit a5f0e4da1c5e87a9537501f75b039450cd66f23b Author: Chris DeGrendele Date: Thu Jul 25 22:34:21 2019 -0700 commit the changes Src/Particle/AMReX_TracerParticles.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 40ee9785d6b0e211cf3933084e17e5aeb3450264 Merge: d2442fa9b ae1f992c2 Author: Chris DeGrendele Date: Thu Jul 25 22:24:47 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into tracerparticles_2 commit d2442fa9b57831d9925386cc7f1b78cc76d932e1 Author: Chris DeGrendele Date: Thu Jul 25 22:10:38 2019 -0700 fixed off by 1 index error again Src/Particle/AMReX_TracerParticle_mod_K.H commit 0756a5ba736948d1d7aa398c10cec0bf7a3ef632 Author: Chris DeGrendele Date: Thu Jul 25 22:07:35 2019 -0700 tracer Src/Particle/AMReX_TracerParticle_mod_K.H commit c232b0d0893e79a6f8bdbf733e0eae8381be39be Author: Andrew Myers Date: Fri Jul 26 00:01:23 2019 -0400 more work on refactoring the particle communication code Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 19a391d613115ab54c7a6e71c914ce6bb2080d51 Author: Andrew Myers Date: Thu Jul 25 22:46:09 2019 -0400 remove some unused variables Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit f64e2cdb94b52df3d6f6a42063cefc34aca837c0 Merge: 589f976be ae1f992c2 Author: Andrew Myers Date: Thu Jul 25 22:36:14 2019 -0400 Merge branch 'development' into redistribute_opt commit ae1f992c22a84dfb7927acd8788435fabe86d6f1 Author: Andrew Myers Date: Thu Jul 25 22:31:45 2019 -0400 make sure these variables are initialized Src/Base/AMReX_Utility.cpp commit 8b8e7dd4da5f6bba4bac5489ccb553867a454efd Author: Andrew Myers Date: Thu Jul 25 20:50:18 2019 -0400 remove sync I just added Src/Base/AMReX_Utility.cpp commit feaa261f1ce9ce7f5f6f11542741a71320ae9cfd Merge: 33061f019 46026bf13 Author: Andrew Myers Date: Thu Jul 25 20:41:04 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 33061f01999a48c2bd806726458c5c8626b1c9ca Author: Andrew Myers Date: Thu Jul 25 20:40:40 2019 -0400 turn on TINY_PROFILE by default Tests/GPU/RandomNumberGeneration/GNUmakefile commit 46026bf1399174ebcb3b99751c31f157f2675e6b Merge: 8be85ba2a d10808444 Author: Weiqun Zhang Date: Thu Jul 25 17:31:40 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8be85ba2a688792409623c7b8a6a05c5fc155890 Author: Weiqun Zhang Date: Thu Jul 25 17:31:01 2019 -0700 when there are callbacks in MFIter, use two streams only Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuElixir.cpp Src/Base/AMReX_MFIter.cpp commit d108084444bc76cd7e4641aaeebdd48951839a21 Author: kngott Date: Thu Jul 25 17:19:35 2019 -0700 OverlapMask on the GPU. Src/Base/AMReX_MultiFab.cpp commit 20cbb7918fe81c73c7e76fd4696dfb15e7512b26 Author: Andrew Myers Date: Thu Jul 25 20:15:09 2019 -0400 Should call device synchronize after initializing the random seeds Src/Base/AMReX_Utility.cpp commit 84bac46d82daf34a603c67da32aa7b92b7c9e97a Author: Andrew Myers Date: Thu Jul 25 20:03:59 2019 -0400 parmparse nstates and ndraw in the random number generation test Tests/GPU/RandomNumberGeneration/main.cpp commit fefbecacf3451023eb7c339ea65adbc9190800b4 Author: Brandon Runnels Date: Thu Jul 25 17:25:51 2019 -0600 wip - currently works but bottom solve is failing Tests/LinearSolvers/MultiComponent/MCNodalLinOp.H Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit 92426d391fb364dc36d7158ea23b7c07a19dcffd Author: Andrew Myers Date: Thu Jul 25 18:51:48 2019 -0400 don't need separate variables for host and device size of the state array Src/Base/AMReX_Utility.cpp commit f6878072146abb91622743a696be9579ea0e899b Author: Andrew Myers Date: Thu Jul 25 18:46:07 2019 -0400 remove unused function Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit b6144c1a856935bbbf4fb44d965311417ecffaea Author: Andrew Myers Date: Thu Jul 25 18:45:39 2019 -0400 some renaming Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 104941ce0790458165d431f8adc18c1ae9c1bdeb Author: Andrew Myers Date: Thu Jul 25 17:58:36 2019 -0400 some reorganization Src/Base/AMReX_Utility.cpp commit 48d8e73ab6d888cb1da5ea308c359131050447d7 Author: Andrew Myers Date: Thu Jul 25 17:51:36 2019 -0400 also use the locks in amrex::RandomNormal Src/Base/AMReX_Utility.cpp commit 9b37e151c0f4c6564fdec3c61ac333b5521f9698 Author: Andrew Myers Date: Thu Jul 25 17:50:31 2019 -0400 update random number gpu test Tests/GPU/RandomNumberGeneration/main.cpp commit fb743125b2c57909e045ac35cc53988aea603304 Author: Andrew Myers Date: Thu Jul 25 17:50:10 2019 -0400 also add a free_state function to release the lock Src/Base/AMReX_Utility.cpp commit 97deb3d982dc045de45ac8679c3e00500f39d5eb Author: Andrew Myers Date: Thu Jul 25 17:40:21 2019 -0400 use same nstates variable to keep track of both the random states and the lock array Src/Base/AMReX_Utility.cpp commit b176a9b0295f25af43493427edaa249f98218b30 Author: Andrew Myers Date: Thu Jul 25 17:39:20 2019 -0400 fix index bug in amrex::Random Src/Base/AMReX_Utility.cpp commit 4f997b2b3d21d43ec3e7afec6af63ce6c510d721 Merge: b92641b6d d5f5e0d49 Author: Andrew Myers Date: Thu Jul 25 14:37:57 2019 -0700 Merge pull request #532 from ChrisDeGrendele/gpu_rng Random number generation on gpus commit 5e4d505143599bc146512b129bee7bcca3322f0c Author: Brandon Runnels Date: Thu Jul 25 15:33:37 2019 -0600 re-committed with spurious files removed Tests/LinearSolvers/MultiComponent/MCNodalLinOp.H Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/Make.package Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit b92641b6d62a0103090be0c1ab375e24c7cd9dc5 Author: kngott Date: Wed Jul 24 14:19:09 2019 -0700 Remove hanging variable. Src/Base/AMReX_Utility.cpp commit bd15b5b613f9fe73b52b952160c780805fbd8852 Author: atmyers Date: Thu Jul 25 10:04:16 2019 -0700 change add command in build_and_deploy.sh build_and_deploy.sh commit e7e497568ad404a47cbff86b003bb04304eb0839 Author: Weiqun Zhang Date: Thu Jul 25 09:18:52 2019 -0700 fix c++ std flag when pgi is used as nvcc host compiler Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 2b9dcff39ab02780eb4acb86ca5432bdb2b88242 Author: Weiqun Zhang Date: Wed Jul 24 18:23:03 2019 -0700 fix id_rsa_travis path build_and_deploy.sh commit d5f5e0d4918f86250153e46e4a3d631f3fedd0cf Author: Chris DeGrendele Date: Wed Jul 24 17:26:56 2019 -0700 get_state should only be declared if we're using gpus Src/Base/AMReX_Utility.cpp commit 5e64ad21cce30f49c291b3d1fa6160af36c6a316 Author: Weiqun Zhang Date: Wed Jul 24 17:09:37 2019 -0700 move doc to AMReX-Codes.github.io build_and_deploy.sh commit b3edd79f132dfa2ee1ee7362c0833d4f7f5349be Author: Chris DeGrendele Date: Wed Jul 24 17:01:04 2019 -0700 fixed whitespaces Src/Base/AMReX_Utility.cpp commit 4272c1561aba4dd6e5d7940dc23f57a2ef6cb39c Author: Chris DeGrendele Date: Wed Jul 24 16:58:28 2019 -0700 fixed Src/Base/AMReX_GpuUtility.cpp commit 9a3e547ba272783a20dae4b44fcab94ee0df86d8 Author: Chris DeGrendele Date: Wed Jul 24 16:48:41 2019 -0700 Forgot }; Src/Base/AMReX_Utility.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit 487846a6915ad01fe424ee32ffe9ded5e07d75db Author: Chris DeGrendele Date: Wed Jul 24 16:42:15 2019 -0700 Tracer Particle GPU support Src/Base/AMReX_Utility.cpp Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particle_mod_K.H Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/launc_gpu.sh Tests/GPU/RandomNumberGeneration/main.cpp Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile commit 1c6f79eec6b419a1ef30dec9ae8b9d3ff87e3da9 Author: Chris DeGrendele Date: Wed Jul 24 16:28:59 2019 -0700 Random Number Generation on GPUs Src/Base/AMReX_GpuUtility.cpp Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/launc_gpu.sh Tests/GPU/RandomNumberGeneration/main.cpp Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit ff91d72b795de73129c27ba12e4974466208498a Author: Chris DeGrendele Date: Wed Jul 24 15:55:20 2019 -0700 one last thing Src/Base/AMReX_GpuUtility.H commit ac80f65870dafb78463457aae2089ce421772ce7 Author: Chris DeGrendele Date: Wed Jul 24 15:51:41 2019 -0700 removed more files Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Backtrace.0 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Backtrace.0 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/viz.py commit a9ab86ccf182afb110bcdc04a50985f76623a7c3 Author: Weiqun Zhang Date: Wed Jul 24 15:47:46 2019 -0700 trigger travis LICENSE commit b0713f29ce919b74b7df7e70073d62dd53447934 Author: Chris DeGrendele Date: Wed Jul 24 15:47:25 2019 -0700 Removed old func decleration Src/Base/AMReX_Utility.H commit 062d0bfcb04da34088914dbf38ef42b5714c19d3 Author: Chris DeGrendele Date: Wed Jul 24 15:44:22 2019 -0700 removed more unnecessary commits Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/out.txt Tests/GPU/Particles/Redistribute/Backtrace.0 Tests/GPU/RandomNumberGeneration/out.txt.REMOVED.git-id Tutorials/GPU/NeighborList/#MDParticleContainer.cpp# commit 4b857626a1706e60fdca133b8e6693276c6de288 Author: Chris DeGrendele Date: Wed Jul 24 15:40:17 2019 -0700 Deleted accidental pushes Src/Base/#AMReX_FArrayBox.H# Src/Base/#AMReX_FArrayBox.cpp# Src/Base/#AMReX_GpuUtility.cpp# Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/AMReX_TracerParticles.cpp Src/Particle/out.txt Tests/GPU/Particles/Redistribute/Backtrace.0 Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/launc_gpu.sh Tests/GPU/RandomNumberGeneration/main.cpp Tests/GPU/RandomNumberGeneration/out.txt.REMOVED.git-id Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000.REMOVED.git-id Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_D_00000.REMOVED.git-id Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_D_00000.REMOVED.git-id Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_H Tutorials/GPU/NeighborList/#MDParticleContainer.cpp# Tutorials/Particles/NeighborList/Backtrace.0.0 commit 3ccab6c251411e9e2a1680fc2c4c6692626bcda4 Author: Chris DeGrendele Date: Wed Jul 24 15:33:02 2019 -0700 Merged back into Random() funct Src/Base/AMReX_Utility.cpp commit 70bf151be40210a3e0e8840ddcb7274b29c3474c Merge: b36efca32 d12f632ee Author: Chris DeGrendele Date: Wed Jul 24 15:22:36 2019 -0700 synced with no devicevector version commit 589f976befb551cdfa7aeafd32c328504cedf060 Author: Andrew Myers Date: Wed Jul 24 17:54:15 2019 -0400 just do construction of the map on the CPU Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleBufferMap.cpp commit 78e25e62096f5f44f823dddef41d39be2e168ede Merge: e10e02ee5 d12f632ee Author: Weiqun Zhang Date: Wed Jul 24 14:46:27 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b36efca325aec4dd1bb059f74050cd16d89f7ed8 Author: Chris DeGrendele Date: Wed Jul 24 14:36:25 2019 -0700 GPU random number generation Src/Base/AMReX_Utility.cpp commit d12f632ee38cf8434f3ec0cc9fa7fc3570de7246 Author: jmsexton03 Date: Wed Jul 24 14:13:37 2019 -0700 Update run.summit w/1 resource set per GPU comment Tutorials/GPU/run.summit commit 0c3303e6ea5d58fcc6aa47784219b65b8c4ca41e Author: Andrew Myers Date: Wed Jul 24 16:49:50 2019 -0400 forgot to add these files Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleBufferMap.cpp commit a2601327fbb228e91e9ebcd88a7e42f08aa6f738 Author: Andrew Myers Date: Wed Jul 24 16:49:18 2019 -0400 some tweaks to the ParticleBufferMap class Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tests/Particles/NeighborParticles/script.sh commit 0c2f3fa94b423031262db8fec65624f38508beb0 Author: Andrew Myers Date: Wed Jul 24 15:22:24 2019 -0400 reorganize some of the recent changes to the neighbor particle code Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit cc3ac385c34404fcaed3d978b414ef6080ab733d Author: Andrew Myers Date: Wed Jul 24 13:57:21 2019 -0400 remove commented code Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit f40b3d76d511b8bdd1b1232b1be92586ce4ab923 Author: Andrew Myers Date: Wed Jul 24 13:56:53 2019 -0400 some cleanup in BuildRedistributeMask Src/Particle/AMReX_ParticleContainerI.H commit e334d63cfbc03436a2237235416c7c9232bee53a Author: Brandon Runnels Date: Wed Jul 24 11:16:20 2019 -0600 implementing nodal multicomponent mlmg test Tests/LinearSolvers/MultiComponent/Make.package Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit 915745d6cf21b17b361e986fb45e42351a5dde65 Author: kngott Date: Tue Jul 23 16:57:39 2019 -0700 MultiFab functions test. Tests/GPU/ScratchPad/GNUmakefile Tests/GPU/ScratchPad/inputs_3d Tests/GPU/ScratchPad/main.cpp commit eaa9c05bf70db0f7bfca47835f667efba5902f09 Author: kngott Date: Tue Jul 23 16:57:06 2019 -0700 Self-dot and updated MultiFab::norm2 function. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit d1aa84f93b0220fff36ae9d6679cccaea8dd693d Author: Andrew Myers Date: Tue Jul 23 19:41:37 2019 -0400 remove this unit test, as it has been rolled into the other one Tutorials/GPU/NeighborParticlesUnitTest/CMakeLists.txt Tutorials/GPU/NeighborParticlesUnitTest/CheckPair.H Tutorials/GPU/NeighborParticlesUnitTest/Constants.H Tutorials/GPU/NeighborParticlesUnitTest/GNUmakefile Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborParticlesUnitTest/Make.package Tutorials/GPU/NeighborParticlesUnitTest/README.md Tutorials/GPU/NeighborParticlesUnitTest/inputs Tutorials/GPU/NeighborParticlesUnitTest/main.cpp Tutorials/GPU/NeighborParticlesUnitTest/script.sh commit 1840541e0deb27039dbcdb373d3977e2ad0ff7e1 Merge: 23c6a180b d0f607e88 Author: Andrew Myers Date: Tue Jul 23 19:37:37 2019 -0400 Merge branch 'development' into mfix_hackathon commit d0f607e88f5f30def91d358882f5f65541c642d9 Merge: 2352c6302 859eb6ffc Author: Andrew Myers Date: Tue Jul 23 19:36:54 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2352c6302c3968b2f5761f7df2acb86d3906d201 Author: Andrew Myers Date: Tue Jul 23 19:36:42 2019 -0400 remove use of thrust vector as global variable Src/Base/AMReX_Utility.cpp commit 23c6a180b47d3f24f1526075bd46ad809e8a641d Author: Andrew Myers Date: Tue Jul 23 18:43:39 2019 -0400 move test to Tests Tests/Particles/NeighborParticles/CMakeLists.txt Tests/Particles/NeighborParticles/CheckPair.H Tests/Particles/NeighborParticles/Constants.H Tests/Particles/NeighborParticles/GNUmakefile Tests/Particles/NeighborParticles/MDParticleContainer.H Tests/Particles/NeighborParticles/MDParticleContainer.cpp Tests/Particles/NeighborParticles/Make.package Tests/Particles/NeighborParticles/README.md Tests/Particles/NeighborParticles/inputs Tests/Particles/NeighborParticles/main.cpp Tests/Particles/NeighborParticles/script.sh commit e0405fad2b9a08832f11edd080c221e57cc8091d Author: Andrew Myers Date: Tue Jul 23 18:41:02 2019 -0400 consolidate and reorganize test Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/inputs Tutorials/GPU/NeighborListUnitTest/main.cpp Tutorials/GPU/NeighborListUnitTest/script.sh commit 39717e44261a6231ae8fcaf6087048482e3a414c Author: Andrew Myers Date: Tue Jul 23 18:14:08 2019 -0400 use the wrapped version of exclusive_scan Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Tutorials/GPU/NeighborParticlesUnitTest/script.sh commit 6d17024fdbc65162e6710404cf111215394e5a38 Author: Andrew Myers Date: Tue Jul 23 18:11:15 2019 -0400 modify print statements in test Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/main.cpp commit 45bc81f1af301de472b0a2df76955182798b0565 Author: Andrew Myers Date: Tue Jul 23 17:35:07 2019 -0400 compute num_copies in a cleaner way Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 0e9f709bbb9f1750db1fb1973930c7ca93ca65b3 Author: Andrew Myers Date: Tue Jul 23 17:14:54 2019 -0400 std::cout -> amrex::Print() Tutorials/GPU/NeighborListUnitTest/main.cpp commit 14fcb8d8c3aed51dee5848ff331ad81236c2953f Author: Andrew Myers Date: Tue Jul 23 17:14:18 2019 -0400 fix rcv buffer offset calculation Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit f7e851b3bfee7e6650d9b1ac1b7c1fe2d0c84b23 Author: Andrew Myers Date: Tue Jul 23 16:32:12 2019 -0400 remove some now unused functions Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit af9ef562b21f87749ed5e62f216a43768c5dff19 Author: Andrew Myers Date: Tue Jul 23 16:15:55 2019 -0400 fix timer name Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 13e37ae058d2c8a9adb78097889c047882118df0 Author: Andrew Myers Date: Tue Jul 23 16:15:34 2019 -0400 this doesn't need to be a member Src/Particle/AMReX_NeighborParticles.H commit 31cb3ca14db3de30356471c209e763e452acc6e0 Author: Andrew Myers Date: Tue Jul 23 16:07:09 2019 -0400 put this operator in the amrex namespace so amrex::Print() can find it Tutorials/GPU/NeighborListUnitTest/main.cpp commit 5cf139eb7bee03bb8390edf4ea0a5a9fef03bc6d Author: Andrew Myers Date: Tue Jul 23 15:38:46 2019 -0400 fix mpi neighbor particle test Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 808ba1f747681e7d49cf4d87d0e1dad9e2e8a89b Author: Andrew Myers Date: Tue Jul 23 13:50:29 2019 -0400 modify some prints Tutorials/GPU/NeighborListUnitTest/main.cpp commit e3202f1dbc0ae441311e178d6fde0def28da9b9a Author: Andrew Myers Date: Tue Jul 23 13:49:52 2019 -0400 some work towards fixing the MPI portion of updateNeighbors... almost right now. Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit a705898c8c62528e9042be48cae3ac87c13bde44 Author: Andrew Myers Date: Tue Jul 23 13:23:18 2019 -0400 templated overload of << for pair Tutorials/GPU/NeighborListUnitTest/main.cpp commit 08c988e301fd0bada0dbfcc416ab27424d449364 Author: Andrew Myers Date: Tue Jul 23 13:22:58 2019 -0400 modify test to compare both min and max of the inter-particle spacing Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit dde9e1aac8f2b0c649887babddf47b2839086a1c Author: Andrew Myers Date: Mon Jul 22 20:20:08 2019 -0400 some work on debugging parallel Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit e10e02ee55f12a447b2275d2e074b43febf6248c Author: Weiqun Zhang Date: Mon Jul 22 15:23:53 2019 -0700 fix the fix that tried to remove hardwired warp size Src/Base/AMReX_FabArrayUtility.H commit 859eb6ffceb13b4c2cc12ba6beb9493571039fb8 Merge: 197237e1d c8ba1d76e Author: Weiqun Zhang Date: Mon Jul 22 11:20:13 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 197237e1da0c3d0dd0e2259aac5c19ddbfb32999 Author: Weiqun Zhang Date: Mon Jul 22 11:19:55 2019 -0700 add compiler generated move for AmrMesh and AmrCore Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrMesh.H commit c8ba1d76e81faa171240aa6fe964da707deb422e Merge: 232e0ae7d 1da27415a Author: WeiqunZhang Date: Mon Jul 22 09:45:52 2019 -0700 Merge pull request #527 from Alpine-DAV/task/2019_07_blueprint_updates bugfixes for conduit blueprint support commit b64c1b73e986ccf03ebb01e96ddf3785887a18a6 Author: Ann Almgren Date: Sun Jul 21 16:07:07 2019 -0700 Fix spelling so 'git grep' searches will find the right thing Src/Particle/AMReX_ParticleContainerI.H commit 232e0ae7d99e444c2b35248baf80811ddb8c6888 Merge: 9e24752ba 6614b20ab Author: mic84 Date: Fri Jul 19 18:28:39 2019 -0700 Merge pull request #526 from rupertnash/development CMake install step: make header modification more cross-platform commit 9e24752ba5124c0cd0fdb333dd48626325b116a4 Merge: d78cd92f0 07679922a Author: Weiqun Zhang Date: Fri Jul 19 16:22:21 2019 -0700 Merge branch 'hackathon' into development commit 79c526b1a18bd913e98027f6800355ba82b9e788 Merge: bdd0c8ec8 9446d4139 Author: Andrew Myers Date: Fri Jul 19 14:45:37 2019 -0400 Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon commit bdd0c8ec8826490ec663e426778b3395fb304026 Author: Andrew Myers Date: Fri Jul 19 14:45:06 2019 -0400 need to change where we are setting the number of neighbors from the remotes Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 1da27415ab0ec9135e38e3c63a7e93076a988ac1 Author: Cyrus Harrison Date: Fri Jul 19 10:11:31 2019 -0700 clarify comment Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp commit 07679922a86d4ab0c5df370afdb9c2464b519b47 Merge: aeb0059e3 0c0b033cf Author: Weiqun Zhang Date: Fri Jul 19 09:19:54 2019 -0700 Merge branch 'weiqun/hackathon' into hackathon commit aeb0059e3a91a80058bf2b106fdee77c70750510 Merge: 7d1d31ed3 e8c9afeaa Author: Weiqun Zhang Date: Fri Jul 19 09:18:59 2019 -0700 Merge branch 'hackathon' of github.com:AMReX-Codes/amrex into hackathon commit 7d1d31ed3665381deae2c2e9451f2ae4cfd33de8 Author: Weiqun Zhang Date: Fri Jul 19 06:23:21 2019 -0700 libamrex: move AMReX_Config.H inside include guard Tools/GNUMake/Make.rules commit 6614b20ab8eb39a9c031658ad3c2a25b9d9e0fdb Author: Rupert Nash Date: Fri Jul 19 14:26:19 2019 +0100 insert include AMReX_Config.H within include guard Tools/CMake/modify_installed_headers.cmake commit 73ab017b410e628587fe6d89b3d74e3e58bc9624 Author: Rupert Nash Date: Fri Jul 19 13:17:57 2019 +0100 make header modification use cmake to be more cross-platform Tools/CMake/modify_installed_headers.cmake commit 19c01e9bb8cd8844c06bdb28611fb1b78bbcaf20 Author: Andrew Myers Date: Fri Jul 19 03:41:19 2019 -0400 some towards fixing the mpi Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 4df2382d0d22fb76df19d1855e896eebdb5f626d Author: Andrew Myers Date: Thu Jul 18 19:41:52 2019 -0400 exchange the total number of rcv bytes Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 3fc1981e2a23a08396161b602893e3bc1cb0e2cc Author: Andrew Myers Date: Thu Jul 18 19:08:15 2019 -0400 fix proc_box_offsets Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 2bf381b70b3dd7147f680b6c1ac02a1fc9f4d380 Author: Andrew Myers Date: Thu Jul 18 18:41:37 2019 -0400 taking out a print statement Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 29f650fd1f6daad25d2f1001864b8efb3b894735 Author: Andrew Myers Date: Thu Jul 18 18:38:44 2019 -0400 computing proc ids and offsets Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 6d7f264dcdd6b652774fe243e737b0a7b1c641bd Author: Andrew Myers Date: Thu Jul 18 17:53:19 2019 -0400 pack particles into the send buffer such that all the boxes bound for the same proc id are together Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 9d6195416542bcb90cdc1e7b3fe7c2a792478937 Author: Andrew Myers Date: Thu Jul 18 17:25:54 2019 -0400 don't need to do any communication to figure out which procs sent what boxes to me Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 02510d342e077bf1e69c90624b0d05f618f14ba6 Author: Andrew Myers Date: Thu Jul 18 16:46:18 2019 -0400 a test getBoxRcvCounts function Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 9446d413967fd8ceab2f9bc0c35e743a5a0f2e11 Author: Ann Almgren Date: Thu Jul 18 09:54:55 2019 -0400 Fix printing so that we only print off the processor that owns grid 0 Tutorials/GPU/NeighborListUnitTest/main.cpp commit 0b7911edd34bec37f899038276ef55adc67de476 Merge: 3b44c3fc7 b7005481e Author: Ann Almgren Date: Thu Jul 18 09:45:15 2019 -0400 Merge branch 'mfix_hackathon' of https://github.com/amrex-codes/amrex into mfix_hackathon Conflicts: Tutorials/GPU/NeighborList/main.cpp commit 3b44c3fc7199ff8540a1b9cd01e454f4f06efe6d Author: Ann Almgren Date: Thu Jul 18 09:34:42 2019 -0400 Slight clean-up of main Tutorials/GPU/NeighborList/main.cpp commit b7005481e8bc9cd77f9ac87284df3bafb2a2cffb Author: Andrew Myers Date: Thu Jul 18 00:05:12 2019 -0400 also look at particle positions in the neighbor list test Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/main.cpp commit 485da8fce65f49df64bd3f716c946f7528ce6bbe Author: Andrew Myers Date: Wed Jul 17 23:31:02 2019 -0400 change some printing behavior Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp commit 9bffc48ef18149b09afc47938be6c97e8f1d1b38 Author: Andrew Myers Date: Wed Jul 17 23:21:05 2019 -0400 add a final call to redistribute Tutorials/GPU/NeighborList/main.cpp commit 5eb842f205f07210d8853e4491732c7c0cf10bba Author: Andrew Myers Date: Wed Jul 17 23:12:38 2019 -0400 don't print min dist unless requested Tutorials/GPU/NeighborList/main.cpp commit 785bf3aee1d20bb7c6d432d4469d11cb6151dbe4 Author: Andrew Myers Date: Wed Jul 17 23:10:31 2019 -0400 don't print the neighbor list unless requested Tutorials/GPU/NeighborList/main.cpp commit e8c9afeaa55f8d92c6b4b058f4e4cfd40a653b37 Author: kngott Date: Wed Jul 17 17:40:13 2019 -0700 Fix summit script flags for CUDA aware MPI. Tutorials/GPU/run.summit commit 71aa55e15e031c74c683578896d035b6c27b8259 Merge: 88e7d6d82 386316a19 Author: Andrew Myers Date: Wed Jul 17 19:31:45 2019 -0400 merging. commit 88e7d6d829dfab05638c7fff7795fc726183e48d Author: Andrew Myers Date: Wed Jul 17 19:26:25 2019 -0400 modify inputs for neighbor list test Tutorials/GPU/NeighborListUnitTest/inputs commit cfa7f01190358c79f0e9ef6a09c723b401f3ea09 Author: Andrew Myers Date: Wed Jul 17 19:24:30 2019 -0400 missed a box offset Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 386316a1975998f7efc8898d8f472a61fde9b9b8 Author: Ann Almgren Date: Wed Jul 17 19:16:13 2019 -0400 This has the CPU version of the checkParticles() version -- it gives the "correct" answer with 1 MPI process but not with 2 MPI processes. Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit 016c227e5f1ff8cc603bd9a45882042f66c4e2fd Author: Andrew Myers Date: Wed Jul 17 18:44:57 2019 -0400 src -> dst Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 8e1248ab3964690acfdda6f7ffd68872d6bae3b9 Author: Andrew Myers Date: Wed Jul 17 18:29:11 2019 -0400 implement update and Fill in terms of the new halo functions Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 383f42fdf2c8af74850fcd256d9ea4f8a2650119 Author: Ann Almgren Date: Wed Jul 17 18:19:08 2019 -0400 We need to explicitly call the sychronize before printing Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit 1e34d2491abb8ad747e882b13808890340671453 Author: Ann Almgren Date: Wed Jul 17 18:16:07 2019 -0400 Don't try to access "mine" when it's not actually set Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit 01ed6c451ea5464f48be0c5f60de7662ff7fc135 Author: Ann Almgren Date: Wed Jul 17 18:12:41 2019 -0400 Actually lets use num_ppc = 1 Tutorials/GPU/NeighborListUnitTest/inputs commit 5b7e43e25f8ba4b7e7406c4178f8318c44c9a4ba Author: Ann Almgren Date: Wed Jul 17 18:12:08 2019 -0400 This is the inputs for this test Tutorials/GPU/NeighborListUnitTest/inputs commit 32fdf9d64799fc187a7749d8c4f1a8bca659c428 Author: Ann Almgren Date: Wed Jul 17 18:10:53 2019 -0400 Change the print statements to work in parallel Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit 9b9a7a4935badfda570aa11c2de798a0a03d7f7b Author: Weiqun Zhang Date: Wed Jul 17 15:08:26 2019 -0700 add optional shared memory to ParallelFor Src/Base/AMReX.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H commit fa3ca1809b7101c5b587069fbd9209ea227c735d Author: Andrew Myers Date: Wed Jul 17 17:15:21 2019 -0400 remove commented out code Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 5850e5d5d93923ab7551aa1c70cc51c5bba1c22b Author: Ann Almgren Date: Wed Jul 17 17:03:18 2019 -0400 This does all the testing on CPU even when the neighbor list is built on GPU. Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborParticlesUnitTest/inputs Tutorials/GPU/NeighborParticlesUnitTest/main.cpp commit 9e6db163057d4baf998ef915703278b5d4ac52b0 Merge: a6ae2f9b6 9477744c5 Author: Andrew Myers Date: Wed Jul 17 16:58:19 2019 -0400 Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon commit a6ae2f9b6814cd3d8a611b5f469b9d005acfbcfa Author: Andrew Myers Date: Wed Jul 17 16:56:48 2019 -0400 apply periodic when packing the buffer Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit d9676a13a449a4015f165102571cfd7308b8f273 Author: Andrew Myers Date: Wed Jul 17 16:43:41 2019 -0400 compute the dst indices correctly Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 87667c5376faa0d4338d0008e8b1f7c3bda286ee Author: Andrew Myers Date: Wed Jul 17 16:14:09 2019 -0400 don't reset the counters inside the mfiter loop to sort the snd buffer by destination only Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 2c1c5730a0883c077196cf4a688afae4a9e23e45 Author: Andrew Myers Date: Wed Jul 17 15:43:58 2019 -0400 implement pack and unpack Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 9477744c5ac0f4675131f740ba490e31a560c8c2 Author: Ann Almgren Date: Wed Jul 17 15:00:45 2019 -0400 New unit test for testing BuildNeighborList which creates particle-neighbor lists Tutorials/GPU/NeighborParticlesUnitTest/CMakeLists.txt Tutorials/GPU/NeighborParticlesUnitTest/CheckPair.H Tutorials/GPU/NeighborParticlesUnitTest/Constants.H Tutorials/GPU/NeighborParticlesUnitTest/GNUmakefile Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborParticlesUnitTest/Make.package Tutorials/GPU/NeighborParticlesUnitTest/README.md Tutorials/GPU/NeighborParticlesUnitTest/inputs Tutorials/GPU/NeighborParticlesUnitTest/main.cpp Tutorials/GPU/NeighborParticlesUnitTest/script.sh commit 932fe23eecec65f070a5747bb94a78c3fac3e682 Author: Andrew Myers Date: Wed Jul 17 15:00:45 2019 -0400 resize the snd_buffer to the appropriate size Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 19a0b0ed02f5479de4425fc7515f12e98eaef877 Author: Cyrus Harrison Date: Wed Jul 17 11:45:38 2019 -0700 fix export of blueprint files for mult-domain, fix wrapping of multiple fields, add cycle info Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp commit 1916c22ca09ab274579d393ad7bebf01458a18c4 Author: Andrew Myers Date: Wed Jul 17 14:34:37 2019 -0400 handle periodicity; compute box counts and offsets Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 9a0221ac14aff30471aaecfac89475d5b0eef4b5 Author: Andrew Myers Date: Wed Jul 17 14:10:54 2019 -0400 seperate out computing the halo particles and computing the copy plan Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit d78cd92f07f4649d72e6f52726448333d2c06ce9 Author: Max Katz Date: Wed Jul 17 10:56:44 2019 -0700 Add option to change _device suffix for GPU pragma Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 4f96c55d54f20c94b1b86fd73697830fdc712379 Author: Max Katz Date: Wed Jul 17 10:01:13 2019 -0700 Add pragma gpu option to disable host version Tools/F_scripts/write_cuda_headers.py commit 538516fedb6d31e87dc89b853497beb6bac2c155 Author: Max Katz Date: Tue Jul 16 23:15:02 2019 -0700 Allow PGI -gopt to be disabled Tools/GNUMake/comps/pgi.mak commit d118719c6105c3aa6edcf1560608534b412cf12a Author: Andrew Myers Date: Wed Jul 17 01:09:24 2019 -0400 some work towards reimplementing neighbor particle communication Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit f9886599367e36f0631fb7ad233cb7540d4e9988 Author: Ann Almgren Date: Tue Jul 16 20:43:48 2019 -0400 New unit test for FillNeighbors and UpdateNeighbors Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/README.md Tutorials/GPU/NeighborListUnitTest/main.cpp commit b2a4a785abbf720c7a8dd200af9ac3c36be5257b Author: Ann Almgren Date: Tue Jul 16 19:14:11 2019 -0400 add inputs Tutorials/GPU/NeighborListUnitTest/inputs commit c19c1d299b12e71f76f82848f41aa83d9ed31e8f Author: Ann Almgren Date: Tue Jul 16 19:13:55 2019 -0400 Starting point for new unit test Tutorials/GPU/NeighborListUnitTest/CMakeLists.txt Tutorials/GPU/NeighborListUnitTest/CheckPair.H Tutorials/GPU/NeighborListUnitTest/Constants.H Tutorials/GPU/NeighborListUnitTest/GNUmakefile Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/Make.package Tutorials/GPU/NeighborListUnitTest/main.cpp Tutorials/GPU/NeighborListUnitTest/script.sh commit 786fc90640c1296b5706918ba50b4b540fffddb4 Author: Max Katz Date: Tue Jul 16 14:52:44 2019 -0700 Add attributes(host) attributes(device) macro Tools/GNUMake/Make.defs commit a2985282547946c04f283059e3851badfe43f247 Author: Ann Almgren Date: Tue Jul 16 16:45:15 2019 -0400 Add run-time option to control whether we compute and print the minimum distance between particles Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp commit 5146e6000f14460ff40d1fa4f9c1a2da2a8ed052 Merge: 0a93f84d6 adee7bfc3 Author: Ann Almgren Date: Tue Jul 16 15:39:57 2019 -0400 Merge branch 'mfix_hackathon' of https://github.com/amrex-codes/amrex into mfix_hackathon Conflicts: Tutorials/GPU/NeighborList/main.cpp commit 0a93f84d61cf8eb16cd85c2443020dc89d68e2c8 Author: Ann Almgren Date: Tue Jul 16 15:38:24 2019 -0400 Update this GPU neighborlist tutorial to make it closer to the MFiX-Exa conditions (2.5 particle diameters per grid cell, for example) Tutorials/GPU/NeighborList/Constants.H Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/README.md Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp commit 13b74f310ba57155ca4232e7e006ddd918b31c9e Author: Johannes Blaschke Date: Tue Jul 16 11:40:32 2019 -0700 need to skip ebfacets that coincide with cell boundaries when looking for eb-facet edges Src/EB/AMReX_EB_geometry.F90 commit adee7bfc36aee81fd874f40e5dcc319cebfc8a0c Author: Andrew Myers Date: Tue Jul 16 14:14:42 2019 -0400 remove extra set acceleration to 0.0 Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit ab0138277d631809acd913676fd56980e5ec2439 Merge: 39552f356 9b053eae7 Author: Andrew Myers Date: Tue Jul 16 13:56:40 2019 -0400 Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon commit 39552f356b1e40dea2b6f189eac9d6152581338d Author: Andrew Myers Date: Tue Jul 16 13:55:53 2019 -0400 add some more sanity checking Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 9b053eae7663180981a6f2bc667dcb5add786fb8 Author: Michele Rosso Date: Tue Jul 16 13:46:17 2019 -0400 Make dt an input parameter and set it to a reasonable default value Tutorials/GPU/NeighborList/main.cpp commit 58cd5c3ef3ffdcb4eb318ae91d17bd10a32ede2d Author: Weiqun Zhang Date: Tue Jul 16 10:04:35 2019 -0700 return -1 as mask if particle id is negative Src/Particle/AMReX_Functors.H Src/Particle/AMReX_ParticleContainerI.H commit 370ec1588ebf24c3a24936acd6cb5eec30dd42ea Author: Weiqun Zhang Date: Tue Jul 16 06:58:25 2019 -0700 add a new version of RealBox::contains Src/Base/AMReX_RealBox.H commit d238ef120f5c070be6eea1add0493457d426c5c2 Author: Andrew Myers Date: Tue Jul 16 04:05:14 2019 -0400 tweak inputs Tutorials/GPU/NeighborList/inputs commit 03dad45b6ad1e8984bb35532ab7973d7d5fc3133 Author: Andrew Myers Date: Tue Jul 16 04:05:01 2019 -0400 print out an error metric Tutorials/GPU/NeighborList/main.cpp commit ae7588123b75fc877a2d7a4213de8df2eaba9e00 Author: Andrew Myers Date: Tue Jul 16 04:04:29 2019 -0400 function to print out the min distance between particles over the whole simulation Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 066138910044c6ff4ca9041af556941b0ad4e20f Author: Andrew Myers Date: Tue Jul 16 04:03:58 2019 -0400 tweak CheckPair Tutorials/GPU/NeighborList/CheckPair.H commit 7132148a28752f76791dd58e858333e33ae44681 Author: Andrew Myers Date: Tue Jul 16 03:06:53 2019 -0400 fix typo Tutorials/GPU/NeighborList/main.cpp commit c2c41c540efd703cf61a45d8537f74d180a5f607 Author: Andrew Myers Date: Tue Jul 16 03:04:04 2019 -0400 parmparse rebuild int and num_ppc Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp commit a48ebe553c49af9fd273cd950b86103efda2bf3d Author: Andrew Myers Date: Mon Jul 15 20:59:25 2019 -0400 need to clear the neighbors before we re-generate the halo information Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit f54514166c4e5dc97fddbad0d74d5efe17e192f6 Author: Michele Rosso Date: Mon Jul 15 17:22:13 2019 -0700 CMake: always link to Threads Src/Base/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in commit eba7f955061fab67c41b981ee01301142f479fff Author: Andrew Myers Date: Mon Jul 15 17:47:29 2019 -0400 only count real particles Src/Particle/AMReX_ParticleContainerI.H commit 13a17a585292be5e3b0736d5e0e3f62fa7f670fa Author: Andrew Myers Date: Mon Jul 15 17:28:55 2019 -0400 don't include neighbor particles in ascii files Src/Particle/AMReX_ParticleContainerI.H commit a6d2a742ad5fdd47d3bb37fa5a61588abd760081 Merge: 5f4d2b389 243a3c6ca Author: Ann Almgren Date: Mon Jul 15 15:05:25 2019 -0400 Merge branch 'mfix_hackathon' of https://github.com/amrex-codes/amrex into mfix_hackathon commit 5f4d2b389e6ef8298bd113c6474b7325ab8464f4 Author: Ann Almgren Date: Mon Jul 15 15:04:19 2019 -0400 Add flag to allow nvprof to work on ascent. Tutorials/GPU/NeighborList/script.sh commit 243a3c6cab645ee1a7e5742a31a78b98ed67a5a0 Merge: 32a2aaf4a 19e29493e Author: Andrew Myers Date: Mon Jul 15 14:50:48 2019 -0400 Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon commit 19e29493e6348e6853f1bec710aaabcbde2feb2e Author: Oscar Luis Antepara Zambrano Date: Mon Jul 15 14:49:23 2019 -0400 Increasing the number of particles by 8 per cell Tutorials/GPU/NeighborList/main.cpp commit 4e7ccb1bdb320ab695fbc4dfbe459c821dcb26d1 Author: Oscar Luis Antepara Zambrano Date: Mon Jul 15 14:43:58 2019 -0400 adding a print statement for number of particles generated Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 32a2aaf4a12accc3498585776b5ae97d770f8e80 Author: Andrew Myers Date: Mon Jul 15 14:38:56 2019 -0400 rebuild the neighbor list every 25 time steps Tutorials/GPU/NeighborList/main.cpp commit df8cd54cd1c759a70b7d9dc70134594c78afcbfe Author: Oscar Luis Antepara Zambrano Date: Mon Jul 15 14:30:30 2019 -0400 adding a print statement for number of particles generated Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit e70516e242b243a94124548bb11895505829eda4 Author: Andrew Myers Date: Mon Jul 15 12:17:43 2019 -0400 adding a run script for the hackathon Tutorials/GPU/NeighborList/script.sh commit 0c0b033cf9a643fe46b25d4f2866ae224e8b978a Author: Weiqun Zhang Date: Mon Jul 15 09:00:36 2019 -0700 check for nullptr after malloc Src/Base/AMReX_Arena.cpp commit bb8717ca509171aab238ff2c4a78f446a67c77c0 Author: Johannes Blaschke Date: Sun Jul 14 22:40:17 2019 -0700 ooops... forgot this Src/EB/AMReX_EB_levelset_F.F90 commit 2ba32709ff6512e441dcf23d9af772043d881467 Author: Johannes Blaschke Date: Sun Jul 14 22:34:10 2019 -0700 fix off-by-epsilon error when filling level-set Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset_F.F90 commit 106298c8779289554cc515490b42df8db3cc104e Author: Weiqun Zhang Date: Sun Jul 14 12:53:18 2019 -0700 replace usleep with std::this_thread::sleep_for Src/Base/AMReX_VisMF.cpp commit 162b38449b4415c865b6b346f593444db218e2cf Author: Weiqun Zhang Date: Sun Jul 14 07:07:32 2019 -0700 get around Cray Src/Particle/AMReX_ParticleContainerI.H commit e1d345f957b63f95036fc8e3dcecd634bcb3de1f Author: Weiqun Zhang Date: Sat Jul 13 22:41:47 2019 -0700 fix for Cray Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit acd2980959a7333476020293233e6085100603d4 Author: Weiqun Zhang Date: Sat Jul 13 21:47:21 2019 -0700 fix a number of warnings Src/EB/AMReX_EB2_IF_Cylinder.H Src/EB/AMReX_EB2_IF_Scale.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7ed1a9fc3e46493fa5dcbef2e7a78fd18013d95b Author: Weiqun Zhang Date: Sat Jul 13 21:16:43 2019 -0700 remove old fortran amrex_eb2_build_cells Src/EB/AMReX_EB2_F.H Src/EB/AMReX_eb2_3d.F90 commit 45e1900aadb3815ba391de8894e166d1099bf25e Author: Weiqun Zhang Date: Sat Jul 13 21:14:49 2019 -0700 wrong move Src/EB/AMReX_EB_LSCoreBase.cpp commit 56edcd3dfd9bc07da900abbef13e662fdccd91df Author: Weiqun Zhang Date: Sat Jul 13 20:34:13 2019 -0700 fix bug in a new IOProcessor function Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_VisMF.cpp commit 2b738f916ad72783d96b21bd2d034c9148ba1f8d Author: Weiqun Zhang Date: Sat Jul 13 20:29:00 2019 -0700 clean up Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H commit b5f83484f54b514d6fb157694820e75bee4e9340 Author: Weiqun Zhang Date: Sat Jul 13 19:44:45 2019 -0700 add a default constructor to DataDeleter Src/Base/AMReX_BaseFab.H commit 0c1494e8e38c7a3a6baf235753ff89967adfcf21 Merge: 5becd01bb 07347b918 Author: Weiqun Zhang Date: Sat Jul 13 18:11:12 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5becd01bb2503a4e62d2e819293a313b17eb21a4 Author: Weiqun Zhang Date: Sat Jul 13 18:10:50 2019 -0700 minor. std::async already creates a temporary in its internal buffer, so it's safe to use const& Src/Base/AMReX_VisMF.cpp commit 07347b918d85ecffb05a71c7d3dc3bd5c3a5ad7c Merge: 147989685 43d7f2974 Author: atmyers Date: Sat Jul 13 17:12:21 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 147989685819bc32fb85780becdd1f88fc802c8f Author: atmyers Date: Sat Jul 13 17:12:09 2019 -0700 add remaining reduction operations (logical and and logical or) Src/Particle/AMReX_ParticleUtil.H commit 43d7f29740f89d54a3b5ab9e06f5c6a52bc3e55c Author: Weiqun Zhang Date: Sat Jul 13 13:45:16 2019 -0700 WriteAsync: tweak sleep time Src/Base/AMReX_VisMF.cpp Tests/VELOC/multifab/main.cpp commit 7928f0ad5fc19f04925196c0ea565017e34fdca8 Author: Weiqun Zhang Date: Sat Jul 13 10:28:14 2019 -0700 collect WriteAsyn status Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Tests/VELOC/multifab/main.cpp commit cf23bba6b455853b06a020493b08962929093e30 Author: Weiqun Zhang Date: Fri Jul 12 21:01:22 2019 -0700 make sure AMREX_CXX_* is properly included Src/Base/AMReX_TypeTraits.H commit 2d050a22e8a6942e1de41284d5baf0f6ace286f7 Merge: 5c84569d6 c3e1f4a1e Author: WeiqunZhang Date: Fri Jul 12 19:17:32 2019 -0700 Merge pull request #518 from eschnett/development Avoid warning about (safely) uninitialized variable commit c3e1f4a1e0171c7715bd01bcec76e76ed045d70b Author: Erik Schnetter Date: Fri Jul 12 21:34:19 2019 -0400 Avoid warning about (safely) uninitialized variable Src/Base/AMReX_FabArrayCommI.H commit 5c84569d61b5b09c29fdbb1e4ba27ecf910f799e Merge: ce92ad203 5a81038f6 Author: Andrew Myers Date: Fri Jul 12 17:05:21 2019 -0700 Merge branch 'development' into particle_reductions commit ce92ad2038d82031b2cef0ad02ae38bdfdee73ad Author: Andrew Myers Date: Fri Jul 12 17:02:10 2019 -0700 fix copy/paste errors Src/Particle/AMReX_ParticleUtil.H commit f4333764982aa0131e9d906e88ae374ac5041693 Author: Andrew Myers Date: Fri Jul 12 16:57:26 2019 -0700 fix typo Src/Particle/AMReX_ParticleUtil.H commit 995ca68ad4cd9a4d847168e0604d0de96e2c6f91 Merge: c7c584478 37a894deb Author: Andrew Myers Date: Fri Jul 12 19:32:50 2019 -0400 Merge branch 'particle_reductions' of github.com:AMReX-Codes/amrex into particle_reductions commit 37a894debc921d16ef5cac1dcb3f162bae181192 Author: Andrew Myers Date: Fri Jul 12 16:33:37 2019 -0700 use decltype instead of extra template parameter Src/Particle/AMReX_ParticleUtil.H commit c7c584478e2a96e60f51f8052306a0998f8bf629 Author: Andrew Myers Date: Fri Jul 12 19:32:29 2019 -0400 fix typos Src/Particle/AMReX_ParticleUtil.H commit a472e4a65f8d94ae870dbc0b084ad80bbf1ceeb5 Author: Andrew Myers Date: Fri Jul 12 16:08:00 2019 -0700 simplifing Src/Particle/AMReX_ParticleUtil.H commit 05dfe296bddb445f2b22a7db6c9545d21d0c6c08 Author: Andrew Myers Date: Fri Jul 12 16:03:35 2019 -0700 also template on the lambda return type Src/Particle/AMReX_ParticleUtil.H commit e66431f8aa48286d370431750edf5c972f042c9b Author: Andrew Myers Date: Fri Jul 12 15:29:50 2019 -0700 add ReduceRealMax and ReduceRealMin functions as well. Src/Particle/AMReX_ParticleUtil.H commit 5a81038f625033708c2b3686f612a890e6f4b4b4 Author: Weiqun Zhang Date: Fri Jul 12 18:28:10 2019 -0400 fix for IBM compiler on summit that still use a very old gcc Src/Base/AMReX_Extension.H Src/Base/AMReX_TypeTraits.H commit 4a0bdbc0f4cb92ff1b607aad21a66be966883245 Author: Andrew Myers Date: Fri Jul 12 14:45:55 2019 -0700 add a ReduceRealSum for particle data Src/Particle/AMReX_ParticleUtil.H commit 18ae19a33f986c3a414ce26da318e744ea0c45a4 Merge: f9447aedd c99378b6b Author: Michele Rosso Date: Fri Jul 12 14:34:04 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f9447aeddb1f09543ac3ade8061f0f63458dbac2 Author: Michele Rosso Date: Fri Jul 12 14:33:42 2019 -0700 CMake: add pthreads to dependency list for non-MPI builds Src/Base/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in commit c99378b6b3d5716d018942e81f7b3acee510d5d9 Author: Weiqun Zhang Date: Fri Jul 12 14:30:06 2019 -0700 add -pthread to llvm Tools/GNUMake/comps/llvm.mak commit 811cdc7bf94b324cd74a6738334ea396c34d7499 Author: Weiqun Zhang Date: Fri Jul 12 14:21:21 2019 -0700 add -pthread to intel Tools/GNUMake/comps/intel.mak commit d2a387c86d1d5acfc38b6c144773590d48eb5b07 Author: Weiqun Zhang Date: Fri Jul 12 14:06:06 2019 -0700 pass -pthread to g++ Tools/GNUMake/comps/gnu.mak commit 2570f97d56c7e58903c2ad6981433707d2bad0f2 Author: Weiqun Zhang Date: Fri Jul 12 13:18:11 2019 -0700 more aggressive inline with AMREX_FORCE_INLINE Docs/sphinx_documentation/source/GPU.rst Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_Algorithm.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_LOUtil_K.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_algoim_K.H Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/Particle/AMReX_Particle_mod_K.H Tests/GPU/CudaGraphs/GraphBoundary/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H Tutorials/GPU/Advection_AmrCore/Source/Tagging.H Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/mykernel.H Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/NeighborList/CheckPair.H Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit be58fefaa54d61ac206f358c6a326fc580ad0bd2 Author: Weiqun Zhang Date: Fri Jul 12 09:43:31 2019 -0700 modify the veloc test Tests/VELOC/multifab/main.cpp commit a4a4beee762433dafc5da5f2562441b3852f1de1 Merge: 1d2c2a70a d64794988 Author: Weiqun Zhang Date: Fri Jul 12 09:23:45 2019 -0700 Merge branch 'development' into weiqun/asynco commit d6479498828a3b3bed0e0b044559e69d4c2a256d Merge: 3d9d8505a 731313767 Author: Weiqun Zhang Date: Fri Jul 12 09:22:12 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 731313767a0286850cfaf4f841e469b9accf00a6 Author: Stefan Vater Date: Fri Jul 12 16:43:06 2019 +0200 Doc update (#515) Doc update from @svater Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit a19b7c5564c0dffb0f1df9945e6bf6e1cdc576d0 Author: Andrew Myers Date: Thu Jul 11 20:19:01 2019 -0700 also wrap thrust::exclusive_scan, providing CPU implementation Src/Base/AMReX_CudaContainers.H commit 1d2c2a70aa4cc2091fa41265be7c12891de4a06e Author: Weiqun Zhang Date: Thu Jul 11 19:34:33 2019 -0700 make the veloc test more general Tests/VELOC/multifab/GNUmakefile Tests/VELOC/multifab/main.cpp commit 8822f00bbe24066bc48a17087ee8d197ab5adf3a Author: Weiqun Zhang Date: Thu Jul 11 19:10:03 2019 -0700 fix another bug in WriteAsync Src/Base/AMReX_VisMF.cpp commit 2d467ce395cc9f97f597c0ffa153034d32634b95 Merge: a0a3519a5 0ba3c26c0 Author: Andrew Myers Date: Thu Jul 11 17:28:17 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ef84e7887c849a1ae61677526f44f22f242defc2 Merge: ff97fa401 2d467ce39 Author: Christopher DeGrendele Date: Thu Jul 11 17:27:57 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 59d942e8f1f966c6e88df81f488b6d0b64ef3af5 Author: Weiqun Zhang Date: Thu Jul 11 17:27:03 2019 -0700 fix index Src/Base/AMReX_VisMF.cpp commit a0a3519a5c4bb529d365bd427d891cf6188666d1 Author: Andrew Myers Date: Thu Jul 11 17:26:44 2019 -0700 fix box_threads_and_blocks for AMREX_SPACEDIM < 3 Src/Base/AMReX_GpuDevice.cpp commit ff97fa40129e578148eb6929fa6eab44d033a9fe Merge: 29d2d4861 0ba3c26c0 Author: Christopher DeGrendele Date: Thu Jul 11 17:04:39 2019 -0700 merge with upstream commit 1126d925565725bdb0d8a5c65cb93b16151f9021 Author: Weiqun Zhang Date: Thu Jul 11 16:54:24 2019 -0700 VisMF::WriteAsync for multi cpus Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Tests/VELOC/multifab/main.cpp commit 29d2d4861e0ad289bcf68760629308c492c856d6 Author: Christopher DeGrendele Date: Thu Jul 11 16:42:45 2019 -0700 commented out Src/Base/AMReX_Utility.cpp commit 131c5fa91baa429e918519fa4b2e9833d736340c Author: Christopher DeGrendele Date: Thu Jul 11 16:11:23 2019 -0700 temp Src/Base/#AMReX_GpuUtility.cpp# Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/launc_gpu.sh Tests/GPU/RandomNumberGeneration/main.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000.REMOVED.git-id Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_D_00000.REMOVED.git-id Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_D_00000.REMOVED.git-id Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_H commit 0ba3c26c029aa363cfa8ffdecd7f9c3d088782f4 Merge: 6d8cf4f26 c82865310 Author: Ann Almgren Date: Thu Jul 11 15:07:23 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 6d8cf4f26747fc4f6a9953532a839f2ec7e66891 Author: Ann Almgren Date: Thu Jul 11 15:07:14 2019 -0700 fix formatting Src/Particle/AMReX_TracerParticles.cpp commit c82865310f40d43bd784d6f0a6265af9bc7bcd62 Author: kngott Date: Thu Jul 11 14:37:44 2019 -0700 Fix typo. Tutorials/GPU/run.summit commit d5da22490d3137d7559ceea77f5a8054b29d8f51 Merge: 5bb99f977 c82680df9 Author: Christopher DeGrendele Date: Thu Jul 11 14:33:15 2019 -0700 Merge branch 'development' of https://github.com/ChrisDeGrendele/amrex into development commit c82680df99189f8ca77b4f446904a746d993536f Author: Christopher Degrendele Date: Thu Jul 11 17:32:34 2019 -0400 CIC grid error - I pushed this earlier but I guess it didn't actually push Src/Particle/AMReX_TracerParticle_mod_K.H commit 959653566eb85771be58ce86ed5931dece337cb0 Merge: f6c2ab5cc 8827bc3b9 Author: Andrew Myers Date: Thu Jul 11 14:30:03 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f6c2ab5cc6c51dbc467993d3fdab70b456b22b69 Author: Andrew Myers Date: Thu Jul 11 14:29:48 2019 -0700 a wrapper around thrust::inclusive_scan for portability between GPU and CPU codes Src/Base/AMReX_CudaContainers.H Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 8827bc3b9668a311f0a510ee557d07041b6ca57c Author: Jean M. Sexton Date: Thu Jul 11 14:15:52 2019 -0700 Add nvprof profiler flags to run.summit script Tutorials/GPU/run.summit commit 31334d8f25ef96a6688a37093928e23dd42c4cb0 Author: Christopher Degrendele Date: Thu Jul 11 17:04:19 2019 -0400 deleted unnecessary file Src/Particle/#AMReX_TracerParticles.H# commit 131939d38b54aec45bbb271fbab61cbffdfa9d4c Author: Christopher Degrendele Date: Thu Jul 11 17:03:55 2019 -0400 Didn't mean to change this file Src/Particle/#AMReX_TracerParticles.H# Src/Particle/AMReX_ParticleContainerI.H commit 5b2a91a4cc15af3bc5e12b352bedda0643ec14ba Author: Andrew Myers Date: Thu Jul 11 11:53:41 2019 -0700 remove the 'unsigned short int' version of the atomicCAS wrapper, which we don't need and is only available in 10.1 Src/Base/AMReX_GpuUtility.H commit cb06fc26260ff04e5e772cc22b48f6b9a33b537d Author: Weiqun Zhang Date: Thu Jul 11 11:37:37 2019 -0700 finished VisMF::WriteAsync for single cpu Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_Utility.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 6789d309463574fc3d0bdd489d8418c7f8309426 Author: Weiqun Zhang Date: Thu Jul 11 11:36:26 2019 -0700 use memcpy to avoid potential alignment issue Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp commit 5bb99f97714b8cbeb2f1f9eee651b2e72af0fd95 Merge: 5827e0c17 21f159ddf Author: Christopher DeGrendele Date: Thu Jul 11 10:05:56 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b08fdf902a8e444f9e6d63010bbd63044db4915f Merge: 77d5b1e6a 21f159ddf Author: Kevin Gott Date: Wed Jul 10 22:09:52 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit 21f159ddf90f809aeaa0e66e18c5c2480c131632 Author: Andrew Myers Date: Wed Jul 10 17:07:58 2019 -0700 fix indentation Src/Base/AMReX_GpuUtility.H commit e65bdba45f7260421ab840ddd466c101275fd008 Author: Andrew Myers Date: Wed Jul 10 17:03:48 2019 -0700 add wrappers around Cuda's atomicCAS Src/Base/AMReX_GpuUtility.H commit 3d9d8505a67786138b8c434701cd325e01e8a5ef Author: Weiqun Zhang Date: Wed Jul 10 13:18:10 2019 -0700 use mlock on memory in The_Pinned_Arena when USE_CUDA=FALSE Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp Src/Base/AMReX_EArena.H Src/Base/AMReX_EArena.cpp commit 68800a804ec6004b8b011198557f90f1a3f80fc8 Author: Jean M. Sexton Date: Wed Jul 10 13:07:30 2019 -0700 Remove --pretty-print from AMReX_BLBackTrace.cpp since this gives an error on cori-gpu Src/Base/AMReX_BLBackTrace.cpp commit 7e14f7843ded496755aba2fd9813a54026ac237b Author: Weiqun Zhang Date: Wed Jul 10 10:49:01 2019 -0700 add optional communicator argument to some VisMF functions Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 8d012014ece7a20224b27a1b52dd15253f381a2a Merge: 6df597a38 eab70c9ef Author: Weiqun Zhang Date: Tue Jul 9 14:16:57 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6df597a38cd21228ddee1903b84629010e08aed9 Author: Weiqun Zhang Date: Tue Jul 9 14:16:47 2019 -0700 use pinned memory Tests/VELOC/multifab/main.cpp commit eab70c9ef0a86bb7e1a5773daf2f51da211dd936 Merge: f88f85f45 8cd6bac61 Author: Andrew Myers Date: Tue Jul 9 13:25:15 2019 -0700 Merge pull request #512 from KiranEiden/keiden/amrex Fix issues RealBox equality check commit f88f85f45e45bbfd838b2393a8fe258fc3594419 Merge: 3e7595874 3e7238b07 Author: Weiqun Zhang Date: Tue Jul 9 13:17:50 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3e75958749508293a53c74a8109c366fd7dad47f Author: Weiqun Zhang Date: Tue Jul 9 13:17:09 2019 -0700 add BaseFab::release Src/Base/AMReX_BaseFab.H Tests/VELOC/multifab/GNUmakefile Tests/VELOC/multifab/inputs Tests/VELOC/multifab/main.cpp commit 8cd6bac61017143a5d3969aa1418343dd33c4360 Author: Kiran Eiden Date: Tue Jul 9 13:09:55 2019 -0700 Switched to <= for RealBox equality check Src/Base/AMReX_RealBox.cpp commit 01ed464f7eee27d77f3dd0b28e8b68a30d73f7ff Author: Kiran Eiden Date: Tue Jul 9 12:34:38 2019 -0700 Revert to doing exact comparison by default Using machine epsilon to do inexact comparison is a bit confusing - it's probably better to have the user supply their own value if they want a tolerance. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 51a8b84c0d04c7dda02831538204cb70b2cd9559 Author: Kiran Eiden Date: Tue Jul 9 11:54:23 2019 -0700 Switch to using machine epsilon Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 3e7238b07e03c1153307311dc3cc7785f9361f06 Author: Andrew Myers Date: Tue Jul 9 11:43:17 2019 -0700 make the default eps for contains be the roundoff error for Real Src/Base/AMReX_RealBox.H commit 14147fa3e0d4281a062a74b5f6b1c2710c7efab5 Merge: 084781521 ac062bf45 Author: Andrew Myers Date: Tue Jul 9 11:33:59 2019 -0700 Merge pull request #511 from KiranEiden/development Added function for checking RealBox equality commit ac062bf45fcdcda3fa81db4d0468b7b9fc17cea6 Author: Kiran Eiden Date: Tue Jul 9 11:21:39 2019 -0700 Added exclamation point to comment for consistency Src/Base/AMReX_RealBox.H commit 3653841cdf2a144ae65c89705144cb74c6321405 Author: Kiran Eiden Date: Tue Jul 9 11:16:28 2019 -0700 Added function for checking RealBox equality Added the AlmostEqual function to the amrex namespace, which checks that the domains represented by two real boxes are the same within a tolerance. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 0847815211ceeedd80f1e860bd3c158ce9aa9a0d Merge: ef6a8be24 66334cb07 Author: WeiqunZhang Date: Tue Jul 9 09:35:49 2019 -0700 Merge pull request #510 from AMReX-Codes/checkinput Enforce AMR validity checks on max_level commit 0cd8d6e653df34d257b10fcff3acccd8d691c31b Author: Weiqun Zhang Date: Tue Jul 9 09:24:10 2019 -0700 VeloC test: write and read MultiFab Tests/VELOC/multifab/GNUmakefile Tests/VELOC/multifab/Make.package Tests/VELOC/multifab/Readme Tests/VELOC/multifab/inputs Tests/VELOC/multifab/main.cpp Tests/VELOC/multifab/veloc.cfg commit dacc1c421d270ed2f0df6141890cc65f7bece0b0 Author: Weiqun Zhang Date: Tue Jul 9 08:58:17 2019 -0700 add DistributionMappin::readFrom and writeOn Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit d16534ebb41e3daf3e4f86e28fa542e7d9f8422e Author: Weiqun Zhang Date: Tue Jul 9 06:47:59 2019 -0700 dtoh_memcpy and htod_memcpy for MultiFabs Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MultiFabUtil.H commit 66334cb079eff0c371473b30d2e69413de801157 Author: Max Katz Date: Mon Jul 8 19:27:50 2019 -0700 Enforce AMR validity checks on max_level The inputs validity check on the AMR quantities was not checking on max_level. So, e.g., if you had amr.max_level=0 then you could do things which would not make sense, like have amr.blocking_factor be larger than amr.max_grid_size. Src/Amr/AMReX_Amr.cpp commit 33b0ea1139e02697c92a116f0a19b2a806e073ae Merge: ada159824 ef6a8be24 Author: Weiqun Zhang Date: Mon Jul 8 16:33:46 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ef6a8be2437d8e2c7941eced9cc54d28792a306c Author: Michele Rosso Date: Mon Jul 8 18:53:21 2019 -0400 CMake: make public the OpenMP flags passed to CUDA host compiler Tools/CMake/AMReX_Config.cmake commit ada159824a46539cd8513704de5e6566c7f9a23e Author: Weiqun Zhang Date: Mon Jul 8 11:27:47 2019 -0700 use PhysBCFunctNoOp in amrex Tutorials/Particles/ElectrostaticPIC/main.cpp commit 7c53f0131f22031fdbe6ffd835df85f4ba2b7a78 Merge: 25073e2bb a7dbede01 Author: Weiqun Zhang Date: Mon Jul 8 10:44:57 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 25073e2bb49620eadbdf1d6a4b1d48d4606c1783 Author: Weiqun Zhang Date: Mon Jul 8 10:44:47 2019 -0700 add a comment Src/EB/AMReX_EBCellFlag.H commit a7dbede0144b0e522377f1875c91782ebf3abd97 Author: Max Katz Date: Mon Jul 8 00:28:15 2019 -0700 Only write initial checkpoint if checkpoints are requested Src/Amr/AMReX_Amr.cpp commit 1ccad8ac0c95380046c41b14296ef7260d583715 Merge: 9a4fd73c5 e41149eec Author: Weiqun Zhang Date: Sun Jul 7 17:06:49 2019 -0700 Merge branch 'weiqun/dev' into development commit e41149eec8a3796d013aaf37e2e9e7041f7ddc37 Author: Weiqun Zhang Date: Sun Jul 7 16:49:31 2019 -0700 fix new index typo due to typo Src/EB/AMReX_EB2_3D_C.cpp commit 2a576387faf4cd0260220d0efe5fb59ce4ab1454 Author: Weiqun Zhang Date: Sun Jul 7 15:45:45 2019 -0700 build 3d eb cells on gpu Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EBCellFlag.H commit 07b4ee757400bf2a63087449b4b1c8e01f49e4d4 Author: Weiqun Zhang Date: Sat Jul 6 22:31:26 2019 -0700 WIP: build 3d eb cells on gpu Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_Level.H commit 9a4fd73c5148ca8ca9146fd725a9b5c4c8930ea7 Merge: 844fdcbe9 b0f1479b9 Author: Weiqun Zhang Date: Sat Jul 6 19:22:55 2019 -0700 Merge branch 'weiqun/dev' into development commit b0f1479b904ac8a2afde53f8571c0710eddfbbab Author: Weiqun Zhang Date: Sat Jul 6 17:16:53 2019 -0700 3d EB: build faces on gpu Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_eb2_3d.F90 commit 844fdcbe9e768cde7b24c3e60764c6bb68546fd1 Author: Weiqun Zhang Date: Sat Jul 6 08:10:59 2019 -0700 assuming -lgomp only works gcc Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 829ca05e630c932a6474a7c5d82b7bd5b9cdc87e Merge: 49fb948dd 063d3df4b Author: Weiqun Zhang Date: Sat Jul 6 07:59:48 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 063d3df4b99f19a783b8c1d60a1f85f316d9745d Author: Michele Rosso Date: Fri Jul 5 15:51:43 2019 -0700 CMake: fix bug in config file Tools/CMake/AMReXConfig.cmake.in commit b00040b057bf789f4905420b040b3abee100b057 Author: Michele Rosso Date: Fri Jul 5 14:30:33 2019 -0700 CMake: manually pass OpenMP flag to CUDA host compiler Tools/CMake/AMReX_Config.cmake commit e657cdec0b96d5406865e5f0596aa4053fd3f558 Author: Michele Rosso Date: Fri Jul 5 12:46:56 2019 -0700 CMake: use C++ bindings for MPI in addition to C bindings. This fixes bugs with certain MPI implementations still using C++ bindings. Src/Base/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in commit 49fb948dd595949f9363d6403969303ec6079833 Author: Weiqun Zhang Date: Fri Jul 5 12:10:35 2019 -0700 2d EB: build_cells on gpu Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_eb2_2d.F90 commit d67e5473d107e2f705bf5125f43cb7258bdd96c7 Author: Michele Rosso Date: Fri Jul 5 10:54:04 2019 -0700 CMake: allow builds with both CUDA and OMP Tools/CMake/AMReX_Options.cmake commit 4619a738a3a71ff40c86d5e9066f7977ae1b4fb4 Author: Andrew Myers Date: Fri Jul 5 13:43:36 2019 -0400 remove restriction that OMP and CUDA/HIP can't be enabled at the same time. Tools/GNUMake/Make.defs commit 7f8f9bb79494afe477acc46b1057960ee2036417 Merge: f3f57faf9 fdc40e3a9 Author: Weiqun Zhang Date: Fri Jul 5 10:41:57 2019 -0700 Merge branch 'development' into weiqun/dev commit fdc40e3a923c12f5e87c62cbf25535e8048d0a41 Merge: 768cfebe4 2a425f243 Author: Weiqun Zhang Date: Fri Jul 5 10:40:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f3f57faf97815585e90098557e2eb5fba584a067 Author: Weiqun Zhang Date: Fri Jul 5 10:40:34 2019 -0700 EB: build_faces on gpu Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_eb2_2d.F90 commit 2a425f2438c227a43757248529bb61f5d1ebe718 Author: Andrew Myers Date: Fri Jul 5 10:33:47 2019 -0700 use value semantics instead of pointers for rhoarr Src/Particle/AMReX_ParticleContainerI.H commit d26a384296606160c545e20e9be4abeefe7a7790 Author: Andrew Myers Date: Fri Jul 5 10:14:31 2019 -0700 initialize rhoarr pointer to nullptr Src/Particle/AMReX_ParticleContainerI.H commit 283f94cf94ff070b7f8972129b61a40a8d47c324 Author: Andrew Myers Date: Fri Jul 5 10:04:25 2019 -0700 update AssignCellDensitySingleLevel to handle the case where OMP and CUDA are on, but we are not in a launch region Src/Particle/AMReX_ParticleContainerI.H commit 44e9e434dedb56db7de5a56c77bb64dbfb7901b1 Author: Weiqun Zhang Date: Fri Jul 5 08:10:10 2019 -0700 WIP: 2d compiles Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_Level.H commit 2a23fdea1b06755b1f8f9348da00d270681d31db Author: Weiqun Zhang Date: Fri Jul 5 07:55:31 2019 -0700 add LoopOnCpu to get rid of nvcc warnings Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_Loop.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_EB2_GeometryShop.H commit 02702ff93c93d39232e6d0a5800faf17a0c26ece Author: Weiqun Zhang Date: Fri Jul 5 06:28:53 2019 -0700 WIP: EB2::build_faces on gpu Src/Base/AMReX_Box.H Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Level.H Src/EB/CMakeLists.txt Src/EB/Make.package commit 06463cb673e2def560fd5ec366664b10207db333 Author: Ann Almgren Date: Thu Jul 4 19:01:20 2019 -0700 pass bottom_reltol and bottom_abstol through the MacProjector Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 768cfebe4a554e8eb07bdde71fddf5e7d7c10b1e Author: Weiqun Zhang Date: Thu Jul 4 13:22:05 2019 -0700 EB: get intercepts on gpu if we can Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Level.H commit b6357ebf3d9f29d306daf274bd368c0ac2040dfb Author: Weiqun Zhang Date: Wed Jul 3 20:35:03 2019 -0700 old versions of eu-addr2line do not support pretty-print Src/Base/AMReX_BLBackTrace.cpp commit 3388f80b9b9d7629e7ed764feade2e288e1ce132 Merge: a64322906 9688c2462 Author: Weiqun Zhang Date: Wed Jul 3 18:42:35 2019 -0700 Merge branch 'development' into weiqun/dev commit a6432290623e83ebdfb61d3f1ad69316fc27f52f Author: Weiqun Zhang Date: Wed Jul 3 18:30:34 2019 -0700 around a possible gcc bug Src/Base/AMReX_BLBackTrace.cpp commit 9688c2462e97dacbeaeb378c88230582d6f32d7b Author: Ann Almgren Date: Wed Jul 3 17:11:47 2019 -0700 Need to only touch inverse_tags if enable_Inverse() is true Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 5cb23803a6671072aa5b579d5ddf6468dfce0c42 Author: Andrew Myers Date: Wed Jul 3 16:23:44 2019 -0700 Fix problem where the size of inverse_tags wasn't getting reset to 0 properly Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit d33e8ab9488892e730d39069fffa6b88a60ac721 Author: Weiqun Zhang Date: Wed Jul 3 15:23:32 2019 -0700 fix typo Src/Base/AMReX_BLBackTrace.cpp commit f1b0dc3126ee8f64907ae0e68beb8668113b1cfb Author: Weiqun Zhang Date: Wed Jul 3 15:17:24 2019 -0700 use eu-addr2line if present Src/Base/AMReX_BLBackTrace.cpp commit dba1e7a1bd8846e578ebd9fea099456112a4bb69 Merge: cb5168234 57852530e Author: Ann Almgren Date: Wed Jul 3 14:58:27 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit cb516823443ac99e62b9388b7378bf45df7aea89 Author: Ann Almgren Date: Wed Jul 3 14:58:16 2019 -0700 default enable_inverse to false Src/Particle/AMReX_NeighborParticlesI.H commit 57852530e2181926d91e6ca61ee0961d7aa3dffe Merge: 3b9c4e5b8 0daa9725d Author: Andrew Myers Date: Wed Jul 3 17:17:26 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3b9c4e5b8125c593bb73b0cb0dc9bc7ebf995c1a Author: Andrew Myers Date: Wed Jul 3 17:17:05 2019 -0400 workaround for compiler bug in gcc < 4.9 Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp Src/Particle/AMReX_Particle.H commit 0daa9725d843b0274e4ef634792542ab646f5ba2 Author: Michele Rosso Date: Wed Jul 3 14:13:41 2019 -0700 CMake: add -fimplicit-none to Fortran flags preset Tools/CMake/AMReXFlagsTargets.cmake commit 12838b811ca76ff5a464d3ed7c8da23f7979be65 Author: Weiqun Zhang Date: Wed Jul 3 12:35:44 2019 -0700 GNU make: load Make.local-pre if present Tools/GNUMake/Make.defs commit 365d5faac4d00201c72cfd36a850d09596702044 Author: Weiqun Zhang Date: Wed Jul 3 10:26:41 2019 -0700 fix warning for clang Src/Base/AMReX_TypeTraits.H commit 9e626237a71caeaa44af8fc550c78dbf217fcb08 Author: Weiqun Zhang Date: Wed Jul 3 13:14:07 2019 -0400 workaround gcc 4 Src/Base/AMReX_BaseFab.H Src/Base/AMReX_TypeTraits.H commit 9e970bbd081f64803d54b1ef98e2e6092ecc2697 Author: Weiqun Zhang Date: Wed Jul 3 09:40:38 2019 -0700 add EXPORT_DYNAMIC to llvm-flag.mak Tools/GNUMake/comps/llvm-flang.mak commit 0e4c2fd67c82d9383356cc4e5a23d559c9d9872b Author: Weiqun Zhang Date: Wed Jul 3 09:26:00 2019 -0700 Backtrace on mac: llvm is supported Src/Base/AMReX_BLBackTrace.cpp Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/llvm.mak commit c3227249d416391387e6c5bc93333ff8600a5353 Author: Weiqun Zhang Date: Wed Jul 3 07:22:03 2019 -0700 move dynamic load flags to gnu.mak Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak commit 33815bacd7acd7cd5c35ea92bfddb6cf40d1c961 Author: Weiqun Zhang Date: Wed Jul 3 07:02:33 2019 -0700 turn dynamic load by default for Darwin+gcc Tools/GNUMake/Make.defs commit 7e11843d448d738e1accabfbd6c309d9d3e50a9d Author: Weiqun Zhang Date: Wed Jul 3 06:41:39 2019 -0700 use atos for backtrace on mac Src/Base/AMReX_BLBackTrace.cpp commit e6755c205dd753e678ac819f523d5443dc614439 Merge: 256a73917 0544a7f6a Author: Weiqun Zhang Date: Tue Jul 2 20:47:45 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 256a73917bf20854e2822083c2321754c49ebb63 Author: Weiqun Zhang Date: Tue Jul 2 20:47:28 2019 -0700 If available, print the tiny profiler stack when backtracing Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 0544a7f6a26eafd1b6b126264eb9e30de79443ce Author: Weiqun Zhang Date: Tue Jul 2 19:10:19 2019 -0700 set handler for SIGFPE Src/Base/AMReX.cpp commit b27f10392a658a3be285dfd524bbfd18b08e2987 Author: Weiqun Zhang Date: Tue Jul 2 18:49:42 2019 -0700 For backtrace, do not omit frame pointer Src/Base/AMReX_BLBackTrace.cpp Tools/GNUMake/comps/gnu.mak commit 3c5ec487fa177081e372f18eec35c711ca8b5eaf Author: Weiqun Zhang Date: Tue Jul 2 18:23:53 2019 -0700 backtrace on Mac Src/Base/AMReX_BLBackTrace.cpp Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak commit 8ec490d359a54cda4a3586255bc4925680b86018 Author: Weiqun Zhang Date: Tue Jul 2 15:43:30 2019 -0700 enable floating pointer exception and backtrace for Mac Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp commit 4cace2d0cc89617daee331021ffd892926a51cdd Author: Weiqun Zhang Date: Mon Jul 1 21:20:34 2019 -0700 fix 2d problem in my last commit Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 88b156506be8ba6cc6d29f84a122938d3fe579b5 Author: Weiqun Zhang Date: Mon Jul 1 20:43:14 2019 -0700 Linear Solver: option to set non-zero domain bc locations Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit 9fc854d5c20dfd06ede71235043bc8a04b57177d Author: Weiqun Zhang Date: Mon Jul 1 19:07:45 2019 -0700 fix parse_bt.py Tools/Backtrace/parse_bt.py commit 9d2c3af7ebb75582854a58caae5bc38ef435bdd8 Author: Weiqun Zhang Date: Mon Jul 1 18:50:37 2019 -0700 addr2line: skip libc.so because it causes troubles Src/Base/AMReX_BLBackTrace.cpp Tools/Backtrace/parse_bt.py commit 754903a6d9f01066936cc204a98ca5d70cd0e6c3 Author: Weiqun Zhang Date: Mon Jul 1 18:33:05 2019 -0700 try to use the address in () for addr2line if we can Src/Base/AMReX_BLBackTrace.cpp commit 60c962c721b74e791986c01de6b8999a3619d3f0 Author: Weiqun Zhang Date: Mon Jul 1 18:16:16 2019 -0700 Revert "backtrace: use the address returned by backtrace, not the one extraced from bactrace_symbols" This reverts commit a5794ef4a68f11d45a05e1fe20290afee42f4b0a. Src/Base/AMReX_BLBackTrace.cpp Tools/Backtrace/parse_bt.py commit a5794ef4a68f11d45a05e1fe20290afee42f4b0a Author: Weiqun Zhang Date: Mon Jul 1 16:04:19 2019 -0700 backtrace: use the address returned by backtrace, not the one extraced from bactrace_symbols Src/Base/AMReX_BLBackTrace.cpp Tools/Backtrace/parse_bt.py commit f90a295750dafdcb1d99879d3ffcdfac2c626870 Merge: 648b18fac 6fe1d9f67 Author: Weiqun Zhang Date: Mon Jul 1 09:16:01 2019 -0700 Merge branch 'weiqun/dev' into development commit 648b18facb8dd665c828a1fe9c59afc213c90262 Author: Weiqun Zhang Date: Mon Jul 1 09:13:27 2019 -0700 update CHANGES CHANGES commit 6fe1d9f6714fa5315d62bee8a3fd89ec121e5deb Author: Weiqun Zhang Date: Sat Jun 29 13:30:24 2019 -0700 fix warnings Src/Base/AMReX_PhysBCFunct.H Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_algoim.cpp Src/EB/AMReX_algoim_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit c9f296356b4ea22422f6d1ab0240eb49cf8844c2 Author: Weiqun Zhang Date: Sat Jun 29 11:47:57 2019 -0700 option to turn off Wshadow because there are so many in thrust. fix some warnings Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_EArena.cpp Src/Base/AMReX_Lazy.cpp Src/Base/AMReX_Machine.cpp Tools/GNUMake/comps/gnu.mak Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/EBCNS/Source/CNS.cpp commit cb962dc7c74c9c004a70554fa4f5467608780f4f Author: Weiqun Zhang Date: Sat Jun 29 11:05:06 2019 -0700 provide default constructor to EBCellFlag because nvcc cannot generate default device version Src/EB/AMReX_EBCellFlag.H commit 9a9dc9c4586948d01838a618cfe646f25a45e66d Author: Weiqun Zhang Date: Sat Jun 29 07:17:10 2019 -0700 put amrex::min and amrex::max in new file AMReX_Algorithm.H. add max_lbound and min_ubound functions Src/Base/AMReX_Algorithm.H Src/Base/AMReX_Box.H Src/Base/AMReX_Utility.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H commit 5827e0c1785f1bac79a528e9c0296a4bf253ed18 Author: Christopher DeGrendele Date: Fri Jun 28 14:48:40 2019 -0700 fixed the same indice error from before on CIC grids Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 4b5531659800a79c48aaad8833f9c96c26a34bf1 Author: Weiqun Zhang Date: Fri Jun 28 10:32:02 2019 -0700 clean up Src/Base/AMReX_BaseFab.H Src/Particle/AMReX_ParticleContainerI.H commit 5f3f1a83fe82907e31fc0650e6c418f2994b1ad7 Author: Weiqun Zhang Date: Thu Jun 27 21:50:27 2019 -0700 for non-trivially_default_contructible types, do placement new on gpu to avoid touching memory on cpu. This will help BaseFab> and BaseFab. Src/Base/AMReX_BaseFab.H commit c50d3b00ab8dfb7d884d1149bbdacd4cd76ed06e Merge: e7c05438b 49f3c405e Author: Michele Rosso Date: Thu Jun 27 16:05:32 2019 -0700 Merge branch 'mr/cmake' into development commit 49f3c405e5ae0f356f1802d2a56f52683e5c7977 Author: Michele Rosso Date: Thu Jun 27 16:05:06 2019 -0700 CMake: add module to perform typecheck. Tools/CMake/AMReXTypecheck.cmake commit 12295594ab5c9d7938606bedda5c3ca2538a542c Author: Weiqun Zhang Date: Thu Jun 27 14:15:53 2019 -0700 update documentation and launch tutorial Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit 92cf67a242523995843a68dbbe27a74fe0ab7827 Author: Weiqun Zhang Date: Thu Jun 27 13:22:25 2019 -0700 use amrex::Loop Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/Launch/main.cpp commit e7c05438bc0c3a8a405b57d9249ba57f7562b9d7 Author: Weiqun Zhang Date: Thu Jun 27 12:43:17 2019 -0700 add amrex::Loop and amrex::LoopConcurrent Src/Base/AMReX_Box.H commit a7bc34a9797e9c43cd96df6143901897bd88e91c Author: Christopher Degrendele Date: Thu Jun 27 15:29:32 2019 -0400 Mac routine is now dimension agnostic. This is ready for testing Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit f4d93081d017ed8edd2c5e65009fe1bdfbeb1083 Merge: c781aad03 5f72fe0e0 Author: Michele Rosso Date: Thu Jun 27 11:39:38 2019 -0700 Merge branch 'development' into mr/cmake commit c781aad03e649338061da0376fb078db1c9857b4 Author: Michele Rosso Date: Thu Jun 27 11:14:12 2019 -0700 CMake: clean up Tools/CMake/AMReX_Utils.cmake commit 5f72fe0e0ce209acad0f7b38be664c0259537649 Author: Ann Almgren Date: Thu Jun 27 08:11:27 2019 -0700 Fix typo Src/EB/CMakeLists.txt commit 0c355b89df69e4cc07884d2e7eaccef9317d4617 Author: Weiqun Zhang Date: Thu Jun 27 07:49:55 2019 -0700 fix index bug Src/EB/AMReX_EBMultiFabUtil.cpp commit ec29247c4bdac6728186d0857cb993f51949b118 Author: Weiqun Zhang Date: Thu Jun 27 07:47:43 2019 -0700 fix index bug Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 8cbdec34974579d011ca936d669c9b10ffc54aa1 Author: Weiqun Zhang Date: Thu Jun 27 07:04:16 2019 -0700 fix cmake Src/EB/CMakeLists.txt Src/EB/Make.package commit 8d41be6b388131e43f1d1450563511b1ea5b1ba7 Author: Weiqun Zhang Date: Wed Jun 26 20:45:34 2019 -0700 remove deprecated Fortran routine Src/EB/AMReX_eb2_3d.F90 commit 4d211ed3bead6eea6f501f142d4bc1ef7c2edd35 Author: Weiqun Zhang Date: Wed Jun 26 20:13:45 2019 -0700 EB: build types on gpu Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit 2b76bff200e75d737b24e347c2511e426ba52594 Author: Weiqun Zhang Date: Wed Jun 26 15:54:44 2019 -0700 EB: fill leveset on gpu Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB_levelset.H commit 663d92367de1bc30428e3a62085df98698f74885 Author: Michele Rosso Date: Wed Jun 26 16:56:06 2019 -0700 CMake: update evaluate_genex Tools/CMake/AMReX_Utils.cmake commit 0c8a510ea278d9823b43aa8202823e3a317b1738 Merge: b8b961e41 7165274ef Author: Weiqun Zhang Date: Wed Jun 26 13:42:34 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7165274efcdf5681a1e87d0f93e8bdb4002e22f3 Author: Weiqun Zhang Date: Wed Jun 26 13:40:27 2019 -0700 make sure we don't dereference nullptr Src/Base/AMReX_FabArray.H commit 38bd36a1a1eba6204be8eda17a29e35877122ece Author: Christopher Degrendele Date: Wed Jun 26 16:12:12 2019 -0400 Fixed a bug and deleted unnecessary lines Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 1127512d0ba40282ff691d553ab01f4613d4c1ea Author: kngott Date: Wed Jun 26 13:08:41 2019 -0700 Fix labels in launch test. Tests/GPU/FusedLaunches/main.cpp commit b8b961e4124540b22e58fd9f9ab73efc4211a8c4 Merge: 852b2ed3b f6a798af2 Author: Weiqun Zhang Date: Wed Jun 26 12:24:32 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 852b2ed3b440600b59f13cc9393f8f90baccf990 Author: Weiqun Zhang Date: Wed Jun 26 12:18:24 2019 -0700 gpu: set covered cells and faces Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil_C.H Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Src/EB/CMakeLists.txt Src/EB/Make.package Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit f6a798af2f4ff6c9fdc2d5f68734b2af66672eed Author: kngott Date: Wed Jun 26 11:49:40 2019 -0700 Updated launch tester. Tests/GPU/FusedLaunches/main.cpp commit 9796f26e46aeb46033197500cbb3d23da69fa818 Author: Christopher Degrendele Date: Wed Jun 26 12:19:38 2019 -0400 removed unwanted files Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Backtrace.0 commit 9b84068c0d3cc07e43a329bb42e2b8e2a19e8809 Author: Weiqun Zhang Date: Wed Jun 26 09:05:11 2019 -0700 gpu: EBAmrUtil Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBAmrUtil_F.H Src/EB/AMReX_EBAmrUtil_nd.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit 87dfe837414ee20aa28e0bc749421a160b7f0576 Merge: 375861d8c 29bf4c9d1 Author: kngott Date: Tue Jun 25 19:47:07 2019 -0700 Merge branch 'development' into kngott/fused commit 29bf4c9d12ca6c80370487a69f8c21e58ca0619c Author: kngott Date: Tue Jun 25 19:46:48 2019 -0700 Adjust make system for Brian's new modules. Tools/GNUMake/sites/Make.nersc commit ea72119ce758e38a97ec98665adbcdbe22195281 Author: Weiqun Zhang Date: Tue Jun 25 17:13:08 2019 -0700 Fix nodal solver owner mask. This will break regression tests. Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit e5b9f9be4fce571076469a3bcb712296eef0cf52 Author: Andrew Myers Date: Tue Jun 25 16:07:01 2019 -0700 fix an off-by-one index error Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 2b389a4e6df5952eb0476afe3e84d036cdd1fe94 Author: Andrew Myers Date: Tue Jun 25 16:04:59 2019 -0700 change this variable name to keep yt happy Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 131af99347f4959902946d0e82da2e3751e5c1ee Merge: f08b0d145 1afd7c079 Author: Weiqun Zhang Date: Tue Jun 25 15:43:29 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f08b0d145578fb7742f743119a2581233419754b Author: Weiqun Zhang Date: Tue Jun 25 15:43:19 2019 -0700 BoxList: make sure block size is not zero Src/Base/AMReX_BoxList.cpp commit 1afd7c0794a413bd32b7600a0e7da8d8b27b45ae Merge: ec0d2c1e7 5fcdcfe52 Author: WeiqunZhang Date: Tue Jun 25 15:33:45 2019 -0700 Merge pull request #508 from OscarAntepara/oscar Adding bottomSolver_maxIter and solver_maxIter to the MacProjector commit 5fcdcfe523195ceb8f89125a89c0afbc8d117e15 Author: Oscar Antepara Date: Tue Jun 25 15:03:29 2019 -0700 Adding bottomSolver_maxIter and solver_maxIter to the MacProjector Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit ec0d2c1e77fab8094d8cb1f469d2f1244efdc71d Author: Michele Rosso Date: Tue Jun 25 14:20:10 2019 -0700 Typechecker: add support for _Bool type Tools/typechecker/typechecker.py commit 3695191ad7408dea8d5cb3b96be4c7178800ea95 Merge: 6c7513e63 504daae2c Author: Michele Rosso Date: Tue Jun 25 13:41:46 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 6c7513e6323db3b3da8923815e2bc1f61db407eb Author: Michele Rosso Date: Tue Jun 25 13:41:38 2019 -0700 Fix bug in doc that prevents latexpdf to compile Docs/sphinx_documentation/source/BuildingAMReX.rst commit e82c4fe0dbe7493f7e07345d71333fce07875c86 Author: Christopher Degrendele Date: Tue Jun 25 16:06:10 2019 -0400 f Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Header Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00000 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00001 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00002 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00003 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00004 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00005 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00006 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00007 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00008 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00009 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00010 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00011 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00012 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00013 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00014 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00015 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00016 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00017 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00018 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00019 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_H Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_1/phi_D_00000 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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_H commit bc64f66353e5659f946ba3d1dabcb6f4f6872f1a Author: Christopher Degrendele Date: Tue Jun 25 15:27:59 2019 -0400 Removed plotfile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Header Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_0/Cell_H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_1/Cell_D_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_1/Cell_H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_2/Cell_D_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_2/Cell_H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Header Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_0/DATA_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_0/Particle_H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_1/DATA_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_1/Particle_H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_2/DATA_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_2/Particle_H commit bbc2d03221254831d5e396fdca5b6904605531a7 Author: Christopher Degrendele Date: Tue Jun 25 15:27:12 2019 -0400 Reorganized Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Backtrace.0 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Header Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00000 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00001 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00002 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00003 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Tue Jun 25 12:03:46 2019 -0700 fix jump to case label error Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp commit 1eb0d65e79c34bdeb8654bac397d7afef7254448 Author: Weiqun Zhang Date: Tue Jun 25 10:57:17 2019 -0700 add noexcept to some functions Src/Base/AMReX_PlotFileDataImpl.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Base/AMReX_PlotFileUtil.H commit 0aaa8e91e11a879b0dd3ca1726e4d7ad3aec0995 Author: Weiqun Zhang Date: Tue Jun 25 09:19:11 2019 -0700 add amrex_set_finest_level to amrex_amrcore_module Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 commit 52f81640c37272e536983d808d3f23cd83019447 Author: Max Katz Date: Tue Jun 25 04:16:42 2019 -0700 Add more RegionTags to AmrLevel Src/Amr/AMReX_AmrLevel.cpp commit 375861d8cadfdcf9f53779297b5980c56ba9967e Merge: 7aca5e105 9265fcc73 Author: kngott Date: Mon Jun 24 15:46:26 2019 -0700 Merge branch 'development' into kngott/fused commit 9265fcc7363581ceeeb4deeada998b80327c705e Merge: bcb7a6086 45a9f4e9d Author: Michele Rosso Date: Mon Jun 24 14:43:13 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit bcb7a608604eb198b38a5018944574aa2accace7 Author: Michele Rosso Date: Mon Jun 24 14:43:01 2019 -0700 CMake: fix bug in OpenMP support Tools/CMake/AMReX_Config.cmake commit 45a9f4e9dbcb73e4639c99e1340362bff13af028 Merge: 1410499cb dd39829f3 Author: Weiqun Zhang Date: Mon Jun 24 12:52:11 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a9811bc9e1a1c1df5ce781b4ce936f77f19cb2c4 Author: Christopher Degrendele Date: Mon Jun 24 13:21:26 2019 -0400 CIC routine is now dimension agnostic, MAC routine has a bug Src/Particle/AMReX_Particle.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 1410499cb5bfb81cac5617e506ee3217722acf17 Author: Weiqun Zhang Date: Mon Jun 24 08:24:42 2019 -0700 YAFluxRegister: no need to test fab ptr Src/Boundary/AMReX_YAFluxRegister.cpp commit dd39829f329a21997513a85a676f2a438b727a2a Author: Max Katz Date: Mon Jun 24 08:14:01 2019 -0700 Add statedata region tags Src/Amr/AMReX_AmrLevel.cpp commit e19e3d6abe753fdbb67070c37b6baedeef45d7ea Author: Weiqun Zhang Date: Mon Jun 24 07:02:20 2019 -0700 need to BaseFab's DataAllocator ctors host and device Src/Base/AMReX_BaseFab.H commit 2e33fdc274d27207360d088a80b6941c485a0494 Merge: 91f1db2b2 590d26130 Author: Weiqun Zhang Date: Sun Jun 23 17:43:21 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 91f1db2b28f3ac074de2583d8385dbef00e296a3 Author: Weiqun Zhang Date: Sun Jun 23 17:43:10 2019 -0700 make sure FabArray works for non-BaseFab FAB Src/Base/AMReX_FabArray.H commit 590d2613028554d420cb2fc144b8a5644432e9da Author: Andrew Myers Date: Sun Jun 23 19:57:05 2019 -0400 better to apply periodic shift for the remotes on the CPU, since they are to be copied off anyway Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 1af7c643c4f6064b2f4052e5425951808a1be403 Author: Weiqun Zhang Date: Sun Jun 23 16:53:06 2019 -0700 minIndex and maxIndex for iMultiFab Src/Base/AMReX_iMultiFab.cpp commit 91714378256a24c6dc8e386d35c9ed361aceabdd Author: Andrew Myers Date: Sun Jun 23 19:19:38 2019 -0400 copy directly to pinned memory; use std::memcpy instead of cudaMemcpy Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit ece4af197db2bcfca4ee482a8b0e7beb2e6c60a1 Author: Max Katz Date: Sun Jun 23 09:22:41 2019 -0700 Add StateData tag to MFs Src/Amr/AMReX_StateData.cpp commit 82feafd878298aafc90c1ae89f323b74dd128b23 Author: Weiqun Zhang Date: Sun Jun 23 09:06:20 2019 -0700 fix for C++11 Src/Base/AMReX_BaseFab.H commit d2bca5ed416d08e07d1024c97e09d25e1de9582c Author: Weiqun Zhang Date: Sun Jun 23 07:31:30 2019 -0700 add MultiFab::queryMemUsage Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 77d74e3e70d64e5318dde870507f8bd1806b7410 Author: Weiqun Zhang Date: Sun Jun 23 07:12:18 2019 -0700 add tags to MultiFab/FabArray and use them to track memory usage Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 071557b77ceca7c4ffc98b7331a0050b0d6f32fb Merge: fc9e8f81a 93ac54bf4 Author: Weiqun Zhang Date: Sat Jun 22 22:38:30 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fc9e8f81a2bc72bcdf67649fb418551560e1a9d1 Merge: 2d0e22516 0bbb6bf2e Author: Weiqun Zhang Date: Sat Jun 22 22:38:12 2019 -0700 Merge branch 'mlmg-2d' into development commit 93ac54bf4a8f2cb1f195c5526fef74a8e054d9b6 Author: Max Katz Date: Sat Jun 22 21:41:01 2019 -0700 Add option to perform asynchronous MF prefetch Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MFIter.H commit f0feb384b25d567f69fb177c14471619a87311ad Merge: 6b6ab38f6 2d0e22516 Author: Andrew Myers Date: Sat Jun 22 23:25:31 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6b6ab38f64e4a27f2e0c53ec04c67daf9ce2c476 Author: Andrew Myers Date: Sat Jun 22 23:24:49 2019 -0400 use std::memcpy instead of cudaMemcpy for host-to-host transfers Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 2d0e2251643d93b8bdd7b827b7951e1bb4126ca4 Author: Weiqun Zhang Date: Sat Jun 22 18:35:41 2019 -0700 use arena in FabArray Src/Base/AMReX_FabArray.H commit fcead2beec1a4d67471937265610292db85e8121 Author: Weiqun Zhang Date: Sat Jun 22 17:56:46 2019 -0700 --no-edit Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_MultiCutFab.H commit 191a4179f329553aed51a0a88e375d01f424f36d Author: Andrew Myers Date: Sat Jun 22 21:10:56 2019 -0400 also get rid of the transform when packing the MPI buffers Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 293d646ea78d9593fc244497172aef4acba13ee3 Author: Andrew Myers Date: Sat Jun 22 20:26:44 2019 -0400 avoid the thrust::transform call, which is also blocking Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 859450e0c12d1fdb4f730979adf6537023437494 Author: Andrew Myers Date: Sat Jun 22 19:23:38 2019 -0400 use an async copy here instead of thrust::copy, which is blocking Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit d42cb88d85c9fb12ab96e2526a90b6fc7a9dd81a Author: Weiqun Zhang Date: Fri Jun 21 17:53:29 2019 -0700 BaseFab: remove allocator template paramter. instead make allocator base of BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_TypeTraits.H commit c16d19c808e09c6eb73dde93a59764b3acbfa4ba Author: Weiqun Zhang Date: Fri Jun 21 17:09:33 2019 -0700 BaseFab no longer needs BaseFabData as base Src/Base/AMReX_BaseFab.H commit 6bf7f89e744746c60b2851ca1e894905ae47a964 Author: Weiqun Zhang Date: Fri Jun 21 16:13:44 2019 -0700 remove asyncfab Src/Base/AMReX.cpp Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAsyncFab.H Src/Base/AMReX_GpuAsyncFab.cpp Src/Base/AMReX_GpuAsyncFabImpl.H Src/Base/AMReX_GpuAsyncFabImpl.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit c44df3e619ecc10792e57b621e968592d1207fae Author: Weiqun Zhang Date: Fri Jun 21 16:11:02 2019 -0700 update license information Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/index.rst commit c62e4c96437e1244713b348a3fd29469807d69b2 Merge: 2aa10bab7 910e17989 Author: Andrew Myers Date: Fri Jun 21 15:32:35 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit abf33debda9ccbfdd9b15e70d9b19b6d45ca4127 Merge: cf742655b 910e17989 Author: Michele Rosso Date: Fri Jun 21 10:32:05 2019 -0700 Merge branch 'development' into mr/cmake commit 910e17989a9a3059465a056946c7229b6dcd7136 Author: Weiqun Zhang Date: Thu Jun 20 17:11:35 2019 -0700 remove fab device ptr Docs/sphinx_documentation/source/BuildingAMReX.rst Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabAllocator.H Src/Base/AMReX_FabAllocator.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_FabFactory.H Src/Base/AMReX_GpuAsyncFabImpl.H Src/Base/AMReX_GpuAsyncFabImpl.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_VisMF.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_InterpBndryData.cpp Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Tests/GPU/AsyncFab/GNUmakefile Tests/GPU/AsyncFab/Make.package Tests/GPU/AsyncFab/main.cpp Tests/GPU/libamrex_CUDA/main.cpp Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/GNUMake/Make.defs commit 2aa10bab76349453fb7c94b5ca92687feb058865 Merge: 6f0adc081 45de01f7a Author: Andrew Myers Date: Thu Jun 20 17:52:07 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 45de01f7aa25793893d9bbc18c950fa35abe2157 Merge: 8e7cc93d0 50721056c Author: Marc Day Date: Thu Jun 20 13:56:41 2019 -0700 Merge pull request #505 from esclapez/dev_CleanDiffSameDomainRefined Clean the screen output of DiffSameDomainRefined. commit 8e7cc93d0cd555737f5cb60c541a3970c618915d Author: Andrew Myers Date: Thu Jun 20 13:55:41 2019 -0700 Revert "change names in tutorial documentation and update license information" This reverts commit 66a1e8a55997a8396a3c5d6904c9e3837c75cea4. Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/conf.py Docs/sphinx_tutorials/source/index.rst build_and_deploy.sh commit 50721056ca127e432a3f33c819015daab1701d51 Author: Lucas Esclapez Date: Thu Jun 20 13:31:57 2019 -0700 Missing \n from previous commit ... Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit 491033a3fdd70db70612334bf380fd875a8f5cbd Author: Lucas Esclapez Date: Thu Jun 20 13:20:40 2019 -0700 Clean the screen output of DiffSameDomainRefined. Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit ebe558b3be32321b30f35c9b39e3d5731aeebcd8 Author: Weiqun Zhang Date: Thu Jun 20 11:12:22 2019 -0700 add amrex_set_boxarray, distromap and geometry to amrex_core_module Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 commit 6f0adc081b3dd99e54e30fdde41b33ebc3d96225 Author: Andrew Myers Date: Thu Jun 20 13:14:26 2019 -0400 add early exit for EnforcePeriodicGPU at the end of RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 0d008b645172b7806c0ab97886cf9a1487809b2e Author: Andrew Myers Date: Wed Jun 19 20:43:41 2019 -0400 change some HostToHost to HostToDevice Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit e88163d0fe5699f9261c8a93a9afbd6962008727 Author: Andrew Myers Date: Wed Jun 19 20:29:08 2019 -0400 some optimizations for FillNeighborsGPU Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 58cd50a62a24a5f850fe0955d7d99b74c5c48a19 Merge: 19b3157b1 c76e60eaa Author: Christopher Degrendele Date: Wed Jun 19 18:56:04 2019 -0400 Merge branch 'development' of git://github.com/AMReX-Codes/amrex into development commit 19b3157b1af742abe37522517d677b88e440c431 Author: Chris DeGrendele Date: Wed Jun 19 15:03:15 2019 -0700 added umac interpolate function Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit c76e60eaaba1433e30e9047139dcc63121071f03 Author: Weiqun Zhang Date: Wed Jun 19 13:45:29 2019 -0700 documentation: minor fix Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/InputsLoadBalancing.rst commit d05898a8ba29bdba3b139775d233a4d9cf07ad98 Author: Weiqun Zhang Date: Wed Jun 19 13:31:58 2019 -0700 documentation: kernel launch Docs/sphinx_documentation/source/GPU.rst commit 73640ad27db7941dec79f3b226f515532e2c707b Author: Weiqun Zhang Date: Wed Jun 19 13:24:39 2019 -0700 documentation: kernel launch Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst commit 9066abae218e6326f9df65c7ab18b69f00a6a5ac Author: Weiqun Zhang Date: Wed Jun 19 10:14:27 2019 -0700 documentation: AsyncArray and Elixir Docs/sphinx_documentation/source/GPU.rst commit 8a7927bdc6cbc3137864c881b66f03c95290c53a Author: Weiqun Zhang Date: Tue Jun 18 16:18:02 2019 -0700 AMREX_OMP_OFFLOAD -> AMREX_USE_OMP_OFFLOAD. Remove AsyncFab from documentation Docs/sphinx_documentation/source/GPU.rst Tools/GNUMake/Make.defs Tutorials/GPU/Launch/MyKernel_F.F90 Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/main.cpp commit dd2c955f46da7e2b73b9c98c7421a823719c4df4 Author: Weiqun Zhang Date: Tue Jun 18 14:59:26 2019 -0700 documentation: update boundary Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU_Chapter.rst commit 2fc15e15294d563324ad53215382359ef0c73f51 Author: Weiqun Zhang Date: Tue Jun 18 14:55:51 2019 -0700 documentation: update boundary Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/LinearSolvers.rst commit 1481c0a45d171be170f11c4d75b4bf4b81b3b7ee Author: Weiqun Zhang Date: Tue Jun 18 14:37:08 2019 -0700 documentation: update kernel section Docs/sphinx_documentation/source/Basics.rst commit beb3194d8f3163b2d7b050bfc4d44e8aedc27d6b Author: Weiqun Zhang Date: Tue Jun 18 14:03:10 2019 -0700 documentation: update tiling section to use C++ Docs/sphinx_documentation/source/Basics.rst commit e993ec3b5af2f3d0af666dc4b7465631f1537371 Author: Weiqun Zhang Date: Tue Jun 18 13:23:12 2019 -0700 add Array4::nComp and update documentation for Dim3 and Array4 Docs/sphinx_documentation/source/Basics.rst Src/Base/AMReX_Array4.H commit b02380381a0d43a284d1e39d5046c727ebea89be Author: Andrew Myers Date: Wed Jun 19 13:00:52 2019 -0700 add some more verbosity to the build_and_deploy script to make it easier to debug build_and_deploy.sh commit 79479d07fc4ae392e01fac9a89c9cef955a47084 Author: Andrew Myers Date: Wed Jun 19 14:27:11 2019 -0400 need to use different names for these derived type components Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit 7aca5e105eaa5c85f0abc5f3d0bfb7558ed93680 Author: kngott Date: Tue Jun 18 16:36:02 2019 -0700 Update for hip changes. Tests/GPU/FusedLaunches/main.cpp commit 6d761c749c978a2507c3389d1ca2f4a05858a569 Merge: 118244e70 aae3f7582 Author: kngott Date: Tue Jun 18 16:33:09 2019 -0700 Merge branch 'development' into kngott/fused commit ef3389bb2b357e70fdd00579e5f9dec65533e211 Author: Andrew Myers Date: Tue Jun 18 16:02:17 2019 -0700 remove unused variable Src/Particle/AMReX_TracerParticles.cpp commit 617aac1272c15adb670536ba474b5d1db9192c70 Author: Andrew Myers Date: Tue Jun 18 15:55:26 2019 -0700 use different approach in interp_2 Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 9cec506dd15185bf86c7c1ef4c1d0ca86476e6bc Author: Andrew Myers Date: Tue Jun 18 15:34:13 2019 -0700 add a debugging print Src/Particle/AMReX_TracerParticles.cpp commit fb7b7899fd4a8e81166fdc53149f5d2b61744ba9 Author: Christopher DeGrendele Date: Tue Jun 18 15:30:21 2019 -0700 s Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit cf742655b84c1fa9344366c25f623af6afc86ed5 Merge: b73a83d08 aae3f7582 Author: Michele Rosso Date: Tue Jun 18 14:45:38 2019 -0700 Merge branch 'development' into mr/cmake commit aae3f75822080736f456f270ed9eb06f78f989cd Author: Michele Rosso Date: Tue Jun 18 14:36:23 2019 -0700 CMake: turn off tutorials by default CMakeLists.txt Docs/sphinx_documentation/source/BuildingAMReX.rst commit 2d4a7aba08ff6cabdb86bbb7c88f3d2cc5caeb40 Merge: e19e10705 dd60dc605 Author: Michele Rosso Date: Tue Jun 18 14:34:51 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e19e107059b4616dd022793d52fa6c11ac985e62 Author: Michele Rosso Date: Tue Jun 18 14:34:45 2019 -0700 CMake: allow user to build and install plotfile tools. Fixes issue #501 CMakeLists.txt Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/Plotfile/CMakeLists.txt commit 77d5b1e6a93a51d0b82d0c949984f9eb602aae94 Author: kngott Date: Tue Jun 18 13:55:24 2019 -0700 Add timer regions to GraphBoundary test. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 49a087a17ce4f2bed50cb63e6f72f26b3a1053d1 Merge: 34ed0239a dd60dc605 Author: kngott Date: Tue Jun 18 13:53:37 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit dd60dc605e37834306a18f0a7436b162634ba082 Author: kngott Date: Tue Jun 18 13:53:03 2019 -0700 Fix include guards. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H commit e0c2f717286b8a75fc94d3f3a18459fc92f580b3 Author: Christopher DeGrendele Date: Tue Jun 18 13:34:07 2019 -0700 revert back to no idx Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/.#AMReX_TracerParticles.cpp Src/Particle/AMReX_TracerParticle_mod_K.H commit e5fcaadfcacb8d8808103bccb63874627b5f07a7 Author: Christopher DeGrendele Date: Tue Jun 18 13:25:52 2019 -0700 cpu Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/.#AMReX_TracerParticles.cpp Src/Particle/AMReX_TracerParticle_mod_K.H commit 185218af2c60720e952ea338e5267b0930415394 Author: kngott Date: Tue Jun 18 13:18:50 2019 -0700 Turn off OpenMP if GPU. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 0d53195165d22cc46bdf90dce24b0e7cdffed62c Author: kngott Date: Tue Jun 18 12:51:08 2019 -0700 Update BCs and Patch calls for GPUs. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H Tutorials/GPU/Advection_AmrCore/Source/Make.package Tutorials/GPU/Advection_AmrCore/Source/bc_fill.H Tutorials/GPU/Advection_AmrCore/Source/bc_fill_nd.F90 commit 4d65b9ff195f40aa16da4fb0dcd090cc47334947 Author: kngott Date: Mon Jun 17 20:31:25 2019 -0700 Add GPU tagging. Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H Tutorials/GPU/Advection_AmrCore/Source/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 Tutorials/GPU/Advection_AmrCore/Source/Tagging.H commit 033e103adc7bf405577329bddd57516dfa9ddb39 Author: Christopher DeGrendele Date: Tue Jun 18 11:39:33 2019 -0700 This now compiles on CPUs Src/Particle/AMReX_TracerParticle_mod_K.H commit 80e5d068c2ce362ec5d86bf10938d2107075a887 Author: Christopher DeGrendele Date: Tue Jun 18 11:29:13 2019 -0700 function parameters Src/Particle/#AMReX_ParGDB.H# Src/Particle/#AMReX_ParticleContainerI.H# Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 7f9c319b51f31ccb0a589c5e8a81fad61093c7e8 Author: Ann Almgren Date: Tue Jun 18 10:53:36 2019 -0700 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 08cc2209ec2f17f4f36420c6e3c5a8f530377834 Author: Andrew Myers Date: Tue Jun 18 10:51:48 2019 -0700 change function signature of the interp function Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 9d456183b8d36200e0035ba792ff3a5caf0da09a Merge: 66a1e8a55 2e720cce9 Author: WeiqunZhang Date: Tue Jun 18 10:48:42 2019 -0700 Merge pull request #504 from KiranEiden/keiden/amrex Fixed typo in print_backtrace_info commit 2e720cce925e3771d2fb6548e68b256e873f9c2f Author: Kiran Eiden Date: Tue Jun 18 10:40:46 2019 -0700 Fixed typo in print_backtrace_info Src/Base/AMReX_BLBackTrace.cpp commit be500b06b7fd38d62a47f47fc1b88450aa29028f Author: Christopher DeGrendele Date: Tue Jun 18 10:33:59 2019 -0700 push Src/Particle/AMReX_Particle.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 66a1e8a55997a8396a3c5d6904c9e3837c75cea4 Author: Weiqun Zhang Date: Tue Jun 18 10:03:19 2019 -0700 change names in tutorial documentation and update license information Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/conf.py Docs/sphinx_tutorials/source/index.rst build_and_deploy.sh commit e3a542f6d14aba1d56a4c222f59ea25fba389103 Author: Weiqun Zhang Date: Tue Jun 18 09:16:38 2019 -0700 point to parse_bt.py in backtrace message Src/Base/AMReX_BLBackTrace.cpp Tools/Backtrace/parse_bt.py commit 7edf2a9c96db0c3b28653c9951cd5bad9d710520 Merge: 10c8682a4 318dc951c Author: WeiqunZhang Date: Tue Jun 18 08:48:46 2019 -0700 Merge pull request #503 from AMReX-Codes/mz increase precision of output commit 318dc951c8d8b28d6c4771d781ea4c3d5bb44a2c Author: Michael Zingale Date: Tue Jun 18 11:38:51 2019 -0400 increase precision of output so we can use the results for mapping for problem inits to roundoff Tools/Plotfile/fextract.cpp commit 3a61bad82c9396d4610aeadb60fd717986a975fd Author: Christopher DeGrendele Date: Tue Jun 18 08:04:46 2019 -0700 testing Src/Particle/AMReX_TracerParticle_mod_K.H commit 10c8682a46336dff7c658ad81a0edd07e331ef7d Author: Weiqun Zhang Date: Mon Jun 17 20:43:27 2019 -0700 fix typecheck. It doesn't like __attribute__ Src/Base/AMReX_Extension.H Tools/GNUMake/Make.rules commit 217167b0e1a5ded4e647644bc9ecdb9f0475e9b3 Merge: bb35be534 49b5191d1 Author: Andrew Myers Date: Mon Jun 17 20:21:21 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bb35be534646a2499e7b8e689ccc07795ff9f42f Author: Andrew Myers Date: Mon Jun 17 20:21:02 2019 -0700 a better check for OpenMP < 3.1 Src/Particle/AMReX_Particle.H commit 49b5191d19c9cba066961a1e725acd7a220504c3 Merge: 8dc4071ef abb991019 Author: Ann Almgren Date: Mon Jun 17 20:14:35 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 8dc4071ef0d15d8fe6e9c3a7fa0bc943a5bc8820 Author: Ann Almgren Date: Mon Jun 17 20:11:07 2019 -0700 Need to test on apz(i,j,k+1) not apz(i,j,k) when testing the hi-side terms Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 34ed0239a6047ea25b9dbf04f5e50397f0970e5b Author: kngott Date: Mon Jun 17 18:04:30 2019 -0700 Fix header. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H commit abb99101967db07ca31d0e7736298171a5f44df2 Author: Weiqun Zhang Date: Mon Jun 17 16:13:48 2019 -0700 fix omp race condition Src/Base/AMReX_BoxArray.cpp commit cb93b55c21e83ed6243b4a29df22f3520731871f Author: Christopher DeGrendele Date: Mon Jun 17 15:06:06 2019 -0700 Trial 2 Src/Base/#AMReX_FArrayBox.H# Src/Base/#AMReX_FArrayBox.cpp# Src/Particle/#AMReX_ParGDB.H# Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/AMReX_Particle.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 1c99b1338b37747d8fb2c2e96344ac9587b90f2b Merge: d7c8c3c8a 46c05b129 Author: Weiqun Zhang Date: Mon Jun 17 09:21:23 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d7c8c3c8a2af379658980e882a95887639f680a0 Author: Weiqun Zhang Date: Sun Jun 16 18:22:28 2019 -0700 add MacProjector::setBottomVerbose function Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit 46c05b129f2a72bf81856045877236942d2da1fa Merge: b4bd2202f 340a85f9e Author: Andrew Myers Date: Sun Jun 16 17:31:31 2019 -0700 Merge branch 'development' into sum_neighbors commit 340a85f9e8bf0cc3659bddd831f2a772f7a856a5 Author: Weiqun Zhang Date: Sat Jun 15 17:13:26 2019 -0700 make sure it works with OMP < 3.1 Src/Base/AMReX_MultiFab.cpp commit b4bd2202f3e2619701a4e22ded926bbad5cddb24 Author: Andrew Myers Date: Sat Jun 15 16:31:48 2019 -0700 add test integer comp to neighbor list tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/neighbor_list_2d.f90 Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit 0ed5d0d1a446cb7a13f00b7ede92d0b62e3754d9 Author: Andrew Myers Date: Sat Jun 15 16:31:24 2019 -0700 add sumNeighbors for int comps too Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit 445ebec3cab3c6089f13d5a597196e64c20e585a Merge: 3c30a8133 5c01ebd8d Author: Weiqun Zhang Date: Sat Jun 15 16:25:12 2019 -0700 Merge branch 'hip' into development commit af21c228afdfc70a52cf9eab963cd6a9dce786b1 Author: Andrew Myers Date: Sat Jun 15 16:16:47 2019 -0700 more descriptive variable name Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit f502f972c3d483876c0ca8947cc80e687f90f751 Author: Andrew Myers Date: Sat Jun 15 16:15:00 2019 -0700 fix bug in sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit f9915fb34569985fa6dbfbfcf041fc012841fb62 Author: Andrew Myers Date: Sat Jun 15 15:29:17 2019 -0700 unpack the communicated data Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleContainerI.H commit aefe1bcb382be2c27f56cc0bb9a269fd8fa8fd2b Author: Andrew Myers Date: Sat Jun 15 15:28:46 2019 -0700 ignore this unused Src/Base/AMReX_FabArrayCommI.H commit 36735775a198067099025fb46a7de0512d86a0c5 Author: Andrew Myers Date: Sat Jun 15 14:38:21 2019 -0700 minor formatting changes Src/Particle/AMReX_NeighborParticles.H commit 96ceaf4a076077b52559374407a061007f8b4353 Author: Andrew Myers Date: Sat Jun 15 14:35:55 2019 -0700 implementing MPI portion of sumNeighbors Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleContainerI.H commit 3c30a8133218def80b2945228dd51fa072edf91f Merge: 19d1a66ba 4e769bfc5 Author: Weiqun Zhang Date: Sat Jun 15 14:12:20 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0cbcb8e46488cc83064c11d5c229322f0cda0a32 Author: Andrew Myers Date: Sat Jun 15 13:59:13 2019 -0700 implement local form of sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit a8f852b57f62995518b177d1945ebefe6343dc48 Author: Andrew Myers Date: Sat Jun 15 13:32:10 2019 -0700 adding a level to the InverseCopyTag Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 282c7ec7343aaebe993e152f8adec7d035fb0ba7 Author: Andrew Myers Date: Sat Jun 15 13:24:08 2019 -0700 starting to work on implementing the sumNeighbors MPI exchange Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 5c01ebd8d640e6bf556f78297427c2775c19830e Author: Weiqun Zhang Date: Sat Jun 15 13:04:55 2019 -0700 fix typo in interp 2d Src/AmrCore/AMReX_Interp_2D_C.H commit 631c60077c5338b443acd85005d72bd59d1ec4fe Merge: 2d98120f3 d32ff0b75 Author: Weiqun Zhang Date: Sat Jun 15 12:50:41 2019 -0700 Merge branch 'hip' of github.com:AMReX-Codes/amrex into hip commit 2d98120f387b902f5653a71917bcd240fde27e39 Author: Weiqun Zhang Date: Sat Jun 15 11:49:30 2019 -0700 add lbound, ubound and length for Array4. remove fabPtr and AsyncFab from Interpolater Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_Array4.H commit 4e769bfc531247a4dc5ecd16f36ad4b623ef304a Author: Andrew Myers Date: Sat Jun 15 00:16:00 2019 -0400 fix off-by-one error Src/Particle/AMReX_ParticleContainerI.H commit d32ff0b759a39d854163ab71557efaba35452cc5 Author: atmyers Date: Fri Jun 14 20:26:52 2019 -0700 getting rid of some fabPtr in the particle classes Src/Particle/AMReX_Functors.H Src/Particle/AMReX_ParticleContainerI.H commit 2c8edd8137553383491acfb8c35800d0f73b05e5 Author: Weiqun Zhang Date: Fri Jun 14 18:43:57 2019 -0700 use Array4 in neighbor particles Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit d9011fc25bcb7c63f753301cc544260fbe35b7ec Author: Weiqun Zhang Date: Fri Jun 14 18:43:06 2019 -0700 fix commit 69791966a864e27 Src/Amr/AMReX_AmrLevel.cpp commit 7a4194de7852d93f69f7097754cfbf8219450830 Author: Weiqun Zhang Date: Fri Jun 14 18:16:51 2019 -0700 put Array4 and Dim3 into their own files so that we can have Array4::operator() taking IntVect Src/Base/AMReX_Array.H Src/Base/AMReX_Array4.H Src/Base/AMReX_Box.H Src/Base/AMReX_Dim3.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_IntVect.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 7ae5228c5af6bb39ecec887f87dda70b3a4d89c8 Author: Andrew Myers Date: Fri Jun 14 17:25:54 2019 -0700 fix compilation error in sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit a30bce88c891858009b7ab76a854fd1e1f59f181 Author: Andrew Myers Date: Fri Jun 14 17:23:57 2019 -0700 fix comments Src/Particle/AMReX_NeighborParticles.H commit 12b126e87598f951c8a10ae05284f37f89e797e7 Author: Andrew Myers Date: Fri Jun 14 17:22:55 2019 -0700 output operator for InverseCopyTag Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 5b829d456cccf535b492e8dfb3ade1f74535a6fc Merge: 41014e267 16d211031 Author: Andrew Myers Date: Fri Jun 14 17:16:33 2019 -0700 Merge branch 'development' into sum_neighbors commit 41014e267219cd9f5e948bba81b3d4babcb41f75 Author: Andrew Myers Date: Fri Jun 14 17:14:55 2019 -0700 use getter for enableInverse Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 302d2c748912468b08bd83e5941835574e7fe692 Author: Andrew Myers Date: Fri Jun 14 17:12:33 2019 -0700 make enable_inverse static Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 508ce00c47ff9e0398a7e4fb840244421b956096 Author: Andrew Myers Date: Fri Jun 14 17:11:31 2019 -0700 getters / setters for enable inverse Src/Particle/AMReX_NeighborParticles.H commit 1862718af2b9a4618c33afa9de926e8d8d9e76a5 Author: Andrew Myers Date: Fri Jun 14 17:10:04 2019 -0700 abort if calling sumNeighbors without enable_inverse Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 8457f4595ef398df7598c2ab885537bb22bf9354 Author: Andrew Myers Date: Fri Jun 14 17:08:51 2019 -0700 remove Redistribute-based implementation of sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit c705af94069dcbdb8972f5be56f4e67100b7e1a3 Author: Andrew Myers Date: Fri Jun 14 17:08:13 2019 -0700 wrap the inverse neighbor particle stuff in a boolean flag Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 2b6296201ac384173e461cbb4d01c4b1cfd9e500 Author: Christopher DeGrendele Date: Fri Jun 14 16:04:55 2019 -0700 not yet working gpu code Src/Particle/#AMReX_ParticleContainerI.H# Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 7c22bf1fa59e7133c6c69374e82253097b0b8326 Merge: 69791966a 19d1a66ba Author: Weiqun Zhang Date: Fri Jun 14 16:04:44 2019 -0700 Merge branch 'development' into hip commit 69791966a864e2703f3e51bda0a58c4cfef050b3 Author: Weiqun Zhang Date: Fri Jun 14 16:03:59 2019 -0700 update Amr/ to avoid fabPtr Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_Extrapolater.cpp Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 7baa200d89f28e4662d5a9fa6ee28a9e90ae67f2 Author: Andrew Myers Date: Fri Jun 14 12:53:05 2019 -0700 keep track of information needed to reverse the neighbor particle communication. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 66df989ccbe05afa8fbab2c19decf86174df85e2 Author: Andrew Myers Date: Fri Jun 14 11:10:38 2019 -0700 calling sumNeighbors in the main evolve loop Tutorials/Particles/NeighborList/main.cpp commit 85ed015a98d583e202a430b2d15fd338c253738d Author: Andrew Myers Date: Fri Jun 14 11:10:14 2019 -0700 add a test comp to the neighbor particle tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/neighbor_list_2d.f90 Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit 1a469a0a50a75aeafa9824152a13447a2b1946ac Author: Andrew Myers Date: Fri Jun 14 11:08:57 2019 -0700 add Redistribute-based implementation of sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 082c57c5767636fe7346f59c365a0bd7a14c1acc Author: Andrew Myers Date: Fri Jun 14 11:08:28 2019 -0700 add dispatch for CPU implementation of sumNeighbors Src/Particle/AMReX_NeighborParticlesI.H commit 7461573e8e84289b0a643eada9d835c9ec235077 Author: Andrew Myers Date: Fri Jun 14 11:07:48 2019 -0700 initialize a tmp PC from a known ParGDB Src/Particle/AMReX_Particles.H commit d59eea3586b67cf8193e361661ff8ed5407f55bd Author: Andrew Myers Date: Fri Jun 14 11:07:18 2019 -0700 adding a sum neighbors method for the NeighborPC Src/Particle/AMReX_NeighborParticles.H commit 16d2110317f7899edae1da752724a89fe2457fac Author: Jean M. Sexton Date: Fri Jun 14 10:06:10 2019 -0700 Add GPU debugging section, make ReduceSum include function prototype in documentation Docs/sphinx_documentation/source/GPU.rst commit 19d1a66ba37070e7203c47e11ed9a384ba73a792 Author: Weiqun Zhang Date: Fri Jun 14 09:31:53 2019 -0700 MLMG: fab Ptr to Array4 Src/Boundary/AMReX_MultiMask.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit f2dbaef853bf0d1135d91e6cd4f73c2a8b9583dc Author: Ann Almgren Date: Fri Jun 14 09:32:48 2019 -0700 Remove mfix-specific text Docs/sphinx_documentation/source/InputsProblemDefinition.rst commit 534bd6bafddbe1954a5dc29dc5fc03f83b3a7323 Author: Weiqun Zhang Date: Fri Jun 14 09:23:28 2019 -0700 Mask: add constructors taking Array4 Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/AMReX_YAFluxRegister.cpp commit 7d966002680cc049fb4d4914e10c5502c383e74b Author: Ann Almgren Date: Fri Jun 14 09:21:18 2019 -0700 Add default load balancing strategy Docs/sphinx_documentation/source/LoadBalancing.rst commit 58c58bd963eb333ecb9e2a2a004708bf5e43e3ac Merge: 3765e3113 ac849b567 Author: Weiqun Zhang Date: Fri Jun 14 08:56:23 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ac849b567f6bb488257bf0a83ba8611291c4b375 Author: Jean M. Sexton Date: Thu Jun 13 16:03:02 2019 -0700 Add Run-time Inputs chapter based off amrex-specific portions of MFIX-Exa documentation Docs/sphinx_documentation/source/InputsCheckpoint.rst Docs/sphinx_documentation/source/InputsLoadBalancing.rst Docs/sphinx_documentation/source/InputsPlotFiles.rst Docs/sphinx_documentation/source/InputsProblemDefinition.rst Docs/sphinx_documentation/source/InputsTimeStepping.rst Docs/sphinx_documentation/source/Inputs_Chapter.rst Docs/sphinx_documentation/source/index.rst commit fa5ffb15b54dd1b4db86a5f15b3edbfedef60dc0 Author: Andrew Myers Date: Thu Jun 13 15:11:48 2019 -0700 remove outdated limitations from the GPU section Docs/sphinx_documentation/source/GPU.rst commit 650dd3ac16f95a97bfc68d4921c19640d5b16005 Author: Andrew Myers Date: Thu Jun 13 15:06:59 2019 -0700 fix a formatting problem Docs/sphinx_documentation/source/Particle.rst commit e0f6ed6eff91778c35ec2c446abacd558d6b71a3 Author: Andrew Myers Date: Thu Jun 13 15:03:15 2019 -0700 note the prefix for the amrex.use_gpu_aware_mpi flag Docs/sphinx_documentation/source/GPU.rst commit dd87d9f6e0d4016ebfbc23764d80f0bdca17e2b3 Author: Andrew Myers Date: Thu Jun 13 14:47:35 2019 -0700 add some documentation about inputs parameters relevant for the behavior of amrex particles, including IO and GPU performance Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/Particle.rst commit 3765e31135350ff91888b1b7ce816733d8278c22 Merge: 025ff90cc 6439e5e40 Author: Weiqun Zhang Date: Thu Jun 13 14:30:55 2019 -0700 Merge branch 'hip' into development commit 6439e5e40a3220ba40cac9d46077ac8f3b75a6e8 Author: Weiqun Zhang Date: Thu Jun 13 14:02:13 2019 -0700 PhysBCFunct: pass host fab to m_f Src/Base/AMReX_PhysBCFunct.H commit 025ff90ccf7b5bb19c51e2dfca89f7567a0ea9e9 Merge: 0fb0d2b02 0e3d17676 Author: Andrew Myers Date: Thu Jun 13 13:43:28 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0e9659c3b6055ca42e4e44f46eecf67c2a189557 Author: Weiqun Zhang Date: Thu Jun 13 13:39:41 2019 -0700 update amrex_avg_down* Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/Base/AMReX_MultiFabUtil_nd_C.H Src/EB/AMReX_EBMultiFabUtil.cpp Tests/Slice/main.cpp Tests/SliceWithInterp/main.cpp commit 6638056d02c06bcb4c334896e298c5326a7ba2d6 Author: Weiqun Zhang Date: Thu Jun 13 13:27:19 2019 -0700 add noexcept Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp commit 0fb0d2b0269f6d5e7c3ccfbf4e95425abd6e99a1 Author: Andrew Myers Date: Thu Jun 13 12:55:32 2019 -0700 remove these now unimplemented functions - they are in the Gpu:: namespace directly now Src/Base/AMReX_GpuDevice.H commit 0e3d17676096eaa0d45340d2930c7615f219d303 Author: Andrew Myers Date: Thu Jun 13 12:55:21 2019 -0700 use explicit device-to-host copies here rather than relying on page faults Src/Particle/AMReX_ParticleContainerI.H commit b73a83d082a71e54a0eb6432061a5135b6042b53 Author: Michele Rosso Date: Thu Jun 13 12:25:12 2019 -0700 CMake: update documentation. Docs/sphinx_documentation/source/GPU.rst commit f04990d73bd0268a9a1911c81799ec8b7d8b86f1 Author: Michele Rosso Date: Thu Jun 13 12:14:01 2019 -0700 CMake: improve CUDA support. * Set C++ and CUDA required standard via CMake compile features * Force CUDA setup in application codes if ENABLE_CUDA=on Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_SetupCUDA.cmake Tutorials/GPU/NeighborList/CMakeLists.txt commit 5cc30dbfd7d4f9b7ebbc7159257869f81e42c279 Author: Weiqun Zhang Date: Thu Jun 13 11:33:54 2019 -0700 fab to array4 in a number of MultiFabUtil functions Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit 38a093af5a735abe82abdfee4cd83e107ad2f51c Author: Weiqun Zhang Date: Thu Jun 13 09:38:53 2019 -0700 remove fabPtr from avg_cc_to_fc Src/Base/AMReX_BaseFab.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_Utility.H Tutorials/EB/Poisson/Poisson.cpp commit 0bbb6bf2e9bc637b529729e6066a310b3c389f49 Merge: 6949d7f1b c52a1512a Author: Weiqun Zhang Date: Wed Jun 12 17:35:26 2019 -0700 Merge branch 'development' into mlmg-2d commit c52a1512a3d422551ad41baf1bdedf44f06a85de Author: Weiqun Zhang Date: Wed Jun 12 17:22:43 2019 -0700 Add IndexType to FArrayBox contructed from Array4 to avoid assertion failure Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_IArrayBox.H commit f8a3aef2a7aba7f6657e23b7dc8d76ac154c3dfd Merge: 2be8f52b8 09030e1a0 Author: Michele Rosso Date: Wed Jun 12 16:01:53 2019 -0700 Merge branch 'development' into mr/cmake commit 6949d7f1b29fb2d89dde3c8449ca191effc3d94a Merge: d7a6a222c 45864247f Author: Weiqun Zhang Date: Wed Jun 12 14:17:46 2019 -0700 Merge branch 'development' into mlmg-2d commit d7a6a222c5b6bf3ae38b32799bc9f033ebd6e093 Author: Weiqun Zhang Date: Tue Jun 11 21:15:37 2019 -0700 reimplement the treatment of metric terms in MLMG Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H commit 09030e1a05faa0a05ced7fd182080bab4037be1f Author: Michele Rosso Date: Wed Jun 12 11:08:21 2019 -0700 CMake: fix var_NOT-FOUND bug Tools/CMake/AMReX_Config.cmake commit 5cc62c3d0b2c3ae54711ad5bc8a2a6ec66eb935f Merge: b3e1c3e3c 45864247f Author: Kevin Gott Date: Wed Jun 12 13:30:37 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit 45864247fd836da4ab53cddec00e48c91285425e Author: Weiqun Zhang Date: Tue Jun 11 20:37:53 2019 -0700 fix enable_if Src/Particle/AMReX_Particles.H commit e5394eb36466e9c831a3ebf9b2c517337f46c9bc Merge: 8aa918da7 f78799166 Author: Michele Rosso Date: Tue Jun 11 18:55:08 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8aa918da775c3aa775578ffd0622a9f2ca3d4805 Author: Michele Rosso Date: Tue Jun 11 18:54:22 2019 -0700 CMake: add nvToolsExt library to link line Tools/CMake/AMReX_Config.cmake commit 4d9c108d67ca87e8d8c96808b2953cc04dfbf553 Author: Michele Rosso Date: Tue Jun 11 18:41:37 2019 -0700 CMake: fix CUDA tutorials Tutorials/GPU/Launch/CMakeLists.txt Tutorials/GPU/NeighborList/CMakeLists.txt commit ff1b785deb405d1c6b6ef9a30b3349547c968918 Author: Michele Rosso Date: Tue Jun 11 18:30:05 2019 -0700 CMake: fix incorrect required Fortran flag for PGI compiler Tools/CMake/AMReXFlagsTargets.cmake commit f7879916611afef6f72c94560da149f39094a044 Author: Andrew Myers Date: Tue Jun 11 20:57:08 2019 -0400 std::enable_if_t is C++14, using another approach Src/Particle/AMReX_Particles.H commit b3e1c3e3c49178da6ee173cc7062ea8dc3e3da2a Merge: fccff75ef 5a13bb9f0 Author: Kevin Gott Date: Tue Jun 11 20:27:01 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit fccff75efbd11d1d4d374f1c1895126e093a368f Author: kngott Date: Tue Jun 11 17:22:41 2019 -0700 Strictly define regions in test. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 2e74ec473bbef46d895a5b133638e06dee41ed8d Author: kngott Date: Tue Jun 11 17:09:14 2019 -0700 Move copyFromBuffer graph creation to try to get some additional overlap with MPI. Src/Base/AMReX_FabArrayCommI.H commit 5a13bb9f03ffee3295379beb0c0eeb8ab5e48033 Author: Michele Rosso Date: Tue Jun 11 16:56:28 2019 -0700 CMake: enforce C++14 standard Tools/CMake/AMReX_Config.cmake commit cb2ea241c5c2b26cd113f6bd676e80b8355e98a3 Author: kngott Date: Tue Jun 11 16:19:21 2019 -0700 Change FillBoundary graphs to include memcpy. Src/Base/AMReX_FabArrayCommI.H commit 5fd2e9d62b399476e0503343bd61b6c6234e4eec Author: kngott Date: Tue Jun 11 15:51:54 2019 -0700 Add speedup calc to FillBoundary test. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit f99ad2d4d5a8bac0c72284748a2eab30faf89b4b Author: kngott Date: Tue Jun 11 14:45:26 2019 -0700 Add check to memcpy if not added to the graph. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 2be8f52b878a147f30240b6a491dfeb31d81e4f8 Author: Michele Rosso Date: Tue Jun 11 15:03:33 2019 -0700 CMake: document latest changes Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/GPU.rst commit 07d5c72d756bfabba94e79904c0ce530a56d0f57 Author: Michele Rosso Date: Tue Jun 11 15:03:11 2019 -0700 CMake: use a component-centric approch in exported config file Tools/CMake/AMReXConfig.cmake.in commit da6e3ca2b36b0164bb08c0e1f0966a8657475256 Merge: cc2022b93 7406a57ee Author: WeiqunZhang Date: Tue Jun 11 13:41:31 2019 -0700 Merge pull request #497 from mattbement/master add an option to enable PIC to the configuration script commit cc2022b9363221baa99b97c429cc39f06a4ae302 Merge: 5ff599167 825a16ad4 Author: Andrew Myers Date: Tue Jun 11 13:29:17 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5ff599167366da305ff2599bba934475a326254b Author: Andrew Myers Date: Tue Jun 11 13:29:02 2019 -0700 prevent implicit conversion of 'const char *' to 'bool' from selecting this function overload Src/Particle/AMReX_Particles.H commit 825a16ad47d44fca24baabc96524656ef90b4ca3 Merge: c644395e2 71d93fdc0 Author: Weiqun Zhang Date: Tue Jun 11 12:51:13 2019 -0700 Merge branch 'hip' into development commit c644395e2ce2fad3052eaa430259df0805e215cf Merge: 313a8ed2f 210c71dda Author: Weiqun Zhang Date: Tue Jun 11 12:51:01 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1924fd9d429a7c31f23080ae4e2f89584e740bae Author: kngott Date: Tue Jun 11 12:23:39 2019 -0700 De-sync FB local copy graph. Src/Base/AMReX_FabArrayCommI.H commit 71d93fdc03fba5920e8413ca8719d4effe69026d Author: Weiqun Zhang Date: Tue Jun 11 12:22:51 2019 -0700 fix make file for linking with mpif90 Tools/GNUMake/sites/Make.unknown commit fc62aecb01c117104c3e7d415e9eb569865ccf5a Author: kngott Date: Tue Jun 11 12:15:46 2019 -0700 Change CudaGraph execute to use Gpu::Device function. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 51ee1d18c98ea7efb9476ccace88017177a5659b Author: Weiqun Zhang Date: Tue Jun 11 11:20:59 2019 -0700 use omp atomic capture instead of critical Src/Base/AMReX_MultiFab.cpp commit 8d51c4768fbc2d033f0572a65ae108a63e2a5c9f Author: Weiqun Zhang Date: Tue Jun 11 10:15:34 2019 -0700 MultiFabUtil: use Array4 Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil.cpp commit cd65b11cc0158db4355f81beef05c18a4eeaa7f6 Merge: 88e02bb39 210c71dda Author: Michele Rosso Date: Tue Jun 11 10:41:37 2019 -0700 Merge branch 'development' into mr/cmake commit 6622a3e891c2ba15d3a37814bb1f53362140bb45 Merge: 62e5904c5 210c71dda Author: kngott Date: Tue Jun 11 10:32:13 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 77cb031db47b9f12def1d3e59b92568e697d3fc7 Author: Weiqun Zhang Date: Tue Jun 11 10:10:23 2019 -0700 fix for non-MPI Src/Base/AMReX_ccse-mpi.H commit a6c17fed76e6903da3276efe37cbe7168e976e4d Author: Weiqun Zhang Date: Tue Jun 11 09:45:18 2019 -0700 add Gpu::Atomic::Exch and reimplement MultiFab::minIndex and maxIndex Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_MultiFab.cpp commit 62e5904c5d286e1f5cd061b16ac298e4c9bca790 Author: kngott Date: Tue Jun 11 01:13:30 2019 -0700 Implement and test graph building with cudaEvents. Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp commit 127eeb8328b1a0e6dc31728966e9ef8dba4c511c Author: kngott Date: Tue Jun 11 01:09:36 2019 -0700 Properly order graphs to hide FB build. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 483d5eddf385e4709d139bffe05bdf8b6de8c99e Author: kngott Date: Tue Jun 11 01:05:41 2019 -0700 Add additional graph building options to setVal graph test. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 9d3f9d1a1ebed97b15177617db12d0486fc0a7e8 Author: kngott Date: Tue Jun 11 01:02:22 2019 -0700 Turn off synchs in all graph creation loops in FillBoundary. Src/Base/AMReX_FabArrayCommI.H commit 5a32de13af5c7c7a461283306238ab6a5ced4627 Author: kngott Date: Tue Jun 11 00:51:22 2019 -0700 Add StreamItInfo and option to turn off syncing. Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_GpuUtility.cpp commit d972ece09f7455096d7a61330703e8165c67c86a Author: Weiqun Zhang Date: Mon Jun 10 18:37:37 2019 -0700 reimplement minIndex Src/Base/AMReX_MultiFab.cpp commit 210c71dda5a21435805f32e4ea016a84bf273120 Author: Michele Rosso Date: Mon Jun 10 16:32:22 2019 -0700 Modify macro for consistency Src/Base/AMReX_Gpu.H commit 7406a57eea75b15e613aaf92b237385a67c3ed3e Author: Matt Bement Date: Mon Jun 10 14:49:22 2019 -0600 add an option to enable position independent code to the configuration script Tools/libamrex/configure.py commit bccd41b81667fcae817e3a32d0cdd2a00ca0ebb0 Author: kngott Date: Mon Jun 10 13:38:54 2019 -0700 Add optional flag to make graphExecution asynchronous. Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 313a8ed2faa07def0243d904aff39ebcc75585b8 Author: Weiqun Zhang Date: Mon Jun 10 13:23:54 2019 -0700 add MultiFab::norminf Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 1c7576fc206df1b8fcd7ed356d2c43d785318ca2 Author: Weiqun Zhang Date: Mon Jun 10 13:22:43 2019 -0700 Box constructor for extracting Box from Array4 Src/Base/AMReX_Box.H commit 5db0f45d7dff60599991abd2feeaedd5c28dad55 Author: Weiqun Zhang Date: Mon Jun 10 13:20:31 2019 -0700 remove const so that comiler generates operator= for BndryFuncArray Src/Base/AMReX_PhysBCFunct.H commit acdff3e9f3999e1d74332894264eef6b6ef9498c Author: Weiqun Zhang Date: Mon Jun 10 13:09:13 2019 -0700 fix DEBUG build Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H commit d8a26f72c74279032481deb94f80f46946c55a00 Author: Weiqun Zhang Date: Mon Jun 10 10:55:18 2019 -0700 add comment on initVal Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 36e4c4dd0dd7a62462106cbda076cb5a00bacb4e Merge: 343f3f653 67dd208f6 Author: kngott Date: Sun Jun 9 23:25:52 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 4b54eb6373deda6af97567a7203c4ca5128c35be Author: Weiqun Zhang Date: Sun Jun 9 18:50:34 2019 -0700 update FArrayBox Src/Base/AMReX_FArrayBox.H commit 0be8699e3ecd797f45b2a1970436796ae29affba Author: Weiqun Zhang Date: Sun Jun 9 18:18:40 2019 -0700 update reduce for amd device Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuReduce.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 5415ea9bdf6e17c5c2abb260b74869d4e48b2b7a Author: Weiqun Zhang Date: Sun Jun 9 17:20:25 2019 -0700 avoid fabPtr in FabArrayUtility Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayUtility.H commit 1a03289d8daca897221961ff9b95a4572c3d6d06 Author: Weiqun Zhang Date: Sun Jun 9 15:57:05 2019 -0700 update Tutorials Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/EBCNS/Source/CNS_advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp Tutorials/GPU/Launch/MyKernel_F.F90 Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/main.cpp commit d84114f6e0eed6e45737ba1b28bd964b58db6af8 Author: Weiqun Zhang Date: Sun Jun 9 10:48:16 2019 -0700 add a new field int ncomp to Array4. add new constructor to fabs so that we can make fab from Array4 on device Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_IArrayBox.H Tutorials/GPU/Launch/main.cpp commit 67dd208f648ae431895adf93d83ea0787b0e8d9c Author: Weiqun Zhang Date: Sat Jun 8 21:04:56 2019 -0700 remove AsyncFab from StateData::FillBoundary Src/Amr/AMReX_StateData.cpp commit 2913e1d0a4f6fefa5f53113d54fc91a18adaed39 Author: Weiqun Zhang Date: Sat Jun 8 18:38:12 2019 -0700 update boundary fill functions to take Array4 instead of FArrayBox Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp commit 63d8b3f876765339732dfdfd2cc2250163408e31 Merge: 324ce2342 4956dcca1 Author: Weiqun Zhang Date: Sat Jun 8 10:47:17 2019 -0700 Merge branch 'development' into hip commit 4956dcca1f9cd6710273a532dfa1f263a07e9642 Author: Weiqun Zhang Date: Sat Jun 8 10:46:42 2019 -0700 Fix the Poisson solver issue with dirichlet EB in periodic domain. It was mistakenly treated as singlular. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Tutorials/EB/Poisson/main.cpp commit 324ce234212d8e4cb31655873ac7111ba9489c3b Author: Weiqun Zhang Date: Sat Jun 8 10:23:04 2019 -0700 update FillDomainBoundary for gpu Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_PhysBCFunct.H commit 89be080c4cc50fef19091b1899297f2794bd3dc3 Author: Weiqun Zhang Date: Fri Jun 7 23:10:13 2019 -0700 allow z-direction cylinder in 2d Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF_Cylinder.H Tutorials/EB/Poisson/main.cpp commit 0bafa80ba19945d490c8f7ac9c75be98c1173e53 Author: Weiqun Zhang Date: Fri Jun 7 17:51:20 2019 -0700 BL_BACKTRACING -> AMREX_BACKTRACING Docs/Notes/Readme.backtrace Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Tools/GNUMake/Make.defs commit 9742528bed6b92d0d27de9c8a8e4a8a361044f98 Author: Weiqun Zhang Date: Fri Jun 7 17:44:40 2019 -0700 BL_TESTING -> AMREX_TESTING Tools/GNUMake/Make.defs Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/GPU/EBCNS/Source/CNS_io.cpp commit 758c3458490eb28d4d25c0ceffe8adcb9d35ebf8 Author: Weiqun Zhang Date: Fri Jun 7 17:39:33 2019 -0700 BL_TINY_PROFILING -> AMREX_TINY_PROFILING Src/Base/AMReX_BLProfiler.H Tools/GNUMake/Make.defs commit bbfe45aaa255e6908c229bf60aa012bf0aa2e748 Author: Weiqun Zhang Date: Fri Jun 7 17:35:30 2019 -0700 BL_MEM_PROFILING -> AMREX_MEM_PROFILING Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BArena.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MultiFab.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Tools/GNUMake/Make.defs Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 88d5b94de0e9b8e5387728553716ff4c59b2aefe Author: Weiqun Zhang Date: Fri Jun 7 17:25:44 2019 -0700 make BArena use malloc and free directly, which is supposed to be for CPU memory Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp commit d5319abf13a0863cf12184afc3d21c07af558d8f Author: Weiqun Zhang Date: Fri Jun 7 16:01:25 2019 -0700 update __CUDA_ARCH__ Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Extension.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuQualifiers.H commit 548477b0c40d0df4bbed21ccd8563f918085bf74 Author: Weiqun Zhang Date: Fri Jun 7 15:46:00 2019 -0700 hip: update Arena Src/Base/AMReX_Arena.cpp commit 88e02bb39df4cfe8b61aa8c65f6a589c9e416281 Merge: dee0e9b97 4d001942d Author: Michele Rosso Date: Fri Jun 7 15:07:36 2019 -0700 Merge branch 'development' into mr/cmake commit 4d001942dd0bc99b4af5ab4360a5924492807623 Author: Michele Rosso Date: Fri Jun 7 15:07:12 2019 -0700 CMake: add option to enable pinned memory Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 9e535915359b4f9d34b8084552eac157f251a58c Author: Michele Rosso Date: Fri Jun 7 14:42:02 2019 -0700 Revert "add AMREX_USE_GPU if ENABLE_CUDA" This reverts commit df9808bb32daa487c5c63d93a6b47a4f95497c40. AMREX_USE_GPU was already passed to the compiler for CUDA builds. Tools/CMake/AMReX_Defines.cmake commit 6ee029145a49768178800ef29e8601d736fba5b0 Author: Weiqun Zhang Date: Fri Jun 7 14:35:19 2019 -0700 add -DAMREX_FAB_IS_MANAGED Src/Base/AMReX_FabAllocator.cpp Tools/GNUMake/Make.defs commit d9e2d5533a8b35835b6235d16cbb5499c484641e Author: atmyers Date: Fri Jun 7 12:53:54 2019 -0700 change the order of these loops to be cache-friendly Src/Particle/AMReX_Particle_mod_K.H commit 46607d6bdfe50f822842ca17be9e670ddc8e780a Author: Weiqun Zhang Date: Fri Jun 7 12:12:56 2019 -0700 No need to use the legacy hipThreadIdx_* etc. Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuRange.H commit c1891211faa5bcd07a37320332f765490fe686a3 Author: atmyers Date: Fri Jun 7 10:37:29 2019 -0700 std::min/max -> amrex::min/max Src/Particle/AMReX_Particle_mod_K.H commit 34eb0c5d67b1c4217bf69092dad3970b0a3b13af Merge: 3dd7af396 2b4297e2e Author: Weiqun Zhang Date: Fri Jun 7 07:47:13 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2b4297e2e95be8fe049272ee75b1fecaff8a0c67 Author: Weiqun Zhang Date: Thu Jun 6 19:17:08 2019 -0700 fix 1d nodal Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit 3dd7af396123bb0bd5db49c75f9a5318c02d2fe4 Merge: a1a02ce80 60d6c21d0 Author: Weiqun Zhang Date: Thu Jun 6 19:05:16 2019 -0700 Merge branch 'development' into hip commit 60d6c21d062c8754985bbd36346f7c02d1f6aab5 Author: Weiqun Zhang Date: Thu Jun 6 17:19:48 2019 -0700 simplify EB/Poisson tutorial Tutorials/EB/Poisson/Make.package Tutorials/EB/Poisson/Poisson.cpp Tutorials/EB/Poisson/Poisson_F.H Tutorials/EB/Poisson/main.cpp Tutorials/EB/Poisson/poisson.F90 commit a1a02ce8092877be2a4037f357e2594dd4eeb429 Author: Weiqun Zhang Date: Thu Jun 6 14:34:46 2019 -0700 fix leading underscore Src/AmrCore/AMReX_AmrParticles.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_MultiFabUtil_Perilla.H Src/EB/AMReX_EB_LSCore_F.H Src/Extern/ProfParser/AMReX_AVGDOWN_F.H Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/Extern/amrdata/AMReX_DataServices.H commit e191c6ac05a787d9aaaef63cb9af56b0e744e4d6 Author: Weiqun Zhang Date: Thu Jun 6 14:14:06 2019 -0700 update launch macros and functions for hip Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunch.cpp Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosC.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuRange.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp Tests/GPU/Test/main.cpp commit fba880ff02f2d05f2a118d04099c8f3e779db1b0 Author: Weiqun Zhang Date: Thu Jun 6 13:18:39 2019 -0700 reorganize launch macros and functions Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunch.cpp Src/Base/AMReX_GpuLaunchMacrosC.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 23857740b2a6eb857fc26c90200b7d0c26058cb6 Author: Weiqun Zhang Date: Thu Jun 6 12:19:19 2019 -0700 update Range for hip Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuRange.H Src/Base/CMakeLists.txt Src/Base/Make.package commit e0fcbdbf6d519380e7fa3d108d84ff9108cbd2a5 Merge: e0e025828 ef6084e1b Author: WeiqunZhang Date: Thu Jun 6 12:09:28 2019 -0700 Merge pull request #495 from AMReX-Codes/mlcgfix fixed an error in the sxay function definition commit ef6084e1b11bdfcc407260400c74893f5390446f Author: Brandon Runnels Date: Thu Jun 6 12:46:49 2019 -0600 fixed an error in the sxay function definition Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit a17b0ffd86fc66ad8d7d001c7c887dbc39a86359 Author: Weiqun Zhang Date: Thu Jun 6 11:19:07 2019 -0700 hip: CudaMemory -> GpuMemory Src/Base/AMReX_Box.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuMemory.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 01bdfa4e4342209e7684cb1fee3edcf155026c68 Author: Weiqun Zhang Date: Thu Jun 6 10:28:46 2019 -0700 update Elixir for hip Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuElixir.H Src/Base/AMReX_GpuElixir.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 4085a3101a059d813f0e2ff06f1a08663ff04ac0 Author: Weiqun Zhang Date: Thu Jun 6 09:25:17 2019 -0700 remove unused variable Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e0e025828c3b8dc39f07855482f17012d7ebc241 Merge: 58ac0b987 614cc47f6 Author: WeiqunZhang Date: Thu Jun 6 09:19:43 2019 -0700 Merge pull request #489 from AMReX-Codes/nodeghostcells-pr Merge nodeghostcells into development commit 614cc47f698ee0e7adc59ab648ba24b6a6a9b0e1 Author: Brandon Runnels Date: Wed Jun 5 16:03:38 2019 -0600 changed ncomp in fine_mask to 1 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit d3838ce6bc6d06f8a6bbae058aea4e29a25b6edc Author: Brandon Runnels Date: Wed Jun 5 15:54:10 2019 -0600 addressed weiqun's comments Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H commit 1e62c8a14e2966ba19ae17b34df9ad843f40ce85 Merge: e5cac5b88 58ac0b987 Author: Brandon Runnels Date: Wed Jun 5 14:44:48 2019 -0600 Merge branch 'development' into nodeghostcells-pr commit 58ac0b98774a961d1977e074c052325431991120 Merge: 475a58732 e645f917d Author: Weiqun Zhang Date: Tue Jun 4 22:04:06 2019 -0700 Merge branch 'hip' into development commit 475a58732c25149a6316aa872f630cb28b3b9a71 Merge: 04faaca15 c825490f9 Author: Weiqun Zhang Date: Tue Jun 4 22:03:55 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit dee0e9b971361d7ad38b7f2342135104d61c9f03 Author: Michele Rosso Date: Tue Jun 4 18:11:02 2019 -0700 CMake: add doc regarding exported targets Docs/sphinx_documentation/source/BuildingAMReX.rst commit 343f3f6530b2c382dc3e9bfe494f149e26f50bd4 Author: kngott Date: Tue Jun 4 16:22:29 2019 -0700 Add pinned std::vector allocator and Vector. Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H commit c825490f941dace5d18858654a4521c5cd08dbd3 Merge: c4c111456 606aed47e Author: Andrew Myers Date: Tue Jun 4 16:09:04 2019 -0700 Merge pull request #494 from AMReX-Codes/init_redist_gpu Init redist gpu commit 8658a786190a61b94f6e20b01d3483ead9c254d0 Author: kngott Date: Tue Jun 4 13:52:42 2019 -0700 Updating graph tests for hip. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 8204d86a0a7373ae9900446222da6187cbf91394 Author: kngott Date: Tue Jun 4 13:45:41 2019 -0700 Adjust for hip merge. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.cpp Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp commit 0907cf8fdab2b456ef5ea4066c2d55ba1f1fb454 Author: kngott Date: Tue Jun 4 13:21:28 2019 -0700 Fix merge on GpuDevice Src/Base/AMReX_GpuDevice.cpp commit 6a7306828e088694896fbc9a8c9bc68f53bd467b Merge: e68a37d3c e645f917d Author: kngott Date: Tue Jun 4 13:15:30 2019 -0700 Merge branch 'hip' into kngott/cudaGraphs commit e68a37d3cf2d87155d033a8730a45132e1f44b83 Author: Weiqun Zhang Date: Mon Jun 3 17:06:06 2019 -0700 add AMREX_USE_GPU if ENABLE_CUDA Tools/CMake/AMReX_Defines.cmake commit 512f51f9ab5650d43b490eb3a9908b383208df3e Author: Weiqun Zhang Date: Mon Jun 3 15:23:48 2019 -0700 add runtime boolean parameter `amrex.fpe_abort_on_out_of_gpu_memory` to address Issue #485. Src/Base/AMReX_Arena.cpp commit dd3cc8e993ac40c11e83ff2207fd97457389c687 Author: Cyrus Harrison Date: Fri May 31 10:57:41 2019 -0700 blueprint support: allow mpi tasks without mesh data Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp commit 53a706c0b8b93b1c21c1eb44c0b8d4c4fe600b9d Author: Cyrus Harrison Date: Thu May 30 10:18:08 2019 -0600 use BL_SINGLE_PRECISION_PARTICLES to select particle data type Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit 4f486dcc7d42f08c679b8c3c08248cee2f12ce84 Author: kngott Date: Tue Jun 4 11:23:06 2019 -0700 [WIP]: currently breaks FB, working version in development -> test putting memcpy into cudaGraph. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphWithMemcpy/GNUmakefile Tests/GPU/CudaGraphs/GraphWithMemcpy/Make.package Tests/GPU/CudaGraphs/GraphWithMemcpy/inputs_3d Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp Tests/GPU/CudaGraphs/GraphWithMemcpy/run.corigpu commit e645f917dd88b591835fac01c9f32b497858e7a8 Author: Weiqun Zhang Date: Tue Jun 4 09:59:28 2019 -0700 fix the use of numCudaStreams Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit bce3ad68608b402964f71b5576222885f93acd06 Author: Weiqun Zhang Date: Tue Jun 4 09:48:39 2019 -0700 fix merge Src/Base/AMReX_Arena.cpp commit fcdef8cad5adef0ab91ceda24b7ec0da59d6f5d1 Merge: 6c4474412 04faaca15 Author: Weiqun Zhang Date: Tue Jun 4 09:46:25 2019 -0700 Merge branch 'development' into hip commit 04faaca157d9f5311c07aa8fc7aa741a876a2754 Merge: 34cc6be5b c4c111456 Author: Weiqun Zhang Date: Tue Jun 4 09:38:58 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c4c11145640bbb50510b61dcf21814a0f7d74385 Merge: d90dcdfaf fceb7e626 Author: WeiqunZhang Date: Tue Jun 4 09:36:27 2019 -0700 Merge pull request #476 from AMReX-Codes/kngott/cudaGraphs [WIP] Adding CUDA graph support to FillBoundary commit 606aed47eec35dbef069e154ebd43a17314eb635 Author: Jean M. Sexton Date: Tue Jun 4 09:30:31 2019 -0700 Updated RedistributeMPI to use HostVector if AMREX_USE_CUDA=TRUE, fixed fortran indexing bug in particle test Src/Particle/AMReX_ParticleContainerI.H Tests/GPU/Particles/Redistribute/test_3d.F90 commit 317c0b001a96323a6472dd9703416e47befad499 Author: Jean M. Sexton Date: Thu May 23 05:40:48 2019 -0700 Added HostVector to thrust::copy version of RedistributeMPI for the RedistributeCPU version Src/Particle/AMReX_ParticleContainerI.H commit 34cc6be5b055d43e42266278ab01ef7cd059983d Merge: d90dcdfaf fceb7e626 Author: Weiqun Zhang Date: Mon Jun 3 17:23:35 2019 -0700 Merge branch 'kngott/cudaGraphs' into development commit 6c4474412a32cc5cae7bf32509d67545174da4bc Author: Weiqun Zhang Date: Mon Jun 3 17:16:42 2019 -0700 fix AMREX_HIP_OR_CUDA macro Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit d90dcdfaffb286ae9f17cb5fae4a372419252345 Author: Weiqun Zhang Date: Mon Jun 3 17:06:06 2019 -0700 add AMREX_USE_GPU if ENABLE_CUDA Tools/CMake/AMReX_Defines.cmake commit df9808bb32daa487c5c63d93a6b47a4f95497c40 Author: Weiqun Zhang Date: Mon Jun 3 17:06:06 2019 -0700 add AMREX_USE_GPU if ENABLE_CUDA Tools/CMake/AMReX_Defines.cmake commit 4c7e477193d7cbccd092dd3ca82a8ef7ec84446e Author: Weiqun Zhang Date: Mon Jun 3 16:49:54 2019 -0700 rename some Cuda* files to Gpu* Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncFab.H Src/Base/AMReX_GpuAsyncFab.cpp Src/Base/AMReX_GpuAsyncFabImpl.H Src/Base/AMReX_GpuAsyncFabImpl.cpp Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuUtility.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/F_scripts/write_cuda_headers.py commit a87000ae21a18ee0d11c7e43c095a191178e2c94 Author: Weiqun Zhang Date: Mon Jun 3 16:33:30 2019 -0700 fix merge Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaGraph.H commit b3360971ea7c8a24e4ec9043fb76291ceb6b1c1e Merge: 1ca21e17a fceb7e626 Author: Weiqun Zhang Date: Mon Jun 3 16:25:45 2019 -0700 Merge branch 'kngott/cudaGraphs' into hip commit 00c4f657b93ce94c729396f286fbd4102606720c Author: Weiqun Zhang Date: Mon Jun 3 15:23:48 2019 -0700 add runtime boolean parameter `amrex.fpe_abort_on_out_of_gpu_memory` to address Issue #485. Src/Base/AMReX_Arena.cpp commit fceb7e6264878fbf7ec3c80b1e72b27a6ee758b7 Author: Weiqun Zhang Date: Mon Jun 3 12:59:06 2019 -0700 make cuda graph opt-in Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 2e08dc482af397d7f44d55af76c467cbaca735fc Merge: 91dbbd21d b372630d2 Author: Weiqun Zhang Date: Mon Jun 3 12:51:18 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 91dbbd21d29aa5bcc98355d089cb7f8e6659d241 Author: Weiqun Zhang Date: Mon Jun 3 12:39:53 2019 -0700 allow empty tags Src/Base/AMReX_FabArrayCommI.H commit 47e2cfcb27f8cff7472e308d9b429a7d4d679be7 Author: Weiqun Zhang Date: Mon Jun 3 09:49:36 2019 -0700 check __cplusplus instead gcc version. add constexpr Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaGraph.H commit 68ed0414fe43737e4e4273d9b9c9e71d12835f69 Merge: b372630d2 3e44dd633 Author: WeiqunZhang Date: Mon Jun 3 09:20:59 2019 -0700 Merge pull request #491 from Alpine-DAV/task/2019_05_blueprint_updates conduit blueprint integration updates commit b372630d20d4f02db18f00ed9a123ca49c9bc970 Merge: f3a1a1b21 24a24023c Author: Weiqun Zhang Date: Mon Jun 3 07:49:02 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f3a1a1b2128fa7964935caa2fe18c0ab7f044778 Merge: f536ee205 ef3c8a97d Author: Weiqun Zhang Date: Mon Jun 3 07:47:35 2019 -0700 Merge branch 'master' into development commit f536ee20544c383133c14c46a7f688d4c58d735f Author: Weiqun Zhang Date: Sun Jun 2 09:16:51 2019 -0700 fix merge Src/AmrCore/AMReX_FluxReg_3D_C.H commit 8b512382acafe7540cc549e57d59509424ddc5d9 Merge: 288df8082 4b5e6781e Author: Weiqun Zhang Date: Sun Jun 2 09:15:20 2019 -0700 Merge branch 'weiqun/dev' into development commit 24a24023c03769728b1e8034fefb699ae143d25b Author: Tan Nguyen Date: Sat Jun 1 16:55:31 2019 -0700 fix a memory deallocation bug Src/Amr/AMReX_Amr.cpp commit f819cdb9fb0f77fc460486e62c8483b8c5626e6d Merge: c8216a869 69237b982 Author: Tan Nguyen Date: Sat Jun 1 15:44:05 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c8216a8699b8dcb91fd4e045001c980be603d938 Author: Tan Nguyen Date: Sat Jun 1 15:43:41 2019 -0700 upcxx backend that survived a few production tests Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrTask/rts_impls/mpi/Makefile Src/AmrTask/rts_impls/mpi/PackageQueue.H Src/AmrTask/rts_impls/mpi/PackageQueue.cpp Src/AmrTask/rts_impls/mpi/Perilla.cpp Src/AmrTask/rts_impls/mpi/PerillaConfig.H Src/AmrTask/rts_impls/mpi/PerillaRts.H Src/AmrTask/rts_impls/mpi/PerillaRts.cpp Src/AmrTask/rts_impls/runtime_common/Perilla_common.cpp Src/AmrTask/rts_impls/runtime_common/RGIter.cpp Src/AmrTask/rts_impls/runtime_common/RegionGraph.H Src/AmrTask/rts_impls/runtime_common/RegionGraph.cpp Src/AmrTask/rts_impls/runtime_common/RegionQueue.H Src/AmrTask/rts_impls/runtime_common/RegionQueue.cpp Src/AmrTask/rts_impls/upcxx/Makefile Src/AmrTask/rts_impls/upcxx/PackageQueue.H Src/AmrTask/rts_impls/upcxx/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx/Perilla.H Src/AmrTask/rts_impls/upcxx/Perilla.cpp Src/AmrTask/rts_impls/upcxx/PerillaConfig.H Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/inputs Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp Tools/GNUMake/Make.upcxx commit 4b5e6781ebb234c1c443184d3c3995c69fe955a5 Author: Weiqun Zhang Date: Sat Jun 1 09:01:28 2019 -0700 fix calls to interp and protect Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_GpuControl.H Src/EB/AMReX_EBInterpolater.H Src/EB/AMReX_EBInterpolater.cpp commit fd76d044f1217e276360798aaa4d894828ee7d2b Author: Weiqun Zhang Date: Sat Jun 1 08:15:07 2019 -0700 add RunOn parameter to virtual Interpolater::interp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp commit 288df80820feb337e1764d6023983f2c46dc5d7b Merge: 15f299ab3 b48912444 Author: Weiqun Zhang Date: Sat Jun 1 07:56:22 2019 -0700 Merge branch 'weiqun/dev' into development commit b489124447a5bbb6b9a5c0ebc06fc7fa0cd833d1 Author: Weiqun Zhang Date: Fri May 31 22:13:30 2019 -0700 Add RunOn parameter to FluxRegister::FineAdd Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp commit 15f299ab3091426d568edd36670c59fbdc71d187 Author: Weiqun Zhang Date: Fri May 31 22:13:30 2019 -0700 Add RunOn parameter to FluxRegister::FineAdd Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp commit 5d4ca8053cb653427e5a12625eb01a9071ddd5cf Author: Weiqun Zhang Date: Fri May 31 15:36:00 2019 -0700 add RunOn parameter to some YAFluxRegister functions and fix MLMG Src/Base/AMReX_GpuControl.H Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit d7a47b2c48c88fb063cdc35becb858b34b6b915b Merge: ca721a542 929a6e691 Author: Weiqun Zhang Date: Fri May 31 13:53:08 2019 -0700 Merge branch 'weiqun/attribute_weak' into development commit ca721a542a998447477ee8c9383f2b9ff2757519 Merge: 69237b982 b1f2ff4c4 Author: Weiqun Zhang Date: Fri May 31 13:52:22 2019 -0700 Merge branch 'weiqun/amrex' into development commit ef3c8a97ded20c78b4f7178e6f41e4d82d432538 Merge: b33a70551 899631ce1 Author: Weiqun Zhang Date: Fri May 31 13:50:55 2019 -0700 Merge branch 'development' commit 69237b982bd98db6d9e932d4417344bbcb2ff731 Merge: 899631ce1 1313eaca4 Author: Marc Day Date: Fri May 31 12:31:28 2019 -0700 Merge pull request #492 from burlen/development fix some issues w SENSEI tutorials commit 1313eaca4ee5b32da0ec8f5ee87d0e595c162377 Author: Burlen Loring Date: Fri May 31 12:06:56 2019 -0700 clean up SENSEI AmrLevel tutorial Build & run with sensei by default and fix path to source code Tutorials/SENSEI/Advection_AmrLevel/Exec/Make.Adv Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs commit 20101167a580326a6bb0cfa360b6766db1eb6008 Author: Burlen Loring Date: Fri May 31 12:01:44 2019 -0700 clean up SENSEI AmrCore tutorial Build & run with sensei by default and fix path to source code Tutorials/SENSEI/Advection_AmrCore/Exec/Make.Adv Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/inputs commit 2dabf2810d66cf4c69a3cdcbab884a1fc9d9185e Author: Burlen Loring Date: Fri May 31 10:58:34 2019 -0700 remove UniformVelocity from SENSEI AmrLevel tutorial Using SENSEI with amrex::Amr class is already covered in the SingleVortex tutorial. Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Make.package Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probin commit 899631ce1843b30fd0c77e184302e7bdf246b0ee Author: kngott Date: Fri May 31 11:20:23 2019 -0700 Fix check for mvapich vs. openmpi on CoriGPU. Tools/GNUMake/sites/Make.nersc commit c735da03b1f5cc68d741e443fd7027b06f70f8ca Author: Andrew Myers Date: Fri May 31 11:01:23 2019 -0700 test on particle_lvl_offset here, instead of dxi and pdxi Src/Particle/AMReX_ParticleContainerI.H commit 453f84d3e30e2fc77e75d1f8bf69745123a2da61 Author: Andrew Myers Date: Fri May 31 10:59:23 2019 -0700 remove unused variables Src/Particle/AMReX_ParticleContainerI.H commit 3e44dd633413fb22dd91d4d1d3f0f0365c793aa0 Author: Cyrus Harrison Date: Fri May 31 10:57:41 2019 -0700 blueprint support: allow mpi tasks without mesh data Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp commit be8e9b0937113824ad433581490dcb8d68900342 Author: Andrew Myers Date: Fri May 31 10:39:02 2019 -0700 make this runtime assertion into a compile-time one Src/Particle/AMReX_ParticleContainerI.H commit b33a70551be30a41b05455f6c48f1ed6c3a05ecf Author: Weiqun Zhang Date: Fri May 31 08:04:29 2019 -0700 update CHANGES CHANGES commit 1ca21e17aac6d0789666f7d23d471684e0a18a10 Author: Weiqun Zhang Date: Thu May 30 15:51:08 2019 -0700 rename some Cuda* files to Gpu* Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_GpuUtility.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 1aad2d2c8d0b0ed5364f9170087dd86d945164e1 Author: Weiqun Zhang Date: Thu May 30 15:40:20 2019 -0700 add AMREX_DEVICE_COMPILE macro and update CudaUtility for hip Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuControl.H Src/Particle/AMReX_NeighborList.H commit 81898b81371cb2c4a29cd8629b9c2512010a77e0 Author: Weiqun Zhang Date: Thu May 30 14:00:04 2019 -0700 hip: update AsyncFab Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit a7efc0ed9dde2f7e8a22eb4bc124eb4b6173b360 Author: Weiqun Zhang Date: Thu May 30 13:31:23 2019 -0700 hip: update BaseFab and allow __managed__ when cuda is backend Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuQualifiers.H commit bd6a81b4c44366184e8ade48f592eb28617da438 Author: Weiqun Zhang Date: Thu May 30 12:38:38 2019 -0700 move some functions and classes to namespace amrex::Gpu. update Gpu::AsyncArray Docs/sphinx_documentation/source/GPU.rst Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MFIter.cpp Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Tests/GPU/Test/main.cpp Tests/GPU/TestB/main.cpp Tests/GPU/TestC/main.cpp Tools/F_scripts/write_cuda_headers.py Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp commit fc0c5b5528bcbea53bd344335ea022ff8bfdd740 Merge: 97d59bb77 978cc240e Author: Andrew Myers Date: Thu May 30 15:17:13 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 97d59bb77c1870291c48b1e1408bf617932996b1 Author: Andrew Myers Date: Thu May 30 15:16:49 2019 -0400 need to call define on the particle tile when restarting and runtime soa components are in play Src/Particle/AMReX_ParticleContainerI.H commit e5cac5b881322fa304dfc464d600f7bc6abfa41f Merge: bd5877962 978cc240e Author: Brandon Runnels Date: Thu May 30 11:44:27 2019 -0600 Merge branch 'development' into nodeghostcells-pr commit 1da833e9053c94a7be52ac50c9bff0de4a24833b Author: Cyrus Harrison Date: Thu May 30 10:18:08 2019 -0600 use BL_SINGLE_PRECISION_PARTICLES to select particle data type Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit a7fd7070eb7e556eb47c7f38f80ffe52e2fb799c Author: kngott Date: Thu May 30 00:42:14 2019 -0700 Seperate stopGraphRecording and setGraph. Src/Base/AMReX_FabArrayCommI.H commit 9d2bb614b0de8ae1d8a6ed835d9fe6bf3439ab6c Author: kngott Date: Thu May 30 00:07:24 2019 -0700 Change startRecord and stopRecord locations to work properly with Iter method. Src/Base/AMReX_FabArrayCommI.H commit b6121ada6f2ec09ccd5b70d8a43c7645e22700cc Author: kngott Date: Wed May 29 23:20:16 2019 -0700 Fix initialization list for CopyMemory. Src/Base/AMReX_CudaGraph.H commit 8dbcb505ca5c0c88e6ad3b045db51aa4ec924682 Author: kngott Date: Wed May 29 22:34:47 2019 -0700 Add instantiate error check to debug mode. Src/Base/AMReX_CudaDevice.cpp commit eb37cc7f52ebdac3d033c80d4d39cb03d738fd62 Author: kngott Date: Wed May 29 22:32:37 2019 -0700 DEBUG -> AMREX_DEBUG Src/Base/AMReX_MFIter.cpp commit ef112b4324d45ccfac8d1cca16a48a6db6f7c260 Author: Weiqun Zhang Date: Wed May 29 17:25:14 2019 -0700 fix for cuda Src/Base/AMReX_CudaDevice.H commit 72bb15410611d3f6d28f2954dc7911a1a1cba669 Author: Weiqun Zhang Date: Wed May 29 17:22:16 2019 -0700 add AMREX_HIP_OR_CUDA macro Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_GpuControl.H commit a305732e7c953e81687a50edb6894aac715781cb Author: Weiqun Zhang Date: Wed May 29 16:51:44 2019 -0700 hip: Device::Finalize() Src/Base/AMReX_CudaDevice.cpp commit 21a98e477ad0456919480412fb2640cfd42b3130 Merge: d89f895f0 978cc240e Author: Weiqun Zhang Date: Wed May 29 16:30:45 2019 -0700 Merge branch 'development' into hip commit bd58779627d9e1cdd288d45ee42f954d824a5b3d Author: Brandon Runnels Date: Wed May 29 17:28:42 2019 -0600 added additional residual correction Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit b592e65a3414528209c9a1c0744fa6970531166f Author: Brandon Runnels Date: Wed May 29 17:27:05 2019 -0600 implemented compatibility enum in mlmg - running unit tests Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 978cc240e1cb7272168ff66857dacc17bfd5567f Author: Weiqun Zhang Date: Wed May 29 16:14:38 2019 -0700 MLNodeLaplacian: make normalization threshold a parameter and set the default to 1.e-10 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 52e0d0fbfd971b3f129c3506d4103df8162c770d Merge: 577181c35 a4c45709e Author: Weiqun Zhang Date: Wed May 29 14:51:24 2019 -0700 Merge branch 'algoim' into development commit 577181c3588d069a2a9b546738a63feb4751c9d7 Merge: 534887c06 3b056f043 Author: Weiqun Zhang Date: Wed May 29 14:49:32 2019 -0700 Merge branch 'algoim' into development commit 534887c0610995b2e3957b5d2866c552f9760fb2 Merge: 8009e4e29 343159425 Author: Weiqun Zhang Date: Wed May 29 14:49:21 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d89f895f0e98a89b334827c662211644ad3a9efb Author: Weiqun Zhang Date: Mon May 27 07:10:29 2019 -0700 hip: device and streams Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayUtility.H Tools/F_scripts/write_cuda_headers.py commit 3431594253b7683bc817f168de7712a31eb730ed Author: Andrew Myers Date: Wed May 29 11:26:55 2019 -0700 fix a couple of bugs in the dx != particle_dx version of deposit_cic Src/Particle/AMReX_Particle_mod_K.H commit 60a17fc8930cdceed04d7cc3a2f80f91b2f4dda1 Author: Andrew Myers Date: Wed May 29 11:26:33 2019 -0700 remove unused variables Src/Particle/AMReX_ParticleContainerI.H commit 427d989e2bb5f2197aba6bbf325d4d7997c5ca1d Author: Weiqun Zhang Date: Wed May 29 10:50:56 2019 -0700 executeGraph can be const Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_FabArrayCommI.H commit 3e205fca3cfb20273c8c3e793359d9deb083700e Author: Weiqun Zhang Date: Wed May 29 10:24:31 2019 -0700 Real --> value_type Src/Base/AMReX_FabArrayCommI.H commit 118244e7016b795c3992da329ac53b1431b3fba3 Author: kngott Date: Tue May 28 17:25:59 2019 -0700 Reorganize into a function-based test to allow easy reading and easy scale testing of different launch strategies. Tests/GPU/FusedLaunches/main.cpp commit b28efcd8cc0050fe1587d9cf95a2809750659e28 Author: kngott Date: Tue May 28 16:41:10 2019 -0700 Store cudaStream as cudaStream_t. Src/Base/AMReX_CudaDevice.cpp commit 1819b8d5f13aedef7a63aed899e1655b7436c4fb Merge: 211884633 e70fdbb63 Author: Andrew Myers Date: Tue May 28 15:49:19 2019 -0700 Merge branch 'development' into pic_c++ commit a4c45709eab6cd4130d080ca289f8fa727f9c5c5 Author: Michele Rosso Date: Tue May 28 15:28:54 2019 -0700 CMake: get rid of Algoim and Blitz (finally) Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake Tools/CMake/AMReX_Options.cmake commit 21188463386b342f5f7941811efcd6e0c1014d08 Author: Andrew Myers Date: Tue May 28 15:01:47 2019 -0700 fix AMREX_SPACEDIM Src/Particle/AMReX_Particle_mod_K.H commit 11425edaafeabf94489aa2bfe90438c368c113af Author: Andrew Myers Date: Tue May 28 15:01:26 2019 -0700 correct function signature for amrex_interpolate_cic Src/Particle/AMReX_ParticleContainerI.H commit e70fdbb63067db3aee698ee5800de094e87fd3df Merge: e6ddfdd80 8031759e0 Author: WeiqunZhang Date: Tue May 28 14:33:26 2019 -0700 Merge pull request #486 from burlen/development fix SENSEI_INSITU build commit 0d6ce3d5c42ed5f8ece1b2b3c2d91bc464e60478 Author: Andrew Myers Date: Tue May 28 14:22:04 2019 -0700 implement these functions for AMREX_SPACEDIM != 3 Src/Particle/AMReX_Particle_mod_K.H commit efb00a760abb89d05d6fa69b0c7ea2193bfb20eb Author: Andrew Myers Date: Tue May 28 14:21:47 2019 -0700 Fix this test for AMREX_SPACEDIM != 3 Tests/Particles/AssignDensity/main.cpp commit 474d62c5cfeeaeddf35c577749bfa7a487313810 Author: Weiqun Zhang Date: Tue May 28 14:02:00 2019 -0700 add explicit GraphSafeGuard Src/Base/AMReX_GpuControl.H commit 8031759e02726945298f093a85de01cf2ddfd89b Author: SENSEI SC18 VM Date: Tue May 28 14:01:33 2019 -0700 fix SENSEI_INSITU build Tools/GNUMake/Make.defs commit a108ccf37750b2b3affe3236c23cb218b3e42ee9 Author: Weiqun Zhang Date: Tue May 28 13:58:42 2019 -0700 tidy Src/Base/AMReX_FabArrayCommI.H commit 0b7ad307666c950d7c97ad5d4ff09db463e77aba Merge: cabd6fd36 8009e4e29 Author: Weiqun Zhang Date: Tue May 28 13:53:34 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit cabd6fd362d7330b84a8756ecf9b0837b5098306 Merge: 525e9bf65 3f51a6e96 Author: Weiqun Zhang Date: Tue May 28 13:42:02 2019 -0700 Merge branch 'kngott/cudaGraphs' of github.com:AMReX-Codes/amrex into kngott/cudaGraphs commit 83c3e75eebcaab074db4615de173d6b1ba66ed24 Author: Andrew Myers Date: Tue May 28 13:25:03 2019 -0700 remove the OMP Deposition helper - this is done in BaseFab now Src/Particle/AMReX_OMPDepositionHelper_nd.F90 Src/Particle/CMakeLists.txt Src/Particle/Make.package commit df66628d0096af0a9fbc70e71b9f69a2cb2b0519 Author: Andrew Myers Date: Tue May 28 13:19:15 2019 -0700 hardwired 1 -> ncomp Src/Particle/AMReX_ParticleContainerI.H commit f2211d1d6b637c92291c122e2c089c27b0b143de Author: Andrew Myers Date: Tue May 28 13:05:30 2019 -0700 remove now unused Fortran routines Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 7c6adf6b7ab7d2826f5337d6dc8858d9459b4153 Author: Andrew Myers Date: Tue May 28 12:45:27 2019 -0700 implement and use C++ versions of the particle deposition routines Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_Particles.H commit accf4622abe226f3b8a2e67587f76407db31382d Merge: 981e2f1ea e6ddfdd80 Author: Andrew Myers Date: Tue May 28 10:19:49 2019 -0700 Merge branch 'development' into pic_c++ commit 3b056f043f4a47dca21ec570bcab2b8d86642541 Author: Weiqun Zhang Date: Tue May 28 09:37:04 2019 -0700 update node eb solver test Tests/LinearSolvers/NodeEB/MyTest.cpp commit 269e3cb2859c22a1be7973388a53e2999c4a9791 Author: Weiqun Zhang Date: Tue May 28 09:21:40 2019 -0700 remove Src/Extern/Algoim and update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst Src/Extern/Algoim/AMReX_algoim_integrals.H Src/Extern/Algoim/AMReX_algoim_integrals.cpp Src/Extern/Algoim/CMakeLists.txt Src/Extern/Algoim/Make.package Tests/Algoim/GNUmakefile Tests/LinearSolvers/NodeEB/GNUmakefile Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.algoim commit 8009e4e29661a3ad2894ff2b4d0990dc37316003 Author: Weiqun Zhang Date: Mon May 27 22:07:27 2019 -0700 turn on omp for computing integrals using algoim Src/EB/AMReX_algoim.cpp commit 52ca58c3470c9b7d5f8e2ea3f9eab85f76647eea Author: Weiqun Zhang Date: Mon May 27 22:05:14 2019 -0700 switch to new algoim in 3d nodal solver Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e6ddfdd801b86e14af4b57f71050227b4fa39537 Merge: cd36da0fd 745c9e465 Author: Weiqun Zhang Date: Mon May 27 19:07:43 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cd36da0fd3eb4f9984dea3efd8c7c0982c0e5f88 Author: Weiqun Zhang Date: Mon May 27 18:58:42 2019 -0700 algoim: make it gpu ready Src/EB/AMReX_algoim.cpp Src/EB/AMReX_algoim_K.H commit e115fb5356ad30a65623e6d66403abce67b48842 Author: Weiqun Zhang Date: Mon May 27 18:06:35 2019 -0700 algoim: add gpu qualifier, constexpr and inline Src/EB/AMReX_algoim_K.H Tests/Algoim/main.cpp commit d1d7fc7627b8eaf137fab36e5a709b92741239cd Author: Weiqun Zhang Date: Mon May 27 17:53:45 2019 -0700 algoim: replace std::bitset with our own bitwise operation Src/EB/AMReX_algoim_K.H commit 610ecd43c9d3d718bcf2896f3701df0dc7c8a54b Author: Weiqun Zhang Date: Mon May 27 17:19:16 2019 -0700 algoim: use gpu friendly containers Src/EB/AMReX_algoim_K.H commit 5a45ebbb994394a56f2fea657868c54441921e1a Author: Weiqun Zhang Date: Mon May 27 16:51:57 2019 -0700 algoim: simplify BoundingBox Src/EB/AMReX_algoim_K.H commit d036829bfe713dba8613e22e73f44bd3ef6ff89b Author: Weiqun Zhang Date: Mon May 27 16:38:44 2019 -0700 algoim: simplify Interval Src/EB/AMReX_algoim_K.H commit 2feb605023885c9d52829e38b3d46889d16d9071 Author: Weiqun Zhang Date: Mon May 27 16:33:07 2019 -0700 algoim: use array instead of vector because the number of roots is at most 2 Src/EB/AMReX_algoim_K.H commit dfdf5236e9b96cc427cf493eb72b9a98bdf7ea95 Author: Weiqun Zhang Date: Mon May 27 16:21:12 2019 -0700 alogim: use fixed size array instead of vector because we know the maximal size it can get to. Src/EB/AMReX_algoim_K.H commit f68bf2214e3f559a5b57c9ee6ae5fdfdd82bcd2f Author: Weiqun Zhang Date: Mon May 27 12:37:41 2019 -0700 set precision in algoim test Tests/Algoim/main.cpp commit c9d017a92cad98767255293c020a5cceeb9d01b4 Author: Weiqun Zhang Date: Mon May 27 12:07:19 2019 -0700 test algoim performance Tests/Algoim/main.cpp commit b38e1e04078f7c55c773a3487bee7cff6c48024c Author: Weiqun Zhang Date: Mon May 27 11:36:45 2019 -0700 update cmake to include algoim Src/EB/AMReX_algoim.cpp Src/EB/CMakeLists.txt Src/EB/Make.package commit 75096365fcabf6524a7240d865a01d0bd211e29c Author: Weiqun Zhang Date: Mon May 27 11:03:01 2019 -0700 add algoim test Src/EB/AMReX_algoim_K.H Tests/Algoim/GNUmakefile Tests/Algoim/Make.package Tests/Algoim/main.cpp commit 745c9e4653b2f7bf62ac7af685bffbcb9b5c7c57 Author: Andrew Myers Date: Mon May 27 10:56:51 2019 -0700 add missing AMREX_D_TERM macros to fix SPACEDIM != 3 Src/Particle/AMReX_ParIterI.H commit 0bf18c475a15bb25c9734c036f288935ec274ec9 Author: Weiqun Zhang Date: Mon May 27 07:50:57 2019 -0700 copy algoim to Src/EB and remove its dependency on blitz Src/EB/AMReX_algoim.H Src/EB/AMReX_algoim.cpp Src/EB/AMReX_algoim_K.H Src/EB/Make.package commit 981e2f1ea29976ba61c25f0c82f31a15ec2d4a47 Author: Andrew Myers Date: Fri May 24 14:18:51 2019 -0700 start C++ implementations of amrex pic routines Src/Particle/AMReX_Particle_mod_K.H commit 72e2dac3b6e1cbfc9449090457bc5ea53b413854 Author: Kevin Gott Date: Fri May 24 14:16:13 2019 -0700 Doc typo. Docs/sphinx_documentation/source/GPU.rst commit 25a07c957b7d018c6cd42b5c3ac840656354ad35 Author: Andrew Myers Date: Fri May 24 13:43:21 2019 -0700 add missing stream sync Src/Particle/AMReX_ParIterI.H commit 8bc1cb1005e400630aa0a618dede48bb4971e544 Author: Andrew Myers Date: Fri May 24 13:19:33 2019 -0700 amrex_build_nl also doesn't exist any more Src/Particle/AMReX_Particles_F.H commit a108a25e78bd7a44b2a7dbee93ced00d615cde91 Author: Andrew Myers Date: Fri May 24 13:18:53 2019 -0700 remove now un-used Fortran routines from the particle code Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H commit 4eaa4dd0716a113e5fd53d5629860d548e093c0f Author: Andrew Myers Date: Fri May 24 13:18:32 2019 -0700 don't need these functors any more Src/Particle/AMReX_Functors.H commit 079575170d3c531f325735f278d989d28a20e1a4 Author: Andrew Myers Date: Fri May 24 13:18:07 2019 -0700 switch to C++ in get/set particle position Src/Particle/AMReX_ParIterI.H commit e3840f9732d67dd744eb9c59b0fa8dd00a9d6b95 Author: Weiqun Zhang Date: Thu May 23 17:07:27 2019 -0700 AMREX_CUDA_MAX_THREADS -> AMREX_GPU_MAX_THREADS Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_fort_mod.F90 Tools/CMake/AMReX_Defines.cmake Tools/GNUMake/Make.defs commit 0b6d91ee3079344d5f1a6359b4250abd00323b1d Author: Weiqun Zhang Date: Thu May 23 17:02:29 2019 -0700 hip: error checking Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuError.H commit f1429079d50b27f0770753a8c17dd89fac0bb0e3 Author: Weiqun Zhang Date: Thu May 23 15:25:39 2019 -0700 hip: inLaunchRegion Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp commit 68db8f708636d29b441b532efc0d5cd6355383b9 Author: Andrew Myers Date: Thu May 23 15:13:45 2019 -0700 fix a few more warnings Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrParticles.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 commit 3f51a6e960e462e4fe92c7cde27a6fe532920910 Author: Kevin Gott Date: Thu May 23 17:51:14 2019 -0400 Adjustments for older GNU versions. Src/Base/AMReX_CudaGraph.H commit 0df1e6b3b9d23443bec287741e57eeaba7eb5f1b Author: Kevin Gott Date: Thu May 23 17:50:15 2019 -0400 Add check for cuda version due to API change. Src/Base/AMReX_CudaDevice.cpp commit 4b390f5b687de00db5063a42e9236d0e6f5160b8 Author: Weiqun Zhang Date: Thu May 23 14:47:30 2019 -0700 make: add HIP_PLATFORM Src/Base/AMReX_GpuQualifiers.H Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit ee1537750c1c033f1fb83d909893c013a480bab3 Merge: 5843e73fe 16ac0c078 Author: Kevin Gott Date: Thu May 23 16:59:44 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit 319cecd5a42a03e60b42bed78052037e71fef453 Author: Andrew Myers Date: Thu May 23 13:56:11 2019 -0700 fixing some more parameter shadowing / unused variable warnings Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_filcc_mod.F90 Src/Boundary/AMReX_BndryRegister.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 16ac0c07867b8a75637896a10f43f41e9682e4ea Author: Andrew Myers Date: Thu May 23 13:21:32 2019 -0700 fix some parameter shadowing warnings Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit b8739674a808c11de6ad4c72a4f506a085971389 Author: Weiqun Zhang Date: Thu May 23 13:06:43 2019 -0700 start hip with nvcc as backend Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/hip.mak commit de2596e3dd3082f65bb18806f9a25917bdb93fca Merge: bfea077f5 eb7155121 Author: Andrew Myers Date: Thu May 23 14:24:14 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bfea077f53304a55e1a493ccc0779f97010b636f Author: Andrew Myers Date: Thu May 23 14:23:37 2019 -0400 correct this size of these vectors to account for possibly runtime-added components Src/Particle/AMReX_ParticleContainerI.H commit 175f4792bbf8184030d6f9b5e8bdb5a3ff05b666 Author: Andrew Myers Date: Thu May 23 14:03:26 2019 -0400 add assertion to catch problems earlier Src/Particle/AMReX_ParticleContainerI.H commit 3fe970489f97233ac4b8c8d765ab0a643d6d52f8 Author: Andrew Myers Date: Thu May 23 13:58:54 2019 -0400 fix size of comp_name and boolean write arrays Src/Particle/AMReX_ParticleContainerI.H commit eb7155121e5c60ece6bbcbacd717feea879dd6a3 Author: Weiqun Zhang Date: Thu May 23 10:48:22 2019 -0700 Tensor solver: fix periodic bc Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit d3f7e55e2e43a0435ede13123d199c00427a51d6 Author: Weiqun Zhang Date: Wed May 22 16:15:03 2019 -0700 remove explicit from ErrorFunc and ErrorFunc2 because codes rely on implicit conversion Src/AmrCore/AMReX_ErrorList.H commit 5943432cf2f7c3274b83a80866914bef00c6e0a3 Author: Weiqun Zhang Date: Wed May 22 16:10:21 2019 -0700 MLNodeLap: tweak normalization parameter to reduce the number of bicg iterations Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 2d8c923ecbe4fc2a336fd7845f4982e99c2f4921 Author: Weiqun Zhang Date: Wed May 22 16:07:56 2019 -0700 Allow implicit conversion from int to BoundCond. Src/Boundary/AMReX_BoundCond.H commit fe80097cb63522ec8958ff1beda8ddcfe350fdf5 Author: Weiqun Zhang Date: Wed May 22 15:24:50 2019 -0700 fix a bunch of warnings by cppcheck mostly on explicit ctor Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_Interpolater.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_Print.H Src/Base/AMReX_RealVect.H Src/Base/AMReX_TinyProfiler.H Src/Boundary/AMReX_BoundCond.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBInterpolater.H Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp commit 37d9ebb3267274f5af67c0482282744e655235ef Author: kngott Date: Wed May 22 14:49:40 2019 -0700 Updated fused Test. Tests/GPU/FusedLaunches/main.cpp commit 3de50d9bcf72dc358b8a08adfdae632456f97af4 Author: kngott Date: Wed May 22 14:49:30 2019 -0700 Function to get num streams from Device. Src/Base/AMReX_CudaDevice.H commit 599cdb8dda46c336ba10ffd9749c0f42f74261a9 Author: Weiqun Zhang Date: Wed May 22 14:20:38 2019 -0700 initialize values so that static analysis tools don't complain Src/AmrCore/AMReX_AmrCore.cpp commit dce3a0eb00904e9ca764715f73caa69e21b81e9b Author: Weiqun Zhang Date: Wed May 22 13:51:43 2019 -0700 fix out of bound error for 1d Src/Base/AMReX_Geometry.cpp commit 63d37bfba6597e3487f16e65c1331ac67c1ced64 Author: Weiqun Zhang Date: Wed May 22 14:42:09 2019 -0400 update nvml path on summit Tools/GNUMake/sites/Make.olcf commit b1f2ff4c44dcd6585a9382868ba9ec894a765b8f Author: Weiqun Zhang Date: Tue May 21 19:20:37 2019 -0700 FPinfo: pass the correct Geometry Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2_IndexSpaceI.H commit 1bccc04eb73175976b838bbde720b2b71adb8c66 Author: Weiqun Zhang Date: Tue May 21 16:44:04 2019 -0700 Geometry: functions to reset the default Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 7a0738eacf23fdf4cd8b35136d5acc0a9fe22428 Author: Weiqun Zhang Date: Tue May 21 16:33:47 2019 -0700 Geometry default ctor: copy from AMReX stack if we can Src/Base/AMReX.H Src/Base/AMReX_Geometry.cpp commit 739520def4bbc459791fdfb3fcf943176cc49913 Author: Weiqun Zhang Date: Tue May 21 16:08:00 2019 -0700 fix periodicity flags after Amr restart Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit e7a7734850757f2d8ed71498bcf63b3fa986b19c Author: Weiqun Zhang Date: Tue May 21 13:44:50 2019 -0700 add periodic to Geometry I/O Src/Base/AMReX_Geometry.cpp commit 26e12516bfe661ee68cf59314e3b96e2b15b38e5 Author: Weiqun Zhang Date: Tue May 21 13:43:59 2019 -0700 add IntVector ctor taking Array as argument Src/Base/AMReX_IntVect.H commit 12da1ac4b9eb366be289d15d0d29967a090b41c4 Author: Weiqun Zhang Date: Tue May 21 13:43:28 2019 -0700 tidy Src/Base/AMReX_CoordSys.cpp commit ee5e7bfcff8a998e31f388fea9562f6a78b3ed89 Author: kngott Date: Tue May 21 12:38:18 2019 -0700 Fused Launches Test, first draft. Tests/GPU/FusedLaunches/GNUmakefile Tests/GPU/FusedLaunches/Make.package Tests/GPU/FusedLaunches/inputs_3d Tests/GPU/FusedLaunches/main.cpp Tests/GPU/FusedLaunches/run.corigpu commit 02c15dc1ba8f92b4d05256abfbfada9f5d8af1d2 Author: Weiqun Zhang Date: Tue May 21 09:03:52 2019 -0700 fix a typo in documentation Docs/sphinx_documentation/source/Basics.rst commit c0079c513234e20c7b22f61d915e35b438ec241b Author: Weiqun Zhang Date: Mon May 20 16:47:56 2019 -0700 DefaultGeometry: use the one at the top of AMReX stack. Src/Base/AMReX_Geometry.H commit 3d681c08792d3130095c413684cb2e1bf455081c Merge: ba1943af8 ab6281555 Author: Weiqun Zhang Date: Mon May 20 16:17:21 2019 -0700 Merge branch 'development' into weiqun/amrex commit ab62815554b32e969ca3cf0fbb12592319fcb027 Author: Weiqun Zhang Date: Mon May 20 16:16:32 2019 -0700 added DefaultGeometry function Src/Base/AMReX_Geometry.H commit ba1943af8b6cd0d7e8d22a337f480638ca5dd7c5 Merge: 36c664a20 6565e29f1 Author: Weiqun Zhang Date: Mon May 20 15:53:40 2019 -0700 Merge branch 'development' into weiqun/amrex commit 6565e29f1488b3b2dda2e220f96b259cbeee26fb Author: Weiqun Zhang Date: Mon May 20 15:40:57 2019 -0700 MLEBABecLap: fix index bug Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 36c664a202e9cb0aca3fc8fc8000f0c315c1d385 Merge: 4e1ed235c da7e7b8c9 Author: Weiqun Zhang Date: Mon May 20 15:26:51 2019 -0700 Merge branch 'development' into weiqun/amrex commit da7e7b8c9bc0efe108511d04cad2b2c128e994e6 Author: Weiqun Zhang Date: Mon May 20 13:30:58 2019 -0700 added some geometry functions to help migration Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/Base/AMReX_Geometry.H commit 4e1ed235cc85817bd42f7f04e1d70a02ecabfd70 Author: Weiqun Zhang Date: Mon May 20 12:16:35 2019 -0700 fix an old tutorial OldTutorials/DataServicesTest0/DataServicesTest0.cpp commit 9d68de498c403ebab36cc9c4005417076f48737d Author: Weiqun Zhang Date: Mon May 20 11:26:53 2019 -0700 Geometry: fix tests and tutorials Docs/sphinx_documentation/source/Basics.rst Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBflux_grad/MyTest.cpp Tests/LinearSolvers/NodeEB/MyTest.cpp Tools/C_util/WritePlotFile.cpp Tutorials/GPU/EBCNS/Source/CNS_init_eb2.cpp Tutorials/GPU/EBCNS/Source/CNS_io.cpp Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 5843e73fee89ac1595ed14314781f78af4354c96 Author: kngott Date: Mon May 20 11:08:42 2019 -0700 Clean up copy with graphs test. 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Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_io.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_io.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_io.cpp Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/physbc.cpp commit ec0fa51b4e110a9e4ec3e151a8dd2cb3df513550 Author: Weiqun Zhang Date: Mon May 20 10:22:10 2019 -0700 Geometry: update EB Src/EB/AMReX_EB2_Level.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb2.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp commit f73135f7443e5c0da2f24dc4a8c57dcfb1dd4857 Author: Weiqun Zhang Date: Mon May 20 09:55:07 2019 -0700 MLEBTensorOp: forgot to set scalars Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 14a17354c64fcd7f1f8990fa03dd2d8674d54db4 Author: Weiqun Zhang Date: Sun May 19 21:43:27 2019 -0700 Geometry: update Particle Src/Particle/AMReX_ParticleContainerI.H commit 2b8ddb67d961d52ede9d1cd563b8769e49143baf Author: Weiqun Zhang Date: Sun May 19 21:33:43 2019 -0700 Geometry: update Amr Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 2aa60332fbc4817ee9c7aca33ea581050aa1cbdd Author: Weiqun Zhang Date: Sun May 19 18:59:59 2019 -0700 Geometry: put the first Geometry object to the top of AMReX stack and use arguments passed in whenever available. AmrMesh: repsect constructor parameters when building Geometry Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/Base/AMReX_Geometry.cpp commit ac79021b80cabded2fca11043999345e3e6763b8 Author: Weiqun Zhang Date: Sun May 19 17:16:45 2019 -0700 Geometry::define: fix comparison Src/Base/AMReX_Geometry.cpp commit 5eb6f851bcfeef0fe219484bb73d35298cd1aed1 Author: Weiqun Zhang Date: Sun May 19 14:34:40 2019 -0700 add scalars to Tensor solver Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 8f78df8f979e4857c43fb38d426203b57486971b Author: Weiqun Zhang Date: Sun May 19 13:59:24 2019 -0700 Geometry: update AmrCore Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_Geometry.H commit 01081da0482f8e8f802477fe7f1201e541382438 Author: Weiqun Zhang Date: Sun May 19 12:13:55 2019 -0700 Geometry: update linear solver Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit cf23b20c0d5601cdca2d069439c719971e006687 Author: Weiqun Zhang Date: Sun May 19 11:41:10 2019 -0700 fix comments in inputs Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_3d Tutorials/Basic/HeatEquation_EX3_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX3_C/Exec/inputs_3d commit e0edc4378a31f9d7f3ca09017549a441339aa2eb Author: Weiqun Zhang Date: Sun May 19 11:34:06 2019 -0700 Geometry: update F_Interfaces Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit f94cb4563a3701481e05febc1b50a30970b63d57 Author: Weiqun Zhang Date: Sun May 19 10:27:21 2019 -0700 removed static data from Geometry and updated Base Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileUtil.cpp commit b808fad3cc215667a5175826f9ca0388bbc1a928 Author: Weiqun Zhang Date: Sat May 18 15:27:51 2019 -0700 WIP Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 51b2c6a287d9e6ca316d1af55e51fdd9b3658775 Author: Weiqun Zhang Date: Sat May 18 14:36:38 2019 -0700 AMReX stack Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp commit b377f1b187575b31aa79617ab39a7c01e3976b49 Author: Weiqun Zhang Date: Sat May 18 09:25:36 2019 -0700 EB2::IndexSpace: make sure it's safe to push pointers that are already owned by the stack. Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp commit d18ee0c635c775b67abd57e7fc65ee61a8c06c43 Author: Weiqun Zhang Date: Fri May 17 16:57:17 2019 -0700 MLMG: if the solution multifab has ghost cells, set them to zero, otherwise uninitialized values might get used. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 3c308ce0fa21afd85b80e653199bb9487bc5c22c Author: Weiqun Zhang Date: Fri May 17 14:50:36 2019 -0700 Nodal Poisson tutorial: multi-level Src/Base/AMReX_PhysBCFunct.H Tutorials/LinearSolvers/NodalPoisson/Make.package Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest_F.H Tutorials/LinearSolvers/NodalPoisson/init_prob.F90 commit a71415bbf9a3f13ab4643f8f7c2c58ee51ef3000 Author: kngott Date: Fri May 17 14:12:35 2019 -0700 Small fix. Src/Base/AMReX_CudaDevice.cpp commit 9d006b6b531f6d423a49ad972655cc99b62da8e5 Author: kngott Date: Fri May 17 14:10:03 2019 -0700 Update BuildingGraphs for easier reading. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 29e546d0a42f183224bf9ac16c67a1d2c514114b Author: Andy Nonaka Date: Fri May 17 09:50:22 2019 -0700 (more) cleanup only; make macros more readable/distinguishable from each other Src/Base/AMReX_ArrayLim.H commit 250e0653b3cb4bf5848f06baf7ee0f3c23fad1d6 Merge: b8cac2bff ca5bcfabe Author: Andy Nonaka Date: Fri May 17 09:48:39 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b8cac2bff9e12bb8cfb3284e5ee354d9af2b39f2 Author: Andy Nonaka Date: Fri May 17 09:48:15 2019 -0700 cleanup only; make macros more readable/distinguishable from each other Src/Base/AMReX_ArrayLim.H commit ca5bcfabef01039e93bff8c985da05261d05fa49 Merge: e15561a02 163d44b08 Author: Andrew Myers Date: Thu May 16 21:03:05 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e15561a0236cd10cf2fe468da9c475271b85e71d Author: Andrew Myers Date: Thu May 16 20:47:53 2019 -0400 remove debug print Src/Particle/AMReX_ParIterI.H commit 4ccf376f20186fdbdac5d4af3edc93ab916e00d4 Author: Andrew Myers Date: Thu May 16 20:34:16 2019 -0400 bug fix for set particle position, which wasn't properly copying the particles ids Src/Particle/AMReX_Functors.H Src/Particle/AMReX_ParIterI.H commit 1198c9b3a444722ff750ed0cf2ee0cab6e8801ec Author: Andrew Myers Date: Thu May 16 20:33:06 2019 -0400 format fix Src/Particle/AMReX_ParticleTile.H commit d3ffa9166b0dc92935437b366a132b6ec7db29f6 Author: Andrew Myers Date: Thu May 16 20:32:51 2019 -0400 format fix Src/Particle/AMReX_StructOfArrays.H commit 163d44b08f64673b6c3b96c63175428d0c11aaa5 Author: Weiqun Zhang Date: Thu May 16 17:17:11 2019 -0700 EBTensor test: convergence test results Tests/LinearSolvers/EBTensor/results.org commit 8991789213f8c43cce328a0ff5a92a1e4cc14d86 Author: Weiqun Zhang Date: Thu May 16 16:42:29 2019 -0700 MLEBTensor: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 912ed5d8c72eaf87f1080c4ca49cb74d5305a521 Author: Weiqun Zhang Date: Thu May 16 14:58:22 2019 -0700 EBTensorOp: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit a3f4c71c4bcfc4cde9be9bf61053b1176fce6172 Author: Weiqun Zhang Date: Thu May 16 14:55:24 2019 -0700 EBTensor test Src/EB/AMReX_EBFabFactory.H Tests/LinearSolvers/EBTensor/GNUmakefile Tests/LinearSolvers/EBTensor/Make.package Tests/LinearSolvers/EBTensor/MyTest.H Tests/LinearSolvers/EBTensor/MyTest.cpp Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp Tests/LinearSolvers/EBTensor/MyTest_K.H Tests/LinearSolvers/EBTensor/inputs Tests/LinearSolvers/EBTensor/main.cpp commit 525e9bf651fe634161f924b18487c26cdf573625 Author: Weiqun Zhang Date: Thu May 16 16:42:29 2019 -0700 MLEBTensor: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 003436a9f5a7ceadd16ca116b542a470d482bc9b Author: Weiqun Zhang Date: Thu May 16 14:58:22 2019 -0700 EBTensorOp: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit bb6b5e9c45892458571c0a527f5773f453ca0b00 Author: Weiqun Zhang Date: Thu May 16 14:55:24 2019 -0700 EBTensor test Src/EB/AMReX_EBFabFactory.H Tests/LinearSolvers/EBTensor/GNUmakefile Tests/LinearSolvers/EBTensor/Make.package Tests/LinearSolvers/EBTensor/MyTest.H Tests/LinearSolvers/EBTensor/MyTest.cpp Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp Tests/LinearSolvers/EBTensor/MyTest_K.H Tests/LinearSolvers/EBTensor/inputs Tests/LinearSolvers/EBTensor/main.cpp commit 9c636cf2d9c3985357dd13b73b83115fec17bfcd Author: Brandon Runnels Date: Thu May 16 13:05:06 2019 -0600 fixes error where solution only converges in mlmg with verbosity >= 0 - need a better solution Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5c4964ee4619f440e0784b8a526b8e4b4e0383d5 Author: kngott Date: Wed May 15 23:49:14 2019 -0700 Additional graph fixing. Src/Base/AMReX_CudaDevice.cpp commit 159168c32518f09ddc0c5f4c6ffde97e21d3df30 Author: kngott Date: Wed May 15 20:51:25 2019 -0700 Add cudaGraph and cudaGraphExec destroy calls. Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaGraph.H commit 8674d16021d7788e79d5386824a71d61546dc3ba Author: Weiqun Zhang Date: Wed May 15 14:59:37 2019 -0700 rm setGraphRegion call from linear solver tutorial Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit 828f0a76f8c623bce7d6d21476825c248f188851 Author: Weiqun Zhang Date: Wed May 15 14:59:11 2019 -0700 add GraphSafeGuard Src/Base/AMReX_GpuControl.H commit f440ead98c4038bf48e1bb1f8e8d556b3e703208 Author: Weiqun Zhang Date: Wed May 15 14:51:44 2019 -0700 add AMReX_CudaGraph.H to cmake Src/Base/CMakeLists.txt commit df1826963afc3ff693864fbe217f1822f5de30f1 Merge: c91ee3745 8fe800d00 Author: Weiqun Zhang Date: Wed May 15 14:48:04 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 8fe800d00c4117d49a1f89b60a34470ff611417e Author: Weiqun Zhang Date: Wed May 15 11:04:45 2019 -0700 MLEBTensor: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 3efe7f91cd1d5419e662b0c37a6a28f4fc19a2c6 Author: Weiqun Zhang Date: Tue May 14 16:33:23 2019 -0700 EB_average_down_boundaries: fix for multi-component Src/EB/AMReX_EBMultiFabUtil.cpp commit c91ee3745111a77264d12b79c285332212d88340 Author: kngott Date: Tue May 14 15:33:18 2019 -0700 Tweak to be more consistent with non-graphed code. Src/Base/AMReX_FabArrayCommI.H commit 8ef9b58d79a8243e37fce147d052505e03281b4e Author: Weiqun Zhang Date: Tue May 14 13:35:49 2019 -0700 MLEBTensor: fix sign Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 4d888e79341d4741bcdcf65ae3ad3d99c620a13e Author: Weiqun Zhang Date: Tue May 14 12:45:55 2019 -0700 Tensor solver: finish the coarsening of bulk viscosity Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 4d8e0ed9ff18a81a3c8209b164cf9860c7820f93 Author: atmyers Date: Mon May 13 17:02:12 2019 -0700 Make OK and Redistribute respect the launch region flag. Src/Particle/AMReX_ParticleContainerI.H commit f14a00c9e40e5ea61fdaa62ebf93e3a168a7d037 Author: kngott Date: Mon May 13 15:26:39 2019 -0700 Fix GraphBoundary test error check to include user-specified number of components and ghost cells. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 82ec2e7987cbdfbb74be7914c40fab1dc6ad2784 Author: kngott Date: Mon May 13 15:26:03 2019 -0700 Cleanup in Building test. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit bbb1768ef679e2a3e0ece2e05d740490793e1b9c Merge: 5c4ef4f13 e954997b5 Author: Andrew Myers Date: Mon May 13 15:45:29 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5c4ef4f13d129e829695c06213fbf6ab1730f76f Author: Andrew Myers Date: Mon May 13 15:45:14 2019 -0400 these define calls are needed when using the runtime soa capability on the GPU Src/Particle/AMReX_ParticleContainerI.H commit e954997b5c7768eac063f5f6b175653793d43706 Author: Weiqun Zhang Date: Mon May 13 12:03:31 2019 -0700 Noal RAP: don't renormalize if the diagonal component is too small compared to the global maximum Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a4c7ab982efb6ac3f85965df383634d3f1b9a907 Author: Weiqun Zhang Date: Mon May 13 09:56:23 2019 -0700 MLEBTensorOp: fix EB flux Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 761869bce01b4eb4b29c9c200d1419f401cecfda Merge: d31b3fa85 d50bb8520 Author: Ann Almgren Date: Mon May 13 09:55:01 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit d31b3fa85fb375883b6d32b33c3f2eccc4dc4908 Author: Ann Almgren Date: Mon May 13 09:54:32 2019 -0700 Set USE_MPI = FALSE in GNUMakefile since this version of diffmultifab only works in serial Tools/C_util/DiffMultiFab/GNUmakefile commit d50bb85205d633f2338e2f3fee59832416375a3a Author: Weiqun Zhang Date: Mon May 13 09:20:08 2019 -0700 Edison is gone Src/Base/AMReX_Machine.cpp Tests/HDF5Benchmark/GNUmakefile Tests/Slice/GNUmakefile Tools/CMake/AMReX_Machines.cmake Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nersc commit 5d47e2be23105075c2314bd29e8cce48d43c85ad Merge: 9dbeb3804 26bd9bb8c Author: Weiqun Zhang Date: Sun May 12 12:45:51 2019 -0700 Merge branch 'master' into development commit 26bd9bb8cfa50057b00644313406def720e0ddf6 Author: Weiqun Zhang Date: Sun May 12 12:45:23 2019 -0700 add citation to README.md README.md commit 9dbeb38046895f9da8c2077cf3c28f3c5e48a3e4 Merge: 349338589 9814f9204 Author: Weiqun Zhang Date: Sun May 12 10:47:41 2019 -0700 Merge branch 'master' into development commit 9814f92043cc6960b4b072d63698e6f678c04b48 Author: Weiqun Zhang Date: Sun May 12 10:40:19 2019 -0700 add JOSS status badge README.md commit b8ed63a64da40dc9562d7bdb4ca84d7680b583d3 Author: Weiqun Zhang Date: Sun May 12 08:37:51 2019 -0700 fix IAMR DOI paper/paper.bib commit 1aca4ebd695c3158bccb16f7673019710f8ef88a Merge: f9cc19632 d0aa7c819 Author: WeiqunZhang Date: Sun May 12 07:54:25 2019 -0700 Merge pull request #481 from kyleniemeyer/patch-4 Update paper.bib commit d0aa7c819ceb1d4864b239839b6358d4feccc130 Author: Kyle Niemeyer Date: Sun May 12 00:41:03 2019 -0700 Update paper.bib paper/paper.bib commit f9cc19632ae12087cddc8269e6b283ac17a3aeb0 Merge: ed18c1f0d 16a24db43 Author: asalmgren Date: Sat May 11 20:59:53 2019 -0700 Merge pull request #480 from kyleniemeyer/patch-3 Update paper.bib commit ed18c1f0dadc44b13a30350ee1b442c33ad5279c Merge: 92a53bda9 070eaba1b Author: asalmgren Date: Sat May 11 20:55:25 2019 -0700 Merge pull request #479 from kyleniemeyer/patch-2 Fixes case of multiple references in paper commit 16a24db433dc41e869c23da03ef4c12cd001683a Author: Kyle Niemeyer Date: Sat May 11 20:51:33 2019 -0700 Update paper.bib paper/paper.bib commit 070eaba1b430149802cecc084f541da96ef7094f Author: Kyle Niemeyer Date: Sat May 11 20:43:01 2019 -0700 Fixes case of multiple references in paper paper/paper.md commit 92a53bda9c1c236520e8ef60d1ea7883c98014b2 Author: Weiqun Zhang Date: Sat May 11 19:15:22 2019 -0700 paper: minor changes paper/paper.md commit 178a691a54cd08506c4a531bcdd61e61769c8c6a Author: Weiqun Zhang Date: Sat May 11 18:52:48 2019 -0700 spell out JCP paper/paper.bib commit 1b9e09bbc7f2cb5e67c01b7ffdd118cf731be6d0 Author: Weiqun Zhang Date: Sat May 11 18:48:51 2019 -0700 Fix paper.bib paper/paper.bib paper/paper.md commit 38ba904d77fe9e2186f2cba9013f060e0b71f8a5 Merge: f8e92b80f 39a198738 Author: Weiqun Zhang Date: Sat May 11 18:41:59 2019 -0700 Merge branch 'master' of github.com:AMReX-Codes/amrex commit f8e92b80f56e867261ba4666e5e38654330ec4ce Author: Weiqun Zhang Date: Sat May 11 18:41:48 2019 -0700 Fix paper.bib paper/paper.bib commit 39a19873838dcbdbfbca185ab44220fb91a72ef9 Author: Ann Almgren Date: Sat May 11 17:37:22 2019 -0700 Update with many references. paper/paper.bib paper/paper.md commit 34933858958b331337cd953c0cb2d25838a406c9 Merge: 078f85d89 ed11b5e0e Author: Ann Almgren Date: Sat May 11 17:37:33 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 078f85d89a38ac85bbed612f57655d279ba8532d Author: Ann Almgren Date: Sat May 11 17:37:22 2019 -0700 Update with many references. paper/paper.bib paper/paper.md commit ed11b5e0e19cb56fd5f333ec34012807dc120cda Merge: e8d58f802 8c51b8af0 Author: Weiqun Zhang Date: Sat May 11 17:24:16 2019 -0700 Merge branch 'weiqun/mlmg' into development commit 8c51b8af02a730a2ec17c353d16080acf37efa87 Author: Weiqun Zhang Date: Sat May 11 17:19:16 2019 -0700 MLEBTensor: calling cross terms Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 11c17318144bd0f883ccce11dcdb2839327eee24 Author: Weiqun Zhang Date: Sat May 11 16:46:38 2019 -0700 MLEBTensor: 2d cross terms Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 65ccd1eafaf575e42b302bc3495d41896639f252 Author: Weiqun Zhang Date: Sat May 11 15:31:23 2019 -0700 MLEBTensor: 3d cross terms Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit a8a5eb8e8c62d45751d6162f3c853b3574cb14f0 Author: Ann Almgren Date: Fri May 10 17:12:49 2019 -0700 Add references for SUNDIALS, hypre, PETSc and xSDK. paper/paper.bib paper/paper.md commit b36a8428fb88d554871c16b49c63a9e574445773 Author: Ann Almgren Date: Fri May 10 16:28:34 2019 -0700 Add city and country to the author affiliations. paper/paper.md commit e8d58f802faf26220345727bf278af9fb08d3e99 Author: Ann Almgren Date: Fri May 10 17:12:49 2019 -0700 Add references for SUNDIALS, hypre, PETSc and xSDK. paper/paper.bib paper/paper.md commit f4118f5be894e1f745ae5c2740fcecdf0ee451d2 Author: Weiqun Zhang Date: Fri May 10 17:08:48 2019 -0700 WIP: MLEBTensorOp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit af7cab1765a8c69ee3c1039b93d4ab0fff7d2f9e Merge: 58d4c08d3 451066888 Author: Ann Almgren Date: Fri May 10 16:28:52 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 58d4c08d37fa56bcfadc1ee4354ca093c70e2b0f Author: Ann Almgren Date: Fri May 10 16:28:34 2019 -0700 Add city and country to the author affiliations. paper/paper.md commit c20f084f6e1a66ff3ee737019947529d2b34cd07 Author: Weiqun Zhang Date: Fri May 10 15:39:01 2019 -0700 MLEBTensor: fill the corners of regular fabs too Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 1fa7ad1388ebc366db1d87b61048868434ea6d36 Author: Weiqun Zhang Date: Fri May 10 13:55:45 2019 -0700 MLEBTensor: save fluxes in MultiFab so that we don't have to have 2 ghost cells Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 7cf9062ef32dd596ba9268d9cb95eac026219339 Merge: 13da3a462 4f03be844 Author: WeiqunZhang Date: Fri May 10 14:15:40 2019 -0700 Merge pull request #478 from kyleniemeyer/patch-1 Typographic edits in paper commit 4f03be844d30dd254fddeb2ab5d3079b1829cba6 Author: Kyle Niemeyer Date: Fri May 10 14:13:34 2019 -0700 Typographic edits in paper paper/paper.md commit ac59fe275f0a4859b7fcd2087d53a6bd9761cbcc Author: Andrew Myers Date: Fri May 10 12:14:49 2019 -0700 size should be capacity here Src/Base/AMReX_PODVector.H commit 451066888fc0e4139437b7698119678bad9f59cc Merge: 21d8a427f b6a7b719c Author: Weiqun Zhang Date: Fri May 10 11:18:37 2019 -0700 Merge branch 'weiqun/mlmg' into development commit b6a7b719cbd29e8e3de752b31ad0e053e27fff0a Author: Weiqun Zhang Date: Fri May 10 10:55:43 2019 -0700 MLEBABecLap: fix typo Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H commit e4c5386e3fc3b018da8cbf0d3b5685c9fb8213cb Author: Weiqun Zhang Date: Fri May 10 09:42:08 2019 -0700 MLEBABecLap: fix new bug in mask Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H commit 376f57d6cf922344e833312944e70cb2ab6bf122 Author: Weiqun Zhang Date: Fri May 10 09:01:26 2019 -0700 WIP: MLEBTensor Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 60e3a2a111b5036674314aa0b1082baeb8eeec0c Author: Weiqun Zhang Date: Thu May 9 18:38:19 2019 -0700 MLEBTensor: cross term fluxes Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 89c62f87f1e7e2f77135711e118525aeda8754ba Author: kngott Date: Thu May 9 17:24:06 2019 -0700 Readme for CudaGraph tests. Tests/GPU/CudaGraphs/Readme.txt commit 8184c385360b3062c1c2a3e802fdc0e37979e944 Author: kngott Date: Thu May 9 17:15:53 2019 -0700 Clean up older, redundant graph tests. Tests/GPU/CudaGraphs/ArrayReuse/GNUmakefile Tests/GPU/CudaGraphs/ArrayReuse/Make.package Tests/GPU/CudaGraphs/ArrayReuse/inputs_3d Tests/GPU/CudaGraphs/ArrayReuse/main.cpp Tests/GPU/CudaGraphs/ArrayReuse/run.corigpu Tests/GPU/CudaGraphs/GraphCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphCopy/Make.package Tests/GPU/CudaGraphs/GraphCopy/inputs_3d Tests/GPU/CudaGraphs/GraphCopy/main.cpp Tests/GPU/CudaGraphs/GraphCopy/run.corigpu Tests/GPU/CudaGraphs/GraphIterReuseCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphIterReuseCopy/Make.package Tests/GPU/CudaGraphs/GraphIterReuseCopy/inputs_3d Tests/GPU/CudaGraphs/GraphIterReuseCopy/main.cpp Tests/GPU/CudaGraphs/GraphIterReuseCopy/run.corigpu commit 54f15cd2db930ffd4d1bdc627f1025f90b68ce51 Author: Andrew Myers Date: Thu May 9 16:08:24 2019 -0700 also use the PODVector on CPU code (for now, to test it) Src/Base/AMReX_CudaContainers.H commit c14c9b16e470557490d9bcde38dc7518b9eaf946 Author: Weiqun Zhang Date: Thu May 9 15:15:26 2019 -0700 MLEBABecLap: prepare it for tensor solve Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 Src/LinearSolvers/MLMG/Make.package commit 21d8a427f73c680846f89a8cbc1a82a17c4b9de2 Author: Andrew Myers Date: Thu May 9 14:55:38 2019 -0700 correct the number of comps when writing particle data to plt files Src/Particle/AMReX_ParticleContainerI.H commit 67784e0c1aadea9942459c9fd0f5e98a1f92261e Author: Weiqun Zhang Date: Thu May 9 12:45:57 2019 -0700 MLEBABecLap: switch to new gsrb with multi-component b coefficient Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 0e76d0280b95cb4f54ce2f4e4e89c27185b5076a Author: Weiqun Zhang Date: Thu May 9 11:19:57 2019 -0700 simplification Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit b15b1d2a8da7b0b997f8e483b471ff2b8a7e2d3c Author: Weiqun Zhang Date: Thu May 9 10:47:36 2019 -0700 WIP: MLEBTensorOp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 7dcd6e1e65ad294f549977c92cf8752d9443286c Author: Weiqun Zhang Date: Thu May 9 09:03:28 2019 -0700 make some functions public for cuda Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H commit b4893f43a39d88aa1f685c32ea3d74c3d4c66857 Author: Weiqun Zhang Date: Wed May 8 18:34:58 2019 -0700 MLEBABecLap: fix new bug introduced when removing HO EB Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit c1a85dc5a2f28a5c4c95e845f216115cb1fee70b Author: Andrew Myers Date: Wed May 8 19:43:20 2019 -0400 mark these functions as noexcept, since we don't catch those ever Src/Base/AMReX_PODVector.H commit e4a58ce8d4c8c558848db44b27f595edef9730aa Author: Weiqun Zhang Date: Wed May 8 16:39:48 2019 -0700 MLEBTensorOp: add eb kappa Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H commit 3c8c4516ff05b5c43b41131054d22ec8c834b5a0 Author: Andrew Myers Date: Wed May 8 19:25:52 2019 -0400 split this constructor for PODVector into two Src/Base/AMReX_PODVector.H commit b7be90fa07d3adff0a72a52654e73c8c418725da Author: Andrew Myers Date: Wed May 8 19:20:56 2019 -0400 don't need thrust::raw_pointer_cast anymore Src/Particle/AMReX_ParticleContainerI.H commit f2ed00545be6be1b94197db8bb782ae70deef8e9 Author: Weiqun Zhang Date: Wed May 8 15:48:07 2019 -0700 MLEBABecLap 2D: remove blend beta Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 025cde7d1893fe83b264c7fb0228813d32c1f949 Merge: f7a796f4b 37c3faf70 Author: Weiqun Zhang Date: Wed May 8 15:39:29 2019 -0700 Merge branch 'development' into weiqun/mlmg commit 37c3faf70c7c03c84462c5d1470d7ae2ae472b43 Author: Weiqun Zhang Date: Wed May 8 15:38:23 2019 -0700 add a missing header Src/Base/AMReX_ParmParse.H commit f7a796f4bfdc5595db5017e04618e9c5d8b17545 Author: Weiqun Zhang Date: Wed May 8 15:00:24 2019 -0700 MLEBABecLap: update for multi-component Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 commit 39c836c57e814030b0e68c499af7793d0623190b Author: Andrew Myers Date: Wed May 8 18:08:38 2019 -0400 copying the grid start and stop indices using thrust_copy instead of the copy constructor Src/Particle/AMReX_ParticleContainerI.H commit e93dab73c74cbc6b4b305bac3521d7ec89cb6c31 Author: Kevin Gott Date: Wed May 8 16:32:16 2019 -0400 Fix run.summit script. -N = email, not number of nodes. Tutorials/GPU/run.summit commit 25528e43bb3d53adcaf3a8348a7a9b77dbb9f5c5 Author: Andrew Myers Date: Wed May 8 16:27:59 2019 -0400 remove debug print statement Src/Base/AMReX_PODVector.H commit f66ed9c3d3b487dd697a72d0c8c2bbb059c72be9 Author: Weiqun Zhang Date: Wed May 8 13:04:40 2019 -0700 MLEBABecLap: remove HO EB Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit fcb52dd3726dcf3ebe8ac567bb93a10dc71acb84 Author: kngott Date: Wed May 8 12:47:05 2019 -0700 Proper CUDA Callback calls for CUDA 9 & CUDA 10, Part 2. Src/Base/AMReX_CudaAsyncFab.cpp commit f9bf8841668e4a4256cff480a60dee15e8d8b725 Author: kngott Date: Wed May 8 12:41:55 2019 -0700 Proper CUDA Callback calls for CUDA 9 & CUDA 10. Src/Base/AMReX_CudaAsyncFab.cpp commit 84f3abce80345f0f2020427055d0ef64d1c8aeb4 Author: kngott Date: Wed May 8 12:20:28 2019 -0700 Hide max_cuda_streams function when USE_CUDA=FALSE. Src/Base/AMReX_CudaDevice.H commit 618ef094876af9d8755937226ec248bf5b22f728 Author: Weiqun Zhang Date: Wed May 8 12:01:47 2019 -0700 MLTensor: limit kappa to mg level 0 Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 5518eff068513bbc71be2a8af35e5dfd0fbaa67a Merge: 9783b79d7 fa43d9a79 Author: kngott Date: Wed May 8 11:49:01 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 2071003f8a4792fc40c5b738da969277b6dbde03 Author: Weiqun Zhang Date: Wed May 8 09:41:22 2019 -0700 MLTensor: move as much as possible into the laplacian Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 9783b79d7d861e6c866094969b0b5cd79a3a082f Author: kngott Date: Wed May 8 11:47:25 2019 -0700 Clean up. Src/Base/AMReX_FabArrayCommI.H commit 13da3a4627acdf7a8671b2ed377e145628f32f04 Author: Ann Almgren Date: Wed May 8 11:43:08 2019 -0700 Oops -- forgot to actually remove the text LICENSE commit fa43d9a7997ca3bbd1af94ac164d942e7ad59d01 Author: Ann Almgren Date: Wed May 8 11:43:08 2019 -0700 Oops -- forgot to actually remove the text LICENSE commit e069976b36c585bb4e8f1045fa72d0a3d5562d7f Author: kngott Date: Wed May 8 11:42:23 2019 -0700 Fix indentation in FillBoundary w/ Graphs. Src/Base/AMReX_FabArrayCommI.H commit fc619fdce1f0553333b71ae848d35ff2f84a0c61 Author: Ann Almgren Date: Wed May 8 11:40:17 2019 -0700 Update license.txt -> LICENSE and replace modified BSD by standard 3-clause BSD. LICENSE README.md commit 18f452ae4f256e7d37f44f59a00ebd0c8fed0a3d Author: Ann Almgren Date: Wed May 8 11:40:17 2019 -0700 Update license.txt -> LICENSE and replace modified BSD by standard 3-clause BSD. LICENSE README.md commit 6e574f9a2afb86ab45714912b9b9f334cb205b56 Merge: f7586cd9e 66d8a46bd Author: kngott Date: Wed May 8 11:35:01 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit f7586cd9ec324429c84b7f2c6d03860907be28b0 Author: kngott Date: Wed May 8 11:34:18 2019 -0700 Add number of ghost cells and components to test inputs. Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d commit 8ce293ad8a4c6b78f77c60d4011a8238b4b55967 Author: kngott Date: Wed May 8 11:32:55 2019 -0700 Add runtime flag to turn on/off graphs to LinearSolver Tutorial. Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit 91199880018afb6f281ba1ad383608e2810f5461 Author: kngott Date: Wed May 8 11:31:56 2019 -0700 Rename re-used timer. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 18bb26fd9817c257cda18e2e7c70b51ba9307f03 Author: kngott Date: Wed May 8 11:31:22 2019 -0700 Clean up FillBoundary graph test. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 2cf8523fa64cfd341c3d7b6923bb1005afd5eb02 Merge: 9545d80be 66d8a46bd Author: Andrew Myers Date: Wed May 8 13:53:47 2019 -0400 Merge branch 'development' into atmyers/vector_memory_usage commit 42073726f446ac8dd0743f4b3c04d607da891767 Author: Weiqun Zhang Date: Tue May 7 22:12:38 2019 -0700 MLTensor: apply the cross terms at all levels Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit e48a89f893c3d6457e70910161f03eb50c3fdd0b Author: Weiqun Zhang Date: Tue May 7 19:34:45 2019 -0700 WIP: MLEBTensorOp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 66d8a46bde5baf7ac3e410fd560d6705fc38668c Author: Ann Almgren Date: Tue May 7 18:06:28 2019 -0700 Add notes about being able to install amrex using spack. Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst Docs/sphinx_documentation/source/GettingStarted.rst commit 95b428ac6bbf51334c1f94d0c4fe0f8215482c00 Author: Weiqun Zhang Date: Tue May 7 16:09:28 2019 -0700 MLEBTensorOp: stubs Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/Make.package commit af07eb7a5be433e4e44a2cb46848ca5d64ca938f Author: Weiqun Zhang Date: Tue May 7 15:54:36 2019 -0700 MLTensor: bc at corners Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 9047db69c7f4b4cd9808fd4c251dbb2f620ad1e7 Author: Weiqun Zhang Date: Mon May 6 16:07:47 2019 -0700 MLMG: when using EB, the coarest domain size is now >= 4. Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit fb079185c4f07af9b98948afc3e24acceb842105 Author: Weiqun Zhang Date: Mon May 6 14:46:07 2019 -0700 MLTensor: simplification Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 31757085d71708d94b978fbda0aae3b0e67d57d6 Author: Weiqun Zhang Date: Mon May 6 14:10:43 2019 -0700 MLTensor: include all cross terms Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit a6f69d55d37d1f2da2c3bad91f1932005da8f44c Author: Ann Almgren Date: Sun May 5 15:57:15 2019 -0700 fix typos Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit 1dfef654a951a6a9fe82d59fd36ccaaf56cdac8e Author: Ann Almgren Date: Sun May 5 15:42:35 2019 -0700 more on gridding Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit 7251c87a4d94f89bc934d7a6b8690ea272aed50b Merge: fab14b6c0 bc89383e9 Author: Ann Almgren Date: Sun May 5 15:08:11 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit fab14b6c0a29dbb63e7401f97a8116b46b8f5574 Author: Ann Almgren Date: Sun May 5 15:07:59 2019 -0700 update to gridding stuff Docs/sphinx_documentation/source/DualGrid.rst Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit bc89383e99e36f873bfeb984f847b8456c972cc2 Merge: e2b9b5d69 c992ae224 Author: Weiqun Zhang Date: Sun May 5 13:53:12 2019 -0700 Merge branch 'weiqun/mlmg' into development commit c992ae2241d0eba9666cd441f91899568ab48673 Author: Weiqun Zhang Date: Sun May 5 13:52:57 2019 -0700 comments about the tensor solver Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H commit e2b9b5d6978f5110f88ca7cbb12ab3275f23d412 Author: Ann Almgren Date: Sun May 5 12:56:26 2019 -0700 fix formatting Docs/sphinx_documentation/source/LoadBalancing.rst commit da28ba423c088f52f34231f861678a3b34fb1b66 Author: Ann Almgren Date: Sun May 5 12:39:17 2019 -0700 Add short text about load balancing Docs/sphinx_documentation/source/DualGrid.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit e9afc6f7e62bb7b6d4db17bd3f83823d649b30f9 Author: Ann Almgren Date: Sat May 4 20:16:07 2019 -0700 Remove gridding from AmrCore now that it lives in its own section. Docs/sphinx_documentation/source/AmrCore.rst commit b6d1e4fa4b0e9c6c1958b1c1d28954a4c8df7f05 Author: Ann Almgren Date: Sat May 4 20:10:06 2019 -0700 fix typo Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit 1a128f70b5e702f8251beea610224ed051dd28be Author: Ann Almgren Date: Sat May 4 20:02:35 2019 -0700 Add text about dual gridding. Docs/sphinx_documentation/source/DualGrid.rst Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit ee13c67359f375d36e9166f88a4719675b86eea3 Author: Ann Almgren Date: Sat May 4 19:48:31 2019 -0700 More clarification Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit 284f84250c89ace2e0085459e5b7f0d256c216ea Author: Ann Almgren Date: Sat May 4 19:27:58 2019 -0700 fix typo Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 080490b983e63a210b9bb806d97d365781183c93 Author: Ann Almgren Date: Sat May 4 19:26:46 2019 -0700 more fixes for grid creation Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 9d7870ed20cfe5c181bb32b97e3e7ab3bbe35c0b Author: Ann Almgren Date: Sat May 4 19:21:39 2019 -0700 more grid creation update Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit f964bd8469d66ea9d8c9d0240773057608e8b294 Author: Ann Almgren Date: Sat May 4 19:03:44 2019 -0700 More detail Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 1427d5404b4b6c47c2fa5c89d897f8d5ef4ecf3c Author: Ann Almgren Date: Sat May 4 18:31:12 2019 -0700 Add refine_grid_layout Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 366c966f7bc4708a3f28659657af5fed2eedf120 Author: Ann Almgren Date: Sat May 4 18:16:08 2019 -0700 Fix oops re cpp use Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 843d168baad6175b21d4a5d65acfc3b8b00ec2fc Author: Ann Almgren Date: Sat May 4 18:14:15 2019 -0700 More update on grid creation Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 2ec6dfac0074fbcb06e5485adeb95e6a12e66a7b Author: Ann Almgren Date: Sat May 4 17:57:54 2019 -0700 More detail re grid creation Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 168eee4d320dcbc5875a71c7c0014635ca4868b6 Merge: 44647b983 cbd29aa71 Author: Ann Almgren Date: Sat May 4 11:20:02 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 44647b983e815a025168286eaab60440c1a12530 Author: Ann Almgren Date: Sat May 4 11:19:43 2019 -0700 Fix the headings for managing grid hierarchy Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit e9f91a3962321e5d9df9f9e175f8deb58130ec53 Author: Weiqun Zhang Date: Sat May 4 09:04:31 2019 -0700 MLTensor: override apply instead of solutionResidual Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 23398439c98d18aafbbeef106343b2c48f0688e5 Author: Weiqun Zhang Date: Fri May 3 21:48:06 2019 -0700 MLTensor: hide setScalars Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit cbd29aa715007223b1bd49d05bf931d4df835e30 Merge: 137f45cf0 421af5572 Author: asalmgren Date: Fri May 3 18:21:47 2019 -0700 Merge pull request #475 from AMReX-Codes/docs-libamrex Expand section on building libamrex commit 421af557231f1526b1e12dee12f750d10ed6c8e4 Author: Donald E. Willcox Date: Fri May 3 18:04:42 2019 -0700 Expand section on building libamrex with details about how to set C++ flags and linker flags for the application code. Docs/sphinx_documentation/source/BuildingAMReX.rst commit 137f45cf070536b8d8725b7936dc4ce27bd265b1 Author: Ann Almgren Date: Fri May 3 17:57:58 2019 -0700 Add Chapter intro for ManagingGridHierarchy Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit aae549bd2e87dee875161dc97d8154295d8b0e31 Author: kngott Date: Fri May 3 17:28:20 2019 -0700 ifdefs to protect CUDA 10 features. Needs testing on Summit. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayCommI.H commit 749a2c8f7053f8f8e934d52cf269f8de730057e7 Merge: 8b04d1ad8 1249b1ca6 Author: Ann Almgren Date: Fri May 3 17:00:50 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 8b04d1ad88f3ef74dd70964159f1e8864ab77249 Author: Ann Almgren Date: Fri May 3 17:00:35 2019 -0700 add separate section on managing the grid hierarchy Docs/sphinx_documentation/source/ManagingGridHierarchy.rst Docs/sphinx_documentation/source/index.rst commit 4e4f1e519a6ca959a991913033e955dbe7fccbd3 Author: kngott Date: Fri May 3 16:00:31 2019 -0700 Update FillBoundary to switchable graph recording methods. Src/Base/AMReX_FabArrayCommI.H commit 3f8424de740c4a2530c0646b010d88a178f7fe31 Author: kngott Date: Fri May 3 15:59:08 2019 -0700 Add flag to switch graph recording methods and single start and stop function to choose. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit 7cc4c4e0b93dbf96d97362efe87b7fc8e2452b1a Author: kngott Date: Fri May 3 15:57:29 2019 -0700 Reorganize and cleanup output. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit d7a382a2e5385cdeb103d522ea8fd808abd60a60 Author: kngott Date: Fri May 3 15:56:12 2019 -0700 Whitespace cleanup. Src/Base/AMReX_GpuControl.H commit 1249b1ca6889665df3c3d30ccce71b8fb10f3b09 Author: Weiqun Zhang Date: Fri May 3 15:27:09 2019 -0700 Fix bndry for hypre and petsc Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 9545d80beec5ecbc12aab92c44bd0265110a7cec Author: Andrew Myers Date: Fri May 3 17:53:49 2019 -0400 fix move assignment operator Src/Base/AMReX_PODVector.H commit 539eb05f9054f303e5a9755cb47f46fd47ee1e4c Merge: aa6741c65 34092a5d8 Author: Weiqun Zhang Date: Fri May 3 14:43:12 2019 -0700 Merge branch 'weiqun/mlmg' into development commit 34092a5d8493aa28d6581f76cb2d69af2c643d43 Author: Weiqun Zhang Date: Fri May 3 14:42:47 2019 -0700 MLTensor: add extra terms to residual Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_K.H Src/LinearSolvers/MLMG/Make.package commit 871c06875d32c1b19781ca400cb75bfb58cacc6b Author: Andrew Myers Date: Fri May 3 17:37:05 2019 -0400 implement erase, assign, insert Src/Base/AMReX_PODVector.H commit 517afa944afbf8431c9a132f63597fe5543dcf01 Author: Weiqun Zhang Date: Fri May 3 12:59:25 2019 -0700 add computeGradient Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 9dadef8b8cd5cf93a6e0564e1271e83353f42b32 Author: Andrew Myers Date: Fri May 3 13:55:06 2019 -0400 can implement these Vector using simple typedefs now Src/Base/AMReX_CudaContainers.H commit e2d3be1bd48dd7cbc6075d9dea183bf3b4dfaecb Author: Andrew Myers Date: Fri May 3 13:54:20 2019 -0400 don't need this allocator to inherit from the thrust one Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_PODVector.H commit 5406c08584d21c0de44ced27cad77819ccecb140 Author: Weiqun Zhang Date: Fri May 3 10:53:21 2019 -0700 MLTensorOp: prepareForSolve Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit e02130b32ec3f03406beb2116393ba1e33cc0a08 Author: Andrew Myers Date: Fri May 3 13:52:49 2019 -0400 use the wrapped version of Gpu::HostVector here Src/Particle/AMReX_ParticleContainerI.H commit 522c58748ef88fac1dc86011bf118e2a8969c2c1 Author: Weiqun Zhang Date: Fri May 3 09:55:51 2019 -0700 MLEBABecLap: update for multi-component Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit aa6741c65786da1bcaa51d3a21f8f9ce50b07f21 Author: Weiqun Zhang Date: Fri May 3 07:15:37 2019 -0700 Fix FillPatch for EB Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H commit 0a08d83f7d451956ad8e9c6b942ca23165c64a9d Author: Maikel Nadolski Date: Fri May 3 10:49:21 2019 +0200 Link against the C version of MPI Src/Base/CMakeLists.txt commit afac4e3890987efbe731cfbf7933585952bcaeac Author: Marc Day Date: Thu May 2 19:19:36 2019 -0700 Fix WritePlotFile to allow few levels in output that in orig, based on length of mf data passed in Tools/C_util/WritePlotFile.cpp commit bdaef55a55aff0cd36a9aa28ed529ffc55ff04e4 Author: Marc Day Date: Thu May 2 18:50:57 2019 -0700 Update isoToVTK.py to be python3-compliant Tools/EBSurfaceTools/isoToVTK.py commit 1d818c3f893601c0cc26eab5f38d26a97fd7dc3b Author: Weiqun Zhang Date: Thu May 2 16:53:22 2019 -0700 MLCellLinOp: update for multi-component Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 718f36ba7411bb803934e12ac1b4e217921adb22 Author: Weiqun Zhang Date: Thu May 2 16:38:54 2019 -0700 MLABecLap: update for multi-component Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 0043eb360cf6824053307d2f263356b4e8d4f264 Author: Andrew Myers Date: Thu May 2 19:00:38 2019 -0400 a vector implementation where we control the growth and reallocation strategy Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_PODVector.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 40c62cc4d0d8ba60a5ff74fe7427380af6314260 Author: Weiqun Zhang Date: Thu May 2 15:30:18 2019 -0700 MLMG: fine mask only needs to have 1 component. BaseFab::norinfmask now assumes the mask has only 1 component. Src/Base/AMReX_BaseFab.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 41a38aba1b3cd47d98f52361fdd7ce272611823c Author: Weiqun Zhang Date: Thu May 2 13:51:48 2019 -0700 new version of contains_inf with IntVect argument for ghost cells Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit d312ff08d3a2e9b44094cb69de2c66378ce4bafa Author: Weiqun Zhang Date: Thu May 2 13:46:21 2019 -0700 new version of SumBoundary with argument for number of ghost cells Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit dbf8aef2be063695b6ffe037578485718a6d3690 Author: Weiqun Zhang Date: Thu May 2 12:09:38 2019 -0700 Remove duplicated code in FillPatch Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit a9a0347f1661a72e727e42e370e45697d3c3f619 Author: Weiqun Zhang Date: Thu May 2 10:04:35 2019 -0700 MLMG nodal rap: change the number of ghost cells to 1 at the bottom Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 948cb60fccc5f7bd84cfd91d3fb83224e0ba5b7f Author: Andrew Myers Date: Thu May 2 13:21:50 2019 -0700 change the assert about the particle type to be even stronger Src/Particle/AMReX_ParticleContainerI.H commit 7fae8b4c18fde89fafe84acc45fe6070846fdb96 Author: Andrew Myers Date: Thu May 2 13:14:19 2019 -0700 let the constructor for the Particle struct be compiler-defined Src/Particle/AMReX_Particle.H commit 278f7aa4776243cd538f888f87d61620b26a27b2 Merge: c39648484 867bd8f56 Author: Andrew Myers Date: Thu May 2 10:04:21 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c39648484de3976b3cd7e80ea166ff5336d894b5 Author: Andrew Myers Date: Thu May 2 10:03:58 2019 -0700 The pointer incrementing logic here was wrong due to the possibility of structure padding. Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit c98d66c8248ebef820820793fcfec6c9192f1d05 Author: Maikel Nadolski Date: Thu May 2 17:58:33 2019 +0200 Do not require CXX libraries for MPI which are deprecated. CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in commit 867bd8f566743cc9eda4aedb877db22f16da8c9c Author: Weiqun Zhang Date: Wed May 1 20:47:18 2019 -0700 fix symmetry issue of nodal rap stencil in 2D Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 8c225f8dc6a65747d6b89778ce444ff52113e72b Author: Weiqun Zhang Date: Wed May 1 19:13:18 2019 -0700 fix symmetry issue of nodal rap stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 805ff0f714c5bdae16c671ef5fb9a2288c86759c Merge: 9b7b0a746 aa0b4e4af Author: kngott Date: Wed May 1 12:22:25 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 9b7b0a746992aba08fcb2f9b6d4ab5ac75809953 Author: kngott Date: Wed May 1 12:21:36 2019 -0700 Output adjustment. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit aa0b4e4afea1a26ff59a2c9bb5625939b239bec0 Merge: f0fe60c36 01bd97c5e Author: Andrew Myers Date: Wed May 1 10:10:46 2019 -0700 Merge pull request #471 from AMReX-Codes/particle_realdescriptor_fix bug fixes for particles when BL_FLOAT is used. commit f0fe60c36e1f7e6315e4109687b68289dccbe0ec Merge: adcf40035 a8e4bfa66 Author: WeiqunZhang Date: Wed May 1 10:07:28 2019 -0700 Merge pull request #472 from maikel/feature/FillPatch_IndexSpace EB: Add an additional overload for FillPatchTwoLevels. commit 641f9dc883e08a1b44be052cbae5f4f72c561f3e Author: Weiqun Zhang Date: Wed May 1 09:11:55 2019 -0700 MLMG: remove assertion to maintain backward compatibility Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 3c2641aef1dec1f8124061a91f846557d13a3395 Merge: ffe5eff88 adcf40035 Author: Weiqun Zhang Date: Wed May 1 09:06:01 2019 -0700 Merge branch 'development' into weiqun/mlmg commit adcf400351198159f6c1cbc618c912ecf033f170 Author: Weiqun Zhang Date: Wed May 1 09:04:52 2019 -0700 update CHANGES CHANGES commit c76bcf6349919f15306b9e7148511ddb8cf17c1e Merge: 2b96cafc6 cad29442c Author: Weiqun Zhang Date: Wed May 1 08:44:20 2019 -0700 Merge branch 'development' commit cad29442cfd4c692e23a477dbb25a00e8b46baaf Author: Tan Nguyen Date: Tue Apr 30 17:29:35 2019 -0700 factor upcxx backend code Src/AmrTask/rts_impls/mpi/Make.package Src/AmrTask/rts_impls/mpi/Perilla.cpp Src/AmrTask/rts_impls/mpi/perilla.mak Src/AmrTask/rts_impls/runtime_common/Make.package Src/AmrTask/rts_impls/runtime_common/Perilla_common.cpp Src/AmrTask/rts_impls/runtime_common/RGIter.cpp Src/AmrTask/rts_impls/runtime_common/RegionGraph.H Src/AmrTask/rts_impls/runtime_common/RegionGraph.cpp Src/AmrTask/rts_impls/runtime_common/WorkerThread.H Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp Src/AmrTask/rts_impls/runtime_common/perilla.mak Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/upcxx/Barrier.H Src/AmrTask/rts_impls/upcxx/Barrier.cpp Src/AmrTask/rts_impls/upcxx/LocalConnection.H Src/AmrTask/rts_impls/upcxx/Make.package Src/AmrTask/rts_impls/upcxx/Perilla.cpp Src/AmrTask/rts_impls/upcxx/PerillaConfig.H Src/AmrTask/rts_impls/upcxx/PerillaRts.H Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp Src/AmrTask/rts_impls/upcxx/Perilla_common.cpp Src/AmrTask/rts_impls/upcxx/RGIter.H Src/AmrTask/rts_impls/upcxx/RGIter.cpp Src/AmrTask/rts_impls/upcxx/RegionQueue.H Src/AmrTask/rts_impls/upcxx/RegionQueue.cpp Src/AmrTask/rts_impls/upcxx/RemoteConnection.H Src/AmrTask/rts_impls/upcxx/WorkerThread.H Src/AmrTask/rts_impls/upcxx/WorkerThread.cpp Src/AmrTask/rts_impls/upcxx/mylock.h Src/AmrTask/rts_impls/upcxx/perilla.mak commit ffe5eff882978dfc6c2ceae6b85af31636bf25cc Author: Weiqun Zhang Date: Tue Apr 30 17:04:10 2019 -0700 MLMGBndry: multi-component Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit eecd1c27bc75fe3d95743dca312d13940d75c433 Author: Weiqun Zhang Date: Tue Apr 30 16:45:12 2019 -0700 MLMG: multi-component BndryCondLoc Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit 2a7d7a29c9647882bba387ea628c06f40d501c71 Author: kngott Date: Tue Apr 30 16:19:01 2019 -0700 FillBoundary MPI graphed and tested on one node. CopyTo, Local & CopyFrom all graphed. Src/Base/AMReX_FabArrayCommI.H commit 01bd97c5e57c037dd3cdb3a89aac56082be1f7fd Author: Andrew Myers Date: Tue Apr 30 15:50:57 2019 -0700 make sure the format and order is consistent for each of the real conversion functions Src/Base/AMReX_FabConv.cpp commit c37b030a9240baffc722b5f1bb3a289c0376c14e Author: Andrew Myers Date: Tue Apr 30 15:26:03 2019 -0700 float -> double Src/Base/AMReX_FPC.cpp commit 671d64ca7d75f5908a39ab64fa4df2cc4f0b1775 Author: Weiqun Zhang Date: Tue Apr 30 15:06:31 2019 -0700 make domain bc vector so that each component could have its own bc type Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H commit f7002c1e3553ae6c9ea630b28811c362d8cf7789 Author: kngott Date: Tue Apr 30 14:57:41 2019 -0700 Get rid of StreamIter loops where not needed. Src/Base/AMReX_FabArrayCommI.H commit 7bdd2860272c5a2da86d0e05880de3cc942a830d Author: Weiqun Zhang Date: Tue Apr 30 14:40:43 2019 -0700 MLTensorOp: derive from MLABecLaplacian Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 4f1cb78034770a43946008dfc72db2c0684e2042 Author: kngott Date: Tue Apr 30 14:38:16 2019 -0700 SendToBuffer Graphed Src/Base/AMReX_FabArrayCommI.H commit e55a71ef7dc2f6b8760906487bf8061109bcafc4 Author: kngott Date: Tue Apr 30 14:36:33 2019 -0700 Better run script. Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu commit d0ca7303d25952ea65d119c39aa3220de03d4bb1 Author: kngott Date: Tue Apr 30 14:36:16 2019 -0700 Small tweaks. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 58cbc7b9b421b5203253a1c44748d99ab17bce1b Author: Tan Nguyen Date: Tue Apr 30 13:26:13 2019 -0700 delete duplicated codes Src/AmrTask/rts_impls/mpi/RegionGraph.H Src/AmrTask/rts_impls/mpi/RegionGraph.cpp commit 354b0363e3d6f351aff26fa7b71714ba7a6596dd Author: Tan Nguyen Date: Tue Apr 30 13:24:12 2019 -0700 delete duplicated codes Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi/Barrier.H Src/AmrTask/rts_impls/mpi/Barrier.cpp Src/AmrTask/rts_impls/mpi/LocalConnection.H Src/AmrTask/rts_impls/mpi/RGIter.H Src/AmrTask/rts_impls/mpi/RGIter.cpp Src/AmrTask/rts_impls/mpi/RegionQueue.H Src/AmrTask/rts_impls/mpi/RegionQueue.cpp Src/AmrTask/rts_impls/mpi/RemoteConnection.H Src/AmrTask/rts_impls/mpi/WorkerThread.H Src/AmrTask/rts_impls/mpi/WorkerThread.cpp Src/AmrTask/rts_impls/mpi/mylock.h commit b4025c682b7b12b333e67c01d355eb01de13fde2 Author: Weiqun Zhang Date: Tue Apr 30 10:23:43 2019 -0700 Start tensor solver Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/Make.package commit a8e4bfa6606a0840317e46964f69cef07e1af9fa Author: Maikel Nadolski Date: Tue Apr 30 09:50:47 2019 +0200 Allows to create FPInfo objects with an associated EB2::IndexSpace. For enabled EB these changes allow to choose the EB2::IndexSpace which will be used for the interpolation regions in FillPatchTwoLevels. This commit also makes it possible to use FillPatchTwoLevels without any EB2::IndexSpace built at a prior stage. In this case it will do the same communication logic as if AMReX would not be built with enabled EB. Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp commit 498593ddd7adc2d52bd379484c194512c7d82f95 Merge: 405feb15c 11beeb82b Author: Tan Nguyen Date: Mon Apr 29 21:52:39 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 405feb15c6a6412798b79128e1141b65e11b9fe0 Author: Tan Nguyen Date: Mon Apr 29 21:51:29 2019 -0700 factor codes in omp and pthreads backends Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi/Barrier.H Src/AmrTask/rts_impls/mpi/Barrier.cpp Src/AmrTask/rts_impls/mpi/LocalConnection.H Src/AmrTask/rts_impls/mpi/Make.package Src/AmrTask/rts_impls/mpi/Makefile Src/AmrTask/rts_impls/mpi/PackageQueue.H Src/AmrTask/rts_impls/mpi/PackageQueue.cpp Src/AmrTask/rts_impls/mpi/Perilla.H Src/AmrTask/rts_impls/mpi/Perilla.cpp Src/AmrTask/rts_impls/mpi/PerillaConfig.H Src/AmrTask/rts_impls/mpi/PerillaRts.H Src/AmrTask/rts_impls/mpi/PerillaRts.cpp Src/AmrTask/rts_impls/mpi/RGIter.H Src/AmrTask/rts_impls/mpi/RGIter.cpp Src/AmrTask/rts_impls/mpi/RegionGraph.H Src/AmrTask/rts_impls/mpi/RegionGraph.cpp Src/AmrTask/rts_impls/mpi/RegionQueue.H Src/AmrTask/rts_impls/mpi/RegionQueue.cpp Src/AmrTask/rts_impls/mpi/RemoteConnection.H Src/AmrTask/rts_impls/mpi/WorkerThread.H Src/AmrTask/rts_impls/mpi/WorkerThread.cpp Src/AmrTask/rts_impls/mpi/mylock.h Src/AmrTask/rts_impls/mpi/perilla.mak Src/AmrTask/rts_impls/mpi_pthreads/Make.package Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/runtime_common/Barrier.H Src/AmrTask/rts_impls/runtime_common/Barrier.cpp Src/AmrTask/rts_impls/runtime_common/LocalConnection.H Src/AmrTask/rts_impls/runtime_common/Make.package Src/AmrTask/rts_impls/runtime_common/PerillaMemCheck.H Src/AmrTask/rts_impls/runtime_common/PerillaMemCheck.cpp Src/AmrTask/rts_impls/runtime_common/RGIter.H Src/AmrTask/rts_impls/runtime_common/RGIter.cpp Src/AmrTask/rts_impls/runtime_common/RegionQueue.H Src/AmrTask/rts_impls/runtime_common/RegionQueue.cpp Src/AmrTask/rts_impls/runtime_common/RemoteConnection.H Src/AmrTask/rts_impls/runtime_common/WorkerThread.H Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp Src/AmrTask/rts_impls/runtime_common/mylock.h Src/AmrTask/rts_impls/runtime_common/perilla.mak Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/upcxx/Barrier.H Src/AmrTask/rts_impls/upcxx/Barrier.cpp Src/AmrTask/rts_impls/upcxx/LocalConnection.H Src/AmrTask/rts_impls/upcxx/Make.package Src/AmrTask/rts_impls/upcxx/Makefile Src/AmrTask/rts_impls/upcxx/PackageQueue.H Src/AmrTask/rts_impls/upcxx/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx/Perilla.H Src/AmrTask/rts_impls/upcxx/Perilla.cpp Src/AmrTask/rts_impls/upcxx/PerillaConfig.H Src/AmrTask/rts_impls/upcxx/PerillaRts.H Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp Src/AmrTask/rts_impls/upcxx/Perilla_common.cpp Src/AmrTask/rts_impls/upcxx/RGIter.H Src/AmrTask/rts_impls/upcxx/RGIter.cpp Src/AmrTask/rts_impls/upcxx/RegionGraph.H Src/AmrTask/rts_impls/upcxx/RegionGraph.cpp Src/AmrTask/rts_impls/upcxx/RegionQueue.H Src/AmrTask/rts_impls/upcxx/RegionQueue.cpp Src/AmrTask/rts_impls/upcxx/RemoteConnection.H Src/AmrTask/rts_impls/upcxx/WorkerThread.H Src/AmrTask/rts_impls/upcxx/WorkerThread.cpp Src/AmrTask/rts_impls/upcxx/mylock.h Src/AmrTask/rts_impls/upcxx/perilla.mak commit 11beeb82bd1d04f05d6aba88efca19f2df5b5f88 Author: Johannes Blaschke Date: Mon Apr 29 21:23:53 2019 -0700 eb level's `fillLevelSet` needs to be public Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB_levelset.H commit 6db482adf6115be422d34ff4e3d317ac71dac9a3 Author: Weiqun Zhang Date: Mon Apr 29 16:55:32 2019 -0700 minor changes for format and consistence Src/AmrCore/AMReX_AmrMesh.cpp commit 0cac7a83148d573f6fadccf9e399776736216378 Author: Weiqun Zhang Date: Mon Apr 29 16:44:49 2019 -0700 MLEBABecLap: loop fusion Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit e9563d164000ba3eb2f251f9710ac3c3249cc525 Author: kngott Date: Mon Apr 29 16:10:38 2019 -0700 CUDA Graphs API works for non-lambdas. Test later for lambdas? Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp commit feff050bd24f6568be508692121c0b30709ef866 Author: Maikel Nadolski Date: Tue Apr 30 00:06:21 2019 +0200 EB: Add an additional overload for FillPatchTwoLevels. * This adds an EB2::IndexSpace paramter to FillPatchTwoLevels. That way one can specify the exact EB2::IndexSpace for the interpolation region. * Add a defaulted FabFactory parameter to the constructor of FPInfo. Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 16de912ecabc31b9550059005e54fdca511fd3a3 Author: Andrew Myers Date: Mon Apr 29 11:01:33 2019 -0700 bug fixes for particles when BL_FLOAT is used. Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabConv.cpp Src/Particle/AMReX_Particles.H commit 3abb14a69f71c5ee6b406394137ad33b71c9b6ea Author: Weiqun Zhang Date: Mon Apr 29 08:58:24 2019 -0700 Fix NodeEB test Tests/LinearSolvers/NodeEB/MyTest.cpp commit 5cc33860d3cc1e50022a416d0b54a80f74caa1a4 Author: Max Katz Date: Sun Apr 28 21:32:18 2019 -0700 Add parameter for dynamic shared memory Tools/F_scripts/write_cuda_headers.py commit a49ca7c2a51c671e7256048c0ead47ebff11db6c Author: Max Katz Date: Sun Apr 28 17:04:14 2019 -0700 Use different format for passing box to pragma Tools/F_scripts/write_cuda_headers.py commit 31511eee6312dcc2eb56c5cb08926156aa1e94d7 Author: Max Katz Date: Sun Apr 28 15:57:19 2019 -0700 Allow the GPU pragma to accept information about the box Tools/F_scripts/write_cuda_headers.py commit 88f7768ba043a328b392ea53e2a1176c306822fa Author: Max Katz Date: Sun Apr 28 15:57:01 2019 -0700 Add version of grid stride calculation that uses box information Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit 8802ac6f661c409b5cf9def5f150eebfe5b8b503 Author: Max Katz Date: Sun Apr 28 15:56:26 2019 -0700 Add functions for shared memory reductions Src/Base/AMReX_fort_mod.F90 commit b1b6e009a1c49a0a4438afc0ce0d605d674ea3b1 Author: Weiqun Zhang Date: Sat Apr 27 11:04:54 2019 -0700 Change the default bottom solver to bicgcg for nodal RAP Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit 4e98a228f8aa588d530479f70eb460c06e0577fb Author: Ann Almgren Date: Sat Apr 27 09:06:34 2019 -0700 Pass the mg_cg_verbose flag through the MacProjector Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit ae61eb954876668d8c2fa4766808e5b68c3160a4 Author: Weiqun Zhang Date: Fri Apr 26 22:51:29 2019 -0700 MLMG bottom solver: add new types cgbicg and bicgcg. They will start with cg or bicg. If fails, it will switch to the other. If the alternative succeeds, the switch becomes permanent. Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a49cfcf7d8cfec03de65d26ac0aec0fff88fc516 Author: Weiqun Zhang Date: Fri Apr 26 22:03:29 2019 -0700 Fix omp bug in nodal solver with RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f15ee11afff2093ee2ada37493436053f4caa879 Author: Weiqun Zhang Date: Fri Apr 26 19:28:57 2019 -0700 Remove use_hypre parameter from MLNodeLaplacian ctor Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 70d617fa0054c8178adb9e951adc329550304200 Author: Michele Rosso Date: Fri Apr 26 20:38:58 2019 -0400 CMake: fix incorrect path Src/CMakeLists.txt commit f96cb4119c444067491834b4dcc177474a5f56a4 Author: Michele Rosso Date: Fri Apr 26 20:32:00 2019 -0400 CMake: fix printing of CUDA options Tools/CMake/AMReX_SetupCUDA.cmake commit 57d324d9d25e6774037870868c5beb953a1441db Author: kngott Date: Fri Apr 26 17:08:13 2019 -0700 Fix the indexes. Src/Base/AMReX_FabArrayCommI.H commit 36052abce4049bd58a15531fa40c6af2a5bed6aa Author: kngott Date: Fri Apr 26 17:07:24 2019 -0700 Free before allocing if resize a sized CudaGraph. Src/Base/AMReX_CudaGraph.H commit 5817608a37aa7884eede6fa23b64de5daad6f46d Author: Michele Rosso Date: Fri Apr 26 16:41:50 2019 -0700 CMake: move CUDA-specific options to AMReX_SetupCUDA.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupCUDA.cmake commit ba2538a32433b7e8162d8a501874c7d69b2bef95 Merge: 699592071 20a27e108 Author: Michele Rosso Date: Fri Apr 26 16:37:10 2019 -0700 Merge branch 'development' into mr/cmake commit ee9e95d3c84507fb24edb8f666c1084bd98ea258 Author: kngott Date: Fri Apr 26 15:34:03 2019 -0700 Default run test case without nvprof. Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu commit d5a2801027ba204cb6e50cecdc5b6d58030d3b71 Author: kngott Date: Fri Apr 26 15:33:31 2019 -0700 Working test case comparing CPU, GPU and CudaGraph versions of FillBoundary. Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit a1a955b3b249fe29f6a484c40ecedd5fee4eb20e Author: kngott Date: Fri Apr 26 15:32:29 2019 -0700 First working version of FillBoundary using Graphs with MPI = 1. Src/Base/AMReX_FabArrayCommI.H commit fe0a2e88e97daa5a7f0780da265a32bf8999bdea Author: kngott Date: Fri Apr 26 15:32:00 2019 -0700 Change FB initialization to resize CudaGraphs. Src/Base/AMReX_FabArrayBase.cpp commit 9a560de6319c09c347c43098ee7541c9f90371ee Author: kngott Date: Fri Apr 26 15:31:26 2019 -0700 Clean up CudaGraph and allow resizing. Src/Base/AMReX_CudaGraph.H commit a11344e510a89c4a852411b49196f264deb1301b Author: kngott Date: Fri Apr 26 15:07:43 2019 -0700 Smarter GraphRegion checks and CPU version of functions. Src/Base/AMReX_GpuControl.H commit 20a27e10855e01044d07e1fdebbcea27ff2fed92 Merge: 1cf1b9f44 a07a2338d Author: Andrew Myers Date: Fri Apr 26 14:27:58 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1cf1b9f441a79706a6efe7f489c9fa38084e9369 Author: Andrew Myers Date: Fri Apr 26 14:27:48 2019 -0700 methods for defining the number of runtime real and integer components in the particle container Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 685c0eaf2fa6b6168e351c3b754dd0108bfc0903 Author: Andrew Myers Date: Fri Apr 26 14:24:13 2019 -0700 update struct-of-arrays test to include runtime-added components Tests/Particles/main.cpp commit a07a2338df106d0cd377aa81decf9576ce96d4f3 Merge: 10cc51429 cb66da428 Author: mic84 Date: Fri Apr 26 13:38:35 2019 -0700 Merge pull request #467 from mwm126/patch-5 Change FindPythonInterp (deprecated) to FindPython commit 445b21b0e45f4d68e4e2d59ca0b05d8f051c93ea Author: Andrew Myers Date: Fri Apr 26 13:03:18 2019 -0700 including the runtime added comps in the ParticleContainer functions Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit cb66da42852da45a053b9acb6b829912cec83f48 Author: Mark Meredith Date: Fri Apr 26 15:54:31 2019 -0400 Change FindPythonInterp (deprecated) to FindPython Since CMake 3.12, FindPython is the preferred way of detecting Python. Also run makebuildinfo_C.py with the detected Python version (instead of assuming env python) Src/CMakeLists.txt commit 6716ad84e69de088a386ff54d2603d8670b5bb5c Author: Andrew Myers Date: Fri Apr 26 12:24:57 2019 -0700 functions for adding runtime real and int components Src/Particle/AMReX_Particles.H commit 2c4c0e2db290b23442287577168122fcc370bb8c Author: Andrew Myers Date: Fri Apr 26 12:21:25 2019 -0700 Have the particle container keep track of how many runtime comps it has Src/Particle/AMReX_Particles.H commit 923bfb00197bbc3e0e546a96d64b6c680c1dec1e Author: Andrew Myers Date: Fri Apr 26 11:48:15 2019 -0700 adding runtime soa components to StructOfArrays Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit 10cc514296e634359690a308bd7f92e8ae34c323 Author: kngott Date: Fri Apr 26 11:34:48 2019 -0700 Further summit script adjustment. Tutorials/GPU/run.summit commit 699592071f1fa08e9313ef9e209f07881f21c426 Author: Michele Rosso Date: Fri Apr 26 10:32:30 2019 -0700 CMake: fix scope of Particle compile definitions Src/Particle/CMakeLists.txt commit b45a4191159365b14ee0d40dffa84ab6e94db307 Merge: ab1a090ee 04d8db7eb Author: WeiqunZhang Date: Fri Apr 26 10:28:02 2019 -0700 Merge pull request #466 from maikel/feature/FabUtils_ngrow_IntVect Add more support for non-uniform grow vectors to MultiFab and FabArrayUtility commit e0ec5c9ed7bfc232d658d63df03d83b19274f06a Author: Michele Rosso Date: Fri Apr 26 10:02:17 2019 -0700 CMake: completely include AMReX_buildInfo.H into build tree. Src/CMakeLists.txt Tools/CMake/AMReXInstallHelpers.cmake commit ab1a090ee2c87df8662e098d1338558e29190f62 Merge: 174fc9cb4 725da0f80 Author: WeiqunZhang Date: Fri Apr 26 09:55:28 2019 -0700 Merge pull request #465 from maikel/feature/Improve_Move_Assignment Improve move assignment operators for BoxArray and DistributionMapping commit 174fc9cb416c69f77ff5905461f07a8b9221f42f Merge: af4ece1fb ce6434991 Author: WeiqunZhang Date: Fri Apr 26 09:19:10 2019 -0700 Merge pull request #464 from rhouim/development Added a trilinear interpolation option for 3D on cpu. This can be us… commit 04d8db7ebba404631db36509f488a05a4e39f0f5 Author: Maikel Nadolski Date: Fri Apr 26 13:19:29 2019 +0200 Add more support for non-uniform grow vectors to MultiFab and FabArrayUtility. Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 725da0f80b8dd55c4c734e6774283d31fcb1df49 Author: Maikel Nadolski Date: Fri Apr 26 11:27:21 2019 +0200 Use rule of six to improve constructors of BoxArray and DistributionMapping Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit af4ece1fbef6265b124a0c998c5bac49f8e9d8bd Merge: 92846c516 e89e3c277 Author: WeiqunZhang Date: Thu Apr 25 21:58:15 2019 -0700 Merge pull request #463 from maikel/feature/AmrMesh_refrat Improve AmrCore and AmrMesh constructors. commit 92846c516c265d4102188bb64004c37c6f60fa82 Merge: cf568821d 476e659da Author: Andrew Myers Date: Thu Apr 25 19:57:47 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cf568821d3ade13bfed3840a43e6658fa91ea04b Author: Andrew Myers Date: Thu Apr 25 19:57:30 2019 -0400 also apply the shift to the remote neighbors (gpu neighbor particles) Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 476e659dad93e9901dffa3caa1c84eca6c03ad3c Author: Weiqun Zhang Date: Thu Apr 25 16:36:08 2019 -0700 Remove debug lines Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 23fb2549a6c482cdfc9eeafb896ad8783b1b4de3 Author: Weiqun Zhang Date: Thu Apr 25 16:33:48 2019 -0700 Nodal 2d solver: save some codes in comments Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f1985849761ffb58c2edab9bfe5333f544be4ab4 Author: Andrew Myers Date: Thu Apr 25 18:51:51 2019 -0400 keep track of periodicity (gpu neighbor particles) Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit a994adb68758aea5fba871129f9996d05d2fd343 Author: Andrew Myers Date: Thu Apr 25 18:51:09 2019 -0400 nested struct for keeping track of neighbor tasks to perform Src/Particle/AMReX_NeighborParticles.H commit 43e138ad496545c42e5e1af0f7a0ca4e19bad8c3 Author: Andrew Myers Date: Thu Apr 25 18:50:39 2019 -0400 functor for shifting neighbor particles periodically so that naive distance calculation will return the shortest distance Src/Particle/AMReX_Functors.H commit 6de9f597cf3ddc463f2d1a6884d27e6b63388b02 Author: Michele Rosso Date: Thu Apr 25 15:27:55 2019 -0700 CMake: add options to enable/disable tutorials CMakeLists.txt commit 6e03e33f31d95f00add682c1c2f5c07120c9caef Author: Michele Rosso Date: Thu Apr 25 15:18:53 2019 -0700 CMake: change location of configuration files Src/CMakeLists.txt Tools/CMake/AMReXInstallHelpers.cmake commit 9da635bf0bba3909f4d93abed85cfb536e0a557a Merge: a81b9c743 b66f1cd11 Author: Brandon Runnels Date: Thu Apr 25 15:46:20 2019 -0600 Merge branch 'development' into nodeghostcells commit e1cdab269aa11647a76446cd9761d544b97e4638 Merge: 18eb7664a b66f1cd11 Author: Weiqun Zhang Date: Thu Apr 25 14:02:13 2019 -0700 Merge branch 'development' into weiqun/mlmg commit 18eb7664a05386f36105f502f56b8b4bdbc27c7e Author: Weiqun Zhang Date: Thu Apr 25 14:01:19 2019 -0700 Nodal RAP: fix R Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit b66f1cd11bc0f6b25d143e9eb470fe0ac735c7e3 Author: kngott Date: Thu Apr 25 12:41:28 2019 -0700 Update script for shared nodes. Will be important to get resources as more users are added to the system. Tutorials/GPU/run.corigpu commit a66aedff421737bf085218b5e2d7f07166a184ff Author: Andrew Myers Date: Thu Apr 25 13:48:46 2019 -0400 store information about the periodic shift in the grid map (gpu neighbor particles) Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit b4d74c99117d31fcb7c9e783929bbe6de573f28e Author: Ann Almgren Date: Thu Apr 25 07:12:57 2019 -0700 Revert "When we run the "bottom solver" at mglev = 0, we want to go ahead and" This reverts commit 43ecb9cecaa700ff77ce900e80180cbf34eba379. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 43ecb9cecaa700ff77ce900e80180cbf34eba379 Author: Ann Almgren Date: Wed Apr 24 17:34:37 2019 -0700 When we run the "bottom solver" at mglev = 0, we want to go ahead and solve to completion, so we set the "bottom solver tolerance" to the tolerance specified in the solve call, rather than 1e-4. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit ce643499192be29fabdcde6e5091e835b850e38b Author: rhouim Date: Wed Apr 24 19:36:03 2019 -0400 Added a trilinear interpolation option for 3D on cpu. This can be used by using cell_bilinear_interp in the FillPatch routines. This was tested with the Advection_AmrCore tutorial and it behaved as expected. Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_Interpolater.cpp commit cc3708a0461936ba957cd4ddac66526f1447b26a Author: Ann Almgren Date: Wed Apr 24 16:32:56 2019 -0700 Change from cell-by-cell testing on volfrac to testing on flag Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit 140761ec309f9145d674303b0bf020767878a65e Merge: cb06bb30a af5e91619 Author: Weiqun Zhang Date: Wed Apr 24 14:11:30 2019 -0700 Merge branch 'development' into weiqun/mlmg commit 9dcbc68ceac9b70446bf9fcfe6c5eba436b02946 Author: kngott Date: Wed Apr 24 14:09:36 2019 -0700 WIP: Starting conversion of 1 Rank FillBoundary. Src/Base/AMReX_FabArrayCommI.H commit 3f209ae6f1072aa0236a96fc4b00bbe284eabf35 Author: kngott Date: Wed Apr 24 14:09:16 2019 -0700 Add graphs to FB object Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 80a418cb3211e37da3dc83538905ee21cdfc99e6 Author: kngott Date: Wed Apr 24 14:08:40 2019 -0700 Add AMReX_CudaGraph.H to AMReX_Gpu.H and add bool declaring if graph is ready. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_Gpu.H commit c76155835f746753124e7ffa2c9322b651e86533 Author: kngott Date: Wed Apr 24 14:07:09 2019 -0700 Label auto const's as Arrayk4's for clarity. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit cb06bb30a57c032ca2277bdc02d53b1bfb7d4455 Author: Weiqun Zhang Date: Wed Apr 24 13:54:44 2019 -0700 WIP: first pass of RAP coarsening Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit af5e91619bbf46ed67aa48499a928c2c21fa7ca4 Author: Michele Rosso Date: Wed Apr 24 11:33:49 2019 -0700 Change '#if AMREX_USE_GPU' to '#ifdef AMREX_USE_GPU' Src/Base/AMReX_FabArray.H commit 3e4e7653663d3e9f1d0b7227c99f92be219481a7 Merge: f8a4694eb 7844b4fd7 Author: Michele Rosso Date: Wed Apr 24 10:47:15 2019 -0700 Merge branch 'development' into mr/cmake commit 7844b4fd7d4c846f994a311b0956f7b92da4987b Author: Ann Almgren Date: Wed Apr 24 10:32:07 2019 -0700 Revert "Don't set regular stencils when volfrac < 1e-12 -- go ahead and" This reverts commit fd5dade48cf3fb52cbd2b3076946b3cd382760ef. Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit fd5dade48cf3fb52cbd2b3076946b3cd382760ef Author: Ann Almgren Date: Wed Apr 24 09:29:53 2019 -0700 Don't set regular stencils when volfrac < 1e-12 -- go ahead and compute the integrals. Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit e89e3c277cc7b5ad8ac58fd81814d77e68801c12 Author: Maikel Nadolski Date: Wed Apr 24 09:47:04 2019 +0200 Use std::move to avoid allocations. Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.cpp commit b7ff3247713c4e84cd3eddb3e4d2df25cf66a970 Author: Maikel Nadolski Date: Wed Apr 24 09:32:08 2019 +0200 Improve AmrCore and AmrMesh constructors. Change the refinement ratio paramter of AmrMesh's constructor from std::vector to amrex::Vector to be more consistent with non-uniform refinement ratios. Add a refrat parameter to AmrCore's constructor. Before this change AmrMesh's refinment parameter was never set to this custom value. Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 530db41797eae40d36066e1904aad2c095dc55bc Author: Weiqun Zhang Date: Tue Apr 23 16:54:49 2019 -0700 WIP: RAP stencil: add A matrix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 948755d2d2053d2760ea541ad3f0aac2b20956df Author: Weiqun Zhang Date: Tue Apr 23 16:19:19 2019 -0700 WIP: RAP stencil: P Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 7ebd60f966413e8caa274fc7752738950704af07 Author: Andrew Myers Date: Tue Apr 23 16:12:48 2019 -0700 formatting fix Docs/sphinx_documentation/source/Testing.rst commit 8ae2c9ca5b910aecf599c9885a137ffd6b12d8c3 Author: Andrew Myers Date: Tue Apr 23 16:11:54 2019 -0700 remove redundant statement (test runner docs) Docs/sphinx_documentation/source/Testing.rst commit cfee094f71d84d87f3add3eb0a9e8c3024870b6d Merge: 9cf51ea96 1bbc83cf7 Author: Andrew Myers Date: Tue Apr 23 16:09:12 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9cf51ea96226d3be3c1b59f1660ef1d20b2325a6 Author: Andrew Myers Date: Tue Apr 23 16:09:00 2019 -0700 fix typo Docs/sphinx_documentation/source/Testing.rst commit c8ab96844e4c2e7b4419c2f2d4d822cddd6dd873 Author: kngott Date: Tue Apr 23 16:07:41 2019 -0700 Store void* in CopyMemory instead of Array4 Src/Base/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit d79237b25db8bee69225c1ca5a55d881fe669a90 Author: Weiqun Zhang Date: Tue Apr 23 15:17:06 2019 -0700 WIP: RAP stencil: interp_from Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 5c29d1da3d631d3b47f38f080e6ceb53754216c4 Author: Weiqun Zhang Date: Tue Apr 23 15:01:19 2019 -0700 WIP: RAP stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 53a168f76c028cee178f9cf022e4a24735535887 Author: kngott Date: Mon Apr 22 19:49:12 2019 -0700 Move to Arenas. Src/Base/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit ee850e27baec9a8c80aba6dea14a4dec6f9af98e Author: kngott Date: Mon Apr 22 17:22:59 2019 -0700 Move AMReX_CudaGraph to Src/Base. Src/Base/AMReX_CudaGraph.H Src/Base/Make.package Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 94a81cc4970584addbd78d5f2d76c84c0556b936 Author: Weiqun Zhang Date: Tue Apr 23 13:16:32 2019 -0700 use Array4 in cuda graph Src/Base/AMReX_Array.H Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit f8a4694eb76c8b87574f153a8effb5f25a2743d7 Author: Michele Rosso Date: Tue Apr 23 11:52:16 2019 -0700 CMake: get interface properties rather than private properties for Flags targets Tools/CMake/AMReX_Config.cmake commit 1bbc83cf7c5cde64e225d39f8c12cb0e1e79f278 Author: Weiqun Zhang Date: Tue Apr 23 11:24:57 2019 -0700 minor Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 022bcad68bf4fbeee44abd53b869bed9a7eb17be Author: Weiqun Zhang Date: Tue Apr 23 11:19:41 2019 -0700 No need to call FillBoundary on integrals because we compute them in ghost cells. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a95848df1d4653be65d17ba908b673ddd7b41eaf Author: Weiqun Zhang Date: Tue Apr 23 10:57:38 2019 -0700 Use Array4 in computing integrals using algoim Src/Extern/Algoim/AMReX_algoim_integrals.H Src/Extern/Algoim/AMReX_algoim_integrals.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit fd09d1d57bc889bbf1051bf88ec5871d981d4378 Author: Weiqun Zhang Date: Tue Apr 23 10:23:18 2019 -0700 Add Make.algoim. USE_ALGOIM -> AMREX_USE_ALGOIM. For hypre and petsc, both _DIR and _HOME are allowed. Src/Extern/Algoim/CMakeLists.txt Src/Extern/Algoim/Make.package Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/GNUmakefile Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.algoim Tools/GNUMake/packages/Make.hypre Tools/GNUMake/packages/Make.petsc commit 75ba20ea4bea9761ee9082fedfb3bf5186aa0f0e Author: Weiqun Zhang Date: Tue Apr 23 08:59:51 2019 -0700 FabArray: m_host_fabs_v is gone. Src/Base/AMReX_FabArray.H commit c15ec2907dfe9f0294f98ef6baa17e681ba44e6f Author: kngott Date: Mon Apr 22 17:07:38 2019 -0700 Remove un-needed MemCpy from CudaGraph. Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H commit 1e0c4d44f763198d8e4d4138d972daac7981a85e Author: kngott Date: Mon Apr 22 17:01:40 2019 -0700 Update test for improved CudaGraph object. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 900276a9faf29b717f0100b82080f39097c7242e Author: Andrew Myers Date: Mon Apr 22 17:00:07 2019 -0700 adding some pages to the documentation about the regression testing Docs/sphinx_documentation/source/Regression_Testing_Chapter.rst Docs/sphinx_documentation/source/Testing.rst Docs/sphinx_documentation/source/index.rst commit ee31daee833669f83d4ce8a1c0f22d962a6de959 Author: Andrew Myers Date: Mon Apr 22 15:51:49 2019 -0700 adding a sample .ini for running the amrex regression tests locally Tools/RegressionTesting/AMReX-tests.ini commit 7dc7789542c003bc3e9be5a454475928d1a743a8 Merge: 1d660a810 4f095bf31 Author: Weiqun Zhang Date: Mon Apr 22 15:41:27 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit a8e0b2d89eda7eff40b80bf97f0d2d1d8bc9d6c9 Merge: b88767d1e 4f095bf31 Author: kngott Date: Mon Apr 22 15:30:39 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 4f095bf3124d2b9b9ac13bd82305fb0f2b7da9f0 Author: kngott Date: Mon Apr 22 15:27:10 2019 -0700 Make Array4 Variables non-const. Src/Base/AMReX_Array.H commit b88767d1e6a28d896ce36dba5e1cb21d2c416662 Author: Weiqun Zhang Date: Mon Apr 22 15:11:05 2019 -0700 Tidy cuda graph classes Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H commit ce9f2a02cd4739d200db6d06103ede0eb94b5799 Merge: 087982fa9 b68fadfc1 Author: Michele Rosso Date: Mon Apr 22 13:46:47 2019 -0700 Merge branch 'development' into mr/cmake commit b68fadfc1071c3e615d7ed65fe641a5910c17f96 Author: Weiqun Zhang Date: Mon Apr 22 12:58:22 2019 -0700 Add prerequisites for building AMReX. This addresses comment #1 in Issue #458. Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst commit 84e222fad80f77577e84877dcb0cafa4ab3eadf4 Author: kngott Date: Mon Apr 22 12:41:21 2019 -0700 Separate CudaGraph object. Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 0f783533b8feffd3e68682816ce443289d83a58f Merge: 10f9372bc 87ca50e70 Author: Weiqun Zhang Date: Mon Apr 22 12:27:23 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 10f9372bc2e64ae211577242b3e5e73f6790cc84 Author: Weiqun Zhang Date: Mon Apr 22 12:27:16 2019 -0700 Update compilestesing.py for python 3 Tools/CompileTesting/compiletesting.py commit 2b96cafc674ac07b2e32fbc3847f529db7976daa Author: Ann Almgren Date: Mon Apr 22 10:31:22 2019 -0700 Add John to core contributor list. README.md commit 87ca50e7025d0191cc49e0e94e68b73d38bf25fa Author: Ann Almgren Date: Mon Apr 22 10:31:22 2019 -0700 Add John to core contributor list. README.md commit a4ca75cdcb4d21ec208ff2534f7ea0be34507561 Author: Ann Almgren Date: Mon Apr 22 06:48:04 2019 -0700 Fix oops in how we read in n_error_buf now that it is locally an IntVect Src/AmrCore/AMReX_AmrMesh.cpp commit 0268c8326c600e5baa73c5f28e4061b4a2dce476 Author: kngott Date: Mon Apr 22 00:31:16 2019 -0700 First draft of working Graph object. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 18b8159006c03f2355681ac46c3a8e08b112d3ac Author: Ann Almgren Date: Sun Apr 21 13:18:53 2019 -0700 Add more detail about using GitHub issues. README.md commit b213ee796cd1b57f2de08b47f96b53e58e8ad65a Author: Ann Almgren Date: Sun Apr 21 13:09:36 2019 -0700 Add list of current "core developers" to AMReX README README.md commit 8183041a3d4461e9680dc3d0e38d5a697eec0d8d Author: Ann Almgren Date: Sun Apr 21 13:18:53 2019 -0700 Add more detail about using GitHub issues. README.md commit 46146292dde1961146071fa66a230de050d42220 Author: Ann Almgren Date: Sun Apr 21 13:09:36 2019 -0700 Add list of current "core developers" to AMReX README README.md commit f0dff6e75ff66c8a03c5de8b4b4aa3b0adaf2877 Author: Weiqun Zhang Date: Sat Apr 20 20:19:58 2019 -0700 Add optional argument for direction to AmrMesh::nErrorBuf function. Add IntVect version, nErrorBufVect. add optional argument for direction to FabArrayBase::nGrow Src/AmrCore/AMReX_AmrMesh.H Src/Base/AMReX_FabArrayBase.H commit 1d660a810b89d5c4f26390b1df58d6e0a411cac4 Merge: 9f23f314c 515df37b2 Author: Weiqun Zhang Date: Sat Apr 20 18:37:00 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit 515df37b2b3735a51fb4671e227d695d32071d2d Author: Weiqun Zhang Date: Sat Apr 20 18:03:42 2019 -0700 add a new BoxArray::growcoarsen function that takes IntVect as ngrow parameter and use it in TagBoxArray Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 11891071c7c736cba4270bf2023e8d57f3c8c46e Author: Weiqun Zhang Date: Sat Apr 20 17:59:58 2019 -0700 return IntVect from TagBoxArray::borderSize Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_IntVect.H commit 9f23f314cb6cd2c0bdb4a05c52480776c91f0a00 Merge: df47ebb5e 3ce3ab881 Author: Weiqun Zhang Date: Sat Apr 20 17:47:53 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit df47ebb5e4bad4e4869d0bf13f7f95b02aac1ce8 Author: Weiqun Zhang Date: Sat Apr 20 17:47:04 2019 -0700 TagBoxArray: host ptr is the owner now Src/AmrCore/AMReX_TagBox.cpp commit 3ce3ab881f9764403baa17420cce613be7dc5f7e Merge: df61a42c9 cf9775d57 Author: WeiqunZhang Date: Sat Apr 20 17:02:45 2019 -0700 Merge pull request #461 from chaw0023/HypreDeclaration Add missing declaration for hypre_int commit cf9775d57b4084e24f8c2892df6fac258b1e2364 Author: Saurabh Chawdhary Date: Sat Apr 20 17:57:45 2019 -0500 Add missing declaration for hypre_int Src/Extern/PETSc/AMReX_PETSc.cpp commit df61a42c97e01f73f9c135ff109c1be36798a8af Author: Ann Almgren Date: Sat Apr 20 15:56:28 2019 -0700 Makes n_error_buf in AmrMesh class an IntVect rather than an int. Note that AmrCore-based codes can use this option by setting n_error_buf_x, n_error_buf_y, n_error_buf_z rather than setting simply n_error_buf in the inputs file, but setting n_error_buf will still work. AmrLevel-based applications are only able to use the int functionality since they don't currently have an errorEst routine that takes an IntVect. AmrCore-based apps may need to change based on this change; AmrLevel-based codes should not have to. Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp commit cad287871f6d6202fc550dac1db4d2cceb4d2577 Merge: 2f5779244 7f819b191 Author: Weiqun Zhang Date: Sat Apr 20 12:01:13 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit 7f819b19119505faac2a050d577ddde3d921ca02 Author: Weiqun Zhang Date: Sat Apr 20 12:00:36 2019 -0700 avoid fortran keyword Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 3f2a8fec28d401d56946b04a878ebd0a479c1d85 Author: Weiqun Zhang Date: Sat Apr 20 11:51:54 2019 -0700 shorten names Tests/Slice/GNUmakefile Tests/Slice/Make.package Tests/Slice/inputs Tests/Slice/main.H Tests/Slice/main.cpp Tests/SliceWithInterp/inputs Tests/SliceWithInterp/main.cpp commit 2f57792441ead08764fb6939634970344d88b345 Author: Weiqun Zhang Date: Sat Apr 20 09:13:06 2019 -0700 Update the new fabDevicePtrAtLocalIdx and fabHostPtrAtLocalIdx functions because m_host_fabs_v has been removed Src/Base/AMReX_FabArray.H commit 9dd2aee2caedc63a30526fda7f0a33635fc2b3aa Merge: c71309755 264d4bf77 Author: Weiqun Zhang Date: Sat Apr 20 08:53:09 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit 264d4bf77bd9ea8c42d78198de080f9c55726c2a Merge: 6d834eef1 a6fdc77b1 Author: WeiqunZhang Date: Fri Apr 19 20:22:37 2019 -0700 Merge pull request #459 from chaw0023/PetscSolveLS Petsc bottom solver in F_interface; update GNUmakefile commit 6d834eef18f07230d87a769597881fc95fdb239f Author: Weiqun Zhang Date: Fri Apr 19 20:09:27 2019 -0700 add inputs.hypre and inputs.petsc to ABecLaplacian_C tutorial Tutorials/LinearSolvers/ABecLaplacian_C/inputs.hypre Tutorials/LinearSolvers/ABecLaplacian_C/inputs.petsc commit c5ab471a585bcbe9e69e86bf2123ba307ecfa841 Author: Weiqun Zhang Date: Fri Apr 19 19:49:39 2019 -0700 PETSc: remove dependency on HYPRE Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/Extern/PETSc/AMReX_PETSc_fort_mod.F90 Src/Extern/PETSc/Make.package commit 087982fa99390df771f2a56581656464abfbf856 Merge: ad0e2bd55 e031ae679 Author: Michele Rosso Date: Fri Apr 19 17:35:40 2019 -0700 Merge branch 'development' into mr/cmake commit ad0e2bd55653fae52948ff38f982510013ebdf3d Author: Michele Rosso Date: Fri Apr 19 17:34:59 2019 -0700 CMake: clean up Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/TestManager.cmake Tools/CMake/select_gpu_arch.cmake commit c3085b6a1aac3ecb0641c0f8ef4e5dbf31cd51c1 Author: Michele Rosso Date: Fri Apr 19 17:31:38 2019 -0700 CMake: fix bug in CUDA flags due to recent changes Tools/CMake/AMReX_Config.cmake commit 299f345cdb656d018767a84e673f9681022013bc Author: Michele Rosso Date: Fri Apr 19 17:17:01 2019 -0700 CMake: treat C++ and Fortran flags in a target-oriented fashion * Define INTERFACE targets for C++ and Fortran flags. * Export those targets so that app codes can use them. Src/CMakeLists.txt Tools/CMake/AMReXFlagsTargets.cmake Tools/CMake/AMReXInstallHelpers.cmake Tools/CMake/AMReX_Compilers.cmake commit a6fdc77b17a19ae4be6b0082e7d144e082d2782c Author: Saurabh Chawdhary Date: Fri Apr 19 18:25:25 2019 -0500 Add Particle fortran interface directory to Pdir GNUmakefile.in commit ae58f6dd2a0734577251b0ac20070ffd631f14f2 Author: Saurabh Chawdhary Date: Fri Apr 19 18:02:07 2019 -0500 Add option for using petsc as bottom solver Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 commit b6dd1be8707f46a0f23f5d097e785c9697bf15f7 Author: Saurabh Chawdhary Date: Fri Apr 19 18:11:31 2019 -0500 Add option --enable-petsc to use PETSc as bottom solver GNUmakefile.in Tools/libamrex/configure.py commit e031ae6797943d4752678dc02f96fa00ec7802a8 Author: kngott Date: Fri Apr 19 15:52:48 2019 -0700 run.summit update #4. Tutorials/GPU/run.summit commit c9e2251e32c3735e60a571721a32cfd882f6ca8c Author: kngott Date: Fri Apr 19 15:40:21 2019 -0700 run.summit update #3. Tutorials/GPU/run.summit commit a528bf6cafe4e470d03daa6814c5c67f2065e4be Author: kngott Date: Fri Apr 19 14:03:30 2019 -0700 More Summit and CoriGPU script updates. Tutorials/GPU/run.corigpu Tutorials/GPU/run.summit commit 3f1e2423abc85065f19e58b078319384369782d6 Merge: ac36e5165 ecdbbcbfc Author: Andrew Myers Date: Fri Apr 19 16:37:52 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ac36e51651e8dc880d87fe31f1a827a00a8025d6 Author: Andrew Myers Date: Fri Apr 19 16:37:40 2019 -0400 remove misleading timer from NeigborList::build Src/Particle/AMReX_NeighborList.H commit e10716e63398bc55836ee45e03e9f2ddc8ff9efe Author: Andrew Myers Date: Fri Apr 19 16:37:07 2019 -0400 change AMREX_ALWAYS_ASSERT to AMREX_ASSERT here Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit ecdbbcbfc158e18fb4d3c8fe06dd6ee02f03d846 Author: kngott Date: Fri Apr 19 12:41:50 2019 -0700 Add Summit and jsrun specs to sample run script. Tutorials/GPU/run.summit commit dafdea5b1628c6893a8cda2c3f3ad1141e36df12 Author: Weiqun Zhang Date: Fri Apr 19 12:36:05 2019 -0700 amrex::Tuple is now an alias to std::tuple Src/Base/AMReX_Tuple.H commit 0baf0cdc439d33a10318945ca062c3169bf1ccd6 Merge: aaadc34db 60b7687a6 Author: Andrew Myers Date: Fri Apr 19 11:23:49 2019 -0700 Merge pull request #440 from RevathiJambunathan/SliceGenerationForDiagnostics_RJ Slice generation for diagnostics rj commit aaadc34db48146f3cffb2ee89c7f70625b019240 Author: Weiqun Zhang Date: Fri Apr 19 10:59:44 2019 -0700 AmrMesh: relax the assumption that the base level domain has even number of cells in each direction Src/AmrCore/AMReX_AmrMesh.cpp commit 73e381e9f4443e9144d273ba75f3ee5e9dbcfa3f Merge: 06a58e9bd c81211585 Author: Andy Nonaka Date: Fri Apr 19 10:36:09 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 06a58e9bde1cdba6298cacd783569aec3129c893 Author: Andy Nonaka Date: Fri Apr 19 10:35:56 2019 -0700 minor tutorial notes Docs/sphinx_documentation/source/EB.rst Docs/sphinx_tutorials/source/EB_Tutorial.rst commit 67058fb0ee21fe224803feb39c3e979e1692574f Author: kngott Date: Fri Apr 19 10:14:40 2019 -0700 Graphs using Graph Class. WIP. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit c81211585e5473fdb954d0c29dbf26a52e89e107 Author: Weiqun Zhang Date: Fri Apr 19 09:32:20 2019 -0700 octree average down leaves: fix component index Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 343ff3d2f6214a93c8f6f46b295277b9d1718f88 Author: Andy Nonaka Date: Fri Apr 19 09:13:01 2019 -0700 EB/Poisson tutoral (enclosed sphere at zero potential with a point charge in the interior); fixed convergence issue - for now must specify Dirichlet domain boundary conditions, even if the fluid doesn't touch the domain boundary (AMReX was thinking the problem was singular) Tutorials/EB/Poisson/inputs Tutorials/EB/Poisson/main.cpp commit 576b755c48d700ba1a5d6f49da7998d946efc448 Author: Andy Nonaka Date: Fri Apr 19 08:34:42 2019 -0700 init_data function Tutorials/EB/Poisson/Make.package Tutorials/EB/Poisson/Poisson.H Tutorials/EB/Poisson/Poisson.cpp Tutorials/EB/Poisson/Poisson_F.H Tutorials/EB/Poisson/main.cpp Tutorials/EB/Poisson/poisson.F90 commit 60b7687a6ac6c5ecfd7b02eb597059f8dc943ef7 Author: RevathiJambunathan Date: Thu Apr 18 23:20:28 2019 -0700 Modified the diagnostic slice generation to inherent the index type of the underlying data. The code reads in lo and hi of the slice, and coarsening ratio. If the input for coarsening ratio is not an exponent of 2, then within the code, the ratio is modified to the nearest exponent of 2. The slice is generated in three steps. First, using the input lo and hi, the slice is generated with geom.CellSize() equal to the computational domain. Note that, in this test case, only one level of refinement is assumed. Next, if a 2D slice is extracted at a location where the data points are not available, then values are interpolated on the slice from the nearest points. Finally, if the coarsening ratio in any direction is > 1, then the data from the refine slice is averaged and stored on the coarsened slice ensuring that the box array sizes for both, refined and coarse slice are equal. I have assumed nghost > 0, since for interpolation, we need values from the ghost cells. The initial values for the baseline slice is such that the 0th,1st, and 2nd component correspond to x-pos y-pos, and z-pos, respectively. Tests/CreateSliceForDiagnosticsWithInterpolation_adjusttocoarsenIfrequired/inputs Tests/CreateSliceForDiagnosticsWithInterpolation_adjusttocoarsenIfrequired/main.cpp commit c8f7df4e52135a95e174c5c07bf7746b26f216ee Merge: a4011bcac 1f04f65b9 Author: Weiqun Zhang Date: Thu Apr 18 21:40:38 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a4011bcac9b6512e7f5776cd16754c2d3e8821f2 Author: Weiqun Zhang Date: Thu Apr 18 21:40:03 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_ParticleContainerI.H Tutorials/EB/MacProj/GNUmakefile Tutorials/EB/MacProj/Make.package Tutorials/EB/MacProj/initEB.H Tutorials/EB/MacProj/initEB.cpp Tutorials/EB/MacProj/main.cpp Tutorials/EB/Poisson/GNUmakefile Tutorials/EB/Poisson/Make.package Tutorials/EB/Poisson/inputs Tutorials/EB/Poisson/main.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 9afd6457542e4475a6055aa23d71df2d398281a1 Author: Weiqun Zhang Date: Thu Apr 18 21:36:25 2019 -0700 octree average_down: support for components and volume weighted Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 000aa22131d4e36389835d516a191e9583ed3452 Author: Weiqun Zhang Date: Thu Apr 18 21:04:16 2019 -0700 fix bug in octree leaf index array Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit 157d59cf4123a8e83999ec53712e3032f29f6517 Author: Weiqun Zhang Date: Thu Apr 18 20:44:56 2019 -0700 average down octree leaves Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 0f5429e6e3b7181b3d1bb01d07908fa9666d1a49 Author: Weiqun Zhang Date: Thu Apr 18 20:44:06 2019 -0700 add FabArray member functions for getting fab ptr given local index Src/Base/AMReX_FabArray.H commit 1f04f65b973e61be03ba1d1c06d3d2daf03db084 Merge: e0c5cfc7e 902f0c642 Author: Andy Nonaka Date: Thu Apr 18 17:45:13 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e0c5cfc7e2930bbf1c47c47a1d779ca0707e85d0 Author: Andy Nonaka Date: Thu Apr 18 17:44:27 2019 -0700 EB Poisson solver example. Needs a little tweaking still as the MG isn't converging well yet. Tutorials/EB/Poisson/GNUmakefile Tutorials/EB/Poisson/Make.package Tutorials/EB/Poisson/inputs Tutorials/EB/Poisson/main.cpp commit 902f0c642015edb6e82419cfc1cb1af7ad1b0643 Author: Andrew Myers Date: Thu Apr 18 19:58:32 2019 -0400 instruct thrust to use pooled memory for it's internal reduce operation in build neighbor list gpu Src/Particle/AMReX_NeighborList.H commit 0688ac20d2b3b03d7d99052f2ec2200013210ad5 Merge: eb9c07acb 63baf3cb4 Author: Andrew Myers Date: Thu Apr 18 19:10:23 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit eb9c07acb9c4580f644cad692effaf06e05fa30b Author: Andrew Myers Date: Thu Apr 18 19:09:34 2019 -0400 cache temporary variables in GPU NeighborList::build to save memory and avoid expensive cudaMalloc/cudaFree calls Src/Particle/AMReX_NeighborList.H commit 63baf3cb4dfde4cd3c4c5b61b0e160cfb4df2e47 Author: Andrew Myers Date: Thu Apr 18 12:34:13 2019 -0700 update PIC tutorial makefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex commit 7695e8f07a0de9f2c969861f31c8f8e0909c4f6c Author: Andrew Myers Date: Thu Apr 18 11:13:44 2019 -0700 dual grid particle restart - still need to skip if the header doesn't exist Src/Particle/AMReX_ParticleContainerI.H commit 21e6f94a6bc0c870de91c44e7d99bf590b74091f Author: Andrew Myers Date: Thu Apr 18 10:59:40 2019 -0700 fix typo Src/Particle/AMReX_ParticleContainerI.H commit 0380809fca54c17a4e9a39a31379e7e75003811d Author: Andrew Myers Date: Thu Apr 18 10:58:17 2019 -0700 in the particle restart, open the data file in binary mode. text mode is not sure to work for all implementations Src/Particle/AMReX_ParticleContainerI.H commit d026c805655394d466c9f375c67ccea584a337a9 Author: Andrew Myers Date: Thu Apr 18 10:57:08 2019 -0700 fix logic in the dual grid restart to handle the case where not all levels have particles Src/Particle/AMReX_ParticleContainerI.H commit d24e9c81c4c53ee9e0764bdf3830ce372f9e2efc Merge: b972db4b9 b498ec9ae Author: Andrew Myers Date: Thu Apr 18 10:52:13 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b498ec9aebcf81cdd810e5e464345ca88d5defe1 Merge: a7bcbbd8c 7a7bc18e1 Author: Andrew Myers Date: Thu Apr 18 13:50:23 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b972db4b97e6212da1e97ae6405eeda7bb1ed5df Author: Andrew Myers Date: Thu Apr 18 10:50:18 2019 -0700 fix whitespace errors in Makefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex commit a7bcbbd8cd382e53a47be0c83c137d1a0acdd34a Author: Andrew Myers Date: Thu Apr 18 13:49:59 2019 -0400 add missing file Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 7a7bc18e1743a38657fd1fd463dbce83230e55d2 Merge: dc78bd0f2 7f010c9b2 Author: Andy Nonaka Date: Thu Apr 18 09:42:38 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit dc78bd0f2535c75466db58c0d8ad29ea1abce9f1 Author: Andy Nonaka Date: Thu Apr 18 09:42:26 2019 -0700 cleanup, comment tutorial Tutorials/EB/MacProj/GNUmakefile Tutorials/EB/MacProj/Make.package Tutorials/EB/MacProj/initEB.H Tutorials/EB/MacProj/initEB.cpp Tutorials/EB/MacProj/main.cpp commit d652fdce8487f67ebda190df557b4907031143ea Author: Weiqun Zhang Date: Thu Apr 18 09:14:54 2019 -0700 octree: add BoxArray and DistributionMapping for leaf nodes only Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit 7f010c9b2675d6b56c2c01cfeaf3750181f7a0ac Author: Andrew Myers Date: Wed Apr 17 19:42:21 2019 -0400 move GNUmakefile.libamrex to the proper location Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex commit bc18fc80c66615c71edcdd619600c4153d289b9a Merge: f66a97a3f d0853a069 Author: Andrew Myers Date: Wed Apr 17 19:41:35 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f66a97a3febe8c0e1e4a434ae991d13ba15e02f6 Author: Andrew Myers Date: Wed Apr 17 19:41:11 2019 -0400 Adding a makefile, courtesy of Chris Daley and Weiqun, for building the PIC tutorial using a shared amrex library Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile.libamrex commit 2a4360606ad71ca0706ac9c95c085df497ae23b8 Author: Andrew Myers Date: Wed Apr 17 19:40:28 2019 -0400 add a few more options to the configure.py script for libamrex Tools/libamrex/configure.py commit d0853a0692c6fc16a832bc5a6300dc8a34c85a5a Merge: 29db67e01 e17dc4c90 Author: Andy Nonaka Date: Wed Apr 17 15:37:15 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e17dc4c90644e804818a1809f0e5fb6b128e66d1 Merge: 2136fbeb4 31b75c447 Author: Andrew Myers Date: Wed Apr 17 18:36:44 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 29db67e01c56ff2ebaec5fc7b2e5dba4beb417e8 Author: Andy Nonaka Date: Wed Apr 17 15:36:31 2019 -0700 this tutorial now uses a mac projection to compute flow around a sphere given an initial velocity field of (1,0,0). There is also now a plotfile output that outputs the initial and final velocity and divergence Tutorials/EB/MacProj/main.cpp commit 2136fbeb4dafeaeba0500a748240a33410527084 Author: Andrew Myers Date: Wed Apr 17 18:36:11 2019 -0400 use the share, gpu-enabled initialization routines for all the different versions of the EM PIC Tutorial Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Source/Make.package commit 242d0026cc63ac610956193557befbff59c7fca4 Author: Andrew Myers Date: Wed Apr 17 18:34:57 2019 -0400 update repo name in job submission script Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh commit 8a1c44ac27ecc8f967ced89981ed4b2a256c8d06 Author: Andrew Myers Date: Wed Apr 17 18:14:05 2019 -0400 some tweaks and bug fixes to init particles Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit afe615c7766b6fbd042dac7e2b797ff06d176dad Author: Andrew Myers Date: Wed Apr 17 18:06:36 2019 -0400 minor formatting change Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 commit 61e8f44517bf96e718d637d8b786b55114f41904 Author: Andrew Myers Date: Wed Apr 17 18:02:15 2019 -0400 correct CUDA version of gather_fields routine (EMPIC Tutorial) Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit c5bba7492809b528974569f0abb224c349a2bfd5 Author: Andrew Myers Date: Wed Apr 17 15:00:39 2019 -0400 update python utility to look for the correct number of digits in the output Tools/Py_util/amrex_particles_to_vtp/amrex_binary_particles_to_vtp.py commit c71309755086051f2c0e4703ad6d29bb51945315 Merge: a24e0a889 fd0fd9ca0 Author: Weiqun Zhang Date: Wed Apr 17 11:01:20 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit a24e0a8897cdffe04c07c17ed288a62600f28e7a Author: Weiqun Zhang Date: Wed Apr 17 11:01:11 2019 -0700 no need to build device fabs for the temporary multifab in overridesync Src/Base/AMReX_FabArrayUtility.H commit a8a2399e4e87ff537cd27c22bda43337b6e472cd Author: Andrew Myers Date: Wed Apr 17 13:44:32 2019 -0400 EM PIC Tutorial fix - need to convert this box so that it has the same type as jx (in check_langmuir_solution) Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp commit 7d10a8722bfb2210bc0a9ea578139f9b3e0c39c4 Author: Andrew Myers Date: Wed Apr 17 13:43:03 2019 -0400 mark these functions __host__ __device__ so they can also be run on the host for debugging Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit 31b75c44745cff48ef2480e3f099447275a3d08b Author: Michele Rosso Date: Wed Apr 17 10:07:51 2019 -0700 CMake: add path to typechecker in export config file Tools/CMake/AMReXConfig.cmake.in commit fd0fd9ca0ca71f1201c3139ede50616a12ab6660 Author: Andrew Myers Date: Wed Apr 17 07:47:47 2019 -0700 fix particle restart when finestLevel() goes down Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit b0ca1ea577e13a9a11db7ebbb7bfdf013f31318b Author: Weiqun Zhang Date: Tue Apr 16 21:58:04 2019 -0700 fix a bug in tutorial Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 132c15e405fbff99b7a60393b4421c7dd465cdc4 Author: Weiqun Zhang Date: Tue Apr 16 19:04:17 2019 -0700 fix alias FabArray Src/Base/AMReX_FabArray.H commit 18bed7f4d3815922049d4d495e848565f64c8538 Author: Weiqun Zhang Date: Tue Apr 16 17:03:04 2019 -0700 fix data ptr consistence check Src/Base/AMReX_FabArray.H commit 6cf022043079664e194be7b4dc02087ae7504fae Author: Weiqun Zhang Date: Tue Apr 16 16:56:53 2019 -0700 skip delete for nullptr Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H commit df60503107a62d0f6a9b474a7d5b83dc58097f34 Author: Weiqun Zhang Date: Tue Apr 16 14:43:33 2019 -0700 Option to not create device fabs Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit 56ccba9bea51bbd83e3f3926cd958dffa69981eb Author: Weiqun Zhang Date: Tue Apr 16 14:25:23 2019 -0700 remove unused function Src/Base/AMReX_FabFactory.H commit 41a5b51119f7a12a2db2cf747cee9295c8c20174 Author: Weiqun Zhang Date: Tue Apr 16 14:19:52 2019 -0700 make sure setFab only takes host fab. remove some deprecated functions in CoordSys Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_VisMF.cpp Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_MultiCutFab.cpp commit ae7025a55912cb1ac6c68cd867bd28c9eacc2a72 Author: Tan Nguyen Date: Tue Apr 16 14:00:53 2019 -0700 support on demand mode where an MFIter loop can be easily transformed into the async form Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/pthreads_common/RGIter.H 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Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Make.package Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/main.cpp Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit e2d4a9845c44bc679e11febe0e3bd2ebaf3de2a8 Author: Andrew Myers Date: Tue Apr 16 15:11:16 2019 -0400 formatting change Src/Particle/AMReX_Particles.H commit d62b1750678de777162520d49ae3cce5b12fe3a1 Author: Andrew Myers Date: Tue Apr 16 15:10:44 2019 -0400 offloading init particles in the CUDA version of the EM PIC Tutorial Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit c5d83f538cf291d8bdfb3dc11bb348e17555c010 Author: Andrew Myers Date: Tue Apr 16 15:09:44 2019 -0400 add functions to StructOfArrays that return a GPU-accessible holder for the data pointers. Src/Particle/AMReX_StructOfArrays.H commit 54b34bfe9b3f9e4b77ead0a3ca04855b2e1e3bbe Author: Andrew Myers Date: Tue Apr 16 15:02:25 2019 -0400 implement GPU version of RandomNormal Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 8bab9adee54ab39471fa74c08a9e0eb5104ab3cc Author: Andrew Myers Date: Tue Apr 16 15:01:45 2019 -0400 automatically deallocate the random number arrays in amrex::Finalize Src/Base/AMReX.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit b98061daef33d5cfe685347c91c38923d8713214 Author: Weiqun Zhang Date: Tue Apr 16 10:30:13 2019 -0700 remove deprecated ctors Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp commit 26481ab33b3a527ffb992c31144fb3b2e4db8e73 Merge: 39c1804c4 d666cc265 Author: Weiqun Zhang Date: Tue Apr 16 10:04:01 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit 39c1804c4b2c9c43fa1dc52a2aa30f3082064454 Author: Weiqun Zhang Date: Tue Apr 16 10:02:18 2019 -0700 FabArray: make host fab the main owner and device fab an alias. This will allow for not creating device fabs at all Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_MultiCutFab.H commit d666cc265f6ae49236f7f7f3f57988b5c4ed559e Author: Weiqun Zhang Date: Tue Apr 16 12:59:30 2019 -0400 manually inline static constexpr member for device functions Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp commit a51601e7428cf885be441028eb3f3bdac5efc5be Author: Weiqun Zhang Date: Tue Apr 16 12:08:40 2019 -0400 std::max --> amrex::max in device function Src/EB/AMReX_EB2_IF_Cylinder.H commit 38f1e53f473538a2211a992900677cc1834943d0 Author: kngott Date: Tue Apr 16 08:25:52 2019 -0700 FAB* and Array4 versions both available. Array4 expected due to future unified memory flags. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 69cab283c296b83f86ea5fbb9d368857e5fef518 Merge: 106a5682a 6fe10378c Author: Andrew Myers Date: Mon Apr 15 15:32:17 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 106a5682a986d8492362b40a5512d8098f27715a Author: Andrew Myers Date: Mon Apr 15 15:32:08 2019 -0700 update the neighbor particle documentation to account for the fact that the neighbors are Vector, not Vector now. Docs/sphinx_documentation/source/Particle.rst commit 6fe10378c3daf196fa0bbce21a042575895cd82f Author: Max Katz Date: Mon Apr 15 12:25:28 2019 -0400 Add option to output fextract in scientific notation Tools/Plotfile/fextract.cpp commit c2c93c1ed71fb091517000ae922a8d0740b5557c Author: Weiqun Zhang Date: Fri Apr 12 19:41:09 2019 -0700 put dx_eb computation in a function and use it to fix hypre Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 4e32b05d136d65b9fb6e47daa470cba7d728517e Author: Weiqun Zhang Date: Fri Apr 12 19:21:22 2019 -0700 fix the formular for dx_eb Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 5ac082ec85256c8ce3108f01c8e7e3e08b3034f3 Author: Ann Almgren Date: Fri Apr 12 18:37:20 2019 -0700 oops - missed one declaration -- compiles now Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 03b810e9052c13b77c40fa9b7a7bc075a29a4141 Author: Ann Almgren Date: Fri Apr 12 18:29:20 2019 -0700 Update the stencil used for dphi/dn at EB walls when using Dirichlet bcs. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 55516b137e96510de8e82cd23efc3996ca7fec6a Merge: c8f91df1f e682d934f Author: Michele Rosso Date: Fri Apr 12 17:14:12 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit c8f91df1f4fc08c780c9ba07f583fff01fcdcca4 Author: Michele Rosso Date: Fri Apr 12 17:14:06 2019 -0700 CMake: update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/GPU.rst commit e682d934f184e45769f32eac22e51d7bb6528c7f Merge: cc1d00925 a8b0fe1a4 Author: mic84 Date: Fri Apr 12 16:01:29 2019 -0700 Merge pull request #451 from mwm126/patch-2 Use " sed -i'' " for BSD sed on Mac commit a8b0fe1a4a4c3ae11541f33cefe2d5f80c186a85 Merge: d91fc4b62 cc1d00925 Author: mic84 Date: Fri Apr 12 16:01:17 2019 -0700 Merge branch 'development' into patch-2 commit 8e4dbc1e0dcffc25b6edb369cb6cedff6295172b Author: kngott Date: Fri Apr 12 15:41:08 2019 -0700 1 Graph per Iter methodology added. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Tests/GPU/CudaGraphs/GraphIterReuseCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphIterReuseCopy/Make.package Tests/GPU/CudaGraphs/GraphIterReuseCopy/inputs_3d Tests/GPU/CudaGraphs/GraphIterReuseCopy/main.cpp Tests/GPU/CudaGraphs/GraphIterReuseCopy/run.corigpu commit d91fc4b621747539df981ca7a69841bc2b3b3abb Author: Mark Meredith Date: Fri Apr 12 18:26:29 2019 -0400 Use " sed -i'' " for BSD sed on Mac Tools/CMake/AMReX_InstallExternalLibs.cmake commit dcea92f0c8e9bb8bc50a4d85c572d957b44cc406 Author: kngott Date: Fri Apr 12 14:44:42 2019 -0700 Separate Instantiate Function. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit e56ece2bab84cb55b890a41976bb89868f8dc2af Author: kngott Date: Fri Apr 12 14:34:55 2019 -0700 Change name of Graph functions to prepare for adding multiple capture methods. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Tests/GPU/CudaGraphs/ArrayReuse/main.cpp Tests/GPU/CudaGraphs/GraphCopy/main.cpp Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 0aead5a7bde2728f32060b4e4e4671a3148c5bd3 Author: kngott Date: Fri Apr 12 14:15:33 2019 -0700 Add proper free Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 99abc261b3de4614bd7c71a2f4118e123e3bd59d Author: kngott Date: Fri Apr 12 14:11:45 2019 -0700 Graph Reuse using Device Memory. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 81155d60e26ea2c3a2887cf7d608ffd7922c2253 Author: kngott Date: Fri Apr 12 13:39:06 2019 -0700 FAB lambda variation. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit f4477f5a62cafbf8910c3a8481b5449cedbd0a51 Author: kngott Date: Fri Apr 12 13:28:10 2019 -0700 Array4 and FAB* methods for reusing graph on different MultiFabs. Tests/GPU/CudaGraphs/ArrayReuse/GNUmakefile Tests/GPU/CudaGraphs/ArrayReuse/Make.package Tests/GPU/CudaGraphs/ArrayReuse/inputs_3d Tests/GPU/CudaGraphs/ArrayReuse/main.cpp Tests/GPU/CudaGraphs/ArrayReuse/run.corigpu Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit fe6d5e5415f53d3929ecfffa3791beb0be6fa839 Author: kngott Date: Thu Apr 11 15:22:44 2019 -0700 Missed a noexcept. Src/Base/AMReX_CudaDevice.H commit 01dc07957e0d1fca9bbae251f5bc52ff5674109b Author: kngott Date: Thu Apr 11 15:22:25 2019 -0700 Update callback for Cuda 10. Src/Base/AMReX_CudaAsyncFab.cpp commit 7a46b9d116e726e469800e41b08e548fc4482cf7 Author: kngott Date: Thu Apr 11 15:22:04 2019 -0700 Sync Array fully with development. Src/Base/AMReX_Array.H commit 27556858aa87f6b79a0404ed80cdb62b56716089 Author: kngott Date: Thu Apr 11 14:40:59 2019 -0700 Corrected CommI.H Src/Base/AMReX_FabArrayCommI.H commit fcd183527be08b3f30a854ffd83bc5064cef76a3 Merge: 2e6504d8e cc1d00925 Author: kngott Date: Thu Apr 11 13:55:51 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit cc1d009253e647b033aa6b6fe7d09fc668ac2ee0 Author: Weiqun Zhang Date: Thu Apr 11 12:16:28 2019 -0700 make: when USE_CUDA, make sure comm and space are always defined before substition of compiler flags Tools/GNUMake/Make.defs commit cdb8de6fc5641c6abf2b37e31d05ad90bb8ed5fc Merge: c82d3e236 cd1133e22 Author: Weiqun Zhang Date: Thu Apr 11 12:07:37 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c82d3e23601e22619749f44e52b9c047bcf29030 Author: Weiqun Zhang Date: Thu Apr 11 12:07:19 2019 -0700 hide errors in calling mpic++ -link_info Tools/GNUMake/sites/Make.nersc commit cd1133e229c0a221b765c1be3823622e44cde414 Merge: e1ee32790 188bb5962 Author: Andrew Myers Date: Thu Apr 11 11:07:14 2019 -0700 Merge pull request #450 from AMReX-Codes/init_from_random_restart_gpu_friendly copy particles from host to device in one batch, 3 more funtions commit e1ee32790acca2cbe5bd33796876d72c05ea2d27 Author: Weiqun Zhang Date: Thu Apr 11 10:36:55 2019 -0700 option to fix -pthread for nvcc Tools/GNUMake/Make.defs commit 1ac221a422de0076ec3e7ddbbc43c6c587177b45 Author: Weiqun Zhang Date: Thu Apr 11 07:52:06 2019 -0700 fix sign and unsigned comparison in 1d Src/Base/AMReX_CudaDevice.cpp commit af6e0ce44e51a9f44cf4d2ac53c163f1429fa53e Merge: 7ec432c09 00d24855f Author: WeiqunZhang Date: Wed Apr 10 22:13:10 2019 -0700 Merge pull request #448 from AMReX-Codes/pgi-opt-fix Define PGI_OPT for any choice of AMREX_CCOMP and AMREX_FCOMP in pgi.mak commit 7ec432c09171fdf75e6e8bd12ca8aebdf297704e Author: Weiqun Zhang Date: Wed Apr 10 21:54:33 2019 -0700 have to remove Werror=cross-execution-space-call because of cori Tools/GNUMake/comps/nvcc.mak commit 0b4d19efb18adb782047d7e4295e847784051f99 Author: Weiqun Zhang Date: Wed Apr 10 21:20:35 2019 -0700 simplify USE_HYPRE Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBflux_grad/GNUmakefile Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/NodeEB/GNUmakefile Tools/GNUMake/packages/Make.ascent Tools/GNUMake/packages/Make.hypre Tools/GNUMake/packages/Make.petsc Tutorials/EB/MacProj/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile commit 6fba7be9ce58b69f19038875db4082b7fd86d49e Author: Weiqun Zhang Date: Wed Apr 10 20:40:38 2019 -0700 if -> ifdef for consistence Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrCore/AMReX_TagBox.cpp Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_Machine.cpp Src/Base/AMReX_TypeTraits.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/C_BaseLib/tMF.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp Tutorials/GPU/EBCNS/Source/CNS_io.cpp commit 00d24855f2a5d2f7adf825d3b07f888256c3a887 Author: Donald E. Willcox Date: Wed Apr 10 20:16:05 2019 -0700 Define PGI_OPT even if AMREX_CCOMP is not pgi in case AMREX_FCOMP is pgi. Tools/GNUMake/comps/pgi.mak commit 188bb5962cbbe18435854ac2489244159c7f5dbc Author: Jean Sexton Date: Wed Apr 10 21:48:39 2019 -0400 copy particles from host to device in one batch in InitRandom, InitNRandomPerCell, and Restart Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit a81b9c743246e8f4681c2a045003bef2a5a79e9e Author: Brandon Runnels Date: Wed Apr 10 17:55:03 2019 -0600 added bottom abs tolerance Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 56c9fa7d71c6d9f3f82dd62972fa0899376d2705 Author: Weiqun Zhang Date: Wed Apr 10 16:47:46 2019 -0700 remove .mod files in clean Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex commit 6f7257c0e9d797f78247b1a5e8351c47675e5591 Author: Weiqun Zhang Date: Wed Apr 10 16:33:52 2019 -0700 libamrex: add lib/pkgconfig/amrex.pc GNUmakefile.in Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/cray.mak Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/intel.mak Tools/GNUMake/comps/llvm-flang.mak Tools/GNUMake/comps/llvm.mak Tools/GNUMake/comps/nag.mak Tools/GNUMake/comps/nec.mak Tools/GNUMake/comps/pgi.mak Tools/libamrex/configure.py Tools/libamrex/mkpkgconfig.py Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex commit 317c978f4411dfa1679fe720539208b2d197f641 Merge: 047eddf02 bd684825c Author: Andrew Myers Date: Wed Apr 10 11:35:52 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 047eddf02ccfd740ff666e3c3c6480c499e9e023 Merge: b91808a31 0bbc0ee00 Author: Andrew Myers Date: Wed Apr 10 11:35:39 2019 -0700 Merge branch 'init_from_binary_gpu_friendly' into development commit 0bbc0ee0027ab3e48c655fd99ea555cf3389f2fe Author: Andrew Myers Date: Wed Apr 10 11:34:48 2019 -0700 add sync after InitFromBinary Src/Particle/AMReX_ParticleInit.H commit bd684825c8788c5252da9ed52183116447919eeb Author: Weiqun Zhang Date: Wed Apr 10 10:16:45 2019 -0700 configure: implement the allow_different_compiler option. Add an example makefile to heat equation OpenACC tutorial GNUmakefile.in Tools/libamrex/mkconfig.py Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex commit 2e6504d8e0b76eeaec521d94a84ac6cfba8a1048 Merge: 0a18cff34 4aaf0d8fc Author: kngott Date: Tue Apr 9 17:14:43 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 4aaf0d8fccb306e518c2a4912d448350ec3ebb1a Merge: b91808a31 486539e78 Author: WeiqunZhang Date: Tue Apr 9 17:03:06 2019 -0700 Merge pull request #446 from ghweber/master Add missing include for Conduit/Make.package and missing linker optio… commit b91808a31ec14db121aae6a0acbd56f7a52c3194 Merge: 6c8913512 216b49abd Author: Andrew Myers Date: Tue Apr 9 16:30:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 216b49abd7a285d3baca9a95439c7f03bd0bfda3 Author: Weiqun Zhang Date: Tue Apr 9 15:58:07 2019 -0700 make Array4 is_trivially_copyable Src/Base/AMReX_Array.H commit 6c8913512590390f057dae6337dac1931ef34968 Author: Andrew Myers Date: Tue Apr 9 15:35:53 2019 -0700 add some overloads for backwards compatability Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d2127d26bfe85f828b7803d68e7100e4666428e2 Author: Andrew Myers Date: Tue Apr 9 13:37:50 2019 -0700 fix typo in assert statement Src/Particle/AMReX_ParticleContainerI.H commit 026ecf1f448b375bd42a8247594f886db70ae266 Author: Andrew Myers Date: Tue Apr 9 12:45:20 2019 -0700 fix logic error Src/Particle/AMReX_ParticleContainerI.H commit 0710727f2aa7de451dd503824738e493edf0ce34 Author: Andrew Myers Date: Tue Apr 9 12:33:17 2019 -0700 update Checkpoint call in AssignDensity test Tests/Particles/AssignDensity/main.cpp commit d476de410447b1021ad2656b844f1c46d352e3c8 Author: Andrew Myers Date: Tue Apr 9 12:32:59 2019 -0700 update Header to reflect new num comps Src/Particle/AMReX_ParticleContainerI.H commit 71626307db3755f57379bd1a1ed5f84d4360cd5a Author: Michele Rosso Date: Tue Apr 9 12:16:37 2019 -0700 CMake: improve SUNDIALS support Src/Extern/SUNDIALS4/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/FindSUNDIALS.cmake commit 497c3f06b5afb43e525518fbf658424380d3a991 Author: Andrew Myers Date: Tue Apr 9 11:52:42 2019 -0700 nuke is_checkpoint Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 235f264243599e5dd542984fd86843212580c6f3 Author: Andrew Myers Date: Tue Apr 9 11:29:42 2019 -0700 also add all those versions of WritePlotFile Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 91f0a4d1f2ced9e651e35fe8cfc7973581ad45aa Author: Andrew Myers Date: Tue Apr 9 11:17:33 2019 -0700 more formatting changes Src/Particle/AMReX_ParticleContainerI.H commit 0e63af22785ecd1e9a8dd3297ee6822180590236 Author: Andrew Myers Date: Tue Apr 9 11:15:48 2019 -0700 update ReadParticles to account for these changes Src/Particle/AMReX_ParticleContainerI.H commit 44b01d46e28b6e782f9688ddbc8b356261048e55 Author: Andrew Myers Date: Tue Apr 9 10:57:28 2019 -0700 update ReadParticles Function Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 76311680f60c907b60fd40c9bc05b747fb066ce0 Author: Andrew Myers Date: Tue Apr 9 10:54:42 2019 -0700 formatting changes Src/Particle/AMReX_ParticleContainerI.H commit b97fce2e8a1e3866e8f717a8bff7e4c49ee764aa Author: Andrew Myers Date: Tue Apr 9 10:52:42 2019 -0700 add a new Restart function, implement the specific one in terms of the general Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 0d81f5dd4b6e135bd5c40fd2632df8042e550d6d Merge: 4ffa510fa 5074d83ff Author: Michele Rosso Date: Tue Apr 9 10:52:02 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4ffa510faf8e6088095bd03cfb77365ef76d8063 Author: Michele Rosso Date: Tue Apr 9 10:50:31 2019 -0700 CMake: improve HYPRE support * Add HYPRE detection to AMREX config file * Add minimum required version for HYPRE Src/Extern/HYPRE/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/FindHYPRE.cmake commit ef27155c4aa1bd50eabf300eaad37fb021cc431c Author: Andrew Myers Date: Tue Apr 9 10:48:53 2019 -0700 modify the WriteParticles method to only write out the requested components Src/Particle/AMReX_ParticleContainerI.H commit c3224ec83e9fd7f5a26da9d11da5f8b29f135b33 Author: Andrew Myers Date: Tue Apr 9 10:35:19 2019 -0700 more formatting changes. Src/Particle/AMReX_Particles.H commit 98fc8fd7f2decd01741c63ca99c0fbaf686f8c3e Author: Andrew Myers Date: Tue Apr 9 10:31:36 2019 -0700 implement the special Checkpoint functions in terms of the most general one. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ff5ce628a3134d96e9aeea573814c403e33af67a Author: Andrew Myers Date: Tue Apr 9 10:15:24 2019 -0700 add overloaded versions of Checkpoint that allow for toggling IO on/off for specific particle components. Src/Particle/AMReX_Particles.H commit 91461b7970ee0c8cf0b150d94beb3bc5887bef07 Author: Andrew Myers Date: Tue Apr 9 10:05:40 2019 -0700 formatting changes Src/Particle/AMReX_ParticleContainerI.H commit 8addd98619c6a532083a731b35f9f78fc5277ffd Author: Andrew Myers Date: Tue Apr 9 09:57:10 2019 -0700 copy particles from host to device in one batch Src/Particle/AMReX_ParticleInit.H commit 5074d83ff08ac85ef53b9cc0be8968b2ccbaeafa Merge: 09154aa57 4ebb075fc Author: Andrew Myers Date: Mon Apr 8 21:35:23 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 486539e7843293be3d96b6bf65620513139c82f0 Author: Gunther H. Weber Date: Mon Apr 8 18:35:17 2019 -0700 Move include for conduit packages from Make.defs to Make.conduit Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.conduit commit 09154aa5771c5a7426072e8c34a84e0485897833 Author: Andrew Myers Date: Mon Apr 8 21:35:04 2019 -0400 gpu neighbor list bug fix Src/Particle/AMReX_NeighborList.H commit ac9aeaab2879b7512131d2da8a871f6eefd201d4 Author: Gunther H. Weber Date: Mon Apr 8 17:35:08 2019 -0700 Add missing include for Conduit/Make.package and missing linker options for Conduit/Ascent Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.ascent Tools/GNUMake/packages/Make.conduit commit 4ebb075fc99ccfd3202801ce234b127cc3d6109c Author: Michele Rosso Date: Mon Apr 8 17:20:48 2019 -0700 CMake: add HYPRE support Src/CMakeLists.txt Src/Extern/HYPRE/CMakeLists.txt Tools/CMake/AMReX_Options.cmake Tools/CMake/FindHYPRE.cmake Tutorials/CMakeLists.txt Tutorials/LinearSolvers/ABecLaplacian_C/CMakeLists.txt commit 0531972cb843b6a93843a9b5c90be8fd4538d28a Author: RevathiJambunathan Date: Mon Apr 8 12:31:08 2019 -0700 slicevalues are assigned based on the nearest grid point. Modified initialization of the multifabs such that the values represent the exact x,y,z location in the computational domain to assist with verification of the values assigned to the slice grid points. Tests/CreateSliceForDiagnostics/inputs Tests/CreateSliceForDiagnostics/main.cpp commit c5e7ab3c9731228fd55913c575115175c4b6ec4d Merge: 8d4405e00 af2bcc45b Author: Weiqun Zhang Date: Sat Apr 6 08:16:32 2019 -0700 Merge branch 'development' into weiqun/hypre-node commit 8d4405e00621779bf1b7e6061d2edd005113cd34 Author: Weiqun Zhang Date: Sat Apr 6 08:12:39 2019 -0700 HypreNodeLap: 2d Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 26d2f6c2a098e82396770443e52357a27f87f4c7 Author: Weiqun Zhang Date: Fri Apr 5 21:37:15 2019 -0700 HypreNodeLap: switch to use RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 426464793958ef85434f500a88ba1e2825c9ef0f Author: Weiqun Zhang Date: Fri Apr 5 21:25:35 2019 -0700 HypreNodeLap: set use_hypre only once Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/MyTest.cpp commit 4c4aa0f85885d867123f81f7fea2fd21e59b1bf5 Author: Weiqun Zhang Date: Fri Apr 5 16:37:54 2019 -0700 HypreNodeLap: fix id Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit af2bcc45b4ab467623e998b0a0e8c7093311bf42 Author: Michele Rosso Date: Fri Apr 5 16:36:05 2019 -0700 CMake: add back option I deleted by mistake Tools/CMake/AMReX_Options.cmake commit 280fa93f7ee91cc48a6d66b3fcb2cc339cfe2aaf Author: Weiqun Zhang Date: Fri Apr 5 13:25:26 2019 -0700 reorganize OverrideSync so that it can be used on any FabArray, not just MultiFab Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 6f4f4adc619c4ba741987b0062f1e44b1c761611 Merge: faf9c1de6 795d67029 Author: RevathiJambunathan Date: Fri Apr 5 13:24:08 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into SliceGenerationForDiagnostics_RJ commit 795d67029280b79a52a1fa3694f0bc574bfecd73 Merge: 9fa218b39 12cb3fc57 Author: Michele Rosso Date: Fri Apr 5 11:54:59 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9fa218b395a80119337264b40f05d9cdb2198fc6 Author: Michele Rosso Date: Fri Apr 5 11:54:47 2019 -0700 CMake: change how AMReX CUDA settings are passed to app codes Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_SetupCUDA.cmake commit 12cb3fc5790061ecf5150f67de24c766a58679b6 Author: Marc Day Date: Thu Apr 4 20:32:02 2019 -0700 Put main code in local scope to avoid seg fault bug. Tools/Postprocessing/C_Src/HorizontalAvg.cpp Tools/Postprocessing/C_Src/IntegrateComp.cpp Tools/Postprocessing/C_Src/MultiFabToMatLab.cpp Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp Tools/Postprocessing/C_Src/PtwisePltTransform.cpp commit 9b289bb5a2a74c415789c1e38596e38758b5d867 Author: Michele Rosso Date: Thu Apr 4 17:08:55 2019 -0700 CMake: streamline CUDA setup Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupCUDA.cmake commit 82b9cc5dd931e0c45d81aaaa13cd163e2b89651f Author: Weiqun Zhang Date: Thu Apr 4 16:33:26 2019 -0700 HypreNodelap: implement loadVectors and getSolution Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp commit 1ef26bcb6316197fe0f46dda3ba59d3dc8155346 Merge: 0b1860fd0 ef538d173 Author: Michele Rosso Date: Thu Apr 4 16:24:44 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ef538d173898a6fe3b814fc955b97232c27fad19 Merge: ab6f075bf f34071192 Author: Andrew Myers Date: Thu Apr 4 19:23:41 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ab6f075bf15388b26d3a22c298446e422f51634c Author: Andrew Myers Date: Thu Apr 4 19:23:22 2019 -0400 need to make a local copy of the particle struct pointer to pass into kernels when building the neighbor list Src/Particle/AMReX_NeighborList.H commit f3407119296913781c3e7447af91c2f70aafbc55 Author: Ann Almgren Date: Thu Apr 4 16:06:35 2019 -0700 Change the default box_min_width for EB in the multigrid solves -- when AMREX_USE_EB make the min width 4 instead of 2 Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 5f784d3b66452b17d3b3ac27d33135ef453f6507 Author: Weiqun Zhang Date: Thu Apr 4 14:53:44 2019 -0700 HypreNodeLap: placeholder for loadVectors and getSolution Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 3724b80a470de4fedaa727f3a898c37bb5ef49ec Author: Weiqun Zhang Date: Thu Apr 4 14:40:17 2019 -0700 HypreNodeLap: setup amg solver Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 0b1860fd0b8a46e8fa84e0b7ec45667faaba485b Merge: d9294e811 a5e8b3912 Author: Michele Rosso Date: Thu Apr 4 14:39:04 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a5e8b3912bc670cf94c9f0ac527809d755727fc2 Author: Michele Rosso Date: Thu Apr 4 14:26:44 2019 -0700 CMake: allow 1D builds. Fixes Issue 400 Docs/sphinx_documentation/source/BuildingAMReX.rst Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit 3d1b9f54505083c32c361d02d0e8320f32fe6d7b Author: Michele Rosso Date: Thu Apr 4 13:58:17 2019 -0700 CMake: fix MPI search in config file Tools/CMake/AMReXConfig.cmake.in commit f7065c755ccc9c95159885a61587981a717d68da Author: Weiqun Zhang Date: Thu Apr 4 09:05:46 2019 -0700 MLNodeLaplacian: fill IJ matrix for non-EB Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit faf9c1de6ec6d195e60744faa103285286af5e87 Author: RevathiJambunathan Date: Thu Apr 4 13:29:47 2019 -0700 modified main.cpp to generate error messages if cell size of slice is not an integer multiple of computational domain's cell size. Additional error messages include ensuring that the max_grid_size of box arrays are integer multiples of the coarsening ratio. Tests/CreateSliceForDiagnostics/inputs Tests/CreateSliceForDiagnostics/main.cpp commit b79ca70b454cd95f98d88151aa39522eaedf25c9 Merge: fc2d48fc3 2b9f858c2 Author: WeiqunZhang Date: Thu Apr 4 12:26:59 2019 -0700 Merge pull request #442 from jrood-nrel/fix_fcompare3D_intel Fix fcompare3D for the Intel compiler commit fc2d48fc394a9265174bd64c6978141bd25cdb13 Author: Weiqun Zhang Date: Thu Apr 4 12:25:22 2019 -0700 EB: remove small cells with volume fraction less than 1.e-14 Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 commit d9294e8115c5cd4886c738df14c5eee0a76813eb Author: Michele Rosso Date: Thu Apr 4 10:09:13 2019 -0700 CMake: remove obsolete check Tools/CMake/AMReX_SetupCUDA.cmake commit 2b9f858c2a6c1fe7835b08a256e24d587a7b563a Author: Jon Rood Date: Wed Apr 3 19:37:48 2019 -0600 Fixing line continuation in AMReX_FABUTIL_3D.F so that the Intel compiler can compile this file. Src/Extern/amrdata/AMReX_FABUTIL_3D.F commit c327b9cbd4e9ad122eb6478c5f8a1b9d7e8d0a68 Author: RevathiJambunathan Date: Wed Apr 3 18:01:04 2019 -0700 corrected modification of max grid slice such that IntVect coarseslice can be an integer multiple for any dimension. Tests/CreateSliceForDiagnostics/main.cpp commit 85c722da1739dcbe130a72fdaed35b7e43eb9578 Author: RevathiJambunathan Date: Wed Apr 3 17:38:07 2019 -0700 modified max_grid_size for slice box array to enable slice generation such that the coarse IntVect can be any integer multiple of the baseline slice and not limited to a multiple of two. Tests/CreateSliceForDiagnostics/main.cpp commit 0077d6b0d52cfb9db072be2face4fc9f4b881060 Author: Weiqun Zhang Date: Wed Apr 3 16:41:29 2019 -0700 HypreNodeLap: ask MLNodeLaplacian to fill IJ matrix Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 6a934bd6a5e9d6bf5ef855c1c2eeca1c2b9df09c Author: Weiqun Zhang Date: Wed Apr 3 15:45:33 2019 -0700 HyperNodeLap: set up node id Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/MyTest.cpp commit 0a18cff34e0d962307e60507cc4f876f9ea6e48d Author: kngott Date: Wed Apr 3 14:59:06 2019 -0700 First draft of reusing copy graph on a different MultiFab. Tests/GPU/CudaGraphs/GraphReuseCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphReuseCopy/Make.package Tests/GPU/CudaGraphs/GraphReuseCopy/inputs_3d Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp Tests/GPU/CudaGraphs/GraphReuseCopy/run.corigpu commit a3c33d2ccf862a8bafa911b5c1c90ee36798d145 Author: kngott Date: Wed Apr 3 14:55:59 2019 -0700 Adjust Array4 to allow needed access for CudaGraphs. Hopefully, a better way can be found later. Src/Base/AMReX_Array.H commit 08b185da9ac28c7b2d46741ddfea4b20000cd284 Author: kngott Date: Wed Apr 3 14:54:13 2019 -0700 Adjust GraphRecordingStop to return the graph instead of take by reference. Also comment out graph log output for now. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit adaa02fba55e728607a34db623aab52462c299fc Author: kngott Date: Wed Apr 3 14:52:05 2019 -0700 Turn off FillBoundary preliminary graphing. Need to test more, leave complete marker locations for now. Src/Base/AMReX_FabArrayCommI.H commit b526a676d69eb21cf834fdcf2d684a041da7ab69 Author: Weiqun Zhang Date: Wed Apr 3 12:28:20 2019 -0700 start HypreNodeLap Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/Extern/HYPRE/Make.package Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/MyTest.cpp commit 2503f4ef37bbafbcf3e37bdc79a816b14f0501fe Merge: 35f125a66 6d4fd7bc8 Author: RevathiJambunathan Date: Wed Apr 3 12:17:06 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into SliceGenerationForDiagnostics_RJ commit 35f125a66afa119c2d6f206a1ec91c37d9d41c0c Author: RevathiJambunathan Date: Wed Apr 3 12:16:47 2019 -0700 Adding test case to generate slice for diagnostics Tests/CreateSliceForDiagnostics/GNUmakefile Tests/CreateSliceForDiagnostics/Make.package Tests/CreateSliceForDiagnostics/inputs Tests/CreateSliceForDiagnostics/main.H Tests/CreateSliceForDiagnostics/main.cpp commit 6d4fd7bc8b4057f9b8272481f2999d3b8576eb0c Author: Weiqun Zhang Date: Wed Apr 3 09:49:50 2019 -0700 fix memory issue related to using AsyncFab in non-launch region Src/Base/AMReX_CudaAsyncFabImpl.cpp commit a4ee51d60c29c286daed1052c7de5e6da4288340 Merge: 77f514db1 2e2c19364 Author: Weiqun Zhang Date: Tue Apr 2 17:04:16 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 77f514db1050722643a5d13d58311dcf3e5a868b Author: Weiqun Zhang Date: Tue Apr 2 17:04:05 2019 -0700 make it clear where LIBRARIES can be modified in make system Docs/sphinx_documentation/source/BuildingAMReX.rst commit 2e2c1936447fdb7496b62674b837421782f052ac Merge: 739f30ffd 205ec28e4 Author: Ann Almgren Date: Tue Apr 2 15:44:12 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 739f30ffd5ce74c20d2d40d7a9c712ba87e0f9ad Author: Ann Almgren Date: Tue Apr 2 15:43:23 2019 -0700 Allow VisMF::Read to read an empty MultiFab without an error if and only if we pass in a flag (allow_empty_mf) that explicitly says its ok -- the default is still that it's not ok Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 205ec28e4b00737f935f353f412c89d0bdd9534d Author: Weiqun Zhang Date: Tue Apr 2 15:40:50 2019 -0700 write a debug chekcpoint file for MLNodeLaplaian Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_Utility.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f6d1352c0c97889b5c558a7fc6a7483aa90d9f2f Author: Weiqun Zhang Date: Tue Apr 2 13:24:20 2019 -0700 fix a bug in 2d eb Src/EB/AMReX_eb2_2d.F90 commit 74aeb23b40ecbb85c71ac4efc37ffc42b190db72 Merge: 6872995e7 be96d9c33 Author: Weiqun Zhang Date: Tue Apr 2 13:28:46 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6872995e71a2376755e36bb5bbc0b7446c47afb5 Author: Weiqun Zhang Date: Tue Apr 2 13:24:20 2019 -0700 fix a bug in 2d eb Src/EB/AMReX_eb2_2d.F90 commit be96d9c33c71a771041e88599c123a645de7530b Merge: 8e4a6729d b9496c998 Author: Michele Rosso Date: Tue Apr 2 12:26:47 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8e4a6729d1e7a9bc4b09fb87a0fa00bdfbec555a Author: Michele Rosso Date: Tue Apr 2 12:26:42 2019 -0700 CMake: find OpenMP dependency in AMReX export file Tools/CMake/AMReXConfig.cmake.in commit b9496c998370ff814f85965f8a7d88eae8b5fe51 Merge: b7d5e7aba 45a40a4e5 Author: Andrew Myers Date: Tue Apr 2 14:22:56 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b7d5e7abaa605902d938c4cc905324f0df185c79 Author: Andrew Myers Date: Tue Apr 2 14:22:42 2019 -0400 need to fill the index sequence before using it... Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 45a40a4e5142ed82d58dde36470a6a6fae87521a Author: Michele Rosso Date: Tue Apr 2 11:21:07 2019 -0700 CMake: add missing define for Algoim Src/Extern/Algoim/CMakeLists.txt commit 6fcd9d69daa3ec069e0fda86ac6b9dce021f738f Author: Weiqun Zhang Date: Tue Apr 2 10:18:16 2019 -0700 change the interface of Interpolater::interp. Note that this is a virtual function, so it will break derived classes! Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/EB/AMReX_EBInterpolater.H Src/EB/AMReX_EBInterpolater.cpp commit 517f6df31db90b5ef5ad64a9b02a115e7e676c18 Author: Weiqun Zhang Date: Tue Apr 2 10:13:15 2019 -0700 fix default path to amrex Tools/Plotfile/GNUmakefile commit 9565e8d6365d668eb6c6a773812f0fd7fd03e39e Merge: 916c943bf e8bf23961 Author: Weiqun Zhang Date: Tue Apr 2 10:10:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 916c943bfe27afb635595bdb40bf4071b522bbf7 Author: Weiqun Zhang Date: Tue Apr 2 10:10:22 2019 -0700 remove C_Src/fcompare and fextract to avoid confusion Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/fcompare.cpp Tools/Postprocessing/C_Src/fextract.cpp commit e8bf23961ecec4e04d6e4f67dad0b95e1d93305d Author: Andrew Myers Date: Mon Apr 1 20:50:17 2019 -0400 bail if cuda 9.2 used with USE_EB=TRUE Tools/GNUMake/comps/nvcc.mak commit cd50eb9c7636768a15334e3f01ad3c1463ebd708 Merge: 4ddd58c67 9bdf6484b Author: Andrew Myers Date: Mon Apr 1 20:20:41 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9bdf6484b428d6791aa5266f1f1b66f15654d788 Merge: 659a80a3a 79c2fc7d3 Author: Michele Rosso Date: Mon Apr 1 17:22:50 2019 -0700 Merge branch 'mr/cmake' into development commit 79c2fc7d3241020c5dda1d0073b97a5a514a2058 Author: Michele Rosso Date: Mon Apr 1 17:22:30 2019 -0700 CMake: bump up CMake minimum required version CMakeLists.txt commit 4ddd58c6728fda4c1fbe23d77554f527c5aed4f1 Author: Andrew Myers Date: Thu Mar 28 10:38:22 2019 -0700 mark EBCellFlag functions __host__ __device__ Src/EB/AMReX_EBCellFlag.H commit baf4463b66f9b4fa544b7bf45699ae6b26fd2804 Author: Andrew Myers Date: Thu Mar 28 19:37:13 2019 -0400 early exit for when neighbors don't need to be filled. Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 743bb306e78dc3a49907d13be47fb8d2977af7e3 Author: Andrew Myers Date: Mon Apr 1 20:18:23 2019 -0400 workaround for Thrust bug in Cuda 9.1 Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 7f49eee73aa0337d41e0f3d950ff6854d8e26918 Author: Michele Rosso Date: Mon Apr 1 18:55:10 2019 -0400 Update doc Docs/sphinx_documentation/source/Fortran.rst commit 16c99d836df84c28024df6e2a077e7d123c80ee8 Author: Michele Rosso Date: Mon Apr 1 18:54:27 2019 -0400 CMake: return with error message if CUDA 9.2 is used whit ENABLE_EB=ON Tools/CMake/AMReX_SetupCUDA.cmake commit 659a80a3ab8e1818c3dc9e60fad4822d37e07236 Merge: 3936c7377 9c6ffaeed Author: Weiqun Zhang Date: Mon Apr 1 13:47:56 2019 -0700 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit 3936c73772808a45ce28c4484d9c1b3076898ce8 Author: Weiqun Zhang Date: Mon Apr 1 13:47:45 2019 -0700 Reduce: replace AsyncArray with DeviceScalar Src/Base/AMReX_FabArrayUtility.H commit 9c6ffaeed008d33a32cc9c94e66677c5587d0ad0 Author: Weiqun Zhang Date: Mon Apr 1 13:44:59 2019 -0700 fix UnionIF and IntersectionIF Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Union.H commit 0cf191ae684cd09050206075854a7eb6671fcf12 Merge: 8e2a33ff1 83e253432 Author: Weiqun Zhang Date: Mon Apr 1 13:16:54 2019 -0700 Merge branch 'development' into weiqun/gpu commit 8adf716290037c1efefba3eb854de14bbff33717 Author: Michele Rosso Date: Mon Apr 1 11:18:10 2019 -0700 Fix #ifdef inconsistency Src/Base/AMReX_filcc_mod.F90 commit 83e2534328e8215356391ec20fca06ef00347a59 Author: Michele Rosso Date: Mon Apr 1 11:18:10 2019 -0700 Fix #ifdef inconsistency Src/Base/AMReX_filcc_mod.F90 commit 8e2a33ff140fa9256105f953a7368a9b0a8817d6 Author: Weiqun Zhang Date: Mon Apr 1 13:01:15 2019 -0700 UnionIF: fix typo Src/EB/AMReX_EB2_IF_Union.H commit fd1575c217461a4238177aeb138a2f0ffcd7a8c0 Merge: 6200d3088 b8434d3ae Author: Weiqun Zhang Date: Mon Apr 1 12:33:32 2019 -0700 Merge branch 'development' into weiqun/gpu commit 99c95a68b4896f726f477a6bd7a738fc5d638462 Author: Michele Rosso Date: Mon Apr 1 14:51:40 2019 -0400 Replace some #if with #ifdef Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FabArray.H Src/Particle/AMReX_ParIterI.H commit f33234c7fb76f555a7af8166df50eefbea5ccf29 Author: Michele Rosso Date: Mon Apr 1 11:18:10 2019 -0700 Fix #ifdef inconsistency Src/Base/AMReX_filcc_mod.F90 commit 2b1698e16d03418201771f2d67f2b0945cfd57ec Merge: 75e42783e b8434d3ae Author: Michele Rosso Date: Mon Apr 1 10:46:54 2019 -0700 Merge branch 'development' into mr/cmake commit b8434d3ae5903779eef079a6c318d4b12dd908bb Author: Weiqun Zhang Date: Mon Apr 1 09:07:43 2019 -0700 update changes CHANGES commit f34f31ab260173497a837fcf3cee74b614c7b9e6 Merge: 51b262002 2a61fdfc7 Author: Weiqun Zhang Date: Mon Apr 1 08:58:28 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2a61fdfc7a9642d76e5e7f4fe2f1b4ef09475563 Author: Max Katz Date: Sat Mar 30 12:08:22 2019 -0700 Initialize xlcuf Src/Base/AMReX_CudaDevice.cpp commit 7d92a8a11f16e01391d1aa2d3947194af1346b76 Author: Max Katz Date: Sat Mar 30 12:08:00 2019 -0700 Fix make syntax Tools/GNUMake/Make.rules commit 0121543012dde3d71fc8499f4c378fa6334ac43e Author: Max Katz Date: Sat Mar 30 11:29:29 2019 -0700 Generalize register capping to support xlf Tools/GNUMake/Make.rules commit 90051adc5cbd574b50268a5de85ebdd3fcc79129 Author: Max Katz Date: Sat Mar 30 11:29:17 2019 -0700 Target the specific GPU arch for xlf Tools/GNUMake/comps/ibm.mak commit e10d278823fc93023b4277b4201067dcd60457cb Author: Max Katz Date: Sat Mar 30 10:31:40 2019 -0700 Disallow unrestricted private statements in the Fortran GPU script Tools/F_scripts/gpu_fortran.py commit c8c35da70504fb1e9942e68de8f6c12a9364fd02 Author: Max Katz Date: Sat Mar 30 10:31:18 2019 -0700 Explicitly write out the device version of amrex_filccn Src/Base/AMReX_filcc_mod.F90 commit 51b262002a1c460421bf38336e1854e7372c4603 Author: Weiqun Zhang Date: Fri Mar 29 16:17:33 2019 -0700 User's Guide: parallel descriptor Docs/sphinx_documentation/source/Basics.rst commit 75e42783e82f3463b5f79ba48943388864ea281c Merge: db062be90 c797c1cc8 Author: Michele Rosso Date: Fri Mar 29 15:39:20 2019 -0700 Merge branch 'development' into mr/cmake commit db062be905b298196b14b7b0ed49d00624394514 Author: Michele Rosso Date: Fri Mar 29 15:18:59 2019 -0700 CMake: start moving config and dependecies in the subdir where they are needed Src/Base/CMakeLists.txt Src/CMakeLists.txt Src/Extern/Algoim/CMakeLists.txt Src/Extern/Conduit/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupThirdPartyLibs.cmake commit 6200d30881b46abe9ebe3045bab5e6d51ff8f9bf Author: Weiqun Zhang Date: Fri Mar 29 13:25:41 2019 -0700 constexpr amrex::SpaceDim Src/Base/AMReX_SPACE.H commit c797c1cc88f8a5508f1a60194ec567bc3a5f1a47 Author: Weiqun Zhang Date: Fri Mar 29 13:13:40 2019 -0700 User's Guide: verbosity and make system Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/GettingStarted.rst commit 10dd6c0457e2c3387840db4f0a6ee1367211364a Author: Weiqun Zhang Date: Fri Mar 29 11:07:31 2019 -0700 make it easy to use python3 Docs/sphinx_documentation/Makefile commit a1afcb23f1fa37982cbb23bdb9cb5038541e00b7 Author: Weiqun Zhang Date: Fri Mar 29 08:31:52 2019 -0700 nvcc: error on calling host function from host device function Tools/GNUMake/comps/nvcc.mak commit 7231333cab133c4d5e430b564d6943a8658bc237 Author: Max Katz Date: Thu Mar 28 21:52:27 2019 -0700 Only cap registers if needed Tools/GNUMake/Make.rules commit a1f0000694b6cb5411cf4352da8573784faf58fd Author: Weiqun Zhang Date: Thu Mar 28 17:28:42 2019 -0700 gpu: Intersection and Union IF Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Union.H commit 930035a6158ab49f0e486ec159ea8e86b6255be0 Merge: 2eaed24d1 46d2bbfb8 Author: Tan Nguyen Date: Thu Mar 28 17:11:35 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2eaed24d199213be88d3451dc26ef096fc38b641 Author: Tan Nguyen Date: Thu Mar 28 17:11:18 2019 -0700 OpenMP backend for asyncMFIter Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi_omp/Barrier.cpp Src/AmrTask/rts_impls/mpi_omp/LocalConnection.H Src/AmrTask/rts_impls/mpi_omp/Make.package Src/AmrTask/rts_impls/mpi_omp/PackageQueue.H Src/AmrTask/rts_impls/mpi_omp/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_omp/Perilla.H Src/AmrTask/rts_impls/mpi_omp/Perilla.cpp Src/AmrTask/rts_impls/mpi_omp/PerillaConfig.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_omp/RGIter.H Src/AmrTask/rts_impls/mpi_omp/RGIter.cpp Src/AmrTask/rts_impls/mpi_omp/RegionGraph.H Src/AmrTask/rts_impls/mpi_omp/RegionGraph.cpp Src/AmrTask/rts_impls/mpi_omp/RegionQueue.H Src/AmrTask/rts_impls/mpi_omp/RegionQueue.cpp Src/AmrTask/rts_impls/mpi_omp/RemoteConnection.H Src/AmrTask/rts_impls/mpi_omp/WorkerThread.H Src/AmrTask/rts_impls/mpi_omp/WorkerThread.cpp Src/AmrTask/rts_impls/mpi_omp/perilla.mak Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.H Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/pthreads_common/RGIter.H Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile Src/Base/AMReX_MemPool.cpp commit 46d2bbfb8fbb4353109efc2f7db84cea03cb07eb Merge: d6b74f4b9 7269b933c Author: mic84 Date: Thu Mar 28 17:04:33 2019 -0700 Merge pull request #436 from balos1/development add SUNDIALS 4 support commit f018af3ca5b4110d330efd9b425b6cfa1fdaa606 Author: Weiqun Zhang Date: Thu Mar 28 19:10:48 2019 -0400 add __host__ __device__ to amrex::get for GpuTuple Src/Base/AMReX_Tuple.H commit 5370377fdb6330e79d5eebe3e2a55e70520525f8 Author: Michele Rosso Date: Thu Mar 28 15:37:50 2019 -0700 CMake: use add_subdirectory to include sub-folders into top-level CMakeLists. This change is made possible by CMake 3.13+. By doing so we can get rid of include(), use a more target-centric approach, and have a better localization of dependencies detail. Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/EB/CMakeLists.txt Src/Extern/Algoim/CMakeLists.txt Src/Extern/Conduit/CMakeLists.txt Src/Extern/ProfParser/CMakeLists.txt Src/Extern/SENSEI/CMakeLists.txt Src/Extern/SUNDIALS3/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake commit 96a556e6994bab663d7e80314a86cfaeace17d4d Author: Weiqun Zhang Date: Thu Mar 28 14:17:24 2019 -0700 Tuple: add constexpr Src/Base/AMReX_Tuple.H commit e7e5f0229f203731e5e2a35e3276cf0ab3391a78 Author: Weiqun Zhang Date: Thu Mar 28 13:52:45 2019 -0700 add makeTuple Src/Base/AMReX_Tuple.H commit 8ee93abd9431b1c4b6391816acd479b11dbcb950 Author: Weiqun Zhang Date: Thu Mar 28 13:33:35 2019 -0700 use amrex::Tuple in UnionIF and IntersectionIF Src/Base/AMReX_Tuple.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Union.H commit 13dc9e1a696ca7b9bc3d6934d2518fef22207fb3 Author: Weiqun Zhang Date: Thu Mar 28 10:36:50 2019 -0700 first pass of Tuple Src/Base/AMReX_IndexSequence.H Src/Base/AMReX_Tuple.H commit d6b74f4b9f380592d0ba9b5e10edbdbf867eef2e Author: Weiqun Zhang Date: Thu Mar 28 12:02:25 2019 -0700 fix for clang, thanks to Jon Rood Src/Amr/AMReX_StateDescriptor.H commit c2119f326e3d5c3624f324ff9ab0ebe73ddc0477 Author: Andrew Myers Date: Thu Mar 28 10:40:33 2019 -0700 Revert "mark these functions AMREX_GPU_HOST_DEVICE so they can be used in device code" This reverts commit 40ddf688e40caa3f9253092c57b96957dbe49545. Src/EB/AMReX_EBCellFlag.H commit f9c756aa4c51d7b6c61a729d2a6855397e6a106d Merge: 40ddf688e 2b10462df Author: Andrew Myers Date: Wed Mar 27 19:56:39 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 40ddf688e40caa3f9253092c57b96957dbe49545 Author: Andrew Myers Date: Wed Mar 27 19:56:20 2019 -0400 mark these functions AMREX_GPU_HOST_DEVICE so they can be used in device code Src/EB/AMReX_EBCellFlag.H commit 7269b933cc68488775c9b34c71ff5b0abacb6dd0 Author: Balos, Cody Joe Date: Wed Mar 27 16:13:15 2019 -0700 remove unused file from SUNDIALS4 Src/Extern/SUNDIALS4/farkode_butcher_mod.f90 Src/Extern/SUNDIALS4/fsunlinsol_dense.f90 Src/Extern/SUNDIALS4/fsunnonlinsol_mod.f90 commit 94ec419d8e770c0acee952692aab13ae42c20068 Author: Michele Rosso Date: Wed Mar 27 16:02:24 2019 -0700 CMake: clean-up output for algoim Tools/CMake/AMReX_InstallExternalLibs.cmake commit 2b10462dfd98cadd359f1969307497790bed42ae Author: Weiqun Zhang Date: Wed Mar 27 15:25:48 2019 -0700 removed the use of Tuple and old hypre interface OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp OldTutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F OldTutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H OldTutorials/MultiGrid_C/HypreABecLap/Make.package Src/Boundary/AMReX_BndryData.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_3D.F Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/Make.package commit cadef8b78c5fc6d64a15dd27b380485c40c074c0 Merge: 42d37cbe7 df82fc28d Author: Weiqun Zhang Date: Wed Mar 27 15:03:00 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 89d746a1f86fa59bae1381b2344f72f6b12b33e6 Author: Michele Rosso Date: Wed Mar 27 14:52:50 2019 -0700 CMake: use configuration header to propagate definitions to application codes. * Generate and install AMReX_Config.H * Make defines (except Fortran ones) just a build requirement, i.e. not an install requirement * Modify installed headers to include AMReX_Config.H * Group install code into a single CMake modulex Src/CMakeLists.txt Tools/CMake/AMReXInstallHelpers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/modify_installed_headers.cmake commit df82fc28dc0eff40fab7704ecebfb3ffdeee249f Merge: ebb265836 7cf248727 Author: Ann Almgren Date: Wed Mar 27 14:10:48 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 42d37cbe7174822acd31df1c3c86f977f5bd0536 Author: Weiqun Zhang Date: Wed Mar 27 14:01:41 2019 -0700 gpu: more on EB IF classes Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Ellipsoid.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Plane.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/AMReX_EB2_IF_Sphere.H Src/EB/AMReX_EB2_IF_Torus.H Src/EB/AMReX_EB2_IF_Translation.H commit ebb265836d03830a3757b37242da626a1361aed7 Author: Ann Almgren Date: Wed Mar 27 13:59:44 2019 -0700 dudn --> dphidn for consistency Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 8deeb0dd28f34586080d8aabc42673a8e509d428 Author: kngott Date: Wed Mar 27 13:24:12 2019 -0700 Comments to make reading graph method a little easier. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit e4a06c6c8c848734b67a81a9faafc607b5d66ed0 Author: kngott Date: Wed Mar 27 13:23:37 2019 -0700 Label commented out section. Tests/GPU/CudaGraphs/GraphCopy/main.cpp commit a98f2bde98f8b230fe06359e2ec98ba238dfb00e Author: kngott Date: Wed Mar 27 13:04:13 2019 -0700 Add initial run to get clean timings and adjust timer names. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit d4c82ace86a0a4d5e26746a541921fb97d8b29f0 Author: kngott Date: Wed Mar 27 12:49:13 2019 -0700 Implement the work as a function at the top to easily test Graphs on different MFIter loops. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 7cf2487273e7bf913890f0f05d83e9736837b46a Author: Weiqun Zhang Date: Wed Mar 27 12:07:07 2019 -0700 gpu: eb DifferenceIF Src/EB/AMReX_EB2_IF_Difference.H commit ea982aa99665401acf2d7ca1ebd77b59c8232438 Author: kngott Date: Wed Mar 27 11:42:02 2019 -0700 Adjust graph timers. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 51d30cea1b52879a9f0aaf7e247f8148dafb8a18 Author: Weiqun Zhang Date: Wed Mar 27 11:11:10 2019 -0700 use defaulted ctors Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Cylinder.H commit 62fc189220df15b09b2f2ee3104779f034ef1b15 Merge: e9aff909f b8a5f16c3 Author: Balos, Cody Joe Date: Wed Mar 27 11:03:51 2019 -0700 Merge branch 'development' of https://github.com/amrex-codes/amrex into development commit e9aff909fa4d1083fe7819fb02ab6f7e9d2f1310 Author: Balos, Cody Joe Date: Wed Mar 27 11:00:56 2019 -0700 add SUNDIALS 4 support cmake: support sundials 4 instead of 3 gnumake: support sundials 3 by default or optionally sundials 4 Src/CMakeLists.txt Src/Extern/SUNDIALS4/CMakeLists.txt Src/Extern/SUNDIALS4/Make.package Src/Extern/SUNDIALS4/arkode_interface.f90 Src/Extern/SUNDIALS4/cvode_interface.f90 Src/Extern/SUNDIALS4/farkode_arkstep_mod.f90 Src/Extern/SUNDIALS4/farkode_butcher_mod.f90 Src/Extern/SUNDIALS4/farkode_mod.f90 Src/Extern/SUNDIALS4/fcvode_mod.f90 Src/Extern/SUNDIALS4/fnvector_mod.f90 Src/Extern/SUNDIALS4/fnvector_serial_mod.f90 Src/Extern/SUNDIALS4/fsundials_types_mod.f90 Src/Extern/SUNDIALS4/fsunlinsol_dense.f90 Src/Extern/SUNDIALS4/fsunlinsol_dense_mod.f90 Src/Extern/SUNDIALS4/fsunlinsol_mod.f90 Src/Extern/SUNDIALS4/fsunmatrix_dense_mod.f90 Src/Extern/SUNDIALS4/fsunmatrix_mod.f90 Src/Extern/SUNDIALS4/fsunnonlinsol_mod.f90 Tools/CMake/AMReX_Options.cmake Tools/CMake/FindSUNDIALS.cmake Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.sundials4 Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/GNUmakefile Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/Make.package Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/ark_analytic_f2003.f90 commit 361db6fb5599545fe20376cb68cd8dc45c6e4551 Author: Weiqun Zhang Date: Wed Mar 27 10:13:48 2019 -0700 gpu: eb cylinder Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Cylinder.H commit a725036afba002e616d08dc62bbef8a8c1ef21da Author: Weiqun Zhang Date: Wed Mar 27 09:14:16 2019 -0700 include EB2_IF_Base.H in all IF headers Src/EB/AMReX_EB2_IF_Cylinder.H Src/EB/AMReX_EB2_IF_Difference.H Src/EB/AMReX_EB2_IF_Ellipsoid.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Plane.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/AMReX_EB2_IF_Spline.H Src/EB/AMReX_EB2_IF_Torus.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H commit b8a5f16c381c5c5405645b2d4e68600dc59eb770 Author: Weiqun Zhang Date: Tue Mar 26 23:55:27 2019 -0400 option to disable device sync in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 2709cc3af73a5a32a61265abaf4d5c009b7e37fb Author: Weiqun Zhang Date: Tue Mar 26 22:38:29 2019 -0400 add prefetch to AmrLevel::writePlotFile Src/Amr/AMReX_AmrLevel.cpp commit ac514073416d3925c423f7dc108bd6eec5b7e9fd Author: Weiqun Zhang Date: Tue Mar 26 18:44:50 2019 -0700 add free functions prefetchToHost and prefetchToDevice for FabArray Src/Base/AMReX_FabArrayUtility.H Tutorials/GPU/EBCNS/Source/CNS_io.cpp commit e4029c47ba262588c45602efd38aebe258ddba24 Author: Weiqun Zhang Date: Tue Mar 26 17:05:32 2019 -0700 fix enable_if Src/Base/AMReX_FabArray.H commit bd68aaea0f048a272efbf04f5fba556930d7d39d Merge: f55bfadfd d4bdf49c9 Author: Weiqun Zhang Date: Tue Mar 26 16:51:39 2019 -0700 Merge branch 'weiqun/gpu' into development commit 19478a3e1954d6574503ab03e6200300cda7bbd1 Author: Michele Rosso Date: Tue Mar 26 16:28:58 2019 -0700 Replace #if with #ifdef as per Andrew's suggestion Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_ParallelDescriptor.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleContainerI.H commit d4bdf49c9fa8404deb3c7175531d1f084352d57e Author: Weiqun Zhang Date: Tue Mar 26 16:27:37 2019 -0700 add README Tutorials/GPU/EBCNS/README commit 1cf9824aefe9d4491f449fb9361802af2667e5df Merge: 959071461 a54ba21f1 Author: Weiqun Zhang Date: Tue Mar 26 16:24:58 2019 -0700 Merge branch 'development' into weiqun/gpu commit 9590714612d3d2db028b9ebcbd83ea91983e8e96 Author: Weiqun Zhang Date: Tue Mar 26 14:58:23 2019 -0700 fix enable_if and start gpu version of GeometryShop Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Sphere.H commit f55bfadfdcaab2feb1ee3f81903c060a2ee8d693 Author: Ann Almgren Date: Tue Mar 26 13:38:12 2019 -0700 Need to make the compute_dphidn* routines public Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 2f2ad19cd717ff3befffadd77173718652c58c67 Author: Ann Almgren Date: Tue Mar 26 13:25:50 2019 -0700 Make compute_dphidn hold the lower order stencil and create compute_dphidn_ho to hold the higher-order stencil. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 9458a099ea91fd85b829549646ca7d903a0879a2 Author: Weiqun Zhang Date: Tue Mar 26 12:52:07 2019 -0700 gpu: BoxIF and ComplementIF Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_AllRegular.H Src/EB/AMReX_EB2_IF_Base.H Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Complement.H commit a561d6b2b9cf7f5332ea87f731e5b16566dcd5cc Author: Weiqun Zhang Date: Tue Mar 26 11:49:32 2019 -0700 gpu: copyMultiFabToMultiCutFab Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 4e3e2e34dc1ed334ec174bed40255fee082391a9 Merge: a54ba21f1 96692c116 Author: WeiqunZhang Date: Tue Mar 26 09:18:15 2019 -0700 Merge pull request #435 from jared321/flash_tileID local tile index commit 96692c1161316a670b62039d4422d8e7d9dfc392 Author: Jared O'Neal Date: Tue Mar 26 09:12:00 2019 -0500 Add local tile index to the MFIter's Fortran interface. Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 8e70f01672779af7b0285460f3b3cd9358a3d2f0 Author: Weiqun Zhang Date: Mon Mar 25 16:55:53 2019 -0700 noexcept and inline Src/Base/AMReX_Array.H Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 57d473196e12c1db8d272032938bc6d7740152d6 Author: Weiqun Zhang Date: Mon Mar 25 16:35:28 2019 -0700 remove BoxLib MG and add noexcept Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/EB/AMReX_EB2_Level.H commit af267f6bd7fc79a9a0f86428129e1d177c25df41 Author: Michele Rosso Date: Mon Mar 25 19:16:17 2019 -0400 CMake: change how we set PUBLIC_HEADER and CUDA properties on sources Src/CMakeLists.txt commit c94794ad7f60a814c7d33fc96552cebc35e08752 Merge: 870584201 a54ba21f1 Author: Michele Rosso Date: Mon Mar 25 17:30:19 2019 -0400 Merge branch 'development' into mr/cmake commit 928950d460c7645f6341520c00b811d03e36bc18 Author: Weiqun Zhang Date: Mon Mar 25 13:18:45 2019 -0700 add struct XDim3 Src/Base/AMReX_Array.H commit af6cff52f1e68ed882b20270eaf56d98211048fc Author: Weiqun Zhang Date: Mon Mar 25 13:03:44 2019 -0700 add struct GPUable that can be used as base for EB2's IF classes Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Base.H Src/EB/AMReX_EB2_IF_Sphere.H Src/EB/CMakeLists.txt Src/EB/Make.package commit 35fdae2491647bfe60bb0866919f4059869f19a4 Author: Weiqun Zhang Date: Mon Mar 25 12:40:09 2019 -0700 update plotfile Tutorials/GPU/EBCNS/Exec/Sod/inputs Tutorials/GPU/EBCNS/Source/CNS.H Tutorials/GPU/EBCNS/Source/CNS.cpp Tutorials/GPU/EBCNS/Source/CNS_io.cpp commit c9fe9cdb78a72f593d0e84807a1e78c708709d49 Author: Weiqun Zhang Date: Mon Mar 25 12:15:45 2019 -0700 fix makefile and add noexcept Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Tutorials/GPU/EBCNS/Exec/Make.CNS commit a54ba21f1ae020319b2a051ad0789009aad27089 Author: Weiqun Zhang Date: Mon Mar 25 09:15:27 2019 -0700 particle_compare: fix return type Tools/Postprocessing/C_Src/particle_compare.cpp commit faf5f9584bc2ab308bcec118e7321e316f2d2e01 Author: Max Katz Date: Sun Mar 24 20:09:22 2019 -0700 Print out message that we are initializing CUDA This can take a long time on the P9 platform, so this message is there to reassure the user that in fact something is happening, not a hang. Src/Base/AMReX_CudaDevice.cpp commit efd1db0afadb1144f3dbdbd3cb70a5fa99e44b52 Author: Max Katz Date: Sun Mar 24 07:10:23 2019 -0700 Fix typo Src/Amr/AMReX_AmrLevel.cpp commit cc6298afce527bda9d6a72db5dfa6a8bc3937758 Merge: 853e767be 0ca7e9a99 Author: WeiqunZhang Date: Sat Mar 23 16:25:42 2019 -0700 Merge pull request #434 from AMReX-Codes/convergence some clean ups to the Richardson convergence tool commit 0ca7e9a996281c308464688a567beeeb343ae690 Author: Michael Zingale Date: Sat Mar 23 13:53:19 2019 -0700 make the error files optional implement the verbose option Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit 853e767bea88841bb4ad67f710bf6d773c49c798 Merge: 72f994fa1 a27619f64 Author: WeiqunZhang Date: Sat Mar 23 13:30:35 2019 -0700 Merge pull request #433 from cgilet/development Make public interpolate_to_face_centroid() and interpolate_to_face_ce… commit a27619f64d822ce7588bbcd7c8988c72aec4fe7b Author: cgilet Date: Sat Mar 23 15:51:24 2019 -0400 Make public interpolate_to_face_centroid() and interpolate_to_face_centroid_per_cell() Src/EB/AMReX_EBMultiFabUtil_2d.F90 commit 72f994fa1297e46c0c37e4cbdd3b2ce3c938cf8e Author: Max Katz Date: Sat Mar 23 14:21:15 2019 -0400 character variables should not be allocatable/managed Tools/F_scripts/write_probin.py commit 21e2c8c9338def6f5106f0482161111e2fc1ea43 Author: Max Katz Date: Sat Mar 23 14:01:27 2019 -0400 Only CUDA header script copies files Tools/GNUMake/Make.rules commit 8a597e9126774113b81e9f8db1a27f3c5c87cfae Author: Max Katz Date: Sat Mar 23 13:12:09 2019 -0400 Add some parallelism to the GPU header script Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit a11edc5cf92ea7c4f3c9fd1c88c39e7f35f7ba2d Author: Ann Almgren Date: Sat Mar 23 08:32:11 2019 -0700 Oops -- entered Friesen's ORCID wrong paper/paper.md commit 58b3be3c616c303ccc80c8a6313bc14fcf1e1088 Author: Ann Almgren Date: Sat Mar 23 08:32:11 2019 -0700 Oops -- entered Friesen's ORCID wrong paper/paper.md commit 839d4063e94afc48262bf76e3685c27e10a3a233 Merge: d81b324e4 802a8b6d9 Author: Weiqun Zhang Date: Fri Mar 22 21:48:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d81b324e423a92d193d350fbea0303525e17e10f Author: Weiqun Zhang Date: Fri Mar 22 21:41:17 2019 -0700 add cuda memory prefetch function Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit a9a376131173b744b3f98101190ea51bd702552e Author: Ann Almgren Date: Fri Mar 22 16:51:15 2019 -0700 Fix some capitalization paper/paper.md commit 802a8b6d9014c22c8af03e76e138b7aabb9a1338 Author: Ann Almgren Date: Fri Mar 22 16:51:15 2019 -0700 Fix some capitalization paper/paper.md commit dcb313a925a622ab46f7a39d00eb5a617ac32728 Author: Ann Almgren Date: Fri Mar 22 16:47:15 2019 -0700 Moved JOSS stuff from Docs/JOSS to paper folder so reviewers can find it. paper/Makefile paper/paper.bib paper/paper.md commit 46b637c8e6934b50c678c1713d34064d74ac1867 Author: Ann Almgren Date: Fri Mar 22 16:47:15 2019 -0700 Moved JOSS stuff from Docs/JOSS to paper folder so reviewers can find it. paper/Makefile paper/paper.bib paper/paper.md commit 85ea2c5201980f8d247a6864d625d61761ea733b Merge: a083776bd 048ec2bdf Author: Weiqun Zhang Date: Fri Mar 22 15:47:49 2019 -0700 Merge branch 'weiqun/data_allocator' into development commit a083776bd0cce44ff7fc76f9145ec97986efd688 Merge: 33070a65f a85a15d47 Author: Weiqun Zhang Date: Fri Mar 22 18:40:58 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 33070a65f5ac4bd563a0377a52465c8c04a5535a Author: Weiqun Zhang Date: Fri Mar 22 18:40:19 2019 -0400 set CFLAGS_FROM_HOST to CXXFLAGS_FROM_HOST because nvcc -x cu compiles as C++ Tools/GNUMake/comps/nvcc.mak commit b321c408981ceb8dc832000a869c59f464ee53e8 Author: kngott Date: Fri Mar 22 15:05:17 2019 -0700 Add Graphs to 1 MPI section of FillBoundary. Src/Base/AMReX_FabArrayCommI.H commit 630d8a4bbb35e7385939596b0d4419314743e2ff Author: kngott Date: Fri Mar 22 15:04:27 2019 -0700 Add LaunchRegion and GraphRegion checks to Device::Graph calls. Src/Base/AMReX_CudaDevice.cpp commit f2965ca3e300d0942c519c716fa0879f6cb01e35 Author: kngott Date: Fri Mar 22 15:03:23 2019 -0700 Add static GraphRegion values for Graph Testing. Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp commit 048ec2bdfdf44c93435c99c49e56d05ae806bd3c Author: Weiqun Zhang Date: Fri Mar 22 14:49:09 2019 -0700 add The_Cpu_Arena and CpuDataAllocator. use CpuDataAllocator in parallelcopy meta-data processing Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayBase.cpp commit 158f2d9924bc0e9ec62c9a0786dcdcc036567f4b Author: kngott Date: Fri Mar 22 12:24:57 2019 -0700 Rewrite with Device's graphs functions for testing. Tests/GPU/CudaGraphs/GraphCopy/main.cpp commit 551014a60b2855c44e6836e8454389790e25585d Author: kngott Date: Fri Mar 22 12:24:35 2019 -0700 Change GNUmakefile-s to work with reorganization. Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile Tests/GPU/CudaGraphs/GraphCopy/GNUmakefile commit 15f59366dd13efae3137be07ca5dbc83e85ac147 Author: kngott Date: Fri Mar 22 12:23:25 2019 -0700 Add first draft Graph functions to Device. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile Tests/GPU/CudaGraphs/BuildingGraphs/Make.package Tests/GPU/CudaGraphs/BuildingGraphs/inputs_3d Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp Tests/GPU/CudaGraphs/BuildingGraphs/run.corigpu Tests/GPU/CudaGraphs/CrazyGraphs/GNUmakefile Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp Tests/GPU/CudaGraphs/CrazyGraphs/run.corigpu Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile Tests/GPU/CudaGraphs/GraphBoundary/Make.package Tests/GPU/CudaGraphs/GraphBoundary/Prob.H Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d Tests/GPU/CudaGraphs/GraphBoundary/main.cpp Tests/GPU/CudaGraphs/GraphBoundary/profile.sh Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu Tests/GPU/CudaGraphs/GraphBoundary/run.summit Tests/GPU/CudaGraphs/GraphCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphCopy/Make.package Tests/GPU/CudaGraphs/GraphCopy/inputs_3d Tests/GPU/CudaGraphs/GraphCopy/main.cpp Tests/GPU/CudaGraphs/GraphCopy/run.corigpu commit cabe5ab5e270ceb73a5c765a4076264833fe8918 Author: Weiqun Zhang Date: Fri Mar 22 11:10:07 2019 -0700 add a default template paramter Allocator to BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_TypeTraits.H commit a85a15d470d9c24d38bd834835ed658f7403ae04 Merge: 7605b944c b70cbd660 Author: Ann Almgren Date: Fri Mar 22 10:49:49 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 7605b944c49c1e81eafb3969926d5c72c321990c Author: Ann Almgren Date: Fri Mar 22 10:47:40 2019 -0700 1) Fixed bug in 3d version of amrex_eb_interpolate_to_face_centroid 2) Made 2d versions of amrex_eb_interpolate_to_face_centroid and amrex_eb_interpolate_to_face_centroid_per_cell Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit b70cbd6604f728e23edbf23d11a1034096714ee1 Merge: 3e7a68efa 10babf037 Author: Andrew Myers Date: Fri Mar 22 10:16:45 2019 -0700 Merge pull request #432 from RevathiJambunathan/random_xorwow_RJ Random xorwow -- modified seed with mpi rank commit 3e7a68efa149a5b123870ac0dc6404d47703e5ea Author: Weiqun Zhang Date: Fri Mar 22 10:12:18 2019 -0700 always use -Werror=return-type for gcc Tools/GNUMake/comps/gnu.mak commit 95138e359a5e814288db4e280b30fcc1b100e114 Author: Weiqun Zhang Date: Fri Mar 22 10:01:50 2019 -0700 comment out some profilers Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_VisMF.cpp Src/Particle/AMReX_ParticleContainerI.H commit 5a0965ee69655a62a49a1fac2f22f6e1e2beaf53 Author: Ann Almgren Date: Fri Mar 22 08:06:54 2019 -0700 Add a per-cell interpolate to face centroid routine (taken from mfix). Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit 0ec21fe72223ff03fba442954127d9f8e66fb091 Author: Ann Almgren Date: Thu Mar 21 19:50:19 2019 -0700 Re-word the fork-join sentence Docs/JOSS/paper.md commit af730c3722899e6ff6d8450726daf33f64265ebd Author: Ann Almgren Date: Thu Mar 21 19:43:10 2019 -0700 Fix more typos and remove "(AMR)" from the title. Docs/JOSS/paper.md commit 426ccaf054d7502598efacf17a5cf4d3af8f1f9c Author: Max Katz Date: Thu Mar 21 21:39:43 2019 -0400 Typos Docs/JOSS/paper.md commit d75df993d61d44d98b8d48e6218b292964638945 Author: Max Katz Date: Thu Mar 21 21:37:36 2019 -0400 Change my name Docs/JOSS/paper.md commit fab6d852f9c3a733f5f372fdd1881caf83854188 Merge: d2b8fecc8 bec83ac55 Author: Ann Almgren Date: Thu Mar 21 18:02:59 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit d2b8fecc801704990562ebf32692cfdf0e7d7c64 Author: Ann Almgren Date: Thu Mar 21 18:02:45 2019 -0700 Oops -- forgot John on the author list Docs/JOSS/paper.md commit bec83ac553d60c84a62d0d5820c7dff044c03852 Author: Donald E. Willcox Date: Thu Mar 21 18:02:10 2019 -0700 Fix reference to Zingale et al 2018 Docs/JOSS/paper.md commit 85c91c35d6531d1bb59e26b473babd2021a65262 Author: Ann Almgren Date: Thu Mar 21 17:51:21 2019 -0700 updated references Docs/JOSS/paper.bib commit 20101dd54c2e819af558a128fcbaf6aeddb56dcc Author: Ann Almgren Date: Thu Mar 21 17:45:01 2019 -0700 updated with references Docs/JOSS/paper.md commit d63824cda7535ffc054fd945e36f53878ab0893c Author: Ann Almgren Date: Thu Mar 21 17:22:42 2019 -0700 re-order sections Docs/JOSS/paper.md commit 36b6ede4e0112f010cee71028c0a41c397014f8b Author: Ann Almgren Date: Thu Mar 21 17:21:49 2019 -0700 Modify subsection headings Docs/JOSS/paper.md commit 29871f6440c0902f15b0df9fa0a06b91b75ffc11 Merge: e24e31f40 107452f06 Author: Ann Almgren Date: Thu Mar 21 17:21:09 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit e24e31f40ef5a7723a1716804a7709b56b93bf7d Author: Ann Almgren Date: Thu Mar 21 17:20:58 2019 -0700 This is getting closer... Docs/JOSS/paper.md commit 10babf0375a16d6873c25b0617de66fd68464c9d Author: RevathiJambunathan Date: Thu Mar 21 13:43:29 2019 -0700 cleaned rand, instead of using loc_rand Src/Base/AMReX_Utility.cpp commit 410105913d6ce6fcbb01b3468715b87926b9862c Merge: 595dda107 107452f06 Author: RevathiJambunathan Date: Thu Mar 21 13:31:38 2019 -0700 fixed the conflict with 1D threadId and the newly added 3D threadId in Utility.cpp after merging with development commit 595dda107b1b79dd649e46b603442043b67ce002 Author: RevathiJambunathan Date: Thu Mar 21 13:10:37 2019 -0700 Modified main.cpp in the test file to check for resize and ensuring that the seed generation is working properly for the grown vector Tests/GPU/RandomNumberGeneration/main.cpp commit ce016ccedf633bb194afe833a1b0fd314ef74aca Author: RevathiJambunathan Date: Thu Mar 21 13:09:38 2019 -0700 Modified seed generation to depend on MyProc or mpi_rank, so that each GPU does not have the same seed. And within a GPU, given the same seed, the startsequence of random number generation is threadID dependent. Also, generalized the threadId calculation for 3D block Grid and 3D thread block. Finally, when resize is called, the seed generation is performed only for the newly added vector elements. Note that CheckSeedArraySizeAndResize() should be called to Resize() Src/Base/AMReX_Utility.cpp commit 4862ce28b310704faf8ea58652d42ddd18d568ac Author: kngott Date: Thu Mar 21 12:57:18 2019 -0700 Add FillBoundary Test to repo. Tests/GPU/GraphBoundary/Prob.H Tests/GPU/GraphBoundary/inputs_3d Tests/GPU/GraphBoundary/main.cpp Tests/GPU/GraphBoundary/profile.sh Tests/GPU/GraphBoundary/run.corigpu Tests/GPU/GraphBoundary/run.summit Tests/GPU/GraphCopy/GNUmakefile Tests/GPU/GraphCopy/Make.package Tests/GPU/GraphCopy/inputs_3d Tests/GPU/GraphCopy/main.cpp Tests/GPU/GraphCopy/run.corigpu commit 59f1e467bf859f4cb11d4ea9e3b9702b9e0bd7e6 Author: kngott Date: Thu Mar 21 12:41:59 2019 -0700 Check changing memory layout on CudaGraphs. Tests/GPU/GraphBoundary/main.cpp commit ff086e99b32bb1e81c6c0b2ac6cea42671c779bc Author: kngott Date: Thu Mar 21 00:11:20 2019 -0700 Light cleanup. Tests/GPU/GraphBoundary/main.cpp commit d0ee253ed96ac059b73c70b5970f9845d4b9fdab Author: kngott Date: Wed Mar 20 23:17:10 2019 -0700 Test copy with cudaGraph. Tests/GPU/GraphBoundary/main.cpp commit 107452f062fa134cbf0f3888965122df8a6383bb Author: Weiqun Zhang Date: Wed Mar 20 21:00:45 2019 -0700 fix host version of Random Src/Base/AMReX_Utility.cpp commit 31bea5122c426738500bfb4836f6962ac941500a Author: Weiqun Zhang Date: Wed Mar 20 20:53:03 2019 -0700 add ifdef to cuda function call Src/Base/AMReX_Arena.cpp commit 57a0d8a286ff61491e8236f83f6c74c547817950 Author: Weiqun Zhang Date: Wed Mar 20 16:12:14 2019 -0700 add init eb function Tutorials/GPU/EBCNS/Exec/Sod/GNUmakefile Tutorials/GPU/EBCNS/Exec/Sod/inputs Tutorials/GPU/EBCNS/Source/CNS_init_eb2.cpp Tutorials/GPU/EBCNS/Source/Make.package Tutorials/GPU/EBCNS/Source/main.cpp commit 341f2ea1c40057cbc9f71fad77d5272fcd361108 Author: kngott Date: Wed Mar 20 17:43:33 2019 -0700 Cuda graph testing on lambda-less form of FillBoundary calls. Tests/GPU/GraphBoundary/GNUmakefile Tests/GPU/GraphBoundary/Make.package Tests/GPU/GraphBoundary/inputs_3d Tests/GPU/GraphBoundary/main.cpp Tests/GPU/GraphBoundary/run.corigpu commit 4f0d598ec9206de6f6ccfd17ddcfb3d8023ae779 Merge: 3f0f8c36e 96b97ad5a Author: Andrew Myers Date: Wed Mar 20 15:48:37 2019 -0700 Merge pull request #428 from RevathiJambunathan/random_xorwow_RJ Random number generator on GPU using CUDA - RJ commit 3f0f8c36ed20339e4fa09bc86506035e5499a81c Merge: 6f7684bb5 22ddd1824 Author: WeiqunZhang Date: Wed Mar 20 15:45:04 2019 -0700 Merge pull request #431 from dpgrote/development Added plot_log_per commit 23c94f2414b3b9331d72bccab4af58595132b4f8 Merge: fbf97ef04 96b97ad5a Author: RevathiJambunathan Date: Wed Mar 20 15:41:27 2019 -0700 Merge branch 'random_xorwow_RJ' of https://github.com/RevathiJambunathan/amrex into random_xorwow_RJ commit fbf97ef049a77babb69731dfe51bf9f1a30adf99 Author: RevathiJambunathan Date: Wed Mar 20 15:40:44 2019 -0700 deleting main.H and instead added dependencies in main.cpp file of the in Tests/GPU/RandomNumberGeneration/ Tests/GPU/RandomNumberGeneration/main.H commit e28526881178b87e5078131421040a212f5294fd Author: Weiqun Zhang Date: Wed Mar 20 15:38:38 2019 -0700 start GPU/EBCNS Tutorials/GPU/EBCNS/Exec/Make.CNS Tutorials/GPU/EBCNS/Exec/Sod/GNUmakefile Tutorials/GPU/EBCNS/Exec/Sod/Make.package Tutorials/GPU/EBCNS/Exec/Sod/cns_prob.H Tutorials/GPU/EBCNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/EBCNS/Exec/Sod/cns_prob_parm.H Tutorials/GPU/EBCNS/Exec/Sod/inputs Tutorials/GPU/EBCNS/Source/CNS.H Tutorials/GPU/EBCNS/Source/CNS.cpp Tutorials/GPU/EBCNS/Source/CNSBld.cpp Tutorials/GPU/EBCNS/Source/CNS_K.H Tutorials/GPU/EBCNS/Source/CNS_advance.cpp Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp Tutorials/GPU/EBCNS/Source/CNS_derive.H Tutorials/GPU/EBCNS/Source/CNS_derive.cpp Tutorials/GPU/EBCNS/Source/CNS_index_macros.H Tutorials/GPU/EBCNS/Source/CNS_io.cpp Tutorials/GPU/EBCNS/Source/CNS_parm.H Tutorials/GPU/EBCNS/Source/CNS_parm.cpp Tutorials/GPU/EBCNS/Source/CNS_setup.cpp Tutorials/GPU/EBCNS/Source/CNS_tagging.H Tutorials/GPU/EBCNS/Source/Make.package Tutorials/GPU/EBCNS/Source/diffusion/Make.package Tutorials/GPU/EBCNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/EBCNS/Source/hydro/Make.package Tutorials/GPU/EBCNS/Source/main.cpp commit 96b97ad5a12cc97d2a4e0583113da84d90f943a9 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 15:38:25 2019 -0700 Delete main.H Tests/GPU/RandomNumberGeneration/main.H commit 22ddd18248b6223be76a2e1bd78584ee58ac8246 Author: Dave Grote Date: Tue Mar 19 10:46:18 2019 -0700 Added plot_log_per Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp commit a74ea02410ef8655c0ed214cbdec40b931838b54 Author: RevathiJambunathan Date: Wed Mar 20 15:30:25 2019 -0700 removed main.H file that inluded AMReX header files and instead included them in the main.cpp file. Tests/GPU/RandomNumberGeneration/main.cpp commit 4476763ec0231dbb1da256b62058e18b96c6bd25 Author: RevathiJambunathan Date: Wed Mar 20 15:18:37 2019 -0700 Tests/GPU/RandomNumberGeneration/main.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit 0445d6e9b533da0a9cda9f34bc86ece2fab0ba97 Author: RevathiJambunathan Date: Wed Mar 20 15:05:16 2019 -0700 I had initialized array size with Nbuffer=N*2, but initialized seed with N in for loop, instead of Nbuffer. I have fixed it with Nbuffer. Also note that this array size is to prevent frequent call for resize. the size of array could even be 3*N or 1.5*N. I have put 2*N thinking that should be enough. Either way, user can call CheckSeedArraySizeAndResize() with the required number of CUDA threads launched (N). This function will resize dynamically. Src/Base/AMReX_Utility.cpp commit 10b3fbe0529f77294888db06d885af2cbad4397e Author: RevathiJambunathan Date: Wed Mar 20 14:54:18 2019 -0700 adding the header file for testing random numbers Tests/GPU/RandomNumberGeneration/main.H commit 5b3c105478501110ea3ea6e12d713848191d8bbb Author: RevathiJambunathan Date: Wed Mar 20 14:50:37 2019 -0700 adding the modified test file which calls the Random() function implemented in AMReX_Utility.cpp using either GPU or CPU. Tests/GPU/RandomNumberGeneration/main.cpp commit a120937818ca60ea41cdb27c524daf13b14fb73c Author: RevathiJambunathan Date: Wed Mar 20 14:49:32 2019 -0700 removed #include since it is not used in AMReX_Vector.H and instead included in AMReX_CudaUtility.H. Src/Base/AMReX_Vector.H commit eba1aa01264c64092ec9c58fe0be42a87a9f3152 Author: RevathiJambunathan Date: Wed Mar 20 14:48:02 2019 -0700 cleaned up utility.cpp such that it does not rely on using namespace amrex, or using namespace Gpu, instead using amrex:: or amrex::Gpu:: . Also included *glo_RandStates in an anonymous namespace. Finally, int NrandMax is removed as it is the size of the random seed vector. Instead, I have called dev_RandStates_Seed.size() Src/Base/AMReX_Utility.cpp commit 41d894d0f18e48aee3f8d68cb0daf0b7db3b36d1 Author: RevathiJambunathan Date: Wed Mar 20 14:45:08 2019 -0700 included curand_kernel.h in this file, instead of in AMReX_Vector.H file Src/Base/AMReX_CudaUtility.H commit 6f7684bb504f1a50b6ffcc0b4fd2ea57af5b8a22 Merge: 21c13037f ef738f0d5 Author: WeiqunZhang Date: Wed Mar 20 13:46:08 2019 -0700 Merge pull request #430 from jrood-nrel/nrel_add_rhodes Adding some specific compiler flags for the Rhodes machine at NREL. commit b8f172155c56ab4cebab13eee39f82f284517142 Author: RevathiJambunathan Date: Wed Mar 20 12:59:44 2019 -0700 deleted code (Hash_DistributionMap) in AMReX_Utility.H based on git diff random_xorwow_RJ and development Src/Base/AMReX_Utility.H commit ef738f0d5c7169522894235e5a0e96182f5b5fc6 Author: Jon Rood Date: Wed Mar 20 13:53:57 2019 -0600 Adding some specific compiler flags for the Rhodes machine at NREL. Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nrel commit 8e9b090d29d7051c2c26c7703b073591365f2694 Merge: 75b8f523b 21c13037f Author: RevathiJambunathan Date: Wed Mar 20 12:17:50 2019 -0700 Merge branch 'development' into random_xorwow_RJ commit 75b8f523b569936a81b031723d3cd1d751e5e0cd Author: RevathiJambunathan Date: Wed Mar 20 11:43:52 2019 -0700 modified Utility.cpp to generalize it for runs that do not use the CUDA flag Src/Base/AMReX_Utility.cpp commit cecb2746f0b75e3858ae13ecfc63a995e4193ee1 Merge: edb2bcbe0 43f7771e0 Author: RevathiJambunathan Date: Wed Mar 20 10:55:43 2019 -0700 Merge branch 'random_xorwow_RJ' of https://github.com/RevathiJambunathan/amrex into random_xorwow_RJ commit edb2bcbe0325f595a5350916c04668e54b1f03f3 Author: RevathiJambunathan Date: Wed Mar 20 10:50:40 2019 -0700 modified Utility.cpp to generalize it for runs that do not use the CUDA flag Src/Base/AMReX_Utility.cpp commit 43f7771e0b48ee0c245b00bd223149118d277120 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:44 2019 -0700 Delete test1.out Tests/GPU/RandomNumberGeneration/test1.out.REMOVED.git-id commit 504d54e4f56d18a2f2f79fda427b55fe4539c137 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:35 2019 -0700 Delete profilingdata_rndm.dat Tests/GPU/RandomNumberGeneration/profilingdata_rndm.dat commit cf09fc5072a0d143cc02f8e9e1c678a6766275eb Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:27 2019 -0700 Delete profile_without_skipahead.dat Tests/GPU/RandomNumberGeneration/profile_without_skipahead.dat commit 2794d16610a1819d506589c3ae4c0741efb11631 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:20 2019 -0700 Delete profile_with_skipahead.dat Tests/GPU/RandomNumberGeneration/profile_with_skipahead.dat commit e816387e89ea6f821d8ca4ffd824eaabc00eaef7 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:04 2019 -0700 Delete Backtrace.0 Tests/GPU/RandomNumberGeneration/Backtrace.0 commit 21c13037fd23097c9b890bd4360ee3eabe1d299f Merge: 93707d252 81f80ea98 Author: Weiqun Zhang Date: Wed Mar 20 10:37:40 2019 -0700 Merge branch 'weiqun/bestfit' into development commit 93707d252e69572d0db671735a61416f8b936eb3 Author: Weiqun Zhang Date: Wed Mar 20 13:35:11 2019 -0400 allocate 3/4 of global memory up front in the arena. this can be changed with parmparse parameter amrex.the_arena_init_size Src/Base/AMReX_Arena.cpp commit 6dcce9f1ede35b372d8e121cc8653c460974e457 Merge: 46c5abb44 cb68ed4e4 Author: RevathiJambunathan Date: Tue Mar 19 18:29:10 2019 -0700 adding changes in Utility.H/.cpp after merging with the development branch commit 81f80ea98c81bd47f3791482c90f222302befbec Author: Weiqun Zhang Date: Tue Mar 19 16:41:06 2019 -0700 EArena: use lower bound Src/Base/AMReX_EArena.cpp commit 46c5abb447ee91c48e3c70608276299bb829ce90 Author: RevathiJambunathan Date: Tue Mar 19 16:36:47 2019 -0700 adding changes made in Utility.H/.cpp to include random number generator for device Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_Vector.H commit cb68ed4e415a5fcb4797e10240435a03da6d1ce9 Author: Andrew Myers Date: Tue Mar 19 18:33:06 2019 -0400 ReduceLongMax -> ReduceLongSum Src/Particle/AMReX_ParticleContainerI.H commit 04a8c7814433af86eb4643443cffb116b42d3060 Author: Weiqun Zhang Date: Tue Mar 19 15:08:33 2019 -0700 EArena: memory allocator using best fit strategy Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_EArena.H Src/Base/AMReX_EArena.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 53ce1e1af65ad3e045a915bf2c6dfdda3e2a5193 Author: Michael Zingale Date: Tue Mar 19 10:21:27 2019 -0400 fix makefile Docs/JOSS/Makefile commit 325015b565ab58e05ae8dbdfb30baf9396393291 Author: Ann Almgren Date: Mon Mar 18 19:49:16 2019 -0700 Fix the author ordering so it shows correctly on the web page Docs/JOSS/paper.md commit dee97eff1e5e544999082a583e3268f542771860 Author: Ann Almgren Date: Mon Mar 18 19:13:10 2019 -0700 Add mention of BoxLib and xSDK. Docs/JOSS/paper.md commit e2d01db45b618b762ad1713aa80f8b3eb616396d Author: Ann Almgren Date: Mon Mar 18 19:09:44 2019 -0700 A start of the JOSS paper and bibliography Docs/JOSS/Makefile Docs/JOSS/paper.bib Docs/JOSS/paper.md commit 6ef6e1da53385ea0736bebda210ec6e91dd067a9 Author: Ann Almgren Date: Mon Mar 18 18:52:47 2019 -0700 Remove "Overview" Docs/sphinx_documentation/source/ForkJoin.rst commit be72c86c9d31eb50862beba22702be73a7fae2e5 Author: Ann Almgren Date: Mon Mar 18 18:48:40 2019 -0700 "framework library" --> "framework" Docs/sphinx_documentation/source/index.rst commit 7435d470f9ed18c1a1091c732126a211bbc8080f Merge: 3ef58a9f9 95e37900a Author: Ann Almgren Date: Mon Mar 18 18:41:04 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 3ef58a9f9368432e60c3f04494b1cec2cbbb0042 Author: Ann Almgren Date: Mon Mar 18 18:40:45 2019 -0700 Add ForkJoin to the documentation (as well as the tutorials) Docs/sphinx_documentation/source/ForkJoin.rst Docs/sphinx_documentation/source/figs/fork_join_tasks.png Docs/sphinx_documentation/source/figs/nested_fork_join_tasks.png Docs/sphinx_documentation/source/index.rst commit 95e37900aa57d63c60ac6bcffca61159158b31eb Author: Andrew Myers Date: Mon Mar 18 21:31:21 2019 -0400 keep the temporary variables around to save on memory usage with the Arena Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit e55119ef04d0551033daf8b57cb6f12c2e8c5b5a Author: Andrew Myers Date: Mon Mar 18 21:30:40 2019 -0400 use the managed arena for thrust's interal calculations Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp commit 32e598ac155af8426b2d0d9b5aa4159944e4a11e Merge: 5e41305a3 e4ca314f3 Author: Ann Almgren Date: Mon Mar 18 14:52:11 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 5e41305a3e702c1ca29435aea841eae9e76d783e Author: Ann Almgren Date: Mon Mar 18 14:50:45 2019 -0700 Add disclaimer re Macs Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst commit 929a6e691fb45b49eb9352ae49179a5a1ee391d1 Author: Weiqun Zhang Date: Mon Mar 18 13:23:57 2019 -0700 attribute weak Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_PROB_AMR_F.H Src/Base/AMReX_Extension.H commit e4ca314f3ce884bd25965bd625db440500fe7643 Author: Weiqun Zhang Date: Mon Mar 18 13:22:51 2019 -0700 fix shadow warning Src/Base/AMReX_BCRec.H commit b89a8c35caa5016a19562ab4cf676178468355f1 Author: Kevin Gott Date: Mon Mar 18 16:11:59 2019 -0400 Edit Scratchpad to compile on Summit. Tests/GPU/ScratchPad/main.cpp commit a215812a690f95937b148b0e34d664da86d82f33 Merge: 801fb1c38 5a38f1f31 Author: Weiqun Zhang Date: Mon Mar 18 16:06:38 2019 -0400 Merge branch 'weiqun/noexcept' into development commit 5a38f1f3173e38f907ed07a0823914998228f3a8 Author: Weiqun Zhang Date: Mon Mar 18 16:06:13 2019 -0400 add noexcept to lambda functions Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_derive.cpp Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit 801fb1c38bbeba631a5c76d0b8d129a5aa7c43e3 Merge: 68de1e853 84179b022 Author: Weiqun Zhang Date: Mon Mar 18 12:27:19 2019 -0700 Merge branch 'weiqun/noexcept' of github.com:AMReX-Codes/amrex into weiqun/noexcept commit 84179b0229d994070fa3d8534c294fd2313c5612 Merge: 40c411f87 14d441659 Author: Weiqun Zhang Date: Mon Mar 18 15:25:48 2019 -0400 Merge branch 'development' into weiqun/noexcept commit 68de1e85353f9cf72b8d87c0bd2f340df6346365 Author: Weiqun Zhang Date: Mon Mar 18 12:24:46 2019 -0700 fix a warning Src/Amr/AMReX_StateDescriptor.H commit 14d4416594b17633fb58e871bb78ad8f30400828 Author: Weiqun Zhang Date: Mon Mar 18 14:20:31 2019 -0400 fix make for olcf. Seems that cuda module no longer sets CUDAPATH. Tools/GNUMake/sites/Make.olcf commit 40c411f87c8f0d4a0e65a978ed3a5eec7adcc8c0 Author: Weiqun Zhang Date: Mon Mar 18 10:40:07 2019 -0700 add noexcept to TinyProfiler Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 6580c18faf16a37479a0fa0e8438ba3bed124e34 Merge: b94c3bc32 94746c971 Author: Weiqun Zhang Date: Mon Mar 18 10:25:24 2019 -0700 Merge branch 'development' into weiqun/noexcept commit 977b9c3bb53c9114df960a5d3108d83c31523ceb Author: kngott Date: Mon Mar 18 10:15:30 2019 -0700 Comment adjustments. Tests/GPU/CrazyGraphs/main.cpp commit b94c3bc3241450261b6f2bd527cd4e2c3099fe53 Author: Weiqun Zhang Date: Mon Mar 18 10:15:09 2019 -0700 add noexcept to Amr/ Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp commit d11c4ddf4568c5b04048c9204bf3661ad34b575f Author: Weiqun Zhang Date: Fri Mar 15 17:00:19 2019 -0700 add noexcept to MLMG Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit 45f9e7a51afd154144b1799df89c115d50436f08 Author: kngott Date: Mon Mar 18 01:03:39 2019 -0700 Add lambda launch version. Still needs CUDA 10.1. Tests/GPU/CrazyGraphs/main.cpp commit cb86a8259b468df0b034155d6ca26aed4c3cb9a4 Author: kngott Date: Mon Mar 18 01:03:19 2019 -0700 Add --expt-extended-lambda flag. Tests/GPU/CrazyGraphs/GNUmakefile commit 95106907a52f675201c078663ad029486769264b Author: kngott Date: Sun Mar 17 21:04:15 2019 -0700 Crazy Graphs. Attempt to reuse graphs with different parameters without re-instantiating. Needs CUDA 10.1 to test. Tests/GPU/CrazyGraphs/GNUmakefile Tests/GPU/CrazyGraphs/main.cpp Tests/GPU/CrazyGraphs/run.corigpu commit 3d5505d948240cd4e6791469d6d92c0e4021a3e7 Author: kngott Date: Fri Mar 15 16:58:17 2019 -0700 Reuse a graph. Tests/GPU/CudaGraphs/main.cpp commit 1b4f38021623642c3d382f9c914d2a6c553b64be Author: Weiqun Zhang Date: Fri Mar 15 16:40:53 2019 -0700 add noexcept to Boundary/ Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_LOUtil_K.H Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H commit 2414d66288d7cd4aaa3db6f5e1f0361c4f263520 Author: kngott Date: Fri Mar 15 16:05:55 2019 -0700 Add linked graph over iterations. Tests/GPU/CudaGraphs/main.cpp commit 1570e0162306c01c3e83e9d547203d13ecc18ae7 Author: kngott Date: Fri Mar 15 15:30:11 2019 -0700 One linked MFIter graph & cleaned output. Tests/GPU/CudaGraphs/main.cpp commit c3412db7c753be603b54bfe7d1437944d1f61848 Author: Weiqun Zhang Date: Fri Mar 15 15:21:17 2019 -0700 more noexcepts. remove BroadcastDistributionMap and BroadcastBoxArray Src/Base/AMReX_IndexType.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Orientation.H Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_Vector.H commit 83bc3a01625d2a6a27f154829d7da11cce054bc2 Author: kngott Date: Fri Mar 15 14:17:00 2019 -0700 Individual timers. Tests/GPU/CudaGraphs/main.cpp commit 4b5a033fb6fe633ef9a117df7be5584857f16fe5 Author: RevathiJambunathan Date: Fri Mar 15 14:14:18 2019 -0700 adding test directory for random no. generator on gpus - XORWOW Tests/GPU/RandomNumberGeneration/Backtrace.0 Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/Make.package Tests/GPU/RandomNumberGeneration/main.cpp Tests/GPU/RandomNumberGeneration/profile_with_skipahead.dat Tests/GPU/RandomNumberGeneration/profile_without_skipahead.dat Tests/GPU/RandomNumberGeneration/profilingdata_rndm.dat Tests/GPU/RandomNumberGeneration/test1.out.REMOVED.git-id commit a7707320340595b9e7eb890b010dd889e96bd36a Author: Weiqun Zhang Date: Fri Mar 15 14:13:51 2019 -0700 more excepts and remove iMultiFab's own operator[] Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuError.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 4bf99a9726fc37cf749b2e524a58951890aed4b1 Author: kngott Date: Fri Mar 15 13:11:52 2019 -0700 Touch the memory first to get a fair timing. Tests/GPU/CudaGraphs/main.cpp commit 9de2e4d8587d99430c2b6660027daef46d09aef5 Author: Weiqun Zhang Date: Fri Mar 15 12:40:53 2019 -0700 more excepts Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaElixir.H Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_LayoutData.H commit b8e444b4bc6d379dbfb81552504fbc9b0571b2d3 Author: kngott Date: Thu Mar 14 22:22:45 2019 -0700 Fix the indenting. Tests/GPU/CudaGraphs/main.cpp commit 4d1fd459fec0d8194977835ac3dc01fb90ddd21e Author: kngott Date: Thu Mar 14 22:17:27 2019 -0700 Stream-based graph test. Tests/GPU/CudaGraphs/main.cpp commit eeb4a76cc9b1080848c03457279b41f8dcd316dd Author: kngott Date: Thu Mar 14 22:17:14 2019 -0700 Access maxCudaStreams for Stream based graph test. Src/Base/AMReX_CudaDevice.H commit 89049698ccc008a70c25097404261bc27c587e0b Author: kngott Date: Thu Mar 14 16:47:53 2019 -0700 First draft of CUDA graphs. Tests/GPU/CudaGraphs/GNUmakefile Tests/GPU/CudaGraphs/Make.package Tests/GPU/CudaGraphs/inputs_3d Tests/GPU/CudaGraphs/main.cpp Tests/GPU/CudaGraphs/run.corigpu commit 16e880b73b8a75f0145570365ebc4ab08e0046a1 Author: Weiqun Zhang Date: Thu Mar 14 16:40:29 2019 -0700 more noexcepts Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFabUtility.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxIterator.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_IntVect.H commit 94746c9710253fe7d674a590c22e4379daad22e5 Merge: 1b6af3cb6 83e39b436 Author: Michele Rosso Date: Thu Mar 14 15:18:43 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1b6af3cb63061a11df4b224cd08753f07adfb8ca Author: Michele Rosso Date: Thu Mar 14 15:18:32 2019 -0700 CMake: enable linking against amrex in shared lib mode. Fixes Issue #425 Tools/CMake/AMReX_Config.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit 83e39b43627ffa272a627bde1584e33dfb618ad2 Author: Kevin Gott Date: Thu Mar 14 17:37:36 2019 -0400 Convert relevant amrex::launch's to amrex::ParallelFor in Advection_AmrCore tutorial. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H commit 447f8ee955a84c1bf63b06bbd4b47e463ad04722 Author: Kevin Gott Date: Tue Mar 12 00:18:31 2019 -0400 Remove recursive header calls. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H commit 4022f1dd6b6cb6398e407a731a8df5608e196f97 Merge: 40068ae16 69a51e27d Author: Michele Rosso Date: Wed Mar 13 12:02:20 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 40068ae16af0e76bf90985773aef963341b78299 Author: Michele Rosso Date: Wed Mar 13 11:53:41 2019 -0700 CMake: add support for SUNDIALS3 CMakeLists.txt Docs/sphinx_documentation/source/BuildingAMReX.rst Src/CMakeLists.txt Src/Extern/SUNDIALS3/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Options.cmake Tools/CMake/FindSUNDIALS.cmake Tutorials/CMakeLists.txt Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/CMakeLists.txt Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_finterface/EX1/CMakeLists.txt Tutorials/CVODE/SUNDIALS3_finterface/EX1/main.cpp commit 69a51e27d9e281ca0e87246b1137d17107c09839 Merge: bd274459a d6464aaa5 Author: mic84 Date: Tue Mar 12 14:50:10 2019 -0700 Merge pull request #423 from Alpine-DAV/task/2019_03_ascent_and_conduit_cmake_support add amrex cmake support for including ascent and conduit commit d6464aaa59ff624a3870430af1f2d6b63272922e Author: Cyrus Harrison Date: Tue Mar 12 14:24:41 2019 -0700 add cmake support for including ascent Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupThirdpartyLibs.cmake commit bd274459ae6333b2f1f87997bf5097b4278c49b0 Author: Weiqun Zhang Date: Tue Mar 12 09:15:40 2019 -0700 add include guard so that AMReX_Config.H can be included in C/Fortran codes Tools/libamrex/mkconfig.py commit a2335da0dad9747792cafd21b58217de58721b1c Author: Kevin Gott Date: Mon Mar 11 19:28:12 2019 -0400 Change to simplified simple launch. Tests/GPU/Test/main.cpp Tests/GPU/TestB/main.cpp Tests/GPU/TestC/main.cpp commit 6dfbde769ba2fd83915e0ed9664a6346e425caa7 Author: Kevin Gott Date: Mon Mar 11 15:41:48 2019 -0700 Add >= note to C++ loop discussion. Docs/sphinx_documentation/source/Basics.rst commit 8fda8bab5655d1f86971758458e04cddce10e3d8 Author: Kevin Gott Date: Mon Mar 11 17:21:15 2019 -0400 Less than or equal to. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H commit b070fbd379f232b9604b3918d917e37f300b2305 Author: Max Katz Date: Sun Mar 10 15:49:08 2019 -0400 Make grid-stride loops better aware of numThreadsMin Src/Base/AMReX_CudaDevice.cpp commit aa10d38781573c9dc3a94ee07d8f2540a5fb4323 Author: Max Katz Date: Sun Mar 10 15:48:40 2019 -0400 Specialize rule for AMReX_filcc_mod.F90 when using CUDA Src/Base/Make.package Tools/GNUMake/Make.rules commit 99c3f5f63cc3f412409db1867fa7ed5999f21372 Author: Max Katz Date: Sun Mar 10 08:58:24 2019 -0400 Echo which path we're taking for CUDA fortran compilation Tools/GNUMake/Make.rules commit 99d24aa7ff7f4e7d1b0933aac8f55fca0c82c8db Author: Max Katz Date: Sun Mar 10 05:07:57 2019 -0400 Add hook for setting Device::numThreadsMin Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit 09c15a29f407f6de2fad4cf9347254f75b53bde9 Author: Max Katz Date: Sun Mar 10 03:31:49 2019 -0400 Get amrex_filccn going for the GPU pragma case Src/Base/AMReX_filcc_mod.F90 commit 0440482d855549e36d7da6c252a92b6a19f0b016 Author: Max Katz Date: Sun Mar 10 03:31:15 2019 -0400 Add a device sync in case the user code does bndryFill on the GPU Src/Amr/AMReX_StateData.cpp commit 25a48bb1fba2330169b5076f1cd1e4f5089c1f2b Author: Kevin Gott Date: Fri Mar 8 23:21:46 2019 -0500 Update Tests/GPU/Test: PinnedData idea. Tests/GPU/Test/main.cpp commit ea9243d4b032ac3d132134e40df0daa10ba0d095 Author: Kevin Gott Date: Fri Mar 8 23:17:24 2019 -0500 Update Tests/GPU/TestC: Turning DeviceRegion on and off. Tests/GPU/TestC/main.cpp commit bb7acfb97d35d3b7dd8252beb7fb7daf4e3be472 Author: Kevin Gott Date: Fri Mar 8 22:56:44 2019 -0500 Update GPU/Test/TestB: Fortran return bug. (It's still a bug.) Tests/GPU/TestB/main.cpp commit f955cfd6a121a5d0d7554a4a5498c18f2cb53dc6 Author: Kevin Gott Date: Wed Mar 6 19:28:10 2019 -0500 Macro based launches to function based launches. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit a86a9fdb4b6db15d203f80de262954fac6b6aeb0 Author: Kevin Gott Date: Wed Mar 6 19:27:49 2019 -0500 Add USE_CUDA=TRUE to GPU tutorial makefile. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile commit 38ff7c70874faa9a42d9b91413469de6ab28fc80 Merge: 65c7d13a2 af690cba3 Author: Andrew Myers Date: Fri Mar 8 16:31:32 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 65c7d13a23f5fd2cdc170a8b29fd818b7437d83b Author: Andrew Myers Date: Fri Mar 8 16:31:11 2019 -0800 need to include this header to compile with Cuda 10.1 Src/Base/AMReX_CudaAllocators.H commit 8705842011ed616bb09eeef6430e744099ea415f Author: Michele Rosso Date: Fri Mar 8 18:31:44 2019 -0500 CMake: link to cuda only if ENABLE_CUDA is on Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake commit af690cba3117d4f8533bd1ccd35cd919595eaf64 Author: Ann Almgren Date: Fri Mar 8 10:39:15 2019 -0800 1) Don't pass inhomogeneous flag into gsrb -- we are always in residual-correction form there 2) Make sure to use "integer, value, intent(in)" instead of just "integer, intent(in)" -- lesson learned! Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 1039cbe3dd6d42bd67a21cb1bea66f63d9b04d6a Merge: fe0074b9e 632be646d Author: WeiqunZhang Date: Fri Mar 8 08:40:36 2019 -0800 Merge pull request #421 from AMReX-Codes/regrid_only Add optional flag to RegridOnly for disabling I/O commit 632be646dfb1586519f54f4bd1b500f75b80b904 Author: Max Katz Date: Fri Mar 8 01:08:36 2019 -0500 Add optional flag to RegridOnly for disabling I/O RegridOnly is useful as a public interface to regridding for the user code to call. For cases where the user wants to call it during a simulation, rather than immediately after restart, the I/O options aren't meaningful, so this allows the user to disable that in their call to RegridOnly (while still potentially allowing it in other cases where plotfile_on_restart et al. are desired). Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp commit 0ca64d47e1aa478bae61340ffc8bf2af589fe9c5 Merge: 16d4d63a5 fe0074b9e Author: Cyrus Harrison Date: Thu Mar 7 21:36:26 2019 -0800 merge from development commit 16d4d63a594dd4fa0e25d3a94894c482d5a18290 Author: Cyrus Harrison Date: Thu Mar 7 21:30:00 2019 -0800 plumbing for cmake support for including ascent and conduit Src/CMakeLists.txt Src/Extern/Conduit/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupThirdpartyLibs.cmake commit d992c914148a7bd1dd4993088b4157a97cdb125a Author: Michele Rosso Date: Thu Mar 7 20:34:39 2019 -0500 CMake: look for MPI in config file if required Tools/CMake/AMReXConfig.cmake.in commit 83d0a8f965bfd0f3443b97cb5c2768ac572a42b5 Merge: 95e81ecae fe0074b9e Author: Michele Rosso Date: Thu Mar 7 18:56:04 2019 -0500 Merge branch 'development' into mr/cmake commit 95e81ecae130cb2e530c7ffb91694d7a7298416c Author: Michele Rosso Date: Thu Mar 7 18:55:13 2019 -0500 CMake: some clean-up CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_SetupCUDA.cmake Tools/CMake/comps/AMReX_Cray.cmake Tools/CMake/comps/AMReX_GNU.cmake Tools/CMake/comps/AMReX_Intel.cmake Tools/CMake/comps/AMReX_NVIDIA.cmake Tools/CMake/comps/AMReX_PGI.cmake Tutorials/GPU/NeighborList/CMakeLists.txt commit fe0074b9e556920d692eb8f3478e80701e5242be Author: Weiqun Zhang Date: Thu Mar 7 15:29:41 2019 -0800 add coarsen and refine to Geometry Src/Base/AMReX_Geometry.H commit c1a58d87db04a2a57530a9f5650dd2161bb4247a Merge: 0b21df905 8c6a2fe3d Author: Michele Rosso Date: Thu Mar 7 14:21:13 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0b21df9054bbabcfb7191633fe5bd7d9e640f767 Author: Michele Rosso Date: Thu Mar 7 14:20:51 2019 -0800 CMake: fix typo in configuration file. Tools/CMake/AMReXConfig.cmake.in commit 8c6a2fe3df4258a1ae7fe3fba5240df0033772bb Merge: caf8ada86 33f425ec3 Author: Andrew Myers Date: Thu Mar 7 13:23:16 2019 -0800 Merge pull request #420 from AMReX-Codes/marc/bad_rd_ptr_in_vismf Catch unhandled RealDescriptor logic in VisMf::Write commit caf8ada86e1c0884300b38fbbc792a1604ea98e2 Author: sireeveslbl Date: Thu Mar 7 13:03:50 2019 -0800 Cleaned up diffmultifab's output, and got rid of segfault after amrex finalize Tools/C_util/DiffMultiFab/diffmultifab.cpp commit 855694b1889b274bbd359ea3b34fa3884a96d9f4 Merge: e9cbad95c cf599f630 Author: Ann Almgren Date: Thu Mar 7 11:52:17 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit e9cbad95c70d7b2b7096b2faa45b386222a2af6c Author: Ann Almgren Date: Thu Mar 7 11:48:20 2019 -0800 Add support for higher order stencils at EB boundaries with Dirichlet bc's. This may be unstable so by default it is not used -- to use it you must call setEBHODirichlet() in addition to setEBDirichlet (or setEBHomogDirichlet). There should be no change to the default behavior of any AMReX-based code from this commit. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 commit cf599f6309553b42b03ea12239c44c9fb3baef84 Author: sireeveslbl Date: Thu Mar 7 11:48:16 2019 -0800 Fixed the fix with DiffMultfab, doesn't work with MPI at the moment. Tools/C_util/DiffMultiFab/diffmultifab.cpp commit 33f425ec3e065c8ccc7c9b3d03edb3428da37f41 Author: Marc Day Date: Thu Mar 7 11:15:34 2019 -0800 Catch unhandled RealDescriptor logic in VisMf::Write Src/Base/AMReX_VisMF.cpp commit f7dde771e77d5a97963712cb401b32ab30a3e9f4 Author: Michele Rosso Date: Thu Mar 7 10:40:57 2019 -0800 CMake: fix blitz dependency issue in configuration file. Fixes Issue #418 Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Options.cmake commit 2ef7ceae55b05ffae868bbd56c3d5d6ee9363165 Merge: a3736c4ad b9e4c1ed0 Author: WeiqunZhang Date: Thu Mar 7 09:34:53 2019 -0800 Merge pull request #419 from maikel/bugfix/EB_LSCore Use AMREX_D_DECL for the 2D case. commit b9e4c1ed002ee33446918344201bddea97c7b6dd Author: Maikel Nadolski Date: Thu Mar 7 15:00:18 2019 +0100 Use AMREX_D_DECL for the 2D case. Src/EB/AMReX_EB_LSCoreBase.cpp commit a3736c4ad16b43cc726470120e6515dcd7d93a20 Merge: f10afe756 f496320fa Author: Andrew Myers Date: Wed Mar 6 19:39:49 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f10afe7566a316587d0061b735b292d2e49bdf7f Author: Andrew Myers Date: Wed Mar 6 19:39:14 2019 -0500 do the same early exit in the neighbor particles as in redistribute Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit f496320fa29dd34105849a0bf012feac8c58f8a4 Merge: 0b3acd674 66b488a07 Author: Andrew Myers Date: Wed Mar 6 16:15:36 2019 -0800 Merge pull request #374 from Alpine-DAV/task/2018_11_add_blueprint_particle_support add conduit blueprint support for particles commit 0b3acd674ece90675fcf2dbfcbf220bb3e62fe74 Author: Andrew Myers Date: Wed Mar 6 19:05:59 2019 -0500 only include this file if using cuda Src/Particle/AMReX_NeighborParticles.H commit 641f47ca2edcf78657b0d81779c50f499f85a1be Merge: 4f0733662 b75901c20 Author: Andrew Myers Date: Wed Mar 6 18:49:39 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4f07336627bfa6d30ba0bb447091d7fc3f274a54 Author: Andrew Myers Date: Wed Mar 6 18:49:17 2019 -0500 remove fortran neighbor list Src/Particle/AMReX_Particle_mod_3d.F90 commit ba6f4f0180f6b4159e51e25cc9baacb4468ae3d1 Author: Andrew Myers Date: Wed Mar 6 18:22:18 2019 -0500 add missing files Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 3e0fd673186ee7cbd28279512942bf6ce4bb1562 Author: Andrew Myers Date: Wed Mar 6 18:21:50 2019 -0500 refactor neighbor list stuff so that it can be used in MFIX Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/CMakeLists.txt Src/Particle/Make.package Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/main.cpp commit b75901c2032d16d455b7a836827bbe13dfa0f7a8 Author: Kevin Gott Date: Wed Mar 6 17:35:20 2019 -0500 Fix bugs in Advection_AmrCore GPU tutorial. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H commit 7228e23acab84dabd5ca82d82661f6d1099dbe9b Author: Kevin Gott Date: Mon Feb 18 14:53:53 2019 -0500 unresolved-symbols flag Tests/GPU/buildNotused/GNUmakefile commit 66b488a07404b4b5a1977142c9e7714884dfc920 Merge: 3dd1d297f c716e089a Author: Cyrus Harrison Date: Wed Mar 6 13:38:01 2019 -0800 complete merge from develop (3/6/19) commit 873613548893b41d1c4ac32cfc474f244cf619fc Author: Kevin Gott Date: Wed Mar 6 13:37:21 2019 -0800 First draft of converting Advection_AmrCore to new GPU method. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 3dd1d297f762b041e95505cccc4b58d2b8e85bad Author: Cyrus Harrison Date: Wed Mar 6 13:31:37 2019 -0800 update ascent actions for plots to match current ascent api Tutorials/Blueprint/AssignMultiLevelDensity/main.cpp Tutorials/Blueprint/CellSortedParticles/main.cpp Tutorials/Blueprint/HeatEquation_EX1_C/Source/main.cpp commit ce40e1f1545fc89de0f43efb9e71f0492eb82bb5 Author: Cyrus Harrison Date: Wed Mar 6 13:30:59 2019 -0800 add logic to calc unique domain ids for particle tiles Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit c716e089a9d7e149bd84e8b40bb957422a732495 Author: Andrew Myers Date: Wed Mar 6 15:31:49 2019 -0500 remove missing include file Src/Particle/AMReX_NeighborList.H commit ffea3e87ca591753ab9327fa2a4f9758f49833f9 Author: Weiqun Zhang Date: Wed Mar 6 09:14:30 2019 -0800 add noexcept Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 939cafc8779f20ac99cf59973b94561e158be912 Merge: 20830ed6d 695a53241 Author: Andrew Myers Date: Tue Mar 5 18:49:48 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 20830ed6d21e3c4b721d2852feb2f902bf1c7c8c Author: Andrew Myers Date: Tue Mar 5 18:49:32 2019 -0500 allow arbitrary numbers of grow cells in the gpu neighbor list tutorial Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 695a532417a57641f4e254bab803598475e54e38 Author: Weiqun Zhang Date: Tue Mar 5 15:37:01 2019 -0800 print free gpu global memory Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit c3aca0f4d35f0ecefdf283a7710b0a2385ff96ca Author: Michele Rosso Date: Tue Mar 5 18:03:09 2019 -0500 CMake: fix Tutorials/GPU/neighborList Tutorials/GPU/NeighborList/CMakeLists.txt commit 91c45a9e3cc1bf083cc7ac79b224c2859c7e9592 Merge: 752f93116 4edf4a18e Author: Michele Rosso Date: Tue Mar 5 17:34:52 2019 -0500 Merge branch 'development' into mr/cmake commit 4edf4a18e56fb882a4b4a83a89bf251319f7a650 Merge: 2edecc3dc 69e38b6d4 Author: Weiqun Zhang Date: Tue Mar 5 14:29:42 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2edecc3dc96d74ccce53fd68ab38aa48fc1ffd9b Merge: 28cf6cbb0 98a411499 Author: Weiqun Zhang Date: Tue Mar 5 14:27:59 2019 -0800 Merge branch 'weiqun/fb' into development commit 752f93116c447feb1498a15f1a76957f5db85dd9 Merge: 39ce10987 6a434e42e Author: Michele Rosso Date: Tue Mar 5 17:08:49 2019 -0500 Merge branch 'mr/cmake' of https://github.com/AMReX-Codes/amrex into mr/cmake commit 39ce10987822ac2051ce90c68c11b7bc90619682 Merge: 457ed458f 69e38b6d4 Author: Michele Rosso Date: Tue Mar 5 17:08:23 2019 -0500 Merge branch 'development' into mr/cmake commit 69e38b6d40586e8c84a7e54c8b541447cf6d93df Author: Weiqun Zhang Date: Tue Mar 5 12:57:48 2019 -0800 FillBoundary: tweak local copy Src/Base/AMReX_FabArrayCommI.H commit 98a41149939f53f0311b327818c511db5115775b Author: Weiqun Zhang Date: Tue Mar 5 13:10:05 2019 -0800 fix typo Src/Base/AMReX_FabArrayCommI.H commit 4af02f3f2f3bd375a7890b4edb86126685f16a8a Author: Weiqun Zhang Date: Tue Mar 5 12:57:48 2019 -0800 FillBoundary: tweak local copy Src/Base/AMReX_FabArrayCommI.H commit 28cf6cbb0b417f95997c85214010a1d389c62132 Author: sireeveslbl Date: Tue Mar 5 12:05:30 2019 -0800 Fixed bug in DiffMultiFab Tools/C_util/DiffMultiFab/diffmultifab.cpp commit d099e051b9b04f1e4fbd9b36f9a9ed745b810452 Author: Andrew Myers Date: Tue Mar 5 14:06:13 2019 -0500 missed some device vectors Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit da5f394cef0e650977c9cca33ea337d52aedb75f Merge: c7f2c7a53 7931a1a5d Author: Andrew Myers Date: Tue Mar 5 13:37:54 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c7f2c7a536f6e1844ce0daecdcbe3368d6aaf01a Author: Andrew Myers Date: Tue Mar 5 13:37:16 2019 -0500 switch the device allocator back to using device memory Src/Base/AMReX_CudaAllocators.H commit f12f1ea1490765ffda9ad930b3f10dde449f3e91 Author: Andrew Myers Date: Tue Mar 5 13:31:28 2019 -0500 more Gpu::DeviceVector -> Gpu::ManagedDeviceVector Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_ParticleContainerI.H commit c7f46964943da587835265a65cdd12960c508d99 Author: Andrew Myers Date: Tue Mar 5 13:26:11 2019 -0500 Gpu::DeviceVector -> Gpu::ManagedDeviceVector in NeighborList Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 7931a1a5d58f0084958ad829a79311d8234bdcef Author: Weiqun Zhang Date: Mon Mar 4 12:50:21 2019 -0800 fix pointer consistence checking for non-BaseFab type Src/Base/AMReX_FabArray.H commit 8566f892f0d421defc03be8ec7f561fd4cb28dc7 Author: Brandon Runnels Date: Mon Mar 4 11:31:32 2019 -0700 fixed missing nghost declaration Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit c3751b1e67a7a9f213ab6104d9a0c4f3b1c507c6 Author: Brandon Runnels Date: Sun Mar 3 18:01:04 2019 -0700 updated to keep expected behavior for operators with nghost <= 1 Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 5387506a87b12b6bcf6d53bc528bdaddba924ad1 Merge: a050e083e 6e1acca32 Author: Brandon Runnels Date: Sun Mar 3 16:39:02 2019 -0700 Merge branch 'development' into nodeghostcells commit a050e083e27f29f30970579f7b7032b83f7c7a89 Author: Brandon Runnels Date: Sun Mar 3 15:46:37 2019 -0700 fixed error causing assertion error in ABecLaplacian_C test by updating RHS fill Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a7fad46fb8f74f5259b19f9f4bb4e93e3435f78a Author: Weiqun Zhang Date: Sat Mar 2 12:49:11 2019 -0800 consistence of style README.md commit 91323f27a020c30c004dddb71a7631f916c6694d Merge: 749721f6c 6e1acca32 Author: Weiqun Zhang Date: Fri Mar 1 22:23:17 2019 -0800 Merge branch 'development' commit 6e1acca322a640b3d7290b54fb6a04d1c5455bc3 Author: Weiqun Zhang Date: Fri Mar 1 22:21:45 2019 -0800 fix gpu fillboundary Src/Base/AMReX_FabArrayCommI.H commit 3593511260e60172882de393f2eb0c35cc794e87 Author: Weiqun Zhang Date: Fri Mar 1 21:09:39 2019 -0800 fix launch safe guard Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit eb479b47f2f3c26ed32dcd8d82be575d44a3b507 Author: Weiqun Zhang Date: Fri Mar 1 20:09:27 2019 -0800 assert that the pointers in FabArray are consistent Src/Base/AMReX_BLassert.H Src/Base/AMReX_FabArray.H commit 749721f6cf42bcbff258b99c2cbaeef0ab2f52eb Author: Weiqun Zhang Date: Fri Mar 1 16:52:44 2019 -0800 fix FArrayBox I/O for gpu. resize is not safe. Src/Base/AMReX_FArrayBox.cpp commit aa4e00c0c45c22ab223996dfb80e789ce5e438f6 Author: Weiqun Zhang Date: Fri Mar 1 16:52:44 2019 -0800 fix FArrayBox I/O for gpu. resize is not safe. Src/Base/AMReX_FArrayBox.cpp commit ab2e4b5049960ca297916d30d53f8ba827f52281 Merge: cde06a597 b25ac20f4 Author: Weiqun Zhang Date: Fri Mar 1 08:49:56 2019 -0800 Merge branch 'development' into faballocator commit b25ac20f4e0837c700764494b3e4240dbb924421 Author: Weiqun Zhang Date: Fri Mar 1 08:48:27 2019 -0800 update CHANGES CHANGES commit ef0ab0a3f52004c8c0bcb051c0e45cf36098b6ff Merge: 65b640bc5 b99f44e73 Author: Andrew Myers Date: Thu Feb 28 22:13:35 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 65b640bc58babda414a291d21be698cc056dd316 Author: Andrew Myers Date: Thu Feb 28 22:13:15 2019 -0500 switch the order of these resize operations - could in principle save memory when using the arena Src/Particle/AMReX_ParticleTile.H commit cde06a59746f6fbe5e1d38cdd49045fdfe521453 Author: Weiqun Zhang Date: Thu Feb 28 19:11:03 2019 -0800 CArena: use unordered_set for busy list Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit b99f44e734f98648d4aa97cc03b5d4489dce248b Author: Weiqun Zhang Date: Thu Feb 28 16:00:41 2019 -0800 Arena: removed duplicated codes, and make the memory type hard to change to avoid mistakes. this also makes the DArena use preferred Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp commit 210f3ae188ac1daa74c61a7b0f6957d508c5d3a4 Author: Weiqun Zhang Date: Thu Feb 28 15:16:43 2019 -0800 minor Src/Base/AMReX_FabAllocator.cpp commit f220d84a80691f3afe4079113d150238171bcc79 Merge: da49e80b9 5e7c36a0e Author: Weiqun Zhang Date: Thu Feb 28 14:33:02 2019 -0800 Merge branch 'faballocator' into development commit 5e7c36a0ea135a8c3bc66c3622378f0bdd8298f5 Author: Weiqun Zhang Date: Thu Feb 28 14:06:43 2019 -0800 special allocator for fab because they basically ahve the same size Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_FabAllocator.H Src/Base/AMReX_FabAllocator.cpp Src/Base/AMReX_FabArray.H Src/Base/CMakeLists.txt Src/Base/Make.package commit da49e80b9e8c2f274084978ec11d87756790b03d Author: Andrew Myers Date: Thu Feb 28 15:41:31 2019 -0500 fix debug statement Src/Particle/AMReX_ParticleContainerI.H commit 8a579b78c11187cf9652230a5eeca3b7ed1031b2 Merge: cced122e1 77bc18001 Author: Andrew Myers Date: Thu Feb 28 13:35:24 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cced122e12ae28829ac32b2dd5aa304bdb556889 Author: Andrew Myers Date: Thu Feb 28 13:35:05 2019 -0500 add early exit in the loop over grids in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 77bc18001102990788fba22fc75e37c1d978cb35 Merge: 9c6146408 b11e1008d Author: Andrew Myers Date: Thu Feb 28 08:20:31 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9c6146408f3615d2d46f1221cd7390c2d3db4fe4 Author: Andrew Myers Date: Thu Feb 28 08:20:13 2019 -0800 fix for periodic boundary conditions for particles when single precision is used. Src/Particle/AMReX_ParticleContainerI.H commit b11e1008da794c9cc8851cbaebb14bd54c5a793a Author: Weiqun Zhang Date: Wed Feb 27 20:44:49 2019 -0500 DArena: calculate free memory and print more information Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp commit 855d2edd79e28c83711968c491add583501cb6d1 Merge: e988d7c2c 6376b38d9 Author: Weiqun Zhang Date: Wed Feb 27 16:11:36 2019 -0800 Merge branch 'development' into buddy-allocator commit e988d7c2cb6d242a20c26507ade88640cc15a0eb Author: Weiqun Zhang Date: Wed Feb 27 15:42:58 2019 -0800 DArena: add gpu support Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp commit a485365d2b4009c6808c4ae2af349abcf16cdd19 Author: Weiqun Zhang Date: Wed Feb 27 13:41:55 2019 -0800 buddy memory allocator Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 6376b38d9de59ce1d3b998e1054365271072dc5f Merge: 8741967ed 6a6e73896 Author: Andrew Myers Date: Wed Feb 27 15:18:36 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8741967ed94c4146ee2e0102cc98a14fc58db2c9 Author: Andrew Myers Date: Wed Feb 27 15:17:57 2019 -0500 use The_Arena for all the particle stuff for now. Src/Base/AMReX_CudaAllocators.H commit 6a434e42e3149913d2134bb845c31d6f9dc1ce23 Merge: 5e41e2730 6a6e73896 Author: Michele Rosso Date: Wed Feb 27 11:27:28 2019 -0800 Merge branch 'development' into mr/cmake commit 5e41e2730ed016a047d012bbe46e7511642f867b Author: Michele Rosso Date: Wed Feb 27 11:26:45 2019 -0800 CMake: require version 3.14 only is CUDA is enabled CMakeLists.txt commit 6a6e7389666fe91fe38e08c87e81177ea5a7f9ef Author: Max Katz Date: Tue Feb 26 00:06:10 2019 -0500 Correct spelling of fextrema Tools/Plotfile/GNUmakefile Tools/Plotfile/fextrema.cpp commit 5435457b9ec13c113f4e0a930a39e4bcc37f76ae Author: Weiqun Zhang Date: Mon Feb 25 13:40:17 2019 -0800 Vector version of FillBoundary: switch back to the old way. the new approach needs more works Src/Base/AMReX_MultiFab.cpp commit 540bf01170d29eadf778dabd32a4b0cd6007c54e Author: Max Katz Date: Mon Feb 25 13:01:20 2019 -0800 Update XL compiler locations at LLNL Tools/GNUMake/sites/Make.llnl commit 0f6bcebbe87dd4843a548b24a360d453f33fe1fa Author: Weiqun Zhang Date: Mon Feb 25 11:31:37 2019 -0800 add a new Geometry constructor for convenience Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 90c6cdca5e7d4baa247639800fcab6fb594a4199 Merge: 6a3d4a1b4 5ff892926 Author: Andrew Myers Date: Mon Feb 25 13:44:41 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6a3d4a1b44734176ff467e157beeb90431e856d0 Author: Andrew Myers Date: Mon Feb 25 13:43:38 2019 -0500 NeighborList tutorial - seperate out sorting the particles from doing the copies, so we can re-use the same neighbor list for multiple time steps. Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 5ff892926ff215eeb377262dcb076150d4949b93 Author: Weiqun Zhang Date: Mon Feb 25 10:24:06 2019 -0800 no need to init/finalize fortran mpi anymore Src/Base/AMReX.cpp commit af085c89cb3799ba001fe2c5531bfb7a2c8ef2bd Author: Weiqun Zhang Date: Mon Feb 25 10:20:52 2019 -0800 rm more Fortran BoxLib stuff Src/Base/AMReX.cpp Src/Base/AMReX_BLBoxLib_F.F90 Src/Base/AMReX_error_fi.cpp Src/Base/AMReX_error_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit 740583612b72fb025428e7eb871f6ba339d96a1d Author: Weiqun Zhang Date: Mon Feb 25 09:38:30 2019 -0800 rm more Fortran BoxLib stuff Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BLassert.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_FPC.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_Utility.H commit eb18a252ca372638c28bec9eeac9946c93023711 Merge: 07352b580 dcfa51fe8 Author: Weiqun Zhang Date: Mon Feb 25 09:03:45 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 07352b5804e932c59dd3fcf199a48fb4a10af189 Author: Weiqun Zhang Date: Mon Feb 25 09:02:15 2019 -0800 rm more deprecated files Src/Base/BL_mempool_f.f90 Src/Base/GPackage.mak commit dcfa51fe8a95df16ab4f305fc9c84ea7847c8628 Author: Max Katz Date: Mon Feb 25 11:56:49 2019 -0500 Specialize some AMREX_USE_GPU to AMREX_USE_CUDA Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_FabArrayUtility.H commit e70ede343b4ae1d64f3e009c1317625cb0132cbe Author: Max Katz Date: Mon Feb 25 03:47:06 2019 -0500 Specialize some AMREX_USE_GPU to AMREX_USE_GPU_PRAGMA Src/Base/AMReX_ArrayLim.H commit f67e106fdbbc101b50f22042cec530b1ee1b14b9 Author: Weiqun Zhang Date: Mon Feb 25 08:51:44 2019 -0800 include header Src/Base/AMReX_MemPool.H commit 6c233441043ca952f5c76e2f91a9757cecd8e056 Author: Ann Almgren Date: Mon Feb 25 08:32:29 2019 -0800 Remove F_BaseLib and parts of AMReX that used it. Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/make_api.py Src/Base/AMReX.cpp Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/F_BaseLib/BLProfiler_f90.f90 Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/FParallelMG2.mak Src/F_BaseLib/FParallelMG_RNG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/MemProfiler_f.H Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/MultiFab_C_F.H Src/F_BaseLib/MultiFab_C_F.cpp Src/F_BaseLib/amrex_fabio_c.f90 Src/F_BaseLib/amrex_fort_mod.f90 Src/F_BaseLib/amrex_timer_c.f90 Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 Src/F_BaseLib/bc.f90 Src/F_BaseLib/bc_functions.f90 Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_parmparse.f90 Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_prof_stubs.f90 Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Src/F_BaseLib/bl_space.f90 Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bl_system.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box_f.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/cc_restriction.f90 Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/cutcells.f90 Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/f2kcli.f90 Src/F_BaseLib/f2kcli_crayx1.f90 Src/F_BaseLib/f2kcli_nag.f90 Src/F_BaseLib/f2kcli_win32.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/filler.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/fourth_order_interp_coeffs.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/list_box.f90 Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/memprof.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/ml_nd_restriction.f90 Src/F_BaseLib/ml_restrict_fill.f90 Src/F_BaseLib/mt19937ar.f90 Src/F_BaseLib/multifab_c.f90 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 Src/F_BaseLib/nodal_neumann_bcs.f90 Src/F_BaseLib/nodal_restriction.f90 Src/F_BaseLib/nodal_stencil_bc.f90 Src/F_BaseLib/omp.f90 Src/F_BaseLib/omp_stubs.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 Src/F_BaseLib/particles_f.f90 Src/F_BaseLib/pingpong.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/ppm_util.f90 Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/regrid.f90 Src/F_BaseLib/sort_box.f90 Src/F_BaseLib/sort_d.f90 Src/F_BaseLib/sort_i.f90 Src/F_BaseLib/system_util_c.c Src/F_BaseLib/tag_boxes.f90 Src/F_BaseLib/timer_c.c Src/F_BaseLib/unittests/GNUmakefile Src/F_BaseLib/unittests/gr0_3d.1level Src/F_BaseLib/unittests/tests.f90 Src/F_BaseLib/vector_i.f90 Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_mk/Readme Tools/F_mk/comps/Darwin_ibm.mak Tools/F_mk/comps/Darwin_intel.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_lahey.mak Tools/F_mk/comps/Linux_nag.mak Tools/F_mk/comps/Linux_pathscale.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/Linux_sunstudio.mak Tools/F_mk/comps/aix.mak Tools/F_mk/comps/bgq.mak Tools/F_mk/comps/g95.mak Tools/F_mk/comps/gfortran.mak Tools/F_mk/comps/xlf.mak Tools/Postprocessing/F_Src/CMakeLists.txt Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/Palette Tools/Postprocessing/F_Src/TODO_GHOST Tools/Postprocessing/F_Src/faverage.f90 Tools/Postprocessing/F_Src/faverplot.f90 Tools/Postprocessing/F_Src/fboxinfo.f90 Tools/Postprocessing/F_Src/fcoarsen.f90 Tools/Postprocessing/F_Src/fcompare.f90 Tools/Postprocessing/F_Src/fdump.f90 Tools/Postprocessing/F_Src/fdumpdata2d.f90 Tools/Postprocessing/F_Src/fextract.f90 Tools/Postprocessing/F_Src/fextrema.f90 Tools/Postprocessing/F_Src/ffdcompare.f90 Tools/Postprocessing/F_Src/fintgvar2d.f90 Tools/Postprocessing/F_Src/fnan.f90 Tools/Postprocessing/F_Src/fsnapshot2d.f90 Tools/Postprocessing/F_Src/fsnapshot3d.f90 Tools/Postprocessing/F_Src/ftime.f90 Tools/Postprocessing/F_Src/fvarnames.f90 Tools/Postprocessing/F_Src/fwritecontents2d.f90 Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 Tools/Postprocessing/python/README Tools/Postprocessing/python/column_depth.py Tools/Postprocessing/python/conv_slopes.py Tools/Postprocessing/python/dumpparthistory.py Tools/Postprocessing/python/eos_data.txt Tools/Postprocessing/python/helmeos.py Tools/Postprocessing/python/parseparticles.py Tools/Postprocessing/python/test_helmeos.py Tools/Postprocessing/python/test_parseparticles.py Tools/Postprocessing/python/timestamp_00.REMOVED.git-id Tools/Postprocessing/python/timestamp_02.REMOVED.git-id Tools/Py_util/GNUmakefile Tools/Py_util/README Tools/Py_util/fsnapshot.f90 commit b870d481121651bdff9798ba17a1a14f96e880a7 Author: Max Katz Date: Mon Feb 25 03:31:59 2019 -0500 Do not attempt to set CUDA_ARCH if not defined Tools/GNUMake/comps/pgi.mak commit 8f309b03e211609d13e986ed473d20bdf1837af8 Author: Weiqun Zhang Date: Sat Feb 23 15:23:39 2019 -0800 fix assert message Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 3ea117e6ff47ee358c7a6dbdbcd826b597e7bd93 Author: Weiqun Zhang Date: Sat Feb 23 12:51:14 2019 -0800 MLCellLinOp:: metric factor Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 71331bea7b754cb09609866c2a53c1c23db28316 Author: Weiqun Zhang Date: Sat Feb 23 12:36:53 2019 -0800 MLCellLinOp:: refactor Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 2d6cd66029000afdff1922ef05523fc7144c80d9 Author: Weiqun Zhang Date: Sat Feb 23 10:32:01 2019 -0800 assertion no longer needed because of recent change in Array4 Src/Base/AMReX_BaseFab.H commit 5d6de85d3999904f53d3f76f067984773ad8a834 Author: Weiqun Zhang Date: Sat Feb 23 10:21:37 2019 -0800 pass by value Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/EB/AMReX_EB2_IF_Rotation.H commit 924d2773369435c9f31efc4fb215c81bd49094e7 Author: Weiqun Zhang Date: Sat Feb 23 07:52:38 2019 -0800 pass by value Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_LayoutData.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 37b6f354a3f370391cb5a40486a02c348c61d9b6 Author: Andrew Myers Date: Fri Feb 22 15:55:52 2019 -0800 remove f_baselib from the electrostatic pic tutorial Tutorials/Particles/ElectrostaticPIC/GNUmakefile Tutorials/Particles/ElectrostaticPIC/main.cpp commit 88be86ff6e545ef95d35ce436a7d0a7cba666380 Author: Andrew Myers Date: Fri Feb 22 15:30:54 2019 -0800 remove commented out code OldTutorials/PIC_C/solve_with_mlmg.cpp OldTutorials/TwoGrid_PIC_C/solve_with_mlmg.cpp commit 75454b78ee1d4650365317258fb2c090d0e698a2 Merge: 70bc6ff0d 53c1c663b Author: Andrew Myers Date: Fri Feb 22 15:17:12 2019 -0800 Merge branch 'development' into f_baselib_particles_remove commit 70bc6ff0dc70e5ae6bd1568511802464d0f2dbf0 Author: Andrew Myers Date: Fri Feb 22 15:16:25 2019 -0800 update TwoGrid_PIC_C for the removal of F_Baselib OldTutorials/PIC_C/main.cpp OldTutorials/TwoGrid_PIC_C/GNUmakefile OldTutorials/TwoGrid_PIC_C/Make.package OldTutorials/TwoGrid_PIC_C/main.cpp OldTutorials/TwoGrid_PIC_C/solve_for_accel.cpp OldTutorials/TwoGrid_PIC_C/solve_with_f90.cpp commit 53c1c663b6f63707fc8d78e61fddc8657592d6fb Merge: 8c7ad2c9e 1b73ccf6d Author: Andrew Myers Date: Fri Feb 22 15:04:15 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8c7ad2c9ec0036870f58c8f3d9dac5e8efe130b8 Author: Andrew Myers Date: Fri Feb 22 15:03:27 2019 -0500 make the neighbor list build function templated on check_pair function Src/Particle/AMReX_NeighborList.H Tutorials/GPU/NeighborList/CheckPair.H Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/Make.package Tutorials/GPU/NeighborList/md_K.H commit 1b73ccf6d8fa7e00e3152e9215546e16c2c3c069 Merge: e4cd2dff0 cad64ac43 Author: Weiqun Zhang Date: Fri Feb 22 11:42:44 2019 -0800 Merge branch 'weiqun/gpu' into development commit cad64ac43f7820474eab8ac4091049e4882004ea Author: Weiqun Zhang Date: Fri Feb 22 11:02:25 2019 -0800 fix bug in C++ apply bc Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit adfb83418f8031dbba70adc079d2e3d627028395 Author: Weiqun Zhang Date: Fri Feb 22 09:26:14 2019 -0800 MLCellLinOp: fix index Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit 6e5b3cfcd1894a8d0ce9ab4d38cc5f93fa5eed70 Author: Weiqun Zhang Date: Fri Feb 22 08:00:36 2019 -0800 MLCellLinOP: coef0 on gpu Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit b5ec971285a21c6d7ca5d5d3b4bd5c7aadc76d2a Author: Weiqun Zhang Date: Thu Feb 21 22:02:07 2019 -0800 MLCellLinOp: applybc on gpu Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/Make.package commit e4cd2dff03cae2fe9917bf882c724835e8fb8bc5 Merge: dc462ddd7 891bd8138 Author: Andrew Myers Date: Thu Feb 21 20:31:33 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit dc462ddd7e0212dff946cee17d4ed94490f8ee38 Author: Andrew Myers Date: Thu Feb 21 20:31:13 2019 -0500 start migrating the neighbor list stuff into AMReX proper Src/Particle/AMReX_NeighborList.H Src/Particle/CMakeLists.txt Src/Particle/Make.package Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/Make.package commit d3a2968e6ab2b7c3682c2057bafb759b78586768 Author: Andrew Myers Date: Thu Feb 21 20:21:36 2019 -0500 pstruct[i] -> p Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 822629da7ff387ce90b55b39281377b8aae7e1ef Author: Andrew Myers Date: Thu Feb 21 20:17:45 2019 -0500 allow the user to use range-based for loops for the neighbor list on the GPU Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/Make.package Tutorials/GPU/NeighborList/NeighborList.H Tutorials/GPU/NeighborList/NeighborList.cpp commit 891bd8138d04ab017e4057ec0fcc0ff8b491b7a7 Author: Ann Almgren Date: Thu Feb 21 16:11:04 2019 -0800 Revert "Revert "CMake: change the way Algoim and Blitz are handled"" This reverts commit d93c483d5849c678aeae36d278d169d4af62bb91. CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit b1617f313a703c2b01b65c3ca87471597c72bdd3 Author: Andrew Myers Date: Thu Feb 21 17:53:11 2019 -0500 start to add the NeighborList stuff into a discrete class Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/Make.package Tutorials/GPU/NeighborList/NeighborList.H Tutorials/GPU/NeighborList/NeighborList.cpp Tutorials/GPU/NeighborList/md_K.H commit 02fc3c21c323e159fae9471ad2aa8c6372c46c93 Author: Andrew Myers Date: Thu Feb 21 13:12:15 2019 -0800 remove the EBParticles OldTutorial OldTutorials/EBParticles/EBParticleContainer.H OldTutorials/EBParticles/EBParticleContainer.cpp OldTutorials/EBParticles/GNUmakefile OldTutorials/EBParticles/Make.package OldTutorials/EBParticles/ebparticles_2d.f90 OldTutorials/EBParticles/ebparticles_3d.f90 OldTutorials/EBParticles/ebparticles_F.H OldTutorials/EBParticles/inputs OldTutorials/EBParticles/main.cpp commit 457ed458fc1ce555b77a86696fa7f07a676c65de Author: Michele Rosso Date: Thu Feb 21 15:09:47 2019 -0500 CMake: fix GPU/NeighborList example Tutorials/GPU/NeighborList/CMakeLists.txt commit 2aaf571eae83ca0f65c491596f8d0c64be2e2a8b Merge: 77e2c10d5 d88e7433a Author: Weiqun Zhang Date: Wed Feb 20 20:50:25 2019 -0800 Merge branch 'weiqun/fluxregister' into development commit d88e7433a6890f7443406414921b72bdb717b36f Author: Weiqun Zhang Date: Wed Feb 20 19:17:02 2019 -0800 allow different BoxArrays for average_down_nodal and average_down_edges. new versions of average_down_edges and average_down_faces for single direction Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 77e2c10d5730334057d19fd83663aaf3485a13eb Merge: ffe4d291a 49bd115a5 Author: Daniel Ladiges Date: Wed Feb 20 18:54:52 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ffe4d291abee82bf685d1c6351b69076a5b03593 Author: Daniel Ladiges Date: Wed Feb 20 18:49:30 2019 -0800 Made copy of .mak file in F_BaseLib so it has a sensible name before its death next week (and to keep consistency with FBoxLib). Src/F_BaseLib/FParallelMG_RNG.mak commit 49bd115a5c5de93a6b4179142a85d338ca711f7b Author: Andrew Myers Date: Wed Feb 20 17:23:28 2019 -0800 do this interpolation from coarse in a different way. Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_PhysBCFunct.H commit cdd7a75974c5dde27590337adce72261e18bdd41 Author: Weiqun Zhang Date: Wed Feb 20 16:29:09 2019 -0800 reflux for given direction Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp commit 2409f9306917414638c82e6490ff9161623d17f6 Merge: 8d5b4864f bad1e4ec8 Author: Weiqun Zhang Date: Wed Feb 20 15:54:30 2019 -0800 Merge branch 'weiqun/gpu' into development commit bad1e4ec86005d05eab8f115ce97bbeddf9f7f07 Merge: d150031c8 eca9364d6 Author: Weiqun Zhang Date: Wed Feb 20 16:12:34 2019 -0500 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit d150031c8c77f5f1fde1fd7aacaee90be60d1877 Author: Weiqun Zhang Date: Wed Feb 20 16:12:21 2019 -0500 Array4: add strides as members Src/Base/AMReX_Array.H commit eca9364d67e613e11df6bdede98132ae603db60b Author: Weiqun Zhang Date: Wed Feb 20 13:06:53 2019 -0800 Array4: use printf for device code Src/Base/AMReX_Array.H commit e110ac728c34caf73f70bc0ad81cee4111aa9490 Author: Weiqun Zhang Date: Wed Feb 20 15:44:40 2019 -0500 Array4: constexpr and const Src/Base/AMReX_Array.H commit fd703eded7a055513598952e006deeee64ac82df Author: Weiqun Zhang Date: Wed Feb 20 11:47:20 2019 -0800 print out bounds when access to Array4 is out of bounds Src/Base/AMReX_Array.H commit 2136ee4c3bc31f5a21e25ff352da3a96873b5f94 Author: Andrew Myers Date: Wed Feb 20 14:20:08 2019 -0500 do the clear before Redistribute Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 12a3b9c45b45fd5d08ee404d51fb74f110a86fda Author: Weiqun Zhang Date: Wed Feb 20 11:09:21 2019 -0800 addr2line pretty print Src/Base/AMReX_BLBackTrace.cpp commit 45dc8550f9fc02208c6db0288790f96ae5bb6270 Author: Weiqun Zhang Date: Wed Feb 20 11:06:13 2019 -0800 mlalaplacian on gpu Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_F.H Src/LinearSolvers/MLMG/AMReX_MLALap_K.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit 8d5b4864fb0d4de5bb8746eda19ea735cf82cabf Author: Donald E. Willcox Date: Wed Feb 20 10:39:21 2019 -0800 Rename EX3-CUDA to EX-CUSOLVER Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/GNUmakefile Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/Make.CVODE Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/Make.package Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/README.md Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/extern_probin.template Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_128 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_256 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_32 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_64 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/main.cpp Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/make_cuda.sh Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/make_cuda_cusolver.sh Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/make_serial.sh Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_cuda.cpp Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_cuda_cusolver.cpp Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_serial.cpp Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_system.F90 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_utils.F90 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/test_react.H Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/test_react_F.H commit fcb5fc0586478c2e0d0049e53a0f84f39ce43285 Author: Donald E. Willcox Date: Wed Feb 20 10:38:01 2019 -0800 Remove unnecessary include line for FParallelMG Tutorials/CVODE/SUNDIALS4/EX3-CUDA/Make.CVODE commit 97ab5365bd8834c734b1217169745e01c30fb317 Author: Andrew Myers Date: Tue Feb 19 19:45:01 2019 -0500 call clear and sort from inside fillNeighbors Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/main.cpp commit 70ea36d2cf337b27cfe999476d2767b8fcf65adf Merge: ccd72bb1f 75d789b4b Author: Andrew Myers Date: Tue Feb 19 19:07:30 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ccd72bb1fb43453ca56c6157fd1e088c5a172b76 Author: Andrew Myers Date: Tue Feb 19 19:07:10 2019 -0500 adding and using wrappers around Cuda's atomicInc and atomicDec functions Src/Base/AMReX_CudaUtility.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit ae5d7dad2a6d0b4dd2a6768420986ef1faa1ce0f Author: Weiqun Zhang Date: Tue Feb 19 15:03:46 2019 -0800 mlpoisson: normalize Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H Src/LinearSolvers/MLMG/Make.package commit 75d789b4ba32221685750b5bf621db194dcdb6c4 Author: kngott Date: Tue Feb 19 14:22:01 2019 -0800 GPU docs. Docs/sphinx_documentation/source/GPU.rst commit 18053b1951b785f407690370ae3ad9a1b1c98ad7 Author: Weiqun Zhang Date: Tue Feb 19 14:14:04 2019 -0800 mlpoisson: gsrb Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H commit cd86febcbb686fd95201e8e232eb58c839a59ac7 Author: Andrew Myers Date: Tue Feb 19 12:45:03 2019 -0800 add a NoOpPhysBCFunct and use it in the amr assign density Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_PhysBCFunct.H commit 6a3f565f9136847063876cbeddbeca9cc6d3bf90 Author: Andrew Myers Date: Tue Feb 19 12:39:41 2019 -0800 version of InterpFromCoarseLevel that doesn't use enforce boundary conditions Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 74c07cdc728698b828acd307248f17477683cd55 Merge: 08b9b2e86 588130833 Author: WeiqunZhang Date: Tue Feb 19 10:36:40 2019 -0800 Merge pull request #411 from mwm126/patch-2 Fix USE_ACC error; refactor for readability commit 08b9b2e867c9e69d9cac021243dd69c8a425fe78 Author: Weiqun Zhang Date: Tue Feb 19 10:03:33 2019 -0800 warning instead of ignoring Tests/GPU/libamrex_CUDA/GNUmakefile commit 26a14ea46f495a6d204b0023ec55a795304f7199 Author: Weiqun Zhang Date: Mon Feb 18 10:46:20 2019 -0800 an example of using libamrex with cuda Tests/GPU/libamrex_CUDA/GNUmakefile Tests/GPU/libamrex_CUDA/README.md Tests/GPU/libamrex_CUDA/main.cpp commit f6cab9fbb5d5d802b61ecff623eb9cfdcc564a4a Author: Weiqun Zhang Date: Mon Feb 18 09:24:12 2019 -0800 Elixir: add default constructor and move assignment Src/Base/AMReX_CudaElixir.H commit 58813083353a831b88afa4958c85da77172e1fb8 Author: Mark Meredith Date: Mon Feb 18 08:43:18 2019 -0500 Fix USE_ACC error; refactor for readability I noticed a typo: https://github.com/AMReX-Codes/amrex/blob/master/Tools/libamrex/configure.py#L98 should be "USE_ACC = TRUE". Writing each line in the Makefile with one line of source could help prevent errors like that. Tools/libamrex/configure.py commit cd85e39e1fc93cb06b7e21e85bf5459ef5834be6 Author: Max Katz Date: Sun Feb 17 15:49:08 2019 -0800 Generalize MFIter reduction to allow multiple reduce values Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 487b8184492dd7fb94fdc39fbf3601824f9b0043 Author: Weiqun Zhang Date: Sun Feb 17 14:32:56 2019 -0800 MLPoisson: flux Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H commit da1c9cc3f9d7e0fd23192f09d0495b35a6f22163 Merge: 233e532f7 428ef09c2 Author: WeiqunZhang Date: Sun Feb 17 12:42:41 2019 -0800 Merge pull request #406 from AMReX-Codes/plot_per_fix Add floating point awareness to the plot_per/check_per logic commit 233e532f7b1440c791cf37144836438045207fc1 Author: Weiqun Zhang Date: Sun Feb 17 12:28:21 2019 -0800 generalize FillPatch for non-uniform grow cells Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_PhysBCFunct.H commit 428ef09c2791a6f180caf6fbada0825a4f7371ce Author: Max Katz Date: Sun Feb 17 06:48:35 2019 -0800 Scale epsilon to the current simulation time Src/Amr/AMReX_Amr.cpp commit 2733d5597adece632d7de8c51160b61b8554d2e2 Merge: c9b6dd3a8 d08450efc Author: Max Katz Date: Sun Feb 17 06:32:58 2019 -0800 Merge branch 'development' into plot_per_fix commit fd5ee74d7d2fb79620a9bf45ff96cd78c6eea7a3 Author: Weiqun Zhang Date: Sat Feb 16 21:39:04 2019 -0800 minor change Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H commit e96c037c91d8ef1c5105bcb100a25493bd7a1bf6 Author: Weiqun Zhang Date: Sat Feb 16 21:14:12 2019 -0800 MLPoisson: adotx Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_K.H Src/LinearSolvers/MLMG/Make.package commit d08450efcc7d822a94d9822fc5bfe224b410aec7 Author: Ann Almgren Date: Sat Feb 16 19:27:11 2019 -0800 Add the option to call EB_set_covered with ngrow > 0 so we can cover ghost cells of each Fab. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit de98fb32a1726835151b55425e2b33c23f58c00a Merge: 501b93d8a d93c483d5 Author: Weiqun Zhang Date: Sat Feb 16 18:39:46 2019 -0800 Merge branch 'development' into weiqun/gpu commit 9e94e935e84dad2a702c9d3b317eec04f0eded50 Author: Brandon Runnels Date: Sat Feb 16 17:51:49 2019 -0700 Merge branch development into nodeghostcells Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 939100c077b77845023a4a4d1d4fdf380ae0aff9 Merge: ad09ce0a7 d93c483d5 Author: Brandon Runnels Date: Sat Feb 16 17:33:51 2019 -0700 Merge branch 'development' into nodeghostcells commit ad09ce0a75ecb9e94c6898b7744a98d954e2f308 Author: Brandon Runnels Date: Sat Feb 16 17:33:24 2019 -0700 removed some superfluous functions to be implemented elsewhere Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit ffa23f2f10970f09fd2ca7566920ca353a5f61af Author: Brandon Runnels Date: Sat Feb 16 16:23:39 2019 -0700 working - now cleaning up and updating Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit d93c483d5849c678aeae36d278d169d4af62bb91 Author: Ann Almgren Date: Sat Feb 16 13:59:28 2019 -0800 Revert "CMake: change the way Algoim and Blitz are handled" This reverts commit a4856755c6eabfd91b99842dac09dca8891393de. CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit 501b93d8abe9d2437b819a829f5ef7b13abe3f65 Author: Weiqun Zhang Date: Sat Feb 16 12:10:54 2019 -0800 1d and 2d gsrb Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 8682902d1a9bbaf3ef7e7735ec6f01ec4c9c46ac Author: Max Katz Date: Sat Feb 16 01:25:58 2019 -0800 Add C++11 if PGI is nvcc host compiler Tools/GNUMake/comps/nvcc.mak commit 87db278ff24667ab2088aae2b557426c96441bdc Author: Weiqun Zhang Date: Fri Feb 15 23:06:51 2019 -0800 3d gsrb Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 7c05741cf1579d939efdf85b08b079d75be6fc25 Author: Weiqun Zhang Date: Fri Feb 15 21:18:18 2019 -0800 fix TagBox::coarsen for gpu Src/AmrCore/AMReX_TagBox.cpp commit 8e8c36db6b632e220b4a40316376433915f11b12 Merge: d2afe76c7 5bc08ecb8 Author: Weiqun Zhang Date: Fri Feb 15 20:50:08 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c9127be61b1a13ce23267b6ef2d5147e6798542a Author: Michele Rosso Date: Fri Feb 15 22:11:41 2019 -0500 CMake: add GPU/NeighborList test Tutorials/GPU/Launch/CMakeLists.txt Tutorials/GPU/NeighborList/CMakeLists.txt commit 413edad5376b54da483c6d9927ce9094584602a6 Merge: d464c3220 5bc08ecb8 Author: Michele Rosso Date: Fri Feb 15 20:34:42 2019 -0500 Merge branch 'development' into mr/cmake commit 87b79015d434c481fddaa51d035ab8e1b308ac85 Merge: 75aaf725c 7320b9054 Author: Brandon Runnels Date: Fri Feb 15 18:25:29 2019 -0700 Merge branch 'nodeghostcells' of https://github.com/AMReX-Codes/amrex into nodeghostcells commit d464c32203023488ea60b20e3c73722e08511c61 Author: Michele Rosso Date: Fri Feb 15 20:24:04 2019 -0500 CMake: fix GPU example Tools/CMake/AMReX_Config.cmake Tutorials/GPU/Launch/CMakeLists.txt commit 75aaf725c1e60f36f5a3cccd238bfa5fb71148e8 Author: Brandon Runnels Date: Fri Feb 15 18:22:42 2019 -0700 works for multiple grids in serial, need to determine why mpi does not work Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5bc08ecb8895ddcc20ae66052cdaaee5cba11b4c Merge: edf1944fb 87c3cd753 Author: Andrew Myers Date: Fri Feb 15 19:56:03 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit edf1944fb334440087eb2c78c2a24a7cabeb10f0 Author: Andrew Myers Date: Fri Feb 15 19:55:32 2019 -0500 move the gpu neighbor list thing to Tutorials/GPU Tutorials/GPU/NeighborList/Constants.H Tutorials/GPU/NeighborList/GNUmakefile Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/Make.package Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp Tutorials/GPU/NeighborList/md_K.H commit d2afe76c7052a67db2e4872c467eafc453370e82 Merge: 66499da6c 87c3cd753 Author: Weiqun Zhang Date: Fri Feb 15 16:17:07 2019 -0800 Merge branch 'development' into weiqun/gpu commit 87c3cd753991e06d151c35c4da9ee645f86cb351 Merge: 2e2239112 086ffeac3 Author: Weiqun Zhang Date: Fri Feb 15 15:00:56 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 086ffeac3e5bb49adccef05b6986f7014a0168d7 Author: kngott Date: Fri Feb 15 14:59:53 2019 -0800 Add support for OpenMPI+UCX library on CoriGPU. Tools/GNUMake/sites/Make.nersc commit 2e22391121acefd35c362c56fced50c0006af236 Author: Weiqun Zhang Date: Fri Feb 15 14:55:34 2019 -0800 use always assert Src/Base/AMReX_Array.H Src/Base/AMReX_BLassert.H commit f6df72bd4ea0de1e8e6fb8aa851acb6ce6a05f42 Author: Andrew Myers Date: Fri Feb 15 17:55:00 2019 -0500 removing files added by mistake Tutorials/Particles/NeighborList/AMReX_FPC.tsm Tutorials/Particles/NeighborList/AMReX_ForkJoin.tsm Tutorials/Particles/NeighborList/AMReX_NFiles.tsm Tutorials/Particles/NeighborList/AMReX_SPMD.tsm Tutorials/Particles/NeighborList/AMReX_VisMF.tsm Tutorials/Particles/NeighborList/NeighborListParticleContainer.tsm Tutorials/Particles/NeighborList/main.tsm commit bfa45c0ede545c1dd42670a0c265b3bd091afeca Author: Andrew Myers Date: Fri Feb 15 17:40:41 2019 -0500 also make the cpu version work with non-cubic domains Tutorials/Particles/NeighborList/AMReX_FPC.tsm Tutorials/Particles/NeighborList/AMReX_ForkJoin.tsm Tutorials/Particles/NeighborList/AMReX_NFiles.tsm Tutorials/Particles/NeighborList/AMReX_SPMD.tsm Tutorials/Particles/NeighborList/AMReX_VisMF.tsm Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/NeighborListParticleContainer.tsm Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/main.tsm commit 5c5813d67b649f2705fa228de151e3d5eac7b78e Author: Andrew Myers Date: Fri Feb 15 17:32:38 2019 -0500 let this thing have a non-cubic domain Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 5743bcffe3af4230d801d12a479fa9569b4d2278 Author: Andrew Myers Date: Fri Feb 15 17:17:07 2019 -0500 fix another parallel bug Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 725e6f1d4a754185ec7a6d9125b7ea4efc039635 Author: Andrew Myers Date: Fri Feb 15 16:30:21 2019 -0500 parallel bug fix. Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit d05d25593af8b36e9035add520a85bd345f8069c Merge: efa61ff2e faedb2fcd Author: Brandon Runnels Date: Fri Feb 15 13:11:01 2019 -0700 Merge branch 'nodeghostcells-instr' into nodeghostcells commit efa61ff2ebe4c640d34fd203864addcf1c94daa0 Author: Brandon Runnels Date: Fri Feb 15 13:06:54 2019 -0700 added nghost specification in linop Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit acc2f31d70ce1c0ca9a231be317d226cc65c35e2 Author: Andrew Myers Date: Fri Feb 15 14:46:27 2019 -0500 don't write anything by default in inputs Tests/Particles/GPUNeighborList/inputs commit faedb2fcd0f12afd3757885591b4d1209fbde275 Author: Brandon Runnels Date: Fri Feb 15 12:37:49 2019 -0700 WIP: fillboundary surgery Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit ba563187a5a77d21704c4a0961429c46e0fb3cc8 Merge: 57b47c3b8 a4461a17c Author: Andrew Myers Date: Fri Feb 15 14:34:17 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into gpu_neighbor_list commit 57b47c3b87b706a91676a42dd86fa86d8cbb6c44 Author: Andrew Myers Date: Fri Feb 15 14:32:33 2019 -0500 MPI for gpu fillNeighbors Tests/Particles/GPUNeighborList/GNUmakefile Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit de142a8a07b0df8060b1458c5f90dc3b14c01214 Author: Brandon Runnels Date: Fri Feb 15 10:50:17 2019 -0700 re-instrumented and debugging fillboundary Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit 03c69e55c599d6d4afcbdc384861ee9d6493b959 Author: Michele Rosso Date: Thu Feb 14 21:17:41 2019 -0500 CMake:semi-working CUDA support CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupCUDA.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/comps/AMReX_GNU.cmake Tools/CMake/comps/AMReX_NVIDIA.cmake Tools/CMake/comps/AMReX_PGI.cmake Tutorials/CMakeLists.txt Tutorials/GPU/Launch/CMakeLists.txt Tutorials/GPU/Launch/MyKernel_F.F90 commit a4461a17c6d3f09abc7e06eef05cf7d60a87ca03 Author: kngott Date: Thu Feb 14 15:14:27 2019 -0800 Updated corigpu script. Tutorials/GPU/run.corigpu commit 7aa6daea5f7b25bf98539506061be3aae640bfd1 Author: kngott Date: Thu Feb 14 13:37:00 2019 -0800 Add corigpu run script w/ environment & salloc instructions. Tutorials/GPU/run.corigpu commit 5d658c0ff00a077625b9263e793c13da3d32a9d3 Merge: acf33d839 28b7c7d41 Author: Andrew Myers Date: Thu Feb 14 16:19:57 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into gpu_neighbor_list commit 28b7c7d4177365bd348cbcff4393e2dcb15cdad8 Merge: 895714865 99e2c1030 Author: Andrew Myers Date: Thu Feb 14 13:18:36 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8957148656d5b1dae1849f84403de3bf37b8340d Author: Andrew Myers Date: Thu Feb 14 13:18:25 2019 -0800 routines for 3d neighbor list tutorial Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit acf33d839f04564fb153ea05e13f535323765b8f Author: Andrew Myers Date: Thu Feb 14 15:39:07 2019 -0500 a few bug fixes Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 99e2c1030b0814cee50df6f12154e33d71cadb15 Merge: a4856755c 02e4dc10a Author: Michele Rosso Date: Thu Feb 14 11:47:11 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a4856755c6eabfd91b99842dac09dca8891393de Author: Michele Rosso Date: Thu Feb 14 11:47:02 2019 -0800 CMake: change the way Algoim and Blitz are handled CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit 02e4dc10a5f1b687a0d94603e35f0db6800304e7 Merge: 8db89f69d 4ebff7a98 Author: Weiqun Zhang Date: Thu Feb 14 09:55:01 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8db89f69d062c68c364850ecfb4ed20dac8bacd2 Author: Weiqun Zhang Date: Thu Feb 14 09:54:22 2019 -0800 ParmParse: fix for IntVect Src/Base/AMReX_ParmParse.cpp commit 4ebff7a98034abf0eca3eb94a393eac67e8580c2 Author: Max Katz Date: Thu Feb 14 12:11:23 2019 -0500 Preprocess out -D defines in the CUDA script when searching for pragmas Tools/F_scripts/write_cuda_headers.py commit eb17f4907a1f9277732b6d12148822ad44f66ced Merge: b12c7e641 84554a96f Author: Weiqun Zhang Date: Thu Feb 14 08:21:06 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b12c7e641b1ada11f000ba11aa1d02f118f28d21 Author: Weiqun Zhang Date: Thu Feb 14 08:20:55 2019 -0800 fcompare: handle empty plotfile Src/Base/AMReX_PlotFileDataImpl.cpp Tools/Plotfile/fcompare.cpp commit 84554a96f47bf2a9702d1f46acfdfd3bb18a3d81 Author: Kevin Gott Date: Wed Feb 13 17:50:07 2019 -0800 Updated GPU kernel launch docs. Docs/sphinx_documentation/source/GPU.rst commit f8dd0159ec2a12b58e040c60c8c3c1de89103c6a Author: Weiqun Zhang Date: Wed Feb 13 16:29:34 2019 -0800 remove space from variable names OldTutorials/MultiGrid_C/writePlotFile.cpp OldTutorials/Tiling_Heat_C/writePlotFile.cpp OldTutorials/WaveEquation_C/writePlotFile.cpp commit 833f7dbf19f433c92c9dd2f84e1b9c17f8c52217 Author: Weiqun Zhang Date: Wed Feb 13 16:19:05 2019 -0800 add Palette Tools/Plotfile/Palette commit 93057a03e97c78762fd127340cebc5c81d81354a Author: Andrew Myers Date: Wed Feb 13 18:47:10 2019 -0500 gpu neighbor list running with domain decomposition Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 31177c370af888eb7597236ad214592f724cfe84 Author: Andrew Myers Date: Wed Feb 13 18:37:18 2019 -0500 make OKGPU() work in the presence of neighbor particles Src/Particle/AMReX_ParticleContainerI.H commit 068179d7f66c18581922752bf507633fdd4b13fd Author: Andrew Myers Date: Wed Feb 13 18:12:42 2019 -0500 make numParticles return the number of Real particles (excluding neighbors) Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit 2400ac70a5389d4809df8eacdf5b8dd12c7996c9 Author: Weiqun Zhang Date: Wed Feb 13 14:14:27 2019 -0800 fsnapshot: option to specify coordinates on slice Tools/Plotfile/fsnapshot.cpp commit 6e15ab3ef8318a8c58aa3221302ea46c5d5fd394 Author: Andrew Myers Date: Wed Feb 13 17:00:07 2019 -0500 add fillNeighbors and clearNeighbors Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 1095322e1005ad1bf707f5d79e5bcf9e96cf19a8 Author: Weiqun Zhang Date: Wed Feb 13 13:11:55 2019 -0800 fsnapsht3d Tools/Plotfile/GNUmakefile Tools/Plotfile/fsnapshot.cpp Tools/Plotfile/fsnapshot2d.cpp commit 6464480c9d4bbb39e74b2577913973285ba4bc13 Author: Andrew Myers Date: Wed Feb 13 15:49:36 2019 -0500 copy neighbor particles to their destinations Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 7cf07e9419aed2857f089e2708c6823277c0d5ed Author: Andrew Myers Date: Wed Feb 13 15:34:10 2019 -0500 starting to implement neighbor particle filling Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 10927618ba29e51c528cd0d9121b0722d323c7d7 Author: Andrew Myers Date: Wed Feb 13 15:33:51 2019 -0500 Add getters for numNeighbors Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit d6463c1d015444a491803a0895522e91989d5885 Author: Weiqun Zhang Date: Wed Feb 13 11:28:15 2019 -0800 fsnapshot2d Tools/Plotfile/AMReX_PPMUtil.H Tools/Plotfile/AMReX_PPMUtil.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/Make.package Tools/Plotfile/fcompare.cpp Tools/Plotfile/fextract.cpp Tools/Plotfile/fextreama.cpp Tools/Plotfile/fnan.cpp Tools/Plotfile/fsnapshot2d.cpp commit d3e53077ec78af8250991d4b3b5703f7fac2eb90 Author: Weiqun Zhang Date: Wed Feb 13 09:40:05 2019 -0800 ParmParse: validate input by checking there are nothing left in the stream. For example 1.5.e7 is an invalid double. C++ istream will read it as 1.5 and leaves .e7 in the input stream. Src/Base/AMReX_ParmParse.cpp commit 4c5e77222095f7dd86aa005f44fa6cad445a0efc Author: Weiqun Zhang Date: Wed Feb 13 06:52:41 2019 -0800 Elixir: fix assertion in resize; don't own the pointer if not in gpu launch region Src/Base/AMReX_BaseFab.H commit 7be102528a5a3d3d70dac21b70a9ba87f76ebf60 Author: Andrew Myers Date: Tue Feb 12 20:12:30 2019 -0500 functions for setting the number of neighbor particles Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit 71214b5c2a0e87ae100d69b7e1057d3ef69cbac0 Merge: 4997a9a41 9fe04abe6 Author: Andrew Myers Date: Tue Feb 12 20:00:47 2019 -0500 Merge branch 'development' into gpu_neighbor_list commit 4997a9a4170b5a9ecc0e96077a5e689c3545a02f Author: Andrew Myers Date: Tue Feb 12 19:58:10 2019 -0500 sorting the particles by which neighbor they need to be copied to Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 7320b9054f44ad6410cb020625e481f1c21d0398 Author: Brandon Runnels Date: Tue Feb 12 17:38:27 2019 -0700 removed instrumentation and cleanded up GNUmakefile Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 213169d7a24f036f414f0fd32fd383d92ad15c15 Author: Andrew Myers Date: Tue Feb 12 18:34:50 2019 -0500 build mask data structure for sending particles to neighbors Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 0348ae195493be3998351b7c8fe308247a410d8a Author: Andrew Myers Date: Tue Feb 12 18:34:09 2019 -0500 distinction between real and ghost particles in ParticleTile Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit 9fe04abe6eb7a60019c03b9e43613b78da55ea88 Merge: e1a64f7a2 1318ed728 Author: Weiqun Zhang Date: Tue Feb 12 14:20:40 2019 -0800 Merge branch 'plotfiletools' into development commit 1318ed728e62f1525d82c67189ccfac338a2bfa9 Author: Weiqun Zhang Date: Tue Feb 12 14:20:21 2019 -0800 fextreama: make the output resemble fortran Src/Base/AMReX_CudaLaunch.H Tools/Plotfile/fextreama.cpp commit d1f49fe6c85ba1ae3787aa98bb730c22262c65e6 Author: Weiqun Zhang Date: Tue Feb 12 12:58:20 2019 -0800 fextract Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/fextract.cpp Tools/Plotfile/fextreama.cpp commit 3d19d71a999bd019500a9c2ca7a6f98bed9b3a8d Author: Brandon Runnels Date: Mon Feb 11 17:37:52 2019 -0700 initial working Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit e1a64f7a28ff6de01866388ace519fa2f59b0172 Author: Kevin Gott Date: Mon Feb 11 16:09:46 2019 -0800 Array4 const& Docs/sphinx_documentation/source/Basics.rst commit 316fcc81ece178a5050593581c56e8bbc049b7c7 Author: Kevin Gott Date: Mon Feb 11 13:01:15 2019 -0800 Missing semicolon in example. Docs/sphinx_documentation/source/Basics.rst commit 334d778c3958b56716084ce9476f143e8fdb0c1e Merge: f2d01623f 942e5d162 Author: WeiqunZhang Date: Mon Feb 11 12:07:59 2019 -0800 Merge pull request #408 from mwm126/patch-1 Fix typos commit 942e5d162a565ee5f0425aa4d5b72f84e6f53875 Author: Mark Meredith Date: Mon Feb 11 14:57:42 2019 -0500 Fix typos Docs/sphinx_documentation/source/BuildingAMReX.rst commit f2d01623f721f587a41bc3033f61a7a52be7d9bb Author: Kevin Gott Date: Mon Feb 11 11:47:57 2019 -0800 Update docs from FabView to Array4 style. Docs/sphinx_documentation/source/Basics.rst commit 27f2ac573238f3ac44b65ae106e681d2fc12ade7 Author: Weiqun Zhang Date: Mon Feb 11 14:21:17 2019 -0500 minor change of style Tutorials/GPU/CNS/Source/CNS_advance.cpp commit a95d72be5cc15a850a5e90837ab6adefd14c4085 Author: Weiqun Zhang Date: Mon Feb 11 14:20:27 2019 -0500 elixir: make sure T is trivially dectructible Src/Base/AMReX_BaseFab.H commit 72c02bab45953baf00693773ca84da2c8c9049d5 Author: Weiqun Zhang Date: Mon Feb 11 14:00:07 2019 -0500 fix fab stats Src/Base/AMReX_BaseFab.H commit 5bf393c2ed63c63ea5fc9ca0b429553cff3e22bf Author: Andrew Myers Date: Mon Feb 11 13:34:53 2019 -0500 tweak inputs Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs commit 23cb6133b1859bfc457be8b297b06c584dc72d9b Author: Weiqun Zhang Date: Sun Feb 10 11:00:01 2019 -0800 fix array initialization for C++11 Src/Base/AMReX_PlotFileDataImpl.H commit ef26b56015da6ca0ecc90157c93c3386c607c616 Author: Weiqun Zhang Date: Sun Feb 10 11:00:01 2019 -0800 fix array initialization for C++11 Src/Base/AMReX_PlotFileDataImpl.H commit 6aa0cd8cc08c14a5f9d48f45670309ec4070df1c Author: Weiqun Zhang Date: Sun Feb 10 09:54:20 2019 -0800 AsyncFab: add move ctor Src/Base/AMReX_CudaAsyncFab.H commit 31bdae254c5b108f62cc5e9a0c022343c0c42204 Merge: 5a9dd3393 47ab43431 Author: Weiqun Zhang Date: Sat Feb 9 22:36:53 2019 -0800 Merge branch 'plotfiletools' into development commit 5a9dd33939927ce2877dee639ca70d1f70f90956 Author: Weiqun Zhang Date: Sat Feb 9 22:08:55 2019 -0800 elixir Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaElixir.H Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_Gpu.H Src/Base/CMakeLists.txt Src/Base/Make.package commit cbdccf25628dfa1ad704ef37be94aec8c9abb37d Author: Max Katz Date: Sat Feb 9 21:43:49 2019 -0500 Add AsyncFab function to return the host data Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp commit 47ab43431c4550b1d9ecb7d59ad17e46d0cadbec Author: Weiqun Zhang Date: Sat Feb 9 17:01:48 2019 -0800 fextreams Tools/Plotfile/GNUmakefile Tools/Plotfile/fextreama.cpp commit 1e173b4d6a7cd763fdf2d94bbbaf30a5c7e99200 Author: Weiqun Zhang Date: Sat Feb 9 15:02:15 2019 -0800 finish fcompare Tools/Plotfile/fcompare.cpp commit 2be91abd29a622a02cecce6ecab2854691cf9312 Author: Max Katz Date: Sat Feb 9 17:10:40 2019 -0500 Skip plotfile if there's no variables to plot Src/Amr/AMReX_Amr.cpp commit b91ede01d284ecd89281d80ace376765ca6fca27 Author: Max Katz Date: Sat Feb 9 17:04:33 2019 -0500 Symmetrize small plot with full plot Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp commit 8e5c61668d8965fa56964c39a3f7d7e649cee2c6 Author: Weiqun Zhang Date: Sat Feb 9 13:02:04 2019 -0800 update to using PlotFileData in what we have so far Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_PlotFileDataImpl.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Base/AMReX_PlotFileUtil.H Tools/Plotfile/AMReX_AnyDimUtil.H Tools/Plotfile/AMReX_AnyDimUtil.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/Make.package Tools/Plotfile/fboxinfo.cpp Tools/Plotfile/fcompare.cpp Tools/Plotfile/fnan.cpp Tools/Plotfile/ftime.cpp Tools/Plotfile/fvarnames.cpp commit c9b6dd3a805345b3b40e86e684742a329ead1c8f Author: Max Katz Date: Sat Feb 9 15:39:21 2019 -0500 Fix fp comparison logic using machine epsilon Src/Amr/AMReX_Amr.cpp commit 15748a2f31c297867f97d086cc27a53757413c79 Author: Max Katz Date: Sat Feb 9 10:40:49 2019 -0800 Fix Cori build when linking with Fortran Tools/GNUMake/sites/Make.nersc commit 7aa5c4a58c3be9c9aa99dd139fdf22bb5a629d5d Author: atmyers Date: Sat Feb 9 10:27:40 2019 -0800 add note that the GPU Vector classes now use the memory Arenas provided by AMReX. Docs/sphinx_documentation/source/GPU.rst commit 2cbc641af286607b0ab0c2cb72f3ebe5fcab84fb Author: Ann Almgren Date: Fri Feb 8 23:00:58 2019 -0800 Fix bug in 3D GSRB cell-centered solve. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit b746a889627bb5cc4e03c159d52e17a28fcee9ac Author: Ann Almgren Date: Fri Feb 8 23:00:58 2019 -0800 Fix bug in 3D GSRB cell-centered solve. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit a84ad543870a4412c032dff3f0426ddbf01baf7b Author: Weiqun Zhang Date: Fri Feb 8 20:47:41 2019 -0800 PlotFileData::get for single component Src/Base/AMReX_PlotFileDataImpl.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_VisMF.H commit b8712014f8e896b51aca0259a4a2178f55d09299 Author: Weiqun Zhang Date: Fri Feb 8 17:02:38 2019 -0800 revert changes to AmrData Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Src/Extern/amrdata/CMakeLists.txt Src/Extern/amrdata/Make.package commit 0ea1dcf85848e97fca270ee4c190d539621d6eea Author: Weiqun Zhang Date: Fri Feb 8 16:51:53 2019 -0800 add PlotFileData for reading plotfiles Src/Base/AMReX_PlotFileDataImpl.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/Plotfile/GNUmakefile Tools/Plotfile/ftime.cpp commit 81c63ca4e33510f65c9a7843c718b260461ce653 Author: Brandon Runnels Date: Fri Feb 8 17:49:46 2019 -0700 modifying avergedownandsync Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 74f520d93b1f02511a9d63ad6a3656d94447d1be Merge: e60c3dbbd 41c86612d Author: Brandon Runnels Date: Fri Feb 8 17:17:52 2019 -0700 Merge branch 'development' into nodeghostcells commit b82c882750081d945471827c0d2f3e23d1500164 Merge: da798a3b1 c56e5ca23 Author: Weiqun Zhang Date: Fri Feb 8 13:43:17 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c56e5ca231eef7255f0bac72c476b97e3f9260cc Author: Weiqun Zhang Date: Fri Feb 8 13:12:06 2019 -0800 fix Machine for cori gpu and clean up make Src/Base/AMReX_Machine.cpp Tools/GNUMake/sites/Make.nersc commit 9519d79d86d748099f867f2f073102c4ed4cab27 Author: Andrew Myers Date: Fri Feb 8 13:01:57 2019 -0800 don't need travis wait anymore .travis.yml commit 3a6c8e810f44f798aec80d087a8128f1a612df47 Author: Andrew Myers Date: Fri Feb 8 12:44:53 2019 -0800 disable breathe for now build_and_deploy.sh commit e60c3dbbd1e444087a81ddd93c1d64aa55ee87de Author: Brandon Runnels Date: Fri Feb 8 13:36:27 2019 -0700 modified interpCorrection to NOT include ghost cells Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 41c86612da02af7242dfe6ff3b749da8a9fe9d4c Author: Weiqun Zhang Date: Fri Feb 8 10:40:36 2019 -0800 WIP: make for cori gpu Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.nersc commit 4cbbabec9fe4882d2634ce389d3702fe719cb4ba Author: Weiqun Zhang Date: Fri Feb 8 08:46:02 2019 -0800 fcompare wip Src/Base/AMReX.cpp Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/fcompare.cpp Tools/Plotfile/fnan.cpp Tools/Plotfile/ftime.cpp Tools/Plotfile/fvarnames.cpp commit 7073ffa0f249039d7848db851eb65479797e659e Author: Max Katz Date: Fri Feb 8 11:41:13 2019 -0500 Add floating point awareness to the plot_per/check_per logic The current logic can be slightly erroneous due to floating point issues. For example, if the timestep is 0.01 and the plot_per is 0.1, you would expect plotfiles at steps that are multiples of 10, but due to roundoff errors the current logic will sometimes plot in the 11th step instead of the 10th. By adding a small number to both sides of the comparison, we can guarantee plotting on exactly the timestep we intended. Src/Amr/AMReX_Amr.cpp commit aaae94ccb20bb74a99bb5cbf5962b9550d450a33 Merge: cde8229d6 676cea69b Author: Andrew Myers Date: Thu Feb 7 16:26:30 2019 -0800 Merge pull request #405 from MaxThevenet/development add tag to particles already split commit 676cea69ba66b2ccdf8e6405d57eb16552e2dbf5 Author: Maxence Thevenet Date: Thu Feb 7 16:23:52 2019 -0800 add tag to particles already split Src/Particle/AMReX_Particle.H commit cde8229d63cec4a52c1457daa340988d535bf421 Author: Andrew Myers Date: Thu Feb 7 18:17:14 2019 -0500 remove unused variables Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 7d4dfa1555570b39b20673eb74f3e917b19f7384 Author: Andrew Myers Date: Thu Feb 7 17:56:39 2019 -0500 make the nbor_list a map over tiles Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 73df3e41c63113ead79f287f95b56ffe222fc4a6 Author: Andrew Myers Date: Thu Feb 7 17:47:56 2019 -0500 copy the neigbor list to host before printing Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 2b5d0bf90b246fc3a31ba5ef890e5e9a5ff4566f Author: Andrew Myers Date: Thu Feb 7 17:44:00 2019 -0500 read print_neighbor_list from inputs Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 1d345374c6f4a73ff98a55ecf1a599af6e49d08d Author: Andrew Myers Date: Thu Feb 7 17:41:19 2019 -0500 move printNeighborList to its own method Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 686998be828c1e71b913a110aeee3550291c7a55 Author: Andrew Myers Date: Thu Feb 7 17:38:05 2019 -0500 move computeForces to a separate method Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/main.cpp commit f8a1119a38ec87eda659038334fddd60f14e2024 Author: Andrew Myers Date: Thu Feb 7 17:32:08 2019 -0500 make the neighbor list a class member Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 0a81cf9b12636464c5d778348672768e3bc38adf Author: Andrew Myers Date: Thu Feb 7 17:25:11 2019 -0500 thrust::raw_pointer_cast -> dataPtr() Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit a8d1946249c80285d96a5a426a69927e15446464 Author: Andrew Myers Date: Thu Feb 7 17:21:18 2019 -0500 thrust::device_vector -> Gpu::DeviceVector Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 2ad5bad614f5aeb9ede4b0c4105d5185fcf5a8a8 Merge: c525335bb 6b4de63f6 Author: Andrew Myers Date: Thu Feb 7 16:27:50 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c525335bb49f116b76bf38e0832d8f5a2151322f Author: Andrew Myers Date: Thu Feb 7 16:19:47 2019 -0500 don't need a separate cached allocator now Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp commit 48df6fcbf98363676a3c991e9774e9b573b0328c Author: Andrew Myers Date: Thu Feb 7 15:34:10 2019 -0500 remove the remaining device_vector members from ParticleContainer; temporaries now work fine. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 9fd93ab27323c4a8492d135183726fd76b85a34e Author: Andrew Myers Date: Thu Feb 7 15:01:35 2019 -0500 remove some more of the mutable thrust::device_vector members from the ParticleContainer Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 45fa9cd5b2561872c46424e6df82eec35886769a Author: Andrew Myers Date: Thu Feb 7 14:52:32 2019 -0500 remove some of the mutable thrust::device_vector members from the ParticleContainer Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 6ea1bebb09f66813622055271f34a96403c2aaa2 Author: Andrew Myers Date: Thu Feb 7 14:46:06 2019 -0500 thrust::device_vector -> Gpu::DeviceVector Src/Particle/AMReX_Particles.H commit e8daa3c420edfd90ced989bb7696e90064451b53 Author: Andrew Myers Date: Thu Feb 7 14:34:27 2019 -0500 use the Arena in Gpu::DeviceVector Src/Base/AMReX_CudaContainers.H commit d4a616dd3591b384d7104c13658888abc64d8fc6 Author: Andrew Myers Date: Thu Feb 7 14:34:05 2019 -0500 add thrust allocators that are implemented in terms of AMReX's Arenas Src/Base/AMReX_CudaAllocators.H commit ffd2a3fe062fe64627686961767c8c17cebcf8f4 Author: Brandon Runnels Date: Thu Feb 7 11:12:56 2019 -0700 fixed mlcg to be consistent Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 6b4de63f6e0434fe5c0e8e5478731bec80e65863 Author: Ann Almgren Date: Thu Feb 7 06:44:51 2019 -0800 Remove IMEX_Advec_Diff_C from the Tutorials documentation Docs/sphinx_tutorials/source/SDC_Tutorial.rst commit 3f7088a49c3b4878052e862bcd452929f2c79756 Author: Ann Almgren Date: Thu Feb 7 06:44:07 2019 -0800 Remove IMEX_Advec_Diff_C per Minion's guidance -- this is deprecated. Tutorials/SDC/IMEX_Advec_Diff_C/GNUmakefile Tutorials/SDC/IMEX_Advec_Diff_C/Make.package Tutorials/SDC/IMEX_Advec_Diff_C/advance.cpp Tutorials/SDC/IMEX_Advec_Diff_C/advance_2d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_2d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_3d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/inputs_2d Tutorials/SDC/IMEX_Advec_Diff_C/inputs_3d Tutorials/SDC/IMEX_Advec_Diff_C/main.cpp Tutorials/SDC/IMEX_Advec_Diff_C/myfunc.H Tutorials/SDC/IMEX_Advec_Diff_C/myfunc_F.H commit 53d4c0a3ed3c4159f5dbb292188f0358fbb37410 Author: Weiqun Zhang Date: Wed Feb 6 20:50:44 2019 -0800 clean up Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp commit 8ca1dbc065049971094b6fcc92561df0382b4962 Author: Weiqun Zhang Date: Wed Feb 6 17:55:57 2019 -0800 fnan Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Tools/Plotfile/GNUmakefile commit a265c0a1d5d92f64d20becb798556f2049ec54c0 Author: Weiqun Zhang Date: Wed Feb 6 16:30:33 2019 -0800 ftime Tools/GNUMake/Make.rules Tools/Plotfile/GNUmakefile Tools/Plotfile/fboxinfo.cpp Tools/Plotfile/ftime.cpp Tools/Plotfile/fvarnames.cpp commit 8c80a3299957af0e361a74ff632bd6e8caaf08b4 Author: Andrew Myers Date: Wed Feb 6 19:20:42 2019 -0500 restore cuda-aware mpi option to the particle container. Src/Particle/AMReX_Particles.H commit 6afc477f607378656b05a74b467fe2ae767a8abd Author: Andrew Myers Date: Wed Feb 6 19:20:25 2019 -0500 a vector based on same Src/Base/AMReX_CudaContainers.H commit 3ca4c173bc132007de204fddd50d661b2c2ab591 Author: Andrew Myers Date: Wed Feb 6 19:20:14 2019 -0500 a new allocator that can toggle between pinned and device memory at runtime Src/Base/AMReX_CudaAllocators.H commit 8ea054eb4e6b465637f5a3e9a63876a2cae1872f Author: Weiqun Zhang Date: Wed Feb 6 16:11:05 2019 -0800 fvarnames Tools/Plotfile/GNUmakefile Tools/Plotfile/fvarnames.cpp commit 46bf0a6c851968ab671b92f41eb99796bd061926 Author: Weiqun Zhang Date: Wed Feb 6 15:47:18 2019 -0800 dimension agnostic fboxinfo Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Tools/Plotfile/AMReX_AnyDimUtil.H Tools/Plotfile/AMReX_AnyDimUtil.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/Make.package Tools/Plotfile/fboxinfo.cpp commit 3714926b9508f01f79a602a0d8f1c9efc23b01b5 Author: Andrew Myers Date: Wed Feb 6 18:45:26 2019 -0500 some reorganization Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/main.cpp commit 3e078c66a2ef6df8518dea6daf043c1da42a3e54 Author: Andrew Myers Date: Wed Feb 6 18:33:14 2019 -0500 fix bug Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 2f4e526bc2bc5903ab01b666d985cb62cb82e385 Author: Andrew Myers Date: Wed Feb 6 18:06:33 2019 -0500 removing is_per Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 1c042152ac8b10c2926eee599280d49352f22fba Author: Andrew Myers Date: Wed Feb 6 18:06:00 2019 -0500 implement looping over the neighbor list and moving the particles Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 500934cec055fa0dea360691af579db2ef17583d Author: Andrew Myers Date: Wed Feb 6 17:08:26 2019 -0500 hardwire nppc to (1, 1, 1) Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 0f677bbad39d1cda47739e225dcc188144e58271 Author: Andrew Myers Date: Wed Feb 6 17:07:49 2019 -0500 tweak cutoff Tests/Particles/GPUNeighborList/Constants.H commit 6102c91b84f9234e29f6303ea8323e789da73d85 Author: Andrew Myers Date: Wed Feb 6 16:28:05 2019 -0500 workaround for relaxed constexpr bug in cuda 9.2 Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 34cad51a8538a3e421baf7ca9c52081a146566a5 Author: Andrew Myers Date: Wed Feb 6 13:17:01 2019 -0800 tweak build and deploy build_and_deploy.sh commit 9238a3e3da15f1d056144e353ed7b91040d8d1b7 Author: Andrew Myers Date: Wed Feb 6 12:53:04 2019 -0800 add travis_wait before running the build script .travis.yml commit 093e21e855dcee39d57036fe7bd0f85973f5cd3e Author: Andrew Myers Date: Wed Feb 6 12:27:42 2019 -0800 hide more output build_and_deploy.sh commit 156800ff9a05dda14bac7ef0e7055a77d9fda363 Author: Andrew Myers Date: Wed Feb 6 11:56:05 2019 -0800 hide the doxygen output, which puts us over the log file length limit on Travis CI build_and_deploy.sh commit 1975f1bef9f9ee4dbaffd6353a9b2adb917f85a6 Author: Andrew Myers Date: Wed Feb 6 11:27:06 2019 -0800 restore stuff for latexpdf .travis.yml commit f716c1ec7855c6d39c90a3d34884875c933ecfb4 Author: Andrew Myers Date: Wed Feb 6 11:06:06 2019 -0800 don't specify python3.6 in the build_and_deploy script build_and_deploy.sh commit 0195cc654bfa2c5d2437fa38f31295f217f035ba Author: Andrew Myers Date: Wed Feb 6 10:45:16 2019 -0800 also need libmpich-dev .travis.yml commit 7f334444316527fadd3affce7c2f92338726b973 Author: Andrew Myers Date: Wed Feb 6 10:40:50 2019 -0800 remove extra addons entry .travis.yml commit e1cd32ec8d0b2c9db4c76d9359f706a4117fec0f Author: Andrew Myers Date: Wed Feb 6 10:22:08 2019 -0800 tweak installed packahed .travis.yml commit e1bac9fba731d6ff9a4a5a84853359eca6161683 Merge: 81e1a48db 9b498798f Author: Andrew Myers Date: Wed Feb 6 10:14:42 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 81e1a48db7b77fd72889151db02cd0c430e50c50 Author: Andrew Myers Date: Wed Feb 6 10:14:30 2019 -0800 remove ubuntu-toolchain-r-test .travis.yml commit cf4ad88b1907534cc7e25a8b598a81135347de1e Author: Weiqun Zhang Date: Tue Feb 5 21:45:59 2019 -0800 add PlotfileData as a wrapper of DataServices Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Src/Extern/amrdata/CMakeLists.txt Src/Extern/amrdata/Make.package commit 9b498798f2b743beb4347db246e9f3671bd43c7d Merge: c0a0a1b20 aae1e389b Author: Andrew Myers Date: Tue Feb 5 21:29:11 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c0a0a1b20487bc5b07f132a4643da612bdb0fcd8 Merge: f9167057d 7a51ec74f Author: Andrew Myers Date: Tue Feb 5 21:28:47 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit aae1e389be1fdd3f16f1cbd8f0d3e65ca4e9fbe4 Author: Marc Day Date: Tue Feb 5 18:28:38 2019 -0800 Add sig for WritePltFile that takes an alternative prob domain array Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp commit f9167057d2ac2deea44ae4f2137ebe479fc4a47f Author: Andrew Myers Date: Tue Feb 5 21:28:28 2019 -0500 fix bug involving asynchronous mem copies with Cuda Src/Particle/AMReX_ParticleContainerI.H commit 7a51ec74f14bdd60fd6b2d082a64fc1f32c4c13f Author: Andrew Myers Date: Tue Feb 5 17:53:04 2019 -0800 specify sources .travis.yml commit 7b254ea26fc7685b33a71de0d08b371f2bf8e655 Author: Andrew Myers Date: Tue Feb 5 17:43:49 2019 -0800 add python to PATH .travis.yml commit 182494f93815e1f95e79d51d17b31da0073b010c Author: Andrew Myers Date: Tue Feb 5 17:37:49 2019 -0800 tweak pip install line .travis.yml commit 2381bba51c1eabf3a44ee65943a38c2b2723f300 Author: Andrew Myers Date: Tue Feb 5 17:35:46 2019 -0800 change language. .travis.yml commit 6c5b69981e1528d64716ea2e4040e4af304d118f Author: Andrew Myers Date: Tue Feb 5 17:30:25 2019 -0800 trying to fix the Travis build environment .travis.yml commit 74bc78064c0e86384345a17816cb8d63bd19b424 Merge: bae6b14c2 34e2b1e60 Author: Andrew Myers Date: Tue Feb 5 17:22:25 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 34e2b1e60bade5687bf02cf37e249329c0cdd02c Author: Kevin Gott Date: Tue Feb 5 20:15:36 2019 -0500 Get rid of 9.2.x limitation in GPU docs. Docs/sphinx_documentation/source/GPU_Chapter.rst commit 0795a00963a42a72f8989cb87fd82fa7637e2d15 Merge: d38878212 349a8360a Author: Ann Almgren Date: Tue Feb 5 17:10:00 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit bae6b14c287d83d43dfb3927ddbd80e7e5777fd1 Author: Andrew Myers Date: Tue Feb 5 17:08:06 2019 -0800 bump python version .travis.yml commit 0cf8d19ba5545fa91382b2106d959550b1c64e21 Author: Brandon Runnels Date: Tue Feb 5 18:07:19 2019 -0700 wip - crude updates to allow ghost cell based reflux Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 349a8360a13cb8af81b2df7433fa3b908809e28a Merge: 286a739c0 dc9138bfa Author: Andrew Myers Date: Tue Feb 5 17:02:52 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 286a739c0e181b708ebf7e43675981b8ea19258a Author: Andrew Myers Date: Tue Feb 5 17:02:41 2019 -0800 mpich2 -> mpich .travis.yml commit d3887821212953f5f7a77dfeb793d4b70d0a4c9f Author: Ann Almgren Date: Tue Feb 5 17:02:11 2019 -0800 Fix oops -- this now compiles. Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit dc9138bfa9ee936314e6bc5de1b361731b925984 Merge: fc76b489f 2349a8f55 Author: Ann Almgren Date: Tue Feb 5 16:58:56 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit fc76b489f784d791a7e061fc1e1c17f7ce26569f Author: Ann Almgren Date: Tue Feb 5 16:58:19 2019 -0800 Move interpolate_to_face_centroid routine from mfix into amrex since it is completely general. Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit 2349a8f55a08ee8c84a85cc540c3fef62ae7068f Merge: 752fa858c ebe912f83 Author: Andrew Myers Date: Tue Feb 5 16:57:28 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 752fa858c60d06b5fe8c642d60639369572e0ecc Author: Andrew Myers Date: Tue Feb 5 16:57:14 2019 -0800 update ubuntu version used by travis .travis.yml commit ebe912f83371535ed77fb64b7af46c9c0cf4600b Author: Kevin Gott Date: Tue Feb 5 19:40:09 2019 -0500 buildNotused, testing how to build AMReX as a library around user-defined functions. Tests/GPU/buildNotused/Extern.H Tests/GPU/buildNotused/GNUmakefile Tests/GPU/buildNotused/MyKernel.H Tests/GPU/buildNotused/MyKernel.cpp Tests/GPU/buildNotused/MyKernelB.H Tests/GPU/buildNotused/MyKernelB.cpp Tests/GPU/buildNotused/Notused.H Tests/GPU/buildNotused/Notused.cpp Tests/GPU/buildNotused/Readme Tests/GPU/buildNotused/main.cpp commit 1fdf0538d75c0c196a273a09ad391bfd772f3d72 Author: Andrew Myers Date: Tue Feb 5 16:25:56 2019 -0800 add AddParticles method and implement copyParticles in terms of that. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 80545e9c9b72f7611be0a0adb9d32932154f675c Author: Andrew Myers Date: Tue Feb 5 18:32:48 2019 -0500 do custom partition by default Src/Particle/AMReX_ParticleContainerI.H commit 77bdd5dd53dd9fc4e538bdb555b8cd17f82d034d Author: Andrew Myers Date: Tue Feb 5 18:32:19 2019 -0500 add option to switch between versions of partition Src/Particle/AMReX_ParticleContainerI.H commit da798a3b1039eff770c4cb7a63b6d2d546ad6131 Author: Weiqun Zhang Date: Tue Feb 5 14:45:39 2019 -0800 add Fortran 2003 style command argument functions Src/Base/AMReX.H Src/Base/AMReX.cpp commit 9409b1f266c426293c8fc24fea59cd6358fb55b2 Author: Weiqun Zhang Date: Tue Feb 5 14:13:07 2019 -0800 fix merge Src/Particle/AMReX_Particles.H commit f830c2bb95da2ac07046e9955086493e893f2256 Author: Weiqun Zhang Date: Tue Feb 5 13:39:54 2019 -0800 fix merge Src/Particle/AMReX_Particles.H commit f690ecf6ca9c1c3266dc5be9fd755e521fa5b551 Merge: 2f2c3cf08 7710e67e9 Author: Weiqun Zhang Date: Tue Feb 5 13:32:47 2019 -0800 Merge branch 'development' into dev-tmp commit 7710e67e9beae8a4ff85f0061ce919e47660060e Merge: 529e816df 95206d278 Author: Weiqun Zhang Date: Tue Feb 5 13:29:14 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2f2c3cf08ae71bfb5beff6d747b4655a6a45b2a5 Merge: 8cbed0da9 d2c67c019 Author: WeiqunZhang Date: Tue Feb 5 13:24:35 2019 -0800 Merge pull request #403 from harpolea/doxygen Doxygen commit 529e816df39274a47e9984bc2eaf3ede0484b2fa Author: Weiqun Zhang Date: Tue Feb 5 13:23:41 2019 -0800 add make option for multiple executables Tools/GNUMake/Make.rules commit 95206d278d3a4afe260856c40d9539b8c983cb65 Author: Ann Almgren Date: Tue Feb 5 12:53:46 2019 -0800 Add EB_set_covered call at end of reflux routine. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d2c67c019deb5e1b23361b5fdc590ed45be04ccd Author: Alice Harpole Date: Tue Feb 5 15:36:19 2019 -0500 moves doxygen and breathe steps to build_and_deply Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/source/conf.py build_and_deploy.sh commit 66499da6ca57cc7a53bc20124f5f30942864be5b Merge: 2e4d7b025 42f8d1df6 Author: Weiqun Zhang Date: Tue Feb 5 10:34:53 2019 -0800 Merge branch 'development' into weiqun/gpu commit 2e4d7b02582588776c885cf1b9f5e92b3b6e7bfa Author: Weiqun Zhang Date: Tue Feb 5 10:33:43 2019 -0800 MLMG on GPU: fix eb and put some comments Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 42f8d1df6829f13969131126c3dc86af0c5580cc Author: Ann Almgren Date: Tue Feb 5 09:57:01 2019 -0800 "OldMiniApps" was too old to be relevant. OldMiniApps/FillBoundary/GNUmakefile OldMiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp OldMiniApps/FillBoundary/README OldMiniApps/FillBoundary/qsub.ipm.bat OldMiniApps/MultiGrid_C/COEF_3D.F OldMiniApps/MultiGrid_C/COEF_F.H OldMiniApps/MultiGrid_C/GNUmakefile OldMiniApps/MultiGrid_C/Make.package OldMiniApps/MultiGrid_C/README OldMiniApps/MultiGrid_C/RHS_3D.F OldMiniApps/MultiGrid_C/RHS_F.H OldMiniApps/MultiGrid_C/main.cpp OldMiniApps/MultiGrid_C/qsub.ipm.bat commit 435dee40d59424259c35598c30c43c8bec446047 Author: Ann Almgren Date: Tue Feb 5 09:42:50 2019 -0800 Remove seriously old post-processing routines from Tools/Postprocessing/F_Src that were specific to certain applications. Tools/Postprocessing/F_Src/old_flame/GNUmakefile Tools/Postprocessing/F_Src/old_flame/fbubble_position.f90 Tools/Postprocessing/F_Src/old_flame/fbubble_position_3d.f90 Tools/Postprocessing/F_Src/old_flame/fcusp.f90 Tools/Postprocessing/F_Src/old_flame/fcylflame.f90 Tools/Postprocessing/F_Src/old_flame/fflamelength.f90 Tools/Postprocessing/F_Src/old_flame/finteg.f90 Tools/Postprocessing/F_Src/old_flame/fturbkin.f90 Tools/Postprocessing/F_Src/old_flame/fwidth.f90 Tools/Postprocessing/F_Src/tutorial/GNUmakefile Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90 Tools/Postprocessing/F_Src/tutorial/fwrite2d.f90 commit bd6b8daa47cee89cd458e6a150d70c835b898d06 Author: Weiqun Zhang Date: Tue Feb 5 09:33:53 2019 -0800 MLMG on GPU: flux Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/Make.package commit 26604b385b9a4c96b15894f95f24fbc3dcee11a2 Author: Weiqun Zhang Date: Tue Feb 5 08:34:22 2019 -0800 remove F_MG from inputs OldTutorials/MultiGrid_C/inputs OldTutorials/MultiGrid_C/inputs-rt-c-neu OldTutorials/MultiGrid_C/inputs-rt-c-ord2 OldTutorials/MultiGrid_C/inputs-rt-f-neu OldTutorials/MultiGrid_C/inputs-rt-f-ord2 OldTutorials/MultiGrid_C/inputs-rt-f-ord3 Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord2 Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord3 Tests/LinearSolvers/ComparisonTest/inputs-rt-Neu Tests/LinearSolvers/ComparisonTest/inputs.3d commit 4aa66c8ad9b0a6aac077fd168305eaca477ffc3b Merge: bb07a2dcf 9c4a00ba8 Author: Andrew Myers Date: Mon Feb 4 20:46:07 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bb07a2dcf73d2ce9723783c5dc53c40ef3d07437 Author: Andrew Myers Date: Mon Feb 4 20:41:18 2019 -0500 fixing bug with freeing the snd_buffer for pinned memory in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d0ebff754e8ddcce2a3748711848f2e4f0708b43 Author: Andrew Myers Date: Mon Feb 4 20:40:36 2019 -0500 fixes for the ThrustPinnedAllocator Src/Base/AMReX_CudaAllocators.H commit 9c4a00ba82bcb2517202fbf970f9ae18ffc3464d Merge: 1f8cf421f 14cc8c91d Author: Andrew Myers Date: Mon Feb 4 17:26:10 2019 -0800 Merge pull request #404 from ylunalin/new_heat_tutorials New heat tutorials commit 1f8cf421f18644ce9d8a4f030178f61d182ec03f Author: Kevin Gott Date: Mon Feb 4 20:13:53 2019 -0500 Clean up hybrid makefile. Tests/GPU/buildHybrid/GNUmakefile commit 529418cb0c33162b0990254ddaf9b40a41667256 Author: Andrew Myers Date: Mon Feb 4 20:11:01 2019 -0500 ifdef the PinnedDeviceVector to be a regular Vector if CUDA is off Src/Base/AMReX_CudaContainers.H commit 83fb3f1cea7df966ea59ee5dec60da23998c1e96 Author: Kevin Gott Date: Mon Feb 4 20:10:48 2019 -0500 Bug fix and eliminate unneeded library and include lines when invoking nvcc and pgfortran. Tests/GPU/buildTest/GNUmakefile commit ce2a824764a1de6f75d77984b176969adc06902e Author: Andrew Myers Date: Mon Feb 4 20:10:12 2019 -0500 add PinnedDeviceVector Src/Base/AMReX_CudaContainers.H commit 14cc8c91d59c003bec7237ba57f715c4152896a3 Merge: c68d326e5 bc4ed41c2 Author: Luna Lin Date: Mon Feb 4 20:04:55 2019 -0500 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into new_heat_tutorials commit c68d326e5cb5a5f19b57f7b5e37466fd9acb8133 Author: Luna Lin Date: Mon Feb 4 20:04:29 2019 -0500 Fixed a typo in the CUDA version, and the multiple lines issue in mykernel.H Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/mykernel.H commit 0a4ba07172ac7a1c7ad2edcce55b6710b6d9f573 Author: Andrew Myers Date: Mon Feb 4 19:59:59 2019 -0500 templated pinned allocator that can be used with thrust::device_vector Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp commit 6ce0de9607f7db0a2df6e2e3de023affe2a737b4 Author: Andrew Myers Date: Mon Feb 4 19:22:10 2019 -0500 remove some private members that aren't used anymore from ThrustCachedAllocator Src/Base/AMReX_CudaAllocators.H commit f63d3f7600b083ef3c519f36f658a45aad29a99f Author: Andrew Myers Date: Mon Feb 4 19:18:02 2019 -0500 a Pinned allocator for use with Thrust Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp commit bc4ed41c2a27e6b736ad2ccd98769cf35ecf1fba Author: Ann Almgren Date: Mon Feb 4 13:01:38 2019 -0800 Remove F_BaseLib. Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 6348c99eed30c106688523ec38fe2c4d6119671a Author: Ann Almgren Date: Mon Feb 4 13:00:26 2019 -0800 Remove F_BaseLib. Tests/LinearSolvers/C_CellMG/GNUmakefile commit 10e526313b3a6ea495906cae71f06565e869bce7 Author: Ann Almgren Date: Mon Feb 4 12:54:19 2019 -0800 Remove use of F_MG solvers OldTutorials/MultiGrid_C/GNUmakefile OldTutorials/MultiGrid_C/main.cpp OldTutorials/PIC_C/solve_with_f90.cpp OldTutorials/README_F commit edbf4c97d228111cc9f46df03a295532d84fc39e Author: Andrew Myers Date: Mon Feb 4 12:50:33 2019 -0800 rename solve_with_f90 OldTutorials/PIC_C/Make.package OldTutorials/PIC_C/solve_with_mlmg.cpp commit 6ca892bbe00a3e7c5a17028661daf7e1d2916d8a Merge: 47436c85b c279841a2 Author: Ann Almgren Date: Mon Feb 4 12:43:36 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 47436c85bab2afe64650abd38d6c8e57ba45835c Author: Ann Almgren Date: Mon Feb 4 12:43:23 2019 -0800 Remove reference to F_MG or C_to_F_MG. Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 8d8b12dbc3beefdc3cc0c36fb7d6c9633e7cce8d Author: Andrew Myers Date: Mon Feb 4 12:34:09 2019 -0800 fix compilation / linking OldTutorials/PIC_C/GNUmakefile OldTutorials/PIC_C/main.cpp OldTutorials/PIC_C/single_level.cpp OldTutorials/PIC_C/solve_for_accel.cpp OldTutorials/PIC_C/solve_with_f90.cpp OldTutorials/PIC_C/two_level.cpp commit 464c2bad38bb5406a448bc9af5a50ec274075ee5 Author: Andrew Myers Date: Mon Feb 4 11:12:15 2019 -0800 update GNUmakefile for new linear solver libraries. OldTutorials/PIC_C/GNUmakefile commit c279841a27ba20a3ac1acf426b3b664596d65d55 Author: Andrew Myers Date: Mon Feb 4 11:01:29 2019 -0800 removed old CUDA Fortran example of PIC deposition. Tests/Particles/ManagedCUDADeposition/GNUmakefile Tests/Particles/ManagedCUDADeposition/Make.package Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/inputs Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp commit 2c728f256ebdf1bed90b898c21a6fc0aab8c685f Author: Ann Almgren Date: Mon Feb 4 10:52:13 2019 -0800 Remove all use of F_MG solvers. Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/bc_interp.f90 Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_rhs.f90 Tests/LinearSolvers/F_MG/grids_2d_1lev Tests/LinearSolvers/F_MG/grids_2d_2lev Tests/LinearSolvers/F_MG/grids_3d_1lev Tests/LinearSolvers/F_MG/grids_3d_2lev Tests/LinearSolvers/F_MG/init_cell_coeffs.f90 Tests/LinearSolvers/F_MG/inputs.2d.fcycle Tests/LinearSolvers/F_MG/inputs.2d.fcycle.dir Tests/LinearSolvers/F_MG/inputs.2d.nodal.cross Tests/LinearSolvers/F_MG/inputs.2d.nodal.dense Tests/LinearSolvers/F_MG/inputs.2d.vcycle Tests/LinearSolvers/F_MG/inputs.2d.vcycle.dir Tests/LinearSolvers/F_MG/inputs.3d.fcycle Tests/LinearSolvers/F_MG/inputs.3d.fcycle.dir Tests/LinearSolvers/F_MG/inputs.3d.nodal.cross Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense Tests/LinearSolvers/F_MG/inputs.3d.vcycle Tests/LinearSolvers/F_MG/inputs.3d.vcycle.dir Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/makefile Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_rhs.f90 Tests/LinearSolvers/F_MG/regression Tests/LinearSolvers/F_MG/t_smoother.f90 Tests/LinearSolvers/F_MG/t_stencil.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 393c23276fa616a12b6e2b975d33269aa35f57dc Author: Ann Almgren Date: Mon Feb 4 10:42:42 2019 -0800 Remove F_MG and C_to_F_MG. Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H Src/LinearSolvers/C_to_F_MG/Make.package Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_norm.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_applyop.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sum.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil_types.f90 Src/LinearSolvers/F_MG/stencil_util.f90 Src/LinearSolvers/F_MG/tridiag.f90 commit 8cbed0da9fea9f0b16d86421847b24ed318e7df0 Author: Weiqun Zhang Date: Mon Feb 4 08:48:31 2019 -0800 BOUND_CHECK as an option Src/Base/AMReX_Array.H Tools/GNUMake/Make.defs commit bb5e91303ac3f36b39d3261fcdfa67c9ed6dce05 Author: Alice Harpole Date: Mon Feb 4 11:09:26 2019 -0500 fixed a few bugs and cleaned up Src/Base/AMReX_iMultiFab.H Src/Extern/CVODE/cvode_interface.f90 Src/Extern/CVODE/fnvector_serial.f90 Src/Extern/CVODE/sundials_fdlsmat.f90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90 Src/SDC/AMReX_SDCstruct.H commit 67485ad8beefb6a7c83ec07d5359b0f9e3ed7958 Merge: f5ec341eb 06e715811 Author: Alice Harpole Date: Mon Feb 4 10:26:06 2019 -0500 fixed merge conflicts commit f5ec341eb87853f79034f4a0d5375b74efa1a39e Author: Alice Harpole Date: Mon Feb 4 10:23:41 2019 -0500 fixed bugs in AMReX_Particles.H Src/Particle/AMReX_Particles.H commit 33c3b059763c55e2e25c10e21202ec3c17f3b72d Author: Weiqun Zhang Date: Sat Feb 2 16:52:02 2019 -0800 MLMG on GPU: normalize Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit a88ff2e992f3a70c281c158cd1a33fac2e35bd4b Author: Weiqun Zhang Date: Sat Feb 2 15:49:38 2019 -0800 fix variable type and function name Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit a2154590230fce32ae1a4399ec44035ae6586a3d Author: Weiqun Zhang Date: Sat Feb 2 15:05:40 2019 -0800 MLMG on GPU: MLABecLap A dot x Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/Make.package commit 06e715811324c5645e561030dbd3e2460416498d Author: Weiqun Zhang Date: Sat Feb 2 14:03:22 2019 -0800 update tutorial documentation Docs/sphinx_tutorials/source/GPU_Tutorial.rst commit 36c163ac211be87d842ee48ef5a1d97b6ed8b8e5 Merge: 5a5b5ffc7 337767790 Author: Luna Lin Date: Sat Feb 2 16:51:22 2019 -0500 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into new_heat_tutorials commit 5a5b5ffc770e10c5f502b407321e3ba6b87325fc Author: Luna Lin Date: Sat Feb 2 16:50:49 2019 -0500 GNUMakefile needed to be tweaked to work with new directory organization. Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/GNUmakefile commit 337767790e4d0d3b3b8ce7755b5624a1ca6911c6 Author: Weiqun Zhang Date: Sat Feb 2 13:49:44 2019 -0800 fix 1d interpbndrydata Src/Boundary/AMReX_InterpBndryData_1D_K.H commit 75cd2e3dd6a7b5245c5c329eb57d04c861fe9d14 Author: Weiqun Zhang Date: Sat Feb 2 13:49:44 2019 -0800 fix 1d interpbndrydata Src/Boundary/AMReX_InterpBndryData_1D_K.H commit 21222a1aac8ab8e6cf4d80856307239840cf1e43 Author: Weiqun Zhang Date: Sat Feb 2 13:49:28 2019 -0800 MLMG on GPU: lin_cc_interp Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H Src/LinearSolvers/MLMG/AMReX_MLMG_K.H Src/LinearSolvers/MLMG/Make.package commit 34a88e4e3b0ede6bc3694cd0a89faa72fb782f17 Merge: 3eb2f4b5b 19a8211e8 Author: Weiqun Zhang Date: Sat Feb 2 08:51:32 2019 -0800 Merge branch 'development' into weiqun/gpu commit 19a8211e85b21d200bcee629a415f236842aa326 Author: Weiqun Zhang Date: Sat Feb 2 11:51:08 2019 -0500 fix the version detection macro Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp Tutorials/GPU/CNS/Source/CNS_K.H commit 3eb2f4b5b3880456a29510b1b156a4c0fcf6b5ea Author: Weiqun Zhang Date: Sat Feb 2 08:26:13 2019 -0800 use amrex::ParallelFor Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_derive.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp commit 526f31eefa29f4d8b7da017216ebb9f26804e8bd Merge: 72f542c13 d1bee05cc Author: Weiqun Zhang Date: Sat Feb 2 01:34:40 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 72f542c139ba5dfa3b1b2878f63d3a68eb381885 Author: Weiqun Zhang Date: Sat Feb 2 00:32:29 2019 -0500 avoid using relaxed constexpr for nvcc 9.2 to get around its bug Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp Tools/GNUMake/comps/nvcc.mak Tutorials/GPU/CNS/Source/CNS_K.H commit d1bee05cc5dc22572123d0f374ba4be4b8d8ef81 Author: Andrew Myers Date: Fri Feb 1 19:58:26 2019 -0500 std::cout -> amrex::Print() Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit b575c698b306edd71a0f913cf228a407b050b849 Author: Andrew Myers Date: Fri Feb 1 19:54:54 2019 -0500 add device function for checking a pair of particles Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/Make.package Tests/Particles/GPUNeighborList/md_K.H commit 9313e3c985be47f719f2f5ca203b47639f79e78a Merge: aefa439c7 ae1893aed Author: Andrew Myers Date: Fri Feb 1 19:40:49 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit aefa439c75fa30665ec15e086dd7529c25d8bfee Author: Andrew Myers Date: Fri Feb 1 19:40:30 2019 -0500 Test for building neighbor list data structure using CUDA/Thrust for Nvidia GPUs Tests/Particles/GPUNeighborList/Constants.H Tests/Particles/GPUNeighborList/GNUmakefile Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/Make.package Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit ae1893aed49e7c734cbb596a756ab1af15dc0391 Merge: 0c9d4855f 85b719bb3 Author: Weiqun Zhang Date: Fri Feb 1 16:13:09 2019 -0800 Merge branch 'weiqun/gpu' into development commit 85b719bb35554a6eb2ab11c5bea2b25fb38cadaa Author: Weiqun Zhang Date: Fri Feb 1 16:11:32 2019 -0800 change the default back to managed Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.olcf commit e62cdd9827b835b3f8eb3d3944492c7268838184 Author: Luna Lin Date: Fri Feb 1 18:13:15 2019 -0500 Added OpenACC + OpenMP versions to HeatEquation_EX1_C and reorganize the tutorial directory. Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/mykernel.H Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.ascent Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.nocuda.script Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.summit Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/mykernel.F90 Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/mykernel.F90 Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/Make.HEAT Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 341cca3c724102193d9d22aa0490fb95237ed5a8 Author: Weiqun Zhang Date: Fri Feb 1 15:04:42 2019 -0800 pinned version of AsyncFabImpl Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit d58b06e9e368eac2af3685e80f99745afcd68953 Author: WeiqunZhang Date: Fri Feb 1 14:11:22 2019 -0800 Add zenodo badge README.md commit 5ab9242b5603f738790cab1d78b411ed17ee3f54 Author: Alice Harpole Date: Fri Feb 1 17:00:20 2019 -0500 add breathe to .travis.yml file .travis.yml commit a077ca49290353cdba0a7ca813ad35b7cb5a4b2e Merge: 6a4f5292e 0c9d4855f Author: Alice Harpole Date: Fri Feb 1 16:56:05 2019 -0500 fixed merge conflicts commit 6a4f5292eb587b133784dd784a3f4b04f037298e Author: Alice Harpole Date: Fri Feb 1 16:48:16 2019 -0500 cleaned up some errors Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Extrapolater.H Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateDescriptor.H Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_NFiles.H Src/Base/AMReX_ParmParse.H Src/Base/AMReX_parstream.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_Mask.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_Tagging.F90 Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/Particle/AMReX_Particle.H commit 04caac76676bb97a4731b4e002824abce0318174 Author: Weiqun Zhang Date: Fri Feb 1 13:15:02 2019 -0800 switch to use pinned memory for fab be default Src/Base/AMReX_BaseFab.H Tools/GNUMake/Make.defs commit 0c9d4855f383cb317d81c3b01a680841815bbe78 Merge: f17a237dc 4568621fa Author: Andrew Myers Date: Fri Feb 1 13:12:24 2019 -0800 Merge pull request #402 from MaxThevenet/splitting Add stuff for splitting commit 4568621fa4bfcc07bf8f1c2afd3b125630737891 Author: MaxThevenet Date: Fri Feb 1 12:59:58 2019 -0800 typo Src/Particle/AMReX_Particle.H commit b83fdf81750f8cc63b7a707c593a881160861f1b Author: Alice Harpole Date: Fri Feb 1 15:43:50 2019 -0500 doxygenised fortran files already containing documentation Docs/sphinx_documentation/make_api.py Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_io_mod.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_LO_UTIL.F90 Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset_F.F90 Src/Extern/CVODE/cvode_interface.f90 Src/Extern/CVODE/fnvector_serial.f90 Src/Extern/CVODE/integrator_stats.f90 Src/Extern/CVODE/sundials_fdlsmat.f90 Src/Extern/Conduit/AMReX_Conduit_Blueprint.H Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90 commit 0e67e5d50a8f5295b46230ad013bfcdffc829521 Author: Brandon Runnels Date: Fri Feb 1 13:20:22 2019 -0700 fixed error causing crse level to fail to converge Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit fc016c468636f68e9f5e71556b59766b8739b985 Author: Alice Harpole Date: Fri Feb 1 14:41:47 2019 -0500 run on all header files (which already had some documentation) Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/add_doxy_headers.py Docs/sphinx_documentation/make_api.py Src/Extern/amrdata/AMReX_DataServices.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/SDC/AMReX_SDCstruct.H commit f17a237dc439eb89b11a642ba977eb5ad979a7d7 Author: Ann Almgren Date: Fri Feb 1 11:34:06 2019 -0800 Fix name of file in CMakeLists.txt Src/Boundary/CMakeLists.txt commit 1ab0d654104701f6443482415266e33d494eeb3c Merge: 314e72eb9 81776d1c6 Author: Weiqun Zhang Date: Fri Feb 1 14:16:09 2019 -0500 Merge branch 'development' into weiqun/gpu commit 81776d1c6212c0265201bd8b2d0031c9e8d112c0 Author: Weiqun Zhang Date: Fri Feb 1 14:15:44 2019 -0500 add -lmpi_ibm for summit Tools/GNUMake/sites/Make.olcf commit 314e72eb967c151183832a3454c841578d78c610 Merge: a50797f28 9ce73ae00 Author: Weiqun Zhang Date: Fri Feb 1 13:52:48 2019 -0500 Merge branch 'development' into weiqun/summit-comm commit 9ce73ae00d19d1040c29f5d11cc117f96d977abc Merge: 21aeb7306 0bb9b0cb7 Author: Weiqun Zhang Date: Fri Feb 1 10:50:48 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0bb9b0cb7cc8dceabfa5d7562c7034ffdb21d68e Merge: e1d7a772f 4aa027096 Author: Andrew Myers Date: Fri Feb 1 13:49:19 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e1d7a772f3b3a0d084b61ddb1f841a4af681ccb8 Author: Andrew Myers Date: Fri Feb 1 13:49:02 2019 -0500 remove redundant code Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit 21aeb730680f5062942e8e63acebdb66ef8fe229 Author: Weiqun Zhang Date: Fri Feb 1 10:46:48 2019 -0800 use isGpuPtr instead of isHostPtr to allow BaseFab in pinned memory; some updates due to Array4 changes Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Tutorials/GPU/CNS/Source/CNS_bcfill.cpp commit 5cd1a2bbfc1f6f45e615790a67c4d6e9f11d4a55 Merge: 4aa027096 286fcccd0 Author: Weiqun Zhang Date: Fri Feb 1 10:01:09 2019 -0800 Merge branch 'weiqun/gpu' into development commit 4aa027096c1e07def93aeb94d159104deeda31ce Author: Weiqun Zhang Date: Fri Feb 1 09:38:07 2019 -0800 fix the one that is supposed to use macro Tutorials/GPU/Launch/main.cpp commit 29bd4e3794f36d996b989eede0d26806178ae623 Merge: a0b46cb7b d2fe706ba Author: Weiqun Zhang Date: Fri Feb 1 09:23:01 2019 -0800 Merge branch 'weiqun/launch' into development commit a0b46cb7b1e6ba5447b0098fae184c24cf9ce550 Author: Weiqun Zhang Date: Fri Feb 1 09:00:51 2019 -0800 update CHANGES CHANGES commit 4fe38fc86f5747f3b8a8347a4161d7bfe4027483 Merge: d56f96626 d20258863 Author: Weiqun Zhang Date: Fri Feb 1 08:52:14 2019 -0800 Merge branch 'development' commit 373f712f3d711a21c49d19bc2fa48565913a8a88 Author: MaxThevenet Date: Fri Feb 1 08:22:35 2019 -0800 special id for splitting Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particles.H commit d20258863d3a84206404374054ce688d4e65bb3d Merge: f08be5f7d 209018d16 Author: Johannes Blaschke Date: Thu Jan 31 17:53:54 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f08be5f7d0fea8ea00d061e040294c6b30efba2a Author: Johannes Blaschke Date: Thu Jan 31 17:53:49 2019 -0800 fix spelling Docs/sphinx_documentation/source/EB.rst commit 209018d16ca6c154178aaade1f131f1cf311ddca Merge: 187aacf17 77fc34b74 Author: Andrew Myers Date: Thu Jan 31 20:17:40 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 187aacf17bfe1cd33adb46993a15b9064c624077 Author: Andrew Myers Date: Thu Jan 31 20:17:20 2019 -0500 use pinned memory for send / rcv buffers in Redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d2fe706ba3807662b48fc488e8442d2507472db7 Author: Weiqun Zhang Date: Thu Jan 31 16:29:14 2019 -0800 change the const behavior of Array4 Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Boundary/AMReX_FabSet.H Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/mykernel.H Tutorials/GPU/Launch/main.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit 77fc34b74888ca2073c98d83e9b7a41b1f96ca48 Author: Johannes Blaschke Date: Thu Jan 31 15:26:43 2019 -0800 thiis kind of manual buffering is not necessary Docs/sphinx_documentation/source/EB.rst Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 3661157516ca5d3135da68df0069ff4094d3d4bd Author: Alice Harpole Date: Thu Jan 31 17:41:55 2019 -0500 Ran on Particles folder Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particles.H commit 101107640b2fe871ca058b426f47c60f4ef9e64b Author: Alice Harpole Date: Thu Jan 31 17:29:27 2019 -0500 ran on EB folder Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Cylinder.H Src/EB/AMReX_EB2_IF_Ellipsoid.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Spline.H Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBSupport.H Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H commit 5e119782589a717649352170657fe9c986cbb035 Merge: 9158daec4 b955ea575 Author: Johannes Blaschke Date: Thu Jan 31 14:25:48 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9158daec4f0d3c948718c6f3e14e2113e4f5b7e9 Author: Johannes Blaschke Date: Thu Jan 31 14:25:44 2019 -0800 move volfrac tagging out of levelset core Src/EB/AMReX_EBAmrUtil.H Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBAmrUtil_F.H Src/EB/AMReX_EBAmrUtil_nd.F90 Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_Tagging.F90 commit 9ddd05f166fdd7e44bbecab6f5783bae77734ec0 Author: Alice Harpole Date: Thu Jan 31 17:15:40 2019 -0500 ran on Boundary folder Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_YAFluxRegister.H Src/EB/AMReX_distFcnElement.H commit 8e6b7191dc1f9e5902c939987aa7ecda5b626465 Author: Alice Harpole Date: Thu Jan 31 16:58:05 2019 -0500 ran on Base folder Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseUmap.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxList.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabConv.H Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_LayoutData.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_Machine.H Src/Base/AMReX_MemPool.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_NFiles.H Src/Base/AMReX_Orientation.H Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParmParse.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealVect.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_parstream.H commit 10ad1891c6a8a6a2eca7686b62addc56600c88f3 Merge: a286d89e3 b955ea575 Author: Weiqun Zhang Date: Thu Jan 31 16:47:32 2019 -0500 Merge branch 'development' into weiqun/launch commit b955ea57538ad82f404690bd13ce98345e2cabb5 Author: Andrew Myers Date: Thu Jan 31 16:27:41 2019 -0500 use the same cuda aware mpi flag as the mesh data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit a50797f28a1be09521828b8057244887cd0f5727 Merge: 3e6f43c81 4e19a67da Author: Weiqun Zhang Date: Thu Jan 31 16:18:55 2019 -0500 Merge branch 'development' into weiqun/summit-comm Conflicts: Src/Base/AMReX_FabArrayBase.H commit 4e19a67da2919f3499f5de503a12f3c63132cf1d Author: Weiqun Zhang Date: Thu Jan 31 13:13:37 2019 -0800 disabel cuda aware mpi by default Src/Base/AMReX_ParallelDescriptor.cpp commit 98a73b60478287ccc0b81039caf2c3124195cbb3 Author: Weiqun Zhang Date: Thu Jan 31 15:59:48 2019 -0500 Cuda --> Gpu Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 6397e9088c0e2769419312fb2451dc8ab5abae10 Author: Weiqun Zhang Date: Thu Jan 31 15:54:29 2019 -0500 use pinned memory when amrex.use_cuda_aware_mpi is false Src/Base/AMReX.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit d926ebd23ca6e925e094a72ba67c0f05cb6a5c47 Author: Alice Harpole Date: Thu Jan 31 15:43:32 2019 -0500 ran on AmrCore folder Docs/sphinx_documentation/add_doxy_headers.py Docs/sphinx_documentation/make_api.py Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_TagBox.H commit 8715c9a730178b81800d1e375eab52aed63ae3ad Author: Alice Harpole Date: Thu Jan 31 15:05:06 2019 -0500 run script on Amr folder Docs/sphinx_documentation/add_doxy_headers.py Docs/sphinx_documentation/source/conf.py Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_Derive.H Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateDescriptor.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_RealVect.H commit 3e6f43c818537c09ac2e17fbe35ccf1413ec4d71 Author: Weiqun Zhang Date: Thu Jan 31 12:40:02 2019 -0500 clean up unused features in fabarray communications Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tests/FillBoundaryComparison/main.cpp commit f69ca1ec87ebcebf0f0dbcb492a860121d4805a3 Author: Andrew Myers Date: Wed Jan 30 23:35:59 2019 -0500 add tupleAdd functor Src/Particle/AMReX_Functors.H Src/Particle/AMReX_ParticleContainerI.H commit da0afe5922ad8aea53cd53021ff869db0fe11345 Author: Andrew Myers Date: Wed Jan 30 23:21:32 2019 -0500 fix non-CUDA compilation Src/Particle/AMReX_ParticleContainerI.H commit ea9af061b8658aea06d2d192987987a6f08b0a54 Merge: d029f97ca 304b9670c Author: Andrew Myers Date: Wed Jan 30 22:19:01 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d029f97cac97e546421f2cd79323f9ac36938d05 Author: Andrew Myers Date: Wed Jan 30 22:13:53 2019 -0500 implement option for non cuda-aware mpi Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 0b649b636b235e36511cf57d38b04dc9e3995f81 Author: Michele Rosso Date: Wed Jan 30 21:04:00 2019 -0500 CMake: replace function to evaluate genex Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 4e94951c1ddee644edb76f6bb4a58ccf9fd58f0e Author: Andrew Myers Date: Wed Jan 30 19:38:23 2019 -0500 remove some misleading timers from GPU routines. Src/Particle/AMReX_ParticleContainerI.H commit 164ba7b59869512ff58ea1ae3bdacde3359c53e9 Merge: f5215e6fb 304b9670c Author: Michele Rosso Date: Wed Jan 30 17:53:09 2019 -0500 Merge branch 'development' into mr/cmake commit 62c8bea88711c7b4a90400b3050ab043d6040f69 Author: Andrew Myers Date: Wed Jan 30 17:32:08 2019 -0500 some more async copy Src/Particle/AMReX_ParticleContainerI.H commit a286d89e38a14da78a633e717180e7d4bd2519db Author: Weiqun Zhang Date: Wed Jan 30 13:32:47 2019 -0800 use auto; add profilers in launch tutorial Src/Base/AMReX_Array.H Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/main.cpp commit 5ca4475bffde515ae75b1ac5c86e7908ba68543d Author: Alice Harpole Date: Wed Jan 30 16:25:35 2019 -0500 Fixed indentation of comments for add_doxy_headers so it now works almost correctly for Amr/AMReX_Derive.H Docs/sphinx_documentation/add_doxy_headers.py commit f6f4ee339c1f2fc80dd13515658e5c2db81f8c0e Author: Andrew Myers Date: Wed Jan 30 16:25:27 2019 -0500 use some Async mem copies Src/Particle/AMReX_ParticleContainerI.H commit 3248bf350d2906cfc9f9d97bb78db4c13dc683bf Author: Alice Harpole Date: Wed Jan 30 15:09:40 2019 -0500 make_api.py is now recursive so will work if directories have subdirectories Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/make_api.py commit 304b9670c8b1c19463682a24812a57331500725e Author: Kevin Gott Date: Wed Jan 30 14:24:22 2019 -0500 Bug fix. Tests/GPU/buildHybrid/GNUmakefile commit 55095657e6c512721fb277eec583d7edc13756d5 Author: Weiqun Zhang Date: Wed Jan 30 11:17:02 2019 -0800 add force inline Src/Base/AMReX_CudaLaunch.H commit 9bace973999f196d45c0d3a811a68aa016495157 Author: Andrew Myers Date: Wed Jan 30 13:53:35 2019 -0500 first attempt at a less thrust-intensive redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit f5215e6fb1f861dbc8d999d5e0365b92d4edfd76 Author: Michele Rosso Date: Wed Jan 30 13:03:11 2019 -0500 CMake: move handling of SENSEI lib to config function Src/Extern/SENSEI/CMakeLists.txt Tools/CMake/AMReX_Config.cmake commit 7d6750121790327e02783d831552ee872dc86c1f Author: Alice Harpole Date: Wed Jan 30 12:14:39 2019 -0500 Added doxygen and breathe to docs build to autogenerate the API Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/make_api.py Docs/sphinx_documentation/source/conf.py Docs/sphinx_documentation/source/index.rst commit 19b92da13d28436c058dfc9baf6ef14c1784a712 Author: Weiqun Zhang Date: Tue Jan 29 21:15:35 2019 -0800 use rvalue in launch_host Src/Base/AMReX_CudaLaunch.H commit ca284b7d818fe9567ace743dc4199b75bfdfdd21 Author: Weiqun Zhang Date: Tue Jan 29 20:49:16 2019 -0800 use rvalue reference for lambda parameter for cpu version Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/Launch/main.cpp commit 7a7383a91341e9681d0c5fb0829ccaabc5d36d1e Author: Weiqun Zhang Date: Tue Jan 29 19:56:12 2019 -0800 add amrex::launch, amrex::ParallelFor and amrex:For functions Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/Launch/main.cpp commit 82eb4d05fae4345a7d2a83bf30d62315de448e00 Merge: f5e0632a6 9c16d851e Author: Brandon Runnels Date: Tue Jan 29 17:59:46 2019 -0700 Merge branch 'nodeghostcells' of github.com:AMReX-Codes/amrex into nodeghostcells commit f5e0632a6d76105d251aebffa5d1a8a3ae5a1a15 Author: Brandon Runnels Date: Tue Jan 29 17:59:21 2019 -0700 wip - implementing update of ghost cells Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 9a058294e0d3734caf76d6e948f8e624d0acf2ec Author: Andrew Myers Date: Tue Jan 29 19:08:24 2019 -0500 remove empty entries from m_not_ours before calling RedistributeMPIGPU Src/Particle/AMReX_ParticleContainerI.H commit 286fcccd0d0b81285311d3cf02021185c4d0b389 Merge: e488e5777 285a4f5fd Author: Weiqun Zhang Date: Tue Jan 29 15:40:23 2019 -0800 Merge branch 'development' into weiqun/gpu commit 816ef26cd916afdcabbbad1d7a7987ddd7e81841 Author: Michele Rosso Date: Tue Jan 29 18:19:22 2019 -0500 CMake: refactor how compile definitions are handled. Src/CMakeLists.txt Src/EB/CMakeLists.txt Src/Extern/ProfParser/CMakeLists.txt Src/Extern/SENSEI/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake Tools/CMake/AMReX_Utils.cmake commit e488e5777f3a8d8c37d2c2c69c09a7a3f6b1da9a Author: Weiqun Zhang Date: Tue Jan 29 14:18:45 2019 -0800 2D InterpBndryData: make it the same as Fortran Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_LOUtil_K.H Src/Boundary/CMakeLists.txt Src/Boundary/Make.package commit 285a4f5fd09cf2ab2642beea7752a90669dc4ecc Author: Kevin Gott Date: Tue Jan 29 16:11:15 2019 -0500 AMReX independent CUDA build tests: one using only C++ with lots of compiler options, one with hybrid Fortran & C++ that focuses on pgfortran, as done in AMReX. Tests/GPU/buildHybrid/GNUmakefile Tests/GPU/buildHybrid/MyKernel.H Tests/GPU/buildHybrid/MyKernel.cpp Tests/GPU/buildHybrid/MyKernelB.H Tests/GPU/buildHybrid/MyKernelB.cpp Tests/GPU/buildHybrid/MyKernel_F.F90 Tests/GPU/buildHybrid/MyKernel_F.H Tests/GPU/buildHybrid/Readme Tests/GPU/buildHybrid/main.cpp Tests/GPU/buildHybrid/run.script Tests/GPU/buildTest/GNUmakefile Tests/GPU/buildTest/MyKernel.H Tests/GPU/buildTest/MyKernel.cpp Tests/GPU/buildTest/MyKernelB.H Tests/GPU/buildTest/MyKernelB.cpp Tests/GPU/buildTest/Readme Tests/GPU/buildTest/main.cpp Tests/GPU/buildTest/run.script commit 47ab93461b0a3ba4ddeecf4a10d9bbf04638e538 Author: Weiqun Zhang Date: Tue Jan 29 12:59:15 2019 -0800 InterpBndryData: fix a sign Src/Boundary/AMReX_InterpBndryData_3D_K.H commit 8cc4eeaa77e793b9491e640994a7fd5fe8cf1859 Author: Andrew Myers Date: Tue Jan 29 11:22:59 2019 -0800 add a private pure virtual function for doing custom behavior after a particle is location is Redistribute(). Will be used in WarpX to do particle splitting /merging. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 6bca97c7d01147d1725a2193656d84ad5a0cfc6c Author: Weiqun Zhang Date: Tue Jan 29 11:12:23 2019 -0800 InterpBndryData: fix bugs Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H commit d611427af9f0b0d694a11b12d5855dd9779ce7c9 Author: Michele Rosso Date: Tue Jan 29 13:52:48 2019 -0500 CMake: more changes to support CUDA. * Add architecture detection * Split compiler flags over multiple files based on the compiler ID * Start adding GPU tests. WARNING: this commit still has a linking problem when CUDA is enabled. CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/comps/AMReX_Cray.cmake Tools/CMake/comps/AMReX_GNU.cmake Tools/CMake/comps/AMReX_Intel.cmake Tools/CMake/comps/AMReX_NVIDIA.cmake Tools/CMake/comps/AMReX_PGI.cmake Tools/CMake/select_gpu_arch.cmake Tutorials/GPU/Advection_AmrCore/CMakeLists.txt Tutorials/GPU/Launch/CMakeLists.txt commit 821a673c765f05ced92c00065d8b789186b45f63 Author: Johannes Blaschke Date: Tue Jan 29 10:36:31 2019 -0800 cleanup Src/EB/AMReX_EB_LSCoreI.H commit 3e0e9ab0feb463c3fa50ffa69ac10c34d6a49d4d Author: Weiqun Zhang Date: Tue Jan 29 09:32:13 2019 -0800 InterpBndryData: pass component index to kernels Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H commit 78d77f010b8975e88b0af96b5bb1bd93faa581bb Author: Weiqun Zhang Date: Tue Jan 29 09:11:19 2019 -0800 using Cuda::AsyncFab and CudaAsyncArray in amrex namespace Docs/sphinx_documentation/source/GPU.rst Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_PhysBCFunct.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit d29b926fb1632a827f8e10cec0dbf08640eb4057 Author: Weiqun Zhang Date: Tue Jan 29 09:02:01 2019 -0800 operator<< for printing bounds of Array4 Src/Base/AMReX_Array.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit 6c28e5422cfb714aa24e4fa1ba90e37690b55056 Author: Weiqun Zhang Date: Mon Jan 28 21:04:30 2019 -0800 fix another bug in new InterpBndryData: refine is not always 2 Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H commit b623c67cfc9641ab786f4bc1a49ad5eb037514a9 Author: Weiqun Zhang Date: Mon Jan 28 18:53:53 2019 -0800 fix bug in new InterpBndryData Src/Boundary/AMReX_InterpBndryData.cpp commit 562a42162d69491e3a455d017f886c68b6bcf8b6 Author: Weiqun Zhang Date: Mon Jan 28 18:42:23 2019 -0800 minor optimization by avoiding BoxArray's virtual function Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/AMReX_YAFluxRegister.cpp commit 90c5ee623c5bbdb8fdb3c87c65f7d67696631514 Author: Weiqun Zhang Date: Mon Jan 28 16:59:04 2019 -0800 InterpBndryData on gpu Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_InterpBndryData_K.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/CMakeLists.txt Src/Boundary/Make.package commit cab50940531deb87a4ec589cd6526465cd96ac61 Merge: 3521ea7b8 2b5dfff38 Author: Johannes Blaschke Date: Mon Jan 28 13:21:56 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3521ea7b88ecabc1a3627713ad6602a766fc4b23 Author: Johannes Blaschke Date: Mon Jan 28 13:21:53 2019 -0800 finish documenting levelset Docs/sphinx_documentation/source/EB.rst commit 2b5dfff38607136014c3551da1ac1af1ec0d2eb8 Merge: 5352cf9fb 8b48487ce Author: Andrew Myers Date: Mon Jan 28 10:50:07 2019 -0800 Merge pull request #401 from ylunalin/new_particle_tutorials Add OpenMP offloading directory in EMPIC. commit a4b47d10dad55e7e042a460c2045d468c530c824 Author: Weiqun Zhang Date: Mon Jan 28 10:29:16 2019 -0800 hopefully make omp and cuda more compatible in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 1c1dd7a1d2e339f806acbd3daab43e1db8022966 Author: Weiqun Zhang Date: Sun Jan 27 17:43:40 2019 -0800 YAFluxRegister: fix tiling bug Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_YAFluxRegister.cpp commit cd9ce18d51074c5110e471350c89e34d6aa73850 Author: Weiqun Zhang Date: Sun Jan 27 15:38:21 2019 -0800 fix index bug in YAFluxRegister gpu kernel Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H commit 4dc97ed6f51cab712a26426ee9b01cdb1c69fd59 Author: Weiqun Zhang Date: Sun Jan 27 13:31:24 2019 -0800 finish YAFluxRegister on gpu Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_1d.F90 Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_2d.F90 Src/Boundary/AMReX_YAFluxRegister_3D_K.H Src/Boundary/AMReX_YAFluxRegister_3d.F90 Src/Boundary/AMReX_YAFluxRegister_F.H Src/Boundary/AMReX_YAFluxRegister_K.H Src/Boundary/AMReX_YAFluxRegister_nd.F90 Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/EB/AMReX_EBFluxRegister_nd.F90 commit 5352cf9fb4f9ca8fe8632b5c383e2e0b3672cb1c Author: Ann Almgren Date: Sat Jan 26 20:07:02 2019 -0800 Revert "using async Iters for Nyx first attempt" This reverts commit db3e728709f2186a302f6558a3a95da848787ce3. Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 4004daf5c6fc7ee52721b4e0d0e70c49e8aac4f7 Author: Johannes Blaschke Date: Fri Jan 25 21:37:58 2019 -0800 added explanation on using fortran level-set modules Docs/sphinx_documentation/source/EB.rst commit efc94c2a581cee77547fb9f096646932ef49d8f7 Merge: 1306808cc 79111defe Author: Johannes Blaschke Date: Fri Jan 25 20:46:44 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1306808cc9a6e2c1917beff10bce004115fed730 Author: Johannes Blaschke Date: Fri Jan 25 20:43:20 2019 -0800 fix indentation Docs/sphinx_documentation/source/EB.rst commit 79111defe50aa6f6ef86eea88e31571efde4818b Merge: 38d95b0d8 31e2d4a64 Author: Johannes Blaschke Date: Fri Jan 25 20:42:40 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 31e2d4a643a3bee6a9843ca9c76b377596849a24 Merge: 2cb5366eb ce3bb4a5b Author: Tan Nguyen 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Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/sample_run_scripts/run_Nyx_LyA_Cori.sh Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/GNUmakefile Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/Make.package Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/main.cpp Src/AmrTask/tutorials/Apps/Nyx_hydro/copyright.txt Src/AmrTask/tutorials/Apps/Nyx_hydro/license.txt commit ce3bb4a5bcb6f743eed82cf6849a62e76871583d Merge: 4794806fb db3e72870 Author: Andrew Myers Date: Fri Jan 25 21:00:57 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4794806fbd8e3ab25ff4ac274059134d54c77f11 Author: Andrew Myers Date: Fri Jan 25 21:00:39 2019 -0500 use the pooling memory allocator for thrust::gather calls as well Src/Particle/AMReX_ParticleContainerI.H commit 189c6d382fb1762d15b2f154e04ffe74aee95fca Author: Andrew Myers Date: Fri Jan 25 20:42:07 2019 -0500 cache grid_begin and grid_end arrays to avoid reallocation. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 847eb05341236bb2555b0fbd0b17d304d62bcf8f Author: Weiqun Zhang Date: Fri Jan 25 17:24:52 2019 -0800 YAFluxRegiser: more on gpu Src/Boundary/AMReX_YAFluxRegister.cpp commit 38d95b0d879264da3b0bc8f2d19589891baa8f93 Merge: 4ba6a33b1 db3e72870 Author: Johannes Blaschke Date: Fri Jan 25 17:21:33 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4ba6a33b1deb448b07116ab67d83619a6b1416c8 Author: Johannes Blaschke Date: Fri Jan 25 17:21:25 2019 -0800 update level-set docs Docs/sphinx_documentation/source/EB.rst commit 73a5d4163b7961a85b4cf8b96bfd46b3ce68a884 Author: Weiqun Zhang Date: Fri Jan 25 16:27:19 2019 -0800 start YAFluxRegister on gpu Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H 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Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/sample_run_scripts/run_Nyx_LyA_Cori.sh Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/GNUmakefile Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/Make.package Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/main.cpp Src/AmrTask/tutorials/Apps/Nyx_hydro/copyright.txt Src/AmrTask/tutorials/Apps/Nyx_hydro/license.txt commit 4860a3985660d756144690cacc23a06335bfd889 Author: Weiqun Zhang Date: Fri Jan 25 15:24:20 2019 -0800 Mask on gpu Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.cpp commit 5076743399442d6ae12514828cae899dafc6bdff Author: Johannes Blaschke Date: Fri Jan 25 14:59:57 2019 -0800 remove unused file Docs/sphinx_documentation/source/Tutorials_Chapter.rst commit eb9857654f46c97144d8e1f9330d89463acecb1b Merge: 49b96b3d8 62952ff0e Author: Johannes Blaschke Date: Fri Jan 25 14:55:52 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 49b96b3d8f9642b0749f19894739b95ff9dd74f4 Author: Johannes Blaschke Date: Fri Jan 25 14:55:48 2019 -0800 1. add levelset doxygen, 2. clean up eb docs formatting, 3. fix gpu docs code highlighting Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/GPU.rst Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit d56f96626fdbe215901260b0636d89b5388d0497 Author: Ann Almgren Date: Fri Jan 25 14:45:02 2019 -0800 Last ORCID has been added .zenodo.json commit 2397070e13bb49890455c93f71886ffd7dd2ca65 Author: Ann Almgren Date: Fri Jan 25 14:38:17 2019 -0800 Add one more ORCID .zenodo.json commit 62952ff0e75f8fb9383adb01f7efc0dc84233652 Author: Weiqun Zhang Date: Fri Jan 25 13:05:42 2019 -0800 add missing grownnodaltilebox Src/Base/AMReX_MFIter.cpp commit 9fafa36d9e3303c61b4cb7ccbdc6f6b0c9c801ef Author: Weiqun Zhang Date: Fri Jan 25 12:38:54 2019 -0800 update FabSet and BndryRegister Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.cpp commit fbc24aba9f2243d93b7a525f8fa132a070dd3624 Author: Weiqun Zhang Date: Fri Jan 25 10:34:40 2019 -0800 fix compiler warning about shadow Src/Base/AMReX_RealBox.H commit 8b48487ced78e91e87f06f833082bb7bdf64a9cc Author: Luna Lin Date: Fri Jan 25 13:05:15 2019 -0500 Add OpenMP offloading directory in EMPIC. Moved C++ header files to Source/ to be shared. Got rid of FTOC macro (use name binding), as well as function definition for PushParticlePosition (never used) in OpenACC/. Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/run.summitdev Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Source/Evolve.H Tutorials/Particles/ElectromagneticPIC/Source/Make.package commit 11062d60fd9177d888925da44843d8092c7633a2 Author: Weiqun Zhang Date: Thu Jan 24 16:12:29 2019 -0800 fix virtual override Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H commit 1d3c6392029ce7639ae6ab01dd72713a468302b8 Author: Weiqun Zhang Date: Thu Jan 24 16:09:59 2019 -0800 some fixes Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit b6a0bd3f9a1b1adfa21cdcd74e46be7a72c31a27 Author: Weiqun Zhang Date: Thu Jan 24 16:00:50 2019 -0800 make functions public for cuda Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H commit 207ae1aa7e77c1f09f86725ad36a6e04a770725e Author: Ann Almgren Date: Thu Jan 24 15:24:31 2019 -0800 Re-add comma that I accidentally deleted .zenodo.json commit 23d46f80adb51aa2fb1d1844028ac9e31cd39cbb Merge: 32243243a 33f404284 Author: Ann Almgren Date: Thu Jan 24 15:21:36 2019 -0800 Merge branch 'master' of https://www.github.com/amrex-codes/amrex commit 32243243a0774b3123aabb708f000d7620cc1399 Author: Ann Almgren Date: Thu Jan 24 15:19:53 2019 -0800 add more data .zenodo.json commit 33f40428415b4e52781953c7201b1f522f0f5820 Author: Weiqun Zhang Date: Thu Jan 24 15:12:53 2019 -0800 fix format .zenodo.json commit 34ae846e9bedb74a7ff270b20f12d1ad050bf536 Author: Ann Almgren Date: Thu Jan 24 15:06:43 2019 -0800 Updated with Graves, Williams and more ORCIDs .zenodo.json commit e448fdd84de5133d1d12bc579ee10da92949d2d2 Merge: 752bf973e 3abc9b37c Author: Ann Almgren Date: Thu Jan 24 15:06:31 2019 -0800 Merge branch 'master' of https://www.github.com/amrex-codes/amrex commit c83302eaa83156ab01dcbbf530e3eab4a17ce220 Author: Weiqun Zhang Date: Thu Jan 24 15:01:51 2019 -0800 mg interp on gpu Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 752bf973eb33e695d2b6ecee997ec095f49d851d Author: Ann Almgren Date: Thu Jan 24 12:01:01 2019 -0800 Update with names and ORCID .zenodo.json commit 3abc9b37cb83b060caddd3355c3de273ff077216 Author: Weiqun Zhang Date: Thu Jan 24 11:26:40 2019 -0800 add a link to license in README README.md commit 859b0a79e25d00a416eabad75127a8b39c8b9750 Author: Weiqun Zhang Date: Thu Jan 24 11:26:40 2019 -0800 add a link to license in README README.md commit 0955e4841851357ac38401a8c34572540d8408e7 Merge: 07e3136de 47ede8794 Author: Weiqun Zhang Date: Thu Jan 24 11:20:25 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9b4aca9757ac875ac54bc65acc1673caa56a9364 Author: Weiqun Zhang Date: Thu Jan 24 11:20:20 2019 -0800 mg_interp in C++ Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MG_K.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit a4573f98fbea7fa6adf9283988082697a393bd0a Author: Ann Almgren Date: Thu Jan 24 11:15:38 2019 -0800 Update README README.md commit 8981cdabdb748c474c166392583f72ab9f97bd0b Author: Ann Almgren Date: Thu Jan 24 11:13:25 2019 -0800 README.txt --> README.md README.txt commit db4668da1bf030036507702297a45fe5c93332a0 Author: Ann Almgren Date: Thu Jan 24 11:09:48 2019 -0800 Update with information about being a "core developer" README.md commit 47ede8794259c7de8c5ae35b9c0c115c3249b755 Author: Ann Almgren Date: Thu Jan 24 11:13:25 2019 -0800 README.txt --> README.md README.txt commit c37afca4373963d39d792a25a3d65a6eb992728f Author: Ann Almgren Date: Thu Jan 24 11:09:48 2019 -0800 Update with information about being a "core developer" README.md commit 07e3136de07eeefa629fb8dea5e634c0d9ff5a54 Author: Weiqun Zhang Date: Thu Jan 24 10:00:37 2019 -0800 add assertion Src/Base/AMReX_Array.H commit 8ac7dc95be9b764394ac58c4f51cc87642c699b3 Author: Weiqun Zhang Date: Thu Jan 24 12:07:10 2019 -0500 ibm compiler flags and pragma Src/Base/AMReX_Extension.H Tools/GNUMake/comps/ibm.mak commit 82bfae30b1f821ba92c8d872616c01ebc55e196c Author: Weiqun Zhang Date: Thu Jan 24 09:30:14 2019 -0800 add zenodo json .zenodo.json commit 17ff5f93cf4411d1cb88e66e252c5bab4091dd81 Author: Michele Rosso Date: Wed Jan 23 19:58:16 2019 -0500 CMake: Fortran interfaces are now disabled by default Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_Options.cmake commit 6c2006882368e06e50e8979d1715dfd04be19a81 Author: Weiqun Zhang Date: Wed Jan 23 14:38:15 2019 -0800 mismatched #if Src/Base/AMReX_Extension.H commit fbe137949dab71f5728bee9e65e16132c745e446 Author: Weiqun Zhang Date: Wed Jan 23 14:36:31 2019 -0800 comment out omp simd Src/Base/AMReX_Extension.H commit 22c15748370d5b8bf46c454b6a1aa56b7aca6338 Author: Weiqun Zhang Date: Wed Jan 23 14:15:02 2019 -0800 add AMREX_PARALLEL_FOR_?D Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_derive.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/Launch/main.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp commit c7589644d7dfe0011a8e3abf6dbd3a104685e3eb Author: Kevin Gott Date: Wed Jan 23 13:11:08 2019 -0800 Docs rewording. Docs/sphinx_documentation/source/BuildingAMReX.rst commit c2fd3948a30b3b269be96ad95e1525866c8cf491 Author: Weiqun Zhang Date: Wed Jan 23 10:46:53 2019 -0800 fix the Poisson test Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H commit 31416813931ed1102866f1fff932dec6a8bcebf2 Author: Weiqun Zhang Date: Wed Jan 23 10:39:37 2019 -0800 fix bug in ProbHiArray Src/Base/AMReX_Geometry.H commit c4efc5569fba1af31a426a1f8afd7105f1d4c268 Merge: 2f19745ea b58f86b4e Author: Andrew Myers Date: Tue Jan 22 20:34:04 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b58f86b4e457b72db16fff43417913a96ef8647a Author: Weiqun Zhang Date: Tue Jan 22 17:03:56 2019 -0800 some fixes for cuda Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H commit 2f19745ea3b64f046b67464df0fb56f43ead7b53 Author: Andrew Myers Date: Tue Jan 22 19:56:42 2019 -0500 swap data pointers instead of making temporary copies when reordering particles in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 57b1fb4405cc00ea55d919e93575c41f1d772ed8 Author: Weiqun Zhang Date: Tue Jan 22 16:37:40 2019 -0800 update Tutorials/LinearSolvers/ABecLaplacian_C for gpu Tutorials/LinearSolvers/ABecLaplacian_C/Make.package Tutorials/LinearSolvers/ABecLaplacian_C/MyTest_F.H Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/LinearSolvers/ABecLaplacian_C/init_prob.F90 commit 8bc605aaecf8f759d34ddcf6e5359a527b226621 Merge: b26c112f7 6510416c5 Author: Johannes Blaschke Date: Tue Jan 22 15:40:56 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b26c112f7baf03b58a97a0f1855a561b535f112b Author: Johannes Blaschke Date: Tue Jan 22 15:40:48 2019 -0800 allow users to specify coarsening level when creating eblevels Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreI.H commit 6510416c5835ee8675649d23cd3100f21817aed0 Author: Weiqun Zhang Date: Tue Jan 22 15:05:46 2019 -0800 remove numpts from BaseFab. After dlen and numpts are removed, the size of BaseFab went down from 80 to 56 bytes Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseUmap.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArray.H Tests/BaseFabTesting/main.cpp Tests/C_BaseLib/tUMap.cpp commit 60caa39d6e297fe92a95183dad71944ce0339c50 Author: Weiqun Zhang Date: Tue Jan 22 14:09:07 2019 -0800 remove dlen from BaseFab Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H commit cf2ab418a49f402570eb1c95e122bbb54f709fba Author: Weiqun Zhang Date: Tue Jan 22 14:04:29 2019 -0800 fix some shadows Src/Base/AMReX_FabArrayCommI.H commit 5dd4679f54a7bfe5da6aaa0ad0e0f6187dc73ed2 Author: Johannes Blaschke Date: Sun Jan 20 22:18:23 2019 -0800 fill boundary not needed Src/EB/AMReX_EB_levelset.cpp commit 0d93c4c68435991f4bfd32cbff35088c54750463 Author: Johannes Blaschke Date: Sun Jan 20 22:05:38 2019 -0800 added static level-set intersection Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 07e28e1904336703804abe5f61e1510812d90c04 Author: Weiqun Zhang Date: Sat Jan 19 11:26:01 2019 -0800 add a new interface to InterpCrseFineBndryEMfield Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_Interpolater.cpp commit 3136ee631154630237ee29ff51ef1e3d47e049db Merge: e7d9d9054 6818acd1f Author: Weiqun Zhang Date: Fri Jan 18 23:05:26 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e7d9d905477fe503282456ec7965dca75dd52068 Author: Weiqun Zhang Date: Fri Jan 18 23:05:01 2019 -0500 pic cuda: optimization and simplification Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit 6818acd1fa8d0c2243dd4b19b4114b166cfa2104 Author: Kevin Gott Date: Fri Jan 18 13:42:59 2019 -0800 AsyncArray example. Docs/sphinx_documentation/source/GPU.rst commit bcb60c4be062e1cf9ea6a9788c119a94ad3b878d Author: Johannes Blaschke Date: Fri Jan 18 13:27:25 2019 -0800 make consistent fucntion signatures Src/Base/AMReX_MultiFabUtil.H commit 889320c21d662cd02b78fe7f694472a7470ce05c Merge: 8840413b3 cf0b4ab87 Author: Weiqun Zhang Date: Fri Jan 18 09:22:41 2019 -0800 Merge branch 'weiqun/pic_cuda' of github.com:AMReX-Codes/amrex into weiqun/pic_cuda commit cf0b4ab87692d6c000b3774c2c4e611fb6471c16 Author: Weiqun Zhang Date: Fri Jan 18 12:15:01 2019 -0500 add RedistributionLocal Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.H commit e6343dcadd5ed413acd643309c5cca0d9c0d3f6f Merge: f48fd529f 2840039ad Author: Weiqun Zhang Date: Fri Jan 18 11:59:15 2019 -0500 Merge branch 'development' into weiqun/pic_cuda commit 2840039ad2af1f2ad907b4e9e15af2561ec7d2f5 Author: Andrew Myers Date: Fri Jan 18 01:38:26 2019 -0800 call local form of Redistribute in the pic tutorial Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 8840413b37c9ff9c8f64dfe787372d4a63217046 Author: Weiqun Zhang Date: Thu Jan 17 20:56:46 2019 -0800 rm Fortran files in the cuda version of empic Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit f48fd529f61ffbdbb575dcd92f4ae6d705426aab Author: Weiqun Zhang Date: Thu Jan 17 16:58:59 2019 -0800 forgot a new file Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit 3d4af362e720eb31bfb955376dfcd35c82d5b2b6 Author: Weiqun Zhang Date: Thu Jan 17 16:52:05 2019 -0800 set cuda stream in particle iterator Src/Particle/AMReX_Particles.H commit e8623494feb2227cf81207b67fdecf8a13e03a62 Author: Weiqun Zhang Date: Thu Jan 17 16:16:16 2019 -0800 current deposition on gpu Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit 75a00ef248be27cb4d38af42b256a4cedfe7fa0f Author: Weiqun Zhang Date: Thu Jan 17 15:37:40 2019 -0800 push e and b in cuda Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp commit 16e3c2c1d5fc41fc0beadd7809fb791d320a296e Author: Weiqun Zhang Date: Thu Jan 17 15:17:14 2019 -0800 field gather and momentum push in cuda Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit 0402d2d3db66c0e818a63dae18c4db7f9aefd280 Author: Weiqun Zhang Date: Thu Jan 17 15:16:45 2019 -0800 make functions in Paticle struct host and device Src/Particle/AMReX_Particle.H commit 4a1c7e9f3f136f7fac0dbf06f7bfff8b84e2b45d Author: Michele Rosso Date: Thu Jan 17 14:44:13 2019 -0800 CMake: begin adding CUDA support CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 9ffb13852aea5e6b8ba2a73f5c545802dc4cb381 Merge: b31cfadf4 49baf862f Author: Weiqun Zhang Date: Thu Jan 17 13:38:08 2019 -0800 Merge branch 'development' into weiqun/pic_cuda commit 28d4ae18825395793621f5d9f5334c46edd1b3f7 Author: Kevin Gott Date: Thu Jan 17 13:31:09 2019 -0800 AsyncFab Example. Docs/sphinx_documentation/source/GPU.rst commit 49baf862fe129b58c313a51b863accdec2ef761d Author: Weiqun Zhang Date: Thu Jan 17 13:06:51 2019 -0800 simplification Src/Base/AMReX_MultiFabUtil.H commit 90d945b5c7d53fb0071c1c9ea87269f228ed639f Author: Weiqun Zhang Date: Thu Jan 17 12:38:11 2019 -0800 EBFArrayBoxFactory cannot be used unless it's inside ifdef AMREX_USE_EB Src/Base/AMReX_MultiFabUtil.H commit 6df4f859355d1467cb06a68e657d7ae44bdd7185 Merge: 95627e723 fdb20be70 Author: Weiqun Zhang Date: Thu Jan 17 15:21:44 2019 -0500 Merge branch 'weiqun/mpi' into development commit fdb20be7053c8f3aa64b2301a96db3810a53e126 Author: Weiqun Zhang Date: Thu Jan 17 15:20:46 2019 -0500 get around gcc-4 Src/Base/AMReX_ParallelDescriptor.cpp commit 95627e7238fc012b5469a9e25a69602628352f33 Author: Johannes Blaschke Date: Thu Jan 17 12:18:05 2019 -0800 add helper functions fore regridding Src/Base/AMReX_MultiFabUtil.H commit b2cf854bb3821f3d0311830789366289dafb0810 Merge: 2905f466a 1a6daf926 Author: Michele Rosso Date: Thu Jan 17 12:09:34 2019 -0800 Merge branch 'development' into mr/cmake commit 0a781554559c1d0f7431fa55a88620cc7abd77e1 Author: Weiqun Zhang Date: Thu Jan 17 11:31:28 2019 -0800 new Mpi_typemap to replace the old implementation using removed MPI constructs Src/Base/AMReX_ParallelDescriptor.cpp commit 0a922f158eff7788bab6f9cd41498e7dc44600f9 Author: Weiqun Zhang Date: Thu Jan 17 11:20:35 2019 -0800 missing amrex:: Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit 1a6daf926c4147bec50abcaa62d79f635cb08787 Author: Weiqun Zhang Date: Wed Jan 16 20:47:23 2019 -0800 derive variables in AmrLevel and CNS tutorial Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS_derive.H Tutorials/GPU/CNS/Source/CNS_derive.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package commit 29fa904a249822198921bef7358b89dfee7af02b Author: Weiqun Zhang Date: Wed Jan 16 17:32:33 2019 -0800 add Fab version of derive function Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp commit fb5b7f82a6f25871ea3084f7bada5d1db2184579 Author: Weiqun Zhang Date: Wed Jan 16 15:42:01 2019 -0800 add fabPtr to AuxBoundaryData Src/Amr/AMReX_AuxBoundaryData.H commit f0f450c2d545d9575b7b952f9ae41de22f777222 Author: Weiqun Zhang Date: Wed Jan 16 15:20:40 2019 -0800 add Gpu::notInLaunchRegion() Src/Amr/AMReX_AmrLevel.cpp commit 7b0189cb7b73dd608b0b08fb9bb8d516c7e2b6ec Merge: 19cf22c4f 349b39be1 Author: Weiqun Zhang Date: Wed Jan 16 12:55:13 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 19cf22c4f7dd1191eb916cff54ddb5abb8421fca Author: Weiqun Zhang Date: Wed Jan 16 12:55:06 2019 -0800 Revert "Readability adjustment." This reverts commit 1ff7c6331398fc5eda770f65ab11910fccf7c2c6. Src/Base/AMReX_ParallelContext.H commit 36baee528d4ca0adcb353abf0757cc85f52df1e5 Merge: 1dec5e7c5 1ff7c6331 Author: Weiqun Zhang Date: Wed Jan 16 12:51:46 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 349b39be1cd08a53c00071581a3c12df063921d7 Author: Kevin Gott Date: Wed Jan 16 12:48:30 2019 -0800 Edit GPU Tutorials to explicitly cite correct the useable cuda modules on summit and summitdev. Docs/sphinx_tutorials/source/GPU_Tutorial.rst commit 1dec5e7c54333679a48fa36d6723734cc89dd994 Author: Weiqun Zhang Date: Wed Jan 16 12:43:09 2019 -0800 more on amr gpu Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_BaseFab.H Src/Boundary/AMReX_FabSet.H commit 1ff7c6331398fc5eda770f65ab11910fccf7c2c6 Author: Kevin Gott Date: Wed Jan 16 11:30:11 2019 -0800 Readability adjustment. Src/Base/AMReX_ParallelContext.H commit cdbbb1e4ff8d3d178da864dfe79961caf0b50758 Author: Kevin Gott Date: Wed Jan 16 11:29:52 2019 -0800 Bit more on ParallelContext. Docs/sphinx_documentation/source/Basics.rst commit fb33a5e6407cc6cc0abd8c72927dd9f634e53876 Author: Kevin Gott Date: Wed Jan 16 11:28:37 2019 -0800 Edit GPU Tutorials Docs. Docs/sphinx_tutorials/source/GPU_Tutorial.rst commit cb35f06d8ae3a8cdd8b674ede5a322bf5b1e9f9e Author: Kevin Gott Date: Wed Jan 16 11:27:35 2019 -0800 Comment on ParallelContext. Docs/sphinx_documentation/source/Basics.rst commit aa6a1fa5fa148d58cd1f6df9f01bf719e6294596 Author: Andy Nonaka Date: Wed Jan 16 11:15:23 2019 -0800 typo Docs/sphinx_documentation/source/Particle.rst commit fc1e3f13fd72e57b0d26ca8a5da207cc672b727e Author: Weiqun Zhang Date: Wed Jan 16 13:23:05 2019 -0500 add ldg function for Array4 Src/Base/AMReX_Array.H Src/Base/AMReX_CudaUtility.H commit c8a816b619aa3439b869d3d3e422b5381bb9adfd Author: Weiqun Zhang Date: Wed Jan 16 11:43:16 2019 -0500 add restrict the pointer member in Array4 and FabView Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H commit 2905f466a3c716e3901b4dbb09deffe3ee0e83a6 Author: Michele Rosso Date: Tue Jan 15 21:12:24 2019 -0800 CMake: treat Algoim and Blitz as imported interfaces CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit fe0eddd1a42004fcd9c1d1abf2a580f3d835397a Author: Johannes Blaschke Date: Tue Jan 15 18:43:34 2019 -0800 make static interfaces more portable Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit f5587131003dafef3baceaa58775cc2ca131a45d Merge: a11b75742 074506b49 Author: Johannes Blaschke Date: Tue Jan 15 17:17:01 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a11b75742ffb0409e55db357d7bb034da41e4a88 Author: Johannes Blaschke Date: Tue Jan 15 17:16:58 2019 -0800 expose more LSCore as static functions Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_levelset.H commit 074506b49d01eed4c231c43dfd1973199f528cd4 Author: Weiqun Zhang Date: Tue Jan 15 16:46:48 2019 -0800 fix another new bug Src/Base/AMReX_FabArrayUtility.H commit 12248ca0894bb41c81851a9816e2f26ccf0dffb9 Author: Weiqun Zhang Date: Tue Jan 15 16:27:12 2019 -0800 fix a new bug Src/Base/AMReX_MultiFab.cpp commit da2f89d84e7dad1d67551d7d21ef3551f3e8d16d Merge: 53405a9d4 488429efb Author: Weiqun Zhang Date: Tue Jan 15 15:59:34 2019 -0800 Merge branch 'weiqun/gpu' into development commit 53405a9d45a792123c9c515b9d920362f95cc3f7 Merge: 27cc720bd 66649b6ab Author: Weiqun Zhang Date: Tue Jan 15 15:59:23 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 488429efb62ca3add617728de518d0930e9417f1 Author: Weiqun Zhang Date: Tue Jan 15 15:54:18 2019 -0800 view -> array Tutorials/GPU/CNS/Source/CNS_K.H commit 12486464eac455700b834831b171970d7c3096d9 Author: Weiqun Zhang Date: Tue Jan 15 14:32:00 2019 -0800 remove some duplicated codes in MultiFab and iMultiFab Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit 1ae7a566d0ab6f679a5df7dedb3cc1a646ec28dd Merge: 5e84be4cd 27cc720bd Author: Weiqun Zhang Date: Tue Jan 15 13:14:00 2019 -0800 Merge branch 'development' into weiqun/gpu commit 5e84be4cdf01db1556427b30d34a4a3b0e9b4022 Author: Weiqun Zhang Date: Tue Jan 15 13:13:54 2019 -0800 update FillBoundary Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 27cc720bd213ff6f94ed84e4d5e1ac5563b2b0bf Author: Weiqun Zhang Date: Tue Jan 15 12:26:22 2019 -0800 update Geometry Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp commit eaae1503f11708d3eaa1b659cd7c36725a1b50e6 Author: Weiqun Zhang Date: Tue Jan 15 11:58:37 2019 -0800 change Array4 so that it can be easily passed to Fortran Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H commit 66649b6abe940bcd7857959431044ca5690324a9 Author: Kevin Gott Date: Tue Jan 15 11:11:34 2019 -0800 Update GPU docs: needs picture change & AsyncFab/AsyncArray examples (w.r.t. new Array4 style)? Docs/sphinx_documentation/source/GPU.rst commit 784f8b45098c1d4b85534273c839608f4be81666 Author: Weiqun Zhang Date: Tue Jan 15 10:34:37 2019 -0800 add profilers Tutorials/GPU/Launch/main.cpp commit 9251a1ead2c8489409a851622739a7c37f1cb2b6 Merge: e420ecc2d 1746f0702 Author: Michele Rosso Date: Tue Jan 15 09:45:24 2019 -0800 Merge branch 'development' into mr/cmake commit e420ecc2d77f388f3d72a6f1af7e43d3ed81a993 Author: Michele Rosso Date: Tue Jan 15 09:32:55 2019 -0800 CMake: finalize move to CMake 3.11 Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit 1746f0702952ec6fb722a9779d57aa2a6673a576 Merge: d40cb1e8b 16f627fbd Author: Weiqun Zhang Date: Mon Jan 14 20:09:39 2019 -0800 Merge branch 'weiqun/gpu' into development commit f428d6fc2fd1fe6c1e88cf8cc916f1eeb07a228e Author: Michele Rosso Date: Mon Jan 14 16:47:09 2019 -0800 CMake: move to CMake 3.11 CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tutorials/Amr/Advection_F/CMakeLists.txt Tutorials/Amr/Advection_octree_F/CMakeLists.txt commit d40cb1e8b6b244171688fc7e402826b957e33bf5 Author: Weiqun Zhang Date: Mon Jan 14 15:57:31 2019 -0800 fix bug in AMREX_FOR Src/Base/AMReX_CudaLaunch.H commit 16f627fbde5bf81f29bd899eab159d4614ef6cd5 Author: Weiqun Zhang Date: Mon Jan 14 15:57:31 2019 -0800 fix bug in AMREX_FOR Src/Base/AMReX_CudaLaunch.H commit 3116021ccfb93de3731241f524ff3ee2ed444dd6 Author: Weiqun Zhang Date: Mon Jan 14 18:28:57 2019 -0500 use AMREX_FOR in ParallelCopy Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFab.cpp commit b5a9dea8e03d4a7ac2d56a27e9833c2e4655630d Author: Weiqun Zhang Date: Mon Jan 14 13:58:12 2019 -0500 use AMREX_FOR Src/Base/AMReX_MultiFab.cpp commit 7e5a55ba86eff616a1ff03af70d508df4801a77f Author: Weiqun Zhang Date: Mon Jan 14 10:54:04 2019 -0800 fix template for no BaseFab type Src/Base/AMReX_FabArray.H commit 31738fbff948219d3704c4e09fa7ffd1d86761a1 Merge: 5f47b8881 7799e6bc4 Author: Weiqun Zhang Date: Mon Jan 14 10:41:50 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5f47b8881419d17b8544df0477971edb20e11d76 Author: Weiqun Zhang Date: Mon Jan 14 10:41:42 2019 -0800 remove the unused buggy code for now Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 7799e6bc4dca73beba082701d0badd780b5aebb1 Author: Kevin Gott Date: Mon Jan 14 08:47:25 2019 -0800 Comments on proper use of tilebox and dynamic tiling overview. Docs/sphinx_documentation/source/Basics.rst commit ce493a179efefa337043efec26bfb0f45b46c2e6 Author: Kevin Gott Date: Mon Jan 14 08:46:33 2019 -0800 Note on ~/amrex in GNUMakefile Docs/sphinx_documentation/source/BuildingAMReX.rst commit 7296686dc0fafd9e19b2fe9cb1a3c8a67f907196 Merge: 06ccd53db 116129ca9 Author: Weiqun Zhang Date: Mon Jan 14 09:41:20 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 06ccd53db2f591ded35cc650ba1eb02ec32f90c3 Author: Weiqun Zhang Date: Mon Jan 14 09:41:12 2019 -0800 forgot a file Tutorials/GPU/HeatEquation_EX1_C/Source/mykernel.H commit 116129ca93a16391bb40ba4c45c79188905b71b4 Author: Tan Nguyen Date: Mon Jan 14 11:20:54 2019 -0600 update known limitations Docs/sphinx_documentation/source/AsyncIter.rst commit 87e0bd0aa5ce76f3b554e2b469b2d7ee1af80232 Author: Tan Nguyen Date: Mon Jan 14 11:13:41 2019 -0600 update known limitation Docs/sphinx_documentation/source/AsyncIter.rst commit 6bdb52349e27ebd0c37ffabd0dcc80eda1a8f845 Author: Tan Nguyen Date: Mon Jan 14 09:08:46 2019 -0800 add known limitation of the async runtime to the userguide Docs/sphinx_documentation/source/AsyncIter.rst commit 6fa0a6a0a1b58257662ae55160634f0e5ef5a099 Author: Weiqun Zhang Date: Mon Jan 14 06:51:06 2019 -0800 fix compilation Src/Base/AMReX_CudaAsyncFabImpl.cpp commit 41e7728d4287e8958ef490e5879283c6ff02a5ea Merge: 8a3284459 9f177bbe5 Author: Weiqun Zhang Date: Sun Jan 13 20:51:10 2019 -0800 Merge branch 'weiqun/for' into development commit 8a3284459d5edc50654f6eb11963c8087cb3b567 Author: Weiqun Zhang Date: Sun Jan 13 20:33:48 2019 -0800 Merge branch 'weiqun/for' into development Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_IntVect.H Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/Launch/main.cpp commit 9f177bbe5379c596a3992145c761fc4a5b3a4c58 Author: Weiqun Zhang Date: Sun Jan 13 20:29:16 2019 -0800 update GPU heat equation example Src/Base/AMReX_FArrayBox.H Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit 0f121a87c50b568c96312970c459a7383f091739 Author: Weiqun Zhang Date: Sun Jan 13 14:42:30 2019 -0800 use AMREX_FOR in CNS tutorial Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/Launch/MyKernel.H commit df86f0c113e6748691b2317ca9a0169d63e141db Author: Weiqun Zhang Date: Sun Jan 13 11:24:12 2019 -0800 simplification of AMREX_FOR and more examples in launch tutorial Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/Launch/main.cpp commit bf0c52e83f61ed72c556a683e409ff0dea73c909 Author: Johannes Blaschke Date: Sun Jan 13 10:17:27 2019 -0800 expand implicit function filling Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit 0eb174ebf63e011e9a1c8ec42ce08bc81817955d Author: Weiqun Zhang Date: Sat Jan 12 22:56:57 2019 -0800 start using AMREX_FOR in CNS tutorial Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_tagging.H commit 7172492bc7d3cc94aabc5c236ffc1439169c31e0 Author: Weiqun Zhang Date: Sat Jan 12 22:44:37 2019 -0800 update Launch Tutorials/GPU/Launch/main.cpp commit f37659e5be01f1688de8947e089fd48d52130340 Author: Weiqun Zhang Date: Sat Jan 12 22:44:13 2019 -0800 reorder BaseFabData structure Src/Base/AMReX_BaseFab.H commit 0d6158e1e1cd7189ce3816a93074311703942ae8 Author: Weiqun Zhang Date: Sat Jan 12 22:05:16 2019 -0800 AMREX_FOR_1D, 3D and 4D Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H commit c577887e653b4aa801c55ffd92b193f461028a41 Author: Weiqun Zhang Date: Sat Jan 12 18:31:03 2019 -0800 add AsyncFab::array and fix const of Array4 Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_IntVect.H Tutorials/GPU/Launch/main.cpp commit be4ad4e6b3b91897bb4fc090f170edbb4cb9c7a5 Author: Johannes Blaschke Date: Sat Jan 12 17:53:18 2019 -0800 cleanup Src/EB/AMReX_EB_LSCoreI.H commit ca034f75210a435ed4bd79b5548c78378ecd3324 Author: Johannes Blaschke Date: Sat Jan 12 17:48:16 2019 -0800 expose ebis level building as a static template class Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreI.H commit 1ac82b4de33988d707ccb76658126655a607dc3b Author: Weiqun Zhang Date: Sat Jan 12 15:11:39 2019 -0800 AMREX_FOR: a new kernel launch approach Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_GpuLaunch.H Tutorials/GPU/Launch/main.cpp commit 48d6dcefd2113537f3ecb50fa9a2169e6255aaa7 Author: Johannes Blaschke Date: Sat Jan 12 14:46:56 2019 -0800 fix eb_pad error Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/Donut/Exec/inputs commit 85010e19e632f5150df7cb57a8643ac2eda4b692 Author: Ann Almgren Date: Sat Jan 12 13:40:23 2019 -0800 Fix typo in push_position_boris -- we were using uxp for all directions instead of uxp, uyp, uzp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 commit 6837cc7a65ed2989bcbdec34ac580e5a3664ebbd Author: Ann Almgren Date: Sat Jan 12 13:38:52 2019 -0800 Fix typo in push_position_boris code example. Docs/sphinx_documentation/source/GPU.rst commit 14eaaba4befca5bdf4fee5dc8ae18db4d430c5c3 Merge: 119d8f6ba 9268abc0e Author: Johannes Blaschke Date: Sat Jan 12 12:21:52 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 119d8f6ba7ec0b14f36388c8a3288bcc43044333 Author: Johannes Blaschke Date: Sat Jan 12 12:21:40 2019 -0800 add profiling Src/EB/AMReX_EB_LSCoreBase.cpp commit 9268abc0ec2b4444c05acb4fc1151debde2ba0ad Merge: 4fcd10905 9b75dd527 Author: Ann Almgren Date: Sat Jan 12 11:51:18 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 4fcd1090557b086b14ac44079777166b193da933 Author: Ann Almgren Date: Sat Jan 12 11:51:06 2019 -0800 Add brackets to fcompare.cpp as well. Tools/Postprocessing/C_Src/fcompare.cpp commit 9b75dd527dfb814e939e2a5dab399e5acf930d67 Merge: b5691424e 778731020 Author: Johannes Blaschke Date: Sat Jan 12 11:49:30 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b5691424ebfc804f6a64a97600db7d2e8c7a8e0f Author: Johannes Blaschke Date: Sat Jan 12 11:49:27 2019 -0800 make sure boxarrays are nodal/cc and ensure this works when DIM!=3 Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit 77873102077f01e201fd7174ac9c1d61d5575ee6 Author: Ann Almgren Date: Sat Jan 12 11:36:32 2019 -0800 Needed to add brackets between Initialize and Finalize so this doesn't segfault. Tools/Postprocessing/C_Src/fextract.cpp commit b31cfadf4e84050a523ce231f512153a87b93486 Author: Weiqun Zhang Date: Fri Jan 11 22:53:01 2019 -0800 cuda: check solution and push e field Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 9610f70749ca11fb9b16d9a593d9997ff718eb43 Author: Weiqun Zhang Date: Fri Jan 11 21:32:01 2019 -0800 fix memory leak in pic tutorial Tutorials/Particles/ElectromagneticPIC/Make.EMPIC Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 04f57cbd41bfe9ac4bce7d2420cd1d3aebad3fd3 Merge: adbc9e96b ff13edfb2 Author: Weiqun Zhang Date: Fri Jan 11 19:43:28 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ff13edfb2d6ff0f4c3df0f77aea6883d900a56c7 Merge: d12d5ee8d 4513af878 Author: Johannes Blaschke Date: Fri Jan 11 16:30:59 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d12d5ee8d7f923f22a350d0f5aa9724ebb466e2a Author: Johannes Blaschke Date: Fri Jan 11 16:30:57 2019 -0800 expose multi-level filling Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit e9428b5df55002b954921edb1f2da574ba208fa1 Author: Johannes Blaschke Date: Fri Jan 11 15:23:35 2019 -0800 static EBSearchBox, needed to expose multi-level filling Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit adbc9e96bfd82386a8fe611a128d38d417aaf9bf Merge: ed4dc8d60 4513af878 Author: Weiqun Zhang Date: Fri Jan 11 16:58:22 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ed4dc8d600b3f66349d5c17d5255710516006fbb Author: Weiqun Zhang Date: Fri Jan 11 16:58:13 2019 -0500 add nvcc argument -maxrregcount Tools/GNUMake/comps/nvcc.mak commit 4513af8782cb901a6bcb7e5e93cfcd5f3462bb98 Author: Andrew Myers Date: Fri Jan 11 15:42:40 2019 -0500 turn off OMP_OFFLOAD by default Tutorials/GPU/Launch/GNUmakefile commit 4532950a5c77b7679991e3385c59af86d85894bb Author: Andrew Myers Date: Fri Jan 11 15:42:02 2019 -0500 restoring the USE_OMP_OFFLOAD option and adding an example to the launch Tutorial Tools/GNUMake/Make.defs Tutorials/GPU/Launch/GNUmakefile Tutorials/GPU/Launch/MyKernel_F.F90 Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/main.cpp commit f02acdce177f3c9fa03b510ffefa7dbe7538e945 Author: Weiqun Zhang Date: Fri Jan 11 09:22:27 2019 -0800 exclude initilizations including cuda and openacc that could take a long time from tiny profiler Src/Base/AMReX.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 9c16d851e4927f6bb423ec76a277f1c361f172c4 Merge: 1b39670db c7224c8b7 Author: Brandon Runnels Date: Fri Jan 11 09:46:32 2019 -0700 Merge branch 'development' into nodeghostcells commit c7224c8b7ca8a9e7f3574d3cd39498864702afe5 Author: Weiqun Zhang Date: Thu Jan 10 16:27:53 2019 -0800 inline some RealBox functions Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit d96739520a9e049c9a50b106d708521bd0ce866f Author: Weiqun Zhang Date: Thu Jan 10 16:12:50 2019 -0800 more constexpr Src/Base/AMReX_Orientation.H commit 02482a8ba14b2545b6364b84b50310882ed8d54d Author: Weiqun Zhang Date: Thu Jan 10 15:44:16 2019 -0800 make the implementation of print_state template Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFabUtil.cpp commit c12ec7afff5421481307deea6d464550ad8d5949 Author: Weiqun Zhang Date: Thu Jan 10 15:24:16 2019 -0800 optional ghost cell argument in print_state Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 41da65c5c4909977bec12f587063346b18784d2f Merge: 1e1898d16 78905bf26 Author: Michele Rosso Date: Thu Jan 10 15:43:30 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1e1898d16b83b9fbf30b9cb37e54095c4544f8fc Author: Michele Rosso Date: Thu Jan 10 15:43:19 2019 -0800 CMake: completely drop support for F_Baselib Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Options.cmake commit 78905bf2629807e1766454a7ae50ed4a4b3bcd17 Author: Weiqun Zhang Date: Thu Jan 10 15:08:13 2019 -0800 amrex::cast for MultiFab kind types Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit e1ede7dc6dfc5b1ca5ff37f0d5c5b11745b5a693 Author: Weiqun Zhang Date: Thu Jan 10 14:40:30 2019 -0800 make some functions constexpr Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H commit bf8713d2a348d4f17dd3cb20b3af6e2f8183f978 Author: Weiqun Zhang Date: Thu Jan 10 13:36:54 2019 -0800 rm deprecated functions Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp commit 61ab029d5ea82a8a20224cfbe7581bd9dea173c4 Author: Michele Rosso Date: Thu Jan 10 15:05:57 2019 -0800 CMake: change how the build type is set Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake Tools/CMake/AMReX_Options.cmake commit 58344d7f338f598c0b5205d4b500f1ca0c72d2db Merge: 29557b19b d43b14257 Author: Johannes Blaschke Date: Thu Jan 10 13:43:49 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d43b1425749931c1b7ed84ff10711850a3358b6c Author: Weiqun Zhang Date: Thu Jan 10 13:09:09 2019 -0800 use new BaseFab interface in various places Src/Base/AMReX_Box.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit ed4e217d248c54712b276cf789fc477e3078a66d Author: Weiqun Zhang Date: Thu Jan 10 13:08:20 2019 -0800 mod gpu launch tutorial to show generic loop launch Tutorials/GPU/Launch/main.cpp commit a7596bcd007a13a8314de2311fa14baab13aef6f Author: Weiqun Zhang Date: Thu Jan 10 09:54:53 2019 -0800 safeguard some CoordSys functions Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_GpuControl.H commit 014c616c7066e688ef1a6c2d45353103d96f55de Author: Weiqun Zhang Date: Thu Jan 10 09:27:34 2019 -0800 inline setBC function Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit e042ce4d7ed38a3ac85c0baaacd7cada2e01849f Author: Weiqun Zhang Date: Thu Jan 10 09:17:53 2019 -0800 rm deprecated BaseIndex class and changed the interface of BaseFab cast Src/Base/AMReX_BaseFabUtility.H Src/Base/AMReX_BaseIndex.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 1a1d7dc8889656cec14742a180b84b3ea9e8ccf8 Merge: 525322786 ceb381c36 Author: Weiqun Zhang Date: Wed Jan 9 19:28:16 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ceb381c364698ec869d5baaa977b48ba776bd23f Author: Ann Almgren Date: Wed Jan 9 17:37:57 2019 -0800 Make a link back from Tutorials to Documentation Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/index.rst commit 9f8ef5e605b30d23b5b7fbea891411b8bd1ee460 Merge: b1ce16671 48994bfac Author: Ann Almgren Date: Wed Jan 9 17:33:46 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit b1ce166714e2bb69cb82ef360190dabca5064384 Author: Ann Almgren Date: Wed Jan 9 17:33:03 2019 -0800 Add link to Tutorials page from the front page. Docs/sphinx_documentation/source/index.rst commit 29557b19bd3d586bb59737643ea29a73da800335 Author: Johannes Blaschke Date: Thu Jan 10 02:17:24 2019 +0100 exposed level-set and volfrac box tagging Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 525322786ee305840e8516f9c9d00dfb1fc8ee02 Author: Weiqun Zhang Date: Wed Jan 9 17:03:57 2019 -0800 compiles Src/Base/AMReX_BaseFab.H commit b63b18806dcb5cfe264300a769ec8b5e234fce6e Author: Weiqun Zhang Date: Wed Jan 9 16:49:31 2019 -0800 more on the new interface in BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayBase.H commit 48994bfac9c80345c45bd06bee3c85677d283aa5 Author: Weiqun Zhang Date: Wed Jan 9 12:02:14 2019 -0800 add missing atomic add Src/Base/AMReX_FabArrayUtility.H commit c6a245ed23b8d71fb208ef27311980a4e7b5e206 Author: Weiqun Zhang Date: Wed Jan 9 11:58:27 2019 -0800 optimization of reuction on summit Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FabArrayUtility.H commit ae6d2a04b8901454bed8857e9d51e7788d5cf600 Author: Weiqun Zhang Date: Wed Jan 9 10:53:05 2019 -0800 add profilers and minor changes Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/CNS/Source/CNS.cpp commit c822650fa14cd90793c0dc0bcf5ece2b7d3d76cc Author: Weiqun Zhang Date: Wed Jan 9 10:50:34 2019 -0800 add copyToHost function to AsyncArray Src/Base/AMReX_CudaAsyncArray.H commit 0a68a6092d7f19946714ce3a4d2bb5344481844c Merge: 5e6f40dd5 3a3aa9be1 Author: Weiqun Zhang Date: Wed Jan 9 10:30:26 2019 -0800 Merge branch 'weiqun/gpu' into development commit 5e6f40dd5f800a6dbbc1771f4f132b7a5819c6ea Merge: 1282e9cd9 cc7ae04e8 Author: Guy Moore Date: Tue Jan 8 21:45:09 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1282e9cd950a36f37c0e200362b0da2144a6e4f4 Author: Guy Moore Date: Tue Jan 8 21:43:58 2019 -0800 Corrected intersphinx with URL Docs/sphinx_documentation/source/conf.py Docs/sphinx_tutorials/source/conf.py commit cc7ae04e8861b04bc59fc2983bc0e6d8a69d49e4 Merge: 840d13a79 d759360fd Author: Ann Almgren Date: Tue Jan 8 17:41:58 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 840d13a79368c473d43697d55d2d5a9d5f2d2f5b Author: Ann Almgren Date: Tue Jan 8 17:35:25 2019 -0800 "to be ran" --> "to be run" Docs/sphinx_documentation/source/GPU.rst commit d759360fd1a1c99d2bb482083827c55702cbb517 Merge: b005bb320 c41f123dd Author: Guy Moore Date: Tue Jan 8 17:21:50 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b005bb32078ab02eb2e9320b7b29edf24c29d498 Author: Guy Moore Date: Tue Jan 8 17:19:30 2019 -0800 Added intersphinx extension to cross-ref between sphinx_documentation and sphinx_tutorials Docs/sphinx_documentation/source/SWFFT.rst Docs/sphinx_documentation/source/Tutorials_Chapter.rst Docs/sphinx_documentation/source/conf.py Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst Docs/sphinx_tutorials/source/conf.py Docs/sphinx_tutorials/source/index.rst commit c41f123ddc94e4fec8fca7c0503dac56e5efff82 Merge: 50846e460 2df279092 Author: WeiqunZhang Date: Tue Jan 8 16:54:01 2019 -0800 Merge pull request #388 from AMReX-Codes/cy-perf Bunch of changes to support MLMG performance analysis and tuning commit 50846e4609a3337e9ad67e35a71816f6a56e1cd5 Author: Weiqun Zhang Date: Tue Jan 8 16:05:31 2019 -0800 use cuda driver api to avoid cuda-memcheck error Src/Base/AMReX_CudaUtility.H Tools/GNUMake/Make.defs commit ae3c8f4b5da22d33cbc94c15dd1e8d9865560a56 Merge: d707c001a ff09a41b9 Author: Cy Chan Date: Tue Jan 8 14:26:21 2019 -0800 Merge branch 'development' into forkjoin commit d707c001a49fc536a5f42df64742422ee0b18b22 Author: Cy Chan Date: Tue Jan 8 14:14:51 2019 -0800 simplify ForkJoin interface a bit remove ngrow argument from reg_mf() number of grow cells in forked MultiFab now matches original MultiFab by default can customize after registration via modify_ngrow() function add overloads to modify_comp_split() and modify_ngrow() for no index argument Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/ForkJoin/MLMG/main.cpp Tutorials/ForkJoin/Simple/MyTest.cpp commit ff09a41b921589115bf39a8ba264fc61ef3795d5 Author: Weiqun Zhang Date: Tue Jan 8 11:02:07 2019 -0800 add SafeLaunchGuard and use it in Interpolaters so that they work with old style FillPatch Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_GpuControl.H commit 5f9c1b5530b4c73f1a881ecf1fe997ba551e4a8f Merge: 2d189f02d 54d0ed8cd Author: Tan Nguyen Date: Tue Jan 8 02:33:26 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2d189f02d98b68ce44ad52efef71fd1f43836985 Author: Tan Nguyen Date: Tue Jan 8 02:33:18 2019 -0800 fix a bug in the upcxx banckend that could lead to deadlock Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp commit 54d0ed8cd9839598e139d2361a3e5c3ea8fca6a2 Merge: 97dc2ca6f 3a977f510 Author: Andrew Myers Date: Mon Jan 7 17:36:20 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 97dc2ca6f0e28970560b9e1ecee6b6970fc20e65 Author: Andrew Myers Date: Mon Jan 7 17:36:10 2019 -0800 only allow this early exit in RedistributeGPU if allPeriodic Src/Particle/AMReX_ParticleContainerI.H commit 3a977f5103fe98f57ca5ae641c4959579bba1a42 Merge: 351c9d504 3e819ca91 Author: Johannes Blaschke Date: Tue Jan 8 00:07:58 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 351c9d504a883054dc0d7f15f7c51e8d68146f87 Author: Johannes Blaschke Date: Tue Jan 8 00:07:33 2019 +0100 expand level-set documentation Docs/sphinx_documentation/source/EB.rst commit 3e819ca91b968389e1150282ae1f0e56a0d7979f Merge: 90a7039ef c24b44c86 Author: Cy Chan Date: Mon Jan 7 14:19:15 2019 -0800 Merge branch 'development' into forkjoin commit 90a7039ef294d16018bceb0baa2a5808582ebaa9 Author: Cy Chan Date: Mon Jan 7 14:18:30 2019 -0800 ForkJoin Tutorial documentation edits and formatting Docs/sphinx_tutorials/source/AMR_Tutorial.rst Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst Docs/sphinx_tutorials/source/conf.py commit 63b7c8603bd48042a93dea4bc5f2c0856576b88e Author: Cy Chan Date: Mon Jan 7 11:41:43 2019 -0800 updates to ForkJoin/MLMG tutorial and documentation Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst Docs/sphinx_tutorials/source/figs/fork_join_tasks.png Docs/sphinx_tutorials/source/figs/mf_remap_hires.png.REMOVED.git-id Docs/sphinx_tutorials/source/figs/nested_fork_join_tasks.png Tutorials/ForkJoin/MLMG/inputs Tutorials/ForkJoin/MLMG/main.cpp commit c24b44c86dc3d24bd0e95b2efb41afe82aa9cfee Author: Johannes Blaschke Date: Mon Jan 7 20:09:03 2019 +0100 expand level-set documentation Docs/sphinx_documentation/source/EB.rst Src/EB/AMReX_EB_levelset.H commit 242bf5b84765f18e60337033d80c614facdf17c7 Merge: 8aa7e758d 40fb2da31 Author: Johannes Blaschke Date: Mon Jan 7 19:16:41 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8aa7e758de1a1d620f0b708d7f7755cc05297ad3 Author: Johannes Blaschke Date: Mon Jan 7 19:15:50 2019 +0100 start adding level-set documentation Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/EB/loc_ls_ex.png commit 1e9d32267810772919863880c1c141ad9b7bb6ab Author: Cy Chan Date: Mon Jan 7 10:04:30 2019 -0800 working on ForkJoin Tutorial Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst Tutorials/ForkJoin/Simple/MyTest.cpp commit 40fb2da3149671227ed067e7808d6f2e4e5fb726 Merge: 6b9176dd4 9766347b4 Author: Weiqun Zhang Date: Mon Jan 7 08:56:01 2019 -0800 Merge branch 'weiqun/interp-3' into development commit 6b9176dd451a4328dcd20ab1b9a86c52ebd95e90 Merge: bbbe2f15c 8bdaa2184 Author: Johannes Blaschke Date: Mon Jan 7 17:16:10 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit bbbe2f15c660e918ce10ac9bc6d084fcdf4f1225 Author: Johannes Blaschke Date: Mon Jan 7 17:16:04 2019 +0100 added more profiling Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit 8bdaa21841e3cf5db422d3b8493e20b4c679dacc Merge: 799338c03 4617c45d5 Author: Andrew Myers Date: Mon Jan 7 06:48:29 2019 -0800 Merge pull request #395 from khou2020/ncmpi Add PnetCDF benchmark commit 4617c45d5b93b713e9b4360282125feb6d4e67f2 Merge: 369b5cfb2 799338c03 Author: Kaiyuan Hou Date: Mon Jan 7 06:04:19 2019 -0600 Merge branch 'development' into ncmpi commit 369b5cfb2db3150aed9e6e2b8e36837ba3ce1c50 Merge: 5a7aaa21c 03d99cd92 Author: Kaiyuan Hou Date: Mon Jan 7 06:03:22 2019 -0600 Merge branch 'master' into ncmpi commit 799338c03d58da812d85ea100014b819afc373dd Merge: e230d2cd3 d8cecb46e Author: Weiqun Zhang Date: Sun Jan 6 18:47:40 2019 -0800 Merge branch 'weiqun/interp-2' into development commit e230d2cd379d9ce7035106f727371b185302c935 Merge: b016bb92d 22d3e2008 Author: Ann Almgren Date: Sun Jan 6 17:31:59 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit b016bb92d988cc40c9b60e948d390d56b8e6fbba Author: Ann Almgren Date: Sun Jan 6 17:31:32 2019 -0800 Add non-const access functions for the level set arrays. Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_levelset.H commit 22d3e200897c8f8a084d5070050923b167b6e1dd Author: Tan Nguyen Date: Sun Jan 6 17:25:26 2019 -0800 a small change in metadata extraction Src/Amr/AMReX_Amr.cpp commit beecea767c42c93e7580ff77e1a24b0360c7f32c Author: Tan Nguyen Date: Sun Jan 6 14:27:11 2019 -0800 fix a bug to avoid potential deadlocks Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.H Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.H commit 7d4ad2430aaf8e62ea496bf8bc5cfc7dc9f0c96e Author: Cy Chan Date: Sat Jan 5 21:29:26 2019 -0800 Move existing ForkJoin tutorial to Tutorials/ForkJoin/Simple demonstrates various ways of passing MultiFabs into forked tasks demonstrates setting task output directory Add second ForkJoin tutorial based on modified OldTutorials/MultiColor_C tutorial demonstrates reusing and nesting fork-joins demonstrates customizing component split across tasks for split MultiFabs Tutorials/ForkJoin/GNUmakefile Tutorials/ForkJoin/MLMG/GNUmakefile Tutorials/ForkJoin/MLMG/Make.package Tutorials/ForkJoin/MLMG/ff.f90 Tutorials/ForkJoin/MLMG/inputs Tutorials/ForkJoin/MLMG/main.cpp Tutorials/ForkJoin/Simple/GNUmakefile Tutorials/ForkJoin/Simple/Make.package Tutorials/ForkJoin/Simple/MyTest.H Tutorials/ForkJoin/Simple/MyTest.cpp Tutorials/ForkJoin/Simple/MyTest_F.H Tutorials/ForkJoin/Simple/inputs Tutorials/ForkJoin/Simple/main.cpp commit f36e9298107dbd0aaa60c582696e79e6cdce841d Author: Cy Chan Date: Sat Jan 5 12:50:58 2019 -0800 modifications to ForkJoin: task_output_dir set through member function instead of constructor defaults to empty string (don't write task output files) dir created in fork_join invocation instead of constructor append to task output files instead of creating unique filenames simplify ComponentBounds() Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Tutorials/ForkJoin/MyTest.cpp commit 3a3aa9be1d5864bc133809d8667dd086fd67e4c3 Author: Weiqun Zhang Date: Sat Jan 5 10:50:02 2019 -0800 rm performCopy because it is no longer used Src/Base/AMReX_BaseFab.H commit aee02c254ce241a3b2f8f7148c65e4618be21d43 Author: Weiqun Zhang Date: Sat Jan 5 08:56:09 2019 -0800 start new BaseFab interface Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H commit e258be2164cb5006a61b9f74e12a1cc87ee4726a Author: Johannes Blaschke Date: Sat Jan 5 15:46:12 2019 +0100 implicit function filling now also has the option to apply threshold Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_utils.cpp commit 54be91cf66bec6696758f6b084e5a63770900812 Merge: 2d7782f63 4ac5219e5 Author: Johannes Blaschke Date: Sat Jan 5 12:18:47 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4ac5219e5d34199ae0be7c48c44f26c05328494f Author: Andrew Myers Date: Fri Jan 4 16:12:42 2019 -0800 minor tweaks Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit 5b24c5a595c2d90e7b5672e4eb8e0f199016f955 Merge: f9863f1c5 7f9ed04ca Author: Andrew Myers Date: Fri Jan 4 15:55:12 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f9863f1c5e075300f9d639786679859b802bfa2c Author: Andrew Myers Date: Fri Jan 4 15:54:59 2019 -0800 add description of the CellSortedParticles tutorial Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit 7f9ed04ca4ffa54878a9612e6073708b87ecb173 Merge: 36f2fa27d b24cb033c Author: Andy Nonaka Date: Fri Jan 4 15:36:17 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 36f2fa27d8f0e98b1cd30a40c24d16d84265ed0f Author: Andy Nonaka Date: Fri Jan 4 15:36:00 2019 -0800 Tutorials/Amr README files copied into documentation Docs/sphinx_tutorials/source/AMR_Tutorial.rst Docs/sphinx_tutorials/source/Basic_Tutorial.rst commit b24cb033cbaedbaeb3d230e2c7beb55e190fa011 Merge: cbf38081c c7105c198 Author: Andrew Myers Date: Fri Jan 4 15:04:51 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cbf38081ca11fd4a635414eafcc080d544675e5c Author: Andrew Myers Date: Fri Jan 4 15:00:10 2019 -0800 move LoadBalance from Tutorials to Tests - it's not really a full Tutorial. Tests/Particles/LoadBalance/GNUmakefile Tests/Particles/LoadBalance/Make.package Tests/Particles/LoadBalance/create_binary_particle_file.py Tests/Particles/LoadBalance/inputs Tests/Particles/LoadBalance/main.cpp Tests/Particles/LoadBalance/visualize_output.ipynb commit ea919c0e3399b7d4585c9c5b008255a40f97002c Author: Andrew Myers Date: Fri Jan 4 14:59:25 2019 -0800 minor changes Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit cdbc60cf0114d67e37c536489ab4a2049ef91e57 Author: Andrew Myers Date: Fri Jan 4 14:50:31 2019 -0800 add a section on the ElectromagneticPIC tutorial Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit ddb3dba437e4deeaa3e6afe6c8e1cc55e400bc15 Author: Andrew Myers Date: Fri Jan 4 14:21:03 2019 -0800 update sphinx documentation for particle tutorials Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit b5f7b0a98a550e6edbd5dae337dabc4bda5de933 Author: Andrew Myers Date: Fri Jan 4 14:20:22 2019 -0800 merge the two NeighborList Tutorials into one 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Andy Nonaka Date: Fri Jan 4 13:15:21 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 994fefcb6ec44a23927f2052d7e459b76866a0e3 Author: Andy Nonaka Date: Fri Jan 4 13:14:56 2019 -0800 add link to amrex documentation Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst commit 076ae6e9b1218fa59d16d225a9b5d8417e432302 Author: Weiqun Zhang Date: Fri Jan 4 11:15:31 2019 -0800 add a function to set the static data for periodicity in Geometry Src/Base/AMReX_Geometry.H commit 2d7782f63864e958b2ae729d55b1a4ad07a7f58a Merge: 87f49051e a17cb6ca8 Author: Johannes Blaschke Date: Fri Jan 4 11:11:23 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a17cb6ca86aadec41a9e204b993232051453f76b Merge: 7925f4eaf aa60ee134 Author: Andrew Myers Date: Thu Jan 3 16:50:07 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7925f4eafd7368e47f03409fe28f16183180908d Author: Andrew Myers Date: Thu Jan 3 16:49:05 2019 -0800 add caveat about one of the code snippets in the GPU docs Docs/sphinx_documentation/source/GPU.rst commit 3b40521414f09929237b437b146e37f0dbfd2012 Author: Andrew Myers Date: Thu Jan 3 16:43:12 2019 -0800 docs typo fix Docs/sphinx_documentation/source/GPU.rst commit aa60ee1349d24bb4da0f1ba5f3a910750c150c59 Author: Weiqun Zhang Date: Thu Jan 3 15:20:47 2019 -0800 removed the unroll line I accidently left there Tutorials/GPU/Launch/MyKernel.H commit ea87277b39073d21b1bbe08abb1f9b23df3ca927 Merge: 9277f4a7e 9766347b4 Author: Weiqun Zhang Date: Thu Jan 3 14:55:30 2019 -0800 Merge branch 'weiqun/interp-3' into weiqun/gpu commit 9277f4a7efa7c5cd3156e1cc22dd411b4d5e3f08 Merge: 336720d0d 82311957c Author: Weiqun Zhang Date: Thu Jan 3 14:55:16 2019 -0800 Merge branch 'development' into weiqun/gpu commit 82311957c1888777aab400b2e4042d9ca9ea6154 Author: Weiqun Zhang Date: Thu Jan 3 14:47:20 2019 -0800 minor changes to gpu documentation Docs/sphinx_documentation/source/GPU.rst commit 21eef7c643d09d00a64b7b5840661275779f1f43 Author: Weiqun Zhang Date: Thu Jan 3 14:46:43 2019 -0800 add a new constructor to AsynArray so that it can be used as scratchpad Src/Base/AMReX_CudaAsyncArray.H commit 1b574ea8936e264bb218e3136af421ff74c055b7 Author: Tan Nguyen Date: Thu Jan 3 13:36:52 2019 -0800 minor changes in asyncIter guide Docs/sphinx_documentation/source/AsyncIter_Chapter.rst commit 2df2790926f33c787b2851d78aed0a81b26d13be Author: Cy Chan Date: Thu Jan 3 12:58:49 2019 -0800 remove MLMG::Initialize/Finalize init MLLinOp the first time MLLinOp::define is called Src/Base/AMReX.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 8b7cc41c747ef9cebc7af508955ebd72d97c5aa2 Merge: ec0fe6fc2 70c2cdb80 Author: Andrew Myers Date: Thu Jan 3 13:00:43 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ec0fe6fc2a727891b3b1a90983e2b175d5e96f84 Author: Andrew Myers Date: Thu Jan 3 13:00:27 2019 -0800 some double -> Real Tools/C_util/WritePlotFile.cpp commit 87f49051ebd5bfb8a145261a2d0fc10091f53c69 Merge: 5822778fe 70c2cdb80 Author: Johannes Blaschke Date: Thu Jan 3 21:21:57 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5822778fed303d45aa8dc895ce2da5ea8d07d96b Author: Johannes Blaschke Date: Thu Jan 3 21:21:25 2019 +0100 clean up method naming convention and doxygen Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit 70c2cdb80efb6d7fc18b28535309510b319b0680 Author: Kevin Gott Date: Thu Jan 3 10:42:23 2019 -0800 Profiling and summary GPU docs with pictures. Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU/Streams.pdf Docs/sphinx_documentation/source/GPU/Streams.png Docs/sphinx_documentation/source/GPU/Streams.pptx Docs/sphinx_documentation/source/GPU/gpu_1.pdf Docs/sphinx_documentation/source/GPU/gpu_1.png Docs/sphinx_documentation/source/GPU/gpu_2.pdf Docs/sphinx_documentation/source/GPU/gpu_2.png Docs/sphinx_documentation/source/GPU/gpu_3.pdf Docs/sphinx_documentation/source/GPU/gpu_3.png commit 6f0c2169a7d99dbd49aa01781c366f385992fc19 Author: Kevin Gott Date: Thu Jan 3 10:41:25 2019 -0800 Doc warnings. Docs/sphinx_documentation/source/AmrCore.rst commit 686bdc061c0c61827a49ae15df7b0a16ab8d3c2b Merge: 97d5e06b8 64cccb5b3 Author: Weiqun Zhang Date: Thu Jan 3 09:55:55 2019 -0800 Merge branch 'weiqun/interp-1' into development commit 84ebe89a1f52b40feec48207fd6b2ab19840cd4a Author: Cy Chan Date: Wed Jan 2 17:48:02 2019 -0800 fix some issues with performance analysis / tuning features add MLMG::Initialize/Finalize move MLCellLinOp software performance counters to static class member clears counters on Finalize add MLLinOp::Initialize/Finalize use unique_ptr to manage comm_cache clears MPI communicator cache via destructor on Finalize add machine::Finalize use unique_ptr to manage machine object clears neighborhood cache via destructor on Finalize add optional argument to DistributionMapping::makeSFC to allow selecting old behavior Src/Base/AMReX.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Machine.H Src/Base/AMReX_Machine.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/main.cpp commit 97d5e06b801075109aaf15b99a8702e8aea2f450 Author: Tan Nguyen Date: Thu Jan 3 01:09:43 2019 -0800 update online guide for async Iters Docs/sphinx_documentation/source/AsyncIter.rst Docs/sphinx_documentation/source/AsyncIter_Chapter.rst commit d91c35b047b0303df10d76d68b63cce201764b6c Author: Andy Nonaka Date: Wed Jan 2 17:15:52 2019 -0800 some more details on ghost cells and fillpatch Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/Basics.rst commit d3ccf6512f8c9df75ed3ae97c11e9e61f82c5cd0 Author: atmyers Date: Wed Jan 2 14:25:59 2019 -0800 adding another early exit to copyParticles Src/Particle/AMReX_ParticleContainerI.H commit 8bc2586ec7820d4640fb40599130b3a4de4ba4d0 Merge: 2facfd56c 7b96d51e4 Author: Cy P Chan Date: Wed Jan 2 12:51:02 2019 -0800 Merge pull request #393 from AMReX-Codes/weiqun/perf Weiqun/perf commit 7b96d51e407ad4f4247f54124591c254ab0f76f4 Merge: ae91167d5 2facfd56c Author: WeiqunZhang Date: Wed Jan 2 12:12:52 2019 -0800 Merge branch 'cy-perf' into weiqun/perf commit 2facfd56cdb17978d6b65b1cec0158ce66d93f20 Merge: d4019b35b 7e4a22107 Author: WeiqunZhang Date: Wed Jan 2 11:29:03 2019 -0800 Merge pull request #392 from AMReX-Codes/development Development commit ae91167d561904b724bf8d74935a67272d708db2 Author: Weiqun Zhang Date: Wed Jan 2 11:26:10 2019 -0800 minor changes: boost license, cmake, etc. Src/Base/AMReX_Machine.H Src/Base/AMReX_Machine.cpp Src/Base/AMReX_Utility.H Src/Base/CMakeLists.txt commit 4aab69a1d009f36bf1318d62cc510715d08df57c Merge: d4019b35b 7e4a22107 Author: Weiqun Zhang Date: Wed Jan 2 10:11:26 2019 -0800 Merge branch 'development' into pr-388 commit 7e4a2210727b98a5b2e540d1b322200687120791 Merge: 03d99cd92 ba634257b Author: Weiqun Zhang Date: Wed Jan 2 10:08:52 2019 -0800 Merge branch 'weiqun/fluxregister' into development commit 03d99cd9283fa024693a3c8efd199a68e223c065 Author: Weiqun Zhang Date: Wed Jan 2 10:06:55 2019 -0800 update changes CHANGES commit 1b39670dbfe93d0d90a6e5481ce3a3f3ba46cb96 Author: Brandon Runnels Date: Wed Jan 2 10:46:27 2019 -0700 tidied up Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7fc583984437beaec4c06ade30dabae8a4c1c875 Merge: adc620037 d31416936 Author: Brandon Runnels Date: Wed Jan 2 10:21:22 2019 -0700 Merge branch 'development' into nodeghostcells commit d3141693601906450d3554bd168c3c7c8a7f4c93 Author: Johannes Blaschke Date: Tue Jan 1 14:19:09 2019 +0100 add utility function automating levelset__eb_pad Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit df6b70dfb4bfda92b18bc551f2ef207c3aa20fe9 Author: Johannes Blaschke Date: Tue Jan 1 14:00:55 2019 +0100 update Doxygen Src/EB/AMReX_EB_levelset.H commit a4840fd52b2d48efab3ad40c5ac123ddea5908f7 Author: Johannes Blaschke Date: Sun Dec 30 17:44:46 2018 +0100 fix level-set thresholding Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit 8f99cdded774ee1057c60fd3effd634a101d7445 Merge: 969527484 2d2b33bfe Author: Johannes Blaschke Date: Sun Dec 30 12:19:21 2018 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9695274843cae98cbae0a238bc28f1185340dd2c Author: Johannes Blaschke Date: Sun Dec 30 12:19:17 2018 +0100 clean up function name and doxygen Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit 2d2b33bfe362b4b25631553911629d4e84215563 Author: Tan Nguyen Date: Sat Dec 29 21:58:46 2018 -0800 remove async metadata at stop time Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp commit e3c16e043d25bc0d26dc4b881328ef64eaa8d450 Author: Ann Almgren Date: Sat Dec 29 17:50:37 2018 -0800 Replace std::cout by amrex::Print() Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit 59027dd9fd3e9e1638d0bd519b18a604f475265c Author: Kevin Gott Date: Sat Dec 29 15:45:45 2018 -0800 Fix numbered list for GPU docs. Docs/sphinx_documentation/source/GPU.rst commit f3afb4965b2e5acd896354e58ad1aa885796526f Author: Tan Nguyen Date: Sat Dec 29 14:04:50 2018 -0800 fix a memory leak bug in the upcxx backend Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.H Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx.pthreads commit d4f3f9d9b3e328dba7399cd9946c5c93d59e50be Author: Johannes Blaschke Date: Sat Dec 29 15:45:28 2018 +0100 update level-set doxygen Src/EB/AMReX_EB_levelset.H commit 5f62d9cb720160078d9f86670e22ee0f65826190 Author: Johannes Blaschke Date: Sat Dec 29 15:40:07 2018 +0100 fix sign error in local leve-set filling Src/EB/AMReX_EB_levelset.cpp commit 6c69eae69baea227af0b7ff40ffe1f550c271cea Author: Johannes Blaschke Date: Sat Dec 29 15:21:53 2018 +0100 clean up LSFactory function names Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit 3183325087590b2040f2b6e116a06ef85b968f9a Author: Johannes Blaschke Date: Sat Dec 29 15:14:28 2018 +0100 profile LSFactory fill local Src/EB/AMReX_EB_levelset.cpp commit cb26be15632c37a8e654ca544b7a330582b22649 Author: Johannes Blaschke Date: Sat Dec 29 15:12:26 2018 +0100 document level-set doxygen Src/EB/AMReX_EB_levelset.H commit eb448815a463f08a325409041364467f81202748 Author: Johannes Blaschke Date: Sat Dec 29 14:59:51 2018 +0100 make eb_facets public Src/EB/AMReX_EB_levelset.H commit 639a1c8c6a1ce7e7d42044702c84c2e1cd218b27 Author: Johannes Blaschke Date: Sat Dec 29 12:09:37 2018 +0100 start adding profiling the level-set Src/EB/AMReX_EB_levelset.cpp commit fdb37a29f28d7970aa2dcebd1eec6e0ad59ea879 Author: Johannes Blaschke Date: Sat Dec 29 11:54:31 2018 +0100 continue documenting more level-set stuff Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit 7492c3a7e01a8c2e67e6909991c758e4ca88ad13 Author: Ann Almgren Date: Fri Dec 28 20:03:49 2018 -0800 Change so that we only print "Bottom solve failed" when mg_verbose > 1 not >= 1 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit c12eddb13f32e06367dbfce1fe7414704b15aac3 Author: Ann Almgren Date: Fri Dec 28 19:01:06 2018 -0800 If the BiCG bottom solver fails then sets the "solution" it found to 0 before going into the "bottom smooth" (if nub > 0). This enables certain solves to converge which don't otherwise. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 28936ea736654798fbc8f9f0a23c5465c9d96272 Author: Kevin Gott Date: Thu Dec 27 15:46:34 2018 -0800 Generic loop launch GPU streams docs. Docs/sphinx_documentation/source/GPU.rst commit ba634257bd78b4e9577f1d5c19f348ea14eee069 Author: Weiqun Zhang Date: Tue Dec 25 15:59:28 2018 -0800 gpu: BndryRegister Src/AmrCore/AMReX_FluxReg_2D_C.H Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp commit 697d794942e94f576bbf360a31cee583fea10bd1 Author: Weiqun Zhang Date: Tue Dec 25 12:57:16 2018 -0800 fix component index in FineAdd Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H commit 27c84ca0b2dddbfffacf135759ba319bad213342 Author: Johannes Blaschke Date: Tue Dec 25 03:15:56 2018 -0800 this used to fail in debug, even though subsequent checks catch bad EB, this cange makes it safe in debug also Src/EB/AMReX_EB_levelset.cpp commit a445e88fa5aad15fe9a7722a749142f010e1d4dd Author: Weiqun Zhang Date: Mon Dec 24 19:35:44 2018 -0800 gpu: FluxRegister in 1D and 2D Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit e7243f899d714ccd1a7956c9b9e11430a27dbcae Author: Weiqun Zhang Date: Mon Dec 24 18:04:21 2018 -0800 gpu: FluxRegister in 3D Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.cpp commit adc620037e161e02da9a5b8950f017f5efc58dc8 Merge: c89645cf1 6dbeea20e Author: Brandon Runnels Date: Mon Dec 24 16:05:47 2018 -0700 Merge branch 'development' into nodeghostcells commit c89645cf17964b98e81905c9dbaaefb9b25fbebf Author: Brandon Runnels Date: Mon Dec 24 16:04:58 2018 -0700 removed unnecessary ghost cell copy for rhs fab GNUmakefile Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6dbeea20ecc7ade3f85e9606c422aa8dcde4d3f0 Author: Tan Nguyen Date: Mon Dec 24 02:09:16 2018 -0800 a few small updates on the upcxx backend Src/Amr/AMReX_Amr.cpp commit 5a7aaa21c77b2dca9c2c0a48e978fca29abc121e Author: Kaiyuan Hou Date: Mon Dec 24 00:19:33 2018 -0600 add performance result Tests/PnetCDFBenchmark/ReadMe commit 2923e3caf18114367784f2007d6c1dd5bb6c079e Author: Weiqun Zhang Date: Sun Dec 23 15:54:58 2018 -0800 WIP: FluxRegister::FineAdd on gpu Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxReg_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit afad6ee6a21bb6ce18dee0df3a24c2b670c72ec5 Merge: 5f85e048f 80bf6f9fb Author: Kevin Gott Date: Sun Dec 23 14:49:01 2018 -0800 Merge branch 'development' into gpu commit 5f85e048f2f78feb4ed9874f1701b88d5d0c162e Author: Kevin Gott Date: Sun Dec 23 14:48:28 2018 -0800 Doc bugs fix. Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst Docs/sphinx_tutorials/source/MUI_Tutorial.rst Docs/sphinx_tutorials/source/SDC_Tutorial.rst commit d8d95b6f910d5ec989b2d625ee5b4321bf08e47f Author: Kevin Gott Date: Sun Dec 23 14:37:44 2018 -0800 GPU how-to tutorial doc. Docs/sphinx_tutorials/source/GPU_Tutorial.rst commit a81c3909a6f8796f709a84b0138d36f8431ee825 Author: Kevin Gott Date: Sun Dec 23 14:37:18 2018 -0800 First draft of GPU docs. Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst commit fd8d0ab2bbcffd5e3f9f259edeb93e449b72a13c Author: Kaiyuan Hou Date: Sun Dec 23 02:00:01 2018 -0600 add comment Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp commit 8a0b1ca51d7ae9a83472c43ae42c884a5ac0cfd5 Author: Weiqun Zhang Date: Sat Dec 22 20:50:14 2018 -0800 WIP: FluxRegister on gpu Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/Boundary/AMReX_FabSet.H commit e6e03c8e271ffc0750e9963e7ba883925b8c9021 Author: Weiqun Zhang Date: Sat Dec 22 16:40:22 2018 -0800 gpu: FabSet Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp commit 80bf6f9fbb2e16a93d88194c773c8d200bc4f76c Merge: 2edfa63bc 1276a8713 Author: Johannes Blaschke Date: Sat Dec 22 23:24:57 2018 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 2edfa63bcd5a114e95c193229407fad9f56d1d88 Author: Johannes Blaschke Date: Sat Dec 22 23:24:52 2018 +0100 expose level-set filling functions as static functions. This makes incorporating level-sets without LSFactory easier Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit 1276a87130770a1da6b9f1c3d81df8063c293d87 Author: Weiqun Zhang Date: Sat Dec 22 12:31:17 2018 -0800 add fabHostPtr and fabDevicePtr to FabArray and make fabPtr's return depends on whether it is in gpu launch region Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_iMultiFab.cpp commit dab9ac7fef26ab4a2456d15eaba7295ddb5317a7 Author: Kevin Gott Date: Sat Dec 22 01:13:24 2018 -0500 Add synch. Tutorials/GPU/Launch/main.cpp commit c96c9525557719492b995926a592a5802d2b5e3e Author: Kevin Gott Date: Sat Dec 22 01:11:40 2018 -0500 Loop lambda works. Remove check. Tutorials/GPU/Launch/main.cpp commit a1a9a28110e9b8af5ccbd337ca9ffab38666fdf8 Author: Weiqun Zhang Date: Fri Dec 21 20:25:17 2018 -0800 make stop time smaller Tutorials/GPU/CNS/Exec/RT/inputs commit 9766347b4f31d8ddb2f59ae1f2c7e8e283473bf4 Merge: de06e07b5 d8cecb46e Author: Weiqun Zhang Date: Fri Dec 21 20:24:14 2018 -0800 Merge branch 'weiqun/interp-2' into weiqun/interp-3 commit d8cecb46e3a1a07dc2e037a3003add561996c928 Merge: 58b722a43 64cccb5b3 Author: Weiqun Zhang Date: Fri Dec 21 20:23:19 2018 -0800 Merge branch 'weiqun/interp-1' into weiqun/interp-2 commit 64cccb5b39609a20c64799675ce0a803e08f3e41 Author: Weiqun Zhang Date: Fri Dec 21 20:22:46 2018 -0800 fix a new bug in interpolater Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H commit 988f2a9c91a143f7f5feda9df183d981a221881a Author: Kevin Gott Date: Fri Dec 21 17:37:33 2018 -0800 Loop launch example. Tutorials/GPU/Launch/main.cpp commit d6be58c7820ce6a3e631f81a02352d6d40cd34b3 Author: Brandon Runnels Date: Fri Dec 21 17:14:52 2018 -0700 implemented amrex_mlmg_lin_nd_interp for 3D GNUmakefile Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit 8b258a92614987b4e715b1b883203246d53dbd89 Merge: 2b2d5fef3 c8e601a89 Author: Weiqun Zhang Date: Fri Dec 21 15:17:24 2018 -0800 Merge branch 'development' into weiqun/interp-1 commit c8e601a891915888ca553133551da332738eebd2 Author: Weiqun Zhang Date: Fri Dec 21 14:39:06 2018 -0800 Tutorials/GPU/CNS: compute T Tutorials/GPU/CNS/Exec/RT/inputs Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_parm.H Tutorials/GPU/CNS/Source/CNS_parm.cpp commit d409b0552662092662b025ca06229c83c31af89d Author: Weiqun Zhang Date: Fri Dec 21 14:12:11 2018 -0800 Tutorials/GPU/CNS: store runtime parameters as managed variables Src/Base/AMReX_GpuQualifiers.H Tutorials/GPU/CNS/Exec/RT/Make.package Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp Tutorials/GPU/CNS/Exec/RT/cns_prob_parm.H Tutorials/GPU/CNS/Exec/RT/inputs Tutorials/GPU/CNS/Exec/Sod/Make.package Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/cns_prob_parm.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_parm.H Tutorials/GPU/CNS/Source/CNS_parm.cpp Tutorials/GPU/CNS/Source/Make.package Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit c98a3cf483da6c95acdb872a3b73849fc89f66bd Author: Brandon Runnels Date: Fri Dec 21 15:01:11 2018 -0700 BR GNUmakefile commit 5bdb87fe2fc8764fdb53254d044d7e433bbbeec8 Author: Weiqun Zhang Date: Fri Dec 21 12:50:09 2018 -0800 need to ifdef Src/AmrCore/AMReX_TagBox.cpp commit c4bec517ad89de6de6b85a92a06b2494fb85675d Author: Weiqun Zhang Date: Fri Dec 21 12:48:35 2018 -0800 TagBox on gpu: we must coarsen both device and host fabs Src/AmrCore/AMReX_TagBox.cpp commit c24e38c249711d23be669aa36e0596fefcc57b9b Author: Weiqun Zhang Date: Thu Dec 20 17:04:58 2018 -0800 Tutorials/GPU/CNS: add RT test Tutorials/GPU/CNS/Exec/RT/GNUmakefile Tutorials/GPU/CNS/Exec/RT/Make.package Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp Tutorials/GPU/CNS/Exec/RT/inputs commit 0e443ced430393f1adfc8fca4b5eb7f598d85a7f Author: Weiqun Zhang Date: Thu Dec 20 17:04:03 2018 -0800 Tutorials/GPU/CNS: add gravity Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit 2d4c124e449c406c0f0c9f789b664c898d06f789 Author: Kaiyuan Hou Date: Fri Dec 21 03:21:35 2018 -0600 update to dev branch Tests/HDF5Benchmark/GNUmakefile Tests/PnetCDFBenchmark/ReadMe Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp Tests/PnetCDFBenchmark/inputs Tests/PnetCDFBenchmark/main.cpp commit 50c89dde3e522d84fc7455646bf1f2e926a3b003 Merge: 76fdccab2 90af069af Author: Kaiyuan Hou Date: Fri Dec 21 00:13:44 2018 -0600 Merge remote-tracking branch 'upstream/development' into ncmpi commit 0e84e413df05b85ae58ebe922796aa0b366afdec Author: Brandon Runnels Date: Thu Dec 20 18:12:45 2018 -0700 updated ghost cell copy and streamlined some of the code Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit 336720d0dc9624860149d92799d806603ed1d754 Author: Weiqun Zhang Date: Thu Dec 20 17:04:58 2018 -0800 Tutorials/GPU/CNS: add RT test Tutorials/GPU/CNS/Exec/RT/GNUmakefile Tutorials/GPU/CNS/Exec/RT/Make.package Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp Tutorials/GPU/CNS/Exec/RT/inputs commit 7b90fe03c41436bc22c2f685ef9e81854dbe2e28 Author: Weiqun Zhang Date: Thu Dec 20 17:04:03 2018 -0800 Tutorials/GPU/CNS: add gravity Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit de06e07b56cf0588b659e97b2c2cc9d4e9fdb573 Author: Weiqun Zhang Date: Thu Dec 20 15:54:13 2018 -0800 clean up and comments Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp commit d80cd7b341df1735ecfb3bed6e267d6b73532d48 Author: Weiqun Zhang Date: Thu Dec 20 15:31:32 2018 -0800 NodeBilinear on gpu Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp commit 58b722a4324b8c943bc7438a2a38e34066b5ceaf Author: Weiqun Zhang Date: Thu Dec 20 11:14:15 2018 -0800 rm old fortran routines for pcinterp Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_INTERP_F.H commit 72a5fc476a795200e806f62ceeee126bea350fb8 Author: Weiqun Zhang Date: Thu Dec 20 11:08:18 2018 -0800 fix volume coordinates for 1d spherical coordinates. note that this is a long-standing issue we never bothered to fix. Src/Base/AMReX_CoordSys.cpp commit ac155134d5449ad31757edb46529bc75dfdc9062 Author: Weiqun Zhang Date: Thu Dec 20 10:45:51 2018 -0800 PCInterp on gpu Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp commit 2b2d5fef3af8e5abdf2e0191165d41b0cd72bab1 Author: Weiqun Zhang Date: Thu Dec 20 10:32:30 2018 -0800 minor optimization Src/AmrCore/AMReX_Interp_3D_C.H commit 90af069af705f73c84ae263d96cd25f5fd3bc94a Author: Johannes Blaschke Date: Thu Dec 20 17:27:50 2018 +0100 update gitignore .gitignore commit 4186034aba5d3533bbbbea9b04b57cdd76cb7df3 Author: Kevin Gott Date: Wed Dec 19 17:50:43 2018 -0800 Fix documentation warnings. Docs/sphinx_documentation/source/Tutorials_Chapter.rst Docs/sphinx_documentation/source/index.rst commit f0954a6972273971405de2980b6e742b2266bd43 Merge: 7e2a0b55c 7c722c158 Author: Kevin Gott Date: Wed Dec 19 17:23:09 2018 -0800 Merge branch 'development' into gpu commit 7e2a0b55c973fa6438816c2d0b2123cdce883fc8 Author: Kevin Gott Date: Wed Dec 19 17:16:30 2018 -0800 Plane docs Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU_Chapter.rst commit 96ed170ed2eef47253734c81d235b7e68e1a648c Merge: 3aaa7c630 7c722c158 Author: Weiqun Zhang Date: Wed Dec 19 16:53:01 2018 -0800 Merge branch 'development' into weiqun/interp-1 commit 7c722c158203ef9f03e1fb36961df85471390c28 Author: Andy Nonaka Date: Wed Dec 19 16:44:42 2018 -0800 bugfix in avgdown_faces... was only operating on component 0 Src/Base/AMReX_MultiFabUtil.cpp commit 8d2cbe4df7ffb80a989a9a5d1b0baa6012e8856a Author: Brandon Runnels Date: Wed Dec 19 17:06:19 2018 -0700 initial working version in 2D Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit fadf6d74ee26c83e5a32a587b03e86fe8329ba96 Author: Johannes Blaschke Date: Thu Dec 20 00:06:54 2018 +0100 act on Weiqun's advice Src/Base/AMReX_MultiFabUtil.H commit a113022a3afbfb1da819b5eee5ed4f65ce6969e8 Author: Johannes Blaschke Date: Thu Dec 20 00:06:36 2018 +0100 fix comment Src/Base/AMReX_MultiFabUtil.H commit 3aaa7c630bae0905e37ea389567f3e2655700b1c Author: Weiqun Zhang Date: Wed Dec 19 14:57:08 2018 -0800 partially updated CellConservativeProtected Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp commit 5a7adf8f329199c131a70c83394b160f970977e8 Merge: b5d488a97 39f6e38bc Author: Johannes Blaschke Date: Wed Dec 19 23:40:41 2018 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b5d488a9749ada77f2388585556f26c44eb25e56 Author: Johannes Blaschke Date: Wed Dec 19 23:40:36 2018 +0100 move multifab utils used by LSCore to a better place and document in doxygen Src/Base/AMReX_MultiFabUtil.H Src/EB/AMReX_EB_LSCoreBase.H commit d4019b35b099a8432fc0c7869be7dae6c07644a5 Author: Cy Chan Date: Wed Dec 19 13:55:52 2018 -0800 some cleanup Src/Base/AMReX_DistributionMapping.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit e4e8b51d5e130d9dcdcd3f96dc0fb97ab666b1d0 Author: Weiqun Zhang Date: Wed Dec 19 13:41:46 2018 -0800 linccinterp in 1d and 2d Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_CoordSys.cpp commit 39f6e38bcbf6cb0b75211f307e07b10d8d3c45f6 Author: Andrew Myers Date: Wed Dec 19 13:46:31 2018 -0800 Adding clearParticles and copyParticles method to ParticleContainer. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit f78d7709b2c6e0a26811b134010d5e17f796ffdc Merge: 226897f28 7cb1250d6 Author: Cy Chan Date: Wed Dec 19 13:29:35 2018 -0800 Merge branch 'development' into cy-perf commit 1129a742654c177e8d56006ed7f2b04cec7ea02c Author: Brandon Runnels Date: Wed Dec 19 14:28:16 2018 -0700 updating C/F interpolation to update ghost cells as well as other cells Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit 988ba4e5b3aaf0d83c5f298bf9a0c4d7bd2593bd Author: Weiqun Zhang Date: Wed Dec 19 12:35:03 2018 -0800 add some comments and clean up Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp commit 02b09c7c0bf35cf665e33c180411f36ef1d642a9 Author: Weiqun Zhang Date: Wed Dec 19 11:13:04 2018 -0800 fix issues in 3D CellConservative Interpolater Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp commit 20d2344592debb97c2903b0805398d1a2502a15c Author: Johannes Blaschke Date: Wed Dec 19 18:12:37 2018 +0100 clean up comments and formatting Src/Base/AMReX_MultiFabUtil.H commit 7cb1250d63e26db700d43595a13b23af7854f89b Author: Tan Nguyen Date: Wed Dec 19 00:39:15 2018 -0800 partially fix a memory leak bug in the upcxx backend Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.H Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/pthreads_common/LocalConnection.H Src/AmrTask/rts_impls/pthreads_common/PerillaMemCheck.cpp Src/AmrTask/rts_impls/pthreads_common/RemoteConnection.H Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.H Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp commit 8635e3f992a4fde24fd8bdb5b57d50ac87cc907c Author: Kevin Gott Date: Wed Dec 19 00:37:30 2018 -0800 WIP: GPU docs. Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU_Chapter.rst commit 6088dea81fe1597b8c42f5d3366fbb3623874125 Author: Weiqun Zhang Date: Tue Dec 18 21:15:58 2018 -0800 fix omp performance in atomicAdd Src/Base/AMReX_BaseFab.H commit dd1313d67cd4e8989cedc7788774d3f86bb2cfae Author: Kevin Gott Date: Tue Dec 18 20:24:10 2018 -0500 Add flag to script to turn off GPUDirect. Tutorials/GPU/run.summit commit 226897f287539d0800b1621099d837e57e1b223a Author: Cy Chan Date: Tue Dec 18 14:07:32 2018 -0800 clean up performance analysis a bit Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Machine.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/inputs Tools/Backtrace/parse_bt.py commit c7919313813ebebcd00fbd612ce256dfbbefdae7 Author: Andrew Myers Date: Tue Dec 18 13:48:24 2018 -0800 get the in and out file names from the command line Tools/Postprocessing/C_Src/cube_extract.cpp commit cfa3bebc62a8b554dc687064c2c493a38de5dd86 Author: Weiqun Zhang Date: Tue Dec 18 13:47:22 2018 -0800 3D CellConservative Interpolater on gpu Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp commit abe0fcd94cedb32d6a0f156faa7dcd77db7ed0fe Author: Andrew Myers Date: Tue Dec 18 13:27:33 2018 -0800 a utility for extracting a sub-region from a plotfile. Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/cube_extract.cpp commit 98b7ad8eeaa293a07acd006aab7caef41101f7c4 Merge: eac94b9fd 4ac48958f Author: Cy Chan Date: Tue Dec 18 13:14:55 2018 -0800 Merge branch 'development' into cy-perf commit 4ac48958f368193ba58a6ee347e0f8b6f8548d47 Author: Andrew Myers Date: Mon Dec 17 15:58:02 2018 -0800 tweak snippet slightly Docs/sphinx_documentation/source/GPU.rst commit aa160e6801c53842600326f0319f58a11f7cbb89 Author: Andrew Myers Date: Mon Dec 17 15:56:30 2018 -0800 add examples of Cuda::HostVector and Cuda::DeviceVector Docs/sphinx_documentation/source/GPU.rst commit 05bb1b845d3a492d142f35446c9f943335e52f9d Author: Andrew Myers Date: Mon Dec 17 15:39:17 2018 -0800 fix markdown Docs/sphinx_documentation/source/GPU.rst commit 55371d8ba1f3774e2e42f28f6b2b295dfb79d85c Author: Andrew Myers Date: Mon Dec 17 15:38:38 2018 -0800 fix highlight section Docs/sphinx_documentation/source/GPU.rst commit 01d1ed13ee76a4c64cef9f139ff6d5460252dc43 Author: Andrew Myers Date: Mon Dec 17 15:36:31 2018 -0800 add OpenACC example to GPU documentation Docs/sphinx_documentation/source/GPU.rst commit 98cdd291b1f75d6a9e2249ad0a08173c3b0908d2 Author: Andrew Myers Date: Mon Dec 17 15:23:18 2018 -0800 remove Cuda Fortran version of EM PIC tutorial Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh commit 534be3a98969b9a5650f379511f764ffa82f65bd Merge: cc9096849 8a9c0becd Author: Andrew Myers Date: Mon Dec 17 15:17:48 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cc90968496f95991d17601a6f1a1decf9f890130 Author: Andrew Myers Date: Mon Dec 17 15:00:09 2018 -0800 these variables are no longer managed Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 commit eac94b9fd96bf2ab5b8913ea80243b6192746588 Author: Cy Chan Date: Mon Dec 17 14:34:12 2018 -0800 DistributionMapping: use ParallelAllGather functions Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelReduce.H commit ecbf70c3332e80aae3687376e4b901ec6cf8330d Author: Kevin Gott Date: Mon Dec 17 14:25:40 2018 -0800 WIP: GPU docs edit. Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU_Chapter.rst commit 0f96430ac540fb2a70c559a4834f6cce52320f1c Author: Kevin Gott Date: Thu Dec 13 15:32:26 2018 -0800 Adjust to remove warning in docs. Docs/sphinx_documentation/source/SWFFT.rst commit 2755085a4e3590fee9a74f7cbc7e605145c9746c Author: Cy Chan Date: Mon Dec 17 14:11:18 2018 -0800 add current subgroup ranks to comm cache hash key Src/Base/AMReX_Machine.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 92102881fe33912e0c3333e9f091426f3359d447 Author: Weiqun Zhang Date: Mon Dec 17 13:59:43 2018 -0800 2d compiles Src/AmrCore/AMReX_Interpolater.cpp commit 48072327dc4416ae6f85341dafb53c85a4f3a957 Author: Andrew Myers Date: Mon Dec 17 13:51:34 2018 -0800 can't use ParticlesAt here Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit d4f1f425d358a9b41d7cccb6375636d435176519 Author: Weiqun Zhang Date: Mon Dec 17 13:51:23 2018 -0800 fix assertion Src/AmrCore/AMReX_Interpolater.cpp commit 48edc0e4f20bd88f983a4f8a6c432bce5a7ee8b6 Author: Weiqun Zhang Date: Mon Dec 17 13:45:58 2018 -0800 fix 2d and minor tweak Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_IntVect.H commit 4c3bf4571959d275a652dcc1542612164007b666 Author: Andrew Myers Date: Mon Dec 17 13:45:07 2018 -0800 Tutorial compiles again Src/Particle/AMReX_Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 7512f78bd89785f15cb5492266be3e24302b7e42 Author: Andrew Myers Date: Mon Dec 17 13:02:59 2018 -0800 remove unused include Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H commit a54d11284dc68611cf0f2f76f05325866bec9072 Author: Cy Chan Date: Mon Dec 17 13:00:46 2018 -0800 move hash_combine() and hash_vector() to AMReX_Utility.H Src/Base/AMReX_Machine.cpp Src/Base/AMReX_Utility.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 429488a8e56d3944ae630f6fc90786fa98bfcc76 Author: Andrew Myers Date: Mon Dec 17 12:58:27 2018 -0800 fix tabs / spaces issue in emacs Tutorials/Particles/ElectromagneticPIC/Make.EMPIC commit f93c7ab15ef0d86ab54737058e60ec6339b9dfe9 Author: Cy Chan Date: Mon Dec 17 12:47:57 2018 -0800 move AMReX_Machine files Src/Base/AMReX_Machine.H Src/Base/AMReX_Machine.cpp Src/Base/Make.package Src/LinearSolvers/MLMG/Make.package commit 8e4e40245bb98b652a9a9be24735583f12bad12f Author: Andrew Myers Date: Mon Dec 17 12:46:09 2018 -0800 update fortran subroutines Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H commit 55e873ac40d08263b65b20278fe0e0a188eda1ec Author: Weiqun Zhang Date: Mon Dec 17 12:37:25 2018 -0800 Unlimited 3D CellConservative Interpolater on gpu Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_IntVect.H commit cc6412f5a38541f913800b626f3f55b25fad890a Author: Andrew Myers Date: Mon Dec 17 12:22:19 2018 -0800 update EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit 381137eb2a5cb881e1993903bdef0f572d2d67b8 Author: Andrew Myers Date: Mon Dec 17 11:57:02 2018 -0800 new form of ParticlesAt that is templated on Iterator type Src/Particle/AMReX_Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit 4886dcf9c6f669b804f5a477e91ab3d20c3f8f50 Author: Andrew Myers Date: Mon Dec 17 11:49:50 2018 -0800 use MakeMFIter instead of iterating over the mask Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit 0b0624df3535093be7d97f16874e0d7ff8f77064 Author: Cy Chan Date: Mon Dec 17 11:47:47 2018 -0800 updates to support non-MPI build Src/LinearSolvers/MLMG/AMReX_Machine.cpp Tests/LinearSolvers/MLMG/inputs commit 49026564f65f731205ad5895fd6aaacb6972ae8c Author: Andrew Myers Date: Mon Dec 17 11:25:40 2018 -0800 forgot namespace Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit 438dd3ac6e9734bfb33fdfb924972e931835f643 Author: Andrew Myers Date: Mon Dec 17 11:22:37 2018 -0800 thrust::copy -> thrust_copy Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit ff5ae4bb57c09f1635ff4fde7f5c75490d3c8109 Author: Andrew Myers Date: Mon Dec 17 11:15:15 2018 -0800 some renaming Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 5b163f85fc10dd335b58f58477e9b89f83411d3a Author: Andrew Myers Date: Mon Dec 17 11:11:18 2018 -0800 add EMParIter Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H commit 8a9c0becdca7696a177f0a3a8be68396fac35c8a Merge: 86e1e1278 33efa5749 Author: Weiqun Zhang Date: Sun Dec 16 18:03:34 2018 -0800 Merge branch 'weiqun/gpu' into development commit 86e1e127848f5c03bf28056f64c5520186dbbff8 Author: Weiqun Zhang Date: Sat Dec 15 15:48:22 2018 -0500 add extra -lmpi_ibm on summitdev Tools/GNUMake/sites/Make.olcf commit 33efa574931cd198b5719f36fbef6fb1d08bad9a Author: Weiqun Zhang Date: Fri Dec 14 22:18:16 2018 -0800 remove FabArray constructor that takes FAB::value_type Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/EB/AMReX_EB2_MultiGFab.cpp commit 6b5318e9031d621186ce0c8370ef52e720b2f808 Author: Weiqun Zhang Date: Fri Dec 14 16:37:39 2018 -0800 add some empty files for interpolater in C++ Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interp_C.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit 29403bfaad219002d7f56e504efac895e7027c7a Author: Weiqun Zhang Date: Fri Dec 14 16:26:24 2018 -0800 put interpolation in time on gpu Src/AmrCore/AMReX_FillPatchUtil.cpp commit a1c11e222bba7164184bbfbf82e77bd60417be65 Author: Weiqun Zhang Date: Fri Dec 14 15:57:35 2018 -0800 Tutorials/GPU/CNS: amr Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Exec/Sod/inputs.amr Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/Make.package commit b514f590c3f5f91f5d12d61b8191091504b7d23e Merge: 2259b720c 5955acf3c Author: Kevin Gott Date: Fri Dec 14 18:22:43 2018 -0500 Merge branch 'development' into gpu commit 2259b720c08dc4ca1f22e0e87da2fe23bd03bc19 Author: Kevin Gott Date: Fri Dec 14 18:19:37 2018 -0500 summit run script works. Turns off GPUDirect. Tutorials/GPU/run.summit commit 5955acf3c08794c5b26a8eb2510426640f606076 Author: Ann Almgren Date: Fri Dec 14 14:56:46 2018 -0800 Oops -- forgot "Real" when I added the brackets. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 33f4175f837cce0775069a6b8603fbfc1d9085a6 Author: Ann Almgren Date: Fri Dec 14 14:45:56 2018 -0800 Update "Amr Task" --> "Asynchronous Iterators (Amr Task)" Docs/sphinx_documentation/source/AsyncIter_Chapter.rst commit 98141c4de2db01919f80592254095fa8b0771674 Author: Weiqun Zhang Date: Fri Dec 14 14:06:39 2018 -0800 minor Src/Amr/AMReX_AmrLevel.H Tutorials/EB/CNS/Source/CNS_setup.cpp commit 15b9610f8577a49610cf6f9a6c91881907cfdc5b Author: Ann Almgren Date: Fri Dec 14 13:50:32 2018 -0800 Change formatting of norm output when verbose >= 4. No change in functionality, only in output. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6855d54c7b7126dc4d89646cb9333312344382a1 Author: Ann Almgren Date: Fri Dec 14 13:44:34 2018 -0800 Zero out the "res" array right after we create it in the nodal solve so that we can use the ghost nodes as a convenience in the stencil (knowing they are now zero) Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 4ec23424d41c4c79c475786c8aff01d700a6f4bc Author: Weiqun Zhang Date: Fri Dec 14 13:30:49 2018 -0800 get rid of some warnings Src/Base/AMReX_CoordSys.cpp commit 79bba81388f7bb806810dbc89e18d1cbbc26b491 Author: Weiqun Zhang Date: Fri Dec 14 13:29:02 2018 -0800 variadic template for amrex::min and max Src/Base/AMReX_Utility.H commit 376a50367d1fd5594a4218060fb6d3c0ea3b5cea Merge: b3cb198d6 33e2e0e2e Author: Andrew Myers Date: Fri Dec 14 11:58:09 2018 -0800 Merge pull request #386 from jrood-nrel/update_nrel_site Update makefiles for NREL machines commit b3cb198d61ba3c51d38f3775bc57dd49a2913f16 Author: Max Katz Date: Fri Dec 14 11:29:02 2018 -0800 Add Lassen @ LLNL Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit 88595df7b35926eab7f7faf4ea0dc545bc3ea250 Author: Max Katz Date: Fri Dec 14 11:28:57 2018 -0800 Cuda -> CUDA Src/Base/AMReX_GpuError.H commit 33e2e0e2ed2798e3898f381db0a8ee5373132011 Author: Jon Rood Date: Fri Dec 14 12:21:56 2018 -0700 Adding note about older compilers on NREL machines. Tools/GNUMake/sites/Make.nrel commit 592f6c9138db37396758b12cab80f203dc5f726c Author: Jon Rood Date: Fri Dec 14 12:07:00 2018 -0700 Using same compiler flags for gcc, gnu, and llvm on NREL's Eagle machine. Tools/GNUMake/sites/Make.nrel commit 0921500fa2b88e6fd331e0e1b48254d82e3cda2f Author: Jon Rood Date: Fri Dec 14 11:49:42 2018 -0700 Updating makefiles for NREL machines. Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nrel commit fee6bc5709185d72aa711e8c6a2505b410fffdfe Author: Ann Almgren Date: Fri Dec 14 09:49:25 2018 -0800 In the nodal solve -- if we set CoarseningStrategy to RAP rather than Sigma -- which is what we do when AMREX_USE_EB is defined -- then we should always use the restriction_rap routine (based on "sten") rather than the standard restriction which sees no geometric information Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit bd9b0f998f8e9b58c9127d2292f5bca4921791f3 Merge: d879a7798 130485b8c Author: Weiqun Zhang Date: Fri Dec 14 07:22:02 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d879a7798e3aef61bd9a6033cd1039c8e13f8b26 Author: Weiqun Zhang Date: Fri Dec 14 07:21:32 2018 -0800 fix some AMREX_PRAGMA_SIMD issues Src/Base/AMReX_BaseFab.H Src/Base/AMReX_COORDSYS_1D_C.H commit 130485b8c27072622d5cabfd1172c3cefe1d682a Merge: e5a4d595a 40b6b76ca Author: Andrew Myers Date: Thu Dec 13 16:50:44 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e5a4d595a6bca5d078b7808ec4adc5cab126f66d Author: Andrew Myers Date: Thu Dec 13 16:50:24 2018 -0800 fix typo Docs/sphinx_documentation/source/index.rst commit 3a0a157a38e2aec5d5bd71a50f154c62f0e61fec Author: Andrew Myers Date: Thu Dec 13 16:49:29 2018 -0800 rename chapters in sphinx documentation Docs/sphinx_documentation/source/AMReX_Profiling_Tools_Chapter.rst Docs/sphinx_documentation/source/AmrCore_Chapter.rst Docs/sphinx_documentation/source/AmrLevel_Chapter.rst Docs/sphinx_documentation/source/AsyncIter_Chapter.rst Docs/sphinx_documentation/source/Basics_Chapter.rst Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst Docs/sphinx_documentation/source/EB_Chapter.rst Docs/sphinx_documentation/source/External_Frameworks_Chapter.rst Docs/sphinx_documentation/source/External_Profiling_Tools_Chapter.rst Docs/sphinx_documentation/source/Fortran_Chapter.rst Docs/sphinx_documentation/source/GPU_Chapter.rst Docs/sphinx_documentation/source/GettingStarted_Chapter.rst Docs/sphinx_documentation/source/IO_Chapter.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst Docs/sphinx_documentation/source/Particle_Chapter.rst Docs/sphinx_documentation/source/Visualization_Chapter.rst Docs/sphinx_documentation/source/index.rst commit 2e0e870f254672fabb5c81f010a294e55c0a7c79 Author: Andrew Myers Date: Thu Dec 13 16:31:40 2018 -0800 make corresponding changes to the OpenACC version Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp commit 30cdec5c20c43040ef800aed150cd2288a55b138 Author: Andrew Myers Date: Thu Dec 13 15:47:27 2018 -0800 formatting changes Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp commit 40b6b76ca5ba9ac05e0090ce66784541bde823eb Author: Weiqun Zhang Date: Thu Dec 13 13:17:18 2018 -0800 small changes Src/Base/AMReX_BaseFab.H Src/EB/AMReX_EB2_GeometryShop.H commit c386e845a6765f9adb34087aee301d84455b30dd Author: Andrew Myers Date: Thu Dec 13 12:29:29 2018 -0800 update generating initial conditions with the changes from WarpX Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp commit e2d985ba82924987764b0b9988bb1768de310e7b Author: Andrew Myers Date: Thu Dec 13 12:17:45 2018 -0800 Just call the base class constructor. Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp commit 54b8d3d0792b0ea06fbe57cf9b5e43e687ad72a9 Author: Andrew Myers Date: Thu Dec 13 12:13:35 2018 -0800 move PIdx to the ParticleContainer subclass; do not need Particles.H any more Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Source/Particles.H commit 5ed16936ba364ad5001aca03848b737b03e71b2b Author: Andrew Myers Date: Thu Dec 13 12:11:15 2018 -0800 Redistribute Strategy is not a thing any more. Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H commit 10d35ebdc4f8b4d65e2e69668db67a8251319663 Author: Andrew Myers Date: Thu Dec 13 12:09:20 2018 -0800 restoring the ElectromagneticPIC Tutorial Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh Tutorials/Particles/ElectromagneticPIC/Make.EMPIC Tutorials/Particles/ElectromagneticPIC/Source/Constants.H Tutorials/Particles/ElectromagneticPIC/Source/IO.H Tutorials/Particles/ElectromagneticPIC/Source/IO.cpp Tutorials/Particles/ElectromagneticPIC/Source/Make.package Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Source/Particles.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 0f01a9b6e2108735d09f5c5fdb81e5ac89b634a8 Merge: 604d5b9c5 f91c594c2 Author: Weiqun Zhang Date: Thu Dec 13 11:09:25 2018 -0800 Merge branch 'development' into gpu commit f91c594c22d698c0ced60d47da786846b89d6e20 Author: Weiqun Zhang Date: Thu Dec 13 10:32:54 2018 -0800 no need to pass GeometryData if it is not needed Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 163ad2ae5da1172d93017e6b420469c9310931fd Author: Weiqun Zhang Date: Thu Dec 13 10:21:49 2018 -0800 rm functions we don't really need Src/Base/AMReX_COORDSYS_3D_C.H Src/Base/AMReX_CoordSys.cpp commit e44a56772a408cb06e785e9d843533b73e8fae2b Author: Weiqun Zhang Date: Thu Dec 13 10:11:34 2018 -0800 add Geometry::isPeriodicArray that returns gpu friendly array Src/Base/AMReX_Geometry.H commit 8e6db26ca163cec4cfbec1b12fdd3e7d532320f7 Author: Weiqun Zhang Date: Thu Dec 13 10:00:33 2018 -0800 move AsyncFab dtor to header Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp commit bb332cdcbc97a4628210c2c36d816238399265ca Author: Weiqun Zhang Date: Thu Dec 13 09:46:04 2018 -0800 add amrex_multifab_read Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tools/CompileTesting/compiletesting.py commit f8022a5146cbe21e6389afb0b5e1ec0dd38397b9 Merge: 5a2549870 ce38c3953 Author: Guy Moore Date: Thu Dec 13 07:42:23 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5a254987032c60a2ae70b2751a192db06cd091c5 Author: Guy Moore Date: Thu Dec 13 07:39:04 2018 -0800 Moved SWFFT tutorials into separate sub-directories, and updated documentation to reflect change Filled MUI documentation Docs/sphinx_documentation/source/SWFFT.rst Docs/sphinx_tutorials/source/MUI_Tutorial.rst Docs/sphinx_tutorials/source/SWFFT/iface_rect.png Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst Tutorials/SWFFT/SWFFT_poisson/GNUmakefile Tutorials/SWFFT/SWFFT_poisson/Make.package Tutorials/SWFFT/SWFFT_poisson/README Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test.H Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test.cpp Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test_F.F90 Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test_F.H Tutorials/SWFFT/SWFFT_poisson/inputs.128 Tutorials/SWFFT/SWFFT_poisson/inputs.32 Tutorials/SWFFT/SWFFT_poisson/inputs.64 Tutorials/SWFFT/SWFFT_poisson/main.cpp Tutorials/SWFFT/SWFFT_poisson/run_me Tutorials/SWFFT/SWFFT_poisson/swfft_solver.cpp Tutorials/SWFFT/SWFFT_simple/GNUmakefile Tutorials/SWFFT/SWFFT_simple/Make.package Tutorials/SWFFT/SWFFT_simple/README Tutorials/SWFFT/SWFFT_simple/SWFFT_Test.H Tutorials/SWFFT/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT/SWFFT_simple/SWFFT_Test_F.H Tutorials/SWFFT/SWFFT_simple/inputs.multipleGrids Tutorials/SWFFT/SWFFT_simple/inputs.oneGrid Tutorials/SWFFT/SWFFT_simple/main.cpp Tutorials/SWFFT/SWFFT_simple/run_me_2d Tutorials/SWFFT/SWFFT_simple/run_me_3d Tutorials/SWFFT/SWFFT_simple/swfft_compute.cpp commit ce38c395377c154cab7fd2caed3f58f8f68087f4 Merge: c01a1bebe 56c0c4815 Author: Ann Almgren Date: Thu Dec 13 06:55:49 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit c01a1bebe7e5bb89d362aa94c4451fc1416cab27 Author: Ann Almgren Date: Thu Dec 13 06:55:33 2018 -0800 Wrap EB_set_covered inside ifdef AMREX_USE_EB Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 604d5b9c5960302ffce3581a224b539678f83899 Author: Kevin Gott Date: Thu Dec 13 01:47:36 2018 -0500 Tweaks to get AmrCore compiling on Summit + making H files for converted Fortran->C++ functions. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H Tutorials/GPU/Advection_AmrCore/Source/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit ff4ed0a50b480638077eba5a0714467f04475e88 Author: Kevin Gott Date: Thu Dec 13 01:42:57 2018 -0500 Add non const bracket operator to GpuArray. Src/Base/AMReX_Array.H commit 56c0c48156fb17d029455c19a3b0fc05f256ae53 Author: Tan Nguyen Date: Wed Dec 12 20:49:37 2018 -0800 add code to detect memory leak Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.H Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/pthreads_common/LocalConnection.H Src/AmrTask/rts_impls/pthreads_common/Make.package Src/AmrTask/rts_impls/pthreads_common/PerillaMemCheck.H Src/AmrTask/rts_impls/pthreads_common/PerillaMemCheck.cpp Src/AmrTask/rts_impls/pthreads_common/RemoteConnection.H Src/AmrTask/rts_impls/pthreads_common/perilla.mak Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/main.cpp commit 8314cc2abadb314624c44fdf1e86007005f594b9 Merge: 9f6039c08 73f6f6c5f Author: Tan Nguyen Date: Wed Dec 12 20:44:30 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 73f6f6c5f44222d627d44b32dad6f81d500d8320 Merge: d39e23b0a 556c7a140 Author: Ann Almgren Date: Wed Dec 12 20:05:16 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit d39e23b0a928c70cbc1de64cbbb4cad2f351f4e4 Author: Ann Almgren Date: Wed Dec 12 20:03:45 2018 -0800 1) Some clean-up of nodal restriction 2) Grow nodal domain by 1000 so that we don't double at Neumann boundaries in divu_cf_contrib when using CoarseningStrategy::RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 556c7a1400d8ed2e194c55447e1deb5c884bf851 Merge: f19b2d4a7 7cefc273e Author: Andrew Myers Date: Wed Dec 12 17:09:34 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f19b2d4a7003061d8c32f45dc0bf0c5a07ebad91 Author: Andrew Myers Date: Wed Dec 12 17:09:03 2018 -0800 Make sure to remove particles that leave the problem domain when running on the GPU. Src/Particle/AMReX_ParticleContainerI.H commit 9f6039c082720cd5e10da0bb3783dbff3388cc24 Merge: 417bccec1 7cefc273e Author: Tan Nguyen Date: Wed Dec 12 16:54:26 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7cefc273efb4a20bc17481a59af735fd779554b9 Merge: 6cac804d9 18a08df95 Author: Weiqun Zhang Date: Wed Dec 12 19:02:22 2018 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6cac804d91b0cb93953296d548ad9adc6b4157fd Author: Weiqun Zhang Date: Wed Dec 12 19:01:59 2018 -0500 more inline Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_MultiFabUtil_nd_C.H commit 461c2a4da9d5fddd6ce6662c617a59eebcbcef18 Author: Weiqun Zhang Date: Wed Dec 12 18:41:41 2018 -0500 inline in FArrayBox Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit 0df85b933526720f51d717a258827ab22603be53 Author: Weiqun Zhang Date: Wed Dec 12 18:29:01 2018 -0500 inline in Box Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit dd80d505869c7d3981bd12e462619230ba4ab950 Author: Weiqun Zhang Date: Wed Dec 12 17:50:03 2018 -0500 clean up Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_FabArrayUtility.H commit f74a7d3bc543f15517e4cb6da0540cfe816588e9 Author: Weiqun Zhang Date: Wed Dec 12 16:53:32 2018 -0500 move MultiFabUtil kernels to headers for inline Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 12879796224bfe4a382972fd3ea14b0bd715d1f0 Author: Weiqun Zhang Date: Wed Dec 12 16:22:21 2018 -0500 return by value to save registers Src/Amr/AMReX_StateData.cpp commit 153b056fea37d23b14d8e10ccb206d869b56eba9 Author: Weiqun Zhang Date: Wed Dec 12 16:05:06 2018 -0500 move CoordSys kernels to headers for inline Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_COORDSYS_3D_C.H Src/Base/AMReX_COORDSYS_C.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 3573170c6eaf1561d6332ee944a23f836c0cbc22 Author: Weiqun Zhang Date: Wed Dec 12 15:47:26 2018 -0500 move FillCC to headers for inline Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_FilCC_C.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/CNS/Source/CNS_bcfill.cpp commit d70fd98a1e5550d57375ebd9d33581cb8ee9dee4 Author: Weiqun Zhang Date: Wed Dec 12 15:06:31 2018 -0500 clean up Tutorials/GPU/CNS/Source/CNS_setup.cpp commit 417bccec1aa6c8967d7c5d2fc34ae90195eec81e Merge: 2ddab9c12 18a08df95 Author: Tan Nguyen Date: Wed Dec 12 11:32:29 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6d8e898b19e4ebb4a72dbb055202d8ecb4189f62 Author: Weiqun Zhang Date: Wed Dec 12 13:08:19 2018 -0500 add AMREX_FORCE_INLINE macro Src/Base/AMReX_Extension.H commit 58d8061409fbc6da1140022f59eb093485fc790d Author: Weiqun Zhang Date: Wed Dec 12 12:59:47 2018 -0500 reorganize Tutorials/GPU/CNS for inline Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/Make.package Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/CNS/Source/hydro/Make.package Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 18a08df955e39789ee8efb474e23a86459bcb806 Author: atmyers Date: Wed Dec 12 08:04:11 2018 -0800 remove inconsistent definition of Real in AMReX_ParticleTile.H Src/Particle/AMReX_ParticleTile.H commit 2ddab9c1201a96dece6e434e1f371e36ba18673c Merge: b4bfc5dd3 56d4adc73 Author: Tan Nguyen Date: Tue Dec 11 21:35:30 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 56d4adc7388751ac692ca55d8648c29128436f9c Author: Andrew Myers Date: Tue Dec 11 16:28:59 2018 -0800 want to tile this loop Src/Particle/AMReX_NeighborParticlesI.H commit 2e2daa13aa1cb52f8ba353c64d89054f6cd5b975 Merge: 657b85fac 4efce4926 Author: Kevin Gott Date: Tue Dec 11 19:19:21 2018 -0500 Merge branch 'development' into gpu commit 4efce4926f95c65cf849e5ae1fd14cf5094ab730 Author: Andrew Myers Date: Tue Dec 11 15:43:47 2018 -0800 same thing here Src/Particle/AMReX_NeighborParticlesI.H commit a9a5ed28c4050aa2a9d8fd0598b0bec79d3e81d6 Author: Andrew Myers Date: Tue Dec 11 15:39:21 2018 -0800 the relevant dmap here is the one associated with the dst level, not the src level Src/Particle/AMReX_NeighborParticlesI.H commit b4bfc5dd327d23e920e0cbb434ca881573f8ef8e Merge: 5dc2627f7 df5c4bc9d Author: Tan Nguyen Date: Tue Dec 11 14:48:50 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5dc2627f79f872704a3c10439ab8a740e8798393 Author: Tan Nguyen Date: Tue Dec 11 14:48:35 2018 -0800 abc Src/Amr/AMReX_Amr.cpp commit df5c4bc9dae068d278020e7af301d546a68a99eb Author: Johannes Blaschke Date: Tue Dec 11 14:46:23 2018 -0800 fix BA type Src/EB/AMReX_EB_LSCoreBase.cpp commit 152bbeb13938add4c9ca4e20cf091323df34bb1b Author: Andrew Myers Date: Tue Dec 11 14:17:20 2018 -0800 add section label Docs/sphinx_documentation/source/GPU.rst commit f4306c14658e2678439f10c670d7866f71211275 Author: Andrew Myers Date: Tue Dec 11 14:13:37 2018 -0800 use cpp formatting Docs/sphinx_documentation/source/GPU.rst commit 00e4b1a68cfa147e4ff32c57317832f93bd5894f Merge: fdc2ced27 1fb29b45e Author: Andrew Myers Date: Tue Dec 11 13:58:11 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fdc2ced272031945c27d1fc08ea6bac036c92cde Author: Andrew Myers Date: Tue Dec 11 13:57:57 2018 -0800 add section on GPU particles to the docs. Docs/sphinx_documentation/source/GPU.rst commit 1fb29b45e7e4123dfeb35340745b634ac910a9a0 Merge: 8e54310cb f03cf4470 Author: Johannes Blaschke Date: Tue Dec 11 13:22:08 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8e54310cb1136955ed38a09eaa9bb71c72ae1015 Author: Johannes Blaschke Date: Tue Dec 11 13:22:04 2018 -0800 LSCore uses a local level-set paradigm now Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset_F.F90 commit f03cf44709dca78388ec95e01956b9a8870f365a Merge: be8c8a5ed 7cf30f602 Author: Andrew Myers Date: Tue Dec 11 12:40:17 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit be8c8a5ed81ca7457ee3f8312974f918847d8fb9 Author: Andrew Myers Date: Tue Dec 11 12:39:40 2018 -0800 proofreading pass of GPU documentation Docs/sphinx_documentation/source/ChapterGPU.rst Docs/sphinx_documentation/source/GPU.rst commit 7cf30f602c879ce0ba9c6df28e508b989276f521 Author: Ann Almgren Date: Tue Dec 11 12:26:32 2018 -0800 Remove memory leak - changes per Weiqun's suggestion. Src/AmrCore/AMReX_Cluster.cpp commit 657b85fac6aa5b73c190a632d94ed7a4808ddaf5 Author: Kevin Gott Date: Tue Dec 11 11:57:32 2018 -0800 Removed print statement. AmrCore GPU rewrite tutorial now works on CPUs. Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp commit 35826e1be096ff6479c731c5dcb89c9cbf1c8895 Author: Kevin Gott Date: Tue Dec 11 11:50:14 2018 -0800 inputs Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs commit f7d9446ace14faba0ca587e4117b0a195b8d00fe Author: Weiqun Zhang Date: Tue Dec 11 13:19:13 2018 -0500 add USE_FORCE_INLINE Src/Base/AMReX_Extension.H Tools/GNUMake/Make.defs commit af791bbe18f2838d91291c30ae61a01c2ceaff3d Merge: 359181abe 90fba2864 Author: Johannes Blaschke Date: Mon Dec 10 21:41:15 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 359181abeda0dbb087babb41839a780b24ea065d Author: Johannes Blaschke Date: Mon Dec 10 21:41:08 2018 -0800 implement tiling for local level-set creation Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp commit c8114b085ce7eb6542e49578a78f48d67f085cce Author: Ann Almgren Date: Mon Dec 10 18:32:19 2018 -0800 Fix some bounds problems Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 76fdccab2b1874cc53b49670cb7d801ca8ba3784 Author: Kaiyuan Hou Date: Mon Dec 10 19:16:54 2018 -0600 update timer name Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp commit a18a99be53f7ef245e602fb8f0188bcefddda903 Author: Kevin Gott Date: Mon Dec 10 17:09:03 2018 -0800 Turn off tiling in AmrCore tutorial for testing. Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 commit 055aa82b815f9aa08953e3ea0224ca0328c8933f Author: Kevin Gott Date: Mon Dec 10 17:08:30 2018 -0800 Continuing to fix Core. Has prints. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp commit 90fba286422f13501100288331350086e5c79b16 Merge: 8decd6850 a5d28e316 Author: Andrew Myers Date: Mon Dec 10 16:35:57 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8decd6850e21a5d2232e9193d9f47e84bc273e47 Author: Andrew Myers Date: Mon Dec 10 16:35:47 2018 -0800 this needs to be 'class' instead of 'typename' to keep gcc < 5 happy Src/EB/AMReX_EB_LSCoreBase.H commit a5d28e3166947e5b72e204cb86a2262bd7980520 Author: Weiqun Zhang Date: Mon Dec 10 16:16:23 2018 -0800 more gpu doc Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/LinearSolvers.rst commit 399dcd8913e0538d4c70e485f6a826fe6c55ce17 Author: Marc Day Date: Mon Dec 10 16:06:22 2018 -0800 Remove GPU macros prior to typecheck Tools/GNUMake/Make.rules commit a885e41bfe1b324a5da2d605547513a3be83728c Merge: 48cfa38d7 701100a8a Author: Andrew Myers Date: Mon Dec 10 16:04:26 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 48cfa38d7bf074feb2137613e46393a152caceee Author: Andrew Myers Date: Mon Dec 10 16:04:08 2018 -0800 fix Tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/main.cpp commit f33171737b9408800c3566ce4ad29925a02a2b15 Author: Andrew Myers Date: Mon Dec 10 15:35:38 2018 -0800 also communicate the level information in the MPI send data for neighbor particles Src/Particle/AMReX_NeighborParticlesI.H commit 701100a8adb47db7432ff9a35b534977cf0beb20 Author: Weiqun Zhang Date: Mon Dec 10 15:02:19 2018 -0800 minor fixes Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/GPU.rst commit e563f593bb5e71083095e6c21268d69d499b94f9 Merge: b049cd144 806109417 Author: Ann Almgren Date: Mon Dec 10 14:12:30 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit b049cd1443dc07a17985f1e2f884963d2b66f0d4 Author: Ann Almgren Date: Mon Dec 10 14:11:20 2018 -0800 Allow multilevel solves with CoarseningStrategy::RAP. Note there is a default assumption that the EB boundary does not cross the coarse-fine interface because the coarse-fine stencil is NOT defined using the EB-aware stencils. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 56179041ee6d4af62d6483cae02c783caa661f96 Author: kngott Date: Mon Dec 10 13:45:10 2018 -0800 Ann found compute flux was wrong. Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp commit 7f7523272294f43e68979dc078d3532a4d64e83e Author: Weiqun Zhang Date: Mon Dec 10 16:07:00 2018 -0500 minor: add some consts Src/Base/AMReX_CudaLaunch.H commit 8061094178c4d024fb8894fee46ff6752b958aa0 Author: Weiqun Zhang Date: Mon Dec 10 12:43:47 2018 -0800 Tutorials/GPU/Launch: inline the C++ kernel Tutorials/GPU/Launch/Make.package Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/Launch/MyKernel.cpp commit a243d2553a2e453b8cbc69a7be814e20c771bdc4 Author: kngott Date: Mon Dec 10 11:33:31 2018 -0800 Fixing errors in fluxes. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp commit 2b74acc14df6d5e390029a288500b993f66aed1c Author: Tan Nguyen Date: Mon Dec 10 00:35:57 2018 -0800 extend the upcxx backend to support RGIter Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.H Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PerillaConfig.H Src/AmrTask/rts_impls/upcxx_pthreads/Perilla_common.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp commit 9179da9376d6ef9358084390f3a897d776a13362 Author: Ann Almgren Date: Sun Dec 9 15:06:42 2018 -0800 Remove "mfix" from routine names Tutorials/EB/Donut/Src/EB_F.H Tutorials/EB/Donut/Src/eb_to_pvf.F90 Tutorials/EB/Donut/Src/main.cpp commit 166efca9be6696735057160895577b10eca695e3 Merge: 45a1d5729 6c3968287 Author: Johannes Blaschke Date: Sun Dec 9 10:27:29 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 45a1d572980a2044bd1c7cad7b140456259074b4 Author: Johannes Blaschke Date: Sun Dec 9 10:27:22 2018 -0800 use tiling to fill level-set Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp commit 6c39682876b673e69e5ba63e9ed63994ca926737 Author: Tan Nguyen Date: Sat Dec 8 22:41:44 2018 -0800 fit a small bug in the mpi backend Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.H Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/pthreads_common/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp commit af2371d62e4df80ee92c32673a35a72cd4822364 Author: Weiqun Zhang Date: Sat Dec 8 21:38:44 2018 -0800 on limitations. this finishes my first pass of gpu documentation Docs/sphinx_documentation/source/GPU.rst commit 643710d9bbb9c4e4455c9f9e48d676cfc4c19149 Author: Weiqun Zhang Date: Sat Dec 8 21:19:34 2018 -0800 on assetion, error check and reduction Docs/sphinx_documentation/source/GPU.rst commit 377204509dc7c279cd8b901f7dc2621e8726ad46 Author: Weiqun Zhang Date: Sat Dec 8 20:44:53 2018 -0800 on AsyncFab Docs/sphinx_documentation/source/GPU.rst commit 32b072068e887465f63389374e15551cdbb5ad47 Author: Michael Zingale Date: Sat Dec 8 22:11:41 2018 -0500 pout -> amrex::Print() Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit 0786ecfefe1890c8c40a9745e8cf543578efc2fe Author: Ann Almgren Date: Sat Dec 8 18:58:00 2018 -0800 Add error message if we reach the end of the new_chop routine without returning the new grids. Src/AmrCore/AMReX_Cluster.cpp commit 22538f570f9d023cd9d52e9152a46e424e15835d Author: Weiqun Zhang Date: Sat Dec 8 18:36:47 2018 -0800 try again Src/AmrCore/AMReX_Cluster.cpp commit 742d53a4efc79608548600aada4316e5db3a0c36 Author: Weiqun Zhang Date: Sat Dec 8 18:35:13 2018 -0800 not sure it's the right fix for ClusterList, but it compiles now Src/AmrCore/AMReX_Cluster.cpp commit 96e6bffb24a7ceddb0a15f5f457430c156e62fec Merge: 3eb0140f2 d65c17104 Author: Weiqun Zhang Date: Sat Dec 8 18:28:17 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3eb0140f2b7da485368ae0246e14bab4da5257a4 Author: Weiqun Zhang Date: Sat Dec 8 18:28:08 2018 -0800 rm FabArray::getDomain and comment out some debug code using it Src/Base/AMReX_FabArray.H Tools/C_util/Convergence/DebugOut.cpp commit d65c17104b7d96b8026ea644b61a9643aee4e7c4 Merge: 72e6867e7 c3989d642 Author: Ann Almgren Date: Sat Dec 8 18:18:51 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 72e6867e7963dfcd0e3dd942d701256db5cd02cd Author: Ann Almgren Date: Sat Dec 8 18:17:01 2018 -0800 Update the creation of the grids for the level set by 1) removing the iteration -- we shoudln't need it 2) Introducting a modified "chop" function which doesn't accept cuts if they don't imporove the grid efficiency. This is available to all grid creation routines if they set the flag use_new_chop to true. The level set routines now do that by default. Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit c3989d642e74767c6f02632e2d5738f2517a2cc1 Author: Weiqun Zhang Date: Sat Dec 8 13:21:44 2018 -0800 on gpu safe classes Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst commit 66fd6db75fb1cf013c23bacc126e7a355b29031e Author: Weiqun Zhang Date: Sat Dec 8 12:02:30 2018 -0800 add writing C++ kernel Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/index.rst commit b26f007e07daf2e4b6614e8d01315f9a9188e854 Author: Weiqun Zhang Date: Fri Dec 7 22:21:57 2018 -0800 Merge branch 'gpu-docs' into development Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/source/AsyncIter.rst Docs/sphinx_documentation/source/ChapterGPU.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/index.rst Src/Base/AMReX_Arena.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak Tutorials/GPU/Launch/GNUmakefile Tutorials/GPU/Launch/Make.package Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/Launch/MyKernel.cpp Tutorials/GPU/Launch/MyKernel_F.F90 Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/Readme.md Tutorials/GPU/Launch/main.cpp commit 2a66f8ac162d3e39ac17cf4232c192121bf37655 Author: Andrew Myers Date: Fri Dec 7 18:10:27 2018 -0800 fix bug involving periodic boundary conditions and NeighborCopyTags Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 7f8ec36d662e9e92352658b2e2c205459ffa8156 Author: Johannes Blaschke Date: Fri Dec 7 18:00:55 2018 -0800 change buffer Src/EB/AMReX_EB_LSCoreBase.cpp commit 8983bdb0ca2355be515b086439541f865f65bacf Author: Andrew Myers Date: Fri Dec 7 16:40:56 2018 -0800 need to remove duplicates whether or not mask is used. Src/Particle/AMReX_NeighborParticlesI.H commit 6854d23eb85a0d711f0fb90c2c3ff1df8e5d1e46 Author: Andrew Myers Date: Fri Dec 7 16:38:54 2018 -0800 change order of output for << operator Src/Particle/AMReX_NeighborParticles.H commit 6499818d6b1b301dada4a1be596ecc17e9c21abe Author: Johannes Blaschke Date: Fri Dec 7 15:22:44 2018 -0800 finished volfrac tagging Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 commit e17f89a09d6e8f85760f12aaa88dfc9e32c726b7 Author: Andrew Myers Date: Fri Dec 7 15:22:19 2018 -0800 add << operators for NeighborIndexMap and NeighborCommTag Src/Particle/AMReX_NeighborParticles.H commit ffd0e1a397c62c963b3f2cab2c6b0dac040ee870 Author: Andrew Myers Date: Fri Dec 7 14:24:01 2018 -0800 change the neighbor list print format Src/Particle/AMReX_NeighborParticlesI.H commit fb897c4254587f1387a50f57eb31558dc93dbea6 Author: Johannes Blaschke Date: Fri Dec 7 13:39:06 2018 -0800 get ready for volfrac tagging Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 9678d9b2d767abdb10578f671a9bd0dff3554238 Author: Andrew Myers Date: Fri Dec 7 13:32:13 2018 -0800 need to always bin the particles for the nl on level 0 Src/Particle/AMReX_NeighborParticlesI.H commit 54c7c99114366779955a792fbda007785ccbdcdf Author: Andrew Myers Date: Fri Dec 7 13:28:37 2018 -0800 have printNeighborList take a prefix argument Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 3321757431b634e01c86dbdb4400cb4875e76a96 Author: Andrew Myers Date: Fri Dec 7 13:20:11 2018 -0800 add method to print out nbor list for debugging. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 45d39b390b623545633c8af1ff4118cc4621e116 Author: kngott Date: Fri Dec 7 11:39:55 2018 -0800 Fix slope.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 3c9896f25ab52e009d1ad2f6390b2bea1a34edda Merge: 49b121b59 835ba726c Author: Andrew Myers Date: Fri Dec 7 11:36:21 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 835ba726c125d7c32478b2a9ac32f880ef6cfa68 Author: Johannes Blaschke Date: Fri Dec 7 11:19:18 2018 -0800 level-set tagging now seperately declared as such Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 commit 5a231bb8379a467721dc6d8bfdada02088da45bf Merge: b45f9c279 329c2aab5 Author: Johannes Blaschke Date: Fri Dec 7 11:12:33 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b45f9c279b471a3ed6f53030c8f1e0b84bf8c78d Author: Johannes Blaschke Date: Fri Dec 7 11:12:26 2018 -0800 clean up tagging Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 commit 329c2aab522d94cb3c2d21b4565486d0d6c5238e Author: Weiqun Zhang Date: Fri Dec 7 10:25:11 2018 -0800 make AsyncFab copy constructor device function only and use_cuda=true only Src/Base/AMReX_CudaAsyncFab.H commit 20c68a15154a438635e265304b3844a8ccf332e1 Author: Weiqun Zhang Date: Fri Dec 7 10:05:16 2018 -0800 Make AsyncFab interface nicer thanks to Marc's suggestion. AsyncFab can be captured by value and AsyncFab::fab() will return a reference to Fab. Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit 94c81be3cd56420cfdb2c08a026f611bded89b7e Merge: b2296e0a5 833b9e123 Author: Andrew Myers Date: Thu Dec 6 16:56:12 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b2296e0a56466e3e230913f192cf443561e91831 Author: Andrew Myers Date: Thu Dec 6 16:55:59 2018 -0800 separate out the printing stuff from Arena::Finalize so it can be used for debugging. Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp commit 833b9e123a86ab12148d37b6329a9ffddd5ef76a Merge: 10be78bd4 47ec80ee8 Author: Weiqun Zhang Date: Thu Dec 6 16:45:11 2018 -0800 Merge branch 'weiqun/fabptr' into development commit 47ec80ee8ed2e6d14dd776e8438156a39fdc9ce3 Merge: 92b013a41 26feb5529 Author: Weiqun Zhang Date: Thu Dec 6 19:32:21 2018 -0500 Merge branch 'weiqun/fabptr' of github.com:AMReX-Codes/amrex into weiqun/fabptr commit 26feb5529352bad23b222b445ac1591d80d8eaf8 Author: Weiqun Zhang Date: Thu Dec 6 16:31:57 2018 -0800 update particle functors to use device ptr Src/Particle/AMReX_ParticleContainerI.H commit 54fa626db5eb4f8f5f13e82de30814db21729fce Author: Weiqun Zhang Date: Thu Dec 6 16:31:28 2018 -0800 add __FILE__ and __LINE__ as arguments ot Cuda::ErrorCheck Src/Base/AMReX_GpuError.H commit 10be78bd43029961d55fc2166e06d6da79b32924 Author: Tan Nguyen Date: Thu Dec 6 16:29:11 2018 -0800 avg_down with region graph iterator Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp commit 49b121b59522c725a8818ab5fe4f24f8f963877a Author: Andrew Myers Date: Thu Dec 6 15:31:01 2018 -0800 this at least runs to completion in serial Src/Particle/AMReX_NeighborParticlesI.H commit a5c895158c3c014a89d437efd3170eb72b6cf84f Author: Johannes Blaschke Date: Thu Dec 6 15:23:53 2018 -0800 don't regrid LSCore if BA/DM don't change Src/EB/AMReX_EB_LSCoreBase.cpp commit 289ffa8fd9a2150ff0e8e6fdb058c79ece840b17 Author: Andrew Myers Date: Thu Dec 6 15:15:44 2018 -0800 fix bug that involved confusing the src level with the dst level Src/Particle/AMReX_NeighborParticlesI.H commit 6ecfce3531cba8b37fc435dfc48bc21f14bfbaf5 Author: Cy Chan Date: Thu Dec 6 15:03:17 2018 -0800 add consolidation threshold parameter to MLLinOp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/main.cpp commit e4638572aa927e0cfeaf137efc8d24a8ac0b044a Author: Andrew Myers Date: Thu Dec 6 14:35:57 2018 -0800 clean up resize containers Src/Particle/AMReX_NeighborParticlesI.H commit 2d3b071b7c2230ab5171cdb2dcda04e7199cc785 Author: Andrew Myers Date: Thu Dec 6 14:33:19 2018 -0800 the buffer tag cache also needs to be an array over levels Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit b193ce6db2741b3f4f219c13546590a9e195f003 Author: Andrew Myers Date: Thu Dec 6 14:04:42 2018 -0800 tweak inputs Tutorials/Particles/NeighborListMR/inputs commit 267c8745b3e1da8d061230add6b8bcedcb270978 Author: Andrew Myers Date: Thu Dec 6 13:45:26 2018 -0800 remove some hard-coded 'const int lev = 0' Src/Particle/AMReX_NeighborParticlesI.H commit 24a1c4eb1402fa2886b5b6b00a7e68dc236ca143 Merge: 9b9370fb9 28a79294b Author: Ann Almgren Date: Thu Dec 6 13:33:23 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 9b9370fb9b72422033dfd4eb85c65cd3b23ad09c Author: Ann Almgren Date: Thu Dec 6 13:30:26 2018 -0800 Abort in the case when the entire domain is covered. Previously this case ended up being viewed as "all_regular" Src/EB/AMReX_EB2_Level.H commit 563859211b05601fcacb1c844dd6778a0277b50a Author: Andrew Myers Date: Thu Dec 6 13:12:51 2018 -0800 use the mask if max_level = 0 Src/Particle/AMReX_NeighborParticlesI.H commit 28a79294bd091b4cccd3473d4d7e5df32245086f Author: Johannes Blaschke Date: Thu Dec 6 13:12:05 2018 -0800 completed local level-set Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit c17cd9ec8214db613424d1ecaa6f738b8f0c710f Author: Andrew Myers Date: Thu Dec 6 13:07:36 2018 -0800 remove unused stuff from NeighborListParticleContainer Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborListMR/inputs Tutorials/Particles/NeighborListMR/main.cpp commit c1954c6c466bf22c31a3b9adff21e3dabac370b9 Author: Andrew Myers Date: Thu Dec 6 13:04:23 2018 -0800 fix and simplify periodic boundary adjustment for neighbors Src/Particle/AMReX_NeighborParticlesI.H commit f2dc968984d447fb2410365f836b424fbc4402a0 Author: Andrew Myers Date: Thu Dec 6 13:03:50 2018 -0800 overload << operator for NeighborCopyTag for ease of debugging Src/Particle/AMReX_NeighborParticles.H commit 6b4083716254764bd1357327a978b510d77ebf06 Author: kngott Date: Thu Dec 6 13:02:02 2018 -0800 Properly use cell number. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit fbe5dd7e75fabea3cc86fc7d5d38620254348db1 Author: Andrew Myers Date: Thu Dec 6 12:39:12 2018 -0800 fixing a couple more bugs Src/Particle/AMReX_NeighborParticlesI.H commit 92b013a41a4045792eea2cc5fe00f6329ca11456 Merge: 6b6714d4c a1fbe4d5a Author: Weiqun Zhang Date: Thu Dec 6 14:01:17 2018 -0500 Merge branch 'development' into weiqun/fabptr commit 8e63ca33d415ce6452dd6e349e717aec0050114d Author: Johannes Blaschke Date: Thu Dec 6 10:53:12 2018 -0800 fix typo Src/EB/AMReX_EB_levelset_F.F90 commit 251007d69631f036729031d31a7e38790e2b3812 Author: Johannes Blaschke Date: Thu Dec 6 10:52:01 2018 -0800 fix level-set thresholding Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit a1fbe4d5ab7d023c7adfb2e553fbabb482592a1d Author: Weiqun Zhang Date: Thu Dec 6 09:44:47 2018 -0800 make gcc happy Src/Base/AMReX_MultiFab.H commit 45812fe55627685d4e58016ebe715dc07ed26f57 Author: Weiqun Zhang Date: Thu Dec 6 09:39:10 2018 -0800 get rid of warning in version checking when users set their own CXX Tools/GNUMake/comps/gnu.mak commit 1fce9884601e59e8be6609470efc52af277d1ce2 Author: Ann Almgren Date: Thu Dec 6 06:34:45 2018 -0800 Instead of IntVect{0,0,0} use IntVect{AMREX_DECL(0,0,0)} Src/EB/AMReX_EB_levelset.cpp commit cf15c194ca04d905ae57462c36489a86f74c29a6 Author: Ann Almgren Date: Thu Dec 6 06:10:16 2018 -0800 Need to return something from eb_facets routine Src/EB/AMReX_EB_levelset.cpp commit 30370232770a99c9700e1d273069136373666cd0 Author: Tan Nguyen Date: Thu Dec 6 01:43:37 2018 -0800 Advection code using RGIter Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._Exec Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._README Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._Source Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._Make.Adv Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._SingleVortex Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._UniformVelocity Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._Prob.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._face_velocity_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._face_velocity_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._inputs Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._probin Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Backtrace.0 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Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/main.cpp commit 95dc5a109e8beec698671e9f7b71c9824e84ff59 Author: Johannes Blaschke Date: Wed Dec 5 21:50:40 2018 -0800 hack level-set threshold Src/EB/AMReX_EB_levelset_F.F90 commit c26ddfe28bea62a27b7c000360cd2dd9ccd09cca Author: Andrew Myers Date: Wed Dec 5 19:04:58 2018 -0800 use AMREX_D_TERM so this works in 2D Src/Particle/AMReX_NeighborParticles.H commit 0496ea055b9b572cdcabfbab1828838659ee597d Author: Andrew Myers Date: Wed Dec 5 19:00:53 2018 -0800 fix a couple of bugs Src/Particle/AMReX_NeighborParticlesI.H commit 4945f2609dad0be78b7e6cefe584f5156c9788ef Author: Johannes Blaschke Date: Wed Dec 5 18:37:43 2018 -0800 bug fixes for eb_search Src/EB/AMReX_EB_levelset.cpp commit f79179671feb76431ceddc098c04fbab43b18ff5 Merge: e3666bf3f 2e0d85ee3 Author: Johannes Blaschke Date: Wed Dec 5 18:06:08 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e3666bf3f1c54a018961f8a8645a2e3cf6f0a402 Author: Johannes Blaschke Date: Wed Dec 5 18:06:04 2018 -0800 work on local level-set filling Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit 6b6714d4c5eebc46de9ce78a6854b1a1e5a5a589 Merge: 080924d89 159bcfb4a Author: Weiqun Zhang Date: Wed Dec 5 16:51:26 2018 -0800 Merge branch 'development' into weiqun/fabptr commit 080924d89e9b7f73880570ee5418d7cbc8155949 Author: Weiqun Zhang Date: Wed Dec 5 16:51:14 2018 -0800 udpate gpu codes ot use fabPtr Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_iMultiFab.cpp Tests/GPU/AsyncFab/main.cpp Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 2e0d85ee351e00f76622a13d00425ade5e60f607 Author: Andy Nonaka Date: Wed Dec 5 16:44:53 2018 -0800 add link to tutorial documentation Docs/sphinx_documentation/source/Chapter4a.rst Docs/sphinx_documentation/source/index.rst commit 0ebea50a0cc6c86e823190f72b990d0431ac3601 Author: Andrew Myers Date: Wed Dec 5 16:23:59 2018 -0800 finish non-mask version of GetNeighborCommTags Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 3d5c5669b37d39eb3e96e5fbb781575eb13b698b Author: Andrew Myers Date: Wed Dec 5 16:10:26 2018 -0800 fix bug in computeRefFac Src/Particle/AMReX_NeighborParticlesI.H commit c8072408cf1ec6904181b691d5da375a568fb5b9 Author: Andrew Myers Date: Wed Dec 5 15:58:44 2018 -0800 add a numLevels() method to ParticleContainer and use it Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_Particles.H commit a29a8a440f6ef7f17b9599cb79762032233f092e Author: Andrew Myers Date: Wed Dec 5 15:51:47 2018 -0800 function to compute net ref ratio between two levels Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 68667ee56e5072e10bbd22c1f363a78a7819f494 Author: Cy Chan Date: Wed Dec 5 15:30:09 2018 -0800 fix bug in remap neighborhoods Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 159bcfb4a4b501df991f2bfe7fe96ce754c31984 Author: Weiqun Zhang Date: Wed Dec 5 14:26:20 2018 -0800 fix fortran function name so that the gpu script works Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 commit 6939d3b3f3652663c498e3c2504c9967cd620962 Author: Weiqun Zhang Date: Wed Dec 5 14:14:33 2018 -0800 WIP: add host alias fabs to FabArray Src/Base/AMReX_FabArray.H commit 9651e2bca7d067810b3a95ed59dc3c6e2f911f44 Author: Weiqun Zhang Date: Wed Dec 5 13:37:47 2018 -0800 add createHostAlias for fab Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_MultiCutFab.H commit e4d9589667341ed28ab6f9ef2ace56e905ca0b19 Author: Andrew Myers Date: Wed Dec 5 12:57:05 2018 -0800 some more refactoring Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit fea2ec1fb5156ba8d821bb2eeeb63f8efcd16eee Author: Ann Almgren Date: Wed Dec 5 12:36:03 2018 -0800 move Parallel/ForkJoin --> ForkJoin Tutorials/ForkJoin/GNUmakefile Tutorials/ForkJoin/Make.package Tutorials/ForkJoin/MyTest.H Tutorials/ForkJoin/MyTest.cpp Tutorials/ForkJoin/MyTest_F.H Tutorials/ForkJoin/inputs Tutorials/ForkJoin/main.cpp commit fbdaec2bbd1aab300c72dd638cb0755acbbea557 Author: Andrew Myers Date: Wed Dec 5 12:25:15 2018 -0800 do_mask -> use_mask Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit bf19a639fc15653083081bb3fb5385c9adc5208b Author: Andrew Myers Date: Wed Dec 5 12:04:47 2018 -0800 split up BuildMasks into two different methods Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 4b27017ece63155b26612be907b9c8bbe8e49d05 Author: Ann Almgren Date: Wed Dec 5 12:01:17 2018 -0800 1) Copy the current Tutorials that use SENSEI into a new Tutorials/SENSEI directory. 2) Remove mentions of SENSEI from Tutorials/Amr. 3) Add items in the sphinx documentation for each Tutorials subdirectory. Docs/sphinx_tutorials/source/Blueprint_Tutorial.rst Docs/sphinx_tutorials/source/Forkjoin_Tutorial.rst Docs/sphinx_tutorials/source/GPU_Tutorial.rst Docs/sphinx_tutorials/source/MUI_Tutorial.rst Docs/sphinx_tutorials/source/SDC_Tutorial.rst Docs/sphinx_tutorials/source/SENSEI_Tutorial.rst Docs/sphinx_tutorials/source/index.rst Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/SENSEI/Advection_AmrCore/CMakeLists.txt Tutorials/SENSEI/Advection_AmrCore/Exec/Make.Adv Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/Prob.f90 Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/SENSEI/Advection_AmrCore/README Tutorials/SENSEI/Advection_AmrCore/README_SENSEI.md Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/SENSEI/Advection_AmrCore/Source/Make.package Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/Make.package Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_nd/Make.package Tutorials/SENSEI/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 Tutorials/SENSEI/Advection_AmrCore/Source/bc_fill_nd.F90 Tutorials/SENSEI/Advection_AmrCore/Source/main.cpp Tutorials/SENSEI/Advection_AmrLevel/CMakeLists.txt Tutorials/SENSEI/Advection_AmrLevel/Exec/Make.Adv Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/Make.package Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/Prob.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/probin Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Make.package Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probin Tutorials/SENSEI/Advection_AmrLevel/README Tutorials/SENSEI/Advection_AmrLevel/README_SENSEI.md Tutorials/SENSEI/Advection_AmrLevel/Source/Adv_F.H Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/SENSEI/Advection_AmrLevel/Source/LevelBldAdv.cpp Tutorials/SENSEI/Advection_AmrLevel/Source/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/main.cpp commit 541ed4233e0c7193a5e931fef74c6183f5a1c4ab Author: Andrew Myers Date: Wed Dec 5 11:57:26 2018 -0800 make BuildMasks protected Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 2a096d00330dd2eae80660ce0a1d6a3d4c75558c Author: Andrew Myers Date: Wed Dec 5 11:32:44 2018 -0800 give NeighborCopyTag explicity default constructor as well Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 0a2a0957d3c83479ed0289fc147e89c287025419 Author: Andrew Myers Date: Wed Dec 5 11:27:53 2018 -0800 finish implementation of non-mask getNeighborTag Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit ca10e0c715a4a2bdd1063f799c72cbe56b86997b Author: Andrew Myers Date: Wed Dec 5 11:17:46 2018 -0800 give NeighborCopyTag a non-default constructor Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit c922fc4d354aa24c357be6df0a0c49719a574f23 Author: Andrew Myers Date: Wed Dec 5 11:13:42 2018 -0800 some work towards implementing the non-mask neighbor tag function Src/Particle/AMReX_NeighborParticlesI.H commit a5b5e0c1b649f8bea398dd705e29ee775bf8736b Author: Andrew Myers Date: Wed Dec 5 10:55:06 2018 -0800 some refactoring Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit cf4c1245e5a487efbfac34bbe3a629a97df6bd6f Author: Ann Almgren Date: Wed Dec 5 10:52:09 2018 -0800 Remove HYPRE tutorial -- there isn't a separate one Docs/sphinx_tutorials/source/HYPRE_Tutorial.rst Docs/sphinx_tutorials/source/index.rst commit a9ec9af6b6c99208e99dfc2ec8556cb30f822957 Author: Ann Almgren Date: Wed Dec 5 10:35:56 2018 -0800 Update with the three specific Tutorial names. Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst commit aa84bcfd6a881834a9bc8f0fd4643b9819e335ba Author: Andrew Myers Date: Wed Dec 5 10:04:22 2018 -0800 correct comment Src/Particle/AMReX_NeighborParticlesI.H commit 0742cfff6b9fcc322f5180da1a0a49c7ab9f8f11 Author: Andrew Myers Date: Wed Dec 5 09:55:30 2018 -0800 selectively switch off building the mask Src/Particle/AMReX_NeighborParticlesI.H commit 54ea4b2ce52c5fec225eba14cb24d687bfd282a5 Author: Andrew Myers Date: Wed Dec 5 09:53:43 2018 -0800 add a static member variable to disable the mask approach Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 893da9b9bc77b5f61d0f8b21a852da15a79513f4 Author: Weiqun Zhang Date: Wed Dec 5 09:15:35 2018 -0800 make distFcnElement2d pure virtual Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp commit 293aa3d64405d04a21f6e8c9021f22d050f7b746 Author: Weiqun Zhang Date: Wed Dec 5 09:00:22 2018 -0800 FabArray::fabPtr functions to return pointer to fab Src/Base/AMReX_FabArray.H commit fc87026de68a2496bd70d9e419c909408b56b296 Author: kngott Date: Wed Dec 5 00:37:47 2018 -0800 Fix initialization error. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit 6fa10a22fbc9a54931b13dcb191fe64dc54ee2a9 Author: kngott Date: Tue Dec 4 15:49:34 2018 -0800 Fix boxes. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit c1c1c7c6b5b8eaed9b20b3c95695556fbcb01085 Author: kngott Date: Tue Dec 4 15:48:32 2018 -0800 Fix conversion of single-plane psi into three dimensional loop. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit 9302eb9e840fd3fede4ee80344d497b3845859e9 Merge: 8fde8801a febd8ccc7 Author: Johannes Blaschke Date: Tue Dec 4 15:44:58 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8fde8801aaa7cc997f8d829b70c6538d287cfc0b Author: Johannes Blaschke Date: Tue Dec 4 15:44:55 2018 -0800 make EBSearchBox compatible of infs and nans Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit febd8ccc77bb83db370651c2dd0500f0ab554234 Author: Tan Nguyen Date: Tue Dec 4 14:45:50 2018 -0800 change RTS name Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_pthreads/Make.package Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.H Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/pthreads_common/Make.package Src/AmrTask/rts_impls/upcxx_pthreads/Make.package Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.H Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/main.cpp Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit b9e907bb831414a7da81e3c8b81b59c478db23e1 Merge: fb717eaea 53249b043 Author: Weiqun Zhang Date: Tue Dec 4 14:30:48 2018 -0800 Merge branch 'weiqun/comm' into development commit fb717eaea0e77eb5f4a5e2bb91d6224847dce917 Author: Tan Nguyen Date: Tue Dec 4 14:06:50 2018 -0800 change directory name for rts backends Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi_omp/Barrier.H Src/AmrTask/rts_impls/mpi_omp/Barrier.cpp Src/AmrTask/rts_impls/mpi_omp/LocalConnection.H Src/AmrTask/rts_impls/mpi_omp/Make.package Src/AmrTask/rts_impls/mpi_omp/PackageQueue.H Src/AmrTask/rts_impls/mpi_omp/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_omp/Perilla.H Src/AmrTask/rts_impls/mpi_omp/Perilla.cpp Src/AmrTask/rts_impls/mpi_omp/PerillaConfig.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_omp/RegionGraph.H Src/AmrTask/rts_impls/mpi_omp/RegionGraph.cpp Src/AmrTask/rts_impls/mpi_omp/RegionQueue.H Src/AmrTask/rts_impls/mpi_omp/RegionQueue.cpp Src/AmrTask/rts_impls/mpi_omp/RemoteConnection.H Src/AmrTask/rts_impls/mpi_omp/WorkerThread.H Src/AmrTask/rts_impls/mpi_omp/WorkerThread.cpp Src/AmrTask/rts_impls/mpi_omp/perilla.mak Src/AmrTask/rts_impls/mpi_pthreads/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi_pthreads/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi_pthreads/Barrier.H Src/AmrTask/rts_impls/mpi_pthreads/Barrier.cpp Src/AmrTask/rts_impls/mpi_pthreads/LocalConnection.H Src/AmrTask/rts_impls/mpi_pthreads/Make.package Src/AmrTask/rts_impls/mpi_pthreads/Makefile Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.H Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.H Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaConfig.H Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.H Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_pthreads/RGIter.H Src/AmrTask/rts_impls/mpi_pthreads/RGIter.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.H Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionQueue.H Src/AmrTask/rts_impls/mpi_pthreads/RegionQueue.cpp Src/AmrTask/rts_impls/mpi_pthreads/RemoteConnection.H Src/AmrTask/rts_impls/mpi_pthreads/WorkerThread.H Src/AmrTask/rts_impls/mpi_pthreads/WorkerThread.cpp Src/AmrTask/rts_impls/mpi_pthreads/mylock.h Src/AmrTask/rts_impls/mpi_pthreads/perilla.mak Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/pthreads_common/Barrier.H Src/AmrTask/rts_impls/pthreads_common/Barrier.cpp Src/AmrTask/rts_impls/pthreads_common/LocalConnection.H Src/AmrTask/rts_impls/pthreads_common/Make.package Src/AmrTask/rts_impls/pthreads_common/RGIter.H Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp Src/AmrTask/rts_impls/pthreads_common/RegionQueue.H Src/AmrTask/rts_impls/pthreads_common/RegionQueue.cpp Src/AmrTask/rts_impls/pthreads_common/RemoteConnection.H Src/AmrTask/rts_impls/pthreads_common/WorkerThread.H Src/AmrTask/rts_impls/pthreads_common/WorkerThread.cpp Src/AmrTask/rts_impls/pthreads_common/mylock.h Src/AmrTask/rts_impls/pthreads_common/perilla.mak Src/AmrTask/rts_impls/upcxx_pthreads/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/upcxx_pthreads/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Barrier.H Src/AmrTask/rts_impls/upcxx_pthreads/Barrier.cpp Src/AmrTask/rts_impls/upcxx_pthreads/LocalConnection.H Src/AmrTask/rts_impls/upcxx_pthreads/Make.package Src/AmrTask/rts_impls/upcxx_pthreads/Makefile Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.H Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.H Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PerillaConfig.H Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.H Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla_common.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RGIter.H Src/AmrTask/rts_impls/upcxx_pthreads/RGIter.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionQueue.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RemoteConnection.H Src/AmrTask/rts_impls/upcxx_pthreads/WorkerThread.H Src/AmrTask/rts_impls/upcxx_pthreads/WorkerThread.cpp Src/AmrTask/rts_impls/upcxx_pthreads/mylock.h Src/AmrTask/rts_impls/upcxx_pthreads/perilla.mak commit 603522f96e977817b4d9109987896ccea342ad1c Author: kngott Date: Tue Dec 4 13:45:12 2018 -0800 Change inputs file for GPU testing. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs commit e634cb0cfd110c7db064f937019c35cb277d7348 Author: kngott Date: Tue Dec 4 13:44:51 2018 -0800 clean up false comment Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit 8c30a284a6f94b57c0309214ca4b5716fdc0bdf6 Author: kngott Date: Tue Dec 4 13:44:30 2018 -0800 Fix swapped function arguments. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 2824565f9fa1d831d159e1e73a2bcd855e420e7a Author: Andrew Myers Date: Tue Dec 4 13:28:52 2018 -0800 change periodic shift logic to be more forgiving Src/Particle/AMReX_NeighborParticlesI.H commit d2efcdd01ebebafae3366721ecd42bd72b42939e Author: Andrew Myers Date: Tue Dec 4 13:27:54 2018 -0800 use and IntVect for the periodic_shift member of NeighborCopyTag Src/Particle/AMReX_NeighborParticles.H commit 9f12fbf90fe74d8021d0d6fbcaa56d8799afc4be Author: Andrew Myers Date: Tue Dec 4 13:27:21 2018 -0800 change variable name to be more consistent Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit a9ff55753417d4d66986a097e2c6a4a6e7cdcd29 Author: Johannes Blaschke Date: Tue Dec 4 13:09:13 2018 -0800 added std::move symmantics to regridding and tweake coarsening Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit 53249b0431c42f00d3fc82d9e4702ff85f448b42 Author: Weiqun Zhang Date: Tue Dec 4 15:10:02 2018 -0500 add profiler Src/Base/AMReX_FabArrayCommI.H commit 12366cea00e7daf8a63d74d3e6a5926705f12c09 Author: Weiqun Zhang Date: Tue Dec 4 11:31:34 2018 -0800 AsyncArray: return earlier if size is zero Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_FabArrayCommI.H commit 8d52683c9df4c51121544324d1248477a0d84c74 Author: Weiqun Zhang Date: Tue Dec 4 11:13:48 2018 -0800 merged fillboundary: gpu version of local copy Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_GpuLaunch.H commit 4f1a2802cf03eba1f69f5b8b86c27f34797c44aa Author: Weiqun Zhang Date: Tue Dec 4 10:27:31 2018 -0800 merged fillboundary: omp version of local copy Src/Base/AMReX_FabArrayCommI.H commit 00ab644ad28d92c7a1fb2dae8a2cdbaab2b61cdc Author: Weiqun Zhang Date: Tue Dec 4 10:05:38 2018 -0800 remove TagVols because they have not been used. gpu version copyFromMem in the new merged fillboundary Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit 2a70e1a68457ff428f6ac473eaedaa3de9d3a656 Merge: 50d4f05b1 17bc6666f Author: Johannes Blaschke Date: Mon Dec 3 18:58:17 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 50d4f05b103f0ca4b1cb740c23e24def6cf73159 Author: Johannes Blaschke Date: Mon Dec 3 18:58:10 2018 -0800 add regrid (i.e. update MF and DM of particular level) to LSCore Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 17bc6666fcb31aba3a702d289d05e1091cd8aeb3 Author: Andrew Myers Date: Mon Dec 3 17:21:36 2018 -0800 != operator for NeighborCopyTag Src/Particle/AMReX_NeighborParticles.H commit eda764d93a4241cfc22da051b48ac4d6ea01acd0 Author: Weiqun Zhang Date: Mon Dec 3 13:44:16 2018 -0800 first pass of merged FillBoundary Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 90fd57696784afdce96d496629aab77c61529064 Merge: 5614e2154 886fa6f08 Author: Andrew Myers Date: Mon Dec 3 16:56:59 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5614e215443af02aedd1b4473d02d3341303d79b Author: Andrew Myers Date: Mon Dec 3 16:56:42 2018 -0800 on-the-fly computation of neighbor particles in a multi-level setting. Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborListMR/inputs Tutorials/Particles/NeighborListMR/main.cpp commit fb08de8539446cdacff7bffce033e85effb4c65e Author: kngott Date: Mon Dec 3 16:50:47 2018 -0800 Primary MFIter loop done and compiling. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 886fa6f08839b2dac38f08e9e15999e33d9bd11d Author: rgrout Date: Mon Dec 3 16:44:12 2018 -0700 Replaces #375 Spline Implicit function for EB (#380) * Added Spline implicit function for EB2 * Testing the FORD Scorpion piston bowl generation * Cleaned up spline implicit function * Modified the case to test the spline functionality * Resolve conflicts and address @WeiqunZhang comments * add missing amrex namespace Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Spline.H Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp Src/EB/CMakeLists.txt Src/EB/Make.package Tutorials/EB/GeometryGeneration/main.cpp commit 95a76aed24ab217fdd5c5d889e04be58f1e7e2c4 Author: Andrew Myers Date: Mon Dec 3 12:29:54 2018 -0800 don't forget to define the dmaps Tutorials/Particles/NeighborListMR/main.cpp commit 7d57eec2aaa2a54893c3e9cca4b4a91886a0bcb4 Author: Andrew Myers Date: Mon Dec 3 12:28:05 2018 -0800 fix parameter shadowing Src/Particle/AMReX_NeighborParticlesI.H commit 7f9d039c612e28deb1d3f1607b94568632786718 Author: Andrew Myers Date: Mon Dec 3 12:25:47 2018 -0800 update inputs file Tutorials/Particles/NeighborListMR/inputs commit 0e6d8b9b4d7bed6c89cde53a4c33562727603f3c Author: Andrew Myers Date: Mon Dec 3 12:24:32 2018 -0800 fix another typo. Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp commit 18cd34acc3ede2e14bda49704916491120d34d06 Author: kngott Date: Mon Dec 3 12:23:17 2018 -0800 Advection broken into functions. Compute_flux & slope left. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp commit c9b75dedf5f691f517aa4f8c68786a7919575470 Merge: ab9a9f810 4bd856071 Author: Andrew Myers Date: Mon Dec 3 12:22:38 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ab9a9f81030a2ec4d49eb31d3fa6975fca354f29 Author: Andrew Myers Date: Mon Dec 3 12:22:06 2018 -0800 fix typo Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp commit 4bd85607144c08b67ec9630e19dc2c472f20a661 Author: Tan Nguyen Date: Mon Dec 3 11:56:06 2018 -0800 add ref guide for RegionGraph Iterator Docs/sphinx_documentation/source/AsyncIter.rst Docs/sphinx_documentation/source/Chapter6aa.rst commit 9fb7c521ea93f576aa043fe4d819d4f295b535b8 Merge: 4f40d3d4f fdccb8348 Author: Andrew Myers Date: Mon Dec 3 10:30:20 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4f40d3d4f44df8ba0fa14eb036a067adf1b9d76f Author: Andrew Myers Date: Mon Dec 3 10:29:47 2018 -0800 fix issue involving component names Tests/HDF5Benchmark/main.cpp commit b835b9b0c34290e7596ac5c8558cc97401f9bd81 Author: Andrew Myers Date: Mon Dec 3 10:24:27 2018 -0800 fix assertion re: containing_bx in InitRandom. Src/Particle/AMReX_ParticleInit.H commit 66445f87db5964cf8fae9aad09e751314f936a59 Author: Andrew Myers Date: Mon Dec 3 10:23:57 2018 -0800 remove unused variable Tests/HDF5Benchmark/main.cpp commit 0c7f8cfd4056ff1bb522ad421aa5521e72a036c4 Merge: b3734c4bc fdccb8348 Author: Weiqun Zhang Date: Mon Dec 3 08:47:26 2018 -0800 Merge branch 'weiqun/gpu' into weiqun/comm commit fdccb8348c485b91bee559bf736e6ca5469e509c Merge: 35cc09c0f 4677ac986 Author: Weiqun Zhang Date: Mon Dec 3 08:46:01 2018 -0800 Merge branch 'weiqun/gpu' into development commit 35cc09c0fc7725207614449cbefee972515581e4 Author: Weiqun Zhang Date: Mon Dec 3 08:44:35 2018 -0800 update CHANGES CHANGES commit 273ca8bb066dd252efe5c3d07199a13155519061 Author: Johannes Blaschke Date: Sun Dec 2 22:21:50 2018 -0800 oopsie Src/EB/AMReX_EB_LSCoreBase.H commit de5cb48a498414ae2be633c72daeaaa7f8e57292 Author: Johannes Blaschke Date: Sun Dec 2 22:15:38 2018 -0800 added valid flags to LSCore class Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit 9ee09d5489def9a8ce26b51bbec1955b491a03f3 Author: Max Katz Date: Sun Dec 2 21:12:43 2018 -0500 Restore some code that was deleted in 70befea Src/Amr/AMReX_Amr.cpp commit d773698da9a4c6af6b89a8c733cd8458a9092de1 Author: Michael Zingale Date: Sun Dec 2 17:55:44 2018 -0500 make the extrema use a mask to find the true extrema in the domain (#378) closes #291 Tools/Postprocessing/F_Src/fextrema.f90 commit ab503ef7c6e96820c03ae0b7a4473fdfb34adcf9 Author: Michael Zingale Date: Sun Dec 2 13:31:02 2018 -0500 increase width of box and zone output Tools/Postprocessing/F_Src/fboxinfo.f90 commit b3734c4bc4b6cbc6935f96109ea99aba2f350acc Author: Weiqun Zhang Date: Sat Dec 1 19:08:00 2018 -0500 shift the lo box the big end and do copy too Src/Base/AMReX_FabArrayCommI.H commit 596a137de63b0c976bb11d5c14fd94998be0186a Author: Weiqun Zhang Date: Sat Dec 1 16:03:31 2018 -0500 add profilers Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 38540fba4289e16a9ac10148c7b3f9980d13485e Author: Weiqun Zhang Date: Sat Dec 1 15:32:51 2018 -0500 fewer kernels in FillBoundary Src/Base/AMReX_FabArrayCommI.H commit 7324ec21e899e11f2336685d41bd001f28ce635c Author: Weiqun Zhang Date: Sat Dec 1 13:38:57 2018 -0500 fix typo Src/Base/AMReX_FabArray.H commit 9697f6eb7ad7a5ba99354ba553cb70b11303b604 Merge: 4677ac986 7c7f14410 Author: Weiqun Zhang Date: Sat Dec 1 13:31:40 2018 -0500 Merge branch 'development' into weiqun/comm commit 7c7f14410b3bce9fab77b4bcf7c4674cf415903f Merge: 2e26882a4 853174938 Author: Weiqun Zhang Date: Sat Dec 1 13:24:28 2018 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2e26882a4a789d23bc3ad7c4537c230aec48c51c Author: Weiqun Zhang Date: Sat Dec 1 13:23:56 2018 -0500 add function to help MPI progress Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 4677ac986cd9e20b6a259b21f914ab3c48514c73 Author: Weiqun Zhang Date: Sat Dec 1 07:40:30 2018 -0800 filcc: multiple passes so that the corners can be dealt Src/Base/AMReX_PhysBCFunct.H commit e0f621eafc69e61e5c03f17893790e668b3586f6 Author: kngott Date: Fri Nov 30 18:08:32 2018 -0800 face velocities into MFIter loop. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 85317493856cdd979424dab660606a4695aa9800 Merge: 4b4c53cc8 223e67a50 Author: Johannes Blaschke Date: Fri Nov 30 13:51:00 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4b4c53cc8f3f520709665d0f977450919818d6b4 Author: Johannes Blaschke Date: Fri Nov 30 13:50:56 2018 -0800 updated amrex build info for macOS Docs/sphinx_documentation/source/BuildingAMReX.rst commit 0df67f14e0ce47a2c11a5a17c18b3f2d1f817b7a Author: Weiqun Zhang Date: Fri Nov 30 13:36:34 2018 -0800 add hoextrap to filcc3d Src/Base/AMReX_FilCC_3D_C.cpp commit 223e67a509d4325ada1fb91ec777a720a2d881d6 Author: Tan Nguyen Date: Fri Nov 30 12:00:54 2018 -0800 ref guide for AMFIter Docs/sphinx_documentation/source/Chapter6aa.rst Docs/sphinx_documentation/source/index.rst commit b21ba19363a3b7904cef88c5b6cd2bcaa0574498 Author: Weiqun Zhang Date: Fri Nov 30 11:26:23 2018 -0800 filcc 2d Src/Base/AMReX_FilCC_1D_C.cpp Src/Base/AMReX_FilCC_2D_C.cpp commit 59728376b8df6d3953397a7110ad44498e07a71f Author: kngott Date: Thu Nov 29 16:49:20 2018 -0800 Init and EstTimeDt Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 3bf5d8b14126ba3dc091ab01fbc32ba87620101b Author: kngott Date: Thu Nov 29 16:49:00 2018 -0800 Init and EstTimeDt Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit b848f5689f4d9920500c71e92cdb5c5234b54f82 Author: kngott Date: Thu Nov 29 16:48:41 2018 -0800 Break apart face velocity. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit 13132f838d089941d54b4bf5b25aedcd4b451e1c Author: kngott Date: Thu Nov 29 16:47:09 2018 -0800 Clean up init function. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit 2f59c4138627e5b3301537a5e79a4945e899216a Author: Andrew Myers Date: Thu Nov 29 19:29:44 2018 -0500 add special case early exit to RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 4a629d4f75560f1620dabfe211c66f980cef9f76 Author: Weiqun Zhang Date: Thu Nov 29 15:48:33 2018 -0800 fix bug Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil_1D.cpp Src/Base/AMReX_MultiFabUtil_2D.cpp Src/Base/AMReX_MultiFabUtil_3D.cpp commit cf026a508c996a49490afe3f1f3a16bbf5afa865 Author: Cy Chan Date: Thu Nov 29 14:54:14 2018 -0800 added Backtrace parser script to Tools/Backtrace/ Tools/Backtrace/parse_bt.py commit 5770dff76889fda6969490719df1893127ec87b8 Author: Weiqun Zhang Date: Thu Nov 29 14:02:19 2018 -0800 make gcc on cori knl happy Src/Base/AMReX.H commit 7f815e30aedb1aea8bd3d0afe6987668181c49d1 Author: Weiqun Zhang Date: Thu Nov 29 13:43:55 2018 -0800 remove all fortran codes in EBMultiFabUtil Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/Base/AMReX_MultiFabUtil_nd.cpp Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_EBMultiFabUtil.cpp commit 2939f7ff6c9a45f51283050275502c8c795ba04c Merge: 3f83a4231 3a9783ffc Author: Weiqun Zhang Date: Thu Nov 29 13:31:42 2018 -0800 Merge branch 'development' into weiqun/gpu commit 3f83a4231344d7ef9c93ceedfe7b12fae13fe2e1 Author: Weiqun Zhang Date: Thu Nov 29 13:23:19 2018 -0800 get_loop_bounds -> amrex_get_loop_bounds for the c bind name because it's global Src/Base/AMReX_fort_mod.F90 commit c65a496813d271079151b6d5cbbb89c442966685 Author: Weiqun Zhang Date: Thu Nov 29 13:06:47 2018 -0800 gpu: amrex_avgdown_with_vol Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/EB/AMReX_EBMultiFabUtil.cpp commit 2cbb5a911175f02baafe2eee231e7caefcd864e1 Author: Andrew Myers Date: Thu Nov 29 12:34:56 2018 -0800 start work on making BuildMasks multi-level Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 8e5293a45748cccccc659e0cb3fbf0c3651b6b02 Author: Weiqun Zhang Date: Thu Nov 29 12:16:41 2018 -0800 gpu: amrex_compute_divergence Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 7814aec884a8967da78409a411258bac49ecb9da Author: Weiqun Zhang Date: Thu Nov 29 11:41:00 2018 -0800 gpu: amrex_avgdown and amrex_avgdown_nodes Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 3a9783ffc1541b97198111dd7b67734f5c10a828 Author: Donald Willcox Date: Thu Nov 29 14:33:57 2018 -0500 Integrate to dt/2 then to dt to show example of reinitializing CVODE. Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda_cusolver.cpp commit 332785a5570ef304c147a43c0715593a8aec2b6e Author: Andrew Myers Date: Thu Nov 29 11:30:25 2018 -0800 update Tutorial Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborListMR/main.cpp commit 8155e58910e0ac2c994fe6003d1b54440fc55b95 Author: Andrew Myers Date: Thu Nov 29 11:30:15 2018 -0800 don't make the neighbor particle methods take a lev argument Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit af76352c6fcf2e6545d05a0f699386a5ae917ff3 Author: Weiqun Zhang Date: Thu Nov 29 10:52:10 2018 -0800 gpu: amrex_avgdown_edges Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H commit 74f5fa3b2919da1f7481fe04a639163da15a1939 Merge: 222703fbc d0c3db03f Author: Andrew Myers Date: Thu Nov 29 10:35:38 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 222703fbcdf898ccb31d47e96f399443e115b8b0 Author: Andrew Myers Date: Thu Nov 29 10:35:21 2018 -0800 add new Test for multi-level neighbor lists Tutorials/Particles/NeighborListMR/GNUmakefile Tutorials/Particles/NeighborListMR/Make.package Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborListMR/inputs Tutorials/Particles/NeighborListMR/main.cpp Tutorials/Particles/NeighborListMR/neighbor_list_2d.f90 Tutorials/Particles/NeighborListMR/neighbor_list_F.H commit 70f5ad5da1fdf6b03356073668b89f1e8fb01086 Author: Weiqun Zhang Date: Thu Nov 29 10:33:42 2018 -0800 gpu: amrex_avgdown_faces Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 4d035ec1bf113e5f00809e0876cfe410a1e2227f Author: Andrew Myers Date: Thu Nov 29 10:32:56 2018 -0800 add additional constructor to NeighborParticleContainer Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit d0c3db03f12b6568a4e7292341b6a195e351c330 Author: Weiqun Zhang Date: Thu Nov 29 13:14:47 2018 -0500 make BL_NO_FORT compile Src/Base/AMReX_iMultiFab.cpp commit bacd9a0d99aabad3adb07f09f4cdaf344a1e8bb4 Merge: 3d77c2d8a eb1403f84 Author: Weiqun Zhang Date: Thu Nov 29 09:23:52 2018 -0800 Merge branch 'development' into weiqun/gpu commit 3d77c2d8a498ba64f883b3c7ec75817497c9a60f Author: Weiqun Zhang Date: Wed Nov 28 16:59:02 2018 -0800 Revert "Tutorials/GPU/CNS: fuse launches" This reverts commit 775aee5056e47cd50247f280e10cbd0069c9c90f. Tutorials/GPU/CNS/Source/CNS_advance.cpp commit 775aee5056e47cd50247f280e10cbd0069c9c90f Author: Weiqun Zhang Date: Wed Nov 28 16:25:12 2018 -0800 Tutorials/GPU/CNS: fuse launches Tutorials/GPU/CNS/Source/CNS_advance.cpp commit 6913553acf820cd15c1bb0a80806df9c207dc06f Author: Weiqun Zhang Date: Wed Nov 28 16:24:37 2018 -0800 capability of fusing independent kernels Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H commit eb1403f84bf5768c6a18abd34b557c6cb2fbd1d4 Author: Andrew Myers Date: Wed Nov 28 14:30:10 2018 -0800 remove unused function Src/Base/AMReX_MFIter.H commit 2a70d5953a9831818c15eb0e8a7d431921c2fe9b Author: kngott Date: Wed Nov 28 13:17:05 2018 -0800 cleanup Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp commit 3c32aa4aa643e88b16e458768e19ba3a54f4b5a2 Author: kngott Date: Wed Nov 28 13:16:54 2018 -0800 Ignore TagBox for now. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit bd92538a478e727db6e8dd0468e3b370c3f32555 Author: kngott Date: Wed Nov 28 13:16:00 2018 -0800 Add maxabs to BaseFab. Src/Base/AMReX_BaseFab.H commit 8e1f6638e228153ca11f8f0f7f5acd2a4ea77c00 Author: Cy Chan Date: Wed Nov 28 13:12:53 2018 -0800 some performance analysis updates Src/Base/AMReX_DistributionMapping.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_Machine.cpp commit e935a2d0230ffccb89dd7f4993e88aa5cb3e9ee0 Author: Weiqun Zhang Date: Wed Nov 28 11:59:10 2018 -0800 fix index bug Src/Base/AMReX_MultiFabUtil.cpp commit 35e074ed0413949d496cdde65f75a163cb69638c Author: Weiqun Zhang Date: Wed Nov 28 11:42:22 2018 -0800 renaming Src/Base/AMReX_Box.H Src/Base/AMReX_MultiFabUtil.cpp commit 5986850555d51ccd6bb8f0946d04aa06403cfc0b Author: Weiqun Zhang Date: Wed Nov 28 10:36:43 2018 -0800 turn off simd for debug Src/Base/AMReX_Extension.H commit b6489523615c349b9cfe2fa8af921b16e053016b Author: Weiqun Zhang Date: Wed Nov 28 10:36:25 2018 -0800 fix bug in iMultiFab::sum Src/Base/AMReX_iMultiFab.cpp commit 7ed4eede7f6ce513b25996175be30ba422ba5139 Author: Weiqun Zhang Date: Wed Nov 28 10:28:58 2018 -0800 consolidate functions for casting from one type of fab to another Src/Base/AMReX_BaseFabUtility.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_nd_C.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 161eed763bd62ae71ecd71209a6398bd27e9535e Author: Weiqun Zhang Date: Wed Nov 28 09:55:04 2018 -0800 add iMultiFab::sum to return long Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_nd_C.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit b9a14d5546dee0bf37a067136aba2b4c5969541a Author: Weiqun Zhang Date: Tue Nov 27 23:05:34 2018 -0800 fix bug in case of tiling Src/Base/AMReX_Box.H Src/Base/AMReX_MultiFabUtil.cpp commit b6e71d2d8cff9c2939f05b044c867380fe5113be Merge: 425673b76 98f9a18d6 Author: Weiqun Zhang Date: Tue Nov 27 16:41:16 2018 -0800 Merge branch 'weiqun/gpu' into development commit 98f9a18d6c077ffac0207160ec1da047fdd7b9c2 Author: Weiqun Zhang Date: Tue Nov 27 16:39:59 2018 -0800 gpu: amrex_avg_cc_to_fc Src/Base/AMReX_Box.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H commit 425673b76142d3bd14be7be6aedaa87749974d96 Merge: 858a1ca7e c33dd3c5a Author: Andrew Myers Date: Tue Nov 27 16:33:21 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c33dd3c5a2d46f3fa6bb68361d827599c6265f5f Author: Weiqun Zhang Date: Tue Nov 27 16:28:01 2018 -0800 avoid using omp simd with pgi Src/Base/AMReX_Extension.H commit 42174424dac4f8ac95f7deb539df20c4fcf11470 Author: Weiqun Zhang Date: Tue Nov 27 16:28:01 2018 -0800 avoid using omp simd with pgi Src/Base/AMReX_Extension.H commit 858a1ca7eea9112b6df32dc4431d0ff90f75730f Author: Andrew Myers Date: Tue Nov 27 16:17:35 2018 -0800 make the neighbors and neighbor_list protected Src/Particle/AMReX_NeighborParticles.H commit be85716aeaa293d4bb7b463b4cfd789e950e3207 Author: Andrew Myers Date: Tue Nov 27 16:16:49 2018 -0800 add some accessor functions for neighbors and neighbor lists Src/Particle/AMReX_NeighborParticles.H commit 1704af23aab2dc4204233a4674f4b158330b280b Author: Cy Chan Date: Tue Nov 27 16:12:13 2018 -0800 Add neighborhood cache Add machine model input parameter parsing Add baseline score for neighborhood comparison Src/Base/AMReX.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_Machine.H Src/LinearSolvers/MLMG/AMReX_Machine.cpp commit 218d5ed53c7222595f63f7773adb17c681aa29f5 Author: Cyrus Harrison Date: Tue Nov 27 15:25:01 2018 -0800 add conduit blueprint support for particles Src/Extern/Conduit/AMReX_Conduit_Blueprint.H Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile Tutorials/Blueprint/AssignMultiLevelDensity/main.cpp Tutorials/Blueprint/CellSortedParticles/CellSortedPC.H Tutorials/Blueprint/CellSortedParticles/CellSortedPC.cpp Tutorials/Blueprint/CellSortedParticles/GNUmakefile Tutorials/Blueprint/CellSortedParticles/Make.package Tutorials/Blueprint/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Blueprint/CellSortedParticles/cell_sorted_F.H Tutorials/Blueprint/CellSortedParticles/inputs Tutorials/Blueprint/CellSortedParticles/main.cpp Tutorials/Blueprint/README.txt commit 1661318478bb5d082fb729ee8a3658b512bd98e6 Author: Andrew Myers Date: Tue Nov 27 15:12:08 2018 -0800 add the level to the internal structs used for keeping track of copies Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 0e6d5d45f11ea8370759c9c1ee9eb8aa097a9c48 Author: Weiqun Zhang Date: Tue Nov 27 15:00:48 2018 -0800 fix eb and comp issues in two previous commits Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 98acf69a9cf77d05c28cad4b8ff85190704a22ee Author: Weiqun Zhang Date: Tue Nov 27 14:34:21 2018 -0800 gpu: amrex_avg_fc_to_cc Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_RealBox.H commit b20e6c6b2e934b3efe1297b0cd41ce826b287b78 Author: kngott Date: Tue Nov 27 14:06:14 2018 -0800 Spelling error. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 55b17631bdf14acb116eea9f1a00b50d982df68c Author: Andrew Myers Date: Tue Nov 27 13:26:20 2018 -0800 also keep track of the level information in the mask Src/Particle/AMReX_NeighborParticlesI.H commit 525f2fd3e12fb2549a7e7c348b26b8297fac558b Author: Andrew Myers Date: Tue Nov 27 13:22:21 2018 -0800 use an enum to keep mask comps straight Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 51613d67b0fe83522e9f1f147edd99ebbb87c7df Author: Andrew Myers Date: Tue Nov 27 13:12:37 2018 -0800 BL_ASSERT -> AMREX_ASSERT Src/Particle/AMReX_NeighborParticlesI.H commit 60b6b9caaa4f2ed87e1410f5320128efc5c36ab9 Author: kngott Date: Tue Nov 27 13:12:31 2018 -0800 Adjust for new PhysBCFunct. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 5f7314cbb63e4508b88b2d68fe4f719d20b9b0fc Author: Andrew Myers Date: Tue Nov 27 13:11:14 2018 -0800 some additional regrid functions Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 7374c1845ad9566b4391e1fb576e8a748d429dc8 Author: kngott Date: Tue Nov 27 13:09:03 2018 -0800 DeviceFab -> AsyncFab Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 34c9e668709088ed9626250ea727c91e1de8c4fc Author: Weiqun Zhang Date: Tue Nov 27 13:00:51 2018 -0800 gpu: amrex_avg_eg_to_cc Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H commit 37696df94f38392aa66e55ffef50b095e82fa866 Author: Andrew Myers Date: Tue Nov 27 12:59:24 2018 -0800 minor Src/Particle/AMReX_NeighborParticlesI.H commit 145a358f304070d1ec142942a0819bbf1d6825d9 Author: Andrew Myers Date: Tue Nov 27 12:53:13 2018 -0800 include mask_ptr in the resizeContainers call Src/Particle/AMReX_NeighborParticlesI.H commit 647ec7ccca607aea8011ed947e494a2c6215b215 Author: Andrew Myers Date: Tue Nov 27 12:50:55 2018 -0800 also make the level mask structure multi-level Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 84359ac2dbb98fb025e46e10b441f60bc122fb7e Author: Andrew Myers Date: Tue Nov 27 12:32:01 2018 -0800 fix off-by-one error Src/Particle/AMReX_NeighborParticlesI.H commit a8f0abde115e2d9eaaf312f95416978f5fc9e821 Author: Andrew Myers Date: Tue Nov 27 12:31:46 2018 -0800 fix scoping issue in Tutorial Tutorials/Particles/NeighborList/main.cpp commit 5025167f4a7150dd1471452be49fbb0dc355d459 Author: Weiqun Zhang Date: Tue Nov 27 12:25:13 2018 -0800 fix the call to get Src/Base/AMReX_FabArrayCommI.H commit 52dcac78ada4d441b813876a0a4d9d983d615270 Author: Andrew Myers Date: Tue Nov 27 12:21:46 2018 -0800 remove unused variable Src/Base/AMReX_PhysBCFunct.cpp commit 2f1ca551bc3807d81e632a5bbce2249c3eb3123b Author: Andrew Myers Date: Tue Nov 27 12:18:07 2018 -0800 add call to resize containers to the appropriate size Src/Particle/AMReX_NeighborParticlesI.H commit b3e6e8a36a4d89cccf53340d340f9135e8170486 Author: Andrew Myers Date: Tue Nov 27 12:10:59 2018 -0800 add method for syncing up the size of neighbors and neighbor_list Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 423f1639185ce324797edbf13894e70b7d16b0ef Author: Andrew Myers Date: Tue Nov 27 12:05:38 2018 -0800 remove the fortran version of buildNeighborList Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit e22fb203cb8f3b77ce7728018f6bf56a2bda6291 Author: Andrew Myers Date: Tue Nov 27 12:03:23 2018 -0800 also update the neighbor_list structure for multilevel Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 9e5d32f9353014d03e29bf500209797c25875672 Author: Andrew Myers Date: Tue Nov 27 11:56:20 2018 -0800 update Tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 3445d53662b553bfeadbee22d2ed67d5b54f71e7 Author: Andrew Myers Date: Tue Nov 27 11:55:34 2018 -0800 make the neighbor particle data structure a vector over levels Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 881e74d519892a8e7e1f6ef3bd55864d2f1c30a1 Author: Weiqun Zhang Date: Tue Nov 27 11:54:01 2018 -0800 gpu: amrex_avg_nd_to_cc Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H commit c60bfca40bcc92a439390bdb2a6ced4b3031ef27 Merge: 4910e319b ddf01ba96 Author: Marc Day Date: Tue Nov 27 10:40:16 2018 -0800 Merge pull request #369 from burlen/sensei_init_ghost_zones Sensei init ghost zones commit 4910e319be95dca91be17997552adb359eefa13a Merge: 60588d2d1 8bc68a05c Author: WeiqunZhang Date: Tue Nov 27 10:28:16 2018 -0800 Merge pull request #372 from knutsvk/development use VisIt compatible plotfile heading commit 8bc68a05ce98c067a3f758e5bb2b80863ac63051 Merge: 5433d9588 60588d2d1 Author: knutsvk Date: Tue Nov 27 18:07:40 2018 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5433d9588db554d36cb11a4c82f26235f65ca7a0 Author: knutsvk Date: Tue Nov 27 18:06:14 2018 +0000 use VisIt compatible plotfile heading Tutorials/EB/CNS/Source/CNS.H commit 60588d2d1206151e96684d8fb568e0ec53d88aa6 Author: Johannes Blaschke Date: Mon Nov 26 22:49:33 2018 -0800 fix spelling mistake Src/Base/CMakeLists.txt commit df50c313bbce1203b68ad87b86dc74a52dbcd2a0 Merge: a3c796db7 b8f7450c2 Author: Johannes Blaschke Date: Mon Nov 26 22:22:01 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a3c796db779ce362469fde641190998084c4e811 Author: Johannes Blaschke Date: Mon Nov 26 22:21:56 2018 -0800 coarsen ghost cells as well Src/EB/AMReX_EB_levelset.cpp commit efb81b1d09de3979f511af9aa547b63dbd10e14a Author: kngott Date: Mon Nov 26 17:50:01 2018 -0800 Fix merge error. Src/Base/AMReX_BaseFab.H commit b8f7450c293ea8d0452ec25a64421dfbe107011c Author: Weiqun Zhang Date: Mon Nov 26 17:48:23 2018 -0800 more inline Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H commit 97e4ed5eefb54713df5b7effd25e5d60f7757a90 Author: Weiqun Zhang Date: Mon Nov 26 17:42:43 2018 -0800 MultiFabUtil: fill slice on gpu Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 Src/Base/AMReX_MultiFabUtil_nd_C.cpp Src/Base/AMReX_RealBox.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 65cbb1576a8754d39bc5fadb184997f9c8df62d8 Author: Weiqun Zhang Date: Mon Nov 26 16:09:09 2018 -0800 MultiFabUtil: start gpu Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 Src/Base/AMReX_MultiFabUtil_nd_C.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 213635d6775844d294568646f8c9af8a2e4b91af Merge: 5d4ce9dcd c37f49b21 Author: Weiqun Zhang Date: Mon Nov 26 18:05:32 2018 -0500 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit c37f49b219da98a28d3b44f3ac56f15670dd7117 Merge: ed44f743b 2e7e32e68 Author: Weiqun Zhang Date: Mon Nov 26 14:52:50 2018 -0800 Merge branch 'weiqun/gpu' into development commit 2e7e32e683e3203cf418ce7636c006cca52c126f Author: Weiqun Zhang Date: Mon Nov 26 13:45:58 2018 -0800 remove unused norm0 function Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 5d4ce9dcd4bbae263210024442f46500cafb9874 Author: Weiqun Zhang Date: Mon Nov 26 16:04:50 2018 -0500 cudaMallocHost -> cudaHostAlloc Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CudaDevice.cpp commit 191d4c715f847dc013109884d11bd4c96663d0d4 Author: Cy Chan Date: Mon Nov 26 12:41:14 2018 -0800 added remap neighborhoods to MLLinOp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_Machine.H Src/LinearSolvers/MLMG/AMReX_Machine.cpp Src/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/AMReX_Machine.H Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/inputs Tests/LinearSolvers/MLMG/main.cpp commit cd2f7c0f58f44ed7aa8405224a90619e61fe2a83 Merge: 055ef5b2b 52ee04e9d Author: kngott Date: Mon Nov 26 12:06:18 2018 -0800 Merge branch 'weiqun/gpu' into gpu commit 055ef5b2b717aa6c07342f92d02dfbdbef9c928c Author: kngott Date: Mon Nov 26 12:00:19 2018 -0800 Remove .f90. Now CPU compiling. (WIP). Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.f90 commit c1615e607ea2bef18bbd9b4ddace82e42f0cb7af Author: kngott Date: Mon Nov 26 11:51:50 2018 -0800 First attempt at slope_3d.cpp. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit ed44f743bfcb09aa8c117276d2a91db0a3158ab5 Author: Ann Almgren Date: Mon Nov 26 11:32:41 2018 -0800 Add the brackets between amrex::Initialize() and amrex::Finalize() Tests/HDF5Benchmark/main.cpp commit 1c5e13e81cdec0ba12b0304b400f6764718d4684 Author: Cy Chan Date: Mon Nov 26 10:36:50 2018 -0800 bug fixes and cleanup Tests/LinearSolvers/MLMG/AMReX_Machine.cpp commit 52ee04e9d3d5185992e34b22b6236f1f3ef075cb Author: Weiqun Zhang Date: Mon Nov 26 09:35:37 2018 -0800 change the interface of WriteMLMF to take Vector of MultiFab const* Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit 58646d3278b37b1cd6ff858014c581f479d66bdb Author: Weiqun Zhang Date: Mon Nov 26 08:56:17 2018 -0800 rm iMultiFab norm funcitons Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 1c6606ac457a79403fe6a12c1294da77847f1f5f Author: Weiqun Zhang Date: Mon Nov 26 11:32:40 2018 -0500 make: add USE_CUDA_FAST_MATH so that we could turn off fast math Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 1532d6054a5dcdefb481b93f3d5dd923d8dfae19 Author: Weiqun Zhang Date: Mon Nov 26 11:23:51 2018 -0500 set shared memory bank size Src/Base/AMReX_CudaDevice.cpp commit 3ac5023b4bc5d8504014b17ba40a3d2fd4d75cda Merge: c8012139e b7f54ed1f Author: WeiqunZhang Date: Mon Nov 26 08:09:05 2018 -0800 Merge pull request #273 from Alpine-DAV/task/2018_06_add_blueprint_and_ascent add optional blueprint and ascent support to AMReX commit c8012139ee40261ad0da31f1d19b2d52d31de375 Merge: 6f0792c81 6898aee6f Author: WeiqunZhang Date: Mon Nov 26 08:06:54 2018 -0800 Merge pull request #371 from knutsvk/development MLNodeLaplacian: overload define() with EBFArrayBoxFactory as input commit 6898aee6f836b21cea251388c67eb980f5616f27 Merge: a8052b700 6f0792c81 Author: knutsvk Date: Mon Nov 26 10:44:26 2018 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3a0dabb5b8bf8f7044bf44fcfdda26aa9dce4711 Author: Kaiyuan Hou Date: Sun Nov 25 23:56:27 2018 -0600 remove hdf5 code Tests/HDF5Benchmark/GNUmakefile Tests/PnetCDFBenchmark/GNUmakefile Tests/PnetCDFBenchmark/Make.package Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp Tests/PnetCDFBenchmark/main.cpp commit 8cab06ca66be3c1d96ebb33d453c5227b726cc16 Author: kngott Date: Sun Nov 25 20:03:26 2018 -0800 slope left (WIP). Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package commit 02a9024ea8a6a15d27a5100690096ba79c5f009b Author: kngott Date: Sun Nov 25 19:59:19 2018 -0800 cpp versions Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 6f0792c81782661fa04e758df452b5afbf5c6822 Merge: 9f8303ba4 141666f10 Author: Weiqun Zhang Date: Sun Nov 25 18:18:08 2018 -0800 Merge branch 'weiqun/comm' into development commit 9f8303ba4b32902bca974450e97def9620012382 Author: Tan Nguyen Date: Sun Nov 25 16:42:13 2018 -0800 update destructors for AMFIter related classes Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Pthread_Common/LocalConnection.H commit 141666f108e526ebad2f8caf018b41a8a6cf3fab Author: Weiqun Zhang Date: Sun Nov 25 15:14:30 2018 -0800 fix bug: forgot for after omp parallel Src/Base/AMReX_FabArrayCommI.H commit 12847a471aaae4315ffe246be9a3653222042258 Author: Weiqun Zhang Date: Sun Nov 25 11:28:39 2018 -0800 fix bugs in the new ParallelCopy Src/Base/AMReX_FabArrayCommI.H commit c4f3a77cb90158ab89e43e17c26dd5cab08d926a Merge: 69372fdca 7b357feba Author: Johannes Blaschke Date: Sat Nov 24 22:01:54 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 69372fdca700c154aa3ba03ef2e0893a123ec449 Author: Johannes Blaschke Date: Sat Nov 24 22:01:45 2018 -0800 some cleanup and fixing parameters Src/AmrCore/AMReX_FillPatchUtil.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Tutorials/EB/Donut/Exec/inputs commit ecd7645fecddd8ae75ea498f5b81045afc417c72 Merge: a191785e3 7b357feba Author: Weiqun Zhang Date: Sat Nov 24 21:17:11 2018 -0800 Merge branch 'development' into weiqun/comm commit 7b357feba36aaf0dba217d952aff62fde65e1342 Author: Weiqun Zhang Date: Sat Nov 24 21:14:28 2018 -0800 add scope Tests/LinearSolvers/ComparisonTest/main.cpp commit 7077ee903422fa6af136c7d2fa45288083f688ab Author: Johannes Blaschke Date: Sat Nov 24 21:07:47 2018 -0800 make use of BL_TO_FORTRAN macros Src/EB/AMReX_EB_LSCoreI.H Tutorials/EB/Donut/Exec/inputs commit f6bce80ee9a3d4c1c7f05555bcdcf6d2c77869ea Author: Johannes Blaschke Date: Sat Nov 24 20:28:46 2018 -0800 higher blocking factor Tutorials/EB/Donut/Exec/inputs commit a191785e3b535b1f406ed259a4815a64c33819e2 Author: Weiqun Zhang Date: Sat Nov 24 19:40:04 2018 -0800 update ParallelCopy Src/Base/AMReX_FabArrayCommI.H commit 82f932bcfee120573ee9cad039dac8019893320e Author: Johannes Blaschke Date: Sat Nov 24 18:14:36 2018 -0800 added adaptive mesh around donut Src/EB/AMReX_EB_LSCoreI.H Tutorials/EB/Donut/Exec/inputs Tutorials/EB/Donut/Src/main.cpp commit fa30aa76a1da0d9d523509372d8b101a52658a8e Author: Weiqun Zhang Date: Sat Nov 24 18:11:10 2018 -0800 update FillBoundary Src/Base/AMReX_FabArrayCommI.H commit a6fbd66f7d1da4234fd677311253634ca2c81114 Author: Weiqun Zhang Date: Sat Nov 24 17:03:25 2018 -0800 fix bug: unpacking must be consistent with packing Src/Base/AMReX_FabArrayCommI.H commit eee869a81c46974c498c94871f1da92f259d3653 Author: Weiqun Zhang Date: Sat Nov 24 16:58:55 2018 -0500 wip: fix race condition in ParallelCopy unpacking Src/Base/AMReX_FabArrayCommI.H commit 6cca89f4130cfbaea2894d0aebee9211d8acdaf9 Author: Weiqun Zhang Date: Sat Nov 24 16:07:07 2018 -0500 clean up Src/Base/AMReX_FabArrayCommI.H commit c427998b8b467b9c7579461366e094d142b823eb Author: Weiqun Zhang Date: Sat Nov 24 15:38:45 2018 -0500 split local copy in ParallelCopy into multiple versons Src/Base/AMReX_FabArrayCommI.H commit 40de547ab972f2adbd79cae73de08648e28131f7 Author: Johannes Blaschke Date: Sat Nov 24 12:16:17 2018 -0800 added bite make to donut Tutorials/EB/Donut/Exec/inputs Tutorials/EB/Donut/Src/eb_to_pvf.F90 Tutorials/EB/Donut/Src/main.cpp commit a154ef0b0736c13881f8f7495f1b564bd5eb4fd0 Author: Weiqun Zhang Date: Sat Nov 24 14:41:22 2018 -0500 change operator< for locality Src/Base/AMReX_FabArrayBase.H commit 216f6e6ab1fd7d2fc373f7e27ceca671c9b2022d Author: Weiqun Zhang Date: Sat Nov 24 14:39:35 2018 -0500 print version Src/Base/AMReX.cpp commit 86b5351631e1db31f2531560c5723b4a1d9cc548 Author: Johannes Blaschke Date: Fri Nov 23 23:20:52 2018 -0800 yay this is a donut... but some of the ebgrids are missing :( Tutorials/EB/Donut/Exec/inputs Tutorials/EB/Donut/Src/main.cpp commit edfb23d23c22b834f95921546038d9992aeaeaf1 Author: Johannes Blaschke Date: Fri Nov 23 23:09:12 2018 -0800 added rudimentary inputs file Tutorials/EB/Donut/Exec/inputs commit 79836c5a8b12da60cea5108b21d9611dee33b9d0 Author: Johannes Blaschke Date: Fri Nov 23 23:04:49 2018 -0800 debug donut example Src/EB/AMReX_EB2_IF_Torus.H Tutorials/EB/Donut/Exec/GNUmakefile Tutorials/EB/Donut/Src/Make.package Tutorials/EB/Donut/Src/main.cpp commit f4662aaf5c04590451a3f70ae689a4eacf9adacc Author: Weiqun Zhang Date: Sat Nov 24 01:47:40 2018 -0500 reorder local copy in ParallelCopy Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 254f0c0ed0d88896257f2222e456c6a1cd4aaec7 Author: Johannes Blaschke Date: Fri Nov 23 22:42:16 2018 -0800 make use of BL_TO_FORTRAN macros Tutorials/EB/Donut/Src/main.cpp commit d5601f3052a793399b24e8fc3e5c182591e8fe3a Merge: 10377ee12 7d49e97eb Author: Johannes Blaschke Date: Fri Nov 23 22:34:22 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 10377ee120f955aefeeac9d3d2219c8d908dde1b Author: Johannes Blaschke Date: Fri Nov 23 22:34:15 2018 -0800 start working on donut example Tutorials/EB/Donut/Exec/GNUmakefile Tutorials/EB/Donut/Src/EB_F.H Tutorials/EB/Donut/Src/Make.package Tutorials/EB/Donut/Src/eb_to_pvf.F90 Tutorials/EB/Donut/Src/main.cpp Tutorials/EB/LevelSet/Src/main.cpp commit 7d49e97ebbe2b0d3b29ab511b56031f7bf5502c1 Merge: cda07930c d3ec30436 Author: Weiqun Zhang Date: Fri Nov 23 17:06:15 2018 -0800 Merge branch 'development' into weiqun/gpu commit d3ec3043682ad03ab9c063a45471701150457555 Author: Weiqun Zhang Date: Fri Nov 23 17:02:46 2018 -0800 rm using std::min and std::max Src/Extern/amrdata/AMReX_DataServices.cpp commit 3a31aedf82b30b227f00ac836e741528a3f798b8 Author: Weiqun Zhang Date: Fri Nov 23 17:00:55 2018 -0800 remove start_profiler Src/Amr/AMReX_Amr.cpp commit cda07930c4898d91c9a678372b50e7b508bab4d5 Author: Weiqun Zhang Date: Fri Nov 23 16:04:11 2018 -0800 ifdef cuda specific stuff Src/Base/AMReX_CudaMemory.H commit 5405e9559e5b398c30a36c1619e8595351037366 Author: Weiqun Zhang Date: Fri Nov 23 16:02:17 2018 -0800 gpu reduce in MultiFab Src/Base/AMReX_MultiFab.cpp commit 53053dcee83e4e69cf041af80b02d2d42cae8948 Author: Weiqun Zhang Date: Fri Nov 23 15:38:50 2018 -0800 fix extern shared for templates Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_FabArrayUtility.H commit 0e52972d59f9241cd47c82f3a98ced1d4e516021 Author: Weiqun Zhang Date: Fri Nov 23 14:51:49 2018 -0800 Gpu reduce in iMultiFab. Removed norm functions from iMultiFab. don't think we need them. If they are indeed needed by codes, we will put them back. Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 8aeef50cd914e32e9f52b57cdd46a2d653fcc4a8 Author: Weiqun Zhang Date: Fri Nov 23 14:47:32 2018 -0800 remove init from reduce Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/CNS/Source/CNS.cpp commit fd0af808d81c66deac2c925a0f26fb14667685e7 Author: Weiqun Zhang Date: Fri Nov 23 13:34:46 2018 -0800 add more FabArray reduce and put them in FabArrayUtility Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/CNS/Source/CNS.cpp commit 570f9e7ff41c5030f712cfa8bdd80ee932637346 Author: Weiqun Zhang Date: Fri Nov 23 11:30:09 2018 -0800 add indentation when printing unused parmparse parameters Src/Base/AMReX_ParmParse.cpp commit 314c43e64a131106ab3e39e304d9cf62881be593 Author: Weiqun Zhang Date: Fri Nov 23 11:20:25 2018 -0800 print out a message after initialize and finalize Src/Base/AMReX.cpp commit a8052b7008cc187061651c4aa4c04be81a2fc550 Author: knutsvk Date: Fri Nov 23 14:00:14 2018 +0100 use the ebfactory version of define in the ebfactory version of constructor Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d76df14022fa9e5e1a183b558c4688feaf77457b Author: knutsvk Date: Fri Nov 23 13:54:28 2018 +0100 use c++14 Tools/GNUMake/comps/llvm.mak commit 6e52f7b571f92c39cdc2d9a1aef21c5a52ba16c4 Merge: 5f174ee0a 7d6811caf Author: knutsvk Date: Fri Nov 23 13:53:39 2018 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5f174ee0a55cb46c167461745a5fed86ba0b565c Author: knutsvk Date: Fri Nov 23 13:53:19 2018 +0100 overload define() to work when given EBFArrayBoxFactory instead of FabFactory as input Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5324e8a457cb94c90d245c52ab55c7adfeca1459 Author: Weiqun Zhang Date: Wed Nov 21 21:33:40 2018 -0800 add typename Src/Base/AMReX_FabArray.H commit 287365b7b75eedf3ef301d540451be0b342198c6 Author: Weiqun Zhang Date: Wed Nov 21 20:57:21 2018 -0800 more FabArray::reduce* Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit bc7d54352020990ce4d25e24abaed7ad0729061a Author: Weiqun Zhang Date: Wed Nov 21 19:05:18 2018 -0800 move MultiFab reduction into FabArray templates Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp commit 7d6811caf7cd1be6800a18847d07abb4d30d8d9c Author: Ann Almgren Date: Wed Nov 21 18:49:20 2018 -0800 give more information before aborting Src/AmrCore/AMReX_AmrMesh.cpp commit dcb1401d5637d7c11330d7840d355f17e8510ee0 Author: Weiqun Zhang Date: Wed Nov 21 16:39:23 2018 -0800 Tutorials/GPU/CNS: fast reduction Src/Amr/AMReX_AmrLevel.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp commit fc73948ef7829210048bbb60f64c6a2d6b292015 Author: Weiqun Zhang Date: Wed Nov 21 16:06:22 2018 -0800 add more reduce functions Src/Base/AMReX_CudaReduce.H commit f272cc68a61be9cb3007c214671c3a818918efaf Author: Tan Nguyen Date: Wed Nov 21 13:06:06 2018 -0800 extract metadata after regridding on a non-base AMR level Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AsyncFillPatch.cpp commit 96568cfaebc631f1d9c7dd8e017e15eac18bfb7d Author: kngott Date: Wed Nov 21 12:18:15 2018 -0800 Put changes into Src_3d until 3d and 2d combined. Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.f90 commit 3ff668716381aa3f4d915e07ee81fbfbcbf09667 Author: kngott Date: Wed Nov 21 12:15:03 2018 -0800 Wrap OpenMP pragma. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit b6e4e28f7477014f1b820a2879d85dbdab0606ed Merge: b8241914a 7027401f5 Author: Weiqun Zhang Date: Tue Nov 20 21:01:50 2018 -0500 Merge branch 'weiqun/gpu' into development commit 7027401f5607381901d20c1d2285a46c41d96a15 Author: Weiqun Zhang Date: Tue Nov 20 19:52:13 2018 -0500 back to use device pagable memory Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit b7f54ed1fa3d118356bcf71c934bc2363b643fdf Merge: f6a412b1b b8241914a Author: Cyrus Harrison Date: Tue Nov 20 11:22:35 2018 -0800 Merge branch 'development' into task/2018_06_add_blueprint_and_ascent commit b8241914a423708507954a0771be46418abac297 Author: dwillcox Date: Tue Nov 20 01:47:57 2018 -0500 Clarify CUDA and PGI versions as well as the make command in the Readme. Tutorials/CVODE/SUNDIALS4/EX3-CUDA/README.md commit 62fad37ef1ecb74879b1210497f0a25765220e87 Author: dwillcox Date: Tue Nov 20 01:38:03 2018 -0500 Update call to cv_cuSolver_SetLinearSolver to support additional arguments. Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda_cusolver.cpp commit 0b1275d18317dcc1fc37db13ab38186a0d64ba06 Author: Max Katz Date: Mon Nov 19 22:46:01 2018 -0500 Write out small plotfile in addition to full plotfile Src/Amr/AMReX_Amr.cpp commit 6c05cb3948c24480e79a18b00f69d5a30fd4b9bd Author: Weiqun Zhang Date: Mon Nov 19 15:56:22 2018 -0800 split warpReduceSum into two versions Src/Base/AMReX_CudaReduce.H commit 6a89dcadb9396b9ea219e1d19d44860b0355796b Merge: f61b78ac8 ef6f45eee Author: Weiqun Zhang Date: Mon Nov 19 15:28:49 2018 -0800 Merge branch 'development' into weiqun/gpu commit f61b78ac8c566ca12aa237e0f09ee637a99e6ce4 Author: Weiqun Zhang Date: Mon Nov 19 15:28:02 2018 -0800 preallocate some memory in amrex::Initialize; switch to using pinned memory for cudaMemcpyAsync Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit ef6f45eeed154138153a30abef31abf2eec200f8 Author: Weiqun Zhang Date: Mon Nov 19 10:50:29 2018 -0800 call __syncwarp for volta Src/Base/AMReX_CudaReduce.H commit 23cd99ddc27b1b5a9ea38b38eea01264a48fdc51 Author: Weiqun Zhang Date: Mon Nov 19 10:23:08 2018 -0800 ifdef Src/Base/AMReX_CudaLaunch.cpp commit 0cb37e1aeaf16a4967dbe70fd5e335c7b373c7ed Author: Ann Almgren Date: Mon Nov 19 09:41:34 2018 -0800 AMREX_CudaReduce.H --> AMReX_CudaReduce.H Src/Base/CMakeLists.txt commit d5aaebe623f794b424be322222f937993cd5be4f Author: Weiqun Zhang Date: Mon Nov 19 09:20:17 2018 -0800 Tutorials/GPU/CNS: set USE_CUDA to TRUE by default Tutorials/GPU/CNS/Exec/Sod/GNUmakefile commit f7a7d8637179b4a892932206acf5a6c038a5b270 Merge: 1c5d1e1d2 e18f6904a Author: Weiqun Zhang Date: Mon Nov 19 08:53:16 2018 -0800 Merge branch 'weiqun/gpu' into development commit 927389db6eef77a3ac707e649dfead863cec18c5 Author: kngott Date: Mon Nov 19 01:24:20 2018 -0800 Fix: phi -> psi. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit 1c5d1e1d27b127299d248d24b54344f54ea840a7 Author: Johannes Blaschke Date: Sun Nov 18 22:32:08 2018 -0800 LSCoreBase returns level-set data Src/EB/AMReX_EB_LSCoreBase.H commit e18f6904a7b79877cf85bc09faa93c85655b1e75 Author: Weiqun Zhang Date: Sun Nov 18 21:46:55 2018 -0800 minor Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_MFIter.cpp commit ddf01ba968fd62c6dfcb8341617cee30c4785c86 Author: Burlen Loring Date: Fri Nov 16 12:55:14 2018 -0800 add option to pin mesh this forces mesh origin to 0,0,0. this works around a bug in visit enabling visualization of moving meshes it's off by deault. Src/Extern/SENSEI/AMReX_AmrDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrInSituBridge.cpp Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.cpp Src/Extern/SENSEI/AMReX_InSituBridge.H Src/Extern/SENSEI/AMReX_InSituBridge.cpp commit 2c4868194d35d1506e9bec7b8479afeb70fda599 Author: Burlen Loring Date: Thu Nov 15 04:50:13 2018 -0800 add functions to fill ghost cells in cell centering conversions Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 7745635a6ff976174178be663b148e24f223113f Author: Kaiyuan Hou Date: Sun Nov 18 00:19:45 2018 -0600 single thread Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp commit b7692f02f86fbe8520e07dd97d56a5e4cb0a4dda Author: Johannes Blaschke Date: Sat Nov 17 15:04:48 2018 -0800 add note for macOS users Tools/CMake/AMReX_InstallExternalLibs.cmake commit 01f96627f44f869e6e6d7819c12e6f9155b3a46c Author: Weiqun Zhang Date: Sat Nov 17 13:27:20 2018 -0800 redo reduction in MultiFab::sum Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_MultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 681241e5b72ed01ff37106743720967047824105 Author: Kevin Gott Date: Sat Nov 17 12:28:56 2018 -0800 Begin cpp version of Src Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.f90 commit f7e0342deac5407d6e0c6119ff565d227349fbea Author: Kevin Gott Date: Sat Nov 17 12:26:52 2018 -0800 Adjustments. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit 20d4d4532a20b2e2c31f6dc5f16f59fa6de27b50 Author: Kevin Gott Date: Sat Nov 17 12:25:20 2018 -0800 Clean up face_velocity. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 commit af23e716c8398e8e92570be8ae78bc4246b63e21 Author: Kaiyuan Hou Date: Fri Nov 16 23:50:23 2018 -0600 compile passed Tests/PnetCDFBenchmark/GNUmakefile Tests/PnetCDFBenchmark/Make.package Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.H Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp Tests/PnetCDFBenchmark/inputs Tests/PnetCDFBenchmark/main.cpp commit 74c6f2462571a476d12f48e16915f2249e0d8de6 Author: Johannes Blaschke Date: Fri Nov 16 20:40:15 2018 -0800 enable ls core to read external tag-levels (needed for mfix) Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 0a34e27f6d3d9c4e57848ffb6b47c4664a293e64 Merge: b598d8053 364afd71f Author: Johannes Blaschke Date: Fri Nov 16 19:10:06 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b598d8053d478f7985a0e9d33a1cfc430355cd8f Author: Johannes Blaschke Date: Fri Nov 16 19:09:31 2018 -0800 no longer need to store extra level_set_cc mf vector Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Tutorials/EB/LevelSet/Src/main.cpp commit e6816d454b9a3b7586109eb87b23b26722d784d1 Author: Weiqun Zhang Date: Fri Nov 16 20:44:04 2018 -0500 add some inline Src/Base/AMReX_CudaUtility.H commit 1b825e8c39e633bcb4e4c4e71cfc63a10806a977 Author: Weiqun Zhang Date: Fri Nov 16 16:20:33 2018 -0800 put setComplement on gpu Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxList.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_PhysBCFunct.H commit 364afd71f5daa53770eaf54e73888d3e8d34f199 Author: Andrew Myers Date: Fri Nov 16 14:25:56 2018 -0800 fix makefile logic Tools/GNUMake/comps/pgi.mak commit a316a11474297f18c1e013a5d384e2fa0af7e20c Author: Cy Chan Date: Fri Nov 16 13:24:47 2018 -0800 add local neighborhood calculation Tests/LinearSolvers/MLMG/AMReX_Machine.H Tests/LinearSolvers/MLMG/AMReX_Machine.cpp Tests/LinearSolvers/MLMG/main.cpp commit 4d461681b1f7f3fc49ac456d1d8b8ff9f052e9ed Merge: b00ce98ac d598e3a3c Author: Andrew Myers Date: Fri Nov 16 14:10:20 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b00ce98ac9872b43e5dcf523c9a505a841c6f62c Author: Andrew Myers Date: Fri Nov 16 14:10:12 2018 -0800 fix merge error Tools/GNUMake/comps/pgi.mak commit d598e3a3ce46a590eeb973849835f5b475ec3d2b Author: Johannes Blaschke Date: Fri Nov 16 13:57:29 2018 -0800 get rid of unused variable Src/EB/AMReX_EB_levelset.cpp commit 992757b9f19a86085a4c42aa542bd4b0f8188c0a Merge: 151a1f1d0 6742063eb Author: Andrew Myers Date: Fri Nov 16 13:16:34 2018 -0800 merging commit 151a1f1d07a870b12202219b1b260a7e004995c7 Author: Andrew Myers Date: Fri Nov 16 13:14:27 2018 -0800 turn on c++14 for pgi if the gcc version is new enough Tools/GNUMake/comps/pgi.mak commit 71b71551097e8c58ea519666987428b0a47f067c Author: Andrew Myers Date: Fri Nov 16 12:49:32 2018 -0800 also parse pgi major and minor version numbers in pgi.mak Tools/GNUMake/comps/pgi.mak commit 6742063eb4e27f72b2c87b3ddc7a7ef4fe032264 Merge: 81df91a3f 825e8e1bb Author: Andrew Myers Date: Fri Nov 16 12:04:49 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 81df91a3fd05e71e2d8f065a11c5680f0a9aeb2b Author: Andrew Myers Date: Fri Nov 16 12:04:34 2018 -0800 do not serialize the initial conditions in the HDF5 benchmark Tests/HDF5Benchmark/main.cpp commit 825e8e1bbc4a0259f45a29b7f18bd4f3e6d04df8 Merge: 3f66e38d0 4aeeccd82 Author: Johannes Blaschke Date: Fri Nov 16 10:40:46 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3f66e38d01e50e046d248363e34cc4f0e2d226db Author: Johannes Blaschke Date: Fri Nov 16 10:40:39 2018 -0800 fix pointer pass-by-reference Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_Tagging.F90 Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 4aeeccd8223b9c4cd00777982bd055f912ec143a Author: Michele Rosso Date: Fri Nov 16 09:32:49 2018 -0800 Add absolute tolerance to MAC projector Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 931363df02c9613e25af9bb83fd2c05d6efe9dfb Author: Weiqun Zhang Date: Thu Nov 15 22:58:51 2018 -0800 move the change to libraries to the end of Make.defs Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 39e2b48541fadb9c6afa3f5d43e87543bf469e8f Author: Weiqun Zhang Date: Thu Nov 15 22:53:31 2018 -0800 fix linking with nvcc Tools/GNUMake/Make.rules Tools/GNUMake/comps/nvcc.mak commit a3675430d9635710805c03c86f7266714790089c Author: Cy Chan Date: Thu Nov 15 17:55:13 2018 -0800 performance analysis: added AMReX_Machine.H/.cpp utilities to determine location on machine Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/AMReX_Machine.H Tests/LinearSolvers/MLMG/AMReX_Machine.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/main.cpp commit 24c3033f66a3fb425be7eaede019bdca0fa36908 Author: Weiqun Zhang Date: Thu Nov 15 16:32:10 2018 -0800 respect NVCC_HOST_COMP Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 2d2ac366e0c66226b846befddb9997382c314729 Author: Weiqun Zhang Date: Thu Nov 15 18:03:35 2018 -0500 fix ibm.mak Tools/GNUMake/comps/ibm.mak commit 86e33d764bdf6880b96281d4d7ff43f9777c3c91 Author: Weiqun Zhang Date: Thu Nov 15 14:56:47 2018 -0800 rename for clarity and update make help Tools/GNUMake/Make.rules commit 9301c8eb784190c0529738a2bbaf5160c76e1b28 Merge: dc76962de 989c90b83 Author: Weiqun Zhang Date: Thu Nov 15 14:45:07 2018 -0800 Merge branch 'development' into weiqun/gpu commit 989c90b838042ca14327537b90ad6e7b5bc09284 Merge: 5403edfe1 244a5374d Author: Weiqun Zhang Date: Thu Nov 15 14:44:01 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit dc76962de8ceb9bd5f2d90c98b0c818de2097a77 Author: Weiqun Zhang Date: Thu Nov 15 14:37:35 2018 -0800 add openacc to ignore list Tools/F_scripts/dep.py commit b5dcbd075be89b210fbfc0ab2bbb10d82d862ab2 Author: Weiqun Zhang Date: Thu Nov 15 13:55:56 2018 -0800 modify make so that we can compile with nvcc+gcc without pgi or ibm Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit fff82f1cde2c01671af29024338f26115ce0b0c1 Author: Weiqun Zhang Date: Thu Nov 15 11:30:35 2018 -0800 a bug in make Tools/GNUMake/comps/nvcc.mak commit 495bb2b38fcf31aeafb7c33162f3561c5e53eea2 Author: Weiqun Zhang Date: Thu Nov 15 11:19:27 2018 -0800 add --ptxas-options=-O3 Tools/GNUMake/comps/nvcc.mak commit 5f7e0e25c123f868646c3a8162cf7982755f3fc7 Author: Weiqun Zhang Date: Thu Nov 15 11:18:22 2018 -0800 add comments Tools/GNUMake/sites/Make.unknown commit 244a5374dfcadd27ba0e51c98d19388bef61514a Merge: 149755ad7 b24fd785b Author: Andrew Myers Date: Thu Nov 15 10:18:30 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 149755ad7ee8b75d5cf09d162ff5aa5ba3fc1adb Author: Andrew Myers Date: Thu Nov 15 10:17:52 2018 -0800 whitelist nec compiler as well Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit 481a8d5bbd423e824de2b8bcdcd33c7b10ba0c7b Author: Weiqun Zhang Date: Thu Nov 15 09:47:18 2018 -0800 typo Src/Base/AMReX_CudaDevice.cpp commit 7e65ef96421d8abcc3a327f1b4d21ca7f89cf82d Author: Weiqun Zhang Date: Thu Nov 15 09:46:31 2018 -0800 move openacc stuff into fortran Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_acc_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit b952c36d843e69c9341b357728a156136bc8ddc7 Author: Weiqun Zhang Date: Thu Nov 15 09:23:40 2018 -0800 update script Tools/F_scripts/write_cuda_headers.py commit 1dee311c510843954f5b8850445f56b3c9f48dbe Author: Weiqun Zhang Date: Thu Nov 15 09:00:06 2018 -0800 move the initialiation and finalization of arenas to amrex::Initialize and Finalize so that these arenas will be deleted before cuda shuts down its runtime Src/Base/AMReX.cpp Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit b24fd785bb2138b778f7d67b4c88b6e2fc2dc617 Merge: 1a0fdf0e5 0e3e59bf9 Author: Johannes Blaschke Date: Wed Nov 14 21:44:40 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1a0fdf0e57de03dd5237f98aacc3c3f862de82ee Author: Johannes Blaschke Date: Wed Nov 14 21:44:29 2018 -0800 modernizing ls core tutorial Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 12e2b6257d187045b22f6f66f79b173b0b58b7b0 Author: Weiqun Zhang Date: Wed Nov 14 16:49:30 2018 -0800 migrated fortran function threads_and_blocks Src/Base/AMReX_CudaDevice.cpp commit 6062586795fe10a66bd8857cff7616bb6b3727b9 Author: Weiqun Zhang Date: Wed Nov 14 15:51:14 2018 -0800 remove AMReX_CudaFort.F90 Src/Base/AMReX_CudaFort.F90 Src/Base/Make.package commit 014aac3b699387d2d6e1ab725fa00d662bcf6409 Author: Weiqun Zhang Date: Wed Nov 14 15:50:15 2018 -0800 remove dependence on cuda fortran Src/Amr/AMReX_Amr.cpp Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaFort.F90 Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_fort_mod.F90 commit 0e3e59bf9c2cb9846870d9579d41001a11183b6d Author: Andrew Myers Date: Wed Nov 14 17:42:59 2018 -0500 support ibm compiler for libamrex Tools/GNUMake/Make.rules Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit 9eca4f9b5920505fb247be6a6dc1d50fcf41b69a Author: Guy Moore Date: Wed Nov 14 13:51:42 2018 -0800 fix sphynx error message Docs/sphinx_tutorials/source/AMR_Tutorial.rst Docs/sphinx_tutorials/source/Basic_Tutorial.rst Docs/sphinx_tutorials/source/Tutorials/Tutorials.rst Docs/sphinx_tutorials/source/index.rst commit 3f8fbd5952a0244dd3abd4f7a8abcfb526af57cc Author: Weiqun Zhang Date: Wed Nov 14 13:28:16 2018 -0800 initialize device in C++ Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuError.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/GNUMake/Make.defs commit 9269430f6af19b370879c9040f0110dff529ea55 Merge: 4ae646b24 13839ccba Author: Guy Moore Date: Wed Nov 14 12:30:27 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4ae646b24546608f8df262c350d464261c92d751 Author: Guy Moore Date: Wed Nov 14 12:27:38 2018 -0800 Fixed LaTex equation for building HTML Docs/sphinx_documentation/source/SWFFT.rst commit 13839ccba64a754a06f6674a533fe58770512495 Author: Weiqun Zhang Date: Wed Nov 14 09:00:17 2018 -0800 don't include EB_LSCore* in 2D because it doesn't compile. cmake not fixed Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/Make.package commit 301d001b4e3178b0ec1c461cf1a2e3f012301b47 Author: Johannes Blaschke Date: Wed Nov 14 08:06:39 2018 -0800 update AMReX CMake system Src/EB/CMakeLists.txt commit 6662a685164dba4d91052fb2e5cd5b0593f07903 Author: Johannes Blaschke Date: Tue Nov 13 22:31:16 2018 -0800 LSCore accepts amr parameters during initialization Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit e8ce21a11132840663386dce33361fb2346fcce9 Author: Guy Moore Date: Tue Nov 13 19:56:10 2018 -0800 Updated SWFFT documentation, and moved SWFFT and CVODE documentation into a single chapter titled "External Frameworks" Docs/sphinx_documentation/source/CVODE.rst Docs/sphinx_documentation/source/CVODE_top.rst Docs/sphinx_documentation/source/Chapter14.rst Docs/sphinx_documentation/source/SUNDIALS3.rst Docs/sphinx_documentation/source/SWFFT.rst Docs/sphinx_documentation/source/SWFFT/figs/grid_1x4x2.png Docs/sphinx_documentation/source/SWFFT/figs/grid_2x2x2.png Docs/sphinx_documentation/source/SWFFT/figs/grid_4x1x2.png Docs/sphinx_documentation/source/SWFFT/figs/grid_4x2x1.png Docs/sphinx_documentation/source/SWFFT/figs/grid_4x4x4.png Docs/sphinx_documentation/source/SWFFT/figs/grid_8x8x1.png Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst commit a7c60915d533f55978e970a008ced42bf6e444f1 Author: Johannes Blaschke Date: Tue Nov 13 16:32:49 2018 -0800 store ls checkpoint Src/EB/AMReX_EB_LSCoreBase.H Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit 5403edfe1f9a1af7e4240672d5021d06e76baf8c Author: Weiqun Zhang Date: Tue Nov 13 16:25:16 2018 -0800 some name changes for xSDK Src/Base/AMReX.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaLaunch.H Tools/F_scripts/write_cuda_headers.py commit 26cf216493e22141e1217569a17130d3be91a3a3 Merge: e6cb569f5 13e8e89ec Author: Johannes Blaschke Date: Tue Nov 13 16:20:34 2018 -0800 Merge branch 'development' into jpb/ls-core commit e6cb569f53ebcb2f28546d8b744b879fb93003ef Author: Johannes Blaschke Date: Tue Nov 13 16:19:52 2018 -0800 update inputs Tutorials/EB/LevelSet/Exec/inputs commit baf0e5c43352670ac7ce1abb3f4dc5c1cbd86afb Author: Weiqun Zhang Date: Tue Nov 13 15:33:40 2018 -0800 remove some unused stuff Src/Base/AMReX_BLFort.H Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaFort.F90 commit 13e8e89ec3867625bf925fb6edac1d82bc240b54 Author: Weiqun Zhang Date: Tue Nov 13 14:40:53 2018 -0800 in BndryFuncArray, we need to loop over components Src/Base/AMReX_PhysBCFunct.cpp commit d09c41f3452f33c72de04631af4d6bfd27e5644d Author: kngott Date: Tue Nov 13 13:49:23 2018 -0800 AMREX_RESTRICT non SIMD BaseFab loops. Try dot and sum for now to test. Src/Base/AMReX_BaseFab.H commit 46d920a8e843793fa4873f04cb5e1c2929d11b2a Author: kngott Date: Tue Nov 13 13:07:44 2018 -0800 Clear DeviceFab pointer after use. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit ecf30f6568be4f1be3d2d027e401957973660889 Author: Weiqun Zhang Date: Tue Nov 13 12:45:16 2018 -0800 fix a new bug in PhysBCFunct Src/Base/AMReX_PhysBCFunct.H commit 3ace8106fc8fda2dd42de84042f237e05c834737 Author: Johannes Blaschke Date: Tue Nov 13 11:47:10 2018 -0800 update levelset amr to be compatible with new changes Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 42affd166f379dfb73785dc84611a0467354c3b1 Merge: 2606dd961 56860a708 Author: Johannes Blaschke Date: Tue Nov 13 11:15:25 2018 -0800 Merge branch 'development' into jpb/ls-core commit 56860a7080f63952b30e1aac7a46b8faac0efcdf Merge: 6f0ce3844 2b59ea10d Author: Weiqun Zhang Date: Tue Nov 13 11:14:11 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2b59ea10dda8a2f158393f8034ef0611df07fd84 Merge: 836940d8b 139230c2c Author: Michele Rosso Date: Tue Nov 13 11:13:31 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 836940d8b6561353795ecf0eed49a3e3290ff940 Author: Michele Rosso Date: Tue Nov 13 11:13:22 2018 -0800 Algoim: output runtime info only in debug mode Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit 6f0ce38441d1536c2f6c0ac5c793851174005015 Merge: c4513513c a124074bc Author: Weiqun Zhang Date: Tue Nov 13 10:10:45 2018 -0800 Merge branch 'weiqun/gpu' into development commit c4513513cc83906b7b6691f2eb6ca8ffd5fd8ae9 Merge: 645163829 139230c2c Author: Weiqun Zhang Date: Tue Nov 13 10:08:19 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a124074bc97376d72f7c7b5ff507354cfe5123ee Author: Weiqun Zhang Date: Tue Nov 13 10:07:54 2018 -0800 fix out of bound Src/Base/AMReX_CudaDevice.cpp commit 139230c2c9193a8827459952f315a49d17025d6a Merge: de52e0213 29d1afb48 Author: WeiqunZhang Date: Tue Nov 13 08:51:32 2018 -0800 Merge pull request #366 from AMReX-Codes/SDC cleaning up redundant MG assignments commit 2606dd961bc05f631c871129895020e7388805b0 Author: Johannes Blaschke Date: Mon Nov 12 23:16:02 2018 -0800 Updated fortran subroutine names to match amrex convention Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_bc_fill_nd.F90 commit 9f5872b7d189b371341c8c3b09c028c6423a8c4c Merge: fbcd628b7 de52e0213 Author: Johannes Blaschke Date: Mon Nov 12 22:57:54 2018 -0800 Merge branch 'development' into jpb/ls-core commit fbcd628b7f8b57ef4430e4db7d312fbea3e357dd Author: Johannes Blaschke Date: Mon Nov 12 22:56:30 2018 -0800 clean up Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp Src/EB/Make.package commit 9b45fdf8816a297260958bd7fd8c5001f673e2ea Author: Johannes Blaschke Date: Mon Nov 12 15:14:41 2018 -0800 yay, fixed performance problem Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelDescriptor.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs commit a750223aa2e18b78885b22d54352db574520d573 Author: kngott Date: Mon Nov 12 14:40:51 2018 -0800 Implement deviceFab. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit de52e0213f95c973f854bda0648f0663cebb83af Author: Tan Nguyen Date: Mon Nov 12 14:25:04 2018 -0800 fixing a memory leak bug in the upcxx backend Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.H Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.cpp commit 29d1afb480828792cb81696d5ba80c256bc7ccc2 Author: Lawrence Minion Date: Mon Nov 12 14:12:00 2018 -0800 cleaning up redundant MG assignments Tutorials/SDC/MISDC_ADR_2d/Exec/inputs_2d Tutorials/SDC/MISDC_ADR_2d/README Tutorials/SDC/MISDC_ADR_2d/Source/SDC_sweeper.cpp Tutorials/SDC/MISDC_ADR_2d/Source/main.cpp commit 4cec047ae74d9c5c87950f8e51e97e91e66a2e07 Author: Tan Nguyen Date: Mon Nov 12 13:37:09 2018 -0800 fixing a memory leak bug Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/rts_impls/Perilla/PackageQueue.H Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Pthread_Common/LocalConnection.H Src/AmrTask/rts_impls/Pthread_Common/RGIter.cpp Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.H Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.cpp Src/AmrTask/rts_impls/Pthread_Common/RemoteConnection.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/inputs Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp commit 66e583b6a229cf8eff1a8c47f237111426b1297f Author: Weiqun Zhang Date: Mon Nov 12 12:34:56 2018 -0800 white spaces Src/Amr/AMReX_AmrLevel.cpp commit 37c555f7799f5ea5fd909a5a59c6ad80d98a1f07 Author: Weiqun Zhang Date: Mon Nov 12 12:25:53 2018 -0800 filcc 1D Src/Base/AMReX_FilCC_1D_C.cpp Src/Base/AMReX_FilCC_3D_C.cpp commit f04ac545a884605446d82702400af89a42ecc8dc Author: kngott Date: Mon Nov 12 09:32:39 2018 -0800 c++ version of face_velocity compiles. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 3c40447fd9e067b87db3bfabf43573e196e4f664 Author: kngott Date: Mon Nov 12 09:31:07 2018 -0800 Protect Prob.cpp. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit bd93aa9dccfc888c4c6acfda10d63ea5b66b4f9c Author: Kevin Gott Date: Sun Nov 11 21:50:29 2018 -0800 First attempt at C++ version of face_velocity. Not compile tested. WIP. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit ba96dac22ee09f36dacc9912c7a69be8cf133ae7 Author: Johannes Blaschke Date: Sun Nov 11 17:47:24 2018 -0800 sync wip Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit 216a674a793688347d6bdc921dc1729473a710aa Author: Johannes Blaschke Date: Sun Nov 11 17:15:55 2018 -0800 work on improving performance of multi-level level-set Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFab.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs commit 03b4bc385914062a3464baebbfc70e0afd9f890e Author: Johannes Blaschke Date: Sun Nov 11 13:59:13 2018 -0800 fix problem where eb_padding wil to small... this does not perform well though Src/AmrCore/AMReX_AmrMesh.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs commit ba4a01b0a3be1838f2ee666f5f4507a2bddf80e0 Author: Weiqun Zhang Date: Sun Nov 11 16:54:06 2018 -0500 use functor instead of function pointer so that we can pass user provided function to kernels Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/GPU/CNS/Source/CNS_bcfill.cpp commit 5e9a90d4dc045d737e1239a21948872b7fa9fd1f Author: kngott Date: Sun Nov 11 11:08:50 2018 -0800 Define C version of get_face_velocity. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit 2f7fa5cf220d176eca7ff3dcdbedc7cd2fa9d247 Author: Weiqun Zhang Date: Sun Nov 11 01:00:02 2018 -0500 have to create a local copy of the member variable for the lambda to capture Src/Base/AMReX_PhysBCFunct.cpp commit d8275704d766f98c4e872b5f2c3cff9342862c76 Author: Weiqun Zhang Date: Sat Nov 10 23:13:43 2018 -0500 no need to use mutex in AsynArray anymore because carena has one Src/Base/AMReX_CudaAsyncArray.cpp commit d6c4708803740e47bc939b3bd6ae384e88f25511 Author: Weiqun Zhang Date: Sat Nov 10 23:10:21 2018 -0500 fix mutex in AsyncFab Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit 891df864fc4c0e5209698d1157792ca5a8b9659d Author: Weiqun Zhang Date: Sat Nov 10 22:57:47 2018 -0500 mutex in CArean Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit 9284aa8120d8fe07dbcaea24d300701528ed6ae2 Author: Weiqun Zhang Date: Sat Nov 10 22:47:27 2018 -0500 avoid using fab.box() in assertion Src/Amr/AMReX_StateData.cpp commit cbca02b9656ec0dda83d7bb22c4c78304551af4f Author: Weiqun Zhang Date: Sat Nov 10 22:46:21 2018 -0500 comment out set nan on gpu for now. will move it to multifab in the future. Src/Base/AMReX_FArrayBox.cpp commit 3d82ea9529f5d193a9ee94a70711a7b1159d48fc Author: Weiqun Zhang Date: Sat Nov 10 19:13:41 2018 -0500 StateData: option to fill domain bc on gpu Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_FilCC_3D_C.cpp Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp commit aa2cb3b7ccae91ef9ce043e3523c18b8e9ee2f83 Author: Weiqun Zhang Date: Sat Nov 10 16:53:49 2018 -0500 first pass of filcc in 3d w/o high-order extrapolation Src/Base/AMReX_FilCC_3D_C.cpp commit d702c2078e00f75f5ecd09b51dfe313d1f2713b0 Author: Johannes Blaschke Date: Sat Nov 10 13:34:27 2018 -0800 going to nodal level-set Src/AmrCore/AMReX_AmrMesh.H Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_Tagging.F90 commit bf68bb5eeefdd16fb61a5d0cca677b3f9aae3414 Author: Weiqun Zhang Date: Sat Nov 10 16:21:23 2018 -0500 inline some BCRec functions Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit 5131f12f2777e643a10e67e8ca14bb1bfdc41286 Author: Weiqun Zhang Date: Sat Nov 10 01:27:04 2018 -0500 more work on GpuBndryFuncFab Src/Base/AMReX_FilCC_1D_C.cpp Src/Base/AMReX_FilCC_2D_C.cpp Src/Base/AMReX_FilCC_3D_C.cpp Src/Base/AMReX_FilCC_C.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 4ebf5a62b1b475468e2d959b7e03e4cd031fe4f1 Author: Weiqun Zhang Date: Sat Nov 10 00:12:02 2018 -0500 add ___host__ __device__ to BCRec Src/Base/AMReX_BCRec.H commit b9d825e25fdec9499f40611eb09ac55fe155c388 Author: Weiqun Zhang Date: Fri Nov 9 23:53:45 2018 -0500 make sure nvcc use the same std version as gcc in case gcc version > 5 Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/nvcc.mak commit 2cc5bd3432c52a2f93b937f4a8f41365c5986925 Author: kngott Date: Fri Nov 9 19:48:40 2018 -0800 Define new initprob and change implementation. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit c18a5a31516b46ea4670da5d1c33d30dd28820af Author: kngott Date: Fri Nov 9 19:46:47 2018 -0800 Update make system. Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv Tutorials/GPU/Advection_AmrCore/Source/Make.package commit da72b81451b36fa1b8c85f594249760c2d6cf7e1 Author: kngott Date: Fri Nov 9 19:31:52 2018 -0800 C++ version of Prob Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.f90 commit 93bc1a8d1196b798dca948fe7b321e4c9521e4c1 Author: kngott Date: Fri Nov 9 19:27:16 2018 -0800 Remove exec. Tutorials/GPU/Advection_AmrCore/Source/a.out commit 4f786e3a8598480c20ea8f7148b3af1b2cf48af1 Author: Andrew Myers Date: Fri Nov 9 16:46:44 2018 -0800 use --std=c++14 when using gcc as the host compiler if the gcc version is new enough Tools/GNUMake/comps/nvcc.mak commit dc20014e5ed82974225e11f5657132b7a65c17cb Author: Johannes Blaschke Date: Fri Nov 9 15:19:04 2018 -0800 sync wip while debug Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs commit 5c302080b5cfdef3343cffcc1d1add944403afb9 Author: Weiqun Zhang Date: Fri Nov 9 14:23:13 2018 -0800 GpuBndryFuncFab WIP Src/Base/AMReX_PhysBCFunct.cpp commit 2642312a28662b1c1534fbf34596d67a72076e20 Merge: 7230b398f e0d4403c1 Author: Andrew Myers Date: Fri Nov 9 14:00:04 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 520eb6f0ded91f75d690748808bf4fc22275bb04 Author: Weiqun Zhang Date: Fri Nov 9 13:54:31 2018 -0800 some work on CpuBndryFuncFab Src/Amr/AMReX_StateDescriptor.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp commit 7230b398f44968a1f1eafe52892b41b1343975ca Author: Andrew Myers Date: Fri Nov 9 13:33:06 2018 -0800 correct neighbor size in NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 894a26aeaba6d4e8f6cae2cd51cb11face8a9535 Author: Andrew Myers Date: Fri Nov 9 13:10:55 2018 -0800 switch the neighbor list structure to use ParticleType instead of char Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 7e05e67e640c307279364e99a3945b1e552e47f5 Author: Andrew Myers Date: Fri Nov 9 13:08:01 2018 -0800 remove neighbor_t from the NeighborList tutorial Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit 5d698f830eaedc3e92e7b86a0e8628a65849a9ec Author: Weiqun Zhang Date: Fri Nov 9 10:08:01 2018 -0800 add default constructor for StateDescriptor::BndryFunc Src/Amr/AMReX_StateDescriptor.H commit 8c6654f13ef82c244bd51e00e8fefdf11fa94924 Author: Weiqun Zhang Date: Fri Nov 9 09:50:52 2018 -0800 clean up Src/Amr/AMReX_StateDescriptor.H Src/AmrCore/AMReX_AmrParticles.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit fca63428c271d9bfa11b7145d438e3914133bc13 Merge: ed068ed15 645163829 Author: Weiqun Zhang Date: Fri Nov 9 08:40:31 2018 -0800 Merge branch 'development' into weiqun/gpu commit 6451638295dbb15766039fc440650905e66da801 Merge: 2400749ea e0d4403c1 Author: Weiqun Zhang Date: Fri Nov 9 08:37:18 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b2c847ac8de1d9601669269712b1ca7e6081041e Author: Johannes Blaschke Date: Thu Nov 8 22:51:12 2018 -0800 yay! level-sets Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit d91e6bdae9aeca1d657f36977648111548b5012a Author: Johannes Blaschke Date: Thu Nov 8 21:53:13 2018 -0800 split basic amr core behaviour and specialized eb-geometry Src/AmrCore/AMReX_AmrCore.H Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_bc_fill_nd.F90 Src/EB/Make.package Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit ed068ed159b290507fd4c2907feeec42e064e7ce Author: Weiqun Zhang Date: Thu Nov 8 21:51:54 2018 -0800 update due to change in FillPatch Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_AmrParticles.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_FPhysBC.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Doc/references.bib Tutorials/Amr/ScalarAdvectionDiffusion/Doc/working_notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv.Diff Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs.tracers Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/probin Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/debug.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.2d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.3d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probdata.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probin Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probdata.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probin Tutorials/Amr/ScalarAdvectionDiffusion/README Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugDump.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/LevelBldAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Adv_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/tagging_params.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/fourthOrderCFInterpTest.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/test.inputs Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_mpi_driver.py Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py Tutorials/Particles/ElectrostaticPIC/main.cpp commit 62238fcd6a45ad8dcfe7f963c0200cf257bbdd35 Author: Johannes Blaschke Date: Thu Nov 8 20:24:12 2018 -0800 LSCore needs to be a template class (so that it can hold gshop objects) .gitignore Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H commit e0d4403c13e952ea50d2b43b111842ed5ae2b16b Author: Ann Almgren Date: Thu Nov 8 18:07:51 2018 -0800 Fix error statements to correctly reflect the routine they're from Src/Particle/AMReX_ParticleContainerI.H commit 8f81d49d7e114dde3cf571c054c6ab726f3495f7 Author: Weiqun Zhang Date: Thu Nov 8 16:45:05 2018 -0800 Redo the FillPatch interface. The change is not backward compatible for AmrCore based codes that use FillPatch Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 5a5fdfc2117756e82a080547a5ad349cf322091f Author: Johannes Blaschke Date: Thu Nov 8 13:57:40 2018 -0800 sync wip Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCore.cpp commit 589e8326270086d33049bd8d3b875d4d4eea33c7 Author: Kevin Gott Date: Thu Nov 8 16:23:19 2018 -0500 AdvCore added to Tutorials/GPU and being worked on. Tutorials/GPU/Advection_AmrCore/CMakeLists.txt Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.f90 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/GPU/Advection_AmrCore/README Tutorials/GPU/Advection_AmrCore/README_SENSEI.md Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 Tutorials/GPU/Advection_AmrCore/Source/a.out Tutorials/GPU/Advection_AmrCore/Source/bc_fill_nd.F90 Tutorials/GPU/Advection_AmrCore/Source/main.cpp commit 921aa68296411b9b94bea79de8ab2194bf253024 Author: Kevin Gott Date: Thu Nov 8 16:22:14 2018 -0500 fix .x issue Src/Base/AMReX_COORDSYS_2D.cpp commit c41e57a74b5ce5eb40e3407b71d3b748ecc11fb5 Merge: 7e5bf5a24 48c89300c Author: Johannes Blaschke Date: Thu Nov 8 10:20:00 2018 -0800 Merge branch 'development' into jpb/ls-core commit 48c89300cb7eb6ee80c58b966413dcef153d490d Merge: 2d6d876fa bbcca5e8d Author: WeiqunZhang Date: Thu Nov 8 09:32:11 2018 -0800 Merge pull request #362 from AMReX-Codes/f2py-microphysics Add compile flags for building a code using the AMReX build system as an f2py library commit 7e5bf5a241b9eb92530acbbe36ee70828b5bb7bc Author: Johannes Blaschke Date: Wed Nov 7 21:16:15 2018 -0800 added first pass at AMR for level-set Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCore.cpp Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_bc_fill_nd.F90 commit b6af74e3774537b4cc66a37036082f39a21d8a79 Author: Weiqun Zhang Date: Wed Nov 7 21:15:03 2018 -0800 DeviceFab -> AsyncFab Src/Base/AMReX.cpp Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaFab.H Src/Base/AMReX_Gpu.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/AsyncFab/GNUmakefile Tests/GPU/AsyncFab/Make.package Tests/GPU/AsyncFab/main.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit e993a388e508359bbc9c55baf310fc37ca827142 Author: Weiqun Zhang Date: Wed Nov 7 21:03:27 2018 -0800 fix bug in CudaAsyncArray Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp commit 2d6d876fa68e3a7310bf7d57a9a34234a11d0354 Merge: 3e352a3a1 157ec60a5 Author: Johannes Blaschke Date: Wed Nov 7 20:55:53 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3e352a3a1c339b8bfd1880e7f6277c3b02802014 Author: Johannes Blaschke Date: Wed Nov 7 20:54:48 2018 -0800 these aren't needed after all Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 157ec60a565ef66c8a6ae9115c9b0e77e4d863a4 Merge: 1689fedb8 4cc74b6f6 Author: Michele Rosso Date: Wed Nov 7 17:26:58 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1689fedb8be006ab6bc4031471bcfae6f4615108 Author: Michele Rosso Date: Wed Nov 7 17:26:23 2018 -0800 CMake: add hack to compile blitz on nersc machines Tools/CMake/AMReX_InstallExternalLibs.cmake commit bbcca5e8d1d450445808d4091df615c8d8cbfd9d Author: Donald E. Willcox Date: Mon Oct 22 21:59:11 2018 -0700 Support for building StarKiller Microphysics as a library with f2py. WIP support for building StarKiller Microphysics as a library with f2py. Add default setting USE_COMPILE_PIC?=FALSE Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/gnu.mak commit 0378e2e7bb3e476f672ac97e47d7aceb9b1bf901 Author: Michele Rosso Date: Wed Nov 7 17:01:11 2018 -0800 CMake: fix mispelled variable Tools/CMake/AMReX_Machines.cmake commit 2400749ea351353c9aba2cae87e5711f6560c2cd Author: Weiqun Zhang Date: Wed Nov 7 17:00:07 2018 -0800 Gpu::AsyncArray Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_Gpu.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/CNS/Source/CNS_bcfill.cpp commit 4cc74b6f6bdee3db88ebc22b9e450d7e276861b7 Merge: 2cb5fbbd2 afc57e26d Author: Johannes Blaschke Date: Wed Nov 7 15:46:35 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4480374724ff0010688c2cd805376ab5b8883565 Author: Weiqun Zhang Date: Wed Nov 7 14:57:46 2018 -0800 new bndry fill function in StateData Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_BCRec.cpp commit 2cb5fbbd2569442d6340f9fab063b7078c5ce9d5 Author: Johannes Blaschke Date: Wed Nov 7 14:09:09 2018 -0800 added FillPatch operations for constant-in-time MFs Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 39f2c54ec9c65aa8c0a252db84efa032d62bbd04 Author: Kevin Gott Date: Wed Nov 7 17:07:48 2018 -0500 protected_divide with zeros BaseFab test. Tests/BaseFabTesting/main.cpp commit 368f0ac66f691ea82d4e88a398e97092fd89802c Author: kngott Date: Wed Nov 7 13:38:16 2018 -0800 Convert remaining stridedPtr to FabView. Src/Base/AMReX_COORDSYS_1D.cpp Src/Base/AMReX_COORDSYS_2D.cpp Src/Base/AMReX_COORDSYS_3D.cpp Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EB2_GeometryShop.H commit b7d5b539263e518247847b07370e99db2f2af52b Author: Kevin Gott Date: Wed Nov 7 15:53:21 2018 -0500 Merge errors. Src/Base/AMReX_BaseFab.H commit ef32672a25c20d0e50e38f0f202ebbb5aca07fef Merge: 8a66b2ed1 cd88e66c4 Author: Kevin Gott Date: Wed Nov 7 15:32:54 2018 -0500 Merge branch 'weiqun/gpu' into gpu Conflicts: Src/Base/AMReX_BaseFab.H commit cd88e66c447964a6006728f39a4b15806c170f9a Author: Kevin Gott Date: Wed Nov 7 15:30:28 2018 -0500 BaseFab with FabView. Src/Base/AMReX_BaseFab.H commit afc57e26d93cfed07ae622f42950f2a905154aae Merge: 278be0da1 052a1912e Author: Andrew Myers Date: Wed Nov 7 12:09:49 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 278be0da114a97cdf9180ed73907abad9690803e Author: Andrew Myers Date: Wed Nov 7 12:09:33 2018 -0800 when running with CUDA, construct the neighbor on the host, then copy it into managed memory. Src/Particle/AMReX_NeighborParticlesI.H commit 052a1912e284ade8dd57bdee86b9b35b6ccb7ccd Author: Weiqun Zhang Date: Wed Nov 7 14:24:45 2018 -0500 fix set_covered for nodal Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H commit ad91fa40a76c8f29171f6a0bddf782cd3957d7f0 Merge: 5ddfcf284 656bf0073 Author: Andrew Myers Date: Wed Nov 7 14:00:10 2018 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5ddfcf28403c075ec58e9f19d3e183a61a73f3c9 Author: Andrew Myers Date: Wed Nov 7 13:59:43 2018 -0500 remove uneccesary casts from these thrust calls. Src/Particle/AMReX_ParticleContainerI.H commit cffccd5ee946a03457b3494877be941a11029317 Author: Andrew Myers Date: Wed Nov 7 13:32:15 2018 -0500 prettify thrust calls Src/Particle/AMReX_ParticleContainerI.H commit 656bf007387dde4f5d337c59e217012f9ce7ba27 Author: Weiqun Zhang Date: Wed Nov 7 13:31:33 2018 -0500 setVal: return if Box is not ok. This is the traditional behavior Src/Base/AMReX_BaseFab.H commit 5c4a95ea5cf0746a00a6c7e76ef46d4ad4da27b7 Merge: e57ab30cd 696793a25 Author: Weiqun Zhang Date: Wed Nov 7 09:07:17 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 696793a25c52fcc1d15c7c6d5851a838738cc380 Author: Weiqun Zhang Date: Wed Nov 7 09:06:33 2018 -0800 fix omp Src/Base/AMReX_MultiFab.cpp commit 94868ad6070836834234ae6d94b55ab0d53cfd5d Author: Weiqun Zhang Date: Wed Nov 7 08:53:26 2018 -0800 include cmath Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Torus.H commit e57ab30cdc6601ad94f0820e0800e4356d3bf8ae Author: Weiqun Zhang Date: Wed Nov 7 08:51:46 2018 -0800 include cmath Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Torus.H commit 7e84b9446f645a814eff111cef10b51fccb6f67d Merge: f753145ca 4ef56b859 Author: Weiqun Zhang Date: Wed Nov 7 07:18:14 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4ef56b859a1c0ff96f9c50758c834bf68439e2d2 Author: Ann Almgren Date: Wed Nov 7 06:51:44 2018 -0800 sqrt --> std::sqrt Src/EB/AMReX_EB2_IF_Torus.H commit 480615462d8c6490b6a2dc5ebf49e91a14b8521e Author: Tan Nguyen Date: Wed Nov 7 02:40:10 2018 -0800 fixing a memory leak bug Src/Amr/AMReX_AmrLevel.cpp commit 4648de6723b8346b77e8b5232e68146871801446 Author: Tan Nguyen Date: Wed Nov 7 02:24:05 2018 -0800 fixing a few memory leak bugs Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit 1527a835783221623c68f7a249df0e55dce60065 Merge: 96c62cf90 5fc026813 Author: Ann Almgren Date: Tue Nov 6 17:45:45 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 96c62cf90e52fe13d0a80f91ea48a2f44d846aef Author: Ann Almgren Date: Tue Nov 6 17:45:22 2018 -0800 Add torus Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF_Torus.H Src/EB/Make.package commit 5fc0268137e1dce781ed2a0e687d6719c55da57e Merge: 4e0870f5c 1abf13141 Author: Michele Rosso Date: Tue Nov 6 17:37:55 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4e0870f5c2d038844d9c885b6dec1d67dfdc1e73 Author: Michele Rosso Date: Tue Nov 6 17:37:49 2018 -0800 CMake: update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst commit 1c1596f418ec375b2be8056dce5238cfba05142c Author: Michele Rosso Date: Tue Nov 6 17:25:36 2018 -0800 Cmake: implement small improvements Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit f753145caa7d153dbd44052ea483e319f18134c6 Author: Weiqun Zhang Date: Tue Nov 6 17:12:24 2018 -0800 add Fab version of Bndry Func Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package commit 266b16903c2288daacfcacbce56cfa820e50a68a Author: Michele Rosso Date: Tue Nov 6 16:53:56 2018 -0800 CMake: add support for 3D nodal projection. Add support for Algoim and Blitz libraries if nodal projection is required. CMake will download and install these libraries if no installation paths is given for them. CMakeLists.txt Src/CMakeLists.txt Src/Extern/Algoim/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake Tools/CMake/AMReX_Options.cmake commit 6475a69c8424e3731a5a0c4f9cbdeb4266a986b4 Author: Michele Rosso Date: Tue Nov 6 16:49:26 2018 -0800 CMake: refactor CMakeLists hierarchy in Extern subdir Src/CMakeLists.txt Src/Extern/CMakeLists.txt Src/Extern/ProfParser/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt commit 1abf13141b8a223dd267efcf493bf4de7b99eb4d Author: Weiqun Zhang Date: Tue Nov 6 14:36:15 2018 -0800 remove some unused print functions Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_PhysBCFunct.cpp commit 07330e81f3af4f20cd540306016f10fd50684dd1 Author: Weiqun Zhang Date: Tue Nov 6 14:07:13 2018 -0800 fix a bug in StateData FillBoundary Src/Amr/AMReX_StateData.cpp commit d3b48480666eeaec5691be2febc1a6572e51ce1b Author: Weiqun Zhang Date: Tue Nov 6 12:52:32 2018 -0800 fix omp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_MultiFab.cpp Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 commit e8eb1251d9019e2bbc6b0a084f691a81b886751e Author: Kevin Gott Date: Tue Nov 6 15:31:56 2018 -0500 First draft of GPU minIndex and maxIndex. Needs atomic IntVect assignment to complete thread-safety. Src/Base/AMReX_MultiFab.cpp commit 9a601bd32f68b9dabb943cd8cc6873790fa2a468 Author: Kevin Gott Date: Tue Nov 6 15:29:27 2018 -0500 Change DeviceScalar from is_pod to is_trivially_copyable. Src/Base/AMReX_CudaMemory.H commit d4154d60b8f9c27cc4c545a71cee9b6beb1cd877 Author: Kevin Gott Date: Tue Nov 6 15:28:49 2018 -0500 BaseFab::indexFromValue. Need tolerance checking. Src/Base/AMReX_BaseFab.H commit 970e5649b8d6cb5023dd1105abe6de79d3de3933 Author: Kevin Gott Date: Mon Nov 5 19:37:26 2018 -0500 Thin wrapper around thrust::copy. Src/Base/AMReX_CudaContainers.H commit 9aa1c559f82d3878fd29aacb8e4fd407954fdbc3 Author: Kevin Gott Date: Mon Nov 5 18:54:14 2018 -0500 Cuda -> Gpu & first attempt at minIndex. Src/Base/AMReX_MultiFab.cpp commit c8efaca8355b05c599971f0d278b34b68fb8437e Author: Kevin Gott Date: Mon Nov 5 13:12:35 2018 -0500 Remaining norm Multifab funcs outlined. Won't compile with USE_CUDA=FALSE until thrust::copy is wrapped. Src/Base/AMReX_MultiFab.cpp commit 90d0f2c358b136194366f1717aef280d996b4cad Author: Weiqun Zhang Date: Tue Nov 6 10:52:19 2018 -0800 use amrex::min and max Src/Base/AMReX_Utility.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 62ca4039c4eb9ac9769bebc857ea3626bf6c0c83 Merge: e125a7593 8a66b2ed1 Author: Weiqun Zhang Date: Tue Nov 6 09:55:14 2018 -0800 Merge branch 'gpu' into development commit e125a75934e3819c668eb1f731e6471fb25f7457 Merge: 35dd527c2 27cc2ebfb Author: WeiqunZhang Date: Tue Nov 6 09:38:39 2018 -0800 Merge pull request #356 from AMReX-Codes/SDC Sdc commit 35dd527c2a5d6df11c30cfb14f1bbd647cf7d312 Author: Andrew Myers Date: Mon Nov 5 18:31:53 2018 -0800 missed a few. Tools/Postprocessing/C_Src/fcompare.cpp commit 20ca7d5725807ac9d28ab7a2a373318a4f7377e5 Merge: 0db027a65 86beaeb50 Author: Andrew Myers Date: Mon Nov 5 18:27:40 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0db027a65383317601e9bec40c565020182bd8a9 Author: Andrew Myers Date: Mon Nov 5 18:27:21 2018 -0800 specifiy amrex::min and amrex::max Tools/Postprocessing/C_Src/fcompare.cpp commit 86beaeb50b73367f9aec6bba3460c850f6c4b163 Author: Ann Almgren Date: Mon Nov 5 17:56:17 2018 -0800 print out the maximum discrepancy in volume fraction but don't abort when the volume fraction or centroids don't match. Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit 8a66b2ed1f59bd676e26d57a4a9e7ec53588e4e3 Author: Weiqun Zhang Date: Mon Nov 5 16:08:53 2018 -0800 bug fixes Src/Base/AMReX_BaseFab.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 27cc2ebfb8c3946f61277e3c33970ee9bab45547 Merge: 6ff294752 d9ba6482f Author: Minion Date: Mon Nov 5 14:58:55 2018 -0800 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit 6ff294752c60571cf293e6b0779d1dff41417c98 Author: Minion Date: Mon Nov 5 14:57:43 2018 -0800 fixing size of quad matrices Src/SDC/AMReX_SDCstruct.cpp commit 7849aeef9a58058eac20aa99d677cc17e0563280 Author: Weiqun Zhang Date: Mon Nov 5 14:54:19 2018 -0800 fix bound checking Src/Base/AMReX_BaseFab.H commit 1ab045832bfc6997894b2185c0439b6107df3998 Merge: f6640d572 396cf411e Author: Ann Almgren Date: Mon Nov 5 14:36:32 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit f6640d5729429dd2889a1634fd9dc0cb75b1b611 Author: Ann Almgren Date: Mon Nov 5 14:36:24 2018 -0800 Fix typos in comments Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 396cf411e231d73e0c66a92d705149b838c1fe8f Author: Andrew Myers Date: Mon Nov 5 16:50:02 2018 -0500 and use the new utility functions in the getParticleTile function Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_ParticleUtil.cpp commit 5cff8b641a72ac78bba27343b62ac479d4d3404b Author: Andrew Myers Date: Mon Nov 5 16:49:23 2018 -0500 add min and max utility functions that work in both host and device code Src/Base/AMReX_Utility.H commit 71c7c23a7856fb9f53b9989a8262d2c28f258ba0 Author: Weiqun Zhang Date: Mon Nov 5 13:43:18 2018 -0800 ostream for Dim3 Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit 7dbdea31990e192644286fa88a26278c4806b563 Author: Weiqun Zhang Date: Mon Nov 5 13:38:32 2018 -0800 Riemann solver and reset eint Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit d9ba6482f59029626061df80b8771e869172754e Merge: fbcda5bbb 559cb7099 Author: Lawrence Minion Date: Mon Nov 5 12:07:59 2018 -0800 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit fbcda5bbbf7a477b433650a08f579007cd1a35bd Author: Lawrence Minion Date: Mon Nov 5 12:06:56 2018 -0800 removing outdated example Tutorials/Basic/SDCAdvDiffusion_C/Exec/.#advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Exec/GNUmakefile Tutorials/Basic/SDCAdvDiffusion_C/Exec/inputs_2d Tutorials/Basic/SDCAdvDiffusion_C/Source/Make.package Tutorials/Basic/SDCAdvDiffusion_C/Source/advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/advance_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_3d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/inputs_3d Tutorials/Basic/SDCAdvDiffusion_C/Source/main.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc.H Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc_F.H Tutorials/Basic/SDCAdvDiffusion_C/Source/pf_quadrature.f90 commit 4b10e6cde42032343633f328ca97451c2da68874 Author: Weiqun Zhang Date: Mon Nov 5 11:22:47 2018 -0800 GPU/CNS: slopes Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit cc698315696eacde71ac9c4b4563f0c7f4554537 Author: Ann Almgren Date: Mon Nov 5 09:45:36 2018 -0800 Update the ALGOIM stuff to be in AMReX namespace and change the convention so ALGOIM_HOME points to the external Algoim directory. Src/Extern/Algoim/AMReX_algoim_integrals.H Src/Extern/Algoim/AMReX_algoim_integrals.cpp Src/Extern/Algoim/Make.package Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/GNUmakefile Tests/LinearSolvers/NodeEB/MyTest.cpp commit 4db7d9076d6940b0d83f51cd1bd1be04c8622e1f Author: Weiqun Zhang Date: Sun Nov 4 17:55:41 2018 -0500 add Dim3 struct and this helps pgi in vectorization Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H Tests/Vectorization/kc.H commit 03da503f09d2a91c7c5ab5d2f560a20c242922af Author: Weiqun Zhang Date: Sun Nov 4 17:19:27 2018 -0500 use the correct pragma for pgi Src/Base/AMReX_Extension.H commit bfea64a2b853e85343a86eef8063c625cd98efd5 Author: Weiqun Zhang Date: Sun Nov 4 13:13:56 2018 -0800 minor tweak Tests/Vectorization/kc.H commit 9b8478d68633dd4542f2d69fcd7547e7f62c0612 Author: Weiqun Zhang Date: Sun Nov 4 11:04:28 2018 -0800 use FabView Tests/Vectorization/kc.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_index_macros.H Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 4507c0d643e73538c917730564cc29de8f7c20d6 Author: Weiqun Zhang Date: Sun Nov 4 13:37:57 2018 -0500 rewrite ctoprim Tests/Vectorization/kc.H commit e46edc98424401e496ffd19ca2611cbd0139a6db Author: Weiqun Zhang Date: Sat Nov 3 21:19:46 2018 -0700 use the new version Tests/Vectorization/kc.H commit 75f55ac6e98cd8d14adad496bbd5ae8d7eaa05bb Author: Weiqun Zhang Date: Sat Nov 3 21:16:32 2018 -0700 FabView: clean up and add bound checking in debug Src/Base/AMReX_BaseFab.H commit 847eed93191f974b07a99bb33d930fb7694a54cf Author: Weiqun Zhang Date: Sat Nov 3 16:48:27 2018 -0700 fix intel deprecaion warning Src/Base/AMReX_Extension.H commit 9a9fa778058b0876aa1240eea7e59c637258351f Author: Ann Almgren Date: Sat Nov 3 16:47:27 2018 -0700 Update the regression tests so we test 2d and 3d -- in 3d we test cylinder with the axis in three coordinate directions Tests/LinearSolvers/NodeEB/GNUmakefile Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp Tests/LinearSolvers/NodeEB/inputs Tests/LinearSolvers/NodeEB/inputs.rt.2d Tests/LinearSolvers/NodeEB/inputs.rt.3d.x Tests/LinearSolvers/NodeEB/inputs.rt.3d.y Tests/LinearSolvers/NodeEB/inputs.rt.3d.z commit 4d8ae5b55f2e367b692ac6807193ad4352d6fede Author: Ann Almgren Date: Sat Nov 3 16:45:56 2018 -0700 Had to change the coarsening since the stencils pointing to the faces are 0 for regular cells when dx = dy = dz. This messes with the coarsening when a full cell is near an almost full cell. We should probably make the same change in the interpolation but for now this works on simple test cases (ie cylinders) Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 5de8f04d317e9aad91ed4c7a385fa435b2ef6a9a Author: Ann Almgren Date: Sat Nov 3 16:45:24 2018 -0700 Remove extra printing Src/Extern/Algoim/Algoim_integrals.cpp commit f52ba695a77004906d8e9f8560896c9a26f1f1a5 Merge: 2ec929062 a255044ab Author: Ann Almgren Date: Sat Nov 3 15:05:12 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 2ec9290625ba18996253928611d12fa6b4e91b79 Author: Ann Almgren Date: Sat Nov 3 15:04:49 2018 -0700 Comment out print statement and setprecision statement Src/Extern/Algoim/Algoim_integrals.cpp commit a255044abf0e9f99e2a7e584d7700cf78b4dd5f8 Author: Max Katz Date: Sat Nov 3 17:20:44 2018 -0400 Fix some divide by zero issues in DistributionMapping Src/Base/AMReX_DistributionMapping.cpp commit 1bd9aad69291f96e693d30c5a7d6e90a5835cc00 Author: Weiqun Zhang Date: Sat Nov 3 13:33:49 2018 -0700 add warm up to the test Tests/Vectorization/main.cpp commit cb5a968b2079859107e45f1bca4a1b9af87ee79c Author: Weiqun Zhang Date: Sat Nov 3 13:01:04 2018 -0700 new headers Tests/Vectorization/kc.H Tests/Vectorization/kdecl.H commit 67fbc910637eb5c1d7f4e74b33d06170faa0a0fe Author: Weiqun Zhang Date: Sat Nov 3 12:57:50 2018 -0700 add ctoprim test Tests/Vectorization/kf.F90 Tests/Vectorization/main.cpp commit 074384fb55c5660a04499cb804ec11b280b8035e Author: Weiqun Zhang Date: Sat Nov 3 12:06:37 2018 -0700 add non-simd version Tests/Vectorization/GNUmakefile Tests/Vectorization/Make.package Tests/Vectorization/kc.cpp Tests/Vectorization/main.cpp commit 96e21c5d0c6485003b93eab900cbb405ea5db7fd Author: Weiqun Zhang Date: Sat Nov 3 11:35:18 2018 -0700 minor Tests/Vectorization/main.cpp commit 2c320d49efda86e0c3f64c09a41a6b5ce9b0e467 Author: Weiqun Zhang Date: Sat Nov 3 11:32:46 2018 -0700 compiler extension macros Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_Extension.H Src/Base/AMReX_REAL.H Src/Base/AMReX_RESTRICT.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/GNUMake/comps/gnu.mak commit 65055b9a8d68575e4c9304e7b6e1fab85133a18b Merge: d482be48a 8ff58db6e Author: Ann Almgren Date: Sat Nov 3 10:54:17 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit d482be48ab310ad3c4a805dea28a2d3256cbd2d8 Author: Ann Almgren Date: Sat Nov 3 10:53:36 2018 -0700 Fix indexing problem in 3D EB nodal restriction operator. (There is still a different issue but this does fix some problems) Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 8ff58db6ef8cad54fa9e2ccbd1435904734106df Merge: 37db0ea10 57572bec8 Author: WeiqunZhang Date: Sat Nov 3 10:45:10 2018 -0700 Merge pull request #359 from AMReX-Codes/mkatz/last_checkpoint Fill in last_checkpoint/last_plotfile after a restart commit 37db0ea1037a689cf1987be1c77eaa6a63f46a3f Merge: 24f5ab414 f1afba2e3 Author: WeiqunZhang Date: Sat Nov 3 10:43:03 2018 -0700 Merge pull request #358 from AMReX-Codes/mkatz/minimalbox_overflow_fix Fix a potential numerical overflow in BoxArray::minimalBox commit 57572bec8ca30d710fb78b6e2e35088e3ba35e29 Author: Max Katz Date: Sat Nov 3 03:05:46 2018 -0400 Fill in last_checkpoint/last_plotfile after a restart Castro and Nyx have logic in main.cpp that says to only dump a checkpoint if the coarse timestep of the last checkpoint is older than the current coarse timestep. In the edge case where the simulation doesn't actually take any timesteps after a restart, this results in a checkpoint and plotfile being written from the same data we restarted from, which unnecessarily clobbers the old data and creates a duplicate checkpoint/plotfile. If the user explicitly wants a new checkpoint on restart, perhaps because they are doing some kind of transformation, they can still take advantage of the flags checkpoint_on_restart and plotfile_on_restart. Src/Amr/AMReX_Amr.cpp commit b522d30ad60b1ce1ee5ae8939b2a46a0276a3d42 Author: Weiqun Zhang Date: Fri Nov 2 23:10:12 2018 -0700 vectorization test Tests/Vectorization/GNUmakefile Tests/Vectorization/Make.package Tests/Vectorization/kc.cpp Tests/Vectorization/kf.F90 Tests/Vectorization/main.cpp commit 72353b69b5b3c47324c22318620b3dc256344b9b Author: Weiqun Zhang Date: Fri Nov 2 23:03:34 2018 -0700 AMREX_PRAGMA_SIMD Src/Base/AMReX_RESTRICT.H Tools/GNUMake/comps/ibm.mak Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit ebd4680eab65547ae7d3ec713a4ea4a8a28410a2 Author: Weiqun Zhang Date: Fri Nov 2 23:02:13 2018 -0700 FabView Src/Base/AMReX_BaseFab.H commit f1afba2e3e8e91c2f656c2dadc03578816551a3e Author: Max Katz Date: Sat Nov 3 00:11:07 2018 -0400 Fix a potential numerical overflow in BoxArray::minimalBox If the number of points per dimension N is such that N^3 is larger than a 32-bit integer (or N^2, for 2D), then this implementation of minimalBox will overflow when accumulating into an n_pts variable. Solved by replacing the value holding the number of points with a long, which is consistent with similar calculations elsewhere in BoxArray. Fixes #357 Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit 4a7f8c24c3538a0f6e8cfd0f980b3bc4084f0fbb Author: Weiqun Zhang Date: Fri Nov 2 16:31:32 2018 -0700 flux to dudt Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 24f5ab414fc5312670f7d096df879aec8e607e83 Author: Weiqun Zhang Date: Fri Nov 2 15:27:26 2018 -0700 std::isnan and isinf -> amrex::isnan and isinf Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit d9d6d67b68a7985af087dc2d00b964b5183a5458 Author: Weiqun Zhang Date: Fri Nov 2 15:25:26 2018 -0700 ptxas info Tools/GNUMake/comps/nvcc.mak commit 78916ca8b6f217a9dad4de8bb3efe45081836b60 Author: Weiqun Zhang Date: Fri Nov 2 14:48:12 2018 -0700 fix omp Src/Base/AMReX_MultiFab.cpp commit 0bf4d42d74e00460875e2741945b8fec23d9b1ef Author: Kevin Gott Date: Fri Nov 2 15:02:33 2018 -0400 Turn off OpenMP+GPU in contains_inf/nan. Src/Base/AMReX_MultiFab.cpp commit 0d5156bc2868aa82b46bdc6fd1c1de88ce4f7224 Author: Kevin Gott Date: Fri Nov 2 14:54:32 2018 -0400 MultiFab::contains_nan and contains_inf to gpu. Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_MultiFab.cpp commit d1f45911e128a754458427d6d43f8989e6f9ff54 Author: Weiqun Zhang Date: Fri Nov 2 11:11:49 2018 -0700 add AMREX_LAUNCH_DEVICE_LAMBDA_BOXIV Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H commit 4970b9cdcf8e660872a9636bbd673eccd6d7544f Author: Weiqun Zhang Date: Fri Nov 2 12:28:58 2018 -0400 fix merge Src/Base/AMReX_BaseFab.H commit deaf67f925e3471cafa2d9ddb887a150c43a2d23 Merge: 41d0cebb2 aefa9f75e Author: Weiqun Zhang Date: Fri Nov 2 12:26:42 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development Conflicts: Src/Base/AMReX_BaseFab.H commit 41d0cebb2b1644b1b633e0abb780b0abfab87405 Author: Weiqun Zhang Date: Fri Nov 2 12:23:08 2018 -0400 hopefully mfic can now compile with USE_CUDA=TRUE Src/Base/AMReX_BaseFab.H Src/EB/AMReX_EBCellFlag.H commit aefa9f75e8d9ca83aa17cba0b564e414a3e7b977 Merge: e68664152 da111633c Author: Weiqun Zhang Date: Fri Nov 2 09:15:27 2018 -0700 Merge branch 'development' into weiqun/merge-b-devicefab commit da111633cb9c2f9892c7122e0228824781c1bb34 Author: Weiqun Zhang Date: Thu Nov 1 21:05:00 2018 -0700 in debug mode, add -Werror=return-type to gcc Tools/GNUMake/comps/gnu.mak commit d3f00ab7f6384bbc363ccbdf86303a3f4792a97b Author: Weiqun Zhang Date: Thu Nov 1 21:00:34 2018 -0700 fix a bug Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 9701371299cd7d302ef2e5c3c568ca7c0e0d5da9 Author: Andrew Myers Date: Thu Nov 1 20:30:07 2018 -0400 use thrust::sort here if running with Cuda Src/Particle/AMReX_NeighborParticlesI.H commit 4da37600c2a33f437266cfb71d0af2fcd159c522 Author: Weiqun Zhang Date: Thu Nov 1 17:25:25 2018 -0700 add ctoprim Src/Amr/AMReX_Amr.cpp Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_index_macros.H Tutorials/GPU/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/Make.package Tutorials/GPU/CNS/Source/hydro/Make.package Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 68ffefb5c31d0037e36b2a38bd3a6b9246e27206 Merge: 055b4d653 9a141b726 Author: Andrew Myers Date: Thu Nov 1 18:44:50 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 055b4d653a9697143de86ee7425b05b2eecdc76e Author: Andrew Myers Date: Thu Nov 1 18:40:10 2018 -0400 remove the index conversion stuff for now. Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_ParticleUtil.cpp commit 9e10e0fe306c1d64063bcdd4ca2b533eacbe7bdb Author: Weiqun Zhang Date: Thu Nov 1 15:26:57 2018 -0700 fix sum Tutorials/GPU/CNS/Source/CNS.cpp commit dd6a5812423f073cc262aa7b004a98d738b0cf03 Author: Weiqun Zhang Date: Thu Nov 1 15:20:59 2018 -0700 estimate dt Src/Base/AMReX_CoordSys.H Src/Base/AMReX_Geometry.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package commit 8b2e6de470d95e8e1ba024e8b4a88c592cfc335f Author: Andrew Myers Date: Thu Nov 1 17:45:33 2018 -0400 fix compilation error Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d301ef0ab2fde61d449ff1736204c154dbebc708 Author: Andrew Myers Date: Thu Nov 1 17:45:15 2018 -0400 forgot to add these files. Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_ParticleUtil.cpp commit 5c285c1d271f9e53a13b645a2546e380e6de07b5 Author: Andrew Myers Date: Thu Nov 1 17:30:11 2018 -0400 pass the bin start and stop indices into the SortParticlesByBin method Src/Particle/AMReX_ParticleContainerI.H commit 76cf6ac992aabc9c91a8b07e2afb7c0afb7a9ff3 Author: Weiqun Zhang Date: Thu Nov 1 14:10:44 2018 -0700 vectorization Src/Base/AMReX_BaseFab.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp commit c49b2777758c9dab3f8524ab542f9ba2d124c98d Author: Andrew Myers Date: Thu Nov 1 17:07:17 2018 -0400 add stub for SortParticlesByBin Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit dc7b453c7cbee9b6ca0b8316b08627fb6977dcb8 Author: Andrew Myers Date: Thu Nov 1 16:58:56 2018 -0400 add new functor for binning particles on a sub-grid basis Src/Particle/AMReX_Functors.H commit e68664152dc5a4384b711df2c7b87eae5ef33692 Author: Weiqun Zhang Date: Thu Nov 1 13:46:44 2018 -0700 comment out resize because it contains cuda api calls thus not safe as callback. add mutex in delete to protect the memory pool Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp commit 2481746147bc49310e9ae29a0d35b3e5b8dccb82 Author: Weiqun Zhang Date: Thu Nov 1 13:46:44 2018 -0700 comment out resize because it contains cuda api calls thus not safe as callback. add mutex in delete to protect the memory pool Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp commit ee81d5436e727349e22873e17918060164e92494 Author: Andrew Myers Date: Thu Nov 1 16:06:15 2018 -0400 move getTileIndex to a separate file, make it run on both host and device Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 471441486a7cd0ec151372ed5d1fb70a098542dc Author: Andrew Myers Date: Thu Nov 1 15:06:47 2018 -0400 mark getTileIndex as __host__ __device__ Src/Particle/AMReX_Particles.H commit 2a7244f12c1727450f53e5f850d0ffe6e708dcc8 Author: Andrew Myers Date: Thu Nov 1 15:05:46 2018 -0400 refactor getTileIndex to not use static members so that it can be called from device code. Src/Particle/AMReX_ParticleContainerI.H commit 9a141b726296a74f658486274a99ec7e05bafd38 Author: Kevin Gott Date: Thu Nov 1 12:00:41 2018 -0700 Reset minIndex. Src/Base/AMReX_MultiFab.cpp commit 02cda9da632126a2eb41622636e05f6105ff8ae9 Author: Kevin Gott Date: Thu Nov 1 14:58:23 2018 -0400 Continuing to convert MultiFab functions. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFab.cpp commit ef6c98f00690eeebd7451b61bd37e1191eeb758f Author: Weiqun Zhang Date: Thu Nov 1 11:05:22 2018 -0700 add cns_initdata Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_index.H Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package commit 6e60b0edda955502ae3d628b867d05fccb726a35 Merge: 76b781001 862170c8a Author: Andrew Myers Date: Thu Nov 1 10:00:41 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 76b781001a19174cafad337e7be787be3d852b4d Author: Andrew Myers Date: Thu Nov 1 10:00:31 2018 -0700 remove unused variables Src/Particle/AMReX_Particles.H commit aca87d9b0772f981b41cacf13cdea4299b3c47fe Author: Weiqun Zhang Date: Thu Nov 1 09:06:02 2018 -0700 DeviceFab:: add async clear and resize Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.cpp commit 3bdf3c82872608e34a4cf9198e2e2d67ed8c1bfd Author: Weiqun Zhang Date: Thu Nov 1 09:06:02 2018 -0700 DeviceFab:: add async clear and resize Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.cpp commit 9e0461f904c549452b19d5c207a2510e3c3549b0 Merge: 5a7046a12 294fb430e Author: Weiqun Zhang Date: Thu Nov 1 08:40:17 2018 -0700 Merge branch 'development' into weiqun/gpu commit 294fb430e2448ac2b43c10f0442e216cebd4ddbc Merge: dcbfdc0b0 0d5866916 Author: Weiqun Zhang Date: Thu Nov 1 08:39:40 2018 -0700 Merge branch 'weiqun/merge-a-coord' into development commit 862170c8af86ebca67fff989878e281db94c37e5 Merge: aabb2e131 294fb430e Author: Ann Almgren Date: Thu Nov 1 08:38:50 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit aabb2e1316726c9adbc5e48c5f96c35812cc9f06 Author: Ann Almgren Date: Thu Nov 1 08:38:37 2018 -0700 Remove VisMF::Write call. Src/Extern/Algoim/Algoim_integrals.cpp commit dcbfdc0b0e0e97e8c58696d98c60522ba2d4d8d2 Author: Weiqun Zhang Date: Thu Nov 1 08:38:20 2018 -0700 update CHANGES CHANGES commit 2ae376784842324b2bf54babe24d2ded7016f542 Author: Ann Almgren Date: Thu Nov 1 08:30:50 2018 -0700 Fix typo in 3d version of mknewu_eb Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 730c383e3fe892f73828491e85f805c1845b7760 Author: Ann Almgren Date: Thu Nov 1 07:15:42 2018 -0700 Make sure to enforce periodicity of 3d nodal EB integrals Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 715c875afff6a23cda4b21c5f60cbcc9776f704c Merge: 187123e5f 3130c7cd0 Author: Ann Almgren Date: Thu Nov 1 07:13:44 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 187123e5f7b2688b51a01f5fa6e582a243ca5cdd Author: Ann Almgren Date: Wed Oct 31 21:16:12 2018 -0700 Fix some sign errors and the scaling of the 3D EB nodal stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 1033b29fe3b4a568890d1a6ff543b9af78316b89 Author: Ann Almgren Date: Wed Oct 31 18:19:24 2018 -0700 Initialize the ghost cells of the intg array elements as well Src/Extern/Algoim/Algoim_integrals.cpp commit 3130c7cd0fe04cc5e52ae3e68590cd3e9c00ea7c Author: Kevin Gott Date: Wed Oct 31 19:40:40 2018 -0400 Update HeatEquation GPU example. Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit 0d5866916aac5cd7a5e868c701f6643506b50126 Merge: b1258d42d 864aa38b1 Author: Weiqun Zhang Date: Wed Oct 31 16:29:24 2018 -0700 Merge branch 'development' into weiqun/merge-a-coord commit 864aa38b1967a9b25724b32126a77ff86ffd7881 Author: Andrew Myers Date: Wed Oct 31 16:24:52 2018 -0700 remove now-unused file Src/Particle/AMReX_RedistributeStrategy.H commit b63298b7f0eeb6f02ee4afa2dd6c1d3e233bf349 Author: Andrew Myers Date: Wed Oct 31 16:18:37 2018 -0700 remove broken tutorials - will fix these and add them back later. Tutorials/GPU/ElectromagneticPIC/Constants.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.H Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/GNUmakefile Tutorials/GPU/ElectromagneticPIC/IO.H Tutorials/GPU/ElectromagneticPIC/IO.cpp Tutorials/GPU/ElectromagneticPIC/Make.package Tutorials/GPU/ElectromagneticPIC/NodalFlags.H Tutorials/GPU/ElectromagneticPIC/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC/Particles.H Tutorials/GPU/ElectromagneticPIC/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC/em_pic_F.H Tutorials/GPU/ElectromagneticPIC/inputs Tutorials/GPU/ElectromagneticPIC/main.cpp Tutorials/GPU/ElectromagneticPIC/script.nompi.sh Tutorials/GPU/ElectromagneticPIC/summit.sh Tutorials/GPU/ElectromagneticPIC/summitdev.sh Tutorials/GPU/ElectromagneticPIC/test.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh Tutorials/Particles/ElectromagneticPIC/Make.EMPIC Tutorials/Particles/ElectromagneticPIC/Source/Constants.H Tutorials/Particles/ElectromagneticPIC/Source/IO.H Tutorials/Particles/ElectromagneticPIC/Source/IO.cpp Tutorials/Particles/ElectromagneticPIC/Source/Make.package Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Source/Particles.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 3f9a7412690dbef0e8abfe0d78ba0e5ad5b0b302 Author: Andrew Myers Date: Wed Oct 31 16:07:07 2018 -0700 remove debug print statement Src/Particle/AMReX_ParticleContainerI.H commit 1b07b2acaa0fe4d1455fc638e232d90aa8de0953 Author: Andrew Myers Date: Wed Oct 31 16:03:27 2018 -0700 force rebuilding the redistribute mask when you ask for more ghost cells than it currently has Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit b1258d42d9e6773d3f2620328e5d79b5fe105f84 Author: Weiqun Zhang Date: Wed Oct 31 12:59:21 2018 -0700 fix offset Src/Base/AMReX_COORDSYS_1D.cpp Src/Base/AMReX_COORDSYS_2D.cpp commit 5a7046a12054a18a6375d07070454a31b99e684e Author: Weiqun Zhang Date: Wed Oct 31 11:04:36 2018 -0700 minor Tutorials/GPU/CNS/Exec/Sod/GNUmakefile commit ab1eb7de8cfaff45bb4c5be10646328d30f5faae Author: Weiqun Zhang Date: Wed Oct 31 10:32:46 2018 -0700 skelton for CNS Tutorials/GPU/CNS/Exec/Make.CNS Tutorials/GPU/CNS/Exec/Sod/GNUmakefile Tutorials/GPU/CNS/Exec/Sod/Make.package Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNSBld.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package Tutorials/GPU/CNS/Source/diffusion/Make.package Tutorials/GPU/CNS/Source/hydro/Make.package Tutorials/GPU/CNS/Source/main.cpp commit b5b603c3434040d7812e9d319f94375b1cecd6b8 Author: Tan Nguyen Date: Wed Oct 31 01:49:47 2018 -0700 refactoring AMFIter codes Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla/Barrier.H Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla/LocalConnection.H Src/AmrTask/rts_impls/Perilla/Make.package Src/AmrTask/rts_impls/Perilla/PackageQueue.H Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla/RGIter.H Src/AmrTask/rts_impls/Perilla/RGIter.cpp Src/AmrTask/rts_impls/Perilla/RegionQueue.H Src/AmrTask/rts_impls/Perilla/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla/RemoteConnection.H Src/AmrTask/rts_impls/Perilla/WorkerThread.H Src/AmrTask/rts_impls/Perilla/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla/mylock.h Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_upc++/Barrier.H Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/LocalConnection.H Src/AmrTask/rts_impls/Perilla_upc++/Make.package Src/AmrTask/rts_impls/Perilla_upc++/Perilla.H Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/AmrTask/rts_impls/Perilla_upc++/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla_common.cpp Src/AmrTask/rts_impls/Perilla_upc++/RGIter.H Src/AmrTask/rts_impls/Perilla_upc++/RGIter.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.H Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla_upc++/RemoteConnection.H Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.H Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla_upc++/mylock.h Src/AmrTask/rts_impls/Perilla_upc++/perilla.mak Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Pthread_Common/Barrier.H Src/AmrTask/rts_impls/Pthread_Common/Barrier.cpp Src/AmrTask/rts_impls/Pthread_Common/LocalConnection.H Src/AmrTask/rts_impls/Pthread_Common/Make.package Src/AmrTask/rts_impls/Pthread_Common/RGIter.H Src/AmrTask/rts_impls/Pthread_Common/RGIter.cpp Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.H Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.cpp Src/AmrTask/rts_impls/Pthread_Common/RemoteConnection.H Src/AmrTask/rts_impls/Pthread_Common/WorkerThread.H Src/AmrTask/rts_impls/Pthread_Common/WorkerThread.cpp Src/AmrTask/rts_impls/Pthread_Common/mylock.h Src/AmrTask/rts_impls/Pthread_Common/perilla.mak commit 52e2ab6955876934add9610ada119485be14d2a2 Author: Weiqun Zhang Date: Tue Oct 30 20:51:40 2018 -0700 forgot to add files Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.H Src/Base/AMReX_CudaFabImpl.cpp commit c21604554eada56ab7e4843b983569042032be18 Author: Ann Almgren Date: Tue Oct 30 18:31:48 2018 -0700 Fix oops Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8a5253cdbb5754d8739368be177948938134408b Author: Ann Almgren Date: Tue Oct 30 18:30:17 2018 -0700 Remove extra print Src/Extern/Algoim/Algoim_integrals.cpp commit e37bb3fc5a1b7092a2b3be1b46c7d96cd468a1ca Merge: e7a7de58b 79c269324 Author: Ann Almgren Date: Tue Oct 30 18:29:21 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit e7a7de58b7ad03d817b553a5842dfa2b92c89bb8 Author: Ann Almgren Date: Tue Oct 30 18:28:53 2018 -0700 In preparation for being able to use Algoim to construct the 3d EB nodal integrals for use in the 3d nodal projection Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/Extern/Algoim/Algoim_integrals.H Src/Extern/Algoim/Algoim_integrals.cpp Src/Extern/Algoim/Make.package Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 64112f8eaba07d5427d11a86a6959fb9f77387d5 Author: Weiqun Zhang Date: Tue Oct 30 18:08:58 2018 -0700 add an example of using DeviceFab Tests/GPU/DeviceFab/GNUmakefile Tests/GPU/DeviceFab/Make.package Tests/GPU/DeviceFab/main.cpp commit 559cb7099a392e36c34bbe81d10b868fcf2464e6 Author: Minion Date: Tue Oct 30 17:03:16 2018 -0700 Moving files to look like other tutorials Tutorials/SDC/MISDC_ADR_2d/Exec/GNUmakefile Tutorials/SDC/MISDC_ADR_2d/Exec/inputs_2d Tutorials/SDC/MISDC_ADR_2d/README Tutorials/SDC/MISDC_ADR_2d/Source/Make.package Tutorials/SDC/MISDC_ADR_2d/Source/SDC_sweeper.cpp Tutorials/SDC/MISDC_ADR_2d/Source/functions_2d.f90 Tutorials/SDC/MISDC_ADR_2d/Source/init_phi_2d.f90 Tutorials/SDC/MISDC_ADR_2d/Source/main.cpp Tutorials/SDC/MISDC_ADR_2d/Source/myfunc.H Tutorials/SDC/MISDC_ADR_2d/Source/myfunc_F.H commit 64cd99e24675a0d43b1ed21cba5ad35a4aaa24c5 Author: Minion Date: Tue Oct 30 16:46:50 2018 -0700 made Nnodes adjustable and cleaner quadrature matrices Src/SDC/AMReX_SDCstruct.H Src/SDC/AMReX_SDCstruct.cpp commit f29ceb098636e9816a066fb4f345c06c7c54b8be Author: Weiqun Zhang Date: Tue Oct 30 16:39:14 2018 -0700 DeviveFab: add new constructor for the omp fab resize idiom Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.H Src/Base/AMReX_CudaFabImpl.cpp commit 1189de10d9bdac07a73be61fc7409d34aa7bed2a Author: Weiqun Zhang Date: Tue Oct 30 18:54:52 2018 -0400 add profiler to CudaFab Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.cpp commit 79c26932410322f359b88005181f15c26d55ddd4 Author: Jean Sexton Date: Tue Oct 30 18:31:28 2018 -0400 Remove old example Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/Make.package Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/SetIC.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/inputs Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/myfunc_F.H Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/ode_mod.f90 commit 58e2b03f69bcb96cb0e35eb8078545c461d660e6 Author: Cy Chan Date: Tue Oct 30 14:03:15 2018 -0700 add flag to turn on/off new features for A/B comparison within the same run want to compare under same node assignment from job scheduler print SLURM_NODELIST in MLLinOp Src/Base/AMReX_DistributionMapping.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 0ff2813e18e4573bbcaa7b4b2656c8b4e11ec6e9 Author: Kevin Gott Date: Tue Oct 30 13:55:22 2018 -0700 Add to documentation: Fortran cannot be instrumented when using Tiny Profiling. Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst commit ef86702ef4cc330b6e47f7edbef1c0ca63204372 Merge: c28684d89 7a3148cb4 Author: Weiqun Zhang Date: Tue Oct 30 16:38:10 2018 -0400 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit 7a3148cb43c04cebc358d45bbb2142e894a508c8 Merge: de25ba1dd 227f62499 Author: Weiqun Zhang Date: Tue Oct 30 13:38:19 2018 -0700 Merge branch 'development' into weiqun/gpu commit de25ba1ddc488deb87a29ae0dd95a92a3e95746f Author: Weiqun Zhang Date: Tue Oct 30 13:24:49 2018 -0700 fix non-cuda build Src/Base/AMReX_CudaFabImpl.cpp commit c28684d893d8190c9bafe36dd70828ff5d89a329 Merge: ad2baf40d de25ba1dd Author: Weiqun Zhang Date: Tue Oct 30 16:24:47 2018 -0400 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit ad2baf40d1cfc77b709733bd038e4f852eceb48c Author: Weiqun Zhang Date: Tue Oct 30 16:16:33 2018 -0400 use AMREX_CUDA_MAX_THREADS instead of hardwired number 256 Src/Base/AMReX_CudaDevice.cpp commit dd63bad3479ccf8e07c44209e36869a862d0d2e7 Author: Weiqun Zhang Date: Tue Oct 30 13:11:44 2018 -0700 implement DeviceFab Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.H Src/Base/AMReX_CudaFabImpl.cpp Src/Base/AMReX_CudaUtility.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 227f62499c8a58f1721d564f82490bdafb67a67a Author: atmyers Date: Tue Oct 30 06:49:03 2018 -0700 use resize instead of clear Src/Particle/AMReX_ParticleContainerI.H commit 7f66c6de69b9887306a1b3aa1e87031ade2acfab Author: atmyers Date: Tue Oct 30 06:29:11 2018 -0700 need to clear ghosts / virtuals after adding them Src/Particle/AMReX_ParticleContainerI.H commit 4cff527c6663b493706041d73ddad14346d1213f Author: Tan Nguyen Date: Tue Oct 30 01:13:29 2018 -0700 correct AMFIter metadata after regridding Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla/RGIter.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla_common.cpp commit c0fda2f9f235f67337fbfd6662345ab4583244c8 Author: Lawrence Minion Date: Mon Oct 29 23:39:35 2018 -0700 fix mfi ordering bug Src/SDC/AMReX_SDCstruct.cpp commit c548b64158c7b342142d00989a9b818992a60351 Author: Lawrence Minion Date: Mon Oct 29 23:10:49 2018 -0700 Adding MISDC example with exact solution Tutorials/SDC/MISDC_ADR_2d/GNUmakefile Tutorials/SDC/MISDC_ADR_2d/Make.package Tutorials/SDC/MISDC_ADR_2d/SDC_sweeper.cpp Tutorials/SDC/MISDC_ADR_2d/functions_2d.f90 Tutorials/SDC/MISDC_ADR_2d/init_phi_2d.f90 Tutorials/SDC/MISDC_ADR_2d/inputs_2d Tutorials/SDC/MISDC_ADR_2d/main.cpp Tutorials/SDC/MISDC_ADR_2d/myfunc.H Tutorials/SDC/MISDC_ADR_2d/myfunc_F.H commit 8e51d61cf72771fc5faf0fac1f729af0a6612ea1 Author: Weiqun Zhang Date: Mon Oct 29 18:06:00 2018 -0700 make BaseFab's data trivially copyable Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_Gpu.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 175f0dc150bcb596292d84faeab3e62a71d46693 Merge: 6b66db074 4aa3cf096 Author: Ann Almgren Date: Mon Oct 29 17:33:18 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 6b66db074f11e4e400c94f218aa77bb45be207af Author: Ann Almgren Date: Mon Oct 29 17:33:04 2018 -0700 Remove unused "auto sfab = ..." lines Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EB_levelset.cpp commit 4aa3cf09644db7f269d2c5b4a88d47506d8bc04a Merge: 6f5f3bede 22f04e44a Author: Andrew Myers Date: Mon Oct 29 20:30:54 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6f5f3bede1ae09268f7ec225e37fdb001f0e136a Author: Andrew Myers Date: Mon Oct 29 20:30:11 2018 -0400 changes needed for Nyx to compile with USE_CUDA=TRUE Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 22f04e44a39c692e524a4542a705e9df4a50b504 Author: Kevin Gott Date: Mon Oct 29 20:00:56 2018 -0400 Consolidate and cleanup GPU tutorials. Tests/GPU/ScratchPad/GNUmakefile Tests/GPU/ScratchPad/Make.package Tests/GPU/ScratchPad/inputs_3d Tests/GPU/ScratchPad/main.cpp Tests/GPU/ScratchPad/run.script Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/inputs Tutorials/GPU/ElectromagneticPIC/summitdev.sh Tutorials/GPU/ElectromagneticPIC_1/Constants.H Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.H Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/GNUmakefile Tutorials/GPU/ElectromagneticPIC_1/IO.H Tutorials/GPU/ElectromagneticPIC_1/IO.cpp Tutorials/GPU/ElectromagneticPIC_1/Make.package Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.H Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC_1/Particles.H Tutorials/GPU/ElectromagneticPIC_1/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC_1/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_1/em_pic_F.H Tutorials/GPU/ElectromagneticPIC_1/inputs Tutorials/GPU/ElectromagneticPIC_1/main.cpp Tutorials/GPU/ElectromagneticPIC_1/make.out Tutorials/GPU/ElectromagneticPIC_1/summit.sh Tutorials/GPU/ElectromagneticPIC_1/summitdev.sh Tutorials/GPU/ElectromagneticPIC_1/test.cpp Tutorials/GPU/ElectromagneticPIC_2/Constants.H Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.H Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/GNUmakefile Tutorials/GPU/ElectromagneticPIC_2/IO.H Tutorials/GPU/ElectromagneticPIC_2/IO.cpp Tutorials/GPU/ElectromagneticPIC_2/Make.package Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.H Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC_2/Particles.H Tutorials/GPU/ElectromagneticPIC_2/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC_2/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_2/em_pic_F.H Tutorials/GPU/ElectromagneticPIC_2/inputs Tutorials/GPU/ElectromagneticPIC_2/main.cpp Tutorials/GPU/ElectromagneticPIC_2/script.nompi.sh Tutorials/GPU/ElectromagneticPIC_2/summit.sh Tutorials/GPU/ElectromagneticPIC_2/summitdev.sh Tutorials/GPU/ElectromagneticPIC_2/test.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/run.ascent Tutorials/GPU/HeatEquation_EX1_C/Exec/run.nocuda.script Tutorials/GPU/HeatEquation_EX1_C/Exec/run.summit Tutorials/GPU/HeatEquation_EX1_C/Exec/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/physbc.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/run_summit_1node.sh Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc_F.H Tutorials/GPU/Readme.txt commit dfe4c1f2640676e3c1f0f11c615fcd4fff8355fe Author: Cy Chan Date: Mon Oct 29 14:31:35 2018 -0700 MLMG: add cache for bottom-solve MPI sub-communicators MPI_Comm_create() is expensive and is called for every gravity solve remove some BL_PROFILE_REGION Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 1d4a4d3d6ee78c53a056850caa8d70ce9834f20e Merge: d94ad31fc d27b3cc50 Author: Guy Moore Date: Mon Oct 29 16:38:38 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d94ad31fce36a5ee41e3d69e45eefc6ab68d3aaa Author: Guy Moore Date: Mon Oct 29 16:36:44 2018 -0700 First commit of MUI-coupling tutorial Tutorials/MUI/Exec_01/GNUmakefile Tutorials/MUI/Exec_02/GNUmakefile Tutorials/MUI/Exec_coupled/cmd_mpirun Tutorials/MUI/Exec_coupled/inputs Tutorials/MUI/Source_01/Make.package Tutorials/MUI/Source_01/init_phi_3d.f90 Tutorials/MUI/Source_01/main_01.cpp Tutorials/MUI/Source_01/myfunc.H Tutorials/MUI/Source_01/myfunc_F.H Tutorials/MUI/Source_02/Make.package Tutorials/MUI/Source_02/main_02.cpp Tutorials/MUI/Source_02/myfunc.H Tutorials/MUI/doc/GNUmakefile Tutorials/MUI/doc/MUIcouplingNotes.tex Tutorials/MUI/doc/iface_rect.png Tutorials/MUI/doc/vis_interface.m commit b5d89747b553ecfd1cd4a6079c0f5b69d15c0087 Author: Cy Chan Date: Mon Oct 29 14:29:43 2018 -0700 change makeSFC() to use box volume instead of just 1.0 for weights should improve load balancing for consolidated multigrid levels Src/Base/AMReX_DistributionMapping.cpp commit 97f573ddbb0ae90750c9465f5344967735d38f1c Author: Lawrence Minion Date: Mon Oct 29 14:12:56 2018 -0700 Added multi-implicit capability Src/SDC/AMReX_SDCstruct.H Src/SDC/AMReX_SDCstruct.cpp commit d27b3cc50a475b3b5cc7136ec73c1161f3dd11e6 Author: Ann Almgren Date: Mon Oct 29 12:22:37 2018 -0700 "conn" in 3d has 27 not 12 components Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f8d7261bfe3c3b7e5cf04a1223fbf898b018ca59 Author: Ann Almgren Date: Mon Oct 29 12:22:06 2018 -0700 Formatting for easier reading Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 220edd81a33de8fc7d956cf9c3d256e5d1c008b8 Author: Ann Almgren Date: Mon Oct 29 12:21:49 2018 -0700 Fix typo: "coarest" --> "coarsest" Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 87fbee771c1478aa2d40b4d9923f3a5947649b74 Merge: d68355726 7c3d66689 Author: Ann Almgren Date: Mon Oct 29 12:20:58 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit d6835572664f4733464c3e2f19123501b7dbf1e7 Author: Ann Almgren Date: Mon Oct 29 12:20:15 2018 -0700 1) Fix typo in newu -- should be (i,j,k,2) not (i,j,2,k) 2) add eps to the denominator when we create sten(i,j,k,ist_inv) -- mimicing 2d Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit cc6dfa6944f44bc7ddbdbed75c2b93a6dcae973e Author: Weiqun Zhang Date: Mon Oct 29 11:54:09 2018 -0700 update Src/Base/AMReX_Box.H Src/Base/AMReX_COORDSYS_1D.cpp Src/Base/AMReX_COORDSYS_2D.cpp Src/Base/AMReX_COORDSYS_3D.cpp Src/Base/AMReX_COORDSYS_C.H Src/Base/AMReX_CoordSys.cpp commit 7c3d66689a88c322a0412e755a1165c323a6af6a Author: Michele Rosso Date: Mon Oct 29 10:30:39 2018 -0700 Fix typo in Makefile Src/Particle/Make.package commit b1f02a0859fa6fd6d98d18d519ae1ab7ebd90a0d Merge: 4e72e97a1 42ffc8db8 Author: Ann Almgren Date: Mon Oct 29 10:18:09 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 4e72e97a10cd1117d0622fb0b31156ec62159b37 Author: Ann Almgren Date: Mon Oct 29 10:17:45 2018 -0700 Make sure that the direction of a cylinder is in the range [0:AMREX_SPACEDIM-1] not [0:AMREX_SPACEDIM] Src/EB/AMReX_EB2.cpp commit 42ffc8db86f762970117a633e649a861ff0c7ab0 Author: Andrew Myers Date: Mon Oct 29 09:55:32 2018 -0700 fix restart Src/Particle/AMReX_ParticleContainerI.H commit 68ea7185e42798f79f1381fa8e745368d0150b18 Merge: 4052ff7cc 70cce32aa Author: Weiqun Zhang Date: Mon Oct 29 09:50:43 2018 -0700 Merge branch 'development' into weiqun/gpu commit 2359a078fcaf37495375831f1e990dccb40e1e3c Author: Ann Almgren Date: Sun Oct 28 20:21:29 2018 -0700 Add the 3D EB nodal stencil. Note that we haven't yet computed the integrals -- this just goes from the 19 core integrals to "conn" to "sten" -- we still need to include the computation of the vol, S_x, S_x^2 integrals etc. Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 70cce32aaf0e0168e46c2d8fa591570b78a72395 Merge: d862ef5a6 ebddada4a Author: Weiqun Zhang Date: Sat Oct 27 20:39:37 2018 -0700 Merge branch 'gpu-merge-test' into development commit ebddada4a291268b52f0dd12be4b8286ac790e16 Author: Weiqun Zhang Date: Sat Oct 27 20:30:25 2018 -0700 udpate build Src/Base/CMakeLists.txt Tools/libamrex/configure.py commit 0e5f8945fd19006a5428eff67d6e520c9a924801 Author: Weiqun Zhang Date: Sat Oct 27 23:17:28 2018 -0400 simplification Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_GpuLaunch.H commit d24f58a66cfb9802d44bb317d4960e580216d10f Author: Weiqun Zhang Date: Sat Oct 27 21:16:57 2018 -0400 add cpu and device version for the range macro Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H commit 6486e1c3851ebc70cecff34a70e3819e3b224529 Author: Weiqun Zhang Date: Sat Oct 27 17:57:26 2018 -0700 add Cuda::Range so that we can use the same macro for int and Box Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuLaunch.H Src/Base/CMakeLists.txt Src/Base/Make.package commit b8264404121ff350877f968283d05b14d764cc7e Author: Weiqun Zhang Date: Sat Oct 27 11:50:47 2018 -0700 some renaming Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit 76529b6a8f255ae870c9e819f30d304a24e89c28 Author: Lawrence Minion Date: Fri Oct 26 17:18:29 2018 -0700 Nuking old Heat Equation Example Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile Tutorials/SDC/HeatEquation_EX1_C/Make.package Tutorials/SDC/HeatEquation_EX1_C/advance.cpp Tutorials/SDC/HeatEquation_EX1_C/advance_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/advance_3d.f90 Tutorials/SDC/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/SDC/HeatEquation_EX1_C/inputs_2d Tutorials/SDC/HeatEquation_EX1_C/inputs_3d Tutorials/SDC/HeatEquation_EX1_C/main.cpp Tutorials/SDC/HeatEquation_EX1_C/myfunc.H Tutorials/SDC/HeatEquation_EX1_C/myfunc_F.H Tutorials/SDC/HeatEquation_EX1_C/pf_quadrature.f90 commit 6fd46648612398aa0afdbe74d34127b2066e2069 Author: Lawrence Minion Date: Fri Oct 26 17:16:13 2018 -0700 Changing example name to reflect IMEX advection diffusion Tutorials/SDC/IMEX_Advec_Diff_C/GNUmakefile Tutorials/SDC/IMEX_Advec_Diff_C/Make.package Tutorials/SDC/IMEX_Advec_Diff_C/advance.cpp Tutorials/SDC/IMEX_Advec_Diff_C/advance_2d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_2d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_3d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/inputs_2d Tutorials/SDC/IMEX_Advec_Diff_C/inputs_3d Tutorials/SDC/IMEX_Advec_Diff_C/main.cpp Tutorials/SDC/IMEX_Advec_Diff_C/myfunc.H Tutorials/SDC/IMEX_Advec_Diff_C/myfunc_F.H commit 209b3e457cd24bccc48bdf8176179a5ec6ea6568 Author: Lawrence Minion Date: Fri Oct 26 17:14:27 2018 -0700 Reworked Tutorial to have a modular SDC form Src/SDC/AMReX_SDCquadrature.F90 Src/SDC/AMReX_SDCstruct.H Src/SDC/AMReX_SDCstruct.cpp Src/SDC/Make.package Tutorials/SDC/HeatEquation_EX3_C/Make.package Tutorials/SDC/HeatEquation_EX3_C/advance.cpp Tutorials/SDC/HeatEquation_EX3_C/advance_2d.f90 Tutorials/SDC/HeatEquation_EX3_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX3_C/inputs_2d Tutorials/SDC/HeatEquation_EX3_C/main.cpp Tutorials/SDC/HeatEquation_EX3_C/myfunc.H Tutorials/SDC/HeatEquation_EX3_C/myfunc_F.H commit d862ef5a626632494d7c3b4f33943098ace97459 Merge: 221058e0a cb4f4ef55 Author: Ann Almgren Date: Fri Oct 26 16:52:39 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 221058e0a78fb149d277556563a5bd44d991ad70 Author: Ann Almgren Date: Fri Oct 26 16:45:52 2018 -0700 Cleaned up notation a little -- no functional change Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit cb4f4ef552936f1d063bc352cdef0f892c1e8672 Author: Weiqun Zhang Date: Fri Oct 26 16:25:28 2018 -0700 add regression test inputs Tests/LinearSolvers/NodeEB/inputs.rt.2d commit 193b1566f1e34dc65a2a7025d6e4cf69de667baf Author: Weiqun Zhang Date: Fri Oct 26 16:08:36 2018 -0700 Nodal EB test Tests/LinearSolvers/NodeEB/GNUmakefile Tests/LinearSolvers/NodeEB/Make.package Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp Tests/LinearSolvers/NodeEB/initEB.cpp Tests/LinearSolvers/NodeEB/inputs Tests/LinearSolvers/NodeEB/main.cpp commit 00b7e49a0478811c4ac706c345a619f4984ea751 Merge: 15562f403 bddce1ae4 Author: WeiqunZhang Date: Fri Oct 26 13:41:30 2018 -0700 Merge pull request #333 from AMReX-Codes/gpu-merge-test gpu-mm branch into development. commit bddce1ae4b70b44b74b8b84a4cda228621d5da78 Author: Weiqun Zhang Date: Fri Oct 26 16:34:03 2018 -0400 fix include in BLFort.H Src/Base/AMReX_BLFort.H commit e9d5b69c9c33b899baa0abb051e457669132acd8 Author: Weiqun Zhang Date: Fri Oct 26 12:43:05 2018 -0700 fix some remaining issues of the reorganization Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_GpuLaunch.H commit 37ec77f6e1d9b5b95d1fb304542bacf2da4df4d0 Author: Weiqun Zhang Date: Fri Oct 26 11:17:45 2018 -0700 update cuda qualifier Src/Base/AMReX_CudaUtility.H commit a18a8ff4dc9eda681db983d96cd4f6a0f3840a11 Author: Weiqun Zhang Date: Fri Oct 26 11:14:22 2018 -0700 update the cuda script Tools/F_scripts/write_cuda_headers.py commit 429ff4e534c52968c983a31f1934a678f70ba1a6 Author: Weiqun Zhang Date: Fri Oct 26 10:54:51 2018 -0700 fix the merge Src/Base/AMReX_Geometry.H Src/Particle/AMReX_Functors.H commit 4321f8876b232e7e6de9d7c9a0817f302afb0cc8 Merge: 0975bc242 11ab1fd53 Author: Weiqun Zhang Date: Fri Oct 26 10:51:21 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-merge-test commit 0975bc2420f2f7edaabb89ffc9896a1ca10b00e3 Author: Weiqun Zhang Date: Fri Oct 26 10:48:43 2018 -0700 add namespace alias Gpu and hide the name cuda from users Src/Base/AMReX_GpuControl.cpp commit 583cfe5fac9b29cfc019b79e6333f72184dfa77d Author: Weiqun Zhang Date: Fri Oct 26 10:42:23 2018 -0700 add namespace alias Gpu and hide the name cuda from users Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuControl.H commit 44c96b8b1358ae94f1d4bdf56a5b6625a5303b6a Author: Weiqun Zhang Date: Fri Oct 26 10:34:18 2018 -0700 add namespace alias Gpu and hide the name cuda from users Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_Cuda.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaQualifiers.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuQualifiers.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Orientation.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_MultiCutFab.H Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Tests/GPU/TestC/main.cpp Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.defs Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HelloWorld_C/main.cpp commit 11ab1fd530bf3bc6a4a526c8850f81af506cd54d Merge: c45c0c007 48b783e2e Author: Andrew Myers Date: Fri Oct 26 10:50:25 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit c45c0c00782361ec5d2323cf5a4aeba2e42f2aea Author: Andrew Myers Date: Fri Oct 26 10:50:03 2018 -0400 start to work on particle tiling for GPU Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleContainerI.H commit 48b783e2e5d9a32d887597af2859a51c38ac04bf Author: atmyers Date: Thu Oct 25 23:35:23 2018 -0400 fix NumberOfParticlesAtLevel Src/Particle/AMReX_ParticleContainerI.H commit 946a55341764f3806dd46284d6577f6dce43e1b7 Author: Andrew Myers Date: Thu Oct 25 23:00:05 2018 -0400 remove functors from AMReX_Particles.H Src/Particle/AMReX_Particles.H commit 458a627db851770a1a0a0c39fec247ed18a27c41 Author: Andrew Myers Date: Thu Oct 25 22:52:11 2018 -0400 template the setPosition functor on particle type Src/Particle/AMReX_ParIterI.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 029cfc794b3b82ebc2d7dc4d983e937c69aef66e Author: Andrew Myers Date: Thu Oct 25 22:51:40 2018 -0400 move functors to separate file Src/Particle/AMReX_Functors.H commit 159ecac124273e9e328bdf8557731ebe11efc6b6 Author: Andrew Myers Date: Thu Oct 25 22:51:11 2018 -0400 fix bug introduced Src/Particle/AMReX_ParticleContainerI.H commit 85f313f053b2e1a741ab45e7b60cbfd5529d1380 Author: Andrew Myers Date: Thu Oct 25 22:11:31 2018 -0400 use the new managed objects in the thrust functors Src/Particle/AMReX_ParticleContainerI.H commit 4defed6eb6865b62d322a95807c677e1c6567ba9 Author: Andrew Myers Date: Thu Oct 25 22:11:14 2018 -0400 add isPeriodic to GeometryData Src/Base/AMReX_Geometry.H commit 3d1112a3283d180bf71826d565485ee2b597a3f7 Author: Andrew Myers Date: Thu Oct 25 21:25:32 2018 -0400 use the AMREX_CUDA_HOST_DEVICE macro Src/Particle/AMReX_ParticleContainerI.H commit d727d151f1adf9317cd3b81e939bd49c045ce04e Author: Weiqun Zhang Date: Thu Oct 25 17:39:44 2018 -0700 tidy Src/Base/AMReX_Arena.cpp commit 57f827bf4c9b86331d5fc4c2c0a4f76b52935922 Merge: 857e66cf0 c4ef60b1c Author: Weiqun Zhang Date: Thu Oct 25 20:25:44 2018 -0400 Merge branch 'gpu-merge-test2' into gpu-merge-test commit 857e66cf0f83e048fae4b7d279093368005b36fe Merge: abf9034ea 15562f403 Author: Weiqun Zhang Date: Thu Oct 25 20:25:33 2018 -0400 Merge branch 'development' into gpu-merge-test commit c4ef60b1cb2eba17a6ec4de3b77d4126f3184564 Author: Weiqun Zhang Date: Thu Oct 25 20:24:03 2018 -0400 reorganize arenas. Managed class uses the managed arena. remove BaseFab Fortran functions Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_CudaMemory.H Src/Base/Make.package commit ea6ced7f1eb5a3b2bd4b7f7cf29633c0c55257f9 Author: Andrew Myers Date: Thu Oct 25 16:01:25 2018 -0400 do not sort the grids here. Src/Particle/AMReX_ParticleContainerI.H commit a123f49d050b06be390db88d97ef0c67f618f918 Author: Andrew Myers Date: Thu Oct 25 15:41:48 2018 -0400 function to sort particles be cell if desired Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 966d62ac8e39bb60b34d979b1c9fbdca4da931f5 Author: Andrew Myers Date: Thu Oct 25 10:32:43 2018 -0400 also use it in the call to sort_by_dest Src/Particle/AMReX_ParticleContainerI.H commit 2e3b85ad28def29b81b2fd0b869966e5afc4c5b8 Author: Andrew Myers Date: Thu Oct 25 10:32:24 2018 -0400 simply use The_Cuda_Arena() internally for thrust Src/Base/AMReX_CudaAllocators.H commit e276b2f674f6bcfdaf2ae138fbf80efaf76c2c27 Author: Weiqun Zhang Date: Wed Oct 24 14:44:53 2018 -0700 make sure communication work with non-cuda-aware mpi Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 9b76e70da6c5de2de9a640c71c58b3782ac23edf Author: Weiqun Zhang Date: Wed Oct 24 14:27:06 2018 -0700 arena reorganization Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit cf1044754d3019f4d608ae5258d24ceac76cc8d4 Author: Weiqun Zhang Date: Wed Oct 24 16:49:42 2018 -0400 the cuda arena based on CArena and cudaMalloc Src/Base/AMReX_Arena.H Src/Base/AMReX_FabArrayBase.cpp commit 481b22acb6859717fefbba0f3140ea50b7ee7d6a Author: Minion Date: Wed Oct 24 13:35:45 2018 -0700 Creating SDCstruct library in Src Src/SDC/AMReX_SDCstruct.H Src/SDC/AMReX_SDCstruct.cpp Src/SDC/Make.package commit 25af27aa1131cfc1dbb3a27ebdeb889718d13511 Author: Minion Date: Wed Oct 24 13:34:25 2018 -0700 moving SDC arrays into struct Tutorials/SDC/HeatEquation_EX3_C/GNUmakefile Tutorials/SDC/HeatEquation_EX3_C/Make.package Tutorials/SDC/HeatEquation_EX3_C/SDCstruct.H Tutorials/SDC/HeatEquation_EX3_C/advance.cpp Tutorials/SDC/HeatEquation_EX3_C/main.cpp Tutorials/SDC/HeatEquation_EX3_C/myfunc.H commit 8985423a70482bdfd6624bbde945a169a98c4e55 Author: Andrew Myers Date: Wed Oct 24 16:21:01 2018 -0400 also keep the recv buffers around to avoid cudaMalloc costs Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 15562f40333022082971643914ea32ead93abd4a Author: Tan Nguyen Date: Wed Oct 24 12:44:50 2018 -0700 regular AMFiter update Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla/Make.package Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla/PerillaRts.H Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla/RGIter.H Src/AmrTask/rts_impls/Perilla/RGIter.cpp Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/Make.package Src/AmrTask/rts_impls/Perilla_upc++/Perilla.H Src/AmrTask/rts_impls/Perilla_upc++/PerillaConfig.H Src/AmrTask/rts_impls/Perilla_upc++/RGIter.H Src/AmrTask/rts_impls/Perilla_upc++/RGIter.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit ca5a1b5d488c51a2298835c44593d8672879c60f Author: Lawrence Minion Date: Wed Oct 24 11:51:28 2018 -0700 making constructor for SDCstruct Tutorials/SDC/HeatEquation_EX3_C/SDCstruct.H Tutorials/SDC/HeatEquation_EX3_C/advance.cpp Tutorials/SDC/HeatEquation_EX3_C/main.cpp Tutorials/SDC/HeatEquation_EX3_C/myfunc.H Tutorials/SDC/HeatEquation_EX3_C/myfunc_F.H commit d2c37a6bddbad40fc835a231a025baa77848dc19 Merge: 21f3c2902 0f1a9106e Author: Andrew Myers Date: Wed Oct 24 13:30:34 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 21f3c290232f9e5ea240214a68dfd7accb996e27 Author: Andrew Myers Date: Wed Oct 24 13:30:00 2018 -0400 fix DEBUG build for gpu Src/Particle/AMReX_ParticleContainerI.H commit 0f1a9106e248609acf36b4c1c0eff352020f323d Author: Kevin Gott Date: Wed Oct 24 13:27:59 2018 -0400 Wrap nvvp naming with appropriate directives. Src/Base/AMReX.H Src/Base/AMReX.cpp commit df72a2ccb8c36f978b9c680ad0280e497e293181 Merge: 78fefbd31 568e27881 Author: Andrew Myers Date: Wed Oct 24 13:21:35 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 78fefbd319dcdb6303de0ce68bc8ce945ec0cd23 Author: Andrew Myers Date: Wed Oct 24 13:18:49 2018 -0400 fix circular includes Src/Base/AMReX_CudaAllocators.H commit 568e27881588acf262de1b2a3f93e29d9b4225a7 Author: Weiqun Zhang Date: Wed Oct 24 08:41:23 2018 -0700 check thread safety when using cuda Src/Base/AMReX_FabArrayBase.cpp commit cb6eed9802b8fdc6c87302074ab1304e8f3f4dc0 Author: Weiqun Zhang Date: Wed Oct 24 08:41:00 2018 -0700 these static functions are host only Src/Base/AMReX_BaseFab.H commit 9b9a0f908574b80a17c7e357f15a3edd4dde2fbe Author: Weiqun Zhang Date: Wed Oct 24 08:35:10 2018 -0700 remove unused variable Src/Base/AMReX_FabArrayBase.cpp commit 8fb644a297bbf498d571ec0d45842314aa01c22b Author: Kevin Gott Date: Wed Oct 24 11:44:19 2018 -0400 Add profiler wrapper to Device's init to clearly identify Cuda driver and Cuda API startups in nvvp. Src/Base/AMReX.H Src/Base/AMReX.cpp commit df0b032a69535b20960eb50011bfa66bf64cfc39 Author: Andrew Myers Date: Wed Oct 24 11:20:51 2018 -0400 clean up a little bit. Src/Base/AMReX_CudaAllocators.cpp commit 64b6423d6b80fdbcabc329f859d2af055da1e9de Author: Andrew Myers Date: Wed Oct 24 11:10:06 2018 -0400 comments Src/Base/AMReX_CudaContainers.H commit 16d6e6fa8e4c641807c66051c1e79ee1b4a62b88 Author: Andrew Myers Date: Wed Oct 24 11:07:32 2018 -0400 restore the managed version of std::vector (could be useful elsewhere) Src/Base/AMReX_CudaContainers.H commit 782063c0f304ae362fa6ebff699072d46b505553 Author: Andrew Myers Date: Wed Oct 24 11:02:29 2018 -0400 rename ManagedVector -> ManagedDeviceVector Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H commit 68008a55e388abec76c3240f91464bb4dd61b2bd Author: Andrew Myers Date: Wed Oct 24 10:55:49 2018 -0400 add missing ifdef Src/Base/AMReX_CudaAllocators.cpp commit fd99d6db63b9592595455b6838d72f8ad0582453 Author: Andrew Myers Date: Wed Oct 24 10:49:06 2018 -0400 add stub from compiling fcompare in Tools/Postprocessing/C_Src Tools/Postprocessing/C_Src/GNUmakefile commit 3f9f9d8afcec96eb19fc2b419de7e1a9b982e3dc Author: Andrew Myers Date: Wed Oct 24 10:42:01 2018 -0400 use preallocated buffer for mpi communication in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 711b34abef843e73a5427cf0c1162c7fcc70d1f6 Author: Andrew Myers Date: Wed Oct 24 10:40:57 2018 -0400 use the ThrustManagedAllocator in the Thrust calls in RedistributeGPU Src/Base/AMReX.cpp Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit c3ade82e32b101b02a9d6df3cd4823890ad7ab02 Author: Andrew Myers Date: Wed Oct 24 10:03:52 2018 -0400 adding a ThrustCachedAllocator for calls to thrust::sort and thrust::partition Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H commit 8d6d1aafe0e19a704152a7f0d1aa56739d6f4943 Author: Weiqun Zhang Date: Tue Oct 23 21:36:45 2018 -0700 fix thread safety Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayCommI.H commit 75609195c1a49f540acec202ac6bb70dd045b716 Author: Weiqun Zhang Date: Tue Oct 23 17:00:58 2018 -0700 fix omp for StreamIter Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayCommI.H commit e98d97fe2a10df573aa454eec1a626f5ede33c44 Merge: 219379b0d 6ae02409e Author: Andrew Myers Date: Tue Oct 23 19:32:36 2018 -0400 Merge branch 'gpu-fb' into gpu-merge-test2 commit 219379b0d58230d2fc6ffa2daf65ca8b93bf9303 Author: Andrew Myers Date: Tue Oct 23 19:31:16 2018 -0400 make The_FA_Arena used the managed CArena (from weiqun) Src/Base/AMReX_FabArrayBase.cpp commit 6ae02409e2f6c25966fc3d82d82650aa4341d950 Author: Weiqun Zhang Date: Tue Oct 23 15:24:35 2018 -0700 use one buffer for all send data Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit 1db5bb236e7532896fc7281c128cffdec8e03678 Merge: 175892ee0 8e1f65055 Author: Lawrence Minion Date: Tue Oct 23 14:50:20 2018 -0700 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit 175892ee07460f89a3d6add0aaa1250ec8bd0a3b Author: Lawrence Minion Date: Tue Oct 23 14:49:42 2018 -0700 changing example size Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile Tutorials/SDC/HeatEquation_EX1_C/inputs_2d commit 5df963c75abb7cb68f31136c75c9e67273d3b079 Author: Weiqun Zhang Date: Tue Oct 23 14:44:56 2018 -0700 use one buffer for all recv data Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit a26f208d29bc3c364e55fc5409698f5dbee51459 Merge: 6aac4a682 a48788daa Author: Weiqun Zhang Date: Tue Oct 23 14:20:06 2018 -0700 Merge branch 'gpu-comm-malloc' into gpu-fb commit a48788daae005f7f2ace89af4940bee03dbd8551 Merge: abfc3af25 07678f261 Author: Weiqun Zhang Date: Tue Oct 23 14:17:15 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-comm-malloc commit 07678f261460570ceef8665484a9edd3aa8736a9 Author: Andrew Myers Date: Tue Oct 23 16:15:56 2018 -0400 changes needed by the new Cuda::ManagedVector Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_TracerParticles.cpp commit 375a7eb1d08b1c9b6d0e8e8835aa24e9473e0de8 Author: Andrew Myers Date: Tue Oct 23 16:14:55 2018 -0400 use thrust as the underlying container type for Cuda::ManagedVector Src/Base/AMReX_CudaContainers.H commit 4d051de0de43b28d43e5fcb4bd48a200b01f9595 Author: Andrew Myers Date: Tue Oct 23 16:14:17 2018 -0400 add custom allocator for use with thrust::device_vector Src/Base/AMReX_CudaAllocators.H commit b30cff0eb5020083e47515fb2ba27bafa58e18d3 Author: Kevin Gott Date: Tue Oct 23 16:10:08 2018 -0400 Revert "Async FillBoundary kernel calls. Further testing/tweaking required." This reverts commit 0b9070719e7e3a7092e9f3c33d60b3e1bb561d1a. Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit bbf7beabf891fb796f83a090744c055dcfc9007d Author: Kevin Gott Date: Tue Oct 23 16:09:46 2018 -0400 Revert "Revert "Add first draft of ASYNC macro and CPU versions of other macros."" This reverts commit 901d17cc2d19fc768fe05db37fc5ef4de6e0cb17. Src/Base/AMReX_CudaLaunch.H commit 901d17cc2d19fc768fe05db37fc5ef4de6e0cb17 Author: Kevin Gott Date: Tue Oct 23 16:07:23 2018 -0400 Revert "Add first draft of ASYNC macro and CPU versions of other macros." This reverts commit 8ef30be7967b6b6f17e5b955bd882c398103a230. Src/Base/AMReX_CudaLaunch.H commit 6aac4a68291278826ba14874ce93eed08d720678 Author: Weiqun Zhang Date: Tue Oct 23 15:54:07 2018 -0400 remove _async Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 4cadfd66fb5eda07b2120ebbb8cedda5f5b04a88 Author: Weiqun Zhang Date: Tue Oct 23 15:29:58 2018 -0400 WIP: StreamIter Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FabArrayCommI.H commit 0b9070719e7e3a7092e9f3c33d60b3e1bb561d1a Author: Kevin Gott Date: Tue Oct 23 12:32:49 2018 -0400 Async FillBoundary kernel calls. Further testing/tweaking required. Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 8ef30be7967b6b6f17e5b955bd882c398103a230 Author: Kevin Gott Date: Tue Oct 23 12:31:10 2018 -0400 Add first draft of ASYNC macro and CPU versions of other macros. Src/Base/AMReX_CudaLaunch.H commit fdd5414712f73b59bac54f2c6049bcbde25444ed Author: Kevin Gott Date: Tue Oct 23 12:29:59 2018 -0400 GPU-ize another norm function. Src/Base/AMReX_MultiFab.cpp commit 080cee792c32bfd834dc8a91fa7ae54ec79402d6 Merge: 590c60434 f4acc9482 Author: Andrew Myers Date: Tue Oct 23 00:04:26 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 590c604348604f6054ef2fb5378e245f46bd4d43 Author: Andrew Myers Date: Tue Oct 23 00:03:42 2018 -0400 further reduce the number of memory allocations in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 4052ff7cc86202a043df479cd09077e2a1b98618 Author: Weiqun Zhang Date: Mon Oct 22 18:15:47 2018 -0700 update header name Src/Base/AMReX_CoordSys.cpp commit c4ef333919b53a8a6c16478d4067eab62bb217b4 Author: Weiqun Zhang Date: Mon Oct 22 18:15:07 2018 -0700 rename for typecheck Src/Base/AMReX_COORDSYS_C.H Src/Base/CMakeLists.txt Src/Base/Make.package commit fcc1923854b31bcb0c78bc1d22137bbfcbd786c5 Author: Weiqun Zhang Date: Mon Oct 22 17:58:51 2018 -0700 CoordSys: Fortran -> C++ and GPU Src/Base/AMReX_Box.H Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_1D.cpp Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_2D.cpp Src/Base/AMReX_COORDSYS_3D.F90 Src/Base/AMReX_COORDSYS_3D.cpp Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 085375494e9a3cb8bb24abf338344cdc723849f9 Merge: 22cd090c5 276cba540 Author: Marc Day Date: Mon Oct 22 17:31:29 2018 -0700 Merge pull request #351 from burlen/sensei_adaptor_bugfix sensei data adaptor fixes commit 276cba5406a18909371a7739b9135e9228dd5e77 Author: Burlen Loring Date: Mon Oct 22 15:15:27 2018 -0700 sensei data adaptor fixes * set data set origin, fixes issue with simulations where the lower left corner in physical space is not at 0,0,0 * fix a memory leak in AmrMeshDataAdaptor * let simulations set control parameters explicilty * validate control parameters during initialization Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp Src/Extern/SENSEI/AMReX_InSituBridge.H Src/Extern/SENSEI/AMReX_InSituBridge.cpp commit f4acc948295f4198c4d60efc4219ad4e3a81614b Author: Kevin Gott Date: Mon Oct 22 17:31:09 2018 -0400 First attempt at a triple macro for (i, j, k) equivalent flux calls. Src/Base/AMReX_CudaLaunch.H commit b51f0192d92313b4db6a66358dec546489bd0b50 Merge: d6ae25ec3 ac6e1ed2f Author: Andrew Myers Date: Mon Oct 22 16:15:32 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit d6ae25ec3fa9d583a04f60f074a8739d8213f2a5 Author: Andrew Myers Date: Mon Oct 22 16:15:08 2018 -0400 avoid repeatedly reallocating memory on the GPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit abfc3af258d9a434237102570bf76273bf6ed213 Author: Weiqun Zhang Date: Mon Oct 22 13:08:25 2018 -0700 rm deprecated upc++ stuff OldTutorials/PGAS_HEAT/GNUmakefile OldTutorials/PGAS_HEAT/Make.package OldTutorials/PGAS_HEAT/advance_3d.f90 OldTutorials/PGAS_HEAT/init_phi_3d.f90 OldTutorials/PGAS_HEAT/inputs_3d OldTutorials/PGAS_HEAT/main.cpp OldTutorials/PGAS_HEAT/test-mpi3/main.cpp OldTutorials/PGAS_HEAT/writePlotFile.H OldTutorials/PGAS_HEAT/writePlotFile.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BLPgas.H Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Tests/FillBoundaryComparison/GNUmakefile Tests/FillBoundaryComparison/main.cpp commit de3b4ba84680bc73301c1493250b7206c7bb3056 Author: Andrew Myers Date: Mon Oct 22 14:57:49 2018 -0400 remove page faults from RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 22cd090c5a70c7028cac4b63d1751e70fdcccc04 Author: Weiqun Zhang Date: Mon Oct 22 11:10:08 2018 -0700 fix a bug in 1d interpolation thanks to Zhonglin Li Src/AmrCore/AMReX_INTERP_1D.F90 commit ac6e1ed2f99d832ab59d345ae7cd03cb4ca8513e Author: Kevin Gott Date: Mon Oct 22 12:55:59 2018 -0400 Fix MultiFab reduction locations in some functions. Src/Base/AMReX_MultiFab.cpp commit 03eb03560a147443fa7e0654946f4aa3d15a2d79 Author: Kevin Gott Date: Mon Oct 22 12:45:34 2018 -0400 Add Cuda namespace to HeatEquation & add script for OLCF Ascent. Tutorials/GPU/HeatEquation_EX0_C/Exec/run.ascent Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit 3bc91be1e84697f5d19352d847a5dcdb2640af99 Author: Weiqun Zhang Date: Mon Oct 22 09:23:17 2018 -0700 fix typo Src/Base/AMReX_CudaLaunch.H commit 05db02e4f2c9c233c153e7244a68dd7df8f52769 Author: Ann Almgren Date: Sun Oct 21 17:50:23 2018 -0700 Add the gradient operation for 3D EB nodal -- this is in the mknewu routine. Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit f97f4ab56ab9f8f415ef84f74cc258673e5e53cd Author: Ann Almgren Date: Sun Oct 21 13:44:05 2018 -0700 Add the 3D EB divergence stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 97a5dd17bd075df3c8a0fb046dda629636ae9df5 Merge: e649272b2 302e474d0 Author: Weiqun Zhang Date: Sun Oct 21 13:22:08 2018 -0700 Merge branch 'gpu-merge-test3' into gpu-merge-test2 commit 302e474d0f8177966d78be760e400419eb52f665 Author: Weiqun Zhang Date: Sun Oct 21 16:15:46 2018 -0400 tweak threading trying to be more page friendly Src/Base/AMReX_CudaLaunch.H commit e649272b2ec910548f8d9cff09df442bdf875f33 Author: Kevin Gott Date: Sun Oct 21 13:15:16 2018 -0400 Small, partial changes. Src/Base/AMReX_MultiFab.cpp commit 2031ff34f7d85a26aae73595bd2b339bbd25dc88 Author: Weiqun Zhang Date: Sat Oct 20 13:38:35 2018 -0700 rm Managed as Base of Box and RealBox. namespace reorganization: amrex::Cuda::Atomic::Add etc. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_RealBox.H commit a7a5389cc5b7b4579cb7fa2a674015c9fb29a82f Author: Weiqun Zhang Date: Sat Oct 20 10:46:13 2018 -0700 try to avoid potential name conflict Src/Base/AMReX_CudaLaunch.H commit 86bd00c115fbd2b7ce7c27ab6ccdec3f3d9e205e Author: Weiqun Zhang Date: Sat Oct 20 10:42:49 2018 -0700 put Strategy and getThreadBox into namespace Cuda Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_FArrayBox.cpp commit acd6f6eb50482e1ec3f662d4fd1c8ced659d3455 Author: Weiqun Zhang Date: Fri Oct 19 21:52:02 2018 -0700 int -> long and inline Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp commit 717229b4389df56ef99c973a04253a7561290783 Merge: 323671933 d14cb41c3 Author: Kevin Gott Date: Fri Oct 19 22:17:33 2018 -0400 Merge branch 'gpu-merge-test3' of https://github.com/AMReX-Codes/amrex into gpu-merge-test3 commit 323671933165ee0faf87281affc95ce061644740 Author: Kevin Gott Date: Fri Oct 19 22:17:25 2018 -0400 Better/(fixed(?)) version of the 1D thread box. Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp commit 0f86f9e4a1d789013c423ca2b87635af78046969 Merge: b7a041012 5a7cfbb9d Author: Marc Day Date: Fri Oct 19 17:44:31 2018 -0700 Merge pull request #346 from burlen/amrmesh_bug_fix fix a bug in sensei AmrMeshDataAdaptor commit d14cb41c3b12df8221ed6dc7c02f87251b72bb72 Merge: 957b7a77a fb62a1051 Author: Weiqun Zhang Date: Fri Oct 19 17:39:03 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-merge-test3 commit fb62a10513e70c1a7326007c848e9fce88262a15 Author: Andrew Myers Date: Fri Oct 19 17:23:53 2018 -0700 make ManagedVector::assign run either on the CPU or GPU depending on Cuda::inLaunchRegion Src/Base/AMReX_CudaContainers.H commit bac6d84b580ae3f8acb9d3eb61f8aa5743e96d35 Author: Andrew Myers Date: Fri Oct 19 17:21:18 2018 -0700 double -> Real Src/Particle/AMReX_Particles.H commit dc8a7ec2d17ef85950a0533c638ebd664ec159b9 Author: Andrew Myers Date: Fri Oct 19 17:15:41 2018 -0700 fix get / set particles for 2D Src/Particle/AMReX_Particles.H commit 21f44b57b662cf1c9a8a42dc1bf7f9f38fef1744 Author: Andrew Myers Date: Fri Oct 19 16:56:22 2018 -0700 use Cuda::ManagedVector in Particles Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H commit 5a7cfbb9d9f7580b9629228a1193ed27cf6b7b4c Author: Burlen Loring Date: Fri Oct 19 16:53:08 2018 -0700 fix a bug in sensei AmrMeshDataAdaptor ref ratios may be empty if only 1 level, and cleanup some code in the tutorial that should not have been committed. Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit c5b8482936911115e08bcb14955df710a89f75f6 Author: Andrew Myers Date: Fri Oct 19 16:32:35 2018 -0700 add HostVector and ManagedVector, move to a different file. Src/Base/AMReX_Cuda.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_Vector.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 45d993a958fd2166fa0abf17c7fab9564fc83710 Author: Andrew Myers Date: Fri Oct 19 16:27:51 2018 -0700 remove executable permissions from these source files. Src/Base/AMReX_MultiFabUtil_Perilla.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit 6909852e0aff465bfbab5e322151fb8fcdbec3ab Author: Andrew Myers Date: Fri Oct 19 16:16:39 2018 -0700 add dataPtr() wrapper to ArrayOfStructs Src/Particle/AMReX_ArrayOfStructs.H commit 144acd74bfa3f0a68212f85012894c8ff1c136b8 Author: Andrew Myers Date: Fri Oct 19 15:59:09 2018 -0700 use a template function to reduce code duplication Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 43091486b26ade527b27067260cffb324db3a1c8 Author: Andrew Myers Date: Fri Oct 19 15:55:37 2018 -0700 mn -> mx again Src/Base/AMReX_MultiFab.cpp commit 5fa5fb94448150cf5319a6ac3ce67cfd936eeb1e Author: Andrew Myers Date: Fri Oct 19 15:55:13 2018 -0700 mn -> mx Src/Base/AMReX_MultiFab.cpp commit 8aee1a4ebd11d2ca2f1a836faba9418720a89784 Author: Andrew Myers Date: Fri Oct 19 15:54:45 2018 -0700 add missing if Src/Base/AMReX_MultiFab.cpp commit bcd324f4355d180fba5c6726c05916e2d054dff6 Merge: 12dba2753 b698d8041 Author: Andrew Myers Date: Fri Oct 19 15:53:22 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 957b7a77a85b9779740835016c6e73c8b528eb4c Merge: f18587738 b698d8041 Author: Weiqun Zhang Date: Fri Oct 19 15:14:53 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-merge-test3 commit f18587738b4dc832d733659c0a7ea7f2f26cbd8a Author: Kevin Gott Date: Fri Oct 19 18:12:26 2018 -0400 fix launches. Src/Base/AMReX_CudaLaunch.H commit 12dba2753d8cecd90597f1ec32aaf60b59a6c32e Author: Andrew Myers Date: Fri Oct 19 14:52:31 2018 -0700 give DeviceVector an assign method Src/Base/AMReX_Vector.H commit 2f9f814d4043abd5161a256a63903518d6222581 Author: Kevin Gott Date: Fri Oct 19 17:47:29 2018 -0400 Launch macros with striding. Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp commit b698d8041c054b33eea3ee9e79807eeae22693f3 Merge: 02c26860e 7fecc0778 Author: Weiqun Zhang Date: Fri Oct 19 14:40:42 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 93d79691c115e91cb3822bf645f3689c2f2b3fe1 Author: Andrew Myers Date: Fri Oct 19 14:31:22 2018 -0700 give both device and managed versions of Get / Set Position to ParIter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 7cc3f09db4a2240068e783cd3d7bad60be1384e1 Author: Andrew Myers Date: Fri Oct 19 14:08:07 2018 -0700 use DeviceVector in the ParIter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit e7c6863a72955c9b8d0e713aaf586850192fa034 Author: Andrew Myers Date: Fri Oct 19 14:07:34 2018 -0700 add a wrapper around thrust::device_vector that does the raw_pointer_cast for you Src/Base/AMReX_Vector.H commit ba94b412bd0e2c355efcd6a6831e441032be815a Merge: 872f8a9b5 b7a041012 Author: Cy Chan Date: Fri Oct 19 13:57:02 2018 -0700 Merge branch 'development' into cy-perf commit 872f8a9b5c0308421d192fcb2c6839bc332b5411 Author: Cy Chan Date: Mon Oct 15 16:22:54 2018 -0700 add verbose_mapper flag and detailed messages for DistributionMapping Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelContext.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7fecc07780a93d019a4c275e1723433ba579f808 Author: Kevin Gott Date: Fri Oct 19 16:31:54 2018 -0400 Testing safe for USE_CUDA=FALSE Tutorials/GPU/HelloWorld_C/main.cpp commit 704563169e97a82ce030a91ac432427c55c28b76 Author: Kevin Gott Date: Fri Oct 19 16:30:09 2018 -0400 Starting MultiFab::norm conversions with norm0. Src/Base/AMReX_MultiFab.cpp commit fb50d2d3fc798c4a6ad78962a2bca52dc77d2a84 Author: Weiqun Zhang Date: Fri Oct 19 16:19:46 2018 -0400 new strategy Src/Base/AMReX_Box.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp commit 02c26860e66ccc0f277971c4a261b6c0323903f7 Author: Weiqun Zhang Date: Fri Oct 19 10:52:32 2018 -0700 add AMReX_Cuda.H so that the user only needs to include this one header. add operator<< for printing dim3. Src/Base/AMReX_Cuda.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 91fb0604d7fe316aa763dc7be2c83711abd90848 Merge: 999aafb91 9ddc51039 Author: Andrew Myers Date: Thu Oct 18 21:22:55 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 999aafb91c3e85652db4e9c8949e888b6c827997 Author: Andrew Myers Date: Thu Oct 18 21:22:28 2018 -0400 add a nice hack to the Ascent makefile so you don't have to mess with CPATH to build Tools/GNUMake/sites/Make.olcf commit 9ddc51039f96f19e5f5d1ff4961b1e1862059c0d Author: Weiqun Zhang Date: Thu Oct 18 17:40:31 2018 -0700 move ptr identification functions to amrex::Cuda:: in AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 1669e0edffd6592e190cb497b758f109ab9d00fb Merge: f17b7cff7 d988fb9a0 Author: Andrew Myers Date: Thu Oct 18 17:19:46 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit d988fb9a01087d2fcb5b42457605a8c0d69f1f70 Author: Weiqun Zhang Date: Thu Oct 18 13:31:06 2018 -0700 fix bugs Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_Device.cpp commit f17b7cff75f9f3faf4ea3398fe6a0b16dc60394b Author: Andrew Myers Date: Thu Oct 18 17:15:38 2018 -0700 only use thrust::device_vector in Get / Set Position if Cuda is on. Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 3c7e91f2bf58ebd09e379c16da18f557ce6438a5 Author: Kevin Gott Date: Thu Oct 18 19:51:53 2018 -0400 Wrap Utility for USE_CUDA=FALSE Src/Base/AMReX_CudaUtility.H commit ec5cccb6d2bca2d126184caf93afb56dcd4201e5 Author: Kevin Gott Date: Thu Oct 18 19:50:57 2018 -0400 Fix DeviceScalar. Src/Base/AMReX_CudaMemory.H commit d9e78c5bf5a84911afce8bd1ca6b1497c71c5d0d Author: Kevin Gott Date: Thu Oct 18 19:30:41 2018 -0400 Max and Min changes and test case. Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/HelloWorld_C/main.cpp commit 11a82011642e64207a366413b531044db62e2012 Author: Weiqun Zhang Date: Thu Oct 18 09:35:21 2018 -0700 add inline so that it compiles Src/Base/AMReX_CudaUtility.H commit b8d3fbd36798179dec64a36f0fdaf94c0ed05ad0 Author: Weiqun Zhang Date: Thu Oct 18 09:32:41 2018 -0700 fix typo Src/Base/AMReX_CudaUtility.H commit e0031fdc03cc2a21a7f91ccd73f437cc421b9368 Author: Kevin Gott Date: Thu Oct 18 03:17:15 2018 -0400 First draft of GPU MultiFab::min and max. Needs testing. Fix in sum. Src/Base/AMReX_MultiFab.cpp commit 56f503d94988bef27d85fe0cda2d55623eb3257a Author: Kevin Gott Date: Thu Oct 18 03:15:13 2018 -0400 atomicMin and atomicMax for float and double. Src/Base/AMReX_CudaUtility.H commit 89dfa8dae8fdadc186dd952c108a80bf7003b1b4 Author: Kevin Gott Date: Wed Oct 17 20:12:39 2018 -0400 GPU versions of Dot, Dotmask, initVal and Sum. Src/Base/AMReX_MultiFab.cpp commit 02b616ff13b7659e1b6754d5c4d3e1f4d9d38310 Author: Andrew Myers Date: Wed Oct 17 17:04:38 2018 -0700 Device::inLaunchRegion() -> Cuda::inLaunchRegion() Src/Base/AMReX_MultiFab.cpp commit 4f1b0acf4720db5a7e3e87694e39002392578b05 Author: Andrew Myers Date: Wed Oct 17 19:55:20 2018 -0400 use macro instead of template thing here Src/Base/AMReX_TypeTraits.H Src/Particle/AMReX_ParticleContainerI.H commit 73aa1732e163651435704121a6f47db41ecc3cbb Merge: d0dacb8cb 4a513d311 Author: Andrew Myers Date: Wed Oct 17 16:42:46 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit d0dacb8cbf9f154501ea25719e97ae6f7c500cc3 Author: Andrew Myers Date: Wed Oct 17 16:42:21 2018 -0700 always have this compile-time check return true if the gcc version is too old to support it Src/Base/AMReX_TypeTraits.H commit 4a513d311d21cc3ce7d1be9c37ddee889dc1699d Author: Weiqun Zhang Date: Wed Oct 17 16:14:03 2018 -0700 put FabArray::initVal on GPU Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.cpp commit 9b65ce6b35ab79bd7f7a356edac29db03a12884d Author: Weiqun Zhang Date: Wed Oct 17 16:12:50 2018 -0700 int -> long in 1d Strategy Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 340f216f6bd5e58fe98488f62019130c880c90e6 Merge: 1cae99ebb abf9034ea Author: Weiqun Zhang Date: Wed Oct 17 15:40:51 2018 -0700 Merge branch 'gpu-merge-test' into gpu-merge-test2 commit abf9034ea967600f2b9d58cc98a8ff08325eb292 Merge: 382da09d1 b7a041012 Author: Weiqun Zhang Date: Wed Oct 17 15:40:28 2018 -0700 Merge branch 'development' into gpu-merge-test commit b7a041012fe6d5008221d88d453423bf57d1ddb4 Author: Weiqun Zhang Date: Wed Oct 17 15:38:09 2018 -0700 CArena: make sure memory blocks from different allocations are not coalesced, otherwise cuda complains about invalid argument in cudaMemcpy. Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit 1cae99ebbbcd84b331f9bf0a839a916dafd1a967 Author: Weiqun Zhang Date: Wed Oct 17 15:38:09 2018 -0700 CArena: make sure memory blocks from different allocations are not coalesced, otherwise cuda complains about invalid argument in cudaMemcpy. Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit 0f1802b78f7c015e4d31c6ddf7a23d0c49f8237d Author: Weiqun Zhang Date: Wed Oct 17 11:31:04 2018 -0700 add some Cuda error checks Src/Base/AMReX_CudaLaunch.H commit f3a969c20371115f4e024741366a13042b7a073a Author: Ann Almgren Date: Wed Oct 17 15:07:45 2018 -0700 Fix a problem that was causing us to lose particles in a triply periodic domain. In the case that required this fix, which used single precision particles, the particle's location was only slightly outside the low domain, but the periodic shift put the particle exactly on the high boundary. The solution is to move the particle to the low boundary when the domain is periodic and the particle lies exactly on the high boundary. The particle will then live in the first cell along the low boundary rather than being labeled as out of bounds outside the high boundary. Src/Particle/AMReX_ParticleContainerI.H commit 787cf9e517ec4cd79b1f4c88719d48d2b86f29a1 Author: Andrew Myers Date: Wed Oct 17 15:06:03 2018 -0700 fix typo in new constructor Src/Particle/AMReX_Particles.H commit a1be7990e9a8e5444ca5e853ae51443e257256f6 Merge: d64e02e11 cdf6166a6 Author: Andrew Myers Date: Wed Oct 17 14:13:08 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d64e02e119b0ebeb6d37456f08251492e126fd50 Author: Andrew Myers Date: Wed Oct 17 14:12:55 2018 -0700 add some ifdefs for when HDF5 is not on Tests/HDF5Benchmark/WritePlotfileHDF5.H Tests/HDF5Benchmark/WritePlotfileHDF5.cpp Tests/HDF5Benchmark/main.cpp commit cdf6166a68c8a69579bac11bd2e8a1f0a2b7ad11 Author: Andrew Myers Date: Wed Oct 17 14:03:52 2018 -0700 read nppc from inputs file Tests/HDF5Benchmark/inputs commit d28a262e6625bd766bf095a1ce89997a533ecd31 Author: Andrew Myers Date: Wed Oct 17 14:01:53 2018 -0700 change default compiler to intel Tests/HDF5Benchmark/GNUmakefile commit 9acea847f51ef0da20a83e19e5f92fb746da11b0 Author: Andrew Myers Date: Wed Oct 17 14:00:35 2018 -0700 add Particle IO to the HDF5Benchmark Tests/HDF5Benchmark/GNUmakefile Tests/HDF5Benchmark/main.cpp commit 8749a22e939225d7dbdc09a0f7a01dfbc4fdbad5 Author: Andrew Myers Date: Wed Oct 17 14:00:17 2018 -0700 add new constructor to ParticleContainer Src/Particle/AMReX_Particles.H commit 94fccde71b7d8e86d07d429bdb013697cbeb42da Merge: 78fcf19b0 db5bdb0fd Author: Andrew Myers Date: Wed Oct 17 15:14:01 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 78fcf19b0329b53a1d467774678949adfb9a09cb Author: Andrew Myers Date: Wed Oct 17 15:13:33 2018 -0400 also assert that the particle type is trivially copyable Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 02f5889df37f82bd18a39e1277e80f9360144250 Author: Andrew Myers Date: Wed Oct 17 15:13:12 2018 -0400 add a new template to work around the fact that gcc < 5 doesn't have std::is_trivially_copyable Src/Base/AMReX_TypeTraits.H commit 4fef58f691c78e05cebcbc6f7ecc49b4f4c97572 Merge: 205402177 d90470823 Author: WeiqunZhang Date: Wed Oct 17 10:25:36 2018 -0700 Merge pull request #344 from jared321/intersectionInFortran Intersection in fortran commit db5bdb0fd32cccc4fe31f17fc7f8abad9543bab6 Author: Weiqun Zhang Date: Wed Oct 17 10:03:45 2018 -0700 change strides back to 1 again Src/Base/AMReX_CudaLaunch.H commit 78bec173fbc0f24f02de6780de8f1f106a2d8737 Author: Weiqun Zhang Date: Wed Oct 17 09:38:05 2018 -0700 shift the box so that the smallend is zero. this will make threading consistent for same size boxes Src/Base/AMReX_CudaLaunch.H commit d90470823ca01cd42d2f998a30f3666d45cc39ad Author: Jared O'Neal Date: Wed Oct 17 11:31:31 2018 -0500 Intersection is no longer done by using C++ routines. It is handled directly in the Fortran box module. Src/F_Interfaces/Base/AMReX_box_fi.cpp Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 37cc4a75827a7125e2bfdcdc284db3a7d940a938 Author: Weiqun Zhang Date: Wed Oct 17 00:13:38 2018 -0400 change strides to 1 till we fix the bug Src/Base/AMReX_CudaLaunch.H commit 26b06d8c80d0dc9489f10db68af8e57de9f8610b Author: Weiqun Zhang Date: Tue Oct 16 17:25:31 2018 -0700 new Strategy giving more work to threads Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/HelloWorld_C/inputs_3d Tutorials/GPU/HelloWorld_C/main.cpp commit f4f3e55573fdc97ff44aba52f06d61ffd373b5ab Merge: cf624acfd 382da09d1 Author: Andrew Myers Date: Tue Oct 16 20:08:31 2018 -0400 Merge branch 'gpu-merge-test' into gpu-merge-test2 commit cf624acfd26ee16baa96e8318ecdb687854eb34a Merge: 8441d60c0 6f760d0ec Author: Andrew Myers Date: Tue Oct 16 19:54:12 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 8441d60c0abe46bb5b7fed10ca221d60e32009d8 Author: Andrew Myers Date: Tue Oct 16 19:53:41 2018 -0400 relax the assumption that the particle type must be POD Src/Particle/AMReX_ParticleContainerI.H commit 82ce7f89a3e5a4c96b7dc74abc2d912fbea4c709 Author: Andrew Myers Date: Tue Oct 16 19:53:20 2018 -0400 give particle a constructor marked host/device Src/Particle/AMReX_Particle.H commit 6f760d0ec37a566dc7f99680cd9f17e763ac4ac4 Author: Kevin Gott Date: Tue Oct 16 19:42:04 2018 -0400 Correct inputs for Dot test. Tutorials/GPU/HelloWorld_C/inputs_3d Tutorials/GPU/HelloWorld_C/inputs_geometry commit 03ed3958d489030b33f1b986f4a71561635d3159 Author: Kevin Gott Date: Tue Oct 16 19:39:27 2018 -0400 Dot test. Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/run.script commit 7484adcf0898370821765d94a13ea123866e4bc5 Author: Weiqun Zhang Date: Tue Oct 16 15:21:19 2018 -0700 update DeviceScalar so that it works outside launch region Src/Base/AMReX_CudaMemory.H commit c8d689c15c126dcfc0e6c2a43ce3273a28de3e5f Author: Weiqun Zhang Date: Tue Oct 16 15:16:32 2018 -0700 Device::inLaunchRegion -> Cuda::inLaunchRegion so that we can access the flag without including AMReX_Device.H Src/Base/AMReX_CudaControl.H Src/Base/AMReX_CudaControl.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Tools/F_scripts/write_cuda_headers.py commit 20540217751f596024a8eb255cd4c13486e9e25d Merge: 5776d2e9a eb175b3f2 Author: Marc Day Date: Tue Oct 16 14:57:25 2018 -0700 Merge pull request #339 from burlen/sensei_insitu_development Sensei insitu development commit 5ad081e62f9418bd23caff646ac34c77b1ed7207 Author: Andrew Myers Date: Tue Oct 16 17:33:28 2018 -0400 make MultiFab::OverrideSync() launchable Src/Base/AMReX_MultiFab.cpp commit 5687b90a780e97b6861625c60d2dad1b3932d084 Merge: e5050cd53 35dc98d1e Author: Andrew Myers Date: Tue Oct 16 17:23:30 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 35dc98d1ee85fb721518e0c3f8b0217b77e421d8 Author: Weiqun Zhang Date: Tue Oct 16 13:08:39 2018 -0700 remove HostDeviceScalar Src/Base/AMReX_CudaMemory.H commit 7ae5f75f3dda2743603794d9241d9dfe2d1756c4 Author: Jared O'Neal Date: Tue Oct 16 15:04:39 2018 -0500 Added box intersection routine in Fortran interface. Src/F_Interfaces/Base/AMReX_box_fi.cpp Src/F_Interfaces/Base/AMReX_box_mod.F90 commit e5050cd5391f5868ad5934ead3b34f31e44d5f59 Author: Andrew Myers Date: Tue Oct 16 15:59:12 2018 -0400 fix parameter shadowing Src/Particle/AMReX_ParticleContainerI.H commit 978d92586e50236804043c4af188c6639da7fb52 Author: Andrew Myers Date: Tue Oct 16 14:30:22 2018 -0400 remove AtomicAccumulate method from ParticleContainer in favor of the one from BaseFab. Src/Particle/AMReX_Particles.H commit 6227feebab8967d50b30ba0a8147c37a16dc84b9 Author: Andrew Myers Date: Tue Oct 16 14:27:27 2018 -0400 fix atomicAdd implementation Src/Base/AMReX_BaseFab.H commit d230a70253e0cd352b2b6bc2e801eeec07472dd2 Author: Andrew Myers Date: Tue Oct 16 14:24:24 2018 -0400 finish implementing atomicAdd for BaseFab Src/Base/AMReX_BaseFab.H commit 77a7e6b23225e0c4b1d617f8a2d63e4b76f50711 Author: Andrew Myers Date: Tue Oct 16 14:16:43 2018 -0400 start to implement atomicAdd for BaseFab Src/Base/AMReX_BaseFab.H commit 34b8900f58e0182fbb143f04a14d8564f8654cfc Author: Michele Rosso Date: Mon Oct 15 15:09:23 2018 -0700 CMake: fix bug in STRIP macro Tools/CMake/AMReX_Utils.cmake commit 458408072accab686366256a2237e8e2fd92162d Merge: 8edfba50e fe7c86fae Author: Andrew Myers Date: Tue Oct 16 13:56:58 2018 -0400 Merge branch 'gpu-merge-test' into gpu-merge-test2 commit 8edfba50e8a07523da463313aa3e8f88c9cb3c16 Author: Weiqun Zhang Date: Tue Oct 16 10:52:51 2018 -0700 move atomics to CudaUtility.H, add DeviceScalar, and simplify reduction for MultiFab::Dot Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_TypeTraits.H Src/Base/CMakeLists.txt Src/Base/Make.package commit fe7c86faed89ee9e6099bc59b2b3ecd204d2e489 Author: Andrew Myers Date: Tue Oct 16 02:11:40 2018 -0400 more timers in Multifab Src/Base/AMReX_MultiFab.cpp commit f2c767a1f9abe65cd73ee910fcec86fcb9aee0ac Author: Andrew Myers Date: Tue Oct 16 00:24:53 2018 -0400 C++ version of amrex_atomic_accumulate Src/Particle/AMReX_Particles.H commit 382da09d11ea2c91c25fcd4e110004047d169433 Merge: b35ad2e44 ed34b99cf Author: Weiqun Zhang Date: Mon Oct 15 17:50:28 2018 -0700 Merge branch 'gpu-merge-test' of github.com:AMReX-Codes/amrex into gpu-merge-test commit b35ad2e4468aa3166a0cd2b7619f26807a1b5ba3 Author: Weiqun Zhang Date: Mon Oct 15 17:50:12 2018 -0700 add some Device:synchronize calls to the two step version of parallel copy Src/Base/AMReX_FabArrayCommI.H commit ed34b99cf09e3054af439545117283cd850b81cb Author: Kevin Gott Date: Mon Oct 15 20:28:30 2018 -0400 Preliminary GNUMake system for Ascent. Just copy of summit for now. Tools/GNUMake/Make.machines Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/sites/Make.olcf commit 5776d2e9a6d891fef75a173ad7069803e9e0b99a Merge: 463427ba1 d6ee42371 Author: Jean M. Sexton Date: Mon Oct 15 17:21:14 2018 -0700 Merge branch 'development' of github.com:amrex-codes/amrex into development commit 463427ba1c3b3ae8f0f888b0d33ba5b3556f68a6 Author: Jean M. Sexton Date: Mon Oct 15 17:20:34 2018 -0700 Add basic documentation for new flags Docs/sphinx_documentation/source/CVODE.rst Docs/sphinx_documentation/source/SUNDIALS3.rst commit d6ee423712f49dc8e74993c8cec38d9da8949be0 Author: Andy Nonaka Date: Mon Oct 15 17:09:25 2018 -0700 wrote a helpful debugging utility, "WriteMLMF" that writes a multilevel plotfile to disk given only: -plotfile name -vector of MultiFabs -vector of Geometrys variable names are written as "Var0", "Var1", etc. refinement ratio is computed from the Geometry vector "time" and "level_steps" are set to zero Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit 9b14a25dcc9f0cc48f4d87de2e58151dfb6d43c2 Merge: d92e74784 f67363da4 Author: Jean M. Sexton Date: Mon Oct 15 17:04:25 2018 -0700 Merge branch 'development' of github.com:amrex-codes/amrex into development commit d92e7478496e6da6bd7278c5d357a09a04850df9 Author: Jean M. Sexton Date: Mon Oct 15 17:04:18 2018 -0700 Updated make system with new sundials compile flags Src/Extern/SUNDIALS3/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.cvode Tools/GNUMake/packages/Make.sundials3 Tutorials/CVODE/SUNDIALS2_finterface/EX1/GNUmakefile Tutorials/CVODE/SUNDIALS2_finterface/EX2/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/SetIC.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_finterface/EX1/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/GNUmakefile commit f67363da4459beeb5110409045f9fd7907a857af Author: Michele Rosso Date: Mon Oct 15 15:50:43 2018 -0700 Replace macro D_DECL() with AMREX_D_DECL to comply with XSDK defaults Src/Base/AMReX_ForkJoin.H commit 3e4e560889d6de8fca8c3f2eb34d499144a31d1e Author: Cy Chan Date: Mon Oct 15 15:43:22 2018 -0700 added software performance counters for MLMG operations smooth, apply, restrict, interpolate turn on with -DAMREX_SOFT_PERF_COUNTERS added some profiling regions for detailed MLMG analysis regions used to tag sends/receives when used with amrprofvis -srlist separate out different MG levels Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 3e4375fe5fdef8e145b10c899857c884309b7aec Author: Weiqun Zhang Date: Mon Oct 15 15:44:57 2018 -0700 add addFromMem and use it for FabArray::ADD Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayCommI.H commit 8b576d579c67d845c7def29acce06fec469fc160 Author: Michele Rosso Date: Mon Oct 15 15:09:23 2018 -0700 CMake: fix bug in STRIP macro Tools/CMake/AMReX_Utils.cmake commit f62009be796fffa9c080d744ca5eec8e57889ec4 Author: Jean M. Sexton Date: Mon Oct 15 14:37:25 2018 -0700 Rearranged Sundials tutorials Tutorials/CVODE/SUNDIALS2_finterface/EX1/GNUmakefile Tutorials/CVODE/SUNDIALS2_finterface/EX1/Make.package Tutorials/CVODE/SUNDIALS2_finterface/EX1/inputs Tutorials/CVODE/SUNDIALS2_finterface/EX1/integrate_ode.f90 Tutorials/CVODE/SUNDIALS2_finterface/EX1/main.cpp Tutorials/CVODE/SUNDIALS2_finterface/EX1/myfunc_F.H Tutorials/CVODE/SUNDIALS2_finterface/EX1/ode_mod.f90 Tutorials/CVODE/SUNDIALS2_finterface/EX2/GNUmakefile Tutorials/CVODE/SUNDIALS2_finterface/EX2/Make.package Tutorials/CVODE/SUNDIALS2_finterface/EX2/inputs Tutorials/CVODE/SUNDIALS2_finterface/EX2/integrate_ode_no_jac.f90 Tutorials/CVODE/SUNDIALS2_finterface/EX2/integrate_ode_with_jac.f90 Tutorials/CVODE/SUNDIALS2_finterface/EX2/main.cpp Tutorials/CVODE/SUNDIALS2_finterface/EX2/myfunc_F.H Tutorials/CVODE/SUNDIALS2_finterface/EX2/ode_mod.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/Make.package Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/SetIC.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/inputs Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/myfunc_F.H Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/ode_mod.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/Make.package Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/SetIC.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/inputs Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/myfunc_F.H Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/ode_mod.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/Make.package Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/inputs Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/inputs_2box Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/inputs_non_vectorized Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/myfunc_F.H Tutorials/CVODE/SUNDIALS3_finterface/EX1/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX1/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX1/inputs Tutorials/CVODE/SUNDIALS3_finterface/EX1/integrate_ode.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX1/main.cpp Tutorials/CVODE/SUNDIALS3_finterface/EX1/myfunc_F.H Tutorials/CVODE/SUNDIALS3_finterface/EX1/ode_mod.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/ark_analytic_fp.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/Make.package 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Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.out Tutorials/CVODE/SUNDIALS4/EX3-CUDA/GNUmakefile Tutorials/CVODE/SUNDIALS4/EX3-CUDA/Make.CVODE Tutorials/CVODE/SUNDIALS4/EX3-CUDA/Make.package Tutorials/CVODE/SUNDIALS4/EX3-CUDA/README.md Tutorials/CVODE/SUNDIALS4/EX3-CUDA/extern_probin.template Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_128 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_256 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_32 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_64 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/main.cpp Tutorials/CVODE/SUNDIALS4/EX3-CUDA/make_cuda.sh Tutorials/CVODE/SUNDIALS4/EX3-CUDA/make_cuda_cusolver.sh Tutorials/CVODE/SUNDIALS4/EX3-CUDA/make_serial.sh Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda.cpp Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda_cusolver.cpp Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_serial.cpp Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_system.F90 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_utils.F90 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/test_react.H Tutorials/CVODE/SUNDIALS4/EX3-CUDA/test_react_F.H commit fdb9416dddcecc10a4fb891be3e4df56734ba452 Merge: 042eb98aa c63ecbbb6 Author: Kevin Gott Date: Mon Oct 15 17:15:07 2018 -0400 Merge branch 'gpu-merge-test' of https://github.com/AMReX-Codes/amrex into gpu-merge-test commit 042eb98aa4d695c7eaae776567a9e50457c646de Author: Kevin Gott Date: Mon Oct 15 17:14:50 2018 -0400 Update tutorials to new macros and library names. All successfully compile. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile commit c63ecbbb62193f6a30f6fa693ff4f6e6797825e6 Merge: b026bc74f 2d8237714 Author: Andrew Myers Date: Mon Oct 15 16:41:01 2018 -0400 Merge branch 'gpu-merge-test' of github.com:AMReX-Codes/amrex into gpu-merge-test commit 2d82377143a41210873c1c21fc8b3a908ce1e9e2 Author: Kevin Gott Date: Mon Oct 15 16:24:44 2018 -0400 AMReX_Device.H included in AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.H commit b026bc74f57a8323ce5df371d1bf901cdcd3e7dc Merge: 5ab12ea9e d0ab3db30 Author: Andrew Myers Date: Mon Oct 15 16:05:39 2018 -0400 Merge branch 'development' into gpu-merge-test commit d0ab3db30f947619139f348881f2662595fd6101 Merge: ef472d7f8 1c1376aea Author: Andrew Myers Date: Mon Oct 15 15:43:18 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ef472d7f8f4072a7d12f5c63a28f3d4942f518c5 Author: Andrew Myers Date: Mon Oct 15 15:42:51 2018 -0400 add a few dimension macros to silence unused variable warnings. Src/Base/AMReX_BaseFab.H commit 5ab12ea9eb0e457e1c8ea20e632e480321c5ca5f Merge: 6b3c9038c 1b2f3bc43 Author: Weiqun Zhang Date: Mon Oct 15 12:11:15 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-merge-test commit 1b2f3bc436a6b40b6bfbe4672080071dbe27569f Author: Weiqun Zhang Date: Mon Oct 15 12:10:46 2018 -0700 fix the_FA_arena initializaiton Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit a980d1266d7aa506ee448e41359eac9b91944a2d Author: Weiqun Zhang Date: Mon Oct 15 11:58:17 2018 -0700 back to the usual version Src/Base/AMReX_FabArrayCommI.H commit e0460837bb02dec767d96efd76f5416b45cceb2b Author: Weiqun Zhang Date: Mon Oct 15 10:39:19 2018 -0700 add NOBOX version of launch macro Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArrayCommI.H commit eb175b3f238729e00aa6b2579e5ab9e30baac979 Author: Burlen Loring Date: Thu Oct 11 15:09:26 2018 -0700 SENSEI sphinx documentation Docs/sphinx_documentation/source/Visualization.rst Docs/sphinx_documentation/source/Visualization/rt_2048_paraview_000500.png.REMOVED.git-id Docs/sphinx_documentation/source/Visualization/rt_2048_visit_000500.png.REMOVED.git-id Docs/sphinx_documentation/source/Visualization/sensei_amrex_arch_sm_824.png commit b346e122b757753aa1ea0f4c992d554859c1afc0 Author: Burlen Loring Date: Thu Apr 19 15:47:10 2018 -0700 SENSEI Integrates the SENSEI in situ framework with AMReX. Adds SENSEI data adaptors, and bridge codes for Amr and AmrMesh classes, and is demonstrated through the Advection AmrLevel and AmrCore SingleVortex Tutorial. .gitignore GNUmakefile.in Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/AmrCore/Make.package Src/CMakeLists.txt Src/Extern/SENSEI/AMReX_AmrDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrInSituBridge.H Src/Extern/SENSEI/AMReX_AmrInSituBridge.cpp Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.H Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.cpp Src/Extern/SENSEI/AMReX_InSituBridge.H Src/Extern/SENSEI/AMReX_InSituBridge.cpp Src/Extern/SENSEI/AMReX_InSituUtils.H Src/Extern/SENSEI/AMReX_InSituUtils.cpp Src/Extern/SENSEI/CMakeLists.txt Src/Extern/SENSEI/Make.package Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.nersc Tools/GNUMake/tools/Make.sensei Tools/libamrex/configure.py Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/Amr/Advection_AmrCore/README_SENSEI.md Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/Amr/Advection_AmrLevel/README_SENSEI.md Tutorials/Amr/Advection_AmrLevel/Source/main.cpp commit 1c1376aeaa8b3251d3506545b890aab48c343ea6 Author: Max Katz Date: Mon Oct 15 05:50:06 2018 -0700 Catch errors in the launch configuration Tools/F_scripts/write_cuda_headers.py commit 64b662227120480dc10a9be2305585f43f09431b Author: Weiqun Zhang Date: Sat Oct 13 16:50:11 2018 -0700 wrap atomic min and max Src/Base/AMReX_CudaLaunch.H commit d9aec518529b384d95beb41a5eb900722aa36dab Author: Weiqun Zhang Date: Sat Oct 13 19:01:39 2018 -0400 abort if not in launch region Src/Base/AMReX_CudaLaunch.H commit c1fcbea770435b7493c489e8184937a14b3dac9f Author: Weiqun Zhang Date: Sat Oct 13 13:35:55 2018 -0700 add some ifdef AMREX_USE_CUDA so that it compiles without cuda Src/Base/AMReX_CudaMemory.H commit 9641d8fefb372ae5a4e0bb50528dece44a3449f2 Author: Weiqun Zhang Date: Sat Oct 13 13:19:29 2018 -0700 add a helper function for reduction Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_MultiFab.cpp commit 3a3c7cd7368b76464b5c437c25c3dca761dabc9b Author: Weiqun Zhang Date: Sat Oct 13 12:29:58 2018 -0700 more gpu stuff to MultiFab and iMultiFab Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit d7b016a27e8792e75b1ab4927ebe574135471be2 Author: Weiqun Zhang Date: Sat Oct 13 11:17:45 2018 -0700 fix typo; avoid new when copying Src/Base/AMReX_FabArrayCommI.H commit 7f490160f5db8bba272414cbdbdb2e97f9f0325f Author: Weiqun Zhang Date: Sat Oct 13 10:18:02 2018 -0700 simplification: as long as we pack and unpack the same way, the buffer does not have to preserve the order in memory Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 299c527c8cc6e2018d6e1c6b8542b8903bd03d58 Author: Weiqun Zhang Date: Sat Oct 13 10:00:53 2018 -0700 fix EB CutFab Src/EB/AMReX_MultiCutFab.H commit 06433412e4e4e0ba04461a801283c8c7149e6e9d Author: Weiqun Zhang Date: Sat Oct 13 00:08:04 2018 -0700 FArrayBox -> FAB in template Src/Base/AMReX_FabArrayCommI.H commit 6b3c9038c15be4fee16cb0588005d6bd5bfdb86a Merge: 05dfa0416 104d3c10d Author: Weiqun Zhang Date: Sat Oct 13 00:03:15 2018 -0700 Merge branch 'development' into gpu-merge-test commit 104d3c10d757a21458f50d034b514ef865c8f152 Author: Weiqun Zhang Date: Sat Oct 13 00:01:45 2018 -0700 fix particle for 1 and 2d Src/Particle/AMReX_ParIterI.H commit 23de189c82239f2d499d7db29d9b6e0720fb5dee Author: Weiqun Zhang Date: Sat Oct 13 00:01:45 2018 -0700 fix particle for 1 and 2d Src/Particle/AMReX_ParIterI.H commit c820a303cba10ee13353157ae2be5760c932d22d Author: Weiqun Zhang Date: Sat Oct 13 00:01:27 2018 -0700 fix macro name Src/Base/AMReX_FabArrayCommI.H commit 55668f1511d0bedf7607b4bd357539d50940758f Author: Weiqun Zhang Date: Fri Oct 12 23:39:42 2018 -0700 finish FabCommI Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 95ae2381b9382b602156f12e6d7d7b2d14078b1d Merge: 3bdfdb7b3 c81138ce7 Author: Weiqun Zhang Date: Fri Oct 12 21:51:32 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 3bdfdb7b3ecc5f89d25b88a159e68bdc31375219 Author: Weiqun Zhang Date: Fri Oct 12 21:50:48 2018 -0700 add AMREX_LAUNCH_HOST_DEVICE_LAMBDA Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit c81138ce7a97aecd30e1fa70f4607e576b25a0b3 Author: Kevin Gott Date: Fri Oct 12 17:03:50 2018 -0400 First version of ManagedMemory object for testing. Src/Base/AMReX_CudaMemory.H commit 7dfe10bb942bfad1d726bfbdc6b3954a743f2d9a Author: Kevin Gott Date: Thu Oct 11 19:31:18 2018 -0400 AMReX_CudaManaged.H -> AMReX_CudaMemory.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaMemory.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/Test/main.cpp Tests/GPU/TestB/main.cpp Tests/GPU/TestC/main.cpp commit 8fe374828b1b363aca08f1d89b6e04d0295b8f2d Merge: 421376b26 05dfa0416 Author: Weiqun Zhang Date: Fri Oct 12 16:41:07 2018 -0700 Merge branch 'gpu-merge-test' into gpu-merge-test2 commit 05dfa0416ddd949027dc0baee69844f920c573ca Merge: 5bedd3b42 6a22de47d Author: Weiqun Zhang Date: Fri Oct 12 16:40:26 2018 -0700 Merge branch 'development' into gpu-merge-test commit 421376b262062be5d432e471f50155dca4296495 Author: Kevin Gott Date: Fri Oct 12 19:32:34 2018 -0400 Fix MultiFab::Dot launch macro name. Src/Base/AMReX_MultiFab.cpp commit acc2c42ebdc8a2a2d351c862b87a8ce3176fa0f6 Author: Kevin Gott Date: Fri Oct 12 19:31:10 2018 -0400 First draft of MultiFab::Dot. Included test in GPU/HelloWorld. Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/run.script commit e9cdcaa87a9303ea757507e6512533dee660c805 Author: Weiqun Zhang Date: Fri Oct 12 19:28:37 2018 -0400 rename launch macros and add AMREX_USE_BASEFAB_CPP Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit 6a22de47d1d5a60fe9ba57483cf602415a9fbabc Author: Andrew Myers Date: Fri Oct 12 18:26:58 2018 -0400 a testbed for profiling the particle redistribute on GPUs Tests/GPU/Particles/Redistribute/Constants.H Tests/GPU/Particles/Redistribute/GNUmakefile Tests/GPU/Particles/Redistribute/Make.package Tests/GPU/Particles/Redistribute/TestParticleContainer.H Tests/GPU/Particles/Redistribute/TestParticleContainer.cpp Tests/GPU/Particles/Redistribute/inputs Tests/GPU/Particles/Redistribute/main.cpp Tests/GPU/Particles/Redistribute/test_3d.F90 Tests/GPU/Particles/Redistribute/test_F.H commit 5b218293bd1e361904495bdec31c48cfe88f85bc Author: Andrew Myers Date: Fri Oct 12 17:48:21 2018 -0400 cut down on the number of temporary memory allocations in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 57299b36f51e4a8e9749595254112814be50ec81 Author: Andrew Myers Date: Fri Oct 12 17:35:41 2018 -0400 add finer-grained profiling information to RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 8db1b1742630690ee7074148256d820e7f4d05ec Author: Andrew Myers Date: Fri Oct 12 17:34:52 2018 -0400 minor Src/Particle/AMReX_ParIterI.H commit 93eb7509f07b90bfcc15712e3c47c35da617f479 Author: Andrew Myers Date: Fri Oct 12 17:34:15 2018 -0400 use cudaMemAdvise to set the preferred location of managed vector data to the GPU Src/Base/AMReX_CudaAllocators.H commit 5bedd3b426b4f309caf109ac3d55708acd9a207b Author: Kevin Gott Date: Fri Oct 12 17:03:50 2018 -0400 First version of ManagedMemory object for testing. Src/Base/AMReX_CudaMemory.H commit 0503f8d585bcbd67fd14b03c2fe54499cc0028a4 Author: Weiqun Zhang Date: Fri Oct 12 16:12:30 2018 -0400 use ThreadBox instead of ThreadComponentBox Src/Base/AMReX_FabArrayCommI.H commit 7743284d3868a878a7209dee6df0591d9b67b58c Author: Weiqun Zhang Date: Fri Oct 12 14:33:53 2018 -0400 lambda launch setVal Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArray.H commit e21d4a8154649ea85f80ab6cce344b2a27338551 Author: Weiqun Zhang Date: Fri Oct 12 13:33:43 2018 -0400 new ThreadComponentBox function Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_Device.cpp commit 50efa757a5dcb219628f856ebcbd4d099db28d1a Author: Weiqun Zhang Date: Fri Oct 12 01:38:11 2018 -0400 ComponentBox Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_FabArrayCommI.H commit 613bce24e2125fec22cb2b177f8e54319c6a1fdf Author: Weiqun Zhang Date: Thu Oct 11 22:34:12 2018 -0700 fix plus Src/Base/AMReX_FabArrayCommI.H commit e41c77b68fdefc9c0665c4c9ff10c01ed9653cae Author: Kevin Gott Date: Thu Oct 11 19:31:18 2018 -0400 AMReX_CudaManaged.H -> AMReX_CudaMemory.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaMemory.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/Test/main.cpp Tests/GPU/TestB/main.cpp Tests/GPU/TestC/main.cpp commit f0bb27fc923267a4ead57d04ad65ee0bba7fc348 Author: Weiqun Zhang Date: Thu Oct 11 16:09:35 2018 -0700 use C++ copy Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayCommI.H commit 4d3b6781d16fd62e453b56eeabadc0d12eb335d4 Merge: 5f4c36d08 39fb3524c Author: Andrew Myers Date: Thu Oct 11 18:21:16 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5f4c36d087f2363959c0a1b1ca6d2d725520a5a1 Author: Andrew Myers Date: Thu Oct 11 18:20:50 2018 -0400 GPU-enabled version of get / set particle position Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit c801250adab2e507c917b9c106a02af1677649f2 Author: Andrew Myers Date: Thu Oct 11 17:19:10 2018 -0400 early exit if there are no particles to redistribute Src/Particle/AMReX_ParticleContainerI.H commit 5d71fc3db924fce08ee5c7ecf343e7afe8a707ed Merge: 4b76bef0c 39fb3524c Author: Weiqun Zhang Date: Thu Oct 11 11:01:34 2018 -0700 Merge branch 'development' into gpu-merge-test commit 39fb3524c1418698b2423ed9c2af068b7ed720f7 Author: Weiqun Zhang Date: Thu Oct 11 10:55:17 2018 -0700 fix OMP Src/F_Interfaces/Base/AMReX_fab_mod.F90 Tutorials/Amr/Advection_F/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_octree_F/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_octree_F/Source/evolve_mod.F90 commit 2d847d219480a67c1bf9c431f0a15a1b3b066a99 Merge: ddcf7e8e7 6735da6ba Author: Andrew Myers Date: Wed Oct 10 19:38:03 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ddcf7e8e7572c3391b77c8eee0e0e876147529dc Author: Andrew Myers Date: Wed Oct 10 19:29:17 2018 -0400 remove early exits, they are wrong Src/Particle/AMReX_ParticleContainerI.H commit 01cbfe8503d08c56af4badf2298ac2b08819b730 Author: Andrew Myers Date: Wed Oct 10 19:28:43 2018 -0400 correct for domain offset in assignParticle(), for consistency with CPU version Src/Particle/AMReX_ParticleContainerI.H commit 4b76bef0c2b4fbf2ad1fdfc1285fdf69eb785506 Author: Weiqun Zhang Date: Wed Oct 10 12:41:52 2018 -0700 fix omp compilation Src/Base/AMReX_Device.cpp Src/Base/Make.package commit 51764b9aad17cc4d354495e37145151eddc002a4 Author: Andrew Myers Date: Wed Oct 10 15:39:46 2018 -0400 fix copy/paste error Src/Particle/AMReX_ParticleContainerI.H commit 5581114564e42fb859fac8e22c04a9b69d46037d Author: Weiqun Zhang Date: Wed Oct 10 12:06:03 2018 -0700 fix fortran boxlib compilation Src/Base/AMReX_CArena.cpp commit e0c35e7f4b8a762c261422dee19cb81d14ebb6e9 Author: Weiqun Zhang Date: Wed Oct 10 12:00:58 2018 -0700 revert change to TinyProfiler Src/Base/AMReX_TinyProfiler.cpp commit b8d38d39dc893bc76b245cd43973b7869a565642 Merge: 09ea88f37 6735da6ba Author: Weiqun Zhang Date: Wed Oct 10 11:57:41 2018 -0700 Merge branch 'development' into gpu-merge-test commit 6735da6ba490f12790a5c74936101ed90cf81743 Author: Johannes Blaschke Date: Wed Oct 10 09:56:37 2018 -0700 fix fortran fcompare crash when given nComp=0 plotfile Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/plotfile.f90 Tools/Postprocessing/C_Src/fcompare.cpp Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fcompare.f90 commit 9d6ec0320214d47148e6b3d30d830d775b810c0e Merge: 9bb651294 fd15682cc Author: Andrew Myers Date: Tue Oct 9 20:35:43 2018 -0700 Merge pull request #334 from RemiLehe/cuda_system Set SYSTEM_CUDA_PATH for unknown machine commit fd15682ccb694dc06cf6d1621440eaf633ba2c4f Author: Remi Lehe Date: Tue Oct 9 20:14:40 2018 -0700 Set SYSTEM_CUDA_PATH for unknown machine Tools/GNUMake/sites/Make.unknown commit 9bb65129461a14162f955238fa0495f07086aa89 Merge: ad3bfc62b 9931dbd8c Author: Johannes Blaschke Date: Tue Oct 9 19:19:13 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ad3bfc62b899b82b92f5ec17faba2d9dd39f0636 Author: Johannes Blaschke Date: Tue Oct 9 19:19:10 2018 -0700 Add feature to write 'just' the header files <- helpful for postprocessing particle-only plotfiles Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 9931dbd8c7e180fb7f6cae4a83ac5fab4379826b Author: Andrew Myers Date: Tue Oct 9 21:17:06 2018 -0400 make sure the requested device number gets passed in to acc_set_device Src/Base/AMReX_CUDA.F90 commit ad814efeb63a130428b4df40e9bbe4c1d75ce285 Author: Andrew Myers Date: Tue Oct 9 21:09:26 2018 -0400 fix RedistributeMPIGPU. Src/Particle/AMReX_ParticleContainerI.H commit d2a76cc8973ce80a3c0f13e022f8f7119e885be6 Merge: 17cbd2f21 7ddd6b8b4 Author: Donald E. Willcox Date: Tue Oct 9 20:14:46 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 17cbd2f21d503c9c36ce08663e68231b4fcec70a Author: Donald E. Willcox Date: Tue Oct 9 20:14:29 2018 -0400 Add sample compile lines. Tutorials/CVODE/EX3-CUDA/make_cuda.sh Tutorials/CVODE/EX3-CUDA/make_cuda_cusolver.sh Tutorials/CVODE/EX3-CUDA/make_serial.sh commit 343e8f993ed27420c79cd219b5e75983a0b809c5 Author: Donald E. Willcox Date: Tue Oct 9 20:14:13 2018 -0400 Add a react example using cuSolver linear algebra for CUDA CVODE. Tutorials/CVODE/EX3-CUDA/GNUmakefile Tutorials/CVODE/EX3-CUDA/Make.CVODE Tutorials/CVODE/EX3-CUDA/Make.package Tutorials/CVODE/EX3-CUDA/README.md Tutorials/CVODE/EX3-CUDA/react_cuda.cpp Tutorials/CVODE/EX3-CUDA/react_cuda_cusolver.cpp Tutorials/CVODE/EX3-CUDA/react_serial.cpp Tutorials/CVODE/EX3-CUDA/test_react.H Tutorials/CVODE/EX3-CUDA/test_react_F.H commit 4bc4a617d17040cf9030d96ac68fc5d1d3eba0fa Author: Donald E. Willcox Date: Tue Oct 9 19:31:44 2018 -0400 Add optional Fortran RHS or C++ RHS to mimic the Fortran RHS interface in StarKiller Microphysics. Tutorials/CVODE/EX3-CUDA/Make.package Tutorials/CVODE/EX3-CUDA/react_cuda.cpp Tutorials/CVODE/EX3-CUDA/react_system.F90 Tutorials/CVODE/EX3-CUDA/react_utils.F90 Tutorials/CVODE/EX3-CUDA/test_react_F.H commit 29f35729a3db89922f5911bc9db6583e4661a5a5 Author: Donald E. Willcox Date: Tue Oct 9 19:30:44 2018 -0400 Add CVODE libraries to rpath. Define CPP_RHS. Tutorials/CVODE/EX3-CUDA/GNUmakefile Tutorials/CVODE/EX3-CUDA/Make.CVODE commit 09ea88f37021db9aff687e5be99010150e3673eb Author: Weiqun Zhang Date: Tue Oct 9 16:14:08 2018 -0700 rm Arena_Initialize from amrex::Initialize Src/Base/AMReX.cpp commit 5336f025e0e634fe71bf15702d6bd7570c8aff8f Author: Weiqun Zhang Date: Tue Oct 9 16:09:55 2018 -0700 revert changes to the_arena Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 3bddee5508dfc865c0d311939e6c91aa541e4472 Author: Weiqun Zhang Date: Tue Oct 9 15:35:09 2018 -0700 fix cmake Src/Base/CMakeLists.txt commit 59d93fa2419e58a8d6d4451428d519e4e220aecf Author: Weiqun Zhang Date: Tue Oct 9 15:16:11 2018 -0700 fix typo Tools/GNUMake/Make.defs commit e9cb3d4c7e0088c70c1c9b085e9b15c26a7a6866 Author: Weiqun Zhang Date: Tue Oct 9 15:07:03 2018 -0700 move device finalization later after memory poll finalization Src/Base/AMReX.cpp commit 9cb1bdaaca4ce6d0591c50567b6df0a82120d159 Author: Weiqun Zhang Date: Tue Oct 9 15:01:03 2018 -0700 comment out a version of getThreadBox Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_FabArrayCommI.H Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp commit 8447a27b89a31bae901f3d48b3b61bbaf32331f3 Author: Weiqun Zhang Date: Tue Oct 9 14:42:39 2018 -0700 Revert "Adjust Box+Type launch to match surroundingNodes method." This reverts commit 40baf4661bb13768125dc12a7d0dabb14e3b72de. Src/Base/AMReX_CudaLaunch.cpp commit 379d6028bfdd474cf075552c17a8deaac1a6c4f1 Author: Weiqun Zhang Date: Tue Oct 9 14:25:51 2018 -0700 add more AMREX_CUDA_HOST_DEVICE Src/Base/AMReX_Box.H commit 40baf4661bb13768125dc12a7d0dabb14e3b72de Author: Kevin Gott Date: Tue Oct 9 16:16:35 2018 -0400 Adjust Box+Type launch to match surroundingNodes method. Src/Base/AMReX_CudaLaunch.cpp commit aaef2ffd2429204aa3051e324c3775254b35592a Author: Weiqun Zhang Date: Tue Oct 9 12:51:22 2018 -0700 update ThreadComponentBox Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArrayCommI.H commit df915ce13aa09f49ef7d1819054dc636954fd286 Author: Weiqun Zhang Date: Tue Oct 9 11:24:06 2018 -0700 add another simple Strategy Src/Base/AMReX_CudaLaunch.H commit 2e4e03813188b7a3df5fbceba233576801ea3391 Author: Weiqun Zhang Date: Tue Oct 9 10:21:39 2018 -0700 fix copy between fab and buffer in FillBoundary Src/Base/AMReX_FabArrayCommI.H commit abc2f40ead07c07d18160734b367052ed4205fcf Author: Weiqun Zhang Date: Tue Oct 9 10:01:51 2018 -0700 for clarity add () Src/Base/AMReX_FabArrayCommI.H commit d48fb6cfa0b5f4376d3d4e76f4a9f388cc08ca3b Merge: 8cef75de2 8c2029d14 Author: Kevin Gott Date: Tue Oct 9 12:38:27 2018 -0400 Merge branch 'gpu-merge-test' of https://github.com/AMReX-Codes/amrex into gpu-merge-test commit 8cef75de2b44d0e6985bcfe1d24c9b954b2836ac Author: Kevin Gott Date: Tue Oct 9 12:38:06 2018 -0400 Add both boxes to the check. Instead add an initial ASSERT or is that done elsewhere? Src/Base/AMReX_FabArrayCommI.H commit 8c2029d1459e2dd0583e19cb9bc330a2e5bfcde7 Author: Weiqun Zhang Date: Tue Oct 9 09:18:27 2018 -0700 We can still do OMP and tiling if not in launch region and not using pragma gpu Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit 09e96fd311d128432cfde8a545613cd39c428107 Author: Kevin Gott Date: Tue Oct 9 11:41:17 2018 -0400 Add missed Box checks to kernel launch functions. Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit 7ddd6b8b45cc274b5f5eea0c32845818d4bbf3d0 Author: Ann Almgren Date: Mon Oct 8 18:45:58 2018 -0700 Update the nodal linear solvers so that we can now call the operator to compute the multilevel nodal divergence, and can call MLMG::getFluxes for nodal as well as cell-centered data. Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 22640e07ba33c4eac3de36a429016c62bab10452 Author: Kevin Gott Date: Mon Oct 8 20:25:30 2018 -0400 Update Function tutorial with new version of launch macro. Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp commit fcd9a283447dd39904e54c29dc725c1c4f2be36d Author: Weiqun Zhang Date: Mon Oct 8 17:17:07 2018 -0700 AMREX_CUDA_LAUNCH_FUNCTION -> AMREX_CUDA_LAUNCH_GLOBAL Src/Base/AMReX_CudaLaunch.H commit dc4235160656c2978e7c4de89c66fba6170af015 Author: Kevin Gott Date: Mon Oct 8 20:11:17 2018 -0400 Changing lambda launch function. Src/Base/AMReX_CudaLaunch.H commit 841dd9f6be8a046d97bbd9c21fabc8dcf6f1e0ba Author: Kevin Gott Date: Mon Oct 8 20:10:52 2018 -0400 More changes to Tutorials. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/make.out Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit ec786baa04e7235a27cbba514f5d6467cdfbad6c Author: Weiqun Zhang Date: Mon Oct 8 16:07:19 2018 -0700 Simplify launching macros Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 4f69bcc6d630e89d14a1ef724e5be03c60d193ae Author: Kevin Gott Date: Mon Oct 8 17:25:31 2018 -0400 Adjust GPU tutorials for new changes and update Readme. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/em_pic_3d.F90 Tutorials/GPU/Readme.txt commit 26039d1db6ec3a4351aed4ed326b7cf49e463a15 Author: Kevin Gott Date: Mon Oct 8 17:05:06 2018 -0400 Fix HeatEquation0. Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit afed7d6fdfe7422d203d30aebe9693bd1ad30867 Author: Kevin Gott Date: Mon Oct 8 17:03:48 2018 -0400 Add threading strategy to FillBoundary lambda calls. Src/Base/AMReX_FabArrayCommI.H commit 71d033aeea8ae81cf79f475c67ed83f92f8cb740 Author: Kevin Gott Date: Mon Oct 8 17:02:53 2018 -0400 Add map to Allocators Src/Base/AMReX_CudaAllocators.H commit 2d6325144bc5021acd9d96c74e9df30359388733 Author: Kevin Gott Date: Mon Oct 8 16:59:47 2018 -0400 verbose fortran attributes Tools/GNUMake/Make.defs commit 025a8d02f1de07f6a0ffa53c782dc5885a04021b Merge: f41b57d8f 3ab4676ee Author: Kevin Gott Date: Mon Oct 8 15:47:06 2018 -0400 Merge branch 'gpu-merge-test' of https://github.com/AMReX-Codes/amrex into gpu-merge-test commit f41b57d8fe17df85f3d192f527bc6a6e4b4836b0 Author: Kevin Gott Date: Mon Oct 8 15:46:49 2018 -0400 AMREX_CUDA_DEVICE to AMREX_CUDA_HOST_DEVICE for lambda launches. Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit 3ab4676ee2c172cdf82ede68daeb07db1a3c1edf Author: Weiqun Zhang Date: Mon Oct 8 12:05:50 2018 -0700 minor Src/Base/AMReX_Device.H Tools/F_scripts/write_cuda_headers.py commit c692b0b10addda79c3cdf0e94ac3037aca34a7cf Author: Kevin Gott Date: Mon Oct 8 14:53:35 2018 -0400 Add threading strategy to all MultiFab functions currently using lambdas. Src/Base/AMReX_MultiFab.cpp commit 6c8a5a057baffe7d38a718e18a44418f54f320e7 Author: Weiqun Zhang Date: Mon Oct 8 10:41:52 2018 -0700 TilingIfNotGPU() Src/Base/AMReX_MFIter.H Src/Base/AMReX_MultiFab.cpp commit c7112eebaf2170e029cd39b8ca8f9e0d1385b82c Author: Weiqun Zhang Date: Mon Oct 8 10:33:35 2018 -0700 remove RunOn Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Tests/C_BaseLib/tFB.cpp commit f68de2156859b851e95e2823ace9c423dd4b7945 Author: Weiqun Zhang Date: Mon Oct 8 09:47:58 2018 -0700 more reorganization Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaFort.F90 Src/Base/AMReX_CudaManaged.H Src/Base/CMakeLists.txt Src/Base/Make.package commit b9125f167b6134519d256abd7dfde5dd4d6fecc8 Author: Weiqun Zhang Date: Mon Oct 8 09:33:25 2018 -0700 reorganization Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CudaQualifiers.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_Managed.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Orientation.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/F_scripts/write_cuda_headers.py commit 9aacfad9647025a96ab544be8197cfc00ef4fc74 Author: Weiqun Zhang Date: Sun Oct 7 12:24:16 2018 -0700 move SetPreferred to where the arena is built now Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.cpp commit 74180285cd558896432d2f2e441e77b41381d220 Author: Weiqun Zhang Date: Sat Oct 6 22:36:07 2018 -0700 fix omp Src/Base/AMReX_FabArrayCommI.H commit 02935819661be0764900ed948ff41b7879d7ca25 Author: Weiqun Zhang Date: Sat Oct 6 22:09:52 2018 -0700 fix some warnings Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab.cpp commit 2e1491a597d7966d7e3d399f5749c779aaa96a36 Author: Weiqun Zhang Date: Sat Oct 6 21:49:49 2018 -0700 put OKGPU inside AMREX_USE_CUDA Src/Particle/AMReX_ParticleContainerI.H commit b7acd64f34d54e91bc5eeb1ba8e8dc7d9ac93014 Author: Weiqun Zhang Date: Sat Oct 6 21:49:49 2018 -0700 put OKGPU inside AMREX_USE_CUDA Src/Particle/AMReX_ParticleContainerI.H commit c05916b696c30001439e2ccd005bb850c60ad18a Author: Weiqun Zhang Date: Sat Oct 6 21:31:09 2018 -0700 fix compilation for USE_CUDA=FALSE Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_Managed.H commit 78ce066f560e88cdedc7dff09078f50b01d2d8db Merge: 56c4304d2 93309ae58 Author: Weiqun Zhang Date: Sat Oct 6 21:22:55 2018 -0700 Merge branch 'development' into gpu-merge-test commit 56c4304d2dc92adbac29722a6a61eb110b6390a1 Author: Weiqun Zhang Date: Sat Oct 6 21:21:41 2018 -0700 revert some changes to Arena Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArrayBase.cpp commit 5dc41cb42fbc29bbd453e55aefa4e6a600b9e113 Author: Weiqun Zhang Date: Sat Oct 6 17:43:07 2018 -0700 minor changes for easy comparison Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit 235a743f226323feffe3bbd7db5f18786c0b23a0 Author: Weiqun Zhang Date: Sat Oct 6 17:29:23 2018 -0700 return old value when set Src/Base/AMReX.H Src/Base/AMReX.cpp commit 078bafef55427e408054bc8fe878932884c22925 Author: Weiqun Zhang Date: Sat Oct 6 17:27:07 2018 -0700 function to set where to run Src/Base/AMReX.H Src/Base/AMReX.cpp commit 8a0269c0797c89a1d57c5eea1a03b15dd9520fcd Author: Weiqun Zhang Date: Sat Oct 6 17:08:03 2018 -0700 WhereToRunDefault -> WhereToRun Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_FabArray.H Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Tests/C_BaseLib/tFB.cpp commit 9c6225fb02b46a8db8649b0892c2e421c49fecde Author: Weiqun Zhang Date: Sat Oct 6 16:41:07 2018 -0700 simplify Geometry::data Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 93309ae58ea8f7ca91e2531ce18084b344f9b8cc Merge: 949322724 4526c78e8 Author: Weiqun Zhang Date: Sat Oct 6 16:33:24 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9493227240ed26b35b95d15c9617884fec31e763 Author: Kevin Gott Date: Mon Oct 1 20:41:06 2018 -0400 toLower and toUpper Utility functions. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 5a2f4642515d8d30b4a2c32826c5168e630eb067 Author: Weiqun Zhang Date: Sat Oct 6 15:47:19 2018 -0700 minor changes for readability Src/Base/AMReX_Array.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Orientation.H commit 7dc4054face985d3a054a9888a6baa0d043fca4c Author: Weiqun Zhang Date: Sat Oct 6 14:29:48 2018 -0700 Managed: remove the device version Src/Base/AMReX_Managed.H commit b1a7b28b4407b9c847efd9f0d53f7b4e16c73296 Author: Weiqun Zhang Date: Sat Oct 6 11:30:13 2018 -0700 reorganization Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Managed.H commit 4526c78e8b606e9e8465f14108d301a3584c42c6 Merge: a7d412fcf 69813c7fe Author: Andrew Myers Date: Sat Oct 6 13:50:17 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a7d412fcf262d9b977e473097639b208a2b3b7e3 Author: Andrew Myers Date: Sat Oct 6 13:49:48 2018 -0400 correctly enforce periodic boundary conditions in the GPU form of Redistribute() Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit bf907665e3be2a65169a949ab6d7f7e96a8a0560 Merge: 699ee4d64 4d2e9fb05 Author: Weiqun Zhang Date: Fri Oct 5 21:00:43 2018 -0700 Merge branch 'gpu-merge-test' of github.com:AMReX-Codes/amrex into gpu-merge-test commit 699ee4d641fb4612804b8b274652fef445bb0c13 Author: Weiqun Zhang Date: Fri Oct 5 20:58:54 2018 -0700 fix conflict Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit 910460fe48550f9821872d8acde5813e25c316a2 Author: Weiqun Zhang Date: Fri Oct 5 20:54:08 2018 -0700 fix conflict Tutorials/Particles/ElectromagneticPIC/Particles.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/script.sh Tutorials/Particles/ElectromagneticPIC/test.cpp commit 4d2e9fb05be6058be66a1cb99d6b943b8d526b5d Author: Kevin Gott Date: Fri Oct 5 20:30:20 2018 -0400 Add threading strategy for copy to match Castro's Sedov. Rest of MultiFab to come soon. Src/Base/AMReX_MultiFab.cpp commit 932cf60bf9145da50b7e00cd920e85a69a65e51c Author: Weiqun Zhang Date: Fri Oct 5 15:13:51 2018 -0700 hide some codes from Fortran BoxLib Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BArena.cpp Src/Base/GPackage.mak commit c81591a31b371f793c0ff73a17f5b1a902836608 Author: Kevin Gott Date: Fri Oct 5 17:35:40 2018 -0400 Library adjustments. Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CArena.cpp commit 74895195147221873572a92f4fdee8e093002589 Author: Andrew Myers Date: Fri Oct 5 16:22:04 2018 -0400 implement OK() routine that can be run on either the GPU or the CPU. Src/Particle/AMReX_ParticleContainerI.H commit d9610df11327256c6fceed0bafcb997dfccaea15 Author: Andrew Myers Date: Fri Oct 5 16:21:39 2018 -0400 make these data members mutable Src/Particle/AMReX_Particles.H commit 69813c7fe7086f60932ad8a7375fc50e4a504530 Merge: c028a005c f5c7d46e8 Author: Jean Sexton Date: Fri Oct 5 13:57:21 2018 -0400 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit c028a005c2732286b4711cc92d8571bcbcc728fa Author: Jean Sexton Date: Fri Oct 5 13:56:58 2018 -0400 Single cell successfully passed through to f90 device function Tutorials/SUNDIALS3/EX1_CUDA_NVEC/Make.package Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_CUDA_NVEC/myfunc_F.H Tutorials/SUNDIALS3/EX1_CUDA_NVEC/ode_mod.f90 commit ea43473d94a33a2e8c042f59a34bb5c519fbfca8 Author: Jean Sexton Date: Fri Oct 5 13:55:39 2018 -0400 c rhs calls user-defined kernel Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp commit f5c7d46e8ebf276781d0152c71884a09714ddc19 Merge: 7ab4fc97b b98e8650d Author: WeiqunZhang Date: Fri Oct 5 10:46:26 2018 -0700 Merge pull request #331 from AMReX-Codes/mc-nodelinop Mc nodelinop commit b98e8650daa512ba00386064a73c57c79fb08322 Author: Brandon Runnels Date: Fri Oct 5 11:40:28 2018 -0600 Update AMReX_MLMG.cpp Removed `setVal` Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7ab4fc97bf575142b9604c878d8432882c9c9039 Merge: 116f12b06 b9157c8ef Author: Jean Sexton Date: Fri Oct 5 13:07:00 2018 -0400 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 116f12b06b8910c0830dfe4b81937e6c7e83fcad Author: Jean Sexton Date: Fri Oct 5 13:06:50 2018 -0400 Added serial C++ driven version of EX1, differences between vectorized version and non-vectorized approaches precision level as tolerances are tightened Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/GNUmakefile Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/Make.package Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/inputs Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/inputs_2box Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/inputs_non_vectorized Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/myfunc_F.H commit 3ce0c9e15a073dfd35aa1c7ae7ac57bb4cc4b526 Author: Brandon Runnels Date: Fri Oct 5 11:03:53 2018 -0600 Update AMReX_MLMG.cpp bug fix Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e0c5cceb5b883d6e967d37945e861341ab6aa022 Author: Brandon Runnels Date: Fri Oct 5 10:54:49 2018 -0600 Update AMReX_MLLinOp.cpp Removed setVal Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 494a5516420d280115992b1c47d4fd49194cd7b6 Author: Brandon Runnels Date: Fri Oct 5 10:53:35 2018 -0600 Update AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e6b57819f0431a63100eeade921f453935c49818 Author: Brandon Runnels Date: Fri Oct 5 10:39:44 2018 -0600 Made n inside loop Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 commit b9157c8eff2c0b9b95641fe52dd1c0c6f0e0a4b6 Merge: 54f5cc49f 402e7396a Author: sireeveslbl Date: Fri Oct 5 09:26:58 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into development commit 402e7396ac7ce88890b6f709c9d1e3b6f4e133bc Author: sireeveslbl Date: Fri Oct 5 09:19:45 2018 -0700 Commented out unnecessary subtractions Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 54f5cc49f441ffc3c3aac1ab82d63d7919d0a571 Author: Ann Almgren Date: Fri Oct 5 08:04:56 2018 -0700 Revert "Put the makeSolvable (ie subtract off the mean) back into the BiCG solver - this" This reverts commit aeea5d24835e5a570c9866e32191906222e6669e. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit fb81213bf4c0ff8d8c2f56fb044afedf68c0f199 Merge: f373cdcf9 aeea5d248 Author: sireeveslbl Date: Thu Oct 4 18:00:27 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mlmg commit f373cdcf99ee29b0d612eb321e0c9befa8ddf0a0 Author: sireeveslbl Date: Thu Oct 4 17:59:15 2018 -0700 Changed MLCG makeSolvable to MLMG makeSolvable, changed computeVolInv to kill bug that was not inverting volume for use EB but all_Regular geometry Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit aeea5d24835e5a570c9866e32191906222e6669e Author: Ann Almgren Date: Thu Oct 4 17:55:54 2018 -0700 Put the makeSolvable (ie subtract off the mean) back into the BiCG solver - this should help. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit acbb76613b59ad8d375162547aa633c97d20e475 Merge: 1aacac585 ad21d22af Author: Weiqun Zhang Date: Thu Oct 4 17:41:51 2018 -0700 Merge branch 'development' into gpu-merge-test commit ad21d22af6549ec2bb24887fd11f5c270ba52c2c Merge: 760562cba bec746bdb Author: Weiqun Zhang Date: Thu Oct 4 17:05:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 760562cbaa6857681a3fdb2b73bd80bb55a3bc5b Author: Weiqun Zhang Date: Thu Oct 4 17:02:20 2018 -0700 Call mlmg's makeSolvable. Calls are commented out because it may not work. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit bec746bdbdbb0c9be94dae84a5fe5f9362538b82 Author: Jean Sexton Date: Thu Oct 4 20:01:06 2018 -0400 Cleaned up some comments Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/GNUmakefile Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/Make.package Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/SetIC.f90 Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/inputs Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/main.cpp Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/myfunc_F.H Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/ode_mod.f90 commit 2bd65af115038f2f92a54687fe913c855b2cbc2e Author: Weiqun Zhang Date: Thu Oct 4 16:58:04 2018 -0700 make MLCGSolver a friend of MLMG and pass MLMG pointer into MLCGSolver ctor Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 747396b6d8303dfe4e1ebe661488bbc929ed879c Author: Jean Sexton Date: Thu Oct 4 19:56:38 2018 -0400 Updated sundials library include statements, seperated N_Vector cuda example from AMREX_GPU_PRAGMA example Src/Extern/SUNDIALS3/Make.package Tools/GNUMake/packages/Make.sundials3 Tutorials/SUNDIALS3/EX1/GNUmakefile Tutorials/SUNDIALS3/EX1/integrate_ode.f90 Tutorials/SUNDIALS3/EX1/ode_mod.f90 Tutorials/SUNDIALS3/EX1_CUDA_NVEC/GNUmakefile Tutorials/SUNDIALS3/EX1_CUDA_NVEC/Make.package Tutorials/SUNDIALS3/EX1_CUDA_NVEC/SetIC.f90 Tutorials/SUNDIALS3/EX1_CUDA_NVEC/inputs Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_CUDA_NVEC/myfunc_F.H Tutorials/SUNDIALS3/EX1_cuda/GNUmakefile Tutorials/SUNDIALS3/EX1_cuda/Make.package Tutorials/SUNDIALS3/EX1_cuda/SetIC.f90 Tutorials/SUNDIALS3/EX1_cuda/main.cpp Tutorials/SUNDIALS3/EX1_cuda/myfunc_F.H Tutorials/SUNDIALS3/EX_ark_analytic_fp/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_fp/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/GNUmakefile Tutorials/SUNDIALS3/EX_cv_brusselator_dns/GNUmakefile commit 4100cf0305db0ae3f9969f966765dc2f19ca5837 Merge: 09885864b 59a45f297 Author: Andrew Myers Date: Thu Oct 4 19:34:51 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 09885864b24699d2865152906cd8eacc9100df77 Author: Andrew Myers Date: Thu Oct 4 19:34:23 2018 -0400 dispatch redistribute to the GPU when possible when compiling with AMREX_USE_CUDA=TRUE Src/Particle/AMReX_ParticleContainerI.H commit 59a45f2976e86c40b64ce51a2d4de243f369f0dc Author: Weiqun Zhang Date: Thu Oct 4 16:23:55 2018 -0700 comment out some new codes Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit a30152418e3e7c97d1fdaad331dd6ffb0d365e87 Merge: 862bb4133 7f0603dae Author: sireeveslbl Date: Thu Oct 4 15:32:48 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 862bb41336da19fc1094b35d81b6a36804eefc8d Author: sireeveslbl Date: Thu Oct 4 15:32:27 2018 -0700 Some clean up in AMReX_MLCGSolver.cpp. Removed leftovers from debugging bicgstab Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 7f0603dae75ca684d63bdd8819f26a6149a94d4e Merge: 43cd3bf6c fd085f2c4 Author: Andrew Myers Date: Thu Oct 4 15:32:18 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 43cd3bf6c74b21f081daf520660c0f727d359fd1 Author: Andrew Myers Date: Thu Oct 4 15:32:04 2018 -0700 work-around for pgi in how we handle OMP in the particle container Src/Particle/AMReX_ParticleContainerI.H commit fd085f2c484a14bb2cd98ae198cc1595efe6fcb2 Merge: 7b83fbb4f 832f4f97c Author: sireeveslbl Date: Thu Oct 4 15:29:14 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into development commit 7b83fbb4f7fdfce6c6d474d0ec18144d62ac425a Merge: 935b3fc79 001814001 Author: sireeveslbl Date: Thu Oct 4 15:17:57 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 832f4f97ce9af9365612bc138c21110e30fa4c64 Merge: 3e3d093ac 001814001 Author: sireeveslbl Date: Thu Oct 4 15:17:44 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mlmg commit 3e3d093acd124732a250e7c121006a899d1945b8 Author: sireeveslbl Date: Thu Oct 4 15:16:59 2018 -0700 Changed BiCGStab to include subtracting out the Mean residual for singular linear operators only. This solved the issue with the sinusoidal RHS on the 5x5x5 problem. I also tested it with the classic CellEB problems, that the original BiCGstab solved. Each test yeilded good results. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 1aacac585964495cc54114ab67e7485e8639fd8a Author: Weiqun Zhang Date: Thu Oct 4 14:20:01 2018 -0700 make more device functions Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Managed.H Src/Base/AMReX_TinyProfiler.cpp commit 001814001a21c3f079ade6c641c850445a5cef81 Merge: 420fdc62c 0bc5aae12 Author: Andrew Myers Date: Thu Oct 4 16:49:03 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 420fdc62ccbfe259977043b2bcf8e5c0d2b69554 Author: Andrew Myers Date: Thu Oct 4 16:32:41 2018 -0400 disambiguate timer Src/Particle/AMReX_ParticleContainerI.H commit 0f0bb696ee1bf012fb7d2e8b346c61c025896025 Author: Andrew Myers Date: Thu Oct 4 16:30:00 2018 -0400 a thrust particle redistribute for both soa and aos data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d7e40df50ca45270bbd8bc3ec5ea10e14ab4d27b Merge: b221f49d0 0bc5aae12 Author: Brandon Runnels Date: Thu Oct 4 13:59:06 2018 -0600 Merge branch 'development' into mc-nodelinop commit 935b3fc79ce52b2ba8097e34e4bfbdfb673facc9 Merge: 0b8ab21da 0bc5aae12 Author: sireeveslbl Date: Thu Oct 4 12:48:32 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mlmg commit 0b8ab21da033bcc1a6111864b8eb9b05ca233ca3 Author: sireeveslbl Date: Thu Oct 4 12:31:06 2018 -0700 Changed BiCGStab to subtract out the mean residual, solves the periodic 5x5x5 problem along with the regular problems. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 664bd2655517ae4ea11006fec645b48eebbf5120 Author: Weiqun Zhang Date: Thu Oct 4 12:10:35 2018 -0700 add AMREX_CUDA_HOST_DEVICE to more functions Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Orientation.H commit 0bc5aae12ced26910d5f7ab13c743a4bc1b013a1 Author: Michele Rosso Date: Thu Oct 4 11:33:45 2018 -0700 CMake: start GPU support Src/Base/CMakeLists.txt Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 5a4985f51cb3556367a6aaac3992579ea928e9a2 Author: Weiqun Zhang Date: Thu Oct 4 10:38:38 2018 -0700 Fix for codes with Fortran main. Add AMREX_CUDA_HOST_DEVICE to some functions Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H Tools/GNUMake/comps/pgi.mak commit 97444e555579354a7804fc9fe856ffb9af7a5928 Author: Weiqun Zhang Date: Thu Oct 4 10:37:39 2018 -0700 make amrex::Assert host and device function Src/Base/AMReX.H Src/Base/AMReX.cpp commit 30a9752716584d5a21ccb77919eaf3ffb33c82d3 Author: Michele Rosso Date: Thu Oct 4 09:52:35 2018 -0700 CMake: fix misspelled file name Src/Particle/CMakeLists.txt commit 0ad85a1132c248700851e1a9e0c7ffebbc7b05db Merge: 5f33ded5b b128b0933 Author: Weiqun Zhang Date: Thu Oct 4 09:20:12 2018 -0700 Merge branch 'development' into gpu-merge-test commit b128b0933e38fb449f7813c0bffc9d954ed35ae5 Merge: c02a8019a 3e87fcabf Author: WeiqunZhang Date: Thu Oct 4 09:19:13 2018 -0700 Merge pull request #315 from AMReX-Codes/devirtualize-fab Devirtualize fab commit 5f33ded5bcb296c8d1d1e6a1859a53c8eb3e3049 Author: Weiqun Zhang Date: Wed Oct 3 22:06:05 2018 -0700 fix some tests Tests/C_BaseLib/tFB.cpp Tests/FillBoundaryComparison/main.cpp commit 28aef88f9087c748d52e3697c3916ab9faad942b Author: Weiqun Zhang Date: Wed Oct 3 21:44:50 2018 -0700 pragma gpu script: add call to device function Tools/F_scripts/write_cuda_headers.py commit 38e820704b1c5e6ffae00f236aaabba370120cac Author: Weiqun Zhang Date: Wed Oct 3 21:42:03 2018 -0700 comment out a specialization Src/Base/AMReX_BaseFab.H commit ba261dba2aba2f9cd585148b79e6bcadc409e801 Author: Weiqun Zhang Date: Wed Oct 3 21:29:49 2018 -0700 remove duplicated declarations and fix missing definition of variable Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Device.cpp commit 3cb7a8f59b6860d5cda9efb552c878763723bb18 Author: Weiqun Zhang Date: Wed Oct 3 21:16:58 2018 -0700 rm BF_init. we initialize The Arena in amrex::Initialize Src/Base/AMReX_BaseFab.H commit 5e667e10e33fcc6b6bfa2517924c9f1191053031 Author: Weiqun Zhang Date: Wed Oct 3 21:08:42 2018 -0700 remove a number of BaseFab Fortran calls because they don't use gpu pragama anyway. so we can simpply use c++ versions Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit a324899bd04c0d4810fc83b2f8de6fd6d9a37ac9 Author: Weiqun Zhang Date: Wed Oct 3 17:30:51 2018 -0700 more fixes Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BoxArray.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit b3648c6ff384f05139b6e10a5ddaf7e0a882c31f Author: Andrew Myers Date: Wed Oct 3 20:19:50 2018 -0400 start porting over the thrust redistribute from the tutorial Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 892d73abf2a7f12099553507a00a99de1c3b6ed1 Author: Andrew Myers Date: Wed Oct 3 20:19:15 2018 -0400 add a wrapper around resize for the ArrayOfStructs Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H commit b3fef8c905e9a5eb883fda188464db74f4b04be8 Author: Weiqun Zhang Date: Wed Oct 3 16:47:25 2018 -0700 fix ArrayLim Src/Base/AMReX_ArrayLim.H commit f9c073cb88e2e2844cb1def9753760cfd9b1b0f0 Author: Weiqun Zhang Date: Wed Oct 3 16:19:26 2018 -0700 fix some FillBoundary arguments Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit d18c260bb475aa23753ef9a842eaa2c2fe03f9bd Author: Weiqun Zhang Date: Wed Oct 3 16:05:49 2018 -0700 fix F_Interfaces Src/F_Interfaces/Base/AMReX_multifab_fi.cpp commit 60d94252634b7336503f7bcfba116d337e6aea42 Author: Weiqun Zhang Date: Wed Oct 3 16:00:38 2018 -0700 HelloWorld compiles Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ForkJoin.H commit 804a444a0d3fc4b1e157053bbba47ee17b09ea4a Author: Kevin Gott Date: Wed Oct 3 15:42:21 2018 -0700 Fix namespace brackets. Src/Base/AMReX_BaseFab.cpp commit 861cbf80d38447fe48473c84d1c78f079816bfae Author: Kevin Gott Date: Wed Oct 3 15:38:50 2018 -0700 Add back TrueUnlessGPU. Src/Base/AMReX_MFIter.H commit 333f65d7ba5290273d62b2f7d3e8b7effff59508 Merge: 94b72209c 3e87fcabf Author: Weiqun Zhang Date: Wed Oct 3 15:29:15 2018 -0700 Merge branch 'devirtualize-fab' into gpu-merge-test commit 3e87fcabf1159442abb99fc0ab3ca5dde5f570e9 Merge: 559affd67 c02a8019a Author: Weiqun Zhang Date: Wed Oct 3 15:26:15 2018 -0700 Merge branch 'development' into devirtualize-fab commit 94b72209c9d7c1abf35151fff6d132376a77a170 Author: Kevin Gott Date: Wed Oct 3 18:25:30 2018 -0400 Adjust arena to match both branches. Src/Base/AMReX_Arena.H commit 037e8896b05b53985b4ca964874c8c6d05fbb6a8 Author: Kevin Gott Date: Wed Oct 3 18:12:13 2018 -0400 Wrap Device::synchronizes. Src/Base/AMReX_FabArrayCommI.H commit c8bf8c76bec5cdebc0522b3f3401f0f0f1f22b61 Author: Kevin Gott Date: Wed Oct 3 18:09:38 2018 -0400 Add missing commas to macros. Src/Base/AMReX_Managed.H commit 9a1bd281aa59e2751c866db45be7007cf03225bc Author: Weiqun Zhang Date: Wed Oct 3 13:50:20 2018 -0700 fix conflicts in Base Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_CudaAllocators.H Src/Base/Make.package commit ad99e9fd35d745b0241669df89820627b1913f0a Author: Weiqun Zhang Date: Wed Oct 3 13:23:06 2018 -0700 fix conflicts in make Src/Particle/AMReX_NeighborParticlesI.H Tools/F_mk/GMakedefs.mak Tools/GNUMake/Make.defs Tools/GNUMake/Make.local.template Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/packages/Make.cvode Tools/GNUMake/tools/Make.craypat Tools/GNUMake/tools/Make.vtune commit c02a8019aee5cb38176893d2666156c004babd02 Author: Jean Sexton Date: Wed Oct 3 15:51:12 2018 -0400 Added SUNDIALS3 EX1 tutorial using CVODE Cuda N_Vector and amrex copyToMem Src/Extern/SUNDIALS3/cvode_interface.f90 Tools/GNUMake/packages/Make.sundials3 Tutorials/SUNDIALS3/EX1_cuda/GNUmakefile Tutorials/SUNDIALS3/EX1_cuda/Make.package Tutorials/SUNDIALS3/EX1_cuda/SetIC.f90 Tutorials/SUNDIALS3/EX1_cuda/inputs Tutorials/SUNDIALS3/EX1_cuda/main.cpp Tutorials/SUNDIALS3/EX1_cuda/myfunc_F.H Tutorials/SUNDIALS3/EX1_cuda/ode_mod.f90 commit 45a91b002cc94d6cb3a16774932e235ac44d3c5c Author: Donald E. Willcox Date: Wed Oct 3 15:24:04 2018 -0400 Add CUDA CVODE example EX3-CUDA. Tutorials/CVODE/EX3-CUDA/GNUmakefile Tutorials/CVODE/EX3-CUDA/Make.CVODE Tutorials/CVODE/EX3-CUDA/Make.package Tutorials/CVODE/EX3-CUDA/README.md Tutorials/CVODE/EX3-CUDA/extern_probin.template Tutorials/CVODE/EX3-CUDA/inputs Tutorials/CVODE/EX3-CUDA/inputs_128 Tutorials/CVODE/EX3-CUDA/inputs_256 Tutorials/CVODE/EX3-CUDA/inputs_32 Tutorials/CVODE/EX3-CUDA/inputs_64 Tutorials/CVODE/EX3-CUDA/main.cpp Tutorials/CVODE/EX3-CUDA/react_cuda.cpp Tutorials/CVODE/EX3-CUDA/react_serial.cpp Tutorials/CVODE/EX3-CUDA/react_utils.F90 Tutorials/CVODE/EX3-CUDA/test_react.H Tutorials/CVODE/EX3-CUDA/test_react_F.H commit 66d1f6482b9a71c235ce99caa74a1327194a9cd0 Merge: 2150dc4b1 f6f7a4c0c Author: Kevin Gott Date: Wed Oct 3 15:13:55 2018 -0400 Merge branch 'development' into gpu-merge-test Conflicts: Src/Base/AMReX_Arena.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_fort_mod.F90 Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tests/Particles/StructOfArrays/GNUmakefile Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/Make.rules Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/main.cpp commit f6f7a4c0c6391e8fcc809538970f5c0d5bfbbf5b Merge: 06f905d40 17a7f5045 Author: Andrew Myers Date: Wed Oct 3 13:15:32 2018 -0400 merging. commit 17a7f50456bb629c6584a0be3f58fd33595055c4 Author: Weiqun Zhang Date: Wed Oct 3 10:00:27 2018 -0700 put Nvar_Arena into AMREX_USE_GPU_PRAGMA Src/Base/AMReX_Arena.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 2150dc4b15837d421feac033e0b217c315cd8583 Author: Kevin Gott Date: Wed Oct 3 12:33:09 2018 -0400 Rename for runOn variable for easy searching/renaming later. Src/Base/AMReX_FabArray.H commit 77b02d212ae2be0801af9e6b1cdd1fee32d3001c Author: Weiqun Zhang Date: Wed Oct 3 08:56:36 2018 -0700 fix cmake Src/Particle/CMakeLists.txt commit c5e355508e8c6297f5abfda2fa140e6dc0bc513c Author: Kevin Gott Date: Wed Oct 3 11:48:48 2018 -0400 FillBoundary and EnforcePeriodicity converted to RunOn selection. Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit b221f49d0672e59a8452a78799a60b88d5277522 Merge: 0213b99d9 dcc46f612 Author: Brandon Runnels Date: Wed Oct 3 07:41:58 2018 -0600 Merge branch 'development' into mc-nodelinop commit 06f905d40830f966a0965e040cf93d4faa236e05 Merge: aa5e5ee97 dcc46f612 Author: Andrew Myers Date: Tue Oct 2 20:02:40 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit dcc46f612ec32a199f7e1076720d10e60ed711af Merge: c4a48a12f 238d6764f Author: Marc Day Date: Tue Oct 2 16:41:06 2018 -0700 Merge branch 'marc/forkjoin_dev' into development commit 238d6764f362ed79287c9e89a395f77e4d4aed60 Merge: 352e295ac c4a48a12f Author: Marc Day Date: Tue Oct 2 16:39:14 2018 -0700 resolve trivial conflict commit 352e295ac130c2503bca0c70484c3cb43d1a4fab Author: Marc Day Date: Tue Oct 2 16:37:21 2018 -0700 Remove commented code lines Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit c4a48a12f0ef08943e92349c5a1235208d3e4685 Author: Weiqun Zhang Date: Tue Oct 2 16:34:13 2018 -0700 add NVCC_HOST_COMP Tools/GNUMake/comps/nvcc.mak commit 7821e732f3c4ac6156228ce785f4517f60bba3c2 Author: Marc Day Date: Tue Oct 2 16:32:26 2018 -0700 Add some functionality to the test code Tutorials/Parallel/ForkJoin/MyTest.H Tutorials/Parallel/ForkJoin/MyTest.cpp commit 14ccb0cd040c6e9dac2f9f0b9c211ccd4b01f75f Author: Marc Day Date: Tue Oct 2 16:20:31 2018 -0700 Add name of output folder to fj ctr, allow to be empty string and to overwrite existing output Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit 6dc5b422406cf144f2582689dfaeadd59b162e0d Author: Kevin Gott Date: Tue Oct 2 18:52:16 2018 -0400 Slight renaming. Src/Base/AMReX.cpp commit a733e05e598350542f093e1eb60f2184a6b89ec4 Author: Weiqun Zhang Date: Tue Oct 2 15:40:51 2018 -0700 use linop getFluxes Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit aa5e5ee97bc31da8e26d08c5f11fd9192c85657b Merge: 7f1ceb460 12683828a Author: Andrew Myers Date: Tue Oct 2 18:13:29 2018 -0400 Merge branch 'atmyers-gpu_particles_reorg' into development commit 7f1ceb460bfefee34295fa696c76c51495d32e16 Merge: a800d462d 654b518fc Author: Weiqun Zhang Date: Tue Oct 2 14:46:41 2018 -0700 Merge branch 'gpu' into development commit cf152a29122e5970665ee4b5e3b9b1c608cc803e Merge: d9a06831d a800d462d Author: Kevin Gott Date: Tue Oct 2 17:43:34 2018 -0400 Merge branch 'development' into gpu-mm commit 0005734598ce96d8970b82c89ff9a26c64b8b74d Merge: a776e26d4 a800d462d Author: Marc Day Date: Tue Oct 2 14:30:24 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit a800d462d702607e6689a45db8c8ba2485d8e9de Merge: 3d5d930a6 3bbda25ac Author: Marc Day Date: Tue Oct 2 14:28:33 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d9a06831d2d910d3e664bd394436f7fae8150565 Merge: 45502483d 3bbda25ac Author: Kevin Gott Date: Tue Oct 2 17:06:31 2018 -0400 Merge branch 'development' into gpu-mm commit 654b518fcca82cfe010f4bb460aa07467061ade4 Merge: 7132db3e7 3bbda25ac Author: Weiqun Zhang Date: Tue Oct 2 14:01:36 2018 -0700 Merge branch 'development' into gpu commit 3bbda25ac3aea96302db5e3979ecda0f999620cd Author: Weiqun Zhang Date: Tue Oct 2 13:59:54 2018 -0700 remove some old unused functions Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 7132db3e7219411ca55ddb2f0d26ce62cfe8cb5f Author: Weiqun Zhang Date: Tue Oct 2 13:35:57 2018 -0700 fix cmake Src/Base/AMReX_BaseFab_nd.F90 Src/Base/CMakeLists.txt commit 45502483d826de993dbf04599efab2298d47dd65 Author: Kevin Gott Date: Tue Oct 2 16:33:30 2018 -0400 Reorganize FillBoundary and EnforcePeriodicity calls. Src/Base/AMReX_FabArray.H commit 3cb09f17abda23bbcae89f26ba64f9dd010b9be2 Merge: 0cf71283e 0330434c8 Author: Weiqun Zhang Date: Tue Oct 2 13:15:23 2018 -0700 Merge branch 'development' into gpu commit 0cf71283e9ac113a943425455a5694f4bd8df72d Author: Weiqun Zhang Date: Tue Oct 2 12:25:00 2018 -0700 minor changes in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 2e2af66c997418451c3397501275d2f6cd1432fe Author: Kevin Gott Date: Tue Oct 2 15:26:17 2018 -0400 Move RunOn and CopyFromTo to AMReX.H Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Managed.H commit aef0d1ec6ff58682367b0a3a812235d7785ac30c Author: Kevin Gott Date: Tue Oct 2 15:19:31 2018 -0400 Make AMReX_Managed.H called under any circumstances. Src/Base/AMReX_Array.H Src/Base/AMReX_MultiFab.cpp commit 29a0ada8d2b3dcf8122b7fea9d13f9388f9afc0a Author: Kevin Gott Date: Tue Oct 2 15:18:43 2018 -0400 Addition of runOn/CopyFromTo runtime default and slight renaming. Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Managed.H commit 12683828a1a10fe9d6f62ae1aa1ba8e0f2b643b7 Author: Andrew Myers Date: Tue Oct 2 15:12:48 2018 -0400 remove variadic tuple stuff from particle tile - taking a different approach Src/Particle/AMReX_ParticleTile.H commit d06d06c9a7990ab248b4bada0352420407c32a75 Author: Andrew Myers Date: Tue Oct 2 15:07:34 2018 -0400 using the managed particle vector in Redistribute Src/Particle/AMReX_ParticleContainerI.H commit 1cd8f16db1ade888455c479a404333378fe03b53 Author: Andrew Myers Date: Tue Oct 2 15:06:47 2018 -0400 use managed vectors in the particle iterator for get / set position Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 0330434c8d7a9681ad6cff72dbf4d759e27bdcec Merge: 1b629dd98 4d3b30304 Author: Tan Nguyen Date: Tue Oct 2 11:59:32 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1b629dd98b7fcac7696a4e649018d81ba6b9a2d9 Author: Tan Nguyen Date: Tue Oct 2 11:58:50 2018 -0700 update asyncFP Src/Amr/AMReX_AsyncFillPatch.cpp commit 6c1766a1eaa64a7cedff1eac9beaaa30e668fb85 Author: Weiqun Zhang Date: Tue Oct 2 10:49:46 2018 -0700 use AMREX_USE_GPU_PRAGMA in the script Tools/F_scripts/gpu_fortran.py Tools/F_scripts/write_cuda_headers.py commit c5e29cc4c67dff939c89cc760c4a7f4e35a91f42 Author: Weiqun Zhang Date: Mon Oct 1 18:10:50 2018 -0700 make make have the old behavior when USE_GPU_PRAGMA is not TRUE Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 4d3b303046ebc98271d0c00173962396f6c429d4 Author: Weiqun Zhang Date: Mon Oct 1 18:17:31 2018 -0700 fix compilation Src/Amr/AMReX_AsyncFillPatch.cpp commit 167c0257de002c6c29f8937e506142f0cdab1d11 Author: Kevin Gott Date: Mon Oct 1 20:41:06 2018 -0400 toLower and toUpper Utility functions. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 3adf9557c2c6938f7efd0202defec3d02de1bd50 Author: Kevin Gott Date: Mon Oct 1 20:40:44 2018 -0400 Small fix. Src/Base/AMReX.cpp commit 4ac83d76293b50ce797e90979b91edf08af08d5a Author: Kevin Gott Date: Mon Oct 1 20:35:00 2018 -0400 Temporary fill of RunOn in lambdas to allow compile testing while default and function interfaces are adjusted. Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit d28b38eb592c0a18b51f9f2cf801869fdaa2002b Author: Tan Nguyen Date: Mon Oct 1 15:28:29 2018 -0700 create a separate file for asyncMFIter code Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/Amr/Make.package commit 0c48c88bdbab0d054e28ef3f332ccf749c2758b5 Author: Kevin Gott Date: Mon Oct 1 15:51:03 2018 -0400 Small GPU Readme to remind difference between tutorials. Tutorials/GPU/Readme.txt commit 1c20672825570473608470350b4c63911fbd126c Author: Kevin Gott Date: Mon Oct 1 15:37:29 2018 -0400 First pass at runtime selection of location of lambdas. Should run poorly with HeatEquation_EX0 (lambda version). Src/Base/AMReX.cpp Src/Base/AMReX_Managed.H Tests/GPU/TestC/main.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit 4c9866ecce59bc9cf165696c300effff6fbfc422 Author: Andrew Myers Date: Mon Oct 1 15:32:01 2018 -0400 add some useful typedefs to the ParIter Src/Particle/AMReX_Particles.H commit 8c4ee539038d5aee876b4923589dfd6ac6146064 Merge: 5a057d085 dc4a6267b Author: Weiqun Zhang Date: Mon Oct 1 12:25:41 2018 -0700 Merge branch 'eb-grow' into development commit dc4a6267bf68a17be3ffb3cda542a6ddd6a1cd89 Author: Weiqun Zhang Date: Mon Oct 1 12:18:48 2018 -0700 update CellEB2 test Tests/LinearSolvers/CellEB2/MyTest.cpp commit ffbaa2c6d5cefc49afd06859f2a5fad4b23786e7 Author: Weiqun Zhang Date: Mon Oct 1 12:02:17 2018 -0700 update EB doc Docs/sphinx_documentation/source/EB.rst Tutorials/EB/CNS/Source/CNS_init_eb2.cpp commit 67b34cc2aaafac1eaadac5327e3fcdf0853a23e5 Author: Weiqun Zhang Date: Mon Oct 1 11:10:28 2018 -0700 finish implementation of ngrow for eb Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2_IndexSpaceI.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp commit 5a057d085a36027b02d2fc4e26f1e5df656db5fd Merge: 4911f909e 8e073533b Author: Guy Moore Date: Mon Oct 1 09:18:10 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8e073533b0cffe6dc78847dd4ec93cfed7907549 Author: Weiqun Zhang Date: Mon Oct 1 08:52:00 2018 -0700 update CHANGES CHANGES commit e56c28918788293fcffce7beaa7a2286dda9502e Merge: 9d22e2340 a11cf25db Author: Weiqun Zhang Date: Mon Oct 1 08:51:10 2018 -0700 Merge branch 'development' commit c0e7ad998388be0527ab23b620ae4ef66b6b2e54 Author: Weiqun Zhang Date: Sun Sep 30 16:40:43 2018 -0700 add aoptional ngrow argument to EB2::Build and start implementation Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IndexSpaceI.H Src/EB/AMReX_EB2_Level.H commit 9215f1d22b4ca60f96fdc0820467442b88d3717b Merge: cfb661c22 a11cf25db Author: Weiqun Zhang Date: Sat Sep 29 11:24:50 2018 -0700 Merge branch 'development' into mlmg commit a11cf25dbd5e6f771c7f6cedfbdea368f9559261 Author: Weiqun Zhang Date: Sat Sep 29 11:24:33 2018 -0700 Merge branch 'mlmg' into development Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit cfb661c226012d1a36242e0bdfb54a9fda0492b0 Author: Weiqun Zhang Date: Sat Sep 29 11:23:34 2018 -0700 fix hypre: make sure to exclude non-valid cells Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 4911f909e46ded55ccd6ba25f73c845ccab5f69c Merge: 6f3b4eb63 afc4caed3 Author: Guy Moore Date: Fri Sep 28 16:32:19 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 6f3b4eb6349709beedc3e350a406fc9253bda002 Author: Guy Moore Date: Fri Sep 28 16:29:12 2018 -0700 Added more comments to README Tutorials/SWFFT_simple/README commit 86104f6fbad729c10ab37b7b825bc691c7bbd89f Merge: 051c791c4 afc4caed3 Author: Kevin Gott Date: Fri Sep 28 18:53:06 2018 -0400 Merge branch 'development' into gpu-mm commit 051c791c4dabc7a466d964c9f969764074dab5c7 Author: Kevin Gott Date: Fri Sep 28 18:48:59 2018 -0400 AMREX_CUDA_HOST_DEVICE added. Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Managed.H Src/Base/AMReX_RealBox.H commit 0db41995ca04dd9562c0090922657e289cc2bc86 Author: Guy Moore Date: Fri Sep 28 14:53:27 2018 -0700 Added scaling comment to README Tutorials/SWFFT_simple/README commit 5d0d7e204007e8e7de4827b8565cc2f212fc15e6 Author: Guy Moore Date: Fri Sep 28 14:48:56 2018 -0700 Confirmed FFT scaling Tutorials/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT_simple/inputs.multipleGrids Tutorials/SWFFT_simple/inputs.oneGrid commit afc4caed3bf642c0f27b088f431d9261e03fd72c Author: Andrew Myers Date: Fri Sep 28 14:46:06 2018 -0700 Revert "use git pull instead of clone to avoid polluting the download statistics" This reverts commit d8ee1ef0d9211f7d8615b04883bf145166b2a0e3. build_and_deploy.sh commit 6d6782004db272be88559bc9f2c5396a06114161 Merge: d8ee1ef0d af73f93d4 Author: Andrew Myers Date: Fri Sep 28 14:36:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d8ee1ef0d9211f7d8615b04883bf145166b2a0e3 Author: Andrew Myers Date: Fri Sep 28 14:32:45 2018 -0700 use git pull instead of clone to avoid polluting the download statistics build_and_deploy.sh commit af73f93d49a0d6d21b10c599078af850a2b3e8d5 Author: Weiqun Zhang Date: Fri Sep 28 14:26:14 2018 -0700 port BoxArray DistributionMapping version of MFIter constructor to Fortran Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 8ca61396525f121934aba97a1a1dd05f419e2508 Author: Andrew Myers Date: Fri Sep 28 14:19:19 2018 -0700 fix typo build_and_deploy.sh commit ffd3e55b04ed026571cfb2d911a7e18188adeac8 Author: Andrew Myers Date: Fri Sep 28 14:07:03 2018 -0700 generate pdf and copy it into source before building html build_and_deploy.sh commit a2f0d4ddcea8bab3266219e7a6032a70508d1bd4 Author: Andrew Myers Date: Fri Sep 28 13:43:36 2018 -0700 build pdf of the docs and link to it from the html version on every commit to development .travis.yml Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/index.rst build_and_deploy.sh commit d17314c4029e5a7f4127e6e44e17c03e32c9db6b Author: Weiqun Zhang Date: Fri Sep 28 13:38:55 2018 -0700 attempt to set computability with deviceQuery Tools/GNUMake/sites/Make.unknown commit 19d17692e4233bf5b9725627a32cda9372184bea Author: Weiqun Zhang Date: Fri Sep 28 13:37:36 2018 -0700 make sure C++ standards are consistently set Tools/GNUMake/comps/nvcc.mak commit 32e0e3917cc5d46f7c0390e2af04c896d38aaa56 Author: Weiqun Zhang Date: Fri Sep 28 13:29:26 2018 -0700 fix shadows Src/Base/AMReX_BArena.cpp Src/Base/AMReX_Device.H commit 2c355925414b55dd95ff232184192643b3f705e4 Author: Guy Moore Date: Fri Sep 28 12:39:53 2018 -0700 Updated README Tutorials/SWFFT_simple/README Tutorials/SWFFT_simple/SWFFT_Test.cpp commit f1a2277801fa0fa90e62d6e796bf3358e3dcbbc1 Merge: f4009f86e 8aaa6483c Author: Guy Moore Date: Fri Sep 28 12:06:13 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f4009f86e4c29215fafdce056a787ab73e04efb4 Author: Guy Moore Date: Fri Sep 28 12:04:24 2018 -0700 Adapted for 2D Tutorials/SWFFT_simple/SWFFT_Test.H Tutorials/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT_simple/SWFFT_Test_F.H Tutorials/SWFFT_simple/run_me Tutorials/SWFFT_simple/run_me_2d Tutorials/SWFFT_simple/run_me_3d Tutorials/SWFFT_simple/swfft_compute.cpp commit 65a241c969fcf345de52d02b0e829de11de305bf Author: Kevin Gott Date: Fri Sep 28 14:16:54 2018 -0400 Adjust C+ BaseFab merge to get GPU HeatEquation Running. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_Box.H commit 8aaa6483cd179413394054e663e204b68a846ae4 Author: Andrew Myers Date: Fri Sep 28 11:15:10 2018 -0700 Fix VisMF for the case where the number of ghost cells can be different in each direction Src/Base/AMReX_VisMF.cpp commit 9bfafef0daaf2e140f8786f1c143ffb2730047eb Author: Guy Moore Date: Fri Sep 28 10:53:59 2018 -0700 Cleaned up SWFFT_simple - removed unecessary code from original SWFFT tutorial Tutorials/SWFFT_simple/Make.package Tutorials/SWFFT_simple/README Tutorials/SWFFT_simple/SWFFT_Test.H Tutorials/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT_simple/SWFFT_Test_F.H Tutorials/SWFFT_simple/inputs.multipleGrids Tutorials/SWFFT_simple/main.cpp Tutorials/SWFFT_simple/swfft_compute.cpp commit 497e6621cc4a5d35f91c1a8cc657c5ba681cc058 Author: Guy Moore Date: Fri Sep 28 10:11:00 2018 -0700 First commit of SWFFT_simple tutorial, in which only a forward FFT is performed Tutorials/SWFFT_simple/GNUmakefile Tutorials/SWFFT_simple/Make.package Tutorials/SWFFT_simple/README Tutorials/SWFFT_simple/SWFFT_Test.H Tutorials/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT_simple/SWFFT_Test_F.H Tutorials/SWFFT_simple/inputs.multipleGrids Tutorials/SWFFT_simple/inputs.oneGrid Tutorials/SWFFT_simple/main.cpp Tutorials/SWFFT_simple/run_me Tutorials/SWFFT_simple/swfft_solver.cpp commit e40b2daf7e64d90326351fbcad0f9306f80ee415 Merge: 7de9ae558 8447e9ac2 Author: Kevin Gott Date: Thu Sep 27 20:21:26 2018 -0400 Merge branch 'development' into gpu-mm: cpp versions of BaseFab funcs Conflicts: Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 7de9ae558e5c578bf361f581125bfa1dda40d204 Author: Kevin Gott Date: Thu Sep 27 13:08:22 2018 -0400 Move GPU tests from Tutorials to Test. Tests/GPU/Test/GNUmakefile Tests/GPU/Test/Make.package Tests/GPU/Test/main.cpp Tests/GPU/Test/run.exitcode Tests/GPU/Test/run.script Tests/GPU/TestB/GNUmakefile Tests/GPU/TestB/Make.package Tests/GPU/TestB/main.cpp Tests/GPU/TestB/return_test.F90 Tests/GPU/TestC/GNUmakefile Tests/GPU/TestC/Make.package Tests/GPU/TestC/main.cpp Tests/GPU/TestC/run.summit Tests/GPU/TestC/run.summitdev commit 8447e9ac2512dd6cc1b6ee999ce87c2f8594ad2a Author: Weiqun Zhang Date: Wed Sep 26 18:11:14 2018 -0700 add an assertion Src/Base/AMReX_BaseFab.H commit 75db0e761bf2f35b323e5b7277770493fe20b36d Author: Max Katz Date: Wed Sep 26 14:02:31 2018 -0400 Prefix CUDA_MAX_THREADS with AMREX Src/Base/AMReX_CUDA.F90 Tools/GNUMake/Make.defs commit d0e3ad5d9cf15e507af4b49e80a3b23f75ec756b Author: Max Katz Date: Wed Sep 26 13:57:48 2018 -0400 Prefix GPUS_PER_SOCKET/NODE with AMREX Src/Base/AMReX_Device.cpp Tools/GNUMake/Make.defs commit 98b121dd9c38d344dfeecf9679f58a0ac794a4f2 Author: Max Katz Date: Wed Sep 26 13:56:07 2018 -0400 Remove CUDA_UM Src/Base/AMReX_BArena.cpp Tools/GNUMake/Make.defs commit 18e9ac7ec6c290757730ca09ef1e9147fabd2535 Author: Max Katz Date: Wed Sep 26 13:54:25 2018 -0400 Remove unused OMP_OFFLOAD Tools/GNUMake/Make.defs commit f8fea4918c11a70d755e725f8ac0f61d5700a5da Author: Weiqun Zhang Date: Wed Sep 26 10:48:15 2018 -0700 make sure global operators are used Src/Base/AMReX_BArena.cpp commit f50cf2263719cf4e8d0732f7bf89121bc3845034 Author: Weiqun Zhang Date: Wed Sep 26 10:44:17 2018 -0700 remove unused variables Src/Base/AMReX_MultiFab.cpp commit 6fc69832298173ec1f48d1a152e8e596a308eb61 Author: Weiqun Zhang Date: Wed Sep 26 10:40:37 2018 -0700 remove unused variable Src/Base/AMReX_FabArray.H commit 83823afa804e5ea85cffbae71c73ae27b3cc90ad Author: Max Katz Date: Tue Sep 25 20:10:21 2018 -0400 Free local communicator Src/Base/AMReX_Device.cpp commit ee231f076d9f8a752000d2c7d3ad458d3f8beef6 Author: Max Katz Date: Tue Sep 25 20:03:39 2018 -0400 Use PD Communicator Src/Base/AMReX_Device.cpp commit 85e7ad8867dae516e0e1a357757d89c142a6e769 Author: Max Katz Date: Tue Sep 25 20:00:43 2018 -0400 Remove unused variable Src/Base/AMReX_Device.H commit 4e24b2a4d9edb3782225dfb9ddf32f3d21a03a03 Author: Max Katz Date: Tue Sep 25 19:59:56 2018 -0400 Add a definition for max_cuda_streams Src/Base/AMReX_Device.cpp commit d9dc8bcec4dcd84506c17b0eef533b1fb72f4435 Merge: 8a4cbe149 0e1878ce1 Author: Andrew Myers Date: Tue Sep 25 15:26:31 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8a4cbe14900b1b266d4e57f9b8a17503247df70f Author: Andrew Myers Date: Tue Sep 25 15:26:12 2018 -0700 add ba / dmap access functions to EBFArrayBoxFactory Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp commit 0e1878ce1167b371baeca7cf44c1f5c9ffe99a8c Author: Tan Nguyen Date: Tue Sep 25 14:33:04 2018 -0700 update async version of FillPatchIter Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_MultiFabUtil_Perilla.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit 502418e1bad5cf43df47360bc6f799f9590cc00b Merge: 0cd513b29 b9d703f47 Author: Weiqun Zhang Date: Tue Sep 25 12:56:33 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0cd513b29e72257b8f72939c30008b026121218d Author: Weiqun Zhang Date: Tue Sep 25 12:54:24 2018 -0700 EB: fix roundoff error issues Src/EB/AMReX_eb2_3d.F90 commit b9d703f4759a2374c0eb721d1606c376aeed0b62 Merge: 8a901fed8 ea6dbf258 Author: WeiqunZhang Date: Tue Sep 25 12:11:21 2018 -0700 Merge pull request #324 from zingale/development work around intel compiler crash commit ea6dbf2589e60ecc95b351056f1d03c6cf80e94a Author: Michael Zingale Date: Tue Sep 25 11:54:47 2018 -0700 work around intel compiler crash Tools/F_scripts/write_probin.py commit 8a901fed8156e588e65f15b60b27476cbcb98a5f Merge: 1c0141d7b bf54f74c3 Author: WeiqunZhang Date: Tue Sep 25 09:23:03 2018 -0700 Merge pull request #322 from wolfram-schmidt/development Development commit 0213b99d98d51171ddb1429cdedd24a77769c77c Merge: 9b435a2b6 1c0141d7b Author: Brandon Runnels Date: Tue Sep 25 09:58:04 2018 -0600 Merge branch 'development' into mc-nodelinop commit 9b435a2b60674969fb4c5570de5b78959d7888b3 Author: Brandon Runnels Date: Tue Sep 25 09:57:36 2018 -0600 updated MLMG solver for multicomponent solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit bf54f74c3cf2ae0947c77f47cf4e51e62b38558a Author: Wolfram Schmidt Date: Tue Sep 25 11:52:20 2018 +0200 Cleaned up nec.mak Tools/GNUMake/comps/nec.mak commit a0c1442b6fec3c03ec44e81fd2c9aeaa2ffd3116 Merge: 919594fe8 1c0141d7b Author: Wolfram Schmidt Date: Tue Sep 25 10:14:15 2018 +0200 Merge remote-tracking branch 'upstream/development' into development commit 1c0141d7b3a9ececcf4d91da3d7e3ff57d8cc09b Author: Jean M. Sexton Date: Mon Sep 24 17:53:47 2018 -0700 Added ARKODE interface for Sundials 3.X from CVODE interface, used with USE_ARKODE=TRUE and USE_SUNDIALS3=TRUE Docs/sphinx_documentation/source/SUNDIALS3.rst Src/Extern/SUNDIALS3/Make.package Src/Extern/SUNDIALS3/arkode_interface.f90 Src/Extern/SUNDIALS3/farkode.f90 Tools/GNUMake/packages/Make.sundials3 Tutorials/SUNDIALS3/EX_ark_analytic_fp/GNUmakefile Tutorials/SUNDIALS3/EX_ark_analytic_fp/Make.package Tutorials/SUNDIALS3/EX_ark_analytic_fp/ark_analytic_fp.f90 commit d30eea1ac4319202d52a7013cab16ed7f808aafd Author: Jean M. Sexton Date: Mon Sep 24 14:00:08 2018 -0700 Added initial documentation for added Sundials version 3.X support Docs/sphinx_documentation/source/CVODE.rst Docs/sphinx_documentation/source/Chapter14.rst Docs/sphinx_documentation/source/SUNDIALS3.rst commit 045c46bed4c8e0a844746342cdee75ee2e904a1b Author: Jean M. Sexton Date: Mon Sep 24 13:18:34 2018 -0700 USE_SUNDIALS3=TRUE links in David's updated fcvode interface for Sundials 3.X, 5 new example added to Tutorials Src/Extern/SUNDIALS3/Make.package Src/Extern/SUNDIALS3/cvode_interface.f90 Src/Extern/SUNDIALS3/fcvode.f90 Src/Extern/SUNDIALS3/fnvector_serial.f90 Src/Extern/SUNDIALS3/fnvector_serial_fprefix.f90 Src/Extern/SUNDIALS3/fsunlinsol_dense.f90 Src/Extern/SUNDIALS3/fsunmat_dense.f90 Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.sundials3 Tutorials/SUNDIALS3/EX1/GNUmakefile Tutorials/SUNDIALS3/EX1/Make.package Tutorials/SUNDIALS3/EX1/inputs Tutorials/SUNDIALS3/EX1/integrate_ode.f90 Tutorials/SUNDIALS3/EX1/main.cpp Tutorials/SUNDIALS3/EX1/myfunc_F.H Tutorials/SUNDIALS3/EX1/ode_mod.f90 Tutorials/SUNDIALS3/EX_cv_analytic_fp/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_fp/Make.package Tutorials/SUNDIALS3/EX_cv_analytic_fp/cv_analytic_fp.f90 Tutorials/SUNDIALS3/EX_cv_analytic_fp/cv_analytic_fp.out Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/Make.package Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.f90 Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.out Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/Make.package Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.f90 Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.out Tutorials/SUNDIALS3/EX_cv_brusselator_dns/GNUmakefile Tutorials/SUNDIALS3/EX_cv_brusselator_dns/Make.package Tutorials/SUNDIALS3/EX_cv_brusselator_dns/cv_brusselator_dns.f90 Tutorials/SUNDIALS3/EX_cv_brusselator_dns/cv_brusselator_dns.out commit 919594fe85584419743e72e1adf25c91a4b4161c Merge: 9d0fe16b1 b9a5b6547 Author: Wolfram Schmidt Date: Mon Sep 24 12:19:18 2018 +0200 Merge remote-tracking branch 'upstream/development' into development commit 9d0fe16b15bca67976994acb28439ec81d96e2d9 Author: Wolfram Schmidt Date: Mon Sep 24 12:18:31 2018 +0200 Another fix for NEC. Src/F_BaseLib/fabio_c.c Tools/GNUMake/sites/Make.hs commit cf475a3fb6f0482a576fcfe6a11cc376797c194e Merge: da04fa61a b9a5b6547 Author: Max Katz Date: Sat Sep 22 09:21:02 2018 -0400 Merge branch 'development' into gpu commit b9a5b6547326c5186a089cbde76ea217919116e8 Author: Kevin Gott Date: Sat Sep 22 02:06:51 2018 -0400 Fix timer. Tests/BaseFabTesting/main.cpp commit ddb2d87ad21a17e89ba88cab835d4153de2f6d29 Author: Kevin Gott Date: Sat Sep 22 01:55:30 2018 -0400 Small change to BaseFabTest. Tests/BaseFabTesting/main.cpp commit 877f48ac235bb136ee84f85128b5da2b8b84e0bc Merge: 87aa025f6 55033748a Author: kngott Date: Fri Sep 21 22:48:07 2018 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit 87aa025f6614068722ac64e56a7bdbaa9e5c7de5 Author: kngott Date: Fri Sep 21 22:47:55 2018 -0700 BaseFab edit for 1 iter. Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit 55033748a0fdd1f979c016449294a54354b02a0a Author: Tan Nguyen Date: Fri Sep 21 14:18:17 2018 -0700 update RGIter Src/Base/AMReX_FabArrayBase.H commit 088a8bb0879f2defd8ea490c43bd19fd7ac823ef Merge: edc3de713 8ad443b0b Author: Tan Nguyen Date: Fri Sep 21 13:43:39 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit edc3de713afe364c18c7b77522e16252b60ab3ca Author: Tan Nguyen Date: Fri Sep 21 13:43:25 2018 -0700 update AsyncFillPatchIter Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/Base/AMReX_MultiFabUtil_Perilla.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/Base/Make.package commit 8ad443b0b88f347bd907ce70059bc3898155361b Author: kngott Date: Fri Sep 21 12:40:03 2018 -0700 Update to BaseFabTest: some results fixed and masks set randomly. Tests/BaseFabTesting/main.cpp commit afe6fe57a8fa34c6b642061ec6431ab1bcb26e69 Author: Weiqun Zhang Date: Fri Sep 21 10:51:34 2018 -0700 For portability, static_cast std::streampos to std::streamoff for comparison with long Src/Base/AMReX_VisMF.cpp commit f44f5798c915c1032b6f30f6350e2176ff8d9fc8 Author: Andrew Myers Date: Fri Sep 21 13:32:36 2018 -0400 wip - beging reorg of gpu particle code Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit da04fa61af9f6cd04ebb1613be70478efa9146a8 Author: Max Katz Date: Fri Sep 21 10:33:01 2018 -0400 Use PGI as host compiler when using OpenACC Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 25179b7eb1b28cb7543554e19d6164d95853bb04 Merge: 26917c856 aab9bd1cd Author: Wolfram Schmidt Date: Fri Sep 21 12:01:19 2018 +0200 Merge remote-tracking branch 'upstream/development' into development commit 559affd6750bdc3bb30939e0ea7c37f53700323d Merge: 8f5e38c7c aab9bd1cd Author: Weiqun Zhang Date: Thu Sep 20 21:15:04 2018 -0700 Merge branch 'development' into devirtualize-fab commit aab9bd1cdeff7f5d90c6c28d4fa7f7d3a3a71a8c Merge: 98cda28ca b538009df Author: Weiqun Zhang Date: Thu Sep 20 21:13:52 2018 -0700 Merge branch 'development' into basefab_T commit b538009dfb3dfbfaac82de97ed785b1f6063a2aa Merge: 695feee9c b33076b85 Author: Weiqun Zhang Date: Thu Sep 20 18:01:15 2018 -0700 Merge branch 'development' into mlmg commit 695feee9cccbec6c60bf5870a71ef889cf62b0d7 Author: sireeveslbl Date: Thu Sep 20 15:53:30 2018 -0700 Fixed PETSC Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit b33076b85c82f4b7e769a98145388fddc31d485e Merge: 86850afe1 ee28ee67c Author: Johannes Blaschke Date: Thu Sep 20 15:51:12 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 86850afe17051fdecd07b6d55744f19eb3350b64 Author: Johannes Blaschke Date: Thu Sep 20 15:51:10 2018 -0700 levelset factory now outputs eb-geometry Src/EB/AMReX_EB_levelset.H commit a776e26d4553a4e0ae8500696078bf6171fc894a Author: Marc Day Date: Thu Sep 20 15:36:29 2018 -0700 pass flux call down to linop Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 98cda28ca016bf0d7e50f79d95d7530b009d42b8 Author: kngott Date: Thu Sep 20 15:24:16 2018 -0700 remove whitespace Tests/BaseFabTesting/inputs commit 6a53f4c5881c80d5a5f194333e8fb8e144ff4b83 Merge: 800520ffc 3d5d930a6 Author: Marc Day Date: Thu Sep 20 15:13:06 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit 3d5d930a667650b623a3c9dd84c3084822ba2681 Author: Marc Day Date: Thu Sep 20 15:12:32 2018 -0700 Add a getFluxes function that takes a solution rather than using the internal one, which may not exist unless solve is called. Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f61302f3e1c8a39797cd6faf233485122b999aa3 Author: kngott Date: Thu Sep 20 14:34:34 2018 -0700 mask fix Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit 8b08251d15b729e2ae043538e5a5db62576e016e Author: kngott Date: Thu Sep 20 13:43:52 2018 -0700 More BaseFabTest adjustments. Tests/BaseFabTesting/main.cpp commit 479adf60df8260c6f4afedd4ec67809d10698fb5 Author: kngott Date: Thu Sep 20 13:37:35 2018 -0700 Less iterations, all basefab routines. Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit f0a8cffdf88921e2fa36f8efc0fd6b3c106f1fa2 Merge: 43a972fe4 224cc1bb3 Author: Weiqun Zhang Date: Thu Sep 20 13:25:49 2018 -0700 Merge branch 'basefab_T' of github.com:AMReX-Codes/amrex into basefab_T commit fa84c2fbcaff3e4e00162a2d2ee96eb62fb842d5 Merge: 8f4772b8c ee28ee67c Author: Max Katz Date: Thu Sep 20 16:14:19 2018 -0400 Merge branch 'development' into gpu commit ee28ee67c98502018c5a98335f267572a0ab3de5 Author: Max Katz Date: Thu Sep 20 16:11:34 2018 -0400 Add template for max reduction Src/Base/AMReX_BLFort.H commit 8f4772b8c5fd75be4046ee1626c27da32417fcf1 Author: Max Katz Date: Thu Sep 20 16:10:23 2018 -0400 Add max reduction Src/Base/AMReX_BLFort.H commit 43a972fe4839dcf0b5398dc284c980ef246c91e0 Author: Weiqun Zhang Date: Thu Sep 20 12:54:02 2018 -0700 minor Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EB2_GeometryShop.H commit 9611046defbadb9c89aac3e2b56b38e08d6a0a61 Author: Max Katz Date: Thu Sep 20 15:21:54 2018 -0400 Split up kernel launch line Tools/F_scripts/write_cuda_headers.py commit ca76cd28ba3cf787ed6773f4775418b05a3a446e Author: Max Katz Date: Thu Sep 20 15:10:08 2018 -0400 Throw an error if not using PGI or XL with CUDA Tools/GNUMake/Make.defs commit 224cc1bb3ea3ee70d92ddc954fc8e0406e316992 Author: kngott Date: Thu Sep 20 11:41:46 2018 -0700 Clean up prints. Tests/BaseFabTesting/main.cpp commit 32cb991f357f9575e09ad4d9192950c186db64ba Author: kngott Date: Thu Sep 20 11:28:03 2018 -0700 Partial test update. Tests/BaseFabTesting/main.cpp commit b693d59c64e5e150837f8c1f2f4d476559d6d26e Author: Weiqun Zhang Date: Thu Sep 20 11:17:57 2018 -0700 fix uninitialized value Src/Base/AMReX_BaseFab.H commit 723017c6c3fd931b7335c2f94ec8dfee279a2d42 Author: Weiqun Zhang Date: Thu Sep 20 10:18:12 2018 -0700 add StridedPtr and use it Src/Base/AMReX_BaseFab.H commit 9412dda96792c9ff6907b4d3a7bdf4b70f59fadc Author: Donald E. Willcox Date: Thu Sep 20 10:18:18 2018 -0400 preserve case for gpu targets in public statements Tools/F_scripts/gpu_fortran.py commit ce13ef65cb4328aa9bb8337ccc560f9a9f7d5452 Author: Alice Harpole Date: Thu Sep 20 09:19:09 2018 -0400 Add charstring compiler flag (#321) Adds -Mcuda=charstring flag to pgi.mak. This is needed for offloading some of the gravity routines to GPU in Castro. Tools/GNUMake/comps/pgi.mak commit 00647e6e08c35ccbce3a0d4ff74f054d62073552 Merge: 3dcf17588 dd674416e Author: Weiqun Zhang Date: Wed Sep 19 21:54:56 2018 -0700 Merge branch 'basefab_T' of github.com:AMReX-Codes/amrex into basefab_T commit 3dcf17588edd71026a3ad401d96a7afc305e8b38 Author: Weiqun Zhang Date: Wed Sep 19 21:54:07 2018 -0700 clean up Src/Base/AMReX_BaseFab.H commit a325765e6900d19e7a6aa8d0994e0283ee6d3ad3 Author: Weiqun Zhang Date: Wed Sep 19 21:39:19 2018 -0700 new version of BaseFab function templates Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit dd674416e89f8ecbcee267ad713aa51f9c96c487 Author: Kevin Gott Date: Wed Sep 19 23:45:23 2018 -0400 Compile worked on BaseFab test. Tests/BaseFabTesting/GNUmakefile Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit fd99cf50edacf595fd9704ecef097be8d1e83a18 Author: Kevin Gott Date: Wed Sep 19 20:47:35 2018 -0400 Add number of components to test. Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit bd1d0fcef3e91ce39005abb9e6bf1d2fb9261c05 Author: Tan Nguyen Date: Wed Sep 19 16:52:04 2018 -0700 add asyncFillPatchIter Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/RGIter.H Src/AmrTask/rts_impls/Perilla/RGIter.cpp commit 8b96839601ff76af8c16e25903b8c8cdde96ea1f Merge: 1113463c8 5f973b8a9 Author: Weiqun Zhang Date: Wed Sep 19 16:39:58 2018 -0700 Merge branch 'basefab_c' into basefab_T commit 1113463c85c25d67028b43b2d4bef2f4181f19a3 Author: Weiqun Zhang Date: Wed Sep 19 16:38:07 2018 -0700 another version of linComb Src/Base/AMReX_BaseFab.H commit bbf511bad712b50ccf21c9337f8b839808a8b130 Author: Brandon Runnels Date: Wed Sep 19 17:01:20 2018 -0600 minor changes to fix NAN errors Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 6e7c60160418782843b3d67372941ed004c164d6 Author: Max Katz Date: Wed Sep 19 18:46:17 2018 -0400 Fix macros Src/Base/AMReX_ArrayLim.H commit 1ceb9772e90672f0a040bb2fc23d32ce81987025 Author: Weiqun Zhang Date: Wed Sep 19 15:42:31 2018 -0700 an alternative version of linComb Src/Base/AMReX_BaseFab.H commit 494c0567ec8aa6274d7955012ad070deb0bca053 Author: Weiqun Zhang Date: Wed Sep 19 15:02:12 2018 -0700 fix bug Src/Base/AMReX_BaseFab.H commit d615236dd7919def5556f9da18e3c38e8b576be2 Author: Ann Almgren Date: Wed Sep 19 14:27:33 2018 -0700 Add the option to set the bottom_solver_type through the MacProjector. Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 9409d21e570f0dce6089481f1b210b36646071eb Author: Weiqun Zhang Date: Wed Sep 19 13:14:30 2018 -0700 first pass to template implementation Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_REAL.H Src/Base/AMReX_RESTRICT.H Src/Base/CMakeLists.txt Src/Base/Make.package commit e6fcfa6ea1cb38ea075277a1039f6c432aa340c0 Author: Andrew Myers Date: Wed Sep 19 16:44:04 2018 -0400 Revert "Respect the COMP choice when compiling with CUDA" This reverts commit 8a597a3c41342058eacfe889f8d7be04e517c4c0. Tools/GNUMake/comps/nvcc.mak commit b3cdcaa69bed05aa595cd8afef18b1c60e8d8ec3 Author: Andrew Myers Date: Wed Sep 19 16:22:24 2018 -0400 remove un-needed boilerplate from CudaManagedAllocator; let compiler define constructors Src/Base/AMReX_CudaAllocators.H commit 5f973b8a913ff3208da9ed085e7996553c431af4 Author: kngott Date: Wed Sep 19 12:14:30 2018 -0700 Working BaseFab test suite. Tests/BaseFabTesting/GNUmakefile Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit 3a49e2eff77a524d45f2be519759d4bdefe562f8 Merge: b93c11e60 dd1fe920a Author: Brandon Runnels Date: Wed Sep 19 12:46:59 2018 -0600 Merge branch 'development' into mc-nodelinop commit b93c11e60938aec9fddba956eb05902335edbd16 Author: Brandon Runnels Date: Wed Sep 19 12:46:25 2018 -0600 updated MLMG for multicomponent solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5a78f5027a4cf0e7848a28c0fee3575e437df936 Author: kngott Date: Wed Sep 19 11:32:57 2018 -0700 First draft of BaseFab Test. Tests/BaseFabTesting/GNUmakefile Tests/BaseFabTesting/Make.package Tests/BaseFabTesting/main.cpp commit dd1fe920a6a9a154ec0506fdf97d238ac0c693d6 Author: Andrew Myers Date: Wed Sep 19 11:30:07 2018 -0700 protect against floating point exceptions in DistributionMapping::makeKnapSack Src/Base/AMReX_DistributionMapping.cpp commit 8a597a3c41342058eacfe889f8d7be04e517c4c0 Author: Max Katz Date: Wed Sep 19 13:02:42 2018 -0400 Respect the COMP choice when compiling with CUDA Tools/GNUMake/comps/nvcc.mak commit 98ab6e68bdbc3d83178b2421f3c21f4f8605a6ad Author: Max Katz Date: Wed Sep 19 13:01:59 2018 -0400 Always use gcc for the preprocessing Tools/GNUMake/Make.rules commit 3923f2a42ceea4f894a006b5d8296b6c4213a090 Author: Weiqun Zhang Date: Wed Sep 19 08:52:07 2018 -0700 expose MLMG and LinOp from MacProjector Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit 26917c8566c617299c669df204cba1c7cdb1c467 Author: Wolfram Schmidt Date: Wed Sep 19 17:21:11 2018 +0200 Added configuration for NEC Aurora (only serial) to GNUMake and excluded GNU extensions not supported by NEC compiler via __NEC__ preprocessor symbol. Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/fabio_c.c Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/comps/nec.mak Tools/GNUMake/sites/Make.hs commit 9b3ac6265189e60f897a73da7a2d54ffaf357121 Author: Max Katz Date: Wed Sep 19 11:10:33 2018 -0400 Catch numbers in subroutine names Tools/F_scripts/write_cuda_headers.py commit 1edfb306cd715bcb7e0d25cb6fd91ed9a3a0a857 Author: Weiqun Zhang Date: Tue Sep 18 21:28:39 2018 -0700 rm slowCopy Src/Base/AMReX_BaseFab.H commit 31c9e7997968a194e5fd1f678c8e0f8933468027 Author: Weiqun Zhang Date: Tue Sep 18 21:08:00 2018 -0700 ifdef out specialization Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 2d333ab237a90a31297478c7e00b024e7cdae0f9 Author: Weiqun Zhang Date: Tue Sep 18 20:28:09 2018 -0700 remove trailing space Tools/GNUMake/Make.defs commit ba21ae6d170ae1ef70813b51599d23f7277048fa Merge: daaf0c641 c679ba5d7 Author: Weiqun Zhang Date: Tue Sep 18 20:26:19 2018 -0700 Merge branch 'basefab_c' of github.com:AMReX-Codes/amrex into basefab_c commit daaf0c6414f39ed340fbbc8c886659b4c3fbb109 Author: Weiqun Zhang Date: Tue Sep 18 20:26:05 2018 -0700 c -> cpp Src/Base/AMReX_BaseFab_c.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit e44304858370f9b238cfec8cbab66a58dd040fca Author: Weiqun Zhang Date: Tue Sep 18 20:18:20 2018 -0700 add AMREX_RESTRICT Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c Src/Base/AMReX_REAL.H commit c679ba5d75eb114ac07b81d4b474ccf6d3f011cc Author: Kevin Gott Date: Tue Sep 18 20:18:31 2018 -0400 Add USE_GPU_PRAGMA option to GNUMakefile. Tools/GNUMake/Make.defs commit 690812fd1516bd03b5861ba63d5a0001829fae0a Author: Weiqun Zhang Date: Tue Sep 18 17:14:43 2018 -0700 fix a test Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit f85a5d7d1dbabdaadab7fa9aae0149e646d866d6 Author: Weiqun Zhang Date: Tue Sep 18 16:41:24 2018 -0700 missing fabs Src/Base/AMReX_BaseFab_c.c commit 3d1cffe4dffc632d363a1c7652af6fee9ad0c35d Merge: 7f0845305 58a9fb74d Author: Brandon Runnels Date: Tue Sep 18 15:41:06 2018 -0600 Merge branch 'development' into mc-nodelinop commit 7f08453057b766cd852d39549c38c509fccc75f1 Author: Brandon Runnels Date: Tue Sep 18 15:38:16 2018 -0600 initial update of mllinop for multicomponent solves Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 31ab19c4bd3fb0487485d3f35f4eecce2db3b80b Author: Weiqun Zhang Date: Tue Sep 18 14:17:41 2018 -0700 removed some BL_NO_FORT's Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_MultiFab.cpp commit 9a047f1dc19781dc0d8e7dc34efddb3e081a1fb6 Merge: 35c790dd9 58a9fb74d Author: Kevin Gott Date: Tue Sep 18 17:03:50 2018 -0400 Merge branch 'development' into gpu-mm Conflicts: Src/Base/AMReX_BaseFab_nd.F90 commit bc204686d7022b9ee421b3fd162086bac98e1eab Author: Weiqun Zhang Date: Tue Sep 18 14:02:24 2018 -0700 update setval_ifnot Src/Base/AMReX_BaseFab.cpp commit 35c790dd9f666f18dc6cfa89b890f7b146e5ada4 Author: Kevin Gott Date: Tue Sep 18 16:56:43 2018 -0400 Remove CPU versions of now Device functions. Src/Base/AMReX_Managed.H commit 510b7bdd549820a1fa26fc0d7e3989ed7bcffd87 Merge: ca28e06da 4fe77f7a5 Author: Weiqun Zhang Date: Tue Sep 18 13:54:03 2018 -0700 Merge branch 'development' into basefab_c commit 4fe77f7a5232dedce2860bf568d25f1d37fe064d Author: Weiqun Zhang Date: Tue Sep 18 13:49:38 2018 -0700 add BaseFab::setValIfNot Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ca28e06da54daa46cea53139aeda89458fdc53eb Author: Weiqun Zhang Date: Tue Sep 18 13:19:10 2018 -0700 use c versions in BaseFab Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 commit b2e8221755bc42c94296318d669c18aca26fc4c1 Merge: 2f75c9c7e 3fbc6ecb5 Author: Donald E. Willcox Date: Tue Sep 18 20:06:31 2018 +0000 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 2f75c9c7e7b82020933505d45f6c41576d7d0e4f Author: Donald E. Willcox Date: Tue Sep 18 20:06:26 2018 +0000 AMREX_ARLIM_ARG with CUDA always returns 3 arguments. Src/Base/AMReX_ArrayLim.H commit 3fbc6ecb5453ec621ebaa526f989c411f2bf3c98 Author: dwillcox Date: Tue Sep 18 15:47:28 2018 -0400 Replace procedure with procedure_device, preserving the case of procedure. Tools/F_scripts/gpu_fortran.py commit ecb145dae43f7bc7f088b2fbd7b02575594d0cf5 Author: Weiqun Zhang Date: Tue Sep 18 11:34:01 2018 -0700 tidy Src/Base/AMReX_BaseFab_c.c commit 7931efa03a80ae63f6e072554162377df8b9d93d Author: Weiqun Zhang Date: Tue Sep 18 11:21:20 2018 -0700 first pass Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 58a9fb74d69855f8049ca393ebb5b2c38d27d248 Author: Weiqun Zhang Date: Tue Sep 18 10:40:51 2018 -0700 eb: add more protection against roundoff errors Src/EB/AMReX_eb2_3d.F90 commit 56c7b28131266cbc1d5baabf2eb71b8df795e245 Merge: e0efa7a19 e9a3e4ed2 Author: Max Katz Date: Tue Sep 18 12:43:47 2018 -0400 Merge branch 'development' into gpu commit e0efa7a1994122f73ac089d342f19f0a06e5b927 Author: dwillcox Date: Tue Sep 18 12:31:34 2018 -0400 Fix a subroutine-detecting bug. Tools/F_scripts/gpu_fortran.py commit e9a3e4ed228b9f80e055c90c7be3b994296db33a Merge: 69c592b88 ba870923e Author: WeiqunZhang Date: Tue Sep 18 09:09:00 2018 -0700 Merge pull request #311 from AMReX-Codes/statedata Statedata commit f0c9a6df5c0f2f6b3f7f1a2974940ce118cbfd6e Merge: df4ba45de 03877e801 Author: Donald E. Willcox Date: Tue Sep 18 05:52:48 2018 +0000 Merge branch 'gpu-fortran-update' into gpu to support StarKiller Microphysics. commit 03877e8018fd1c181fdd4120b5d29e0ba01d72be Author: Donald E. Willcox Date: Tue Sep 18 05:52:27 2018 +0000 GPU Fortran preprocessing script supports StarKiller. Tools/F_scripts/gpu_fortran.py commit 203a75c9fe9e12cbbb26dda1bf26a926cf798021 Author: Weiqun Zhang Date: Mon Sep 17 22:04:47 2018 -0700 more on BaseFab C functions Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c Src/Base/AMReX_BaseFab_f.H commit 69c592b88479d7f561e6378a0b8324f858f8ff80 Author: Tan Nguyen Date: Mon Sep 17 17:12:49 2018 -0700 regular updates Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla_upc++/PerillaConfig.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile commit 9bfe9492a9e478ec3d7d507bb91197b1fa3c3bab Author: Kevin Gott Date: Mon Sep 17 20:05:18 2018 -0400 Test showing Fortran return problem. Tutorials/GPU/TestB/GNUmakefile Tutorials/GPU/TestB/Make.package Tutorials/GPU/TestB/main.cpp Tutorials/GPU/TestB/return_test.F90 commit 6963ebf53a03d3e4a589d1092bd1eb438ac79dd5 Author: Weiqun Zhang Date: Mon Sep 17 16:59:18 2018 -0700 tweak macros Src/Base/AMReX_BaseFab_c.c commit 03fcaeb687b347e8ea127b7c9602c7ec4d21af5f Author: Kevin Gott Date: Mon Sep 17 19:30:44 2018 -0400 Missed parenthesis. Src/Base/AMReX_MultiFab.cpp commit df4ba45debfeb765d07298cf4b0e782e26817d9e Author: Max Katz Date: Mon Sep 17 17:15:57 2018 -0400 Function signatures should be case sensitive in C++ Tools/F_scripts/write_cuda_headers.py commit e195cf01917ba3864a20444a3af162c37a6964a5 Author: Weiqun Zhang Date: Mon Sep 17 13:48:44 2018 -0700 tidy and check in new files Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c commit 855fef569cb1b0cd1518e4fe0618011e8256f9de Author: Weiqun Zhang Date: Mon Sep 17 13:24:10 2018 -0700 start BaseFab_c Src/Base/AMReX_BaseFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit f43c2192d19b84e5ffc30ce09ec0f3292d7973e7 Author: Tan Nguyen Date: Mon Sep 17 12:46:06 2018 -0700 just regular updates Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile Src/Base/AMReX_MemPool.cpp commit 01d1ea223b406dfe500438c8059cbe75b8c60034 Merge: 6ba2b8b7d e167f1a03 Author: Weiqun Zhang Date: Mon Sep 17 11:15:04 2018 -0700 Merge branch 'mlmg' into development commit 6ba2b8b7d02b9770afa785d12cb874bd977baade Merge: 2360e2e86 5b66f1cd9 Author: Weiqun Zhang Date: Mon Sep 17 11:14:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e167f1a0377ce543296a09a8cf0398a3c44cc92c Author: Weiqun Zhang Date: Mon Sep 17 11:13:02 2018 -0700 CellEB2 test: more general at boundary Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/MyTest_F.H Tests/LinearSolvers/CellEB2/mytest_f.F90 commit a0bdf76d92a105cabfe45ea682eded3087370607 Author: dwillcox Date: Mon Sep 17 14:01:59 2018 -0400 Update GPU script for StarKiller Microphysics. Tools/F_scripts/gpu_fortran.py commit 5b66f1cd92eacf48fecdc14861220ca4ab6dea90 Author: Andrew Myers Date: Mon Sep 17 10:54:51 2018 -0700 adding overloaded versions of get_particles, num_particles, and add_particle to the Fortran interfaces Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit 2360e2e86b3d1c71297d9c50ffbfc02dca2bd303 Author: Weiqun Zhang Date: Mon Sep 17 09:38:58 2018 -0700 add a new geometry type to CellEB2 test Tests/LinearSolvers/CellEB2/initEB.cpp commit 12352aaebd2d166edf2043e1ce984d8705668a9e Author: Weiqun Zhang Date: Sun Sep 16 15:43:55 2018 -0700 fix path Tools/CompileTesting/compiletesting.py commit 3e9257ed949477fd3e6c83a0da2d22e783c8fa79 Author: Weiqun Zhang Date: Sun Sep 16 15:38:30 2018 -0700 update compile testing Tools/CompileTesting/compiletesting.py commit 038b48f8306fd9857277491951f864c3348f3fcd Author: Weiqun Zhang Date: Sun Sep 16 15:21:48 2018 -0700 inputs for new EB regression tests Tests/LinearSolvers/CellEB/inputs.rt.2d Tests/LinearSolvers/CellEB/inputs.rt.2d.petsc Tests/LinearSolvers/CellEB/inputs.rt.3d commit 117db3c591c39893524130ad3cffe51a3b900101 Author: Weiqun Zhang Date: Sun Sep 16 15:17:29 2018 -0700 fix return Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit a5fdd7aa11e311315de7eae83b96033e71eb30c2 Author: Weiqun Zhang Date: Sat Sep 15 23:08:56 2018 -0700 writePlotfile Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB/main.cpp commit 6b930dcb6a6e3b3ac27fa16ab14eb074b4260a8c Author: Weiqun Zhang Date: Sat Sep 15 21:32:36 2018 -0700 inputs for new EB regression tests Tests/LinearSolvers/CellEB2/inputs.rt.2d Tests/LinearSolvers/CellEB2/inputs.rt.3d Tests/LinearSolvers/CellEB2/inputs.rt.hypre commit b5ffcd71223d5dc71bd9108b3e2d865eb705bfdf Author: Weiqun Zhang Date: Sat Sep 15 21:10:59 2018 -0700 add a test for BL_NO_FORT Tests/NoFort/GNUmakefile Tests/NoFort/Make.package Tests/NoFort/main.cpp commit 2016e2e80b4ab73ecafe77c70b69d491f1ec1ba8 Author: Weiqun Zhang Date: Sat Sep 15 18:13:06 2018 -0700 doc: make it clear the command line argument is optional. Docs/sphinx_documentation/source/GettingStarted.rst commit ba870923e51245b61864407034db187175957f4e Author: Weiqun Zhang Date: Sat Sep 15 18:13:06 2018 -0700 doc: make it clear the command line argument is optional. Docs/sphinx_documentation/source/GettingStarted.rst commit 8e50c24c72b29678e414aa31eb2545bb27936a5e Author: Weiqun Zhang Date: Sat Sep 15 11:43:08 2018 -0700 more changes for NEC Src/Base/AMReX_ParallelDescriptor_F.F90 Src/Base/AMReX_parmparse_mod.F90 commit 7ca91d255b5204826043d548ae2cfca8bc3630e8 Author: dwillcox Date: Sat Sep 15 13:30:23 2018 -0400 Hack for importing functions and logic for distinguishing function calls. Tools/F_scripts/gpu_fortran.py commit 24e83eb300a073bbca8643f6cda4cb36a307d491 Author: Weiqun Zhang Date: Sat Sep 15 07:31:13 2018 -0700 fix missing prefix Src/Base/AMReX_BaseFab_nd.f90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 commit 9d0b09d5b52bdf093f96f622c24ffdff5ecf8a76 Merge: 74ca9348f 87e26603e Author: WeiqunZhang Date: Fri Sep 14 22:54:51 2018 -0700 Merge pull request #313 from kweide/development More changes for per-fab fluxregister fineadd use from FLASH commit 8f5e38c7cd342f0267485bf22e6e60ed142adb4d Author: Weiqun Zhang Date: Fri Sep 14 21:47:40 2018 -0700 fix more casts Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBFluxRegister.cpp commit fa2e2a74d68975527fd8973b1337a0aab3c7345d Author: Weiqun Zhang Date: Fri Sep 14 21:33:33 2018 -0700 fix cast Tutorials/EB/CNS/Source/CNS.cpp commit 9060af7bb4d9aaca020ea1bd722af2b3ff620bc5 Author: Weiqun Zhang Date: Fri Sep 14 21:22:26 2018 -0700 explicitly write move constructor for StateData hoping to make NEC happy Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit cdd3243e262c2f36b5ebf45e5289e40599938ff2 Merge: 1c51ec0df 74ca9348f Author: Weiqun Zhang Date: Fri Sep 14 21:08:30 2018 -0700 Merge branch 'development' into statedata commit 1978a0dec2bed815f9fe999ed5c37f1f64f2f400 Merge: e55a70c3d 74ca9348f Author: Weiqun Zhang Date: Fri Sep 14 21:03:04 2018 -0700 Merge branch 'development' into devirtualize-fab commit 74ca9348f9dbe4a7898cba7bbcf765efe050df08 Merge: 64bcc3f87 9081c0836 Author: Weiqun Zhang Date: Fri Sep 14 21:01:00 2018 -0700 Merge branch 'development' into mlmg commit c6db1630b726416b1c5683a51e2be308ec8801ab Author: Kevin Gott Date: Fri Sep 14 21:45:34 2018 -0400 BaseFab add, subtract, multiply and divide GPU-ized, including Multifab calls. Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_MultiFab.cpp commit 64bcc3f87c0cb141211dfcfc34e8fa21b15684ae Author: Weiqun Zhang Date: Fri Sep 14 18:02:04 2018 -0700 use dx_eb from module Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit dcc2ab9c8e0b79d9300bfdbc436fe683a67ef38b Merge: 17c31e631 a9cfb02a8 Author: Weiqun Zhang Date: Fri Sep 14 17:56:19 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit 17c31e631f144e66d02a27453f1dcc41f7341ea0 Author: Weiqun Zhang Date: Fri Sep 14 17:56:14 2018 -0700 add makePETSc Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a9cfb02a8b7e99196e725597491b0b1dfe99bbd7 Author: sireeveslbl Date: Fri Sep 14 17:29:13 2018 -0700 Hypre Routines for EB Dirichlet complete. Works for 2D and 3D Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit cf1b212547734e3569183dcc289ce9dd66c67817 Author: Kevin Gott Date: Fri Sep 14 19:23:12 2018 -0400 Make HeatEquation0 lambdas inlined. EmPIC keeps the separate lambdas/macro example. Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit 22936b3c4cba678e0cfc89489e8a5af729f42448 Author: Kevin Gott Date: Fri Sep 14 19:17:07 2018 -0400 Change Remaining BaseFab -> FArrayBox Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 1c96532d375e9436ef7e77f89f403a10b86ac521 Author: Kevin Gott Date: Fri Sep 14 19:02:27 2018 -0400 Rename and distinguish run scripts. Tutorials/GPU/HeatEquation_EX0_C/Exec/run.summit Tutorials/GPU/HeatEquation_EX0_C/Exec/run.summitdev commit 6514c79e4cf2770e924720e9f0f6d1c1601c701e Author: Kevin Gott Date: Fri Sep 14 19:01:45 2018 -0400 Change BaseFab to FArrayBox for lambda capture. First test. Need to explicitly label all FArrayBox functions that use static class objects AMREX_DEVICE_HOST for safety. Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit d55fe127d8f2dc17f12a7a8656b12da60dd839d9 Author: Kevin Gott Date: Fri Sep 14 19:00:43 2018 -0400 Variable and test to turn tiling off if on GPU. Src/Base/AMReX_MFIter.H Src/Base/AMReX_MultiFab.cpp commit cf588c4b48d6cc9a817a1910ac1f64b4588069e7 Author: Kevin Gott Date: Fri Sep 14 18:59:23 2018 -0400 First Multifab function to GPU: copy. HeatEquation now has negligible page faults. Src/Base/AMReX_MultiFab.cpp commit 61d759c232d86ac5025e810dd06347ac403bb187 Author: Kevin Gott Date: Fri Sep 14 18:57:35 2018 -0400 Change inputs Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_3d commit 9171a5b2b9329b1328f6f6f2cae8e797c1e6172e Author: Kevin Gott Date: Fri Sep 14 18:56:46 2018 -0400 EmPIC with Lambdas inlined. Tutorials/GPU/ElectromagneticPIC_2/Constants.H Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.H Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/GNUmakefile Tutorials/GPU/ElectromagneticPIC_2/IO.H Tutorials/GPU/ElectromagneticPIC_2/IO.cpp Tutorials/GPU/ElectromagneticPIC_2/Make.package Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.H Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC_2/Particles.H Tutorials/GPU/ElectromagneticPIC_2/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC_2/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_2/em_pic_F.H Tutorials/GPU/ElectromagneticPIC_2/inputs Tutorials/GPU/ElectromagneticPIC_2/main.cpp Tutorials/GPU/ElectromagneticPIC_2/script.nompi.sh Tutorials/GPU/ElectromagneticPIC_2/summit.sh Tutorials/GPU/ElectromagneticPIC_2/summitdev.sh Tutorials/GPU/ElectromagneticPIC_2/test.cpp commit 08b4e950e26a03a65a530425912440931ebe2195 Author: Kevin Gott Date: Fri Sep 14 18:43:16 2018 -0400 CUDA ifdef wrapper fix. Src/Base/AMReX_Device.cpp commit 887029a32da87a8f3917a119cc0e6ac95c8b7d0e Author: Weiqun Zhang Date: Fri Sep 14 13:58:10 2018 -0700 explicitly use final override. makeHypre linop Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H commit 729f866edaa63eb22b4f78fba1d515633090442b Author: Weiqun Zhang Date: Fri Sep 14 11:33:32 2018 -0700 move getFluxes from MLMG to MLCellABecLap Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 39368764212dbf082bf8ba8fb10aa27fea00774f Author: Weiqun Zhang Date: Fri Sep 14 10:52:32 2018 -0700 add abstract MLCellABecLap class Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/Make.package commit f560e2e1c7084ace63e48668a2e94ce1c1364598 Author: Weiqun Zhang Date: Fri Sep 14 09:28:54 2018 -0700 fix typo Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit 800520ffcbae0867abe6e04871666da777f85691 Merge: 6abf70666 9081c0836 Author: Marc Day Date: Thu Sep 13 23:45:13 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit 9081c0836c93cc6d8e957a7f9f65c9534bf98bcd Author: Cy Chan Date: Thu Sep 13 23:10:50 2018 -0700 added ForkJoin::set_task_output_file() enabled appending to task output files enabled changing task output files in the middle of tasks updates to MultiColor_C OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ParallelContext.cpp commit 6abf70666957254eef4dfb293a55be7e27dbaa87 Author: Marc Day Date: Thu Sep 13 19:41:36 2018 -0700 Make C_CellMG collectives Fork-Join friendly Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit 76c295b9d6f27d3729f0fdecaa4da4cf87320838 Author: Marc Day Date: Thu Sep 13 18:28:01 2018 -0700 Add not-equal for BERec Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit db88a39487d7d82f357b2c33678d3e73b96bca3a Author: Weiqun Zhang Date: Thu Sep 13 17:19:16 2018 -0700 add use_petsc Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp commit 53cf63c8f2ee5bbb89e43e5104f71a55c222d763 Merge: 42a912f6d 7d5d2a064 Author: Weiqun Zhang Date: Thu Sep 13 16:20:58 2018 -0700 Merge branch 'development' into mlmg commit 7d5d2a0648092f814a1d82d0c8fa3c7ebae62a2a Author: Weiqun Zhang Date: Thu Sep 13 16:20:38 2018 -0700 fix a bug in test set up Tests/LinearSolvers/CellEB2/mytest_f.F90 commit b08840c7355f50f6e5b11fc84ab21ce67b780dca Author: Kevin Gott Date: Thu Sep 13 19:08:01 2018 -0400 script and input adjustments Tutorials/GPU/ElectromagneticPIC/summitdev.sh Tutorials/GPU/HeatEquation_EX0_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX0_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script commit 9e13a75c3fa55756919edb91a232462579b47633 Author: Kevin Gott Date: Thu Sep 13 19:00:14 2018 -0400 Addition of non-sync cudaMemcpy wrappers. Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit fff0bcf0df12e46119744fd628be33c911310d17 Author: Kevin Gott Date: Thu Sep 13 18:51:52 2018 -0400 Additional Device::synch Src/Base/AMReX_FabArrayCommI.H commit 47e8febfbe1f94c1b3dc4a2fea0fd06b15acbdf3 Author: Kevin Gott Date: Thu Sep 13 18:51:15 2018 -0400 CUDA wrapper adjustment. Src/Base/AMReX_fort_mod.F90 commit 74e89954c1a6fd97ecd97ce12e466191bb19a833 Author: Kevin Gott Date: Thu Sep 13 18:49:19 2018 -0400 include fix Src/Base/AMReX_CudaAllocators.H commit 226c0b530b07b4305105ec5d72337fdc869f8c40 Author: Kevin Gott Date: Thu Sep 13 18:47:24 2018 -0400 amrex_malloc and amrex_free library fix. Src/Base/AMReX_CUDA_Utility.cpp commit 42a912f6de0375726a6eb4f7f26a36d31702e184 Author: Weiqun Zhang Date: Thu Sep 13 15:16:32 2018 -0700 fix a few things Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 3c742ce8528b48486ac99d127cf1170083eb6237 Author: Weiqun Zhang Date: Thu Sep 13 13:04:21 2018 -0700 some clean up Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 54f2c1d315923d27359cb9107dfffb1094c12024 Merge: 765ee8812 cb4c49653 Author: Marc Day Date: Thu Sep 13 13:16:47 2018 -0700 Merge remote-tracking branch 'origin/development' into marc/forkjoin_dev commit cb4c4965357714e2104558b30e10090eb0136e31 Author: Andrew Myers Date: Thu Sep 13 13:08:50 2018 -0700 tweak .travis.yml again... .travis.yml commit 4be5e4cda0c8356477f12c5c1046bef23bac7da7 Merge: 08423fb65 0f48f3d8f Author: Andrew Myers Date: Thu Sep 13 13:03:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 08423fb655f62b8e15155493ebdb8d531d766fee Author: Andrew Myers Date: Thu Sep 13 13:03:44 2018 -0700 assume 'yes' to queries since this is happening in a script .travis.yml commit 0f48f3d8f0b449464963b1f921f6490821a99e96 Author: Marc Day Date: Thu Sep 13 13:03:30 2018 -0700 Add (another) multifab diff tool that includes grow cells Tools/C_util/DiffMultiFab/GNUmakefile Tools/C_util/DiffMultiFab/diffmultifab.cpp commit c9748733bc2d6519a06d0d085797f1193b9f2077 Author: Andrew Myers Date: Thu Sep 13 12:55:18 2018 -0700 try to use 3.6 instead of 3.4 .travis.yml build_and_deploy.sh commit 305dd23f6a32645b8e82b5162c7ae4b5a0fa24f2 Author: Weiqun Zhang Date: Thu Sep 13 12:54:40 2018 -0700 pass EB b coefficients to hypre Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 490ec265a35da5b0a4983aab18ff8ba88340b3de Merge: f35bc44c0 694f36947 Author: Andrew Myers Date: Thu Sep 13 12:30:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f35bc44c0d8c74c0a80dcf184bfc9aca3bf5aed7 Author: Andrew Myers Date: Thu Sep 13 12:30:28 2018 -0700 specifiy that we want python3 in the build_and_deploy script build_and_deploy.sh commit 3bdae5afa87c01a6755c00a30f65514f6560730d Merge: f0c8a3f51 694f36947 Author: Weiqun Zhang Date: Thu Sep 13 12:27:03 2018 -0700 Merge branch 'development' into mlmg commit 694f369470dbc66a4b81e4224bf06c00cf0294cd Merge: 158d6507a cac96c8e2 Author: Weiqun Zhang Date: Thu Sep 13 12:24:18 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 158d6507a992564c02dbc14450c534b37b636c16 Author: Weiqun Zhang Date: Thu Sep 13 12:24:10 2018 -0700 add a tutorial for geometry generation Tutorials/EB/GeometryGeneration/GNUmakefile Tutorials/EB/GeometryGeneration/Make.package Tutorials/EB/GeometryGeneration/main.cpp commit cac96c8e2b0a68a96183a78a72f69ae40af2d429 Merge: 9490c479e 4ac061964 Author: Andrew Myers Date: Thu Sep 13 12:18:39 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8752fe6d3a2acc1618e7bec02346ea227b08fba2 Author: Weiqun Zhang Date: Thu Sep 13 12:18:36 2018 -0700 add functions for writing plotifles with EB Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit 9490c479e34b6e6e7a7e3d622d071af8e1e7b3ca Author: Andrew Myers Date: Thu Sep 13 12:18:22 2018 -0700 try explicitly using pip3 .travis.yml commit 4ac061964b57b3869f46a100779215b88dc21242 Merge: 648a451c5 9af05c8b4 Author: Andrew Myers Date: Thu Sep 13 12:03:13 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 648a451c508b771abae0e2c0012b01e3f54b461a Author: Andrew Myers Date: Thu Sep 13 12:02:54 2018 -0700 turn on TINY_PROFILING Tests/HDF5Benchmark/GNUmakefile commit b82a57fc6e309521fcfee3ead70f283b0c79136d Author: Andrew Myers Date: Thu Sep 13 12:02:43 2018 -0700 also add the native write plot file to the benchmark Tests/HDF5Benchmark/main.cpp commit 9af05c8b48fd0d9da59fe4848576f9605c6ec948 Author: Andrew Myers Date: Thu Sep 13 11:28:06 2018 -0700 tweak travis.yml again .travis.yml commit 87e26603e9f7349f36ecba288bab639faa7836e7 Author: Klaus Weide Date: Thu Sep 13 13:27:00 2018 -0500 add short comment and cleanup Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp commit 5be85d84a77bd17e72683507c45eacb72806e43c Author: Andrew Myers Date: Thu Sep 13 11:14:05 2018 -0700 switch to using python 3 with travis .travis.yml commit 67a21df1345eb29e2217f639746a0276cd8b668b Merge: ef6847645 a117dcb32 Author: Andrew Myers Date: Thu Sep 13 11:06:23 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ef684764583043db2e8df29093f68cbb67e6c0df Author: Andrew Myers Date: Thu Sep 13 11:06:12 2018 -0700 change python version in travis config .travis.yml commit 94696a5eaa856a7a57ba8ca9c91a56460f462978 Author: Klaus Weide Date: Thu Sep 13 12:59:56 2018 -0500 Changes for per-FAB fluxregister use from Fortran Added optional argument to amrex_fluxregister_fineadd_1fab for requesting zeroing of the coresponding fluxregister data storage before flux data from the current fab are added. Added FineSetVal method to FluxRegister class. Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit a117dcb32631725a4856a660a0ab4a36905d50e2 Merge: 504ea405e 94f19e3ea Author: Andrew Myers Date: Thu Sep 13 10:52:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 504ea405e48bbe2d27bc2110cfb93ee0c7fec57c Author: Andrew Myers Date: Thu Sep 13 10:52:43 2018 -0700 add an HDF5 IO Benchmark test, based on the writer fron Nyx Tests/HDF5Benchmark/GNUmakefile Tests/HDF5Benchmark/Make.package Tests/HDF5Benchmark/WritePlotfileHDF5.H Tests/HDF5Benchmark/WritePlotfileHDF5.cpp Tests/HDF5Benchmark/inputs Tests/HDF5Benchmark/main.cpp commit 5b11781aa3cfa70568d06b2c7a67119426e4dabb Merge: 1b6d906fd 94f19e3ea Author: Weiqun Zhang Date: Thu Sep 13 09:26:39 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 94f19e3eaba8fed0c871287de277e7d8c9a4bcdd Author: Weiqun Zhang Date: Thu Sep 13 09:20:41 2018 -0700 CylinderIF: fix sign bug and clean up Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF_Cylinder.H commit 1b6d906fdb8042328399c1b716881a9d68c1d95a Author: Weiqun Zhang Date: Wed Sep 12 21:16:15 2018 -0700 add Difference and Extrusion for EB Src/Base/AMReX_Array.H Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Difference.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/CMakeLists.txt Src/EB/Make.package Tests/LinearSolvers/CellEB/initEB.cpp Tests/LinearSolvers/CellEB2/initEB.cpp Tutorials/EB/CNS/Source/CNS_init_eb2.cpp Tutorials/EB/MacProj/initEB.cpp commit 26815f1868c9eeb93fe348f216366a52a9443073 Merge: a2ca8fdaa b5192cc64 Author: Johannes Blaschke Date: Wed Sep 12 21:07:32 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a2ca8fdaaa8e69eea54f74d65ad3801e05a0e79f Author: Johannes Blaschke Date: Wed Sep 12 21:07:29 2018 -0700 added infinite CylinderIF by overloading constructor Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF_Cylinder.H commit b5192cc641da8bd0f3cb84e2e421eeae424005c4 Author: Andrew Myers Date: Wed Sep 12 13:58:39 2018 -0700 always have at least ref_ratio ghost cells for the fine levels in AssignDensity Src/AmrCore/AMReX_AmrParticles.H commit 3df57fd5df9ced3d74918dfc628ef14e42f1e5bd Merge: c025461cd 9be9dbdc5 Author: Andrew Myers Date: Wed Sep 12 12:33:34 2018 -0700 merging commit c025461cdb5a40c801e1c54737f683a5a87646a5 Author: Andrew Myers Date: Wed Sep 12 12:25:54 2018 -0700 allow callers to pass in an ngrow parameter into AssignDensity Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_Particles.H commit 0667aaa150e375ea0a7660af740978b352f9940d Author: Max Katz Date: Wed Sep 12 13:46:42 2018 -0400 Add CUDA initialization output Src/Base/AMReX_Device.cpp commit f0c8a3f51e5532e70f40334efd44ebd388e3419c Author: sireeveslbl Date: Wed Sep 12 10:28:43 2018 -0700 Hypre Dirichlet main routines compile, but need to get the eb_b multifab. Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit a1ff7fde3720992374d5fe3c871c3a3d4366d2a1 Merge: ac636be78 b6e7c9a3f Author: Max Katz Date: Wed Sep 12 12:56:39 2018 -0400 Merge branch 'development' into gpu commit 9be9dbdc52fa40bf431545fa4826c71447297b8c Author: Weiqun Zhang Date: Wed Sep 12 09:23:38 2018 -0700 because C++ has double pow(double base, int iexp), there is no reason we don't use it Src/EB/AMReX_EB2_IF_Polynomial.H commit cd0f7c5c5df63b11e92d29fe68b2569d58a7992c Author: Weiqun Zhang Date: Wed Sep 12 08:57:26 2018 -0700 more ParallelDescriptor::second -> amrex::second Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Base/AMReX_VisMF.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_TracerParticles.cpp Tutorials/Amr/Advection_AmrCore/Source/main.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/main.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp Tutorials/CVODE/EX1/main.cpp Tutorials/CVODE/EX2/main.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/main.cpp commit a7192fababe911204e0e9b41729d3a1c26af9b67 Author: Weiqun Zhang Date: Wed Sep 12 08:21:05 2018 -0700 ParallelDescriptor::second -> amrex::second in profiler Src/Base/AMReX_BLProfiler.cpp commit 88a9f4406d13763401e5e3b619d5977a0338beea Author: Weiqun Zhang Date: Wed Sep 12 08:17:36 2018 -0700 update doc Docs/sphinx_documentation/source/GettingStarted.rst commit 38f09b7c31d5b5a0f63c5b6397740ae1f1cf9421 Author: Weiqun Zhang Date: Wed Sep 12 08:08:56 2018 -0700 turn on verbosity by default Src/Base/AMReX.cpp Src/Base/AMReX_Utility.cpp commit 80027298c8a5076f0b17c492cdb1318aa8d3228d Author: Weiqun Zhang Date: Tue Sep 11 22:10:02 2018 -0700 use double in tiny profiler Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit dc719276cb06b3d2950c37198017e99866000732 Merge: 272502a25 8a1c247e2 Author: Weiqun Zhang Date: Tue Sep 11 21:07:54 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 272502a2520b00f5bb26330928ee15332e5ac992 Author: Weiqun Zhang Date: Tue Sep 11 20:54:01 2018 -0700 double precision -> real(amrex_real) Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 commit ac636be78ec8e492f9878a2567c03ac9e77152a8 Author: Max Katz Date: Tue Sep 11 23:33:21 2018 -0400 Fix string concatenation Src/Base/AMReX_Device.cpp commit edf541c301c70579ca77bb018adcb8999e605570 Author: sireeveslbl Date: Tue Sep 11 16:04:03 2018 -0700 Still working on Hypre EB Dirichlet. Some more compilation errors to work out. Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 8a1c247e2d1c50ac9ed4e4955eb05220d6c19de9 Merge: 1d6cefea0 3ed45f021 Author: Johannes Blaschke Date: Tue Sep 11 15:04:23 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1d6cefea03f3bd00a53e21cceaa466d6b9425d64 Author: Johannes Blaschke Date: Tue Sep 11 15:04:13 2018 -0700 elaborate on gcc and cmake Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/Visualization.rst commit 3ed45f021a41ba598b9632906743739c7c551fa6 Merge: 4ff794c13 a442ae307 Author: WeiqunZhang Date: Tue Sep 11 14:37:00 2018 -0700 Merge pull request #310 from kweide/development Fortran build routine for non-owning fab commit a442ae30741a7d992b58f6d97bc140505df565e8 Author: Klaus Weide Date: Tue Sep 11 16:34:23 2018 -0500 Use amrex_error not ERROR STOP Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit 4ff794c134555354e5d181ca5e27850c45156249 Author: Johannes Blaschke Date: Tue Sep 11 14:19:46 2018 -0700 rephrase homebrew install isntructions slightly Docs/sphinx_documentation/source/BuildingAMReX.rst commit c6cd321bd93512fb29fdf73e10533ccdcc9d6062 Author: Johannes Blaschke Date: Tue Sep 11 14:10:18 2018 -0700 elaborate more on gcc install for macOS Docs/sphinx_documentation/source/BuildingAMReX.rst commit aa14dd880da135357c086606a3ecc4814cbfa2f6 Author: Johannes Blaschke Date: Tue Sep 11 14:05:15 2018 -0700 elaborate more on Amrvis install for macOS Docs/sphinx_documentation/source/Visualization.rst commit 35a4e9585cb693453b4dbd7396ad57a73bacb618 Author: Johannes Blaschke Date: Tue Sep 11 13:53:37 2018 -0700 update docs to give more info about building on macOS Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/Visualization.rst commit 7c6c11bb79ae85cc2b8b559d5f895db3777205c4 Author: Klaus Weide Date: Tue Sep 11 13:27:17 2018 -0500 rename a Fortran routine, add argument error checking Changed specific name from amrex_fab_build to amrex_fab_build_alloc. Added some argument size error checking, subject to ifdef AMREX_DEBUG; uses ERROR STOP. Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit 1c51ec0df435c3e4c12fe317375244a86ffac472 Author: Weiqun Zhang Date: Tue Sep 11 11:20:16 2018 -0700 StateData: use unique_ptr internally; declare all five explicitly Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit 54fdc8b923f5baa38d0f22795a530c879ef1e842 Author: Andrew Myers Date: Tue Sep 11 11:11:45 2018 -0700 fix AssignDensity for ref_ratio != 2 Src/AmrCore/AMReX_AmrParticles.H commit 38bb56457c82096fae6c141ea845124fedb664e2 Author: Klaus Weide Date: Tue Sep 11 09:25:12 2018 -0500 Add amrex_fab_build_install New specific subroutine that builds a non-owning (Fortran) FAB from a given (Fortran) data pointer. Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit 2d43c56fffd550061dd96955bd9c6c2ccf677cdb Author: Tan Nguyen Date: Tue Sep 11 01:43:07 2018 -0700 fix a synchronization bug Src/AmrTask/rts_impls/Perilla/Barrier.H Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla/PackageQueue.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla/RegionQueue.H Src/AmrTask/rts_impls/Perilla/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla/WorkerThread.H Src/AmrTask/rts_impls/Perilla/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla_omp/Perilla.cpp Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.H Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla_upc++/Barrier.H Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp commit 2b3dd45e332cae694de1f4d6aa8a506927841fea Author: Klaus Weide Date: Mon Sep 10 19:56:01 2018 -0500 The 1-FAB fineadd now takes a 0-based boxno (aka gridIdx) argument Don't convert from a 1-based to a zero-based index. The new behavior is more consistent with other multifab functions in the Fortran interface that either take or return a grid_index. Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit 497c421b669d3fd532c1c6a4c1896428c783b2a0 Merge: 1b89a5016 33c0aede0 Author: Andrew Myers Date: Mon Sep 10 10:33:59 2018 -0700 Merge pull request #309 from AMReX-Codes/endian use __BYTE_ORDER__ to detect endianess commit 1b89a5016ac44d4b056669339dd9f8d60d241795 Merge: 946ba2856 8568150e6 Author: Weiqun Zhang Date: Mon Sep 10 10:30:10 2018 -0700 Merge branch 'pr-308' into development commit 946ba2856ff1c86a20da406a838f430e7794fc0a Merge: b6e7c9a3f 4a97e1adf Author: WeiqunZhang Date: Mon Sep 10 10:30:00 2018 -0700 Merge pull request #308 from kweide/development Add per-fab version of FineAdd to fluxregister's Fortran interface commit 8568150e63b4948f4749b6a0ebf57bd91a70c496 Author: Weiqun Zhang Date: Mon Sep 10 10:29:15 2018 -0700 cleanup Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp commit 33c0aede0ad5a0665a82d7e960d5f3bbb3f9fe85 Author: Weiqun Zhang Date: Mon Sep 10 09:45:19 2018 -0700 use __BYTE_ORDER__ to detect endianess Src/Base/AMReX_FPC.cpp Src/F_BaseLib/fabio_c.c commit a5b0908e1f3e28e26f4c12799ca9fd7b75b103d7 Author: Michael Zingale Date: Sun Sep 9 10:05:31 2018 -0400 remove ref to interface block Tools/F_scripts/gpu_fortran.py commit 376ffe28c7a26e3e3a0be9617e4b9f231d814c37 Author: Max Katz Date: Sun Sep 9 09:58:16 2018 -0400 Update comments for gpu_fortran.py Tools/F_scripts/gpu_fortran.py commit 9803fde5adc7a248cafd226d389a8d3cc9f5728d Author: Kevin Gott Date: Sun Sep 9 00:53:00 2018 -0400 Add NVML to Summit, Sierra. Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit b8d2ab388a347fec687ef008baa60e3410b87d1f Author: Kevin Gott Date: Sun Sep 9 00:47:25 2018 -0400 String comparison fix. Src/Base/AMReX_Device.cpp commit b6e7c9a3fc03601e9ea1267aa074c45880e45e21 Merge: fc3b1ef98 9c8f9ecf6 Author: Weiqun Zhang Date: Sat Sep 8 20:50:54 2018 -0700 Merge branch 'streampos' into development commit fc3b1ef98ae13150e5986c9affd0cc871ade9d17 Author: Weiqun Zhang Date: Sat Sep 8 18:57:21 2018 -0700 minor cleanup Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp commit 9e460548db6a5791519b078078f2fb0ba50ca81d Author: Weiqun Zhang Date: Sat Sep 8 18:43:56 2018 -0700 add ErrorHandler Src/Base/AMReX.H Src/Base/AMReX.cpp commit b6b402b005434da02a52b9933715018eca6e5422 Author: Weiqun Zhang Date: Sat Sep 8 18:06:10 2018 -0700 clean up Print Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit eb1971c42fd363e4a51ffe784cf7fbef69c2e5d7 Author: Weiqun Zhang Date: Sat Sep 8 17:44:35 2018 -0700 rm unused Serialize/UnSerialize functions Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 7caa763a3277ae90c19bf836b2de7e5973e5ce31 Author: Weiqun Zhang Date: Sat Sep 8 17:30:18 2018 -0700 change tolerance of nodal Poisson solver test Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp commit ff7c6ce78169ed262d434163e3d2dc027c688b44 Author: Weiqun Zhang Date: Sat Sep 8 17:28:48 2018 -0700 add amrex::SetVerbose function Src/Base/AMReX.H Src/Base/AMReX.cpp commit 4a9a07fd16b0f8421cfc689d942a55642dc4d45c Author: Weiqun Zhang Date: Sat Sep 8 11:41:17 2018 -0700 Nodal Poisson solver tutorial Tutorials/LinearSolvers/NodalPoisson/GNUmakefile Tutorials/LinearSolvers/NodalPoisson/Make.package Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest_F.H Tutorials/LinearSolvers/NodalPoisson/init_prob.F90 Tutorials/LinearSolvers/NodalPoisson/main.cpp commit 0dbfbb6db95bcdb19e74609f42d05d4f0839f479 Author: Max Katz Date: Sat Sep 8 11:20:02 2018 -0700 Add warning if oversubscribing GPUs Src/Base/AMReX_Device.cpp commit c9da4bc1bc040eb786edd0dda46f888a83c774a1 Author: Max Katz Date: Sat Sep 8 10:39:45 2018 -0700 Simplify and make more robust the logic for mapping ranks to GPUs Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 4e7e43a162f027a9ca566f1a0d69bc3e2942505c Author: Max Katz Date: Sat Sep 8 10:39:21 2018 -0700 Provide GPU configuration on known systems Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit 2727dccb4ad116be2cab494c511fecb50c94d094 Author: Max Katz Date: Sat Sep 8 07:03:54 2018 -0700 Move Sierra to the rolling MPI release Tools/GNUMake/sites/Make.llnl commit 8bb157fff8433368b9104ffbd83fa3a189f34c66 Author: Max Katz Date: Sat Sep 8 07:03:45 2018 -0700 Add NVML to Summit, Sierra Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit 47f72ef3af5e0e61d7dd88817cb09f6cc4e22eef Author: Max Katz Date: Sat Sep 8 07:02:23 2018 -0700 Fix string comparison issue Src/Base/AMReX_Device.cpp commit e229e2c2cf0c2fd09532aad5d16eb4bd14341fb9 Merge: 20d09285f 78d4e0d72 Author: Weiqun Zhang Date: Fri Sep 7 22:26:08 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 20d09285f1ce2aada904ba2ef3924d8281753901 Author: Weiqun Zhang Date: Fri Sep 7 22:25:54 2018 -0700 fix due to change of average_center_to_face Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 78d4e0d7242717c09fa67c3c779f5f3358ad2f0e Author: Weiqun Zhang Date: Fri Sep 7 22:23:13 2018 -0700 fix new typo Src/Base/AMReX_mempool_mod.F90 commit a6e632c34e3ea7a3d2df0645fcdc97dea2a02ca0 Author: Weiqun Zhang Date: Fri Sep 7 22:11:42 2018 -0700 use pointer bound remapping to avoid an intel compiler bug Src/Base/AMReX_mempool_mod.F90 Src/Base/BL_mempool_f.f90 Src/Base/CMakeLists.txt Src/Base/GPackage.mak Src/Base/Make.package commit d6f295c941890949e22f702bb0709935c7f7d4eb Author: Weiqun Zhang Date: Fri Sep 7 15:06:04 2018 -0700 remove duplication Src/Base/AMReX_MultiFabUtil.cpp commit 9103fd1fe7ab33b49cf3aaddab02ae20da165e7a Merge: cda692808 518a6d2bb Author: Weiqun Zhang Date: Fri Sep 7 14:06:35 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cda692808a71a00251d9bf92463504098cd7d93d Author: Weiqun Zhang Date: Fri Sep 7 14:05:48 2018 -0700 avoid calling popen when intel is used with omp Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit 518a6d2bb6bea387b0c0e3688e6503fd4f673d5c Merge: 2f3091ff2 d48662d16 Author: Andrew Myers Date: Fri Sep 7 12:11:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d48662d169a2cd4f1a534141e4dd1e0a5717a16e Author: Michele Rosso Date: Fri Sep 7 12:11:53 2018 -0700 Add ome more conversion subroutine for vector of array of ptrs Src/Base/AMReX_Array.H Src/Base/AMReX_Vector.H commit 2f3091ff23d1e798ac0caa78261726d000a97c17 Author: Andrew Myers Date: Fri Sep 7 12:11:30 2018 -0700 only allow this version of GetArrOfPtrs to be chosen if T has a FABType Src/Base/AMReX_Array.H commit 189078e82e665f94314ef8d1e74a1155731fe5fd Merge: bf3cb995c 6bab5d322 Author: Kevin Gott Date: Fri Sep 7 15:06:45 2018 -0400 Merge remote-tracking branch 'origin/development' into gpu-mm commit 765ee88128e0f805e86be53e3aca9a0333dc59f7 Merge: 97dbf2b3b 6bab5d322 Author: Marc Day Date: Fri Sep 7 11:15:10 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit 6bab5d322b1cfc34091ea6d46ebd11daebb90edf Merge: 18888cdbb 25e12c549 Author: Michele Rosso Date: Fri Sep 7 11:12:36 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 18888cdbb723a3a904d190d0bbe95fdba4a5741c Author: Michele Rosso Date: Fri Sep 7 11:12:31 2018 -0700 Add signature for average_cellcenter_to_face() Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 97dbf2b3b30461c27286e29086b8b9b664a66a94 Merge: 6d38b7022 25e12c549 Author: Marc Day Date: Thu Sep 6 23:35:38 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit 6d38b7022619e2be6ebaf5a9563a252536553eaf Author: Marc Day Date: Thu Sep 6 23:34:56 2018 -0700 Add profiling info for ForkJoin overhead Src/Base/AMReX_ForkJoin.cpp commit 25e12c549984702cf7bf18a282e22c36aee5ce6b Author: Andrew Myers Date: Thu Sep 6 17:24:02 2018 -0700 add additional constructor for MakeMFIter that knows about dynamic scheduling. Src/Particle/AMReX_Particles.H commit e8988c3ce7801e2edc06bae933035f0f87387e1f Author: sireeveslbl Date: Thu Sep 6 16:00:18 2018 -0700 More work on Dirichlet Hypre, not finished yet. Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 4a97e1adfacc3ff40f9bb9566d0e2e8441b4baeb Author: Klaus Weide Date: Thu Sep 6 14:24:33 2018 -0500 add amrex_fluxregister_fineadd_1fab implementation This is a fineadd method for amrex_fluxregister that adds fluxes from only one fab to a fluxregister. Currently an amrex_fab has to be constructed by the caller and passed, as well as a box number (grid_index, more or less). Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit e55a70c3d4f320c6c9f013be18f01967f97a961a Author: Weiqun Zhang Date: Thu Sep 6 09:29:06 2018 -0700 use factory to delete FAB Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp commit bf3cb995cb6cf0bafa7d7e65f05791a1a6815b16 Author: Kevin Gott Date: Thu Sep 6 05:29:40 2018 -0400 Threading strategy fix. Src/Base/AMReX_BaseFab.cpp commit b0db9113eb67d7ec05ed19052956014f6507c50d Author: Weiqun Zhang Date: Wed Sep 5 21:27:05 2018 -0700 const_cast for MPI-2 Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_ParallelReduce.H commit da8f86e068d7395f014bdfcaaa93983016a89c84 Author: Michele Rosso Date: Wed Sep 5 17:38:25 2018 -0700 Add signature for GetArrOfConstPtrs() Src/Base/AMReX_Array.H commit e2e7973d73101f226957d7165dc25938a331aba5 Author: Weiqun Zhang Date: Wed Sep 5 16:58:23 2018 -0700 remove vitual from BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBInterpolater.cpp Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_MultiCutFab.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 commit 3fec85546799f531714fac8ba3869e4030395662 Author: sireeveslbl Date: Wed Sep 5 16:00:10 2018 -0700 Changed Makefile to reflect location in amrex download Tests/LinearSolvers/CellEB2/GNUmakefile commit 96634380423f2df196b85b91fe96f1cc4109ea74 Author: sireeveslbl Date: Wed Sep 5 15:55:59 2018 -0700 More progress on Hypre EB-dirichlet. Bogus compiler flags are included as to not break anything Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit f6a412b1b93c2394f81dd780852eced063facb3d Author: Cyrus Harrison Date: Wed Sep 5 15:37:27 2018 -0700 restore missing endif Tools/GNUMake/Make.defs commit bed34b12ecfc9fdce32f1b1ef4a3491a37002849 Merge: 2d6ef4f3a 5a997fec0 Author: Cyrus Harrison Date: Wed Sep 5 15:33:53 2018 -0700 merge development branch and resolve conflict commit 2d6ef4f3a57a831550dcd7c27b730e9b2d535175 Author: Cyrus Harrison Date: Wed Sep 5 15:28:46 2018 -0700 add build system var for ascent Tools/GNUMake/Make.defs commit 8d24b366e297457f81b9875a71cda8792eb0034d Author: Cyrus Harrison Date: Wed Sep 5 15:22:24 2018 -0700 move blueprint support Src/Base/Make.package Src/Extern/Conduit/AMReX_Conduit_Blueprint.H Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp Src/Extern/Conduit/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.ascent Tools/GNUMake/packages/Make.conduit Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile Tutorials/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile commit 5a997fec0db563b25a6dbc83910d3cf0204cfae1 Author: Weiqun Zhang Date: Wed Sep 5 14:16:21 2018 -0700 rm SPMD Src/Base/AMReX_FabArray.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMD.cpp Src/Base/AMReX_SPMDI.H Src/Base/AMReX_parstream.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 481e212e678637272ba6d2b72b5ef6ff8b44abb1 Author: Weiqun Zhang Date: Wed Sep 5 13:55:04 2018 -0700 simplification Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit d7ec55af5730ff8df8121f75376d25879fa8fac4 Author: Weiqun Zhang Date: Wed Sep 5 13:13:03 2018 -0700 pass by value so that it support both rvalue and lvalue Src/Base/AMReX_ParallelReduce.H commit e470eec8b40eaa45db63b85737b3d84112ac880f Author: Kevin Gott Date: Wed Sep 5 15:24:15 2018 -0400 Mistype. Src/Base/AMReX_BaseFab.cpp commit d41a2c0fbea1f6f6b2778eeec9408e0d4ddb166d Merge: 318ff60a0 1d010e28f Author: Kevin Gott Date: Wed Sep 5 15:19:23 2018 -0400 Merge remote-tracking branch 'origin/development' into gpu-mm Conflicts: Src/Base/AMReX_ArrayLim.H Src/Particle/AMReX_ParticleContainerI.H commit 318ff60a06288d1ba2bfa3ccfbe45131aa59ad59 Author: Kevin Gott Date: Wed Sep 5 15:03:45 2018 -0400 FillBoundary rewritten onto GPUs. Src/Base/AMReX_FabArrayCommI.H commit 476cc89442041928d78477241eb8e2086fa7190c Author: Kevin Gott Date: Wed Sep 5 14:48:40 2018 -0400 Threading strategy for copy, copyTo and copyFrom. Src/Base/AMReX_BaseFab.cpp commit 4269eef0d683ea2d4960a12ab2bcbb2506f14a57 Author: Kevin Gott Date: Wed Sep 5 14:27:16 2018 -0400 Changes to GPU data class thingee. Tutorials/GPU/Test/main.cpp commit 70d46ab97989eaa6b283174f8640f3af9e0f3de0 Author: Steven Date: Wed Sep 5 10:17:50 2018 -0700 Forgot this one Src/Extern/HYPRE/AMReX_Hypre.cpp commit 55d374bfa6a7f9a25fc9178324dd913fe81eba18 Author: Steven Date: Wed Sep 5 10:16:42 2018 -0700 Hypre Dirichlet Additions, not complete Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 9c8f9ecf6207ff7c0f025f9a816f2fba703605cc Author: Weiqun Zhang Date: Wed Sep 5 10:10:26 2018 -0700 try to fix portablity issue of std::streampos Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_VisMF.cpp commit ba9c6ae77ad38e4fa586607c63a297c13007599a Author: Cyrus Harrison Date: Wed Sep 5 09:59:37 2018 -0700 move Blueprint examples from Test to Tutorials Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile Tutorials/Blueprint/AssignMultiLevelDensity/Make.package Tutorials/Blueprint/AssignMultiLevelDensity/inputs Tutorials/Blueprint/AssignMultiLevelDensity/main.cpp Tutorials/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Blueprint/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/Blueprint/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/Blueprint/HeatEquation_EX1_C/Source/Make.package Tutorials/Blueprint/HeatEquation_EX1_C/Source/advance.cpp Tutorials/Blueprint/HeatEquation_EX1_C/Source/advance_2d.f90 Tutorials/Blueprint/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/Blueprint/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tutorials/Blueprint/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tutorials/Blueprint/HeatEquation_EX1_C/Source/main.cpp Tutorials/Blueprint/HeatEquation_EX1_C/Source/myfunc.H Tutorials/Blueprint/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/Blueprint/README.txt commit 411209a75be742b486ac78a5e4291671374be8dd Author: Kevin Gott Date: Wed Sep 5 12:31:59 2018 -0400 Fortran functions for amrex_gpu_malloc and amrex_gpu_free. Src/Base/AMReX_fort_mod.F90 commit ce480ee80da834c5a2f2b6907dd0d99e3a824f81 Author: Kevin Gott Date: Wed Sep 5 12:31:24 2018 -0400 Initial attempt at Box+component threading strategy. Still need to account for very large kernels (thread > max number of threads). Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_Managed.H commit 614e36ef4a7f7e0c2b11cd03814c8a5d1e23b716 Author: Kevin Gott Date: Wed Sep 5 12:19:56 2018 -0400 amrex_gpu_alloc, amrex_gpu_free and cudaMemCpy wrappers. Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit c3ca0cc94b7c8748ead180051f8c91cdc701e84b Author: Kevin Gott Date: Wed Sep 5 12:08:19 2018 -0400 Additional Box device functions. Src/Base/AMReX_Box.H commit 9b2e953f40eb55b84b9d084d0ac96e61fe611ca8 Author: Kevin Gott Date: Wed Sep 5 12:07:36 2018 -0400 Make main FillBoundary function public to allow kernels. Src/Base/AMReX_FabArray.H commit c15487420a0595c0841cf7341632ad2d9783bf95 Author: Steven Date: Wed Sep 5 07:48:59 2018 -0700 EB Dirichlet Hypre Started. Going through Dirichlet MLMG and adapting it to the Hypre format. Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp commit 8bcb1fd7e53349b5b6aeff50cf931514c0abc440 Author: Kevin Gott Date: Wed Sep 5 02:37:21 2018 -0400 Add error checking to BArena. Src/Base/AMReX_BArena.cpp commit 1d010e28f59331ea45ab5e9d961059e938327c52 Author: Weiqun Zhang Date: Tue Sep 4 17:17:47 2018 -0700 add a number of BL_NO_FORTs so that part of Base can be built without Fortran Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/Make.package commit 9d22e23402af27f2ea6356f67d7a64f59e192ed6 Author: Michele Rosso Date: Tue Sep 4 11:58:18 2018 -0700 CMake:some modification to comply with SPACK requirements Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/MakefileConfig.export.in Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit c1052a0d749e6b9ed5c64b7ad41443a20e635e2c Merge: e3cd0b07d 2f7682928 Author: Weiqun Zhang Date: Tue Sep 4 12:31:47 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e3cd0b07d04691c9ed6a1fff25d541fc1c0dde25 Author: Weiqun Zhang Date: Tue Sep 4 11:30:50 2018 -0700 MLMG: cell-centered fluxes Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 2f76829284d5b68017cb55e4ad5f0c2206184c7e Author: Michele Rosso Date: Tue Sep 4 11:58:18 2018 -0700 CMake:some modification to comply with SPACK requirements Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/MakefileConfig.export.in Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit 90f948159844ec45b9b2f66eaf77e65d584bf133 Merge: 75f3abe5f 4b2542dc1 Author: Weiqun Zhang Date: Mon Sep 3 13:54:44 2018 -0700 Merge branch 'mlmg' into development commit 4b2542dc17b0580d104d9934d44a55da2f2fa154 Merge: f131bf762 0cf77fb99 Author: Weiqun Zhang Date: Mon Sep 3 13:54:24 2018 -0700 Merge branch 'petsc' into mlmg commit 0cf77fb9936052f7bb220bf2660e3d8acb16c629 Author: Weiqun Zhang Date: Mon Sep 3 13:53:28 2018 -0700 follow convention in Extern/HYPRE Src/Extern/PETSc/AMReX_PETSc.cpp commit 00bdbc57a27f093f4e7cf1484bc797a58e5f5f5a Author: Weiqun Zhang Date: Mon Sep 3 13:44:04 2018 -0700 set one row at a time Src/Extern/PETSc/AMReX_PETSc.cpp commit db93a614aa26e66a834ed9ec211e01d9272ea26e Author: Weiqun Zhang Date: Mon Sep 3 13:34:44 2018 -0700 white space Src/Extern/PETSc/AMReX_PETSc.cpp commit 2ce5087db4dae366c6d2f977ae4550dfb2c847ce Author: Weiqun Zhang Date: Mon Sep 3 13:32:48 2018 -0700 Not sure we can assume these petsc calls are omp thread safe. Src/Extern/PETSc/AMReX_PETSc.cpp commit e85e157faac36f01a757faea43bab2aa3f1cb3b2 Author: Weiqun Zhang Date: Mon Sep 3 13:30:01 2018 -0700 adjust petsc preallocatoin. (note that the estimate is for per row, not for all rows in a process.) Src/Extern/PETSc/AMReX_PETSc.cpp commit bc27d78e441215d3975386c601ce7929702205bf Author: Weiqun Zhang Date: Mon Sep 3 12:48:19 2018 -0700 static assert hypre and petsc have the same int Src/Extern/PETSc/AMReX_PETSc.cpp commit fc348441458cdc6bb95ccd04ebfee72ae67a45ea Author: Weiqun Zhang Date: Mon Sep 3 12:43:40 2018 -0700 comment out KSPSetFromOptions Src/Extern/PETSc/AMReX_PETSc.cpp commit f131bf762b6a32d0b7bb465d810839ae13acb0fb Author: Weiqun Zhang Date: Mon Sep 3 12:32:47 2018 -0700 update MLPoisson:FFlux Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 75f3abe5f814140d1290a600f8354f4b2f4667aa Author: Weiqun Zhang Date: Mon Sep 3 12:32:47 2018 -0700 update MLPoisson:FFlux Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit acf1898d1874debdd3c7498c889de54962f5e5d6 Author: Weiqun Zhang Date: Mon Sep 3 12:33:09 2018 -0700 remove HYPRE_DIR/include from petsc Tools/GNUMake/packages/Make.petsc commit 0c3257d20711b7c3562e3570d8f4ebe2300ecc48 Author: Weiqun Zhang Date: Mon Sep 3 12:32:47 2018 -0700 update MLPoisson:FFlux Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 0a7d68dece718240a0adb93c3d877c6d83fcc48f Author: Weiqun Zhang Date: Mon Sep 3 12:16:59 2018 -0700 fix link to petsc on NERSC Tests/LinearSolvers/CellEB/MyTest.cpp Tools/GNUMake/packages/Make.petsc commit b4eca770fa587439bfdb09d087535aae4b6c6c68 Author: Weiqun Zhang Date: Mon Sep 3 12:10:15 2018 -0700 the link flags for various petsc stuff have to be inside ifdef otherwise it won't compile on say NERSC because they want different flags Tests/LinearSolvers/CellEB/inputs Tools/GNUMake/packages/Make.hypre Tools/GNUMake/packages/Make.petsc commit cdd9899d02635a306ae92b1fb54018aef4f49494 Author: Weiqun Zhang Date: Mon Sep 3 11:51:42 2018 -0700 remove hardwired path to petsc Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/CellEB/GNUmakefile commit 42cbd1280d90b0bcddcc249de5f6c31a6ebbe38f Author: Weiqun Zhang Date: Mon Sep 3 11:43:50 2018 -0700 use forward declaration Src/LinearSolvers/MLMG/AMReX_MLMG.H Tutorials/EB/MacProj/GNUmakefile commit 61ded76626446e35eca6748ce9922ba339758b44 Merge: 6994e0510 999851d79 Author: Weiqun Zhang Date: Mon Sep 3 09:40:40 2018 -0700 Merge branch 'mlmg' into petsc commit 999851d79d974ae543af2694804ca3a31e966114 Merge: 1d9197229 04969771e Author: Weiqun Zhang Date: Mon Sep 3 09:39:19 2018 -0700 Merge branch 'development' into mlmg commit 04969771ed55bde0b575bdc47c398e4dc0fef970 Merge: e66a346e7 9ffacd1de Author: WeiqunZhang Date: Mon Sep 3 09:36:56 2018 -0700 Merge pull request #270 from AMReX-Codes/forkjoin Forkjoin commit 9ffacd1de2870ca1f0fcb0300dd2affb39c53607 Author: Weiqun Zhang Date: Mon Sep 3 09:35:53 2018 -0700 move -> forward Src/Base/AMReX_ParallelReduce.H commit e66a346e7e96fb4bfd9200a05df249c57c758f11 Merge: 2716130d8 adb09f392 Author: Weiqun Zhang Date: Mon Sep 3 09:31:41 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit adb09f392c21e50d6e89adf437e5b65acf6f7200 Merge: 2aba10102 5ab4e1042 Author: Weiqun Zhang Date: Mon Sep 3 09:30:51 2018 -0700 Merge branch 'master' into development commit 5ab4e1042647e4429bf55027c73be306279bd45e Author: Weiqun Zhang Date: Mon Sep 3 09:29:50 2018 -0700 update CHANGES CHANGES commit b4fc255bc85c3bcd98eee5c2c22c75c5482f1700 Merge: 782009df1 2aba10102 Author: Michael Zingale Date: Mon Sep 3 12:19:14 2018 -0400 Merge branch 'development' into gpu commit 782009df11c3113593794f8a2e7bb06851f25100 Author: Michael Zingale Date: Mon Sep 3 12:18:59 2018 -0400 sync encodings Tools/F_scripts/preprocess.py commit 2aba10102e454558ea9a0d28e2959123ef0301b2 Author: Michael Zingale Date: Mon Sep 3 12:15:45 2018 -0400 remove unneeded module Tools/F_scripts/dep.py commit 6580f739038a0ecc7a9d4549fe79f65933ab9d79 Author: Michael Zingale Date: Mon Sep 3 12:13:50 2018 -0400 split out preprocess like we do in GPU Tools/F_scripts/dep.py Tools/F_scripts/preprocess.py commit 1359cb411c9fe92c22b56453d91760ea08b09c72 Author: Max Katz Date: Mon Sep 3 11:56:16 2018 -0400 Insert a device sync in CrseInit Src/AmrCore/AMReX_FluxRegister.cpp commit 1d91972293fd0296cbe21717725a793f80c47af4 Author: Weiqun Zhang Date: Sun Sep 2 11:30:56 2018 -0700 MLMG: clean up flux and grad Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit ef7c79c8e24511b3431de463d769c169dd25c37b Author: Klaus Weide Date: Sun Sep 2 00:44:44 2018 -0500 flailing around Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit e23d0acf51aef8fe1ba289c441deea24f3492825 Author: Max Katz Date: Sat Sep 1 19:28:23 2018 -0400 Don't do MFIter reductions if not executing on device Src/Base/AMReX_MFIter.cpp commit 2e4c9ae01def7e7036a6ea1bf2b329c48f050f30 Author: Max Katz Date: Sat Sep 1 19:28:09 2018 -0400 Write amrex_max, etc. device versions by hand Src/Base/AMReX_fort_mod.F90 commit 9566a0d0d857eb90dc301656ef16df9c9aab0879 Author: Max Katz Date: Sat Sep 1 19:27:37 2018 -0400 Start in device launch region Src/Base/AMReX_Device.cpp commit 1828b46a33f7e87a3ab7205c5ccafca6d11307f3 Author: Max Katz Date: Sat Sep 1 18:34:27 2018 -0400 Add an option to disable the device offload Tools/F_scripts/write_cuda_headers.py commit bbbd997dd3c8a2bac0552340e8fc7e1d2e11e36c Author: Max Katz Date: Sat Sep 1 18:17:36 2018 -0400 Write out the host function signature Tools/F_scripts/write_cuda_headers.py commit 75c469c5b46e9ede58f325c63bb9eac0b51d81b5 Author: Max Katz Date: Sat Sep 1 18:04:31 2018 -0400 Add a device synchronize in debug mode Tools/F_scripts/write_cuda_headers.py commit da171a0e75318528a9c23b13f38bf1d0db9ebee1 Author: Weiqun Zhang Date: Sat Sep 1 14:21:33 2018 -0700 implement the locatio option for grad phi Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit d553d266c7fdc776742f147b2641aad19ed3640a Merge: abc62bc09 5e40c6f61 Author: Klaus Weide Date: Sat Sep 1 16:08:55 2018 -0500 Merge branch 'development' of github.com:kweide/amrex into kw-development commit f205aa81db6fde73ba3535d4e0ec022e43dda765 Author: Weiqun Zhang Date: Sat Sep 1 13:49:27 2018 -0700 implement the locatio option for flux Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 8c72f8d71d728ae3e9dbc0bed953ba8312809ad9 Author: Weiqun Zhang Date: Sat Sep 1 08:24:47 2018 -0700 add Location in preparation for getting fluxes at different locations Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 9ebd4a60d46772ff2536dd4fd71da61e4d28a6dc Author: Weiqun Zhang Date: Sat Sep 1 07:49:55 2018 -0700 simplification Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit eccfe39f39c46def58519914b181da91021ba3a8 Author: Marc Day Date: Fri Aug 31 17:26:27 2018 -0700 Modify reductions to use parallel context comm Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit da52e980742189f75fd9ea21c1d7207b5e1800e7 Author: Marc Day Date: Fri Aug 31 16:45:58 2018 -0700 Add grow cells to ForkJoin registration. Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/Parallel/ForkJoin/MyTest.cpp commit 62429e843d5ddde09fee4338c7401c55a35dd40e Author: Weiqun Zhang Date: Fri Aug 31 15:59:31 2018 -0700 CellEB2 test: fix the setup of prob type 2 Tests/LinearSolvers/CellEB2/mytest_f.F90 commit ca71934e9d44c67b48a87c86e950b2eabc867c2b Author: Marc Day Date: Fri Aug 31 14:46:40 2018 -0700 Use ComponentSet instead of std::pair, and use Redistribute instead of copy. Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/Parallel/ForkJoin/MyTest.cpp commit 4f07fc3b4c0e9c8937df6ab3ae0edcfdf8b2ad37 Author: Weiqun Zhang Date: Fri Aug 31 14:44:59 2018 -0700 CellEB2 test: add option for composite or level by level solve Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/inputs commit 2716130d85e005d7bfa8985b7c0033213b3149da Author: Weiqun Zhang Date: Fri Aug 31 13:50:33 2018 -0700 cell centered EB solver: multi-level works Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 1343e8571e138f01edbaba3871ad4196a03f2ce2 Author: Weiqun Zhang Date: Fri Aug 31 13:43:24 2018 -0700 MLMG: add StateMode so that we can properly apply EB bc Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit abc62bc09c0c8094dea77b8d4dc68339fc690c38 Author: atmyers Date: Fri Aug 31 12:39:29 2018 -0700 restore some debugging changes I introduced. Tools/F_scripts/dep.py commit b755d3c2585ae57072e8a0e74710cb25728e9520 Author: atmyers Date: Fri Aug 31 12:38:05 2018 -0700 fix some Python 3 / Unicode issues in dep.py Tools/F_scripts/dep.py commit 6994e0510c07fb18e53b913954d1a5951bd10b3d Author: sireeveslbl Date: Fri Aug 31 11:24:25 2018 -0700 PETSC looks ok Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5a060e8af09ebfbb9c01d2ba76fccd039ee8f40a Author: Weiqun Zhang Date: Fri Aug 31 10:46:15 2018 -0700 EB dirichlet: average down for multi amr levels Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 340035c59d8c8fc2c9f6fb207b8f47d295868809 Author: Weiqun Zhang Date: Fri Aug 31 10:28:37 2018 -0700 add Array versions of various average down functions Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 01162e096e6fe3a6d4e442bb885d449ad4e459cd Merge: f63c63874 61ab86d89 Author: Marc Day Date: Thu Aug 30 19:09:25 2018 -0700 Merge branch 'marc/forkjoin_dev' of github.com:AMReX-Codes/amrex into marc/forkjoin_dev commit f63c63874a3fd24eb5217f10aa749cf1e57123fe Author: Marc Day Date: Thu Aug 30 12:07:22 2018 -0700 Fix bug in tutorial. Tutorials/Parallel/ForkJoin/MyTest.cpp commit c6c76c36b2c141250976030870e2b114ca1688ec Author: Marc Day Date: Thu Aug 30 12:01:28 2018 -0700 Add a simple ForkJoin Tutorial, add a function to the fj class. Tutorial currently gives weird result for duplicated multifabs. Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/Parallel/ForkJoin/GNUmakefile Tutorials/Parallel/ForkJoin/Make.package Tutorials/Parallel/ForkJoin/MyTest.H Tutorials/Parallel/ForkJoin/MyTest.cpp Tutorials/Parallel/ForkJoin/MyTest_F.H Tutorials/Parallel/ForkJoin/inputs Tutorials/Parallel/ForkJoin/main.cpp commit d980a04ded8687bbfb7611f7198f05d407d0b43c Merge: ab479546b 613b99c18 Author: Marc Day Date: Thu Aug 30 18:59:44 2018 -0700 Merge remote-tracking branch 'origin/development' into forkjoin commit 613b99c18989cb425c1f0a70483e5b8f1896dd42 Author: Weiqun Zhang Date: Thu Aug 30 16:43:13 2018 -0700 clean up GNUmakefile.in OldTutorials/EBParticles/GNUmakefile Src/Base/AMReX_BCRec.cpp Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/CMakeLists.txt Src/EB/Make.package Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBflux_grad/GNUmakefile Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/LevelSet/Exec/inputs_eb2 Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H Tutorials/EB/MacProj/GNUmakefile commit 30e876d982d807b4c6c2cd0342c3466f06745b4f Author: Weiqun Zhang Date: Thu Aug 30 16:26:04 2018 -0700 removed old EB Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/source/EB.rst OldTutorials/EBParticles/EBParticleContainer.H OldTutorials/EBParticles/EBParticleContainer.cpp OldTutorials/EBParticles/GNUmakefile OldTutorials/EBParticles/Make.package OldTutorials/EBParticles/ebparticles_2d.f90 OldTutorials/EBParticles/ebparticles_3d.f90 OldTutorials/EBParticles/ebparticles_F.H OldTutorials/EBParticles/inputs OldTutorials/EBParticles/main.cpp OldTutorials/GeometryGeneration/exec/GNUmakefile OldTutorials/GeometryGeneration/exec/coveredSlabs.cpp OldTutorials/GeometryGeneration/exec/coveredslabs.inputs OldTutorials/GeometryGeneration/exec/parabolaWithSphere.cpp OldTutorials/GeometryGeneration/exec/parabolaWithSphere.inputs OldTutorials/GeometryGeneration/exec/sphere.cpp OldTutorials/GeometryGeneration/exec/sphere.inputs OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.cpp OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.inputs OldTutorials/GeometryGeneration/src/CommonCode.H OldTutorials/GeometryGeneration/src/CommonCode.cpp OldTutorials/GeometryGeneration/src/Make.package OldTutorials/GeometryGeneration/src/WriteEBPlotFile.H OldTutorials/GeometryGeneration/src/WriteEBPlotFile.cpp Src/Amr/AMReX_StateData.H Src/CMakeLists.txt Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Graph.H Src/EB/AMReX_EB2_IF_AllRegular.H Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Cylinder.H Src/EB/AMReX_EB2_IF_Ellipsoid.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Plane.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/AMReX_EB2_IF_Sphere.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H Src/EB/AMReX_EB2_IndexSpaceI.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EB2_MultiGFab.H Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 Src/EB/CMakeLists.txt Src/EB/Make.package Src/EB2/CMakeLists.txt Src/EB2/Make.package Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_AnisotropicIF.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFAB.cpp Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIFFactory.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_CH_EBIS_ORDER.H Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_ConstrainedLS.H Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CoordinateSystem.H Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CoveredSlabs.H Src/GeometryShop/AMReX_CoveredSlabs.cpp Src/GeometryShop/AMReX_CutCellMoments.H Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinement.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBFluxFAB.cpp Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBFluxFactory.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_Ellipsoid.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_ExtrudeIF.H Src/GeometryShop/AMReX_ExtrudeIF.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_FixedRefinement.H Src/GeometryShop/AMReX_FixedRefinementImplem.H Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GenericArithmetic.H Src/GeometryShop/AMReX_GenericArithmeticI.H Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeomIntersectUtils.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IFData.H Src/GeometryShop/AMReX_IFData.cpp Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicer.cpp Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregFAB.cpp Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_KDTree.H Src/GeometryShop/AMReX_KDTree.cpp Src/GeometryShop/AMReX_LSProblem.H Src/GeometryShop/AMReX_LSProblem.cpp Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_LoHiSide.H Src/GeometryShop/AMReX_LoHiSide.cpp Src/GeometryShop/AMReX_MetaPrograms.H Src/GeometryShop/AMReX_MinimalCCCM.H Src/GeometryShop/AMReX_MinimalCCCM.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MomentIteratorImplem.H Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_MonomialPowers.H Src/GeometryShop/AMReX_MultiIndex.H Src/GeometryShop/AMReX_MultiIndexImplem.H Src/GeometryShop/AMReX_NoRefinement.H Src/GeometryShop/AMReX_NoRefinementImplem.H Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_Notation.H Src/GeometryShop/AMReX_PXStuff.H Src/GeometryShop/AMReX_PXStuff.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_PolynomialIF.cpp Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLBox.cpp Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLIF.cpp Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLMesh.cpp Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_STLUtil.cpp Src/GeometryShop/AMReX_SmoothAbsoluteValue.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.cpp Src/GeometryShop/AMReX_SmoothIntersection.H Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_SmoothUnion.H Src/GeometryShop/AMReX_SmoothUnion.cpp Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_Stencils.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Src/GeometryShop/AMReX_ZCylinder.H Src/GeometryShop/AMReX_ZCylinder.cpp Src/GeometryShop/CMakeLists.txt Src/GeometryShop/Make.package Src/GeometryShop/_save/AMReX_GeometryShop.H Src/GeometryShop/_save/AMReX_GeometryShop.cpp Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/Make.package Tests/EBAMRTools/regression/aggpwlfp.inputs Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/divergenceOpTest.cpp Tests/EBAMRTools/regression/divop.inputs Tests/EBAMRTools/regression/ebCoarseAveTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebcoarave.inputs Tests/EBAMRTools/regression/ebfineinterp.inputs Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/fluxreg.inputs Tests/EBAMRTools/regression/gradientOpTest.cpp Tests/EBAMRTools/regression/gradop.inputs Tests/EBAMRTools/regression/meshref.inputs Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp Tests/EBAMRTools/regression/nwoebquadcfi.inputs Tests/EBAMRTools/regression/regFluxRegTest.cpp Tests/EBAMRTools/regression/runalltests.mpi.sh Tests/EBAMRTools/regression/runalltests.serial.sh Tests/EBAMRTools/regression/simpleMeshRefine.cpp Tests/EBAMRTools/regression/sphere.inputs Tests/EBEB2/GNUmakefile Tests/EBEB2/Make.package Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs Tests/EBEB2/main.cpp Tests/EBbcent/GNUmakefile Tests/EBbcent/Make.package Tests/EBbcent/main.cpp Tests/GeometryShop/README Tests/GeometryShop/STLGeom/GNUmakefile Tests/GeometryShop/STLGeom/bad.cylinder.inputs Tests/GeometryShop/STLGeom/bad.reactor.inputs Tests/GeometryShop/STLGeom/cylinder.stl Tests/GeometryShop/STLGeom/good.cylinder.inputs Tests/GeometryShop/STLGeom/good.reactor.inputs Tests/GeometryShop/STLGeom/good.sphere.inputs Tests/GeometryShop/STLGeom/reactor.stl Tests/GeometryShop/STLGeom/sphere.stl Tests/GeometryShop/STLGeom/stl.inputs Tests/GeometryShop/STLGeom/stlgeom.cpp Tests/GeometryShop/ebgraphDistributed/GNUmakefile Tests/GeometryShop/ebgraphDistributed/Make.package Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphDistributed/sphere.inputs Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile Tests/GeometryShop/ebgraphSingleGrid/Make.package Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/ebgraphSingleGrid/sphere.inputs Tests/GeometryShop/flatPlate/GNUmakefile Tests/GeometryShop/flatPlate/Make.package Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/flatPlate/flatplate.inputs Tests/GeometryShop/ramp/GNUmakefile Tests/GeometryShop/ramp/Make.package Tests/GeometryShop/ramp/inputs Tests/GeometryShop/ramp/main.cpp Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/Make.package Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/dataarith.inputs Tests/GeometryShop/regression/ebio.2.inputs Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs Tests/GeometryShop/regression/ebnormalizeTest.cpp Tests/GeometryShop/regression/ebnormtest.inputs Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/fabio.inputs Tests/GeometryShop/regression/levelRedistTest.cpp Tests/GeometryShop/regression/levelredist.inputs Tests/GeometryShop/regression/momentConvTest.cpp Tests/GeometryShop/regression/momentconvtest.inputs Tests/GeometryShop/regression/multicelllev.cpp Tests/GeometryShop/regression/multicelllev.inputs Tests/GeometryShop/regression/runalltests.mpi.sh Tests/GeometryShop/regression/runalltests.serial.sh Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs Tests/GeometryShop/regression/simpleMomentExample.cpp Tests/GeometryShop/regression/simplemomentexample.inputs Tests/GeometryShop/runalltests.mpi.sh Tests/GeometryShop/runalltests.serial.sh Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile Tests/GeometryShop/sparseDataSingleGrid/Make.package Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp Tests/GeometryShop/sparseDataSingleGrid/sphere.inputs Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphere/Make.package Tests/GeometryShop/sphere/sphere.inputs Tests/GeometryShop/sphere/sphereConvTest.cpp Tests/GeometryShop/sphere/sphereTest.cpp Tests/GeometryShop/sphereEBISBox/GNUmakefile Tests/GeometryShop/sphereEBISBox/Make.package Tests/GeometryShop/sphereEBISBox/sphere.inputs Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/dirichletTest_F.H Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_F.H Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp Tests/GeometryShop/stencilTestbed/src/Make.package Tests/GeometryShop/stencilTestbed/src/lapl_nd.F90 Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H Tests/GeometryShop/vofStructures/AMReX_EBRedist.H Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/README.txt Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/nbrsTest.cpp Tests/GeometryShop/vofStructures/nbrsTest_mod.F90 Tests/GeometryShop/vofStructures/nbrsTest_nd.f90 Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/umapTest.H Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/umapTest_mod.f90 Tests/GeometryShop/vofStructures/umapTest_nd.f90 Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/EBSurfaceTools/GNUmakefile Tools/GNUMake/Make.defs Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/LevelSet/Exec/GNUmakefile commit 9774819404e1caf31dac39309be4016a2158fe34 Author: sireeveslbl Date: Thu Aug 30 16:10:43 2018 -0700 odd stencil behavior for generating the matrix. Some regions do not have the penta-diagonal design it should have. Looking to investigate this. Src/Extern/PETSc/AMReX_PETSc.cpp commit b926f8d6b4c9530f26add30c72b58cb5001f11dc Author: Ray Grout Date: Thu Aug 30 16:10:01 2018 -0600 Change how vfrac threshold is written out so that amrvis and visit are both happy Tutorials/EB/CNS/Source/CNS_io.cpp commit 473ba9b58ef84aa571712ed706b37acb9de7bd59 Author: Weiqun Zhang Date: Thu Aug 30 13:46:38 2018 -0700 CellEB2: add fine grids Src/EB2/AMReX_EB2_Level.H Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/inputs commit 427ed65caafa636d9e47f80ec88eb62943eadf82 Author: Weiqun Zhang Date: Thu Aug 30 13:32:33 2018 -0700 add CellEB2 test for Dirichlet bc Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/CellEB2/Make.package Tests/LinearSolvers/CellEB2/MyEB.H Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/MyTest_F.H Tests/LinearSolvers/CellEB2/initEB.cpp Tests/LinearSolvers/CellEB2/inputs Tests/LinearSolvers/CellEB2/main.cpp Tests/LinearSolvers/CellEB2/mytest_f.F90 commit 61ab86d89ddc80106e9a4d89bac4cdf2881fa17f Author: Marc Day Date: Thu Aug 30 12:07:22 2018 -0700 Fix bug in tutorial. Tutorials/Parallel/ForkJoin/MyTest.cpp commit 9e4329c64a588c19373b39fd2349a2080a9372ac Author: Marc Day Date: Thu Aug 30 12:01:28 2018 -0700 Add a simple ForkJoin Tutorial, add a function to the fj class. Tutorial currently gives weird result for duplicated multifabs. Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/Parallel/ForkJoin/GNUmakefile Tutorials/Parallel/ForkJoin/Make.package Tutorials/Parallel/ForkJoin/MyTest.H Tutorials/Parallel/ForkJoin/MyTest.cpp Tutorials/Parallel/ForkJoin/MyTest_F.H Tutorials/Parallel/ForkJoin/inputs Tutorials/Parallel/ForkJoin/main.cpp commit 21ddc4f0cce1ba86d6b5ce35574bb74a84e81619 Merge: bb9c90e6c 16c4af11a Author: Marc Day Date: Thu Aug 30 10:34:44 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bb9c90e6ce3f370471655e43577755898bce1805 Author: Marc Day Date: Thu Aug 30 10:34:41 2018 -0700 Add == op for BCRec Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit 16c4af11a566bafc3652dd63e73cebb6430b6099 Author: Weiqun Zhang Date: Thu Aug 30 10:29:14 2018 -0700 new iMultiFab constructor taking IntVect ngrow Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit ab479546b2a79ff0139df460555f97ed9ebbfeb3 Author: Cy Chan Date: Wed Aug 29 22:05:39 2018 -0700 ParallelReduce.H: for MPI_Op lookup, change unordered_map to array Src/Base/AMReX_ParallelReduce.H commit b9724be8936687d03d9b7d23ea79570b898197d0 Author: sireeveslbl Date: Wed Aug 29 16:02:57 2018 -0700 Matrix appears to be correctly populating. However, the KSB solver is throwing a floating point exception. Will continue to debug. Possible culprits: RHS and Sol vectors not correctly being loaded, petsc not being correctly initialized, or something I haven't thought of. Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e1e5eff32eb1f793c5a1a631cba9ed39c8eb74c0 Author: Weiqun Zhang Date: Wed Aug 29 15:59:00 2018 -0700 put limit on eb max coarsening level Src/EB2/AMReX_EB2_IndexSpaceI.H commit 5fef32336b5bac633cba0a89ddda600d7ccab3ca Merge: ed915ae84 2a8625c73 Author: Weiqun Zhang Date: Tue Aug 28 17:15:27 2018 -0700 Merge branch 'development' into mlmg commit ed915ae84fc32db432e5761f6c016744ee67a522 Author: Weiqun Zhang Date: Tue Aug 28 17:15:08 2018 -0700 remove unused variables Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit d3aba2ded4ef78375dd25a69511201e155bd8f0b Author: Weiqun Zhang Date: Tue Aug 28 16:08:34 2018 -0700 3d eb dirichlet: gsrb and normalize Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 657d4cf3a5aa820e79b5a92ef2136e198a39ab82 Author: sireeveslbl Date: Tue Aug 28 15:59:47 2018 -0700 Removed unneeded function Src/Extern/PETSc/AMReX_PETSc.H commit b1ac6e77a5e1405d39f9ad17f54efaef003dc693 Author: sireeveslbl Date: Tue Aug 28 15:57:23 2018 -0700 Wrote the function to connect applications and PETSc routines. There are bugs in the execution that will need to be flushed out. Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6d6c53c958e74fca3e10b89189d8f16fbc6365c7 Author: Weiqun Zhang Date: Tue Aug 28 15:45:34 2018 -0700 3d eb dirichlet a dot x Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit ef35e87ce9f378eb00c4d6b1c73d65e9417c7e66 Author: sireeveslbl Date: Tue Aug 28 14:26:48 2018 -0700 Proper build of Petsc, returned Make.petsc to previous version, single include directory. KSP solver not converging, need to iron out bugs. Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB/inputs Tools/GNUMake/packages/Make.petsc commit 7ab674867475643a895854b83d723ce75b54f419 Author: sireeveslbl Date: Tue Aug 28 13:32:55 2018 -0700 Switched things a bit Tests/LinearSolvers/CellEB/GNUmakefile Tools/GNUMake/packages/Make.petsc commit 5b3ef7c78c7744e94e0b0ee0f24eb8947e48e2dc Author: Weiqun Zhang Date: Tue Aug 28 13:28:15 2018 -0700 update normalize Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 06aed25d7028e47ce3ef0402681d2b9266f027b4 Author: Weiqun Zhang Date: Tue Aug 28 13:03:33 2018 -0700 eb dirichlet: use the simple version Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 7b5d037c980373df3b86533f2031a34bfe909378 Author: sireeveslbl Date: Tue Aug 28 13:02:59 2018 -0700 AMReX with PETSC bottom solve works. Going to go through and remove any unneccessary links/ directories Src/Extern/PETSc/AMReX_PETSc.cpp Tests/LinearSolvers/CellEB/GNUmakefile Tools/GNUMake/packages/Make.petsc commit 17cd9fa57c34931c83fe7cb24e8504fef50c475f Author: sireeveslbl Date: Mon Aug 27 14:16:51 2018 -0700 Killing compilation issues, got the proper linkage. However now am having pointer issues. Will try and fix those. Note this does not compile yet for USE_PETSC=TRUE Src/Extern/PETSc/AMReX_PETSc.cpp Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB/inputs commit 2a8625c73cd0d0eb4eb76e9a26f4e047d9736b2b Merge: d149d24fe dc64d08fe Author: Weiqun Zhang Date: Mon Aug 27 12:30:38 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d149d24fea679f0b8f3c1a3db04edbbe1e10c793 Author: Weiqun Zhang Date: Mon Aug 27 12:28:30 2018 -0700 VisMF::Read can read lower-dimensional files with ghost cells Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_VisMF.cpp commit 0d7547cacee0ddb2fb4cb969b5b5961ecf13356a Author: Weiqun Zhang Date: Mon Aug 27 12:27:25 2018 -0700 mfiter: support no IntVect number of ghost cells Src/Base/AMReX_MFIter.cpp commit dc64d08fe1812add24fac348a49696d4c0a42b48 Author: Tan Nguyen Date: Mon Aug 27 12:24:17 2018 -0700 fix a small buf in the custom Barrier Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp commit 098043097935058b039fdff6d252f497315e8723 Author: Weiqun Zhang Date: Mon Aug 27 10:34:07 2018 -0700 make IntVect operator>> work for data of any dimensions Src/Base/AMReX_IntVect.cpp commit 3d9c8f52f32179e6bc672372ad64a7ca21498e70 Author: Max Katz Date: Sat Aug 25 15:45:15 2018 -0700 Fix up the heat equation GPU tutorial Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit 18e000996386064d540416a819201889be2a5946 Author: Max Katz Date: Sat Aug 25 15:33:42 2018 -0700 Fix typo Tools/F_mk/GMakeMPI.mak commit a7e16417e1b2e93131a0f60312709b678f49b151 Author: Max Katz Date: Sat Aug 25 15:30:35 2018 -0700 Sync up some more with development Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp commit 5ee56f711fc7fc3209a0dd6192129aaeaaba2af3 Merge: 565e7c377 156bb1bb1 Author: Max Katz Date: Sat Aug 25 14:42:40 2018 -0700 Merge branch 'development' into gpu Conflicts: Src/Base/AMReX_ArrayLim.H commit 565e7c3771bbd494ab6c5027e26fb2fdc28795f5 Author: Max Katz Date: Sat Aug 25 14:35:04 2018 -0700 Sync up RealBox with development Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 26b56028a437604079b2d2ed9e5c1b7c8e02e3a9 Author: Weiqun Zhang Date: Sat Aug 25 13:54:00 2018 -0700 dirichlet eb: clean up Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit d301f6c31caa7974058af6691508b09be9766354 Author: Weiqun Zhang Date: Sat Aug 25 11:09:55 2018 -0700 eb dirichlet: version that avoids extrapolation Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit eb95fb356ad43d101e342f079457eb13f6ca3136 Author: Weiqun Zhang Date: Fri Aug 24 22:30:10 2018 -0700 CellEB test: print out the smallest cut cell's volume fraction Tests/LinearSolvers/CellEB/MyTest.cpp commit ea9f5ab9649a63a770bd31b798fe9ff16b74d42e Author: Weiqun Zhang Date: Fri Aug 24 22:03:49 2018 -0700 eb dirichlet: tweak parameters Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit b8990a8d64a17745869fa3978498ee62c1d917cd Author: Weiqun Zhang Date: Fri Aug 24 21:40:24 2018 -0700 eb dirichlet: fix blend function Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Tests/LinearSolvers/CellEB/MyTest.cpp commit e14fe5af840268e43554aab9d241238408145c57 Author: Weiqun Zhang Date: Fri Aug 24 17:15:51 2018 -0700 eb dirichlet: 2d gsrb Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 2e5eee253ec02b7d767b512fb9224b18a1a69fe4 Author: Weiqun Zhang Date: Fri Aug 24 17:15:38 2018 -0700 CellEB test: add parameters for scalars Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit 915d961dd8112f90a4e9a0d79e1843c446130bdc Author: sireeveslbl Date: Fri Aug 24 15:57:28 2018 -0700 Linking issues between PETSc HYPRE and AMReX. Will route out the problem. Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Tests/LinearSolvers/CellEB/GNUmakefile Tools/GNUMake/packages/Make.petsc commit f5470d8f155663022d8ad1260aa9e1e0d014ee83 Author: Weiqun Zhang Date: Fri Aug 24 15:53:30 2018 -0700 pass dirichlet information into gsrb Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 0da813407d405f445e71e135ee41f08d4fddaedb Author: Weiqun Zhang Date: Fri Aug 24 15:43:59 2018 -0700 change the CellEB test initial data Tests/LinearSolvers/CellEB/MyTest.cpp commit d5c81011f62382aaa2b062eee5a270f0a12ca810 Author: Weiqun Zhang Date: Fri Aug 24 15:17:11 2018 -0700 eb dirichlet: a dot x Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 156bb1bb193b01259f6ac6ba4b596b74337e7db0 Author: sireeveslbl Date: Fri Aug 24 13:48:16 2018 -0700 Typo fix Docs/sphinx_documentation/source/EB.rst commit 619d79ca1c04e9c002bb5bf2a3c1df4c1709a20d Author: sireeveslbl Date: Fri Aug 24 13:45:35 2018 -0700 Use Vec functions from PETSc Src/Extern/PETSc/AMReX_PETSc.cpp commit 29f66535b8e88fcece80b1f77fb0c5d3d7417f07 Author: Cy Chan Date: Fri Aug 24 01:27:33 2018 -0700 fixed issue in ParallelReduce for non-integer MPI_Op implementations Src/Base/AMReX_ParallelReduce.H commit e233ff9b869badd71f4b4ebce9d41563004c36e8 Author: Weiqun Zhang Date: Thu Aug 23 17:53:10 2018 -0700 WIP: eb dirichlet Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 0034073b463b89ad2c90c2a219795f9854eeea79 Author: Johannes Blaschke Date: Thu Aug 23 17:47:38 2018 -0700 fix problem with levelset bcs and avoid unncessary tiling Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit 03b21c46093244c7a9a5948d726dde4de4c76026 Author: sireeveslbl Date: Thu Aug 23 16:03:31 2018 -0700 Working on PETSc availability for the bottom solve. Currently am preallocating based on the stencil for our problem. Might be an over estimate, but could also be cheaper than looping through the solution to dictate what is in the diagonal blocks and what is not. Load vector and get solution vector is being modeled after the HYPRE ones, but will change to utilize the PETSc routines. Src/Extern/PETSc/AMReX_PETSc.cpp commit c89bb1c4ec83013aed093cf950933d3d4112e4f1 Author: Weiqun Zhang Date: Thu Aug 23 14:57:44 2018 -0700 pass eb area and beta coefficient into Fortran Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 454aa22ac3b16bd3e7c9cb04b5f4b227055df284 Merge: 65e91937d 0ebe1f0c5 Author: Weiqun Zhang Date: Thu Aug 23 13:37:26 2018 -0700 Merge branch 'development' into forkjoin commit 31df60ec85c47f479ec7bbb58f0dcff9bbd55dcc Author: Weiqun Zhang Date: Thu Aug 23 10:23:13 2018 -0700 add a blend function for EB dirichlet Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 0ebe1f0c5d7d44a5199c5e082573842b9880182f Author: Johannes Blaschke Date: Thu Aug 23 10:11:21 2018 -0700 bug fix: EB tutorial now works without DAMREX_USE_GEOMETRYSHOP Src/EB2/AMReX_EB2_IF_Polynomial.H Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit c0ae1e8caff7bfbe092e662557de26af8a29f6a5 Author: Kevin Gott Date: Thu Aug 23 13:03:38 2018 -0400 Pinned allocator adjustment. Src/Base/AMReX_CudaAllocators.H commit 50ea23a19028c0ddfe44c882d74bcbf7a9e0095c Author: Kevin Gott Date: Thu Aug 23 13:01:55 2018 -0400 PinnedData object draft. Tutorials/GPU/Test/GNUmakefile Tutorials/GPU/Test/main.cpp Tutorials/GPU/Test/run.script commit 4b148a197587e7eef5b99cd88abb605cfa2b2430 Author: Johannes Blaschke Date: Wed Aug 22 21:56:32 2018 -0700 update level set tutorial => user can specify eb or eb2 Src/EB/AMReX_EBTower.H Tutorials/EB/LevelSet/Exec/inputs_eb2 Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 708cb6da6f481deaec9f95c42b941877ea29eba2 Author: Johannes Blaschke Date: Wed Aug 22 17:49:35 2018 -0700 replace pow function in IF_Polynomial with integer-specific version Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_IF_Plane.H Src/EB2/AMReX_EB2_IF_Polynomial.H Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit 0f747c64853aed5fef900c20262902967f49fa0d Author: Weiqun Zhang Date: Wed Aug 22 11:21:31 2018 -0700 fix bug Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 42bcd87b86137830793d62c98c603ad187a4b28f Merge: 491cc8f0f 45d69788f Author: Johannes Blaschke Date: Wed Aug 22 10:48:03 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 491cc8f0f9c52ce4227e3c1fc4cfc5a04dc0d7b0 Author: Johannes Blaschke Date: Wed Aug 22 10:47:54 2018 -0700 upgrade LSFactory to work with EB2 Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_IF_Plane.H Src/EB2/AMReX_EB2_IF_Polynomial.H Src/EB2/AMReX_EB2_IF_Translation.H Src/EB2/AMReX_EB2_IF_Union.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/CMakeLists.txt Src/EB2/Make.package Src/GeometryShop/AMReX_EBIndexSpace.cpp Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 45d69788fd625dfa182c2f85275a98e05eaff732 Author: sireeveslbl Date: Wed Aug 22 10:40:31 2018 -0700 Last of the EB proofreading. Docs/sphinx_documentation/source/EB.rst commit e10d7a767b26d073038331c7129b994441e7980a Author: Ann Almgren Date: Wed Aug 22 06:35:40 2018 -0700 GEOMETRY_SHOP-->GEOMETRYSHOP Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 93af7689615dd9cb7ecc79f5281b1eb52260e55e Author: Ann Almgren Date: Wed Aug 22 06:31:32 2018 -0700 USE_GEOMETRY_SHOP --> USE_GEOMETRYSHOP Tools/GNUMake/Make.defs commit 249af6290b190308bc67303f587da3633831fc40 Author: Max Katz Date: Tue Aug 21 23:50:43 2018 -0700 Fix some variable definitions for nvcc.mak Tools/GNUMake/comps/nvcc.mak commit c55f996a827112d8d9f9efd71f5e71cc5d9fbead Author: Max Katz Date: Tue Aug 21 21:53:23 2018 -0700 Move the fortran preprocessing to the actual compile rule Tools/GNUMake/Make.rules commit f88bcca5051f173a764f98714792870deb7603d4 Author: Max Katz Date: Tue Aug 21 21:11:56 2018 -0700 We no longer need the Fortran passed to the CUDA script Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit 43b0cdef9093b9d1fdd984a79dd611c8f2ebd3f2 Author: Weiqun Zhang Date: Tue Aug 21 17:01:01 2018 -0700 eb avgdown boundaries Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 2609ac24899a582ce51db176e770045a5eed6669 Author: Weiqun Zhang Date: Tue Aug 21 16:27:14 2018 -0700 add boundary area to eb factory Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H commit f596359f6d925d83cfea9a7b1ee40aabf3dcc6d3 Author: sireeveslbl Date: Tue Aug 21 16:06:49 2018 -0700 Proof read edits to new EB documentation. Still working through it. Docs/sphinx_documentation/source/EB.rst commit 8823d007d7b75d7ef605938b6a753d129ecd960d Author: Weiqun Zhang Date: Tue Aug 21 15:53:16 2018 -0700 add function to pass Dirichlet data for EB Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit ba980b866fefa1e1630aa2266a7edad4926920ec Author: Max Katz Date: Tue Aug 21 15:18:59 2018 -0700 cuda header script should also depend on CEXE_sources Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit 94dd0a030b6d91c17949a112c39ee860ace3e16b Merge: b3c6209d9 08995b1aa Author: Weiqun Zhang Date: Tue Aug 21 14:29:32 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b3c6209d95a247ae4d3de86eb58d84b67ff40e7d Author: Weiqun Zhang Date: Tue Aug 21 14:26:34 2018 -0700 EB documentation Docs/sphinx_documentation/source/EB.rst commit 08995b1aa35f3892be63923e475ccd0d00df415b Merge: 75db2acde b3027c25b Author: kngott Date: Tue Aug 21 13:12:43 2018 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit 75db2acde250c324bb26de37a39f63d6943c5209 Author: kngott Date: Tue Aug 21 13:12:15 2018 -0700 Profiler adjustment to allow compile. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit b3027c25be9da522293e185439a422d42fbdb112 Author: Ann Almgren Date: Tue Aug 21 12:55:15 2018 -0700 Need to add flags for using GeometryShop directory Tools/GNUMake/Make.defs commit 3a2b253b66f9d883e4db50dd454471ae2feb6381 Author: sireeveslbl Date: Tue Aug 21 10:04:12 2018 -0700 Consistency in pronouns Docs/sphinx_documentation/source/EB.rst commit 2d4c2597e29d6676bcb645885e4016242bfa10b8 Merge: 16984fc1e 5283952ca Author: Weiqun Zhang Date: Mon Aug 20 17:25:08 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 16984fc1e94d781a155c29abf380c87566caf430 Author: Weiqun Zhang Date: Mon Aug 20 17:25:02 2018 -0700 WIP: EB documentation Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/EB/EB_example.fig.bak Docs/sphinx_documentation/source/EB/eb_fluxes.fig.bak Docs/sphinx_documentation/source/EB/parabsphere.pdf Docs/sphinx_documentation/source/EB/parabsphere.png Docs/sphinx_documentation/source/EB/parabsphere.ps.REMOVED.git-id Docs/sphinx_documentation/source/EB/revolution.pdf Docs/sphinx_documentation/source/EB/revolution.png Docs/sphinx_documentation/source/EB/revolution.ps.REMOVED.git-id Src/EB2/AMReX_EB2_IF_Scale.H commit 65e91937d472e7dfd5ccfb674340a28afb286fc3 Merge: 290b0f152 5283952ca Author: Cy Chan Date: Mon Aug 20 15:32:54 2018 -0700 Merge branch 'development' into forkjoin commit 290b0f152f614ddf7d08b865d9a5466d6f3ee690 Author: Cy Chan Date: Mon Aug 20 15:24:46 2018 -0700 create directory for fork-join task output files Src/Base/AMReX_ForkJoin.cpp commit 5283952ca193bd342eb73596237eb5c607a37962 Author: sireeveslbl Date: Mon Aug 20 14:49:44 2018 -0700 Further Documentation Editing, reviewed Linear Solvers, will do EB next Docs/sphinx_documentation/source/LinearSolvers.rst commit 2d21b89308d70e7cfe142e09a8444d012a69d01a Author: Andrew Myers Date: Mon Aug 20 11:31:39 2018 -0700 bugfix to the fill_slice interpolation routine Src/Base/AMReX_MultiFabUtil_nd.F90 commit eb486fd3c0b2a0eec4cbd2c02aecf949647d52cc Author: Max Katz Date: Mon Aug 20 03:19:20 2018 -0400 Clean up lineinfo/debug differences for CUDA Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 795b012c53f75e7b8e6d99f41cef37a4ed22c165 Author: Max Katz Date: Sun Aug 19 13:28:18 2018 -0400 Sync up write_probin.py with gpu branch Tools/F_scripts/write_probin.py commit e7421210a95191f35ac3006d7a7e199c713fcc71 Author: Max Katz Date: Sun Aug 19 13:25:23 2018 -0400 Clean whitespace Tools/F_scripts/write_probin.py commit e1138b1e8689341485f0201dfe809d0e40661fab Author: Michael Zingale Date: Sun Aug 19 11:04:44 2018 -0400 fix typo in macro Src/Base/AMReX_ArrayLim.H commit 8a94be9e9611f539007de3bfc460d97b6fe5e812 Author: Max Katz Date: Sat Aug 18 23:56:43 2018 -0700 Remove get_fortran_pointer Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_MFIter.H commit 9848001028fbb04d507ac5da032987614b0e8c54 Author: Max Katz Date: Sat Aug 18 23:55:38 2018 -0700 Remove registerRealBox Src/Base/AMReX_MFIter.H commit 1e3ccf553a7ec42f6127d68275cdc0482e9b01a7 Author: Max Katz Date: Sat Aug 18 23:25:14 2018 -0700 Add rzansel @ LLNL Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit 50d1756aa65cf9027203596b42d9c04cfd545d29 Author: Max Katz Date: Sun Aug 19 01:15:49 2018 -0400 Re-enable optimizations for PGI with CUDA Tools/GNUMake/comps/pgi.mak commit 5c318d01f3ccd30f021ec94f6e6a4e7812b0798b Author: Max Katz Date: Sat Aug 18 21:06:56 2018 -0700 Switch to arch specification, default cc35 Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit 08cb1d7c7691ecbca50f0cbd1b8a52835d89b7ba Author: Max Katz Date: Sat Aug 18 21:01:03 2018 -0700 Add debug flags for nvcc Tools/GNUMake/comps/nvcc.mak commit 7f5475151b0c01948d5578b98058837e553ed7da Author: Max Katz Date: Sat Aug 18 22:04:12 2018 -0400 Take the physical boundary fill off the GPU for now Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 commit 1faefc76720e9a79e1afebaea603c5c3cce11f78 Author: Max Katz Date: Sat Aug 18 22:03:35 2018 -0400 Take the derives off the GPU for now Src/Amr/AMReX_AmrLevel.cpp commit b202afde083a8f244ae64829915dad1b23666df1 Author: Max Katz Date: Sat Aug 18 21:45:13 2018 -0400 Create a preprocessed version of the C++ files for diagnostic uses Tools/F_scripts/write_cuda_headers.py commit 8ce7188c06c669e50b8d8fc72f0e304b531f859e Author: Max Katz Date: Sat Aug 18 21:23:02 2018 -0400 ZFILL -> AMREX_ZFILL Src/Base/AMReX_ArrayLim.H commit ea6e4c795e5d53b6cf221d8bf4db9ef2b4371f86 Merge: 07fd20e19 115ea7c38 Author: Max Katz Date: Sat Aug 18 20:13:04 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 115ea7c385ec0f2dd2cdd01c418578615cc01d54 Author: Max Katz Date: Sat Aug 18 19:56:24 2018 -0400 Fix nvcc version check Tools/GNUMake/comps/nvcc.mak commit 07fd20e19d57b3668dc7fd13b20a4ed1fe9e81dc Author: Max Katz Date: Sat Aug 18 19:44:17 2018 -0400 Replace mfi.get_fortran_pointer with macro Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_ArrayLim.H commit 6c0a6db4df51ee4a949eabbb3494d548f73aaf84 Merge: 01b9892d6 ccd3e70f3 Author: Weiqun Zhang Date: Sat Aug 18 13:59:17 2018 -0700 Merge branch 'development' into petsc commit ccd3e70f30504a16c3aa948d7bbae8a304735ffc Author: Weiqun Zhang Date: Sat Aug 18 13:58:28 2018 -0700 no need to include GeometryShop in Tutorials Docs/README.md Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB/inputs Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBConvergenceTest/inputs Tests/LinearSolvers/EBflux_grad/GNUmakefile Tests/LinearSolvers/EBflux_grad/inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.amr Tutorials/EB/CNS/Exec/ShockRef/inputs.regt Tutorials/EB/CNS/Exec/Sod/inputs Tutorials/EB/CNS/Source/main.cpp Tutorials/EB/MacProj/GNUmakefile commit 5e6365b8408ef22a6692bc8f377fa5e7ea1f0512 Author: Weiqun Zhang Date: Sat Aug 18 13:42:20 2018 -0700 put some notes into subdirectory Docs/Notes/Notes.io_implementation Docs/Notes/Readme.backtrace Docs/Notes/Readme.io Docs/Notes/Readme.profiling Docs/Notes/Readme.typecheck Docs/README.md Docs/Readme.sphinx commit 75dd369e746264ec85cdf3d3cffcac235dad9b79 Author: Weiqun Zhang Date: Sat Aug 18 13:33:28 2018 -0700 reset hypre solver in case the solver is reused Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 028acad6856c463fc82d8f0a4638c5051e19e2b4 Merge: babdc7964 06d9bacf3 Author: Weiqun Zhang Date: Sat Aug 18 13:18:00 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit babdc7964de652dd4b525ac016784ff724626d56 Author: Weiqun Zhang Date: Sat Aug 18 13:16:25 2018 -0700 ZFILL -> AMREX_ZFILL Src/Base/AMReX_ArrayLim.H commit ee035aade6d2e23f51108f4d89fbb1c802b05cea Author: Weiqun Zhang Date: Sat Aug 18 13:14:09 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development Src/Base/AMReX_ArrayLim.H commit 25e95b4a3589b190b91233d147dd9178c4bea875 Author: Weiqun Zhang Date: Sat Aug 18 13:08:43 2018 -0700 cleanup Src/EB/AMReX_ebinterp_2d.F90 Src/EB2/AMReX_eb2_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit eedbd40e4c75758051a0eee36dbd7d3fb1c32c6c Author: Weiqun Zhang Date: Sat Aug 18 13:06:58 2018 -0700 fix return Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H commit 796b05b8a065031aacad1bf75a01ce5eedc6dae7 Author: Max Katz Date: Sat Aug 18 15:58:40 2018 -0400 Create fewer streams to shorten initialization time Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit af932c15d8134505a1dd5a15b17c8267d1b6b863 Author: Weiqun Zhang Date: Sat Aug 18 12:48:02 2018 -0700 save parent in factory Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_Level.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 5337abf745959056a69a42cb534b9d82387e9aff Author: Weiqun Zhang Date: Sat Aug 18 08:47:33 2018 -0700 use AMREX_USE_GEOMETRYSHOP. add parent information to EB2::Level and Factory Src/Amr/AMReX_StateData.H Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H commit d38840f0a943f6bde1dbc5721d454869b2857e46 Author: Max Katz Date: Sat Aug 18 06:18:48 2018 -0400 GPU script learns about AMREX_REAL_ANYD Tools/F_scripts/write_cuda_headers.py commit 64c7aeb2eb89b48dc9dd6468e0dc44949808f2e7 Author: Max Katz Date: Sat Aug 18 06:18:30 2018 -0400 Add AMREX_REAL_ANYD Src/Base/AMReX_ArrayLim.H commit 729c84f8bccd807cecd2249e90d7af34972ed258 Merge: a3d678573 06d9bacf3 Author: Max Katz Date: Sat Aug 18 05:39:07 2018 -0400 Merge branch 'development' into gpu commit 06d9bacf35f1e3ad6b04093f991fcb4fb0cf90a8 Author: Max Katz Date: Sat Aug 18 05:23:01 2018 -0400 Add macros for compatibility with GPU branch Src/Base/AMReX_ArrayLim.H commit a3d678573fe6d6697420daa6672238e864db2672 Author: Max Katz Date: Sat Aug 18 05:08:11 2018 -0400 Remove MFIter::registerBox Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit c276cb1ae3886a75f9b12a40fc960adf744b6832 Author: Max Katz Date: Sat Aug 18 05:01:19 2018 -0400 Sync up Box class with development Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit fb160e974d4c7581abda1674ddf72c6e62fac44b Author: Max Katz Date: Sat Aug 18 05:01:07 2018 -0400 Add some missing includes Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H commit c71c43536f9581b3d47af8ee10e15d8f28cf2993 Author: Max Katz Date: Sat Aug 18 04:49:38 2018 -0400 Pass intvect by value for several common macros Src/Base/AMReX_ArrayLim.H Tools/F_scripts/write_cuda_headers.py commit d66734b85a5aa230b17f245051c49b6d650efe92 Author: Max Katz Date: Sat Aug 18 03:29:15 2018 -0400 AMREX_ARLIM_ARG -> AMREX_INT_ANYD Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BaseFab.cpp Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit a60a5e08cc59d633c44025ae4ca8f05a420fe34d Author: Max Katz Date: Sat Aug 18 03:24:23 2018 -0400 Make GPU script aware of BL_TO_FORTRAN Tools/F_scripts/write_cuda_headers.py commit 0c958eb215dc875cf043a10005e66db165b19e62 Author: Weiqun Zhang Date: Fri Aug 17 18:44:41 2018 -0700 MLMG reuse for EB too Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit cc81903911e0ffc480910ca4f6c9bc3eedcde49c Author: Weiqun Zhang Date: Fri Aug 17 18:38:09 2018 -0700 allow MLMG being reused Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 61395dc158d6b3852b75fe5a83d5fbf579ce0339 Author: Andrew Myers Date: Fri Aug 17 17:09:46 2018 -0400 change the default value of USE_CUDA in the OMP HeatEquation example. Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/GNUmakefile commit 5226a6a8087c46546ebac8ac4e02c0f99de5fa4c Author: Andrew Myers Date: Fri Aug 17 17:09:16 2018 -0400 no longer need to do special memory allocation for OMP_OFFLOAD Src/Base/AMReX_BArena.cpp commit 9668e34e275994a81d5f1256bc783505f3b2b4c9 Author: Weiqun Zhang Date: Fri Aug 17 13:54:40 2018 -0700 make EB2 the default Src/EB2/AMReX_EB2.cpp commit 001d25f8fa384a79630fa6721faa612aae1f7e23 Merge: d4a3f3c80 2edabdb09 Author: Weiqun Zhang Date: Fri Aug 17 13:48:08 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 77b396421d2bc18fd73812c9f86d94f3d5c2e017 Merge: 642e93b28 cdd8cb0e2 Author: Andrew Myers Date: Fri Aug 17 16:44:27 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 642e93b28d8814a0ce50e94b8ba41356c8d9e0f1 Author: Andrew Myers Date: Fri Aug 17 16:44:05 2018 -0400 add in missing cudaDeviceSynchronize to FillBoundary (bug only affected NProcs = 1) Src/Base/AMReX_FabArrayCommI.H commit d4a3f3c801ebe1a8f123012a9458ba2004e51e3b Author: Weiqun Zhang Date: Fri Aug 17 13:41:49 2018 -0700 use the new GetVecOfArrOfPtrs Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/EB/MacProj/main.cpp commit 715e0c1e4fd074f435f8ea72327e5bbe5d445ea4 Author: Weiqun Zhang Date: Fri Aug 17 13:37:57 2018 -0700 fix the new GetVecOfArrOfPtrs with enable_if Src/Base/AMReX_Vector.H commit 0334eca80928e427274001de58de1b93e72875d2 Author: Weiqun Zhang Date: Fri Aug 17 13:36:32 2018 -0700 add IsFabArray type traits Src/Base/AMReX_TypeTraits.H commit 40f0c98cec9edb0e95c8c659303754b842f224db Author: Cy Chan Date: Fri Aug 17 13:06:48 2018 -0700 fix bug in ParallelReduce.H for USE_MPI=FALSE Src/Base/AMReX_ParallelReduce.H commit 2edabdb090fbcc0888a3cdf61ed0603a752d6f28 Author: Ann Almgren Date: Fri Aug 17 11:05:24 2018 -0700 Update CMake stuff to take AMREX_ENABLE_GEOMETRY_SHOP option through CMake and convert it to AMREX_USE_GEOMETRY_SHOP flag Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit e33d461af4d779c26b2d1bbd1804acf9be0c9d0d Author: Weiqun Zhang Date: Fri Aug 17 10:55:35 2018 -0700 fix bug in my last commit Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit dce9b3210f27a5f02d14aa152ffbf54f005e4b6a Author: Weiqun Zhang Date: Fri Aug 17 10:47:23 2018 -0700 MacProjector: support regular geometry too Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 2e0bde34bf37c5368855398c6b79a05db2f0f930 Author: Weiqun Zhang Date: Fri Aug 17 10:41:03 2018 -0700 comment out VisMF::Write Tutorials/EB/MacProj/main.cpp commit d7c6c52f88c5aa9f476b8a3ebbbf0bc1054ac0a5 Merge: 29dfbaadc b6572b0b5 Author: WeiqunZhang Date: Fri Aug 17 10:33:59 2018 -0700 Merge pull request #301 from jared321/flash_fluxcorrection Flux correction changes needed for FLASH commit 6d22c43a282079b90e65fa95381fbe37e872d2e5 Author: Kevin Gott Date: Fri Aug 17 13:03:27 2018 -0400 Test program. Tutorials/GPU/Test/GNUmakefile Tutorials/GPU/Test/Make.package Tutorials/GPU/Test/main.cpp Tutorials/GPU/Test/run.exitcode Tutorials/GPU/Test/run.script commit cdd8cb0e28576d52c5b95ce50905da758657107a Author: Max Katz Date: Fri Aug 17 03:36:18 2018 -0400 GPU script now passes AMREX_INT_ANYD wrapped IntVects by value Still needs work; there is an incompatibility between the argument positions in the C++ and the preprocessed headers. Src/Base/AMReX_ArrayLim.H Tools/F_scripts/write_cuda_headers.py commit 936f38fc48c66341bc3bb39cad3e7a68174a8e10 Author: Max Katz Date: Fri Aug 17 02:33:59 2018 -0400 Add capability for script to detect argument location of macros Tools/F_scripts/write_cuda_headers.py commit 29dfbaadc1adf19d96c0aa400f23f8d154f9516d Author: Weiqun Zhang Date: Thu Aug 16 21:44:12 2018 -0700 switch to IAMR sign convention Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/EB/MacProj/main.cpp commit c733a2a23453b4fe71a34046b7de83043e1cf6d9 Author: Weiqun Zhang Date: Thu Aug 16 21:35:10 2018 -0700 add EB2::useEB2 function to update the use_eb2 flag Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp commit 46df61c1b19c211e9c506d6ae37d74fd9124713a Author: Weiqun Zhang Date: Thu Aug 16 18:32:12 2018 -0700 finish MacProjector and tutorial Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/EB/MacProj/main.cpp commit 716bcc4ffea93a7242403a3adbf8c0144a0bbfb8 Author: Weiqun Zhang Date: Thu Aug 16 17:24:12 2018 -0700 remove some debug lines Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 8e76dbc7533642dde83cbf65d78fb29421cab32d Author: Weiqun Zhang Date: Thu Aug 16 17:23:35 2018 -0700 have to remove the new GetVecOfArrOfPtrs because it breaks the old one Src/Base/AMReX_Vector.H commit 687840cefbcd70b6b9b8168712bac431e82a5698 Author: Weiqun Zhang Date: Thu Aug 16 17:15:06 2018 -0700 add new files Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 1696fe655d768f467fae584d701503d736703527 Author: Kevin Gott Date: Thu Aug 16 20:10:09 2018 -0400 Change HeatEquation_EX1 to GPU global functions version. Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 62d8d354723e42c30cd19c03c45be0552440f19a Author: Kevin Gott Date: Thu Aug 16 20:05:17 2018 -0400 Remove un-needed in linear solver heat equation tutorial... for now. Tutorials/GPU/HeatEquation_EX2_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX2_C/Source/Make.package Tutorials/GPU/HeatEquation_EX2_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc_F.H commit 2ae645f1955c692c32100c6dc26dcf1b2616be00 Author: Kevin Gott Date: Thu Aug 16 19:59:23 2018 -0400 Adjustment to GPU Box distribution strategy. Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_IndexType.H commit 7746413ba967f29ffec305f8ed2f859933b50cb4 Merge: 7b84b294d 019aa570e Author: Weiqun Zhang Date: Thu Aug 16 16:55:31 2018 -0700 Merge branch 'development' into mlmg commit 019aa570e4d0d47ee40b254e6a8c8c8c8113f7ea Merge: 9bd4a028c 195666aa0 Author: Weiqun Zhang Date: Thu Aug 16 16:54:51 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9bd4a028c743c7c6ac87984bfdecd4ff864a55c7 Author: Weiqun Zhang Date: Thu Aug 16 16:54:39 2018 -0700 MacProjector: compute rhs and then solve Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Tutorials/EB/MacProj/inputs commit 195666aa01f03d64ebdcd22616f23c0f872faff7 Author: sireeveslbl Date: Thu Aug 16 16:00:11 2018 -0700 Fixed some document typos + some rewording for clarity. Docs/sphinx_documentation/source/Basics.rst commit e5eb1030d3f3675fe08fd7655c0dc18ddcfd3e46 Author: Tan Nguyen Date: Thu Aug 16 14:59:33 2018 -0700 fix a small bug Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp commit aade9c7e7da6e8ce672645ce64e5e0383b734620 Author: Weiqun Zhang Date: Thu Aug 16 14:58:47 2018 -0700 start MacProjector Src/EB2/AMReX_EB2.cpp Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/Make.package Tutorials/EB/MacProj/GNUmakefile Tutorials/EB/MacProj/Make.package Tutorials/EB/MacProj/initEB.H Tutorials/EB/MacProj/initEB.cpp Tutorials/EB/MacProj/inputs Tutorials/EB/MacProj/main.cpp commit 8420a7153db30c0be76891043733b58da02a1992 Merge: 88d1fe3d8 b3392d7a5 Author: kngott Date: Thu Aug 16 14:01:42 2018 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit 7b84b294d6c866e6e640700daeaa34df95296bd1 Author: sireeveslbl Date: Thu Aug 16 13:39:25 2018 -0700 GetVecOfArrOfPtrs implemented for regular class T Src/Base/AMReX_Vector.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Tests/LinearSolvers/EBflux_grad/MyTest.H Tests/LinearSolvers/EBflux_grad/MyTest.cpp commit b3392d7a50ed9dbf4d7e8066059db7542747b0f6 Author: Tan Nguyen Date: Thu Aug 16 13:29:27 2018 -0700 fix a mem leak bug in the runtime backend Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp commit 88d1fe3d87f0786a2b6c8c63cbac1aae88ddf629 Author: kngott Date: Thu Aug 16 13:17:01 2018 -0700 int to long in Profiler to accomodate very large profiling jobs. More similar fixes to likely come later. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit b6572b0b5ed428d08ac1b70dc3fa53779723e5d0 Author: Jared O'Neal Date: Thu Aug 16 14:42:35 2018 -0500 Fixed bug in OverwriteFlux routine. The code was coarsening the grid in the FluxRegister constructor and in the OverwriteFlux function. It now just coarsens at construction. For FLASH, we only need to do flux correction at fine/coarse boundaries. Therefore, altered code to ignore physical boundaries. Src/AmrCore/AMReX_FLUXREG_nd.F90 Src/AmrCore/AMReX_FluxRegister.cpp commit 9e1f388a220b884400052789245565bcd54572b0 Author: Weiqun Zhang Date: Thu Aug 16 12:28:27 2018 -0700 documentation Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/EB/eb_fluxes.eps Docs/sphinx_documentation/source/EB/eb_fluxes.fig Docs/sphinx_documentation/source/EB/eb_fluxes.fig.bak Docs/sphinx_documentation/source/EB/eb_fluxes.pdf Docs/sphinx_documentation/source/EB/eb_fluxes.png Docs/sphinx_documentation/source/LinearSolvers.rst commit dcc3a0c3f438cad6eb09ba0fa0c49c5704a89ca9 Author: sireeveslbl Date: Thu Aug 16 10:12:19 2018 -0700 Killed the 3D bug. EB Grad and Flux work for 2D and 3D Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Tests/LinearSolvers/EBflux_grad/MyTest.cpp commit d72246a1a5e97fd4d3268fe5d501e3a8ad497802 Merge: 5132d4aa6 451d50cb8 Author: Weiqun Zhang Date: Wed Aug 15 18:19:26 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5132d4aa6053822aa9d86c0ef43ac26eafbaa2ad Author: Weiqun Zhang Date: Wed Aug 15 18:19:05 2018 -0700 linear solver documentation Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/Chapter7.rst Docs/sphinx_documentation/source/LinearSolvers.rst Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 451d50cb86d284b171d6c1e2c8e7bd572664cf6f Author: Johannes Blaschke Date: Wed Aug 15 17:26:40 2018 -0700 If you try to build and EBTower 'over' another, the second one is ingored. This is a misleading design pattern => throw error if trying to build EBTower twice (without clearing the old one first) Src/EB/AMReX_EBTower.cpp commit 71e48d0513d3539a68522e178f5b7846d515bb86 Author: sireeveslbl Date: Wed Aug 15 16:20:34 2018 -0700 Flux and Grad 2D are working, flux 3D is working. Debugging Grad 3D Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Tests/LinearSolvers/EBflux_grad/GNUmakefile Tests/LinearSolvers/EBflux_grad/Make.package Tests/LinearSolvers/EBflux_grad/MyEB.H Tests/LinearSolvers/EBflux_grad/MyTest.H Tests/LinearSolvers/EBflux_grad/MyTest.cpp Tests/LinearSolvers/EBflux_grad/initEB.cpp Tests/LinearSolvers/EBflux_grad/inputs Tests/LinearSolvers/EBflux_grad/main.cpp commit d70359ca590e64a5c89301c6de96aa851da827f7 Author: Weiqun Zhang Date: Wed Aug 15 14:55:16 2018 -0700 std::array --> Array Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 22120f0d3b037593e208dc01a3fa3582f5faab3f Author: sireeveslbl Date: Wed Aug 15 11:32:25 2018 -0700 amrex_mlebabeclap_flux/grad compile for both 2D and 3D Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 4c29dbfa4e52d5451babad792e5f74b77677f8f1 Author: Ann Almgren Date: Wed Aug 15 10:04:21 2018 -0700 Don't use ls_ba as a local variable when it's defined in the .H file Src/EB/AMReX_EB_levelset.cpp commit 79115e587021a0fde264828113c8fc1e9e71afb5 Author: Weiqun Zhang Date: Tue Aug 14 18:13:05 2018 -0700 remove using namespace amrex from headers Tutorials/Basic/HeatEquation_EX1_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX2_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX3_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc.H commit 4e5ea54d60b983042893e6b0fb67aafe1c4fde3f Author: Weiqun Zhang Date: Tue Aug 14 18:04:40 2018 -0700 update documentation Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/Visualization.rst Src/Base/AMReX.cpp commit 0e1bf8dc0f657cb89015b8365a7fea0504c21d79 Author: sireeveslbl Date: Tue Aug 14 17:39:21 2018 -0700 Get Gradient of solution implemented for 2D Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit c0572aa5179f0ad3f5bc07247b5515e7db6120c5 Author: Ann Almgren Date: Tue Aug 14 16:04:05 2018 -0700 Remove unused variables Src/EB/AMReX_EBFluxRegister_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit 768047436ac6c39ed485c77cc27eb084404957c2 Merge: 01cc5a795 b42954ee7 Author: Ann Almgren Date: Tue Aug 14 16:02:56 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 01cc5a795b2c7727fe3d2b09c4fe9102ad33afa4 Author: Ann Almgren Date: Tue Aug 14 16:02:32 2018 -0700 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit b42954ee748f31aad2b759139c33f8bb3207a7c7 Author: Weiqun Zhang Date: Tue Aug 14 16:00:59 2018 -0700 update documentation Docs/Readme.typecheck Docs/sphinx_documentation/source/Basics.rst commit 54e23158e526ca32fb6f7378c365638878ac2089 Author: Kevin Gott Date: Tue Aug 14 17:21:15 2018 -0400 Setup for larger comparison testing. Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.cpp Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/inputs Tutorials/GPU/ElectromagneticPIC/summitdev.sh Tutorials/Particles/ElectromagneticPIC/Evolve.cpp commit c460d7cca01d6977706dfd85ac741fa86c29b204 Author: Weiqun Zhang Date: Tue Aug 14 13:49:20 2018 -0700 set dt_level after building bldFineLevels Src/Amr/AMReX_Amr.cpp commit 58af6bbbc696cf719caa35463b90169286c2f5ed Author: Kevin Gott Date: Tue Aug 14 16:13:31 2018 -0400 Global function version of ElectromagneticPIC. Tutorials/GPU/ElectromagneticPIC_1/Constants.H Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.H Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/GNUmakefile Tutorials/GPU/ElectromagneticPIC_1/IO.H Tutorials/GPU/ElectromagneticPIC_1/IO.cpp Tutorials/GPU/ElectromagneticPIC_1/Make.package Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.H Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC_1/Particles.H Tutorials/GPU/ElectromagneticPIC_1/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC_1/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_1/em_pic_F.H Tutorials/GPU/ElectromagneticPIC_1/inputs Tutorials/GPU/ElectromagneticPIC_1/main.cpp Tutorials/GPU/ElectromagneticPIC_1/summit.sh Tutorials/GPU/ElectromagneticPIC_1/summitdev.sh Tutorials/GPU/ElectromagneticPIC_1/test.cpp commit 8ed8342ccebd1edfb8f48a56078d5b5518523e1f Author: Kevin Gott Date: Tue Aug 14 16:11:06 2018 -0400 Fix size check. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp commit a87cb4474b16e8e4a99951a7dd182a73e0cf7dc7 Author: Kevin Gott Date: Tue Aug 14 16:10:42 2018 -0400 Adjusting GPU box setup. Src/Base/AMReX_CUDA_Utility.cpp commit ae99c03811256956b7b15af08199e80832ed3069 Merge: 7d1eb83fb b63478695 Author: Tan Nguyen Date: Tue Aug 14 12:45:35 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7d1eb83fbb7585367902a316c89e4e6d9e693403 Author: Tan Nguyen Date: Tue Aug 14 12:45:27 2018 -0700 first demo of the upcxx backend Src/Amr/AMReX_Amr.cpp commit 2dc26ef627cb38f64fee6914b7b88e54ec9ad569 Author: Tan Nguyen Date: Tue Aug 14 12:35:13 2018 -0700 a demo version of the upcxx backend Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/Base/AMReX.cpp commit b634786956a5e213c38c4b865540d6177a594d54 Author: Weiqun Zhang Date: Tue Aug 14 12:26:14 2018 -0700 update documentation Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/Chapter3.rst commit 603288e70f53d1f2c1b052b485cda343b97d4b00 Author: Max Katz Date: Tue Aug 14 01:54:05 2018 -0400 Catch a corner case in device function naming Tools/F_scripts/gpu_fortran.py commit 4b5b6cb9bc7dd349a01e2267d258227ebdf0a23d Author: Weiqun Zhang Date: Mon Aug 13 18:19:55 2018 -0700 move heat equation example to the end of the chapter on base so that the readers have seen names like MultiFab, BoxArray, etc. at that time Docs/sphinx_documentation/source/Basics.rst Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp commit c4da60a9355d858949286c8151fb9ed1b133fdd6 Author: Kevin Gott Date: Mon Aug 13 20:43:15 2018 -0400 Improved GPU thread distribution method. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CUDA_Utility.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp commit 8638ccc1e4ea90b78e0bc810a0efcb2c49fc5e2b Author: Weiqun Zhang Date: Mon Aug 13 17:41:07 2018 -0700 update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst commit f14f51c97da01f3a19fd699c6598ebfa1348e048 Author: Weiqun Zhang Date: Mon Aug 13 17:40:44 2018 -0700 add hypre to libamrex GNUmakefile.in Tools/libamrex/configure.py commit 1cdf1f952f59bee27b625b11b232447d0fbd8eb4 Author: Weiqun Zhang Date: Mon Aug 13 17:22:21 2018 -0700 add EB to libamrex.a as optional feature GNUmakefile.in Src/Amr/AMReX_StateData.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tools/libamrex/configure.py Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 6b8aeddecc52f5132dd4043248620e8487231a1b Author: Kevin Gott Date: Mon Aug 13 20:02:03 2018 -0400 Implement ParticlesData. Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Particles.H commit 76af532cb52f723750ef09972e19b917a36d2aa5 Author: Weiqun Zhang Date: Mon Aug 13 16:46:26 2018 -0700 update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/Chapter3.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/Introduction.rst commit 3b54e8f672b2b7c6cdb95ec2af8e987fde448564 Author: sireeveslbl Date: Mon Aug 13 16:10:44 2018 -0700 Flux routine for 2D and 3D compile. Will need to test them. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Tests/LinearSolvers/EBConvergenceTest/bcoef.F90 commit 528f27bfb8449dd4d405631da7f52734c6250e74 Author: Weiqun Zhang Date: Mon Aug 13 15:27:14 2018 -0700 less verbose Src/Base/AMReX.cpp Src/Base/AMReX_FabArrayBase.cpp commit 035b24af7fa8d7be46bdb26d7824f5a10be3f281 Author: sireeveslbl Date: Mon Aug 13 14:54:34 2018 -0700 Did 2D comp flux for EB. Didn't break anything. Now for 3D. Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot2D.m commit 13a08eee35bc2a0f291b0844ae40c32e306be2ae Merge: 70ead1df8 633ab9f48 Author: Weiqun Zhang Date: Mon Aug 13 14:45:28 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 70ead1df866e9093a5d12411c2a67c234b9586c9 Author: Weiqun Zhang Date: Mon Aug 13 14:45:01 2018 -0700 fix a bug 3d gsrb for eb Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 633ab9f48c18d5ff9e7c3eed85b3eea34ce480e7 Merge: b2b2f044e d18bba7d1 Author: Daniel Ladiges Date: Mon Aug 13 13:28:52 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b2b2f044e97370e05a34e7419a3877937329d4d5 Author: Daniel Ladiges Date: Mon Aug 13 13:25:50 2018 -0700 Added seperate FParallelMG2.mak file for AMReX-FHDeX, to avoid conflict with existing LLNS code Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/FParallelMG2.mak commit d18bba7d177e5ca0f8282ecacb2d8ba406eedfa4 Merge: 5e01ae0d1 1ba80eb7f Author: Weiqun Zhang Date: Mon Aug 13 12:33:02 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5e01ae0d1ea596a1619347e80bcd0223fea892ec Author: Weiqun Zhang Date: Mon Aug 13 12:30:23 2018 -0700 weight by volume fraction in computing max-norm error Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 8dfe7773f4dfc5698f526bf0cdc14a3dc077a42a Author: Weiqun Zhang Date: Mon Aug 13 10:47:59 2018 -0700 EB linear solver test: add periodic test Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit 1ba80eb7f2d6fe43f677133075f07472a5e66013 Merge: ba1934e2b ca75ca481 Author: asalmgren Date: Mon Aug 13 09:34:27 2018 -0700 Merge pull request #298 from AMReX-Codes/initial_dt_fix Do not initialize dt_level on levels that do not yet exist commit ce57255fc97da415162a1297fd4c3e5e5bfc71ba Author: Brian Friesen Date: Sun Aug 12 02:39:47 2018 -0700 Add OpenMP GPU offload version of HeatEquation_EX1_C tutorial (#296) * Tools: add Piz Daint at CSCS to list of sites/machines * GNUmake: add OpenMP GPU offload flags for XL on Summit/summitdev * Tutorials: create HeatEquation_EX1_C using OpenMP 4.5 GPU offloading Src/Base/AMReX_BArena.cpp Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.cscs Tools/GNUMake/sites/Make.olcf Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/run_summit_1node.sh Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc_F.H commit ca75ca481429819d852eaac44da9c0856d6b515b Author: Max Katz Date: Sun Aug 12 05:23:07 2018 -0400 Do not initialize dt_level on levels that do not yet exist This initialization is problematic if the level 0 timestep when the simulation starts is significantly different from the timestep later on in the simulation when we add refinement. In particular, this will happen if the simulation code shrinks the initial timestep by some factor. If the fine levels are only added later on once the timestep has caught back up to its normal limited level, then the first timestep on the fine level will be effectively limited by the initial level 0 timestep, which can sharply decrease the timestep for no reason. Src/Amr/AMReX_Amr.cpp commit dbb6ea07aeb5a56e1e3645dace1c7ecbefdcb57f Author: Weiqun Zhang Date: Fri Aug 10 18:28:31 2018 -0700 effectively remove the floor on target relative tolerance so that it's easy for testing how small the residual can be Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit ba1934e2b08099a1871f95d3474e9639f783a351 Author: Marc Day Date: Fri Aug 10 17:13:18 2018 -0700 Rewrite this AmrData function in terms of mesh and data that might be provided by something like SENSEI, e.g. (although fake it using plotfile data) Tools/Postprocessing/C_Src/IntegrateComp.cpp commit e766f5f851129e8e99330af9b7fca1c69fc66a53 Author: Weiqun Zhang Date: Fri Aug 10 16:38:10 2018 -0700 typo in profiler name Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit aa8ad3e5ec446a6617e041793fa5c0b104eae4e5 Author: Marc Day Date: Fri Aug 10 16:00:25 2018 -0700 Add a simple AmrData-based integrate function. Tools/Postprocessing/C_Src/IntegrateComp.cpp commit 43736e05292f730b43f34f26d628e149500ac266 Author: sireeveslbl Date: Fri Aug 10 14:17:06 2018 -0700 Forgot to add RHS Tests/LinearSolvers/EBConvergenceTest/RHS.F90 commit 39efc55a19ea159a75c527be49cf8fa5e8fe9397 Author: sireeveslbl Date: Fri Aug 10 14:04:56 2018 -0700 EB convergence testing complete. Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/RHS.F90 Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot2D.m Tests/LinearSolvers/EBConvergenceTest/bcoef.F90 commit 01b9892d66f51caff036e08c75ae15d889f3679d Author: Weiqun Zhang Date: Thu Aug 9 16:53:43 2018 -0700 must re-assign m_factory because rhs must be a different multifab Src/Extern/PETSc/AMReX_PETSc.cpp commit 334fafa0ea8c179691138ab10184d02b2212741d Author: Weiqun Zhang Date: Thu Aug 9 16:52:35 2018 -0700 hypre: must re-assign m_factory because rhs must be a different multifab Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit fbd640ac6005004bffb48060c5e57f6e80a2b2e1 Author: sireeveslbl Date: Thu Aug 9 16:05:38 2018 -0700 Solution is a little off at the physical boundary. Need to fix before moving on. Tests/LinearSolvers/EBConvergenceTest/Make.package Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H Tests/LinearSolvers/EBConvergenceTest/RHS.F90 Tests/LinearSolvers/EBConvergenceTest/acoef.F90 Tests/LinearSolvers/EBConvergenceTest/bcoef.F90 commit 5d7796d017b32a33bff93968c5bc17b9b7583734 Author: Weiqun Zhang Date: Thu Aug 9 16:00:56 2018 -0700 EB solvability Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7bc7628df20629309d72e1fd60fe3ac6e40e5db9 Author: sireeveslbl Date: Thu Aug 9 08:32:06 2018 -0700 Corrected Convergence script, and Octave scprit. 3D constant coefficient shows 2nd Order convergence. Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot3D.m commit 54f7bf7cf3aeca9824973d2fe416b2816906c354 Author: sireeveslbl Date: Wed Aug 8 19:34:41 2018 -0700 Still ironing out some bugs. Looks like the analytic solution isn't being generated correctly for the error calculation in 3D test case. Tests/LinearSolvers/EBConvergenceTest/BC.F90 Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/RHS_2D.F90 Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot3D.m Tests/LinearSolvers/EBConvergenceTest/Results/mfread2.m Tests/LinearSolvers/EBConvergenceTest/Results/mfread3.m commit 7e7381359b61b50616103f769be0d95141ff3ed0 Merge: 1966cb81f d771bcf5d Author: Andrew Myers Date: Wed Aug 8 16:13:12 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1966cb81fab9f7360c7c6ec5a5913f6b423f8cab Author: Andrew Myers Date: Wed Aug 8 16:13:03 2018 -0700 update these function names Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/main.cpp commit d771bcf5d9d319b210a7e0c1f1355e185f913695 Author: Weiqun Zhang Date: Wed Aug 8 16:11:20 2018 -0700 update documentation Docs/sphinx_documentation/source/IO.rst commit 9526d97f230c40b52527c5793cf559ad00a66cfd Author: Andrew Myers Date: Wed Aug 8 15:39:22 2018 -0700 reverse the order of the IOBuffer and fstream variables. Src/Base/AMReX_NFiles.H Src/Base/AMReX_PlotFileUtil.cpp Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_TracerParticles.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 96fea6ac2a01a49cdf7fb5a2712ce15efad34b90 Author: Kevin Gott Date: Wed Aug 8 17:48:41 2018 -0400 MultiFab to iMultiFab + Deviceifying BaseFab functions Src/Base/AMReX_BaseFab.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/inputs commit be2456344bfdbcc44f45aaa9766dd4f634afc255 Author: Kevin Gott Date: Wed Aug 8 14:39:24 2018 -0400 Added simple overall timer and option to output error at each step. Tutorials/GPU/ElectromagneticPIC/main.cpp commit 898b21240eecd7531d4c1235668f446487e9f408 Author: Weiqun Zhang Date: Wed Aug 8 11:08:09 2018 -0700 call pubsetbuf before fstream is opened, otherwise it has no effect for some compilers Docs/Readme.sphinx Docs/sphinx_documentation/source/IO.rst Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit a1e5ed9ca90963776b6855b43cbd002036296aef Author: Kevin Gott Date: Wed Aug 8 13:30:53 2018 -0400 Convert emPIC to use BaseFab Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp commit eae40da887b44424aa4fd0d9bc6168b64217a465 Author: sireeveslbl Date: Tue Aug 7 22:08:27 2018 -0700 3D MyTest now produces results that visually look like the analytical solution. Fixed MultiFabToMatlab 3D so now the binary files aren't garbage. Updated Bash script so user can specify spacedim of test. Todo - Matlab/Octave script for 3D scaling plot. Tests/LinearSolvers/EBConvergenceTest/BC_3D.F90 Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh Tools/Postprocessing/C_Src/MultiFabToMatLab.cpp commit 333ae3f3541bccd0df9d29ba8a8e28fc4318baad Author: sireeveslbl Date: Tue Aug 7 16:12:38 2018 -0700 Working on 3D Problem. There are some kinks to work out still. Tests/LinearSolvers/EBConvergenceTest/BC_2D.F90 Tests/LinearSolvers/EBConvergenceTest/BC_3D.F90 Tests/LinearSolvers/EBConvergenceTest/Make.package Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H Tests/LinearSolvers/EBConvergenceTest/RHS.F90 commit 2c21c72d18e98a7d1d3cd7426edf67b0a38d85fc Author: Kevin Gott Date: Tue Aug 7 18:21:41 2018 -0400 DeviceBox and DeviceDomain replaced with standard AMReX objects. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/summit.sh Tutorials/GPU/ElectromagneticPIC/summitdev.sh commit 085a9932f10a0c02cbd5d6965baa7069885db850 Merge: 8aeb67004 b4ed7b196 Author: Ann Almgren Date: Tue Aug 7 14:08:46 2018 -0700 Merge branch 'master' into development commit b4ed7b196f9b6ba0dda353e73a6f7612bdd6c7c6 Author: Ann Almgren Date: Tue Aug 7 13:41:41 2018 -0700 We have added a new flag -- system::regtest_reduction -- that controls whether or not we use the OpenMP reduction. In AMReX_MultiFab we have replaced "pragma omp parallel reduction(+:sm)" by "pragma omp parallel if (!system::regtest_reduction) reduction(+:sm)" so that if you set system.regtest_reduction = 1 in your inputs file (or command line), you will not see the OpenMP-related variability in MultiFab sum and norm1. You can also use this in your application code. Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_MultiFab.cpp commit 2ca5c5aa1e033a5190e0dc25f136d3364b60af9a Author: sireeveslbl Date: Mon Aug 6 16:18:53 2018 -0700 Convergence test for 2D constant coefficient successfully illustrates second order convergence. Convergence_Data_Gen.sh is a script that generates the EB solution for 32X32 to 1024x1024 grids. In the Results folder, there is an octave script that generates a scaling plot and saves it as a .png for later viewing. Tests/LinearSolvers/EBConvergenceTest/BC.F90 Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh Tests/LinearSolvers/EBConvergenceTest/RHS_2D.F90 Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot2D.m Tests/LinearSolvers/EBConvergenceTest/Results/mfread.m Tests/LinearSolvers/EBConvergenceTest/inputs commit 8aeb67004327c0662229bc81c70da67a7d5eac6d Author: Andrew Myers Date: Mon Aug 6 15:28:15 2018 -0700 fix typo in assert Src/Base/AMReX_Geometry.cpp commit a51af5058c800e77804a065318f7c9dce78a440d Author: Kevin Gott Date: Mon Aug 6 14:39:16 2018 -0400 Corrected run script for summitdev, different version for summit. Tutorials/GPU/ElectromagneticPIC/summit.sh Tutorials/GPU/ElectromagneticPIC/summitdev.sh commit ad69f1499d5a4bcef9f779f85e7aadd223a8793e Author: Andrew Myers Date: Mon Aug 6 09:59:52 2018 -0700 if there is no information about the particle box array in the checkpoint file (true for old checkpoints), assume dual_grid = false. Src/Particle/AMReX_ParticleContainerI.H commit 023bbeb6873ac9dbc21423ebd991bb4870b31408 Merge: a8fdedc53 6ba44195c Author: Andrew Myers Date: Mon Aug 6 10:00:01 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a8fdedc538dcc0eb86848c397a554c59ecc381f4 Author: Andrew Myers Date: Mon Aug 6 09:59:52 2018 -0700 if there is no information about the particle box array in the checkpoint file (true for old checkpoints), assume dual_grid = false. Src/Particle/AMReX_ParticleContainerI.H commit 1381ae45a0f532a9e48794b1dc5c48c3d4ad1c91 Author: sireeveslbl Date: Mon Aug 6 09:10:03 2018 -0700 The BCs appear to be fixed. Tests/LinearSolvers/EBConvergenceTest/BC.F90 Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp commit f7dc10b7888679d9d36b7a236dc18f7787da2c6a Author: sireeveslbl Date: Sun Aug 5 20:23:45 2018 -0700 Seems to be correct, but odd error for small n_cell. Need to find the answer to this problem. Tests/LinearSolvers/EBConvergenceTest/BC.F90 Tests/LinearSolvers/EBConvergenceTest/Make.package Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H commit 6ba44195ced11fab5632638a712a8988ab964b85 Merge: 3e916d54c ba844dbd6 Author: Weiqun Zhang Date: Sat Aug 4 09:31:02 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3e916d54cbfdc7dc5d3c2c5a817c45ee316ba87a Author: Weiqun Zhang Date: Sat Aug 4 09:30:49 2018 -0700 make sure MLMG works when AMREX_USE_EB is defined but EB indexspace is not defined Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit ba844dbd667fd8642f7aa7a2e4e69f1dbb709551 Merge: 448ed444f 66aecd3d9 Author: Tan Nguyen Date: Sat Aug 4 02:06:27 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 448ed444f97fe611ef87a070c32919eadce3af65 Author: Tan Nguyen Date: Sat Aug 4 02:06:02 2018 -0700 upcxx backend Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_upc++/Barrier.H Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/LocalConnection.H Src/AmrTask/rts_impls/Perilla_upc++/Make.package Src/AmrTask/rts_impls/Perilla_upc++/Makefile Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.H Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla.H Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/AmrTask/rts_impls/Perilla_upc++/PerillaConfig.H Src/AmrTask/rts_impls/Perilla_upc++/PerillaRts.H Src/AmrTask/rts_impls/Perilla_upc++/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.H Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla_upc++/RemoteConnection.H Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.H Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla_upc++/mylock.h Src/AmrTask/rts_impls/Perilla_upc++/perilla.mak commit 623b935ae8584a556e57e94c89469a9dfffe69e9 Author: Andrew Myers Date: Fri Aug 3 14:30:41 2018 -0700 streamline particle restart when dual-grid is enabled. Src/Particle/AMReX_ParticleContainerI.H commit 66aecd3d90e4139db2d9e25732dfb5274e8cbbba Author: Andrew Myers Date: Fri Aug 3 17:26:17 2018 -0700 remove a debug print. Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit e31ae6bddf17c3db86a9b8bfda44e0a462c18a22 Author: Andrew Myers Date: Fri Aug 3 17:13:13 2018 -0700 add a bunch of debugging functions to the CellSortedPC Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 91677b5a9f3f2d1cdfbe53b5c263c1e71642ea2b Author: Andrew Myers Date: Fri Aug 3 14:45:52 2018 -0700 fix parameter shadowing Src/Particle/AMReX_ParticleContainerI.H commit d80152c510c19b08af9c87b78b10d1f40b30fa1d Merge: 964cde61a a3150ebc2 Author: Andrew Myers Date: Fri Aug 3 14:33:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 964cde61a2155e45bb0e98f3dd465522f74249e4 Author: Andrew Myers Date: Fri Aug 3 14:33:38 2018 -0700 some work on enabling caching of the cell vectors for the DSMC code Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Particles/CellSortedParticles/main.cpp commit a3150ebc2ca6defa45d92715a4fea7e5d23a4705 Author: Andrew Myers Date: Fri Aug 3 14:30:41 2018 -0700 streamline particle restart when dual-grid is enabled. Src/Particle/AMReX_ParticleContainerI.H commit 96b0e13760aa043fc3aa24a6c2b7fa8b6202a035 Author: Kevin Gott Date: Fri Aug 3 09:49:16 2018 -0400 emPIC working on Summitdev w one rank. Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Device.cpp Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/GNUmakefile Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC/script.nompi.sh Tutorials/GPU/ElectromagneticPIC/script.sh commit bdd98934e52bc425b3a4b2966af6363c0b0b8cbf Author: sireeveslbl Date: Thu Aug 2 11:09:18 2018 -0700 added inputs Tests/LinearSolvers/EBConvergenceTest/inputs commit 50d3a4017a4a09a6f0cc876e40c10a6dc0765bab Author: Weiqun Zhang Date: Wed Aug 1 18:16:15 2018 -0700 WIP: PETScABecLap Src/Extern/PETSc/AMReX_PETSc.cpp commit 4b46a85a7299892785a6c81d573bc114f419743c Author: Weiqun Zhang Date: Wed Aug 1 16:56:21 2018 -0700 WIP: PETScABecLap Src/Extern/HYPRE/Make.package Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/Extern/PETSc/Make.package commit 12cfbf4d1aaf371c61592e6db87acd3d0d813489 Author: Andrew Myers Date: Wed Aug 1 19:26:11 2018 -0400 some reorganization Src/Particle/AMReX_RedistributeStrategy.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Source/Particles.H commit 87d8a087a4755252a94a6b864bdc8fcd3d388aec Merge: 83b848e56 2296e58b0 Author: Andrew Myers Date: Wed Aug 1 15:53:55 2018 -0700 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 83b848e560f9750e1ce88cbd51f72afa867b3324 Author: Andrew Myers Date: Wed Aug 1 15:49:29 2018 -0700 fix compilation problem on Travis build Src/Particle/AMReX_RedistributeStrategy.H Src/Particle/AMReX_RedistributeStrategyCPU.cpp Src/Particle/AMReX_RedistributeStrategyGPU.cpp Src/Particle/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp commit fcc76e32db54098b2d5429e4fa26c4de4af26393 Author: Marc Day Date: Wed Aug 1 14:18:43 2018 -0700 Make sure define is called when reading a coordsys Src/Base/AMReX_CoordSys.cpp commit a817ab604c4194200facb4cd5cc95e34e049112a Author: Ann Almgren Date: Wed Aug 1 14:29:35 2018 -0700 Add the MLMG path to the new files added to CMakeLists.txt which are only included if ENABLE_EB is on. Src/LinearSolvers/CMakeLists.txt commit 9016683614915cd804cc566b1b69c23f1baf97ea Author: Marc Day Date: Wed Aug 1 14:18:43 2018 -0700 Make sure define is called when reading a coordsys Src/Base/AMReX_CoordSys.cpp commit f02a1fc3f0b638220c3a2ebc94b3a717e07294be Author: Weiqun Zhang Date: Wed Aug 1 13:07:34 2018 -0700 add Make.petsc Tools/GNUMake/packages/Make.petsc commit 722241e1e7f72f96194fd990c56691f316bf25ef Merge: 1068a7da5 9ac3da07b Author: Weiqun Zhang Date: Wed Aug 1 13:03:53 2018 -0700 Merge branch 'development' into petsc commit 2296e58b088827667bc54ff7c3519cb57b8d5068 Merge: 42f9fbd50 7854d354d Author: Andrew Myers Date: Wed Aug 1 12:51:00 2018 -0700 Merge pull request #295 from ylunalin/gpu Added collapse clause to acc directives on the triple do loops. commit 9ac3da07b0e4b9dd7ff23b7f3497a8dfb67a278b Author: Weiqun Zhang Date: Wed Aug 1 12:18:15 2018 -0700 minor optimization: use mfi instead of int index Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 7854d354dfe8ff8a0ef504a59ec4209efb500d4c Author: Luna Lin Date: Wed Aug 1 15:14:05 2018 -0400 Added collapse clause to acc directives on the triple do loops. Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 commit ef02ea30568a89a716cf48de74eed1516996b2dd Author: Weiqun Zhang Date: Wed Aug 1 11:14:49 2018 -0700 MLMG: for multiple components, we only need to to do one allreduce Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 57c664b21a28c8549e84c1cc0164e2a59e340e88 Merge: 1a6826139 2c344fa6d Author: Weiqun Zhang Date: Wed Aug 1 11:01:51 2018 -0700 Merge branch 'development' into hypre commit 2c344fa6dd98aa9acf2e744983b24e4d14357a80 Author: Weiqun Zhang Date: Wed Aug 1 11:00:23 2018 -0700 update CHANGES CHANGES commit 8e4c6dbd8605d2a47d43433a105d541fd0a0aa14 Author: Weiqun Zhang Date: Tue Jul 31 23:18:25 2018 -0700 reimplement LayoutData copy ctor and assignment op Src/Base/AMReX_LayoutData.H commit 1a68261392069580c321bd0df047800ba8d660a4 Author: Weiqun Zhang Date: Tue Jul 31 21:34:20 2018 -0700 add boomeramg parameters Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp commit 10764c6c00bf0e1bda32dd0e48db11a06e904302 Author: Weiqun Zhang Date: Tue Jul 31 21:31:08 2018 -0700 clean up Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 914dc018f9e38fc514082af6ddf47af79346090e Author: Weiqun Zhang Date: Tue Jul 31 18:24:15 2018 -0700 remove bd key from LayoutData Src/Base/AMReX_LayoutData.H commit 42f9fbd50d8a0e7f4135bfef6d8ba6ec58d94db5 Author: Andrew Myers Date: Tue Jul 31 20:20:52 2018 -0400 put shared code into a Source directory Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Constants.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/main.cpp Tutorials/Particles/ElectromagneticPIC/Make.EMPIC Tutorials/Particles/ElectromagneticPIC/Source/Constants.H Tutorials/Particles/ElectromagneticPIC/Source/IO.H Tutorials/Particles/ElectromagneticPIC/Source/IO.cpp Tutorials/Particles/ElectromagneticPIC/Source/Make.package Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Source/Particles.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 86899895521a018893a97ade12954241395db9ff Author: Andrew Myers Date: Tue Jul 31 19:53:50 2018 -0400 move the Cuda and OpenACC problem directories into Exec Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Constants.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/IO.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/IO.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/main.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Constants.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/main.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh commit 78151857c38412c67439be1930ec178a3846866c Author: Andrew Myers Date: Tue Jul 31 19:49:01 2018 -0400 some slight renaming Tutorials/Particles/ElectromagneticPIC/Cuda/Constants.H Tutorials/Particles/ElectromagneticPIC/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Cuda/IO.H Tutorials/Particles/ElectromagneticPIC/Cuda/IO.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Cuda/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Cuda/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/Particles.H Tutorials/Particles/ElectromagneticPIC/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Cuda/main.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/script.sh Tutorials/Particles/ElectromagneticPIC/OpenACC/Constants.H Tutorials/Particles/ElectromagneticPIC/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/OpenACC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/OpenACC/IO.H Tutorials/Particles/ElectromagneticPIC/OpenACC/IO.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/OpenACC/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/OpenACC/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/Particles.H Tutorials/Particles/ElectromagneticPIC/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/OpenACC/inputs Tutorials/Particles/ElectromagneticPIC/OpenACC/main.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/script.sh commit 5957a23185e0eca03a0084477b256259911e7084 Author: Andrew Myers Date: Tue Jul 31 19:45:16 2018 -0400 remove the original directory Tutorials/Particles/ElectromagneticPIC/orig/Constants.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/orig/Evolve.H Tutorials/Particles/ElectromagneticPIC/orig/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/orig/GNUmakefile Tutorials/Particles/ElectromagneticPIC/orig/IO.H Tutorials/Particles/ElectromagneticPIC/orig/IO.cpp Tutorials/Particles/ElectromagneticPIC/orig/Make.package Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/orig/Particles.H Tutorials/Particles/ElectromagneticPIC/orig/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/orig/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/orig/inputs Tutorials/Particles/ElectromagneticPIC/orig/main.cpp Tutorials/Particles/ElectromagneticPIC/orig/script.sh commit 1f1ac5cceb4edf074736dc87f41d5bd3856b2aa5 Author: Andrew Myers Date: Tue Jul 31 19:44:37 2018 -0400 finish off the merge between my stuff and Luna's Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.cpp commit 74667c7d8ca2f0a899e0dd2d4da4e5ad346c92bf Merge: be215feeb 70a2b8266 Author: Andrew Myers Date: Tue Jul 31 19:19:55 2018 -0400 merging gpu_particles_refactor into gpu commit be215feebb73660e761890906b762bd67ac8e381 Merge: a3e009611 73cce6faa Author: Andrew Myers Date: Tue Jul 31 16:11:18 2018 -0700 Merge pull request #294 from ylunalin/gpu Try again to merge new GPU particles EMPIC tutorial in. commit 73cce6faad2ddb5e6e49c586495b92d9b6e9abc3 Author: Luna Lin Date: Tue Jul 31 18:40:51 2018 -0400 Fixed the fortran subroutine name binding issue. Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/acc/inputs Tutorials/Particles/ElectromagneticPIC/orig/inputs commit 70a2b826616d01719812f444eeffb00c6fc31888 Author: Andrew Myers Date: Tue Jul 31 17:59:07 2018 -0400 move the GPU particle redistribute code into Src/Particle Src/Particle/AMReX_RedistributeStrategy.H Src/Particle/AMReX_RedistributeStrategyCPU.cpp Src/Particle/AMReX_RedistributeStrategyGPU.cpp Src/Particle/Make.package Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Make.package commit 02abaf3ec71b43da2184f2068b9cd7d154903cd6 Author: Weiqun Zhang Date: Tue Jul 31 14:32:46 2018 -0700 Remove deprecated Tutorial. We now use hypre through MLMG. Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tutorials/HYPRE/ABecLaplacian/ABL.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp Tutorials/HYPRE/ABecLaplacian/ABL_F.F90 Tutorials/HYPRE/ABecLaplacian/ABL_F.H Tutorials/HYPRE/ABecLaplacian/GNUmakefile Tutorials/HYPRE/ABecLaplacian/Make.package Tutorials/HYPRE/ABecLaplacian/inputs Tutorials/HYPRE/ABecLaplacian/main.cpp commit 579122c4c5ae95667754e9c038ea22c8b4a179cb Author: Andrew Myers Date: Tue Jul 31 14:24:18 2018 -0700 use pair index to store particles tiles even when using the GPU Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategy.H Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyCPU.cpp Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyGPU.cpp Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp commit a3e00961169ade69f4b887260abcc82eb09db809 Author: Max Katz Date: Tue Jul 31 17:19:49 2018 -0400 Fix a typo in the IBM makefile Tools/GNUMake/comps/ibm.mak commit 49edffef30469939d026363342b389300d0845f3 Author: Andrew Myers Date: Tue Jul 31 14:10:19 2018 -0700 seperate out the implementation strategy of Redistribute from the ParticleContainer code Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategy.H Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyCPU.cpp Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyGPU.cpp Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Make.package commit 6ff8e87e3419ffe6cab6e7f0eedd92601af965ee Author: sireeveslbl Date: Tue Jul 31 13:48:17 2018 -0700 Testing MultiFab to MatLab converter Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/MultiFabToMatLab.cpp commit ecfc630070d76ac6401472f61cff904b3c9436bb Author: Weiqun Zhang Date: Tue Jul 31 13:35:14 2018 -0700 fix memory leak in HypreABecLap Src/Extern/HYPRE/AMReX_HypreABecLap.cpp commit c283698c519ec51ba367f29c12053e082791222f Author: Weiqun Zhang Date: Tue Jul 31 13:19:29 2018 -0700 HypreABecLap2: avoid memory leak due to hypre bug. Because HypreABecLap memory leak is not fixed yet, switch to HypreABecLap2 in MLMG Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H commit cb6238e86aa2037f1ef1b361e4d785e820fa3544 Author: Max Katz Date: Tue Jul 31 15:15:58 2018 -0400 Make defines consistent Src/Base/AMReX_filcc_mod.F90 commit de30817c36c902d993a779c3800f12b0e53a486d Author: Max Katz Date: Tue Jul 31 15:02:58 2018 -0400 Use unmodified C++ defines for the CUDA script We always use g++ for host compiling when USE_CUDA=TRUE, so we want to use the -D defines, not the -WF defines when COMP=IBM. Tools/GNUMake/Make.rules commit b4fbf94f9048137260d2a52942538468f6adc41d Author: Weiqun Zhang Date: Tue Jul 31 11:14:03 2018 -0700 normalize matrix for regular hypre too Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 64062c4d9a62e9a682a593ff25eff62f26cefaae Author: Luna Lin Date: Tue Jul 31 09:35:53 2018 -0700 Strip trailing whitespaces in cuda/ and orig/. Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/cuda/IO.H Tutorials/Particles/ElectromagneticPIC/cuda/IO.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Make.package Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Particles.H Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/cuda/main.cpp Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/orig/Evolve.H Tutorials/Particles/ElectromagneticPIC/orig/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/orig/IO.H Tutorials/Particles/ElectromagneticPIC/orig/IO.cpp Tutorials/Particles/ElectromagneticPIC/orig/Make.package Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/orig/Particles.H Tutorials/Particles/ElectromagneticPIC/orig/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/orig/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/orig/main.cpp commit ef58fd6eb506c705b82870d17e34859eabe4c8e7 Author: Luna Lin Date: Tue Jul 31 09:32:27 2018 -0700 Convert push_electric(magnetic)_field_x(y,z) subroutine to OpenACC version. Strip whitesopaces in acc/. Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/acc/Evolve.H Tutorials/Particles/ElectromagneticPIC/acc/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/acc/IO.H Tutorials/Particles/ElectromagneticPIC/acc/IO.cpp Tutorials/Particles/ElectromagneticPIC/acc/Make.package Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/acc/Particles.H Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/acc/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/acc/main.cpp commit def166e8b336eb9ffab71c66efc13713ac2705fc Author: Luna Lin Date: Tue Jul 31 08:23:24 2018 -0700 Convert to AMREX_FORT_LAUNCH_PARTICLES functions to OpenACC. Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/acc/em_pic_F.H commit 5c03b1b6c2f6110d4f6325bae51a35c92e13b0fe Author: Weiqun Zhang Date: Mon Jul 30 17:51:06 2018 -0700 refactor hypre classes to reuse the solver for different x and b Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit b4c7ca0c34dab82cb3c518ede18a3aed65cd8f0e Merge: e569b364f e2f4d716f Author: Andrew Myers Date: Mon Jul 30 19:45:02 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit e569b364fcf004ba0521af50a2fd485484e09cab Merge: 94744c8be 357976971 Author: Andrew Myers Date: Mon Jul 30 19:42:00 2018 -0400 fixing merge conflict commit 357976971ecdeb5203cdaa7b1e45320438578855 Author: Max Katz Date: Mon Jul 30 19:32:52 2018 -0400 Need to add source to INCLUDE_LOCATIONS Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX2_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile commit a3ff68ef45b897bc88c018033e3e7d3a38e904f5 Merge: 8f05fe8f4 e2f4d716f Author: Luna Lin Date: Mon Jul 30 19:27:33 2018 -0400 Merge remote-tracking branch 'upstream/gpu' into gpu commit e2f4d716fe5eea7d1b126d688a3317484ba2d99f Author: Max Katz Date: Mon Jul 30 19:18:50 2018 -0400 These flags only belong on Fortran Tools/GNUMake/comps/ibm.mak commit ec15cc9bd5f272f5086f70566963a05fd1cfa3f6 Merge: 2e74b893e d9733c039 Author: sireeveslbl Date: Mon Jul 30 15:33:41 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg commit 2e74b893ea482f80c44a6d5901b3a9f31cc17fd6 Author: sireeveslbl Date: Mon Jul 30 15:33:21 2018 -0700 MLMG to generate solution for testing convergence of EB solver. Going to change PlotFile->matlab to use multifabs to illustrate convergence. The RHS is for the function phi = (x-1/2)/sqrt((x-1/2)^2+(y-1/2)^2), and should be used with the sphere geometry in 2D only, with location 1/2,1/2 and radius 0.25. Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBConvergenceTest/Make.package Tests/LinearSolvers/EBConvergenceTest/MyEB.H Tests/LinearSolvers/EBConvergenceTest/MyTest.H Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H Tests/LinearSolvers/EBConvergenceTest/RHS_2D.F90 Tests/LinearSolvers/EBConvergenceTest/initEB.cpp Tests/LinearSolvers/EBConvergenceTest/inputs Tests/LinearSolvers/EBConvergenceTest/main.cpp commit 8f05fe8f44265660134573ada5d1d8223efabbfd Author: Luna Lin Date: Mon Jul 30 17:03:10 2018 -0400 Added OpenACC only version of the tutorial. Tutorials/Particles/ElectromagneticPIC/acc/Constants.H Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/acc/Evolve.H Tutorials/Particles/ElectromagneticPIC/acc/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/acc/GNUmakefile Tutorials/Particles/ElectromagneticPIC/acc/IO.H Tutorials/Particles/ElectromagneticPIC/acc/IO.cpp Tutorials/Particles/ElectromagneticPIC/acc/Make.package Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/acc/Particles.H Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/acc/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/acc/inputs Tutorials/Particles/ElectromagneticPIC/acc/main.cpp Tutorials/Particles/ElectromagneticPIC/acc/script.sh commit 94744c8beb6e98aa4e04b7768e701314b166aee0 Author: Andrew Myers Date: Mon Jul 30 16:22:19 2018 -0400 wrap these thrust things in AMREX_USE_CUDA Src/Particle/AMReX_StructOfArrays.H commit b723354e84fccaba0de461a977f0a702092f1894 Author: Luna Lin Date: Mon Jul 30 15:43:27 2018 -0400 Fixed a few AMREX_USE_CUDA left behind. Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_3d.F90 commit 43848e1a9e36680d2545ef98b1bd6f2d2889c659 Author: Luna Lin Date: Mon Jul 30 14:55:31 2018 -0400 Moved tutorial files to orig/ subdirectory, create cuda/ subdir, and separate out only cuda enabled codes into it. Tutorials/Particles/ElectromagneticPIC/cuda/Constants.H Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/cuda/IO.H Tutorials/Particles/ElectromagneticPIC/cuda/IO.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Make.package Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Particles.H Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/cuda/inputs Tutorials/Particles/ElectromagneticPIC/cuda/main.cpp Tutorials/Particles/ElectromagneticPIC/cuda/script.sh Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/orig/Constants.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/orig/Evolve.H Tutorials/Particles/ElectromagneticPIC/orig/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/orig/GNUmakefile Tutorials/Particles/ElectromagneticPIC/orig/IO.H Tutorials/Particles/ElectromagneticPIC/orig/IO.cpp Tutorials/Particles/ElectromagneticPIC/orig/Make.package Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/orig/Particles.H Tutorials/Particles/ElectromagneticPIC/orig/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/orig/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/orig/inputs Tutorials/Particles/ElectromagneticPIC/orig/main.cpp Tutorials/Particles/ElectromagneticPIC/orig/script.sh commit d9733c03901bd787aa123d4cb10e2c1a0e302e33 Merge: 47d2ac1f1 1b16867da Author: Weiqun Zhang Date: Sun Jul 29 21:32:28 2018 -0700 Merge branch 'development' into hypre commit 47d2ac1f1a57c2f971c64f5e860921545541bd73 Author: Weiqun Zhang Date: Sun Jul 29 21:23:06 2018 -0700 minor change to get rid of a compiler warning Src/EB2/AMReX_EB2_IF_Rotation.H commit 0c3bfc387db21629c0fb2ed14775a8a87a319f22 Author: Weiqun Zhang Date: Sat Jul 28 18:24:08 2018 -0700 normalize matrix for hypre Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit ef0dfe3d7d42abb2e90751f93216702b32ef92dc Author: Kevin Gott Date: Sat Jul 28 04:46:20 2018 -0400 Test program update. Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/run.script commit 2a4c6984e2efee168167b3c1f2b7587c38b75738 Author: Kevin Gott Date: Sat Jul 28 04:45:52 2018 -0400 ElectromagneticPIC, Lamdba version. Work breakdown needs debugging. Tutorials/GPU/ElectromagneticPIC/Constants.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.H Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/GNUmakefile Tutorials/GPU/ElectromagneticPIC/IO.H Tutorials/GPU/ElectromagneticPIC/IO.cpp Tutorials/GPU/ElectromagneticPIC/Make.package Tutorials/GPU/ElectromagneticPIC/NodalFlags.H Tutorials/GPU/ElectromagneticPIC/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC/Particles.H Tutorials/GPU/ElectromagneticPIC/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC/em_pic_F.H Tutorials/GPU/ElectromagneticPIC/inputs Tutorials/GPU/ElectromagneticPIC/main.cpp Tutorials/GPU/ElectromagneticPIC/script.sh Tutorials/GPU/ElectromagneticPIC/test.cpp commit 2673ea4425d1591281b450ecc3494d0d11dae1c7 Author: Kevin Gott Date: Sat Jul 28 04:42:57 2018 -0400 ElectromagneticPIC function version. Conversion in progress. Need Particles wrapper for GPUs. Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Particles.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/script.sh commit 8e77d2188a1b4a3b4fa98f594664baf3c4a45142 Author: Kevin Gott Date: Sat Jul 28 04:38:00 2018 -0400 Adjustments for ElectromagneticPIC. Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H commit 0e431a0241a4265a986a0fd8eeb65874e4cedfaa Author: Weiqun Zhang Date: Fri Jul 27 21:16:49 2018 -0700 bug fix in eb apply bc Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 commit e5318c77aed8f5e050b9ba9e405baf210c5f8823 Author: Weiqun Zhang Date: Fri Jul 27 18:36:39 2018 -0700 2d high order Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit ba155e9aed09feaba8a60b511f813292f1c5e315 Author: Weiqun Zhang Date: Fri Jul 27 18:32:08 2018 -0700 change the parameter of two spheres so that it doesn't have multi-cuts in 3d Tests/LinearSolvers/CellEB/initEB.cpp Tests/LinearSolvers/CellEB/inputs commit 2c5486753e5c2fa3f9e5d5c338ed173687314b1f Author: Weiqun Zhang Date: Fri Jul 27 18:31:34 2018 -0700 high order bc Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 1b16867daf4f8fd7a4e1ac3a740375c5e38cfd01 Author: Andrew Myers Date: Fri Jul 27 17:25:00 2018 -0700 remove these functions for getting all particle data on a single proc - these are inefficient and not needed. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 5646bd2664540c1403a5e4c1be450e8b70657ee7 Author: Andrew Myers Date: Fri Jul 27 16:52:52 2018 -0700 also provide interfaces to get the particle id and cpu number when initializing particles from Fortran Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_2d.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_3d.f90 commit e90f936dacd94ff874c34555e717f318de41e3ec Author: Weiqun Zhang Date: Fri Jul 27 16:52:22 2018 -0700 eb apply bc Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/Make.package commit c632af7140508f04f7a5652f44abf4f1b9fc9760 Author: Andrew Myers Date: Fri Jul 27 16:38:41 2018 -0700 remove deprecated particle initialization style from the F_Interfaces Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit dc98da8edac41776802adf1afb8267531d59da26 Author: Andrew Myers Date: Fri Jul 27 16:33:33 2018 -0700 add new wrappers to the F_Interfaces and set the Advection_F Tutorial to use them Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_2d.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_3d.f90 Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 commit fb2b4b2160703145540687e44e57210708fc573f Author: Weiqun Zhang Date: Thu Jul 26 18:39:22 2018 -0700 fix bug Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit 76bbf24ac49a095eab5f15537b937280df2ab2b8 Merge: 6833294e4 dab364ead Author: Andrew Myers Date: Thu Jul 26 20:52:43 2018 -0400 Merge branch 'development' into gpu commit 6833294e45fde8b4a7c9f9426905490d68155d85 Merge: c6f222489 eb38d8cd7 Author: Andrew Myers Date: Thu Jul 26 20:52:03 2018 -0400 merging development into gpu commit dab364ead6bcdbce73b8636b29078ca0f945385f Author: Andrew Myers Date: Thu Jul 26 17:50:23 2018 -0700 removed unused variable Src/Particle/AMReX_ParticleContainerI.H commit eb38d8cd75b98b3fb061fbcfaf1514d7b4c1c4ee Merge: 691bb57c7 f9cf22539 Author: Andrew Myers Date: Thu Jul 26 17:42:03 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 691bb57c70239c0022490faa1a214f63fc82b2f1 Author: Andrew Myers Date: Thu Jul 26 17:41:51 2018 -0700 rename these functions to reflect the fact that there are no longer C++ and Fortran versions. Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit fe9f51fdaf3aa7bdbb6ec6a076d068c87b9bf620 Author: Andrew Myers Date: Thu Jul 26 17:30:41 2018 -0700 minor. Src/Particle/AMReX_ParticleContainerI.H commit 1bec1218025ee99b20c364f86ddf92e7a6a326f2 Author: Andrew Myers Date: Thu Jul 26 17:26:01 2018 -0700 minor. Src/Particle/AMReX_ParticleContainerI.H commit 0a1ea32c1f5af29d3a85519504bfcf1a17e7257e Author: Weiqun Zhang Date: Thu Jul 26 15:33:07 2018 -0700 tweak gsrb near the intersection of eb and domain boundary Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit aa7f2fa5cdbbc7b7f530423680eb34bd71db1776 Author: Weiqun Zhang Date: Thu Jul 26 12:18:37 2018 -0700 fix corner cases Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit c6f222489a141ca1379074a29efec59fb1519a89 Author: Andrew Myers Date: Thu Jul 26 14:53:36 2018 -0400 put the detail stuff from StructOfArrays into the amrex namespace. Src/Particle/AMReX_StructOfArrays.H commit 7a309aa33a1fe3ec6f7624230c64abf34c01ca1f Author: Andrew Myers Date: Thu Jul 26 14:51:16 2018 -0400 use the IndexSequence stuff Weiqun added to Base instead of rolling my own. Src/Particle/AMReX_StructOfArrays.H commit 72fc56637cb6ad0d6b7eecd8c2512f36287d13b9 Author: Weiqun Zhang Date: Thu Jul 26 10:27:20 2018 -0700 add MLMG::setBottomTolerance Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit 74f6c3bcad387c9f07eb2477fe88a155eb7d5bae Author: Weiqun Zhang Date: Thu Jul 26 10:18:39 2018 -0700 tweak hypre parameter Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit a1ee2335a73f1119f781b217eee5e68d36677e6a Author: Weiqun Zhang Date: Thu Jul 26 09:16:46 2018 -0700 need to cal EB_average_down_faces Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_F.H commit 1b1eebb25b66b7aade34bf4c4d03b54cad0406ef Merge: 5f3c52f94 49c44894d Author: Weiqun Zhang Date: Thu Jul 26 07:59:18 2018 -0700 Merge branch 'hypre' into mlmg commit 49c44894d550fee0d39c0bf390ec1e5b0ea3862a Author: Weiqun Zhang Date: Thu Jul 26 07:58:22 2018 -0700 fix bug Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit e8c2c3051eed089c257368cc95cdcf686bfda4bc Author: Weiqun Zhang Date: Wed Jul 25 16:55:49 2018 -0700 fix bug Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit fbbef653e65754c05453a0aa5d8412d6774a8a4c Author: Weiqun Zhang Date: Wed Jul 25 16:21:30 2018 -0700 for eb, b coefficients must have one ghost Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 73c6daee1bc820e36c519e6d14d1b18d32ff15f1 Author: Weiqun Zhang Date: Wed Jul 25 16:10:31 2018 -0700 ij matrix for 3d eb Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit f9cf22539b7f38a2bec076ca830f747391f4f0c7 Author: Emmanuel Motheau Date: Wed Jul 25 15:36:47 2018 -0700 Exiting properly the AugmentPlotfile tool if we already have divergence and vorticity already computed, and avoiding useless copy-paste of data Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp commit 54262806bb0317128113da335ac13db6d74ed7d2 Merge: 1733a4832 07980a98c Author: Andrew Myers Date: Wed Jul 25 15:04:09 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 77434b2f5a0e843d99663e06dbc5a4dcb1dd3d32 Author: Weiqun Zhang Date: Wed Jul 25 13:59:39 2018 -0700 ij matrix for 3d all_regular eb Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Tests/LinearSolvers/CellEB/inputs commit 1733a48323447c50e04e351ecc80a474e3c69d81 Author: Andrew Myers Date: Wed Jul 25 13:48:42 2018 -0700 optimize the 'remove_if' logic in ParticleContainer::Redistribute() - note that this will affect the order of particles on the tiles and therefore will cause roundoff differences in the tests. Src/Particle/AMReX_ParticleContainerI.H commit 5a1a672d33ec7af1605748a16a91606ba3e7be5d Author: Weiqun Zhang Date: Wed Jul 25 12:41:47 2018 -0700 tweak hypre parameters Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit bb75f0b6f1ee1a2e617b8272f2c4ccda302fcab7 Author: Weiqun Zhang Date: Wed Jul 25 11:34:13 2018 -0700 add rotated box to CellEB test Tests/LinearSolvers/CellEB/initEB.cpp Tests/LinearSolvers/CellEB/inputs commit 44bd85db255cf1b2d9b10f18b1ef84bfd5b4dfa3 Author: Weiqun Zhang Date: Wed Jul 25 10:35:09 2018 -0700 fix typo Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit eef5300a03bae684b9dee1324c81c5597ed63d88 Author: Weiqun Zhang Date: Tue Jul 24 18:34:25 2018 -0700 add linop_maxorder option to CellEB test Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit e0d37c545d590d9ca4c92461cbb524041e068703 Author: Weiqun Zhang Date: Tue Jul 24 17:11:33 2018 -0700 fix bug Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 300404ac2b129ae4a7de72d1336b178b57c4e82c Author: Weiqun Zhang Date: Tue Jul 24 17:00:15 2018 -0700 WIP: ij matrix for 2d eb Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit 07980a98c1bab00faefdc1bb8fe057e1d87dbef4 Author: Weiqun Zhang Date: Tue Jul 24 13:11:34 2018 -0700 move the computation of indexArray and ownerShip to DistributionMapping Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.cpp commit c528454d6efe855a8851b4fa1b18fc1d2c459cc7 Author: Weiqun Zhang Date: Tue Jul 24 12:31:25 2018 -0700 WIP: hypre for eb Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 19ad1649e251836b4aad7b0a1317a2cca60d005d Merge: 2bf04932e bb2d9caaa Author: Andrew Myers Date: Tue Jul 24 12:14:07 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2bf04932e23e378d520f8e3dcb5780a47c06caee Author: Andrew Myers Date: Tue Jul 24 12:13:58 2018 -0700 Allow for the creation of multiple particle container instances when using the Fortran interfaces. Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/amr_data_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit f2bac735a828fd63a2c86aa7c96595931b6a8f54 Merge: e82229495 bb2d9caaa Author: Andrew Myers Date: Mon Jul 23 21:48:24 2018 -0400 Merge branch 'development' into gpu commit bb2d9caaa0dae9954198ac4309df8c41038c958a Author: Andrew Myers Date: Mon Jul 23 21:47:29 2018 -0400 remove unused code from Src/Particle Src/Particle/AMReX_Particles_1D.F Src/Particle/AMReX_Particles_2D.F Src/Particle/AMReX_Particles_3D.F Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit e82229495de8101dc1553a0e6d22053a5ffd1f1c Merge: da7ba920f 59aa1c7d5 Author: Andrew Myers Date: Mon Jul 23 21:44:24 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit da7ba920f9afb3c5677714022d8354f9664a3365 Author: Andrew Myers Date: Mon Jul 23 21:36:20 2018 -0400 move the thrust-aware struct-of-arrays to Particles so it can be reused elsewhere. Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Src/Particle/CMakeLists.txt Src/Particle/Make.package Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Particles.H commit 59aa1c7d52d5ba80ee6849aeafa453d7ea20e3d2 Author: Michael Zingale Date: Mon Jul 23 21:09:16 2018 -0400 remove old function Tools/F_scripts/write_cuda_headers.py commit 7ba1cffe010c775c9d8343eec8128f0521b44f6b Merge: 0247b40a2 a2aa3c63e Author: Andrew Myers Date: Mon Jul 23 21:06:16 2018 -0400 merging development into gpu commit 0247b40a259a0a30954dbabc9ce79dbf67ea0849 Merge: 97fbf785f 001fd5350 Author: Andrew Myers Date: Mon Jul 23 20:44:53 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 97fbf785fa1ec7c6ece0ff8be9bf607c8f255b52 Author: Andrew Myers Date: Mon Jul 23 20:41:03 2018 -0400 install the CudaAllocators Header in Base Src/Base/Make.package commit 5e4bd1355804cdc318cb95cc97d3d5fa8d2a703b Author: Andrew Myers Date: Mon Jul 23 20:35:05 2018 -0400 update Make.packages Src/Base/Make.package Src/Particle/Make.package commit 45ca10670121afafab6a8ad32b2e434a230d8050 Author: Andrew Myers Date: Mon Jul 23 20:34:39 2018 -0400 use the Base version of the CudaManagedAllocator Src/Particle/AMReX_Particles.H commit ffe1ab70cfea689abfac439203d292fce6f9954f Author: Andrew Myers Date: Mon Jul 23 20:29:28 2018 -0400 remove old deposition example Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp commit cf4f6166005cbd5abb46d6546d5e3816b8b843cb Author: Andrew Myers Date: Mon Jul 23 20:28:52 2018 -0400 fix deposition test Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp commit 001fd5350e81882cb2757b121d59af50bd357dde Author: Michael Zingale Date: Mon Jul 23 20:08:36 2018 -0400 find the fortran targets from the C++ pragmas Tools/F_scripts/write_cuda_headers.py commit 8907f2bc7fd88f7612affdd05297d1079bb5add7 Author: Weiqun Zhang Date: Mon Jul 23 16:50:57 2018 -0700 HYPRE_BoomerAMGSetup only needs to be called once Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 0269e6cd655f65efec8caf79920c7d75d2611139 Author: Weiqun Zhang Date: Mon Jul 23 16:31:27 2018 -0700 fix bct and bcl Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 2bb830685108627ed2d4b2224598166038668bfa Author: Andrew Myers Date: Mon Jul 23 19:21:24 2018 -0400 some Array->Vector Src/Particle/AMReX_CudaManagedAllocator.H Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp commit e92b000e7d66506b4c4fbac140899be5b4c92690 Author: Kevin Gott Date: Mon Jul 23 19:19:19 2018 -0400 HeatEq1 uses standard functions. HeatEq0 uses lambda launchers. Tutorials/GPU/HeatEquation_EX0_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX0_C/Exec/run.nocuda.script Tutorials/GPU/HeatEquation_EX0_C/Exec/run.script Tutorials/GPU/HeatEquation_EX0_C/Source/Make.package Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX0_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX0_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX0_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX0_C/Source/myfunc_F.H commit 8d160d5800f477b4b9c2d367d64b8142364ff8ea Author: Kevin Gott Date: Mon Jul 23 19:11:58 2018 -0400 Done playing with lambdas in HeatEq1. Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H commit 90a2d71859c9fe0ad246041c658db39e80f30326 Author: Weiqun Zhang Date: Mon Jul 23 15:54:24 2018 -0700 2d ij matrix Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit 5f3c52f946609aba512ade99226d79e3e6c78a7c Author: sireeveslbl Date: Mon Jul 23 14:36:51 2018 -0700 EB Avgdown faces works in 2D and 3D Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit f85f8c9de400735cd5e25fab932812b1829229a0 Author: Weiqun Zhang Date: Mon Jul 23 13:41:13 2018 -0700 clean up Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 1114d53447c9418ef8f18be0dedd15a370949c73 Author: Andrew Myers Date: Mon Jul 23 16:37:31 2018 -0400 move the cuda allocator for std::vector into Base so that it may be re-used (not really particle specific) Src/Base/AMReX_CudaAllocators.H Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H commit 64717ba3f443166f7c24cc0d7c4e808c7af383a5 Author: Weiqun Zhang Date: Mon Jul 23 13:33:58 2018 -0700 fix more bugs Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 2ae8ec3fae6796b37d9f54868c6b05a2389b730d Author: Kevin Gott Date: Mon Jul 23 16:27:38 2018 -0400 1st version of Lambda kernel wrappers. May want to rename later. Src/Base/AMReX_Managed.H Tools/GNUMake/comps/nvcc.mak commit e19781312d41fed444294d4c921f7a525d23d99a Author: Weiqun Zhang Date: Mon Jul 23 12:36:14 2018 -0700 bug fixes Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit d96c3d13dcad6014eab6571a5f3ff9cf7455730d Author: Max Katz Date: Mon Jul 23 11:49:28 2018 -0700 Merge particle support into GPU branch (#290) Adds GPU particle support to AMReX, along with several Tutorials. Src/Base/AMReX_BLFort.H Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_Vector.H Src/Particle/AMReX_CudaManagedAllocator.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/Make.package Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp Tests/Particles/ManagedCUDADeposition/GNUmakefile Tests/Particles/ManagedCUDADeposition/Make.package Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/inputs Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp Tests/Particles/StructOfArrays/CudaManagedAllocator.H Tests/Particles/StructOfArrays/GNUmakefile Tests/Particles/StructOfArrays/Make.package Tests/Particles/StructOfArrays/StructOfArrays.H Tests/Particles/StructOfArrays/main.cpp Tools/GNUMake/comps/pgi.mak Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Particles.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/main.cpp Tutorials/Particles/ElectromagneticPIC/script.sh commit dafa1dd927da9cfbb96752de56efd5b1b724823a Author: Weiqun Zhang Date: Mon Jul 23 10:51:19 2018 -0700 WIP: load vectors and get solution Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 5e4fbb846a2b3445a40c17a1726aea3a1f7f2712 Author: Weiqun Zhang Date: Sun Jul 22 18:02:02 2018 -0700 WIP: finish matrix setup Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit b565a7834ae4eeaa17ad55f3be23c75043144af9 Author: Weiqun Zhang Date: Sun Jul 22 08:37:47 2018 -0700 WIP: prepare ij matrix Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit a2aa3c63e3d5b1f21b4772153272cf175f97568e Author: Tan Nguyen Date: Sat Jul 21 23:53:42 2018 -0700 add a routine into Perilla WorkerThread Src/AmrTask/rts_impls/Perilla/WorkerThread.H Src/AmrTask/rts_impls/Perilla_omp/WorkerThread.H commit af16bf2b85ff6a683c6cb66b1aaa6831931d1e6d Author: Tan Nguyen Date: Sat Jul 21 23:34:57 2018 -0700 extend the memory pool to make it compatible with Perilla Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp Src/Base/AMReX_MemPool.cpp commit fcd26442c0986b898f06eebf77866afe4d230b96 Author: Weiqun Zhang Date: Sat Jul 21 21:47:32 2018 -0700 WIP: prepare the solver Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 25cda379c532e26d68d80be695b2b7a1ae293a92 Author: Max Katz Date: Sat Jul 21 12:15:57 2018 -0400 Fix incorrect GPU parameter Src/Amr/AMReX_AmrLevel.cpp commit c93f87752cb0ec69b3b97bf10bcf75f2379d8afb Author: Kevin Gott Date: Fri Jul 20 19:42:00 2018 -0400 Playing with lambdas. Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H commit 6118c9a60308d01c11a137b2d5fd9c2e5db827b3 Merge: 51c6f9313 0e1a0f0b4 Author: Michele Rosso Date: Fri Jul 20 13:09:34 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0e1a0f0b437ff8f3146a12aa33617f28cbc6f9ed Author: Weiqun Zhang Date: Fri Jul 20 06:39:45 2018 -0700 #ifdef so that Vector.H is safe for BoxLib Fortran Src/Base/AMReX_Vector.H commit 3b8eb996bcdac9a11bf09eeb2ee6a3324a7ab3a3 Author: Andrew Myers Date: Thu Jul 19 17:38:54 2018 -0700 remove const I just added Src/Base/AMReX_Array.H commit 51c6f93138cb951ac561e0a0f946985cec5e4b0c Merge: db4f5059e 087f7ae6c Author: Michele Rosso Date: Thu Jul 19 17:10:52 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 087f7ae6c379aa03bac714746f19d72525f165eb Merge: f3ec0972f c2eda1404 Author: Andrew Myers Date: Thu Jul 19 17:07:28 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f3ec0972f868c5f995b5fc68a037e102562494cc Author: Andrew Myers Date: Thu Jul 19 17:07:22 2018 -0700 function for converting from unique_ptr to ptr in the kind of containers used by MLMG to store fluxes and gradients. Src/Base/AMReX_Array.H Src/Base/AMReX_Vector.H commit 88ec0b2550670c4ed4d271df89fe4c9e116a3546 Author: Weiqun Zhang Date: Thu Jul 19 16:13:58 2018 -0700 use HYPRE_Int Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_Hypre_fort_mod.F90 Src/Extern/HYPRE/Make.package Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit e351a2967839c051ba227d07a3193e9c26ce1332 Author: Weiqun Zhang Date: Thu Jul 19 14:33:58 2018 -0700 WIP: ij matrix Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 3efa9e2935f09e98c4d1a2de6443dbc84503908c Author: Kevin Gott Date: Thu Jul 19 16:16:46 2018 -0400 Fixing namespaces. Src/Base/AMReX_Array.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Managed.H commit 4d285332766a059fd94a1f4f283595550ae5659e Author: Weiqun Zhang Date: Thu Jul 19 12:49:03 2018 -0700 option to choose hypre_interface Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit c661af65a432209ff99fc72b9ebac650d4067d9f Author: Weiqun Zhang Date: Thu Jul 19 12:33:39 2018 -0700 clean up semi-structed hypre Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit dc93ed23a4e2cd37f6ef472c1051fd7f14ff3d8d Merge: e89fe4e66 c2eda1404 Author: Kevin Gott Date: Thu Jul 19 14:26:41 2018 -0400 Merge branch 'development' into gpu-mm Conflicts: Src/Base/CMakeLists.txt commit db4f5059e7dd2b20d457afdaac56ab541246cc12 Merge: 3ce935aab c2eda1404 Author: Michele Rosso Date: Thu Jul 19 11:24:24 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e89fe4e66d6d5f4ec8157a9a23fadb92493ae7ba Author: Kevin Gott Date: Thu Jul 19 14:11:10 2018 -0400 Various small changes for GPU C++ particles. Src/Base/AMReX_Array.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_fort_mod.F90 commit 9e2084f31a218929eb27e01a64c65555c5cc037b Author: Weiqun Zhang Date: Thu Jul 19 11:02:00 2018 -0700 2d structed Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 788fc5a3ce1e970b7e4135ff32ff24bceb0585e4 Author: Weiqun Zhang Date: Thu Jul 19 07:09:17 2018 -0700 set hypre logging and limit linop maxorder Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 28521c8a91c02548318fed4fae1ec461950aac7d Author: Weiqun Zhang Date: Thu Jul 19 06:48:58 2018 -0700 match boundary maxorder Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit a76e27d9076c0720267da25c2e5cdb5bdab46eea Author: Weiqun Zhang Date: Wed Jul 18 22:38:49 2018 -0700 WIP: clean up Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit bb5fc714ead25c160d6e33ca6e7d996dd0fe2ef4 Author: Weiqun Zhang Date: Wed Jul 18 17:01:34 2018 -0700 make structed grid interface work Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 8e1f650553a87ff020e9616d85100d25c1ae0ceb Author: Minion Date: Wed Jul 18 16:04:42 2018 -0700 input variables v and nu, fix multi-block error, improve modularity, clean up advance.dpp Tutorials/Basic/SDCAdvDiffusion_C/Exec/GNUmakefile Tutorials/Basic/SDCAdvDiffusion_C/Exec/inputs_2d Tutorials/Basic/SDCAdvDiffusion_C/Source/advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/advance_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/main.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc.H Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc_F.H commit 1752fe40f607ed03d250dcd249b16c2dbd44a387 Author: Weiqun Zhang Date: Wed Jul 18 15:33:34 2018 -0700 start refactoring Hypre Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_3D.F Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/HYPRE/Make.package Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp Tutorials/LinearSolvers/ABecLaplacian_C/inputs Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-abeclap-com Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-poisson-lev commit b712e71c2dc16ed122d9d8dd1b5e54175c55967f Author: Weiqun Zhang Date: Tue Jul 17 18:19:25 2018 -0700 back to use HypreABecLap2 because HypreABecLap3 doesn't work yet Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit f98081877ed1128f0fa004ae574bb3c37147bfd3 Author: Weiqun Zhang Date: Tue Jul 17 17:06:55 2018 -0700 expand some macros Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit d2d11fc3c3495b8696d5c0780670386da02dd5f4 Merge: 3413b5a76 a687aab5d Author: Weiqun Zhang Date: Tue Jul 17 16:55:29 2018 -0700 Merge branch 'mlmg' into hypre commit 3413b5a765c05fdb17ba677ccb1df52000895c9c Merge: 581bfd935 ce857eed2 Author: WeiqunZhang Date: Tue Jul 17 16:41:00 2018 -0700 Merge pull request #246 from shashankNREL/sy/hypre Sy/hypre - HYPRE IJ matrix interface commit a687aab5dc3cbf96fd41fc67d6f8c60758e3ef48 Author: Weiqun Zhang Date: Tue Jul 17 16:40:04 2018 -0700 fix gsrb when eb crosses domain Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit c2eda1404601ccbcb9b879088353d2e6438857ba Merge: f4ad3e63d 8cedfa6d8 Author: WeiqunZhang Date: Tue Jul 17 16:31:32 2018 -0700 Merge pull request #288 from cdaley/development Add a makefile fragment for Clang/Flang commit 8cedfa6d824f338ba6f6a74eecca2343a4e875d9 Author: cdaley Date: Tue Jul 17 16:11:31 2018 -0700 Add a makefile fragment for Clang/Flang Tools/GNUMake/Make.defs Tools/GNUMake/comps/llvm-flang.mak commit 1fba0a3328d2c57e9ca32a9310216a1ed0891156 Author: Weiqun Zhang Date: Tue Jul 17 15:39:33 2018 -0700 use mask for EB and domain bc crosses Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit f4ad3e63dee902a7dadfced6f2c679c44eef6bd7 Author: Weiqun Zhang Date: Tue Jul 17 15:10:26 2018 -0700 fix omp bug in ABecLaplacian_F tutorial Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 commit 66edf60e71eebd2fe4918742138cd6834086d137 Author: Weiqun Zhang Date: Tue Jul 17 15:04:34 2018 -0700 fix make Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile commit 2026409bdbe3fa4aafac7e3d11f3970595617dd0 Author: Weiqun Zhang Date: Tue Jul 17 15:04:20 2018 -0700 avoid using null as variable name Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 2d8cbf141e9c897e53c93aeadbba37e5c747cceb Author: Minion Date: Tue Jul 17 14:56:39 2018 -0700 IMEX advection diffusion example. This works as long as there is only one box Tutorials/Basic/SDCAdvDiffusion_C/Exec/.#advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Exec/GNUmakefile Tutorials/Basic/SDCAdvDiffusion_C/Exec/inputs_2d Tutorials/Basic/SDCAdvDiffusion_C/Source/Make.package Tutorials/Basic/SDCAdvDiffusion_C/Source/advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/advance_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_3d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/inputs_3d Tutorials/Basic/SDCAdvDiffusion_C/Source/main.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc.H Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc_F.H Tutorials/Basic/SDCAdvDiffusion_C/Source/pf_quadrature.f90 commit b28746163c983364f9a8b0830adbc521afbe8714 Merge: 7fc3bca4f f11605d0f Author: Minion Date: Mon Jul 16 19:55:12 2018 -0700 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit 7fc3bca4f925bb6135c2eeff11f430d72cd252af Author: Minion Date: Mon Jul 16 19:52:36 2018 -0700 changing to match new tutorial style Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile Tutorials/SDC/HeatEquation_EX1_C/advance.cpp Tutorials/SDC/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/inputs_2d Tutorials/SDC/HeatEquation_EX1_C/main.cpp Tutorials/SDC/HeatEquation_EX1_C/myfunc_F.H commit e383375cd6b6ca88884dbb69ea1b9fac0d0df0e9 Author: Weiqun Zhang Date: Mon Jul 16 18:24:22 2018 -0700 pass mask to Fortran Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 61904d01ac973ce7abc9c04227898a23bde0fea3 Merge: af7e35009 a5d5e1bf1 Author: Weiqun Zhang Date: Mon Jul 16 18:11:01 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit af7e350091e953cdabca5ad3b23c462547d1900f Author: Weiqun Zhang Date: Mon Jul 16 18:10:25 2018 -0700 add cc mask Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 15abdae568c040962b951bd781290a290cb51c4d Merge: 79650123e f7db6b956 Author: Minion Date: Mon Jul 16 17:58:59 2018 -0700 Merge branch 'development' into SDC commit 7d16226bf29ada54358594dd34f5ab7c40efab01 Author: Weiqun Zhang Date: Mon Jul 16 17:45:26 2018 -0700 simplification Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit a5d5e1bf1876c1597d4b09d4356c12c1008445d6 Merge: 62bf8117d f4e374564 Author: sireeveslbl Date: Mon Jul 16 14:03:49 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg commit 62bf8117d37cf416d4dc8c8e65177350779838f5 Author: sireeveslbl Date: Mon Jul 16 14:03:47 2018 -0700 myTest for merging Tests/LinearSolvers/CellEB/MyTest.cpp commit 02de6ec0e3012136bd401695889b53e9f5e8dbab Author: sireeveslbl Date: Mon Jul 16 14:01:19 2018 -0700 Some changes, need to investigate some bugs, put it back to non-EB face averaging for now Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit f4e374564f12972ad8485fa9328e13072941e296 Author: Weiqun Zhang Date: Mon Jul 16 13:37:59 2018 -0700 3d mlebabeclap and over relaxation Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit f7db6b95620b9fd9e4747d84ae911532715a3932 Author: Tan Nguyen Date: Mon Jul 16 12:45:26 2018 -0700 fix a compile error in the OMP backend of perilla Src/AmrTask/rts_impls/Perilla_omp/Perilla.cpp Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.H Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/inputs commit 78b766b2db6b6a65d2adc23719d2cb901d32734b Author: Weiqun Zhang Date: Mon Jul 16 12:10:31 2018 -0700 2d mlebabeclap Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 2a62bfc383735026b566b18ffd48c0f0cbc7d32f Merge: 48564f3b8 027cac634 Author: Weiqun Zhang Date: Mon Jul 16 10:29:58 2018 -0700 Merge branch 'development' into mlmg commit 027cac63420f117e0b98e02ce603d1264bc76e62 Merge: 7f76f9078 817e87bd2 Author: Weiqun Zhang Date: Mon Jul 16 10:29:19 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7f76f907835f9bd6d49d3bdcef664c47ef5843e4 Author: Weiqun Zhang Date: Mon Jul 16 10:28:50 2018 -0700 move GeometryGeneration to OldTutorials OldTutorials/GeometryGeneration/exec/GNUmakefile OldTutorials/GeometryGeneration/exec/coveredSlabs.cpp OldTutorials/GeometryGeneration/exec/coveredslabs.inputs OldTutorials/GeometryGeneration/exec/parabolaWithSphere.cpp OldTutorials/GeometryGeneration/exec/parabolaWithSphere.inputs OldTutorials/GeometryGeneration/exec/sphere.cpp OldTutorials/GeometryGeneration/exec/sphere.inputs OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.cpp OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.inputs OldTutorials/GeometryGeneration/src/CommonCode.H OldTutorials/GeometryGeneration/src/CommonCode.cpp OldTutorials/GeometryGeneration/src/Make.package OldTutorials/GeometryGeneration/src/WriteEBPlotFile.H OldTutorials/GeometryGeneration/src/WriteEBPlotFile.cpp commit 817e87bd2a74d2025340236c06e86743fb6ae119 Merge: 4a41e5fce 0b3ce7eef Author: WeiqunZhang Date: Mon Jul 16 10:23:01 2018 -0700 Merge pull request #287 from zingale/development close math mode in latex table commit ce857eed216d088415fab222804f9bf9d0ee279e Author: shashankNREL Date: Mon Jul 16 08:15:28 2018 -0600 Accomodating suggestions from Weiqun on the PR Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Tests/LinearSolvers/MLMG/GNUmakefile commit 4a41e5fcef63c1fc7c932fe146dba7b59a16c8c7 Author: Tan Nguyen Date: Mon Jul 16 01:32:52 2018 -0700 add perilla source code Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla/Barrier.H Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla/LocalConnection.H Src/AmrTask/rts_impls/Perilla/Make.package Src/AmrTask/rts_impls/Perilla/Makefile Src/AmrTask/rts_impls/Perilla/PackageQueue.H Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla/PerillaRts.H Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla/RegionQueue.H Src/AmrTask/rts_impls/Perilla/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla/RemoteConnection.H Src/AmrTask/rts_impls/Perilla/WorkerThread.H Src/AmrTask/rts_impls/Perilla/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla/mylock.h Src/AmrTask/rts_impls/Perilla/perilla.mak Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_omp/Barrier.H Src/AmrTask/rts_impls/Perilla_omp/Barrier.cpp Src/AmrTask/rts_impls/Perilla_omp/LocalConnection.H Src/AmrTask/rts_impls/Perilla_omp/Make.package Src/AmrTask/rts_impls/Perilla_omp/PackageQueue.H Src/AmrTask/rts_impls/Perilla_omp/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla_omp/Perilla.H Src/AmrTask/rts_impls/Perilla_omp/Perilla.cpp Src/AmrTask/rts_impls/Perilla_omp/PerillaConfig.H Src/AmrTask/rts_impls/Perilla_omp/PerillaRts.H Src/AmrTask/rts_impls/Perilla_omp/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.H Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla_omp/RegionQueue.H Src/AmrTask/rts_impls/Perilla_omp/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla_omp/RemoteConnection.H Src/AmrTask/rts_impls/Perilla_omp/WorkerThread.H Src/AmrTask/rts_impls/Perilla_omp/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla_omp/perilla.mak Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._Exec Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._README Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._Source Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._Make.Adv Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._SingleVortex Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._UniformVelocity Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._Prob.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._face_velocity_2d.f90 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Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/AdvBld.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_F.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_dt.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_io.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_setup.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._Adv_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._compute_flux_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/Adv_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/compute_flux_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/main.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 48564f3b851af0cec07ab234eb4d52862e3c5d0c Author: Weiqun Zhang Date: Sat Jul 14 12:58:36 2018 -0700 make EB2::maxCoarsening more general Src/Base/AMReX_Box.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/CellEB/MyTest.cpp commit 126f39dc64a3690b7a5692a02e9e8bc15ba573dc Author: Weiqun Zhang Date: Sat Jul 14 11:38:06 2018 -0700 use EB_average_down for solution too Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 6a124e54beaec28acc72a54db8e1a4c26f6a2451 Merge: 81108c1f4 caf348a8d Author: Weiqun Zhang Date: Sat Jul 14 11:33:59 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit caf348a8d6ddc30a3f33dca6dcf4571f311fcb77 Author: sireeveslbl Date: Fri Jul 13 16:18:02 2018 -0700 Changed one arguement Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 41ed9f63132ef7de2e865e51548b441077e13523 Author: sireeveslbl Date: Fri Jul 13 16:00:57 2018 -0700 EB average down faces compiles, and doesn't break code. Still need to test Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H commit 81108c1f49aec3cbeca2a97902c472fa05ad002d Merge: 9cc5b847a d7583ec17 Author: Weiqun Zhang Date: Fri Jul 13 15:06:00 2018 -0700 Merge branch 'development' into mlmg commit d7583ec174a3161e9e88d60dae205931a94f0144 Author: Weiqun Zhang Date: Fri Jul 13 15:05:41 2018 -0700 simplication Src/EB2/AMReX_EB2.cpp commit fcb961551ca3f4395aa4756dba684cf4d57fdaed Author: Weiqun Zhang Date: Fri Jul 13 15:02:23 2018 -0700 ParmParse: get and query using std::array Src/Base/AMReX_ParmParse.H commit 53b936c73f7a8130dfd5a6f00ccfd97ac2088417 Author: Weiqun Zhang Date: Fri Jul 13 14:07:22 2018 -0700 remove old EB from EB/CNS Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Combustor/inputs.testing Tutorials/EB/CNS/Exec/Combustor/inputs_combustor Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.amr Tutorials/EB/CNS/Exec/ShockRef/inputs.regt Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/CNS_init_eb2.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/main.cpp commit 9cc5b847aeaf6e87712cb35cf74eea21eba16750 Author: sireeveslbl Date: Thu Jul 12 22:18:32 2018 -0700 More work on EB average down faces Src/EB/AMReX_EBMultiFabUtil.cpp commit e7d309f4ca8ed1edec477e3b54dc49efd6ca8a94 Merge: 06263a738 f94437c57 Author: Weiqun Zhang Date: Thu Jul 12 22:10:24 2018 -0700 Merge branch 'development' into eb2 commit 1068a7da5333e721f7b8edd64aa8efd19948d512 Author: Weiqun Zhang Date: Thu Jul 12 18:43:48 2018 -0700 start petsc based bottom solver Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/Make.package Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.hypre Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 0b3ce7eef3edd346d9cfb5c91d1befbbbc7421ca Author: Michael Zingale Date: Thu Jul 12 20:28:28 2018 -0400 close math mode in latex table Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit 9fd58f1d4f594f53be9aa7e82a5e875b092aae0b Author: sireeveslbl Date: Thu Jul 12 14:48:33 2018 -0700 EB Average Down Faces not finished yet, but code compiles Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 06263a73855f2995665ec5aa16c3167881cc8fc9 Author: Weiqun Zhang Date: Thu Jul 12 11:16:03 2018 -0700 change inputs back to sphere Tutorials/EB/CNS/Exec/Sod/inputs commit f94437c57f6867ee47113e2fa74f31ab50492407 Author: Weiqun Zhang Date: Wed Jul 11 21:42:27 2018 -0700 update inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.regt commit f7f117c1b8518fa2bb130c031576b8dad9eaaa71 Author: Weiqun Zhang Date: Wed Jul 11 18:26:19 2018 -0700 fix corner case of BoxArray::maxSize Src/Base/AMReX_BoxArray.cpp commit a199794c47dd31982feeddae59193f71c3b58917 Merge: aaa5bc206 f7a3868cd Author: Weiqun Zhang Date: Wed Jul 11 17:37:53 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit aaa5bc206fc43c23d6323ef72358f09ca3fa5ed6 Author: Weiqun Zhang Date: Wed Jul 11 17:37:40 2018 -0700 turn off SIGTERM handling by default to avoid generating tons of Backtrace files after going over the queue time limit Src/Base/AMReX.cpp commit 6b0dc59e25420d7a25abf4de91c56782771c1fb7 Author: sireeveslbl Date: Wed Jul 11 16:20:57 2018 -0700 Working on EB average down faces. Not complete yet. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit f7a3868cd01d64bf5b13d34e1579bce2621395b9 Merge: e8c5a2a14 12ad70a0c Author: Weiqun Zhang Date: Wed Jul 11 16:05:30 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e8c5a2a1428a073ec2037dc55862899df6617167 Author: Weiqun Zhang Date: Wed Jul 11 16:05:12 2018 -0700 fix a bug in PhysBCFunct Src/Base/AMReX_PhysBCFunct.cpp commit 12ad70a0ca00698b8cc8d79d4b28a5eeb2f31730 Author: Weiqun Zhang Date: Wed Jul 11 13:05:02 2018 -0700 avoid conflict with PROFILE Src/Base/AMReX_TinyProfiler.cpp commit f481cf4145987f6a656ae97d23174ecea886ad2c Merge: b99f63b5e 5b46ed8d9 Author: Marc Day Date: Wed Jul 11 12:27:01 2018 -0700 Merge pull request #286 from AMReX-Codes/valentina/timer added timer for MLMG::Solve commit 5b46ed8d99e67f94721fd309cad8540216569cbf Author: Valentina Ricchiuti Date: Wed Jul 11 12:04:11 2018 -0700 added timer for MLMG::Solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 960f19b527f9db74637b195cb1c18f5f7c2a1931 Author: sireeveslbl Date: Wed Jul 11 11:01:54 2018 -0700 Moved to a 4 point interpolation for fluxes Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 7886ad9af152899a96e10209dbaeb469ff48031e Author: Weiqun Zhang Date: Tue Jul 10 18:01:48 2018 -0700 add ghost cells to A coefficient Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit b99f63b5e77414c9cc46aba53184e2c17128ba86 Merge: 3f34528d4 876b0495b Author: Andrew Myers Date: Tue Jul 10 17:24:33 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3f34528d43ca61c9ac17eff8ea66d508bdcac592 Author: Andrew Myers Date: Tue Jul 10 17:10:48 2018 -0700 remove the allow_particles_near_boundaries parameter - no longer needed. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d2f12e4493ec0e7285460d3f12045331735dc3c0 Author: Andrew Myers Date: Tue Jul 10 16:50:16 2018 -0700 remove old multi-level deposition routines (aren't used any more) Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit fbbf3b15d06786d918e5531b82a67794cd59d404 Merge: 547406ea3 876b0495b Author: Weiqun Zhang Date: Tue Jul 10 16:07:37 2018 -0700 Merge branch 'development' into mlmg commit 876b0495b03ec3a5fb89337c83fdbb73e56b040a Author: Weiqun Zhang Date: Tue Jul 10 16:07:13 2018 -0700 compile with PRECISION=FLOAT Src/EB/AMReX_EB_levelset_F.F90 Src/EB2/AMReX_EB2_GeometryShop.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit 547406ea3706dd92655c3d4f930371f183fc03ba Author: sireeveslbl Date: Tue Jul 10 15:32:03 2018 -0700 Other Functions with centroid interpolation Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 62e6da141a594eba627422a1f998344e71f46278 Merge: b8c1c0177 e9a939a89 Author: Weiqun Zhang Date: Tue Jul 10 15:12:57 2018 -0700 Merge branch 'eb2' into development commit 935b19a19f7b6022ba9430231c6686f5128109c4 Merge: 7707c8ea1 1a1c3586e Author: sireeveslbl Date: Tue Jul 10 14:49:05 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg commit 7707c8ea106b4a62d1907179a95592987ec7fb71 Author: sireeveslbl Date: Tue Jul 10 14:49:02 2018 -0700 merging Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 1a1c3586ec91e135a000378b1b4bd6a9fe06a2e8 Author: Weiqun Zhang Date: Tue Jul 10 13:54:23 2018 -0700 fix bugs in adotx Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit c4edfa31bd98e0fde9e4b4c75706ad1b7c708c1c Author: sireeveslbl Date: Tue Jul 10 13:01:48 2018 -0700 Interpolating on a*phi in 'A dot x', utilizing the centroid data Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit b8c1c0177829e56d7df24388206a544ed858dc38 Merge: 59fbdef59 179c3812b Author: Weiqun Zhang Date: Mon Jul 9 17:50:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 59fbdef595764be22bd77627598316826cedd1b4 Author: Weiqun Zhang Date: Mon Jul 9 17:17:04 2018 -0700 catch SIGTERM Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit e9a939a89717495e0f2272794e86545f7140e07d Author: Weiqun Zhang Date: Mon Jul 9 17:47:55 2018 -0700 need to parallel reduce the error code Src/EB2/AMReX_EB2_Level.cpp commit 2e1a9beff733b9e51b058fc15e4e8e8af7a85e46 Author: Weiqun Zhang Date: Mon Jul 9 17:17:04 2018 -0700 catch SIGTERM Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit 7a0ed3f404e3c9adf6e799a69a7d4d0ef968d1bc Author: Weiqun Zhang Date: Mon Jul 9 17:47:55 2018 -0700 need to parallel reduce the error code Src/EB2/AMReX_EB2_Level.cpp commit c8e60428f7ad454ad4d9aee9b1998bd066ff639b Author: Weiqun Zhang Date: Mon Jul 9 17:17:04 2018 -0700 catch SIGTERM Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit 179c3812b08995c500a1ce6e9518023793c34a35 Merge: a697abb10 f571114d6 Author: Emmanuel Motheau Date: Mon Jul 9 16:49:25 2018 -0700 Merge pull request #282 from johnpwakefield/augtool Augtool commit b95231695b48c6d88519debbfa36b6fd0f519193 Author: Weiqun Zhang Date: Mon Jul 9 16:45:07 2018 -0700 increase max_coarsening_level Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/initEB.cpp commit 8fd5ba804fa070a292ae85f691fce73919dece30 Merge: 3892da9b4 c5263e033 Author: Weiqun Zhang Date: Mon Jul 9 16:35:01 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit 3892da9b473dab1f345e9a47327b800058d7cfa3 Merge: ca467a7f7 7e3ae0084 Author: Weiqun Zhang Date: Mon Jul 9 16:34:57 2018 -0700 Merge branch 'eb2' into mlmg commit 7e3ae008428f38d0bbcfac8bf01b102f02979e1d Merge: e29f0b236 a697abb10 Author: Weiqun Zhang Date: Mon Jul 9 16:34:25 2018 -0700 Merge branch 'development' into eb2 commit a697abb101827533d6f11e88a3105de05bad082d Author: Weiqun Zhang Date: Mon Jul 9 16:34:08 2018 -0700 cannot call MPI_Group_free after MPI_Finalize Src/Base/AMReX_ParallelDescriptor.cpp commit ca467a7f742a9854898d623a79d8535fffcea280 Author: Weiqun Zhang Date: Mon Jul 9 16:28:42 2018 -0700 when using EB, limit max coarsening level Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit c5263e0339e25f606107fb992e0fe6950779934c Merge: 1bf59e0c1 f1fa2557a Author: sireeveslbl Date: Mon Jul 9 16:26:19 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg commit 1bf59e0c1790cdd14e5f91769b4e1788290b19b9 Author: sireeveslbl Date: Mon Jul 9 16:25:57 2018 -0700 Wrong dx in interpolation in 2D for a, 3D non-zero alpha now supported. Works with sphere test. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit f1fa2557adbce37e278738ef6349b9c9f515b21b Merge: 150a50cf8 e29f0b236 Author: Weiqun Zhang Date: Mon Jul 9 15:46:42 2018 -0700 Merge branch 'eb2' into mlmg commit e29f0b2366be28d74e512848f21691aa3fb74ab6 Merge: d50a85528 c41536b44 Author: Weiqun Zhang Date: Mon Jul 9 15:46:17 2018 -0700 Merge branch 'weiqun/eb2' into eb2 commit d50a85528036d212897b720cf1ed4aecf948995c Merge: 0b7d415a9 d6b8a51ac Author: Weiqun Zhang Date: Mon Jul 9 15:45:58 2018 -0700 Merge branch 'development' into eb2 commit c41536b44d2ef2feeadf47231022e0cbb97ad902 Author: Weiqun Zhang Date: Mon Jul 9 15:44:57 2018 -0700 make sure fine grids are coarsenable Src/EB2/AMReX_EB2_Level.cpp commit 150a50cf8a2f6d9387ed7dacc9cf3c46cbe6a840 Author: sireeveslbl Date: Mon Jul 9 14:30:18 2018 -0700 Minor change Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 8ca921e23705e47e9b401a537783401b9861972b Author: Weiqun Zhang Date: Mon Jul 9 13:41:48 2018 -0700 rm old comment Src/EB2/AMReX_EB2_Level.H commit 7543b2ecced441bd7596d195e50dc1c308cf6ab7 Author: Weiqun Zhang Date: Mon Jul 9 13:24:16 2018 -0700 EB2: fix maxCoarseningLevel Src/EB2/AMReX_EB2.H commit 17f83e874842a338228b429c194d13d9a7c4f847 Author: Weiqun Zhang Date: Mon Jul 9 13:09:26 2018 -0700 finished implementation of coarsening to different grids Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/MyTest.cpp commit d6b8a51aca5f3e08b473d8aae41c8cbd4b41f6e1 Author: Weiqun Zhang Date: Mon Jul 9 10:57:00 2018 -0700 push communicator to ParallelContext stack earlier so that Abort could work properly Src/Base/AMReX_ParallelDescriptor.cpp commit de4f5c81eeb696e4f3a18a1081d49455646d2fc3 Author: sireeveslbl Date: Mon Jul 9 10:42:49 2018 -0700 Fixed Erroneous Arithmetic Error, and convergence, non-zero alpha is working for 2D. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 35d08e425180123539e697de16b25685a95a734d Author: Weiqun Zhang Date: Sun Jul 8 08:38:58 2018 -0700 MPI_TAG_UB may only be obtained with MPI_COMM_WORLD Src/Base/AMReX_ParallelDescriptor.cpp commit 0a2c5a5e9483bceae1e3def2c85794e7c1cb3bf2 Author: Weiqun Zhang Date: Sat Jul 7 11:09:35 2018 -0700 Fix a bug. Even if boxarray is empty, we may still need to clear various cache. Src/Base/AMReX_FabArrayBase.cpp commit 3ce935aab1c2223d75ae830f3a373caee4bbc108 Author: Michele Rosso Date: Fri Jul 6 17:58:37 2018 -0700 CMake: add test_install to be XSDK compliant CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt Tutorials/CMakeLists.txt commit 5fe36a127533591063ff3bb3d09b6dd4f688e33f Author: Kevin Gott Date: Fri Jul 6 20:13:52 2018 -0400 Add Summit's no CUDA-aware flag. Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script commit 365b953e37f7c94fd13326895bda50b95028dbaf Author: Kevin Gott Date: Fri Jul 6 18:48:18 2018 -0400 run script with GPUDirect off flag. Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script commit 50f8a05724c91e8c05546da2ec49b9c7cadfdd65 Author: Kevin Gott Date: Fri Jul 6 18:44:00 2018 -0400 Rename kernel Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 4f80122ce8da28b2f371d9b3a96147b525c2c248 Author: sireeveslbl Date: Fri Jul 6 15:26:57 2018 -0700 Testing Nonzero Alpha for 2D EB MLMG Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Tests/LinearSolvers/CellEB/MyTest.cpp commit c66be15a755697c6374658aea360d7f64c614dbf Author: Weiqun Zhang Date: Fri Jul 6 10:57:24 2018 -0700 remove optional nmax argument from SFC Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 0038c22528bef9d750b19e9b103a486fe300e63b Merge: 69992f2e7 eee695a18 Author: Michele Rosso Date: Fri Jul 6 10:34:39 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 69992f2e771a16622ef64e5f5cb117189c8c8450 Author: Michele Rosso Date: Fri Jul 6 10:34:34 2018 -0700 CMake: strip MPI and OpenMP variables before using them Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit eee695a1832241640ca4b7f4a4e718c020534b3b Author: Weiqun Zhang Date: Thu Jul 5 18:57:26 2018 -0700 special fix for cray, don't know why it works Src/Base/AMReX_DistributionMapping.cpp commit 914f62280ef31224f6d9e90a0848b5d9955875e6 Author: Michele Rosso Date: Thu Jul 5 17:01:28 2018 -0700 CMake: fix setting for Cray compiler Tools/CMake/AMReX_Config.cmake commit af4f30f7828a963151380dac47777d61804b47ef Merge: 26d69f54b 94c857384 Author: Michele Rosso Date: Thu Jul 5 13:37:09 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 26d69f54b1a99644cbb4ec17cca9b9f6feb153bd Author: Michele Rosso Date: Thu Jul 5 13:37:02 2018 -0700 CMake: fix problem with AppleClang compiler Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 76755cce925c289170785f04f8ea0dd4c9500485 Author: Kevin Gott Date: Thu Jul 5 01:18:14 2018 -0400 Reorganization and small adjustments. Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_Managed.H Src/Base/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit a18c5463d9bbc3c90371f05c6714ba6b6da1a37d Author: Weiqun Zhang Date: Wed Jul 4 18:34:58 2018 -0700 WIP: coarsen to different grids Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp commit c5a36d4abb505e37ae6a039eb9c94cc69b9ba56f Merge: e11950623 0b7d415a9 Author: Weiqun Zhang Date: Wed Jul 4 07:24:13 2018 -0700 Merge branch 'eb2' into mlmg commit 0b7d415a9781482386bd3968cde12d7f8d1bf07b Author: Weiqun Zhang Date: Wed Jul 4 07:17:47 2018 -0700 finish 3d version of amrex_eb2_check_mvmc Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 5222cde56836aa9f1d26bf19b571d3aa43383991 Author: Weiqun Zhang Date: Tue Jul 3 22:06:40 2018 -0700 start 3d version of amrex_eb2_check_mvmc Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit d1234c192a0beddd1014a7ecbbf031f967514f00 Author: Weiqun Zhang Date: Tue Jul 3 22:05:34 2018 -0700 init IArrayBox to INT_MAX in debug/test mode Src/Base/AMReX_IArrayBox.cpp commit e11950623636099ecaeb1a52adefafd2c644a382 Author: Weiqun Zhang Date: Wed Jul 4 07:17:47 2018 -0700 finish 3d version of amrex_eb2_check_mvmc Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 86e2f4cce80e3dd40c4876839d714e8b282be2ae Author: Weiqun Zhang Date: Tue Jul 3 22:06:40 2018 -0700 start 3d version of amrex_eb2_check_mvmc Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 67f937aa0ca85dad70c8665874f5c8cb09bdd050 Author: Weiqun Zhang Date: Tue Jul 3 22:05:34 2018 -0700 init IArrayBox to INT_MAX in debug/test mode Src/Base/AMReX_IArrayBox.cpp commit 94c857384eecac55b3a1a7ff42dacd0660ade13b Author: atmyers Date: Tue Jul 3 18:31:00 2018 -0700 Don't warn when particles are removed at non-periodic boundaries, even with verbose=true. Src/Particle/AMReX_ParticleContainerI.H commit 5c64814a3ec5c34ddec4dfb13257af5ebef78ef2 Merge: 1e12eef59 50ae5b12e Author: Michele Rosso Date: Tue Jul 3 17:26:52 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1e12eef597b8545ba9fb746b6e507ec06fbef702 Author: Michele Rosso Date: Tue Jul 3 17:26:39 2018 -0700 CMake: provide AMReX versioning even when .git is not present CMakeLists.txt Src/CMakeLists.txt commit 50ae5b12ea9b1094d881478006edda5040111e12 Author: Weiqun Zhang Date: Tue Jul 3 17:20:34 2018 -0700 only print when verbose is true Src/Particle/AMReX_ParticleContainerI.H commit f88948557dc6a8e0c0cac66be1fe08eaebe24bcc Merge: 8696a86a9 ebad409cd Author: Weiqun Zhang Date: Tue Jul 3 17:15:16 2018 -0700 Merge branch 'eb2' into mlmg commit ebad409cd08cbbb38309a205c7a4eafa1130f440 Merge: 438f1653e 2668c5a33 Author: Weiqun Zhang Date: Tue Jul 3 17:11:25 2018 -0700 Merge branch 'development' into eb2 commit 8696a86a9e383858f46bc9337c40c008696a3dcf Merge: fb03516ff 438f1653e Author: Weiqun Zhang Date: Tue Jul 3 17:00:03 2018 -0700 Merge branch 'eb2' into mlmg commit fb03516ffe4824975e5f133b20290b6a6f45d575 Author: Weiqun Zhang Date: Tue Jul 3 16:59:44 2018 -0700 don't let linear solver's max_coarsening_level exceed EB2's Tests/LinearSolvers/CellEB/MyTest.cpp commit 2668c5a33ef1cc3991b608b101a1b266936b96f4 Author: Michele Rosso Date: Tue Jul 3 16:49:11 2018 -0700 CMake: fix bug Tools/CMake/AMReX_Options.cmake commit fc5d7f7f44c07a61967bfe39999489e8e142d30e Merge: 830f6db9b b0d12e39c Author: Weiqun Zhang Date: Tue Jul 3 16:48:30 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit 438f1653eb09a6ca6312e69d720f6bee0cc27e67 Author: Weiqun Zhang Date: Tue Jul 3 16:45:03 2018 -0700 fix m_ok Src/EB2/AMReX_EB2_Level.H commit f61c5298612f6b44fdb0fe1a33c9dbeea2e270fa Author: Weiqun Zhang Date: Tue Jul 3 16:35:50 2018 -0700 function to return max coarsening level Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H commit 29494277c70c434d0098ef6490d6f711b820689b Author: Weiqun Zhang Date: Tue Jul 3 15:31:32 2018 -0700 check for multi-cuts and multi-values Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 830f6db9bc902f7ce1178d80b0ee4f788346b2fd Author: Weiqun Zhang Date: Tue Jul 3 16:45:03 2018 -0700 fix m_ok Src/EB2/AMReX_EB2_Level.H commit 73dddbe378c80961018f11abcc064c5d801cd231 Author: Weiqun Zhang Date: Tue Jul 3 16:35:50 2018 -0700 function to return max coarsening level Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H commit 43283ccba78472de118e3743d9fa2e42541d1c07 Author: Weiqun Zhang Date: Tue Jul 3 15:31:32 2018 -0700 check for multi-cuts and multi-values Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 98bdd48c0c969b3c550ab6b6787940326a81c75f Merge: a6d7028a5 391a3a8ad Author: Michele Rosso Date: Tue Jul 3 14:48:39 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a6d7028a59c6f4f05b638a461bc8b93217c65520 Author: Michele Rosso Date: Tue Jul 3 14:48:04 2018 -0700 CMake: one more change Src/CMakeLists.txt commit b0d12e39cd76e394837549ab1dd5597054c00954 Author: sireeveslbl Date: Tue Jul 3 13:11:35 2018 -0700 Fixed Another Bug, for regular convergence Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit a98287ed04e859fe9ad5fb4abfb71ac00dd8a16f Merge: 7bacb0186 95f7869d3 Author: Weiqun Zhang Date: Tue Jul 3 13:03:42 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit 391a3a8ad0da7ccb9f46322ffe2f562b9607afbc Merge: ddbf2bd4e 90764850e Author: Marc Day Date: Tue Jul 3 12:57:28 2018 -0700 Merge pull request #279 from jrood-nrel/update_nrel_makefile Update makefile for NREL site to get higher vectorization from the Intel compiler commit 90764850e01f8d238787ef467af13f9dc0ad64dd Author: Jon Rood Date: Tue Jul 3 13:37:40 2018 -0600 Update makefile for NREL site to get higher vectorization from the Intel compiler. Tools/GNUMake/sites/Make.nrel commit ddbf2bd4ef4ff511bd11b1439a4cf940e432da51 Author: Michele Rosso Date: Tue Jul 3 12:06:56 2018 -0700 CMake: some more improvements Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 95f7869d38e48212832a01dfe329ef00efa10968 Author: sireeveslbl Date: Tue Jul 3 10:12:26 2018 -0700 MyTest Changed to allow for 3D Tests/LinearSolvers/CellEB/MyTest.cpp commit 17aea688ccd1371fa59e5d1aca038a3e5e31fa56 Author: sireeveslbl Date: Tue Jul 3 10:10:18 2018 -0700 Bug Killed, Test Case works for Sphere Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 52717e2d143e6c9d574ca42558553f2b309b2a20 Author: Michele Rosso Date: Mon Jul 2 16:19:37 2018 -0700 CMake: bug fix Tools/CMake/AMReX_Config.cmake commit f2572f354c7f164bd05e27930d408bf181db6c58 Author: Kevin Gott Date: Mon Jul 2 18:56:02 2018 -0400 strip USE_CUDA in make file Tools/GNUMake/Make.defs commit 9d2c88ef119fba3ba9298953627c4c7961caec2d Author: Kevin Gott Date: Mon Jul 2 18:52:47 2018 -0400 Add CUDA streams to MFIter. Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 5dcb9401d870c605c9b1667a79973379d41a69eb Author: Kevin Gott Date: Mon Jul 2 18:50:08 2018 -0400 Adjust Device for AMREX_USE_CUDA=FALSE. Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/Make.package commit 21f4a0119a9009affbd6ae847f31bdc91f5fcc9e Author: Michele Rosso Date: Mon Jul 2 15:49:31 2018 -0700 CMake: update Doc Docs/sphinx_documentation/source/BuildingAMReX.rst commit 8a8b0226c15a81b115152872861b37d4189d6b0e Author: Kevin Gott Date: Mon Jul 2 18:45:17 2018 -0400 Add using CudaAllocators = std allocator for USE_CUDA=FALSE. Src/Base/AMReX_CudaAllocators.H commit 18045ef219bbad954c724c8a8f6bead156a3200d Merge: 8da722c6e ca45d5254 Author: Michele Rosso Date: Mon Jul 2 15:28:58 2018 -0700 Merge branch 'development' into mr/cmake commit 8da722c6ecaecd93c5ffd995abb3165ad8d009bb Author: Michele Rosso Date: Mon Jul 2 15:22:22 2018 -0700 CMake: complete transition to 'Modern CMake' CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Machines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt commit ca45d5254cc935fd6fc36e72c3b6d2f34a0af1a2 Merge: cceea4038 3caa6292f Author: Johannes Blaschke Date: Mon Jul 2 13:38:42 2018 -0700 :Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit cceea40388e6cb15d0770e3f2b670a5a8af211ee Author: Johannes Blaschke Date: Mon Jul 2 13:38:38 2018 -0700 remove meaningless const Src/EB/AMReX_EB_levelset.H commit 3caa6292fa604e9cedeb29e098fd560dcef7ca9e Author: Johannes Blaschke Date: Mon Jul 2 13:11:54 2018 -0700 fixed dummy variable and meaningless const Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset_F.F90 commit 14bf698934e320a63990b9ff5801dbec0fcc658d Author: Weiqun Zhang Date: Mon Jul 2 10:46:08 2018 -0700 makeSFC: switch the order of optional arguments Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 63c651efd555227fb44c831a42f38643abf6fa3f Merge: 1b1fad431 a83507a0e Author: Weiqun Zhang Date: Mon Jul 2 10:42:01 2018 -0700 Merge branch 'sfc' into development commit 1b1fad431ffe4a546ec971a01d1e6fd0b0af951b Merge: 30149e4eb 76f5e80c7 Author: Weiqun Zhang Date: Mon Jul 2 10:41:34 2018 -0700 Merge branch 'knapsack' into development commit 30149e4ebd623991b404a2d90fc40f794d1d8ed3 Author: Weiqun Zhang Date: Mon Jul 2 10:40:21 2018 -0700 update CHANGES CHANGES commit 7bacb018680dac8c6c3e735b82d845828bb46d5b Merge: 432b1218c 954032cf5 Author: Weiqun Zhang Date: Fri Jun 29 18:33:28 2018 -0700 Merge branch 'eb2' into mlmg commit 954032cf52741606e1b92348ce924b6c4f838e2d Author: Weiqun Zhang Date: Fri Jun 29 18:08:26 2018 -0700 detect mutli-values in 2d Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 432b1218cbdbcd908513ccd045f0afa087bd0e60 Author: sireeveslbl Date: Fri Jun 29 16:37:01 2018 -0700 Bugs somewhere, maybe in the interp. Gotta buscar! Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 6c748a75abd100c8db7170139b3bf6f8913af2b9 Author: sireeveslbl Date: Fri Jun 29 15:11:45 2018 -0700 MLEBABecLap_3d compiles, fixed interpolation to multi-D. Needs testing Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit df7b16c20911389890b5cf99171399cdc7ff8f34 Merge: c59f538af ca99e0530 Author: WeiqunZhang Date: Fri Jun 29 14:15:38 2018 -0700 Merge pull request #276 from AMReX-Codes/bugfix_Convergence_tools fix convergence tools in 1D commit c59f538af06a54b951a9135ad7aab5d18183329c Author: Weiqun Zhang Date: Fri Jun 29 13:45:31 2018 -0700 IntVect version of iMultiFab::define Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit d7fd2bb2b60d67c6a81fb4d63e9b133c94d244dd Author: Michele Rosso Date: Thu Jun 28 17:59:26 2018 -0700 CMake: bug fixes Src/Extern/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit cc6ae87b67ea697c9729b101285d9814f5ce8619 Merge: a3afb8634 796e155ac Author: Michele Rosso Date: Thu Jun 28 17:01:19 2018 -0700 Merge branch 'development' into mr/cmake commit a3afb863409f0de3e4c664f437a4aa045ec5665c Author: Michele Rosso Date: Thu Jun 28 16:37:10 2018 -0700 CMake: improve installation step Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit 76f5e80c7269f85ff490ac8c257ccea1a6afcd70 Author: Weiqun Zhang Date: Thu Jun 28 16:34:16 2018 -0700 knapsack: minor cleanup Src/Base/AMReX_DistributionMapping.cpp commit e266b425fa97afe529ffac7bcdeb2eea2f39ec8b Author: Weiqun Zhang Date: Thu Jun 28 16:04:04 2018 -0700 knapsack swap: only need to check the end Src/Base/AMReX_DistributionMapping.cpp commit ca99e05308f88f9e9b2a44b0a9b1c029daf516f2 Author: Emmanuel Motheau Date: Thu Jun 28 13:50:07 2018 -0700 fix convergence tools in 1D Src/Extern/ProfParser/AMReX_AVGDOWN_1D.F Tools/C_util/Convergence/GNUmakefile commit 3318c23dcfc0f35dc4dd3c14e7c1a514efbce471 Author: sireeveslbl Date: Thu Jun 28 13:44:42 2018 -0700 First function compelete Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit f960f6aad75366a5c211c4362e982a0e3fb692b0 Author: Michele Rosso Date: Thu Jun 28 11:01:00 2018 -0700 CMake: use generator expressions when setting compiler flags Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit 0a857b49c2abd557a43160c8fac908d4a478cb68 Author: Weiqun Zhang Date: Thu Jun 28 10:59:02 2018 -0700 knapsack: timer and assertion Src/Base/AMReX_DistributionMapping.cpp commit 796e155ac52a07d486966a70e9e77b0ee85c12c0 Merge: bd82031a3 36ab899cc Author: Johannes Blaschke Date: Thu Jun 28 10:18:38 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit bd82031a3feefd2ad499303aa4734438d6b28dff Author: Johannes Blaschke Date: Thu Jun 28 10:18:34 2018 -0700 boundary level-set initialization ignored periodic directions (filled using FillBoundary anyway) Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 4d89ac16ae29b1a611db4d78c68bb9387233dfbe Author: Weiqun Zhang Date: Thu Jun 28 07:32:34 2018 -0700 knapsack: if the top has only one Box, there is no need to check swapping Src/Base/AMReX_DistributionMapping.cpp commit 49c3bb356915f00b6787168cf6fccad95b67b261 Author: Weiqun Zhang Date: Thu Jun 28 07:21:41 2018 -0700 knapsack: switch order for performance Src/Base/AMReX_DistributionMapping.cpp commit aaa933a7b11cde0d084d7837be6049a455f93b30 Author: Weiqun Zhang Date: Thu Jun 28 07:02:39 2018 -0700 knapsack: list -> vector Src/Base/AMReX_DistributionMapping.cpp commit 36ab899cc67296f632f7da28c2a71e3713036be7 Merge: 5f0327ddc 63fbc614b Author: Marc Day Date: Wed Jun 27 19:30:53 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5f0327ddc5214625981cb7fee20609d74c53a83e Author: Marc Day Date: Wed Jun 27 19:30:26 2018 -0700 Add a utility to append stuff to plotfiles...requires some care to use. following instructions on screen after plotfile modified this way. Tools/C_util/AppendToPlotFile.H Tools/C_util/AppendToPlotFile.cpp commit 63fbc614b4542581114eb6ca5cdc05d2ee414ed0 Merge: e86cf5329 e31932d6d Author: Andrew Myers Date: Wed Jun 27 18:47:10 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e86cf5329f137082f57878c0cd028c0f28838d53 Author: Andrew Myers Date: Wed Jun 27 18:46:40 2018 -0700 force it to rebuild the CellVectors every time Redistribute is called. Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit bce53cba156f1e0bf6fd4448d8103c33d808024b Author: Andrew Myers Date: Wed Jun 27 18:44:20 2018 -0700 lower dt Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 6cb32e97053087b612367fbb0686982e4903461a Author: Andrew Myers Date: Wed Jun 27 18:43:55 2018 -0700 make this loop work with tiling Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Particles/CellSortedParticles/cell_sorted_F.H Tutorials/Particles/CellSortedParticles/main.cpp commit 5f44c2cc57ff22fde2c942a1f4c9adcf088b11a4 Author: Andrew Myers Date: Wed Jun 27 18:38:26 2018 -0700 typo fix Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 9dc4c831e78cb2878e1caed03374b1395201597a Author: Michele Rosso Date: Wed Jun 27 17:56:22 2018 -0700 CMake: update tutorials Tools/CMake/AMReX_Compilers.cmake Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_F/CMakeLists.txt Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/CMakeLists.txt Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 Tutorials/CMakeLists.txt commit e31932d6dc751c97cd9ddbf5a153aaf9be444c56 Author: Ann Almgren Date: Wed Jun 27 17:22:12 2018 -0700 Remove IOIOI cout statements for precreating directory struture Src/Amr/AMReX_Amr.cpp commit 5bd3164afa9aac1bcd5a0f375a9fa1eeed94ed6a Author: Michele Rosso Date: Wed Jun 27 16:16:07 2018 -0700 CMake: set manually C++ std flags to enable transitive dependencies on this property CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake commit fda7766915f13e5c32c2059ea6bfd2f986445e3f Author: Michele Rosso Date: Wed Jun 27 15:02:41 2018 -0700 CMake: some modifications to support different scenarios Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake commit 3335e86bf5439539b67b235ff36df5e0566fdecd Author: Kevin Gott Date: Wed Jun 27 17:27:28 2018 -0400 Remove blockSize from particle blocks_and_threads. Src/Base/AMReX_Device.cpp commit 6e3b58115473de262def5164bf6f6395473041d0 Author: Johannes Blaschke Date: Wed Jun 27 14:06:05 2018 -0700 only manually fill valid non-periodic boundaries Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 13da92224793b3d6dc0518b870f8b7a7a38b8c46 Author: Johannes Blaschke Date: Wed Jun 27 13:30:29 2018 -0700 almost done eliminating all the copy-and-paste bits Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit be135d7b289642ea3baa16bd223d774268ec14df Author: Kevin Gott Date: Wed Jun 27 15:18:01 2018 -0400 Direct, unedited copy of tutorial from gpu_particles. Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Particles.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/main.cpp Tutorials/Particles/ElectromagneticPIC/script.sh Tutorials/Particles/ElectromagneticPIC/test.cpp commit 57fbaaddf0fb317b707c19174884c4793c03c7e4 Author: Michele Rosso Date: Wed Jun 27 10:40:36 2018 -0700 CMake: some bug fixes Tools/CMake/AMReX_Config.cmake commit fbe95bbeb3ac08504451ef9b6afabeb8791275e4 Author: Weiqun Zhang Date: Wed Jun 27 10:34:32 2018 -0700 add inputs Tests/LinearSolvers/CellEB/inputs commit 6781596a7e4f9911b57d6c3f4131df81e928cfff Merge: d87b1da90 ef8d4bab3 Author: Johannes Blaschke Date: Wed Jun 27 10:09:14 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d87b1da904cc40e92ecc7c912fa8f561362e2619 Author: Johannes Blaschke Date: Wed Jun 27 10:08:49 2018 -0700 some more cleaning and removing unncessary arguments Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit f1bcaf745d2ef0da62f4cf6fb3b99f7b4794481b Author: Johannes Blaschke Date: Tue Jun 26 21:57:16 2018 -0700 more cleaning up Src/EB/AMReX_EB_levelset_F.F90 commit 428cb47ce2c882f80f715bc07426c081d53fce52 Author: Johannes Blaschke Date: Tue Jun 26 18:48:27 2018 -0700 working on cleaning copy-and-paste Src/EB/AMReX_EB_levelset_F.F90 commit ef8d4bab3d16885d22fafd95ba06a562a9318b83 Merge: 47b820d2f 4acffee07 Author: Andrew Myers Date: Tue Jun 26 17:52:20 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 47b820d2fcf730f48792b7c4ce5fbd2e8f14e14c Author: Andrew Myers Date: Tue Jun 26 17:52:02 2018 -0700 periodic shift should *repeatedly* shift the particle until it is inside. Src/Particle/AMReX_ParticleContainerI.H commit 697426b2f17884c4356b83d246a92b003551ca06 Author: Michele Rosso Date: Tue Jun 26 17:49:11 2018 -0700 CMake: further improvements Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit 4acffee07cd29abf31730e1b831aa5c5f64a0d81 Author: Johannes Blaschke Date: Tue Jun 26 17:36:10 2018 -0700 fill level set manually in boundary points Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 55479a619c12754862c313aacd3a2637c2b276a4 Author: Michele Rosso Date: Tue Jun 26 15:51:44 2018 -0700 CMake: continue transition to 'modern CMake' CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake commit d81c618f21719fb32b8ed6b39894b3d84d6682b4 Author: Andrew Myers Date: Mon Apr 23 19:10:18 2018 -0400 add macro and helper routine for launching particle kernels Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_Managed.H commit 2f90deb67c9791aa38bd7f756cace75c6b3f1563 Author: Ann Almgren Date: Wed Jun 6 14:56:11 2018 -0400 Add CharVector that can be CUDA memory managed and make neighbors now be managed the way particles are. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_Particles.H commit 77805a6a638370cebb6bb917a893ed70ff9e5141 Author: Andrew Myers Date: Wed Dec 20 14:59:45 2017 -0800 finish fixing gpu_particles branch Src/Particle/AMReX_Particles.H commit 4510dd9939ae0079bc48cc8488067c785be2e331 Author: Andrew Myers Date: Wed Dec 20 10:24:15 2017 -0800 some work on fixing the gpu_particles branch. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 4836d76c7344389aa15372403b7accdace35c89c Author: sireeveslbl Date: Tue Jun 26 14:38:33 2018 -0700 Pulse Inputs to use EB2 stuff Tutorials/EB/CNS/Exec/Pulse/inputs commit f27a6970246d7cc1b591aacfa9724be3a437737c Author: sireeveslbl Date: Tue Jun 26 14:26:55 2018 -0700 MyTest.cpp Tests/EBEB2/MyTest.cpp commit c6f9e437b209b9836c7ca96a20735f1462002781 Author: sireeveslbl Date: Tue Jun 26 14:14:43 2018 -0700 Minor Format Change Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 73fdb7c01c564dca0a3bd47516962ea1011c037b Author: sireeveslbl Date: Tue Jun 26 14:11:52 2018 -0700 Wrote combustor function for EB1 to follow same params as EB2. Edited initialize_EBIS to take additional Geometry argument, for the effective construction of the flattened corner. Removed the old polygon_revolution params in input. Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/main.cpp commit 99d17e26422317b6ef3a4d74876f294b15439d4a Author: Kevin Gott Date: Tue Jun 26 16:54:07 2018 -0400 Fix after merge. Tools/GNUMake/sites/Make.olcf commit e6e53b92bf3770c776d45e9d73504e8add28cf6b Merge: 2306a221e 4d8502ca3 Author: Kevin Gott Date: Tue Jun 26 16:44:37 2018 -0400 Merge with development. commit 2306a221e30459a8109b408ca476753d2fe0ad4a Author: Kevin Gott Date: Tue Jun 26 15:34:50 2018 -0400 HeatEquation Inputs and run.script Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script commit fd8e5fefb930296d3cfe55a47ae06d5a91355895 Author: Max Katz Date: Tue Jun 26 03:03:35 2018 -0700 Automatically generate both host and device functions Tools/F_scripts/gpu_fortran.py Tools/F_scripts/write_cuda_headers.py commit 5a86ca9ba4b8e0ffac3ba1929a97a75f45345822 Author: Max Katz Date: Tue Jun 26 01:26:51 2018 -0700 Move module use statements into subroutines Src/Base/AMReX_BaseFab_nd.F90 commit 6b9eae69aeaf99dac5f992be0daad24e88896f1a Author: Kevin Gott Date: Mon Jun 25 22:13:52 2018 -0400 Split work on GPU to 1 grid cell per GPU thread. Src/Base/AMReX_Box.H Src/Base/AMReX_Managed.H Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp commit e65168f1980529903d1cdc2728b4d640935d5d56 Author: sireeveslbl Date: Mon Jun 25 16:52:17 2018 -0700 Combustor Inputs returned to original problem Tutorials/EB/CNS/Exec/Combustor/inputs commit 4d8502ca3da9479df08d6244a78fe13f9b7e725d Author: Andrew Myers Date: Mon Jun 25 16:31:18 2018 -0700 update the Tests and the Tutorials Tests/Particles/AssignDensity/GNUmakefile Tests/Particles/AssignMultiLevelDensity/main.cpp Tests/Particles/GNUmakefile Tutorials/Particles/CellSortedParticles/GNUmakefile Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/NeighborList/GNUmakefile commit 7e2701896137e6595e3adc8c99f72ad93c500bea Author: Andrew Myers Date: Mon Jun 25 16:30:13 2018 -0700 don't need these includes any more Src/Particle/AMReX_Particles.H commit 75d76b10f85cd976400d472476a86d6700a4bc4e Author: Andrew Myers Date: Mon Jun 25 16:29:56 2018 -0700 ... and actually remove it from Src/Particles Src/Particle/AMReX_ParticleContainerI.H commit 64ea0677ae3da70383052abe5b5f3e4b9fe77f0c Author: Andrew Myers Date: Mon Jun 25 16:29:24 2018 -0700 move implementation of multi-level assign density into Src/AmrCore Src/AmrCore/AMReX_AmrParticles.H commit 99c01ca0c1dfd5657e784d96e48e692fc780b5cf Author: sireeveslbl Date: Mon Jun 25 16:17:25 2018 -0700 Changed inputs for working EB2, need to translate old EB to work with new inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs commit 18b54728fd91f20b8dd6128b6590c44e16ab0c5e Author: Weiqun Zhang Date: Mon Jun 25 16:05:19 2018 -0700 test for CC EB solver Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB/Make.package Tests/LinearSolvers/CellEB/MyEB.H Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB/initEB.cpp Tests/LinearSolvers/CellEB/main.cpp commit da3509b5d272e94e542fa2bae1a2c3c1132ae3fc Author: Weiqun Zhang Date: Mon Jun 25 15:45:35 2018 -0700 add 3d version of amrex_mlmg_eb_cc_interp to public Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit 800390ea20ede398b0ef1efac276f04c3eb3590b Author: sireeveslbl Date: Mon Jun 25 13:14:18 2018 -0700 CNS combustor is finished for EB2, user defines locations of planes, boxes etc Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Source/CNS_init_eb2.cpp commit 50d3411a428f148d88c8032b0155726c7b4d918f Author: Andrew Myers Date: Mon Jun 25 12:15:40 2018 -0700 we need to include EB2 to build now. Tutorials/Particles/EBParticles/GNUmakefile commit c7d4df9b54b15558aa4116b9592dfe70a0c0381b Merge: 526b275f9 b02764fdb Author: Andrew Myers Date: Mon Jun 25 10:48:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 526b275f90f9d58976a8c4071da32883adb8cf13 Author: Andrew Myers Date: Mon Jun 25 10:48:36 2018 -0700 break this timer into two Src/Particle/AMReX_ParticleContainerI.H commit c5358da231cb9c411fab9ed2e7d90fc0d9c323cb Author: Max Katz Date: Mon Jun 25 01:26:58 2018 -0700 Write out the actual CUDA code instead of using the macro Tools/F_scripts/write_cuda_headers.py commit a40fee086f5746bc121cb4db9eeb16171e4ecb12 Author: Max Katz Date: Mon Jun 25 01:14:17 2018 -0700 Also capture Fortran functions Tools/F_scripts/gpu_fortran.py commit 58d8321f068929ed3ff6da4b7b41333b535cc358 Author: Max Katz Date: Mon Jun 25 01:07:37 2018 -0700 Replace with attributes(device) instead of AMREX_DEVICE Tools/F_scripts/gpu_fortran.py Tools/F_scripts/write_cuda_headers.py commit e46cdb267f95bb4721c16cf7d5ea420d0cde6197 Author: Max Katz Date: Sun Jun 24 23:52:37 2018 -0700 Update script info Tools/F_scripts/write_cuda_headers.py commit 9cc7717649b1f07e1954987a17810f438d2f3abd Merge: 7c70d8d29 c3161c486 Author: Max Katz Date: Sun Jun 24 23:46:44 2018 -0700 Merge branch 'gpu' into gpu-gpu commit c3161c48685ce68a2fee272ba993eee56cdfde77 Author: Max Katz Date: Sun Jun 24 23:37:32 2018 -0700 Preprocess CUDA files to look for !$gpu Tools/F_scripts/gpu_fortran.py Tools/GNUMake/Make.rules commit 13c037ea0aa68e0eb70976e01770b21255f2e594 Author: Max Katz Date: Sun Jun 24 23:32:32 2018 -0700 Only do the CUDA header work in the tempdir Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit 9ae00258b6d3228df6dcb42bfafd054ff0ff24fd Author: Max Katz Date: Sun Jun 24 22:56:05 2018 -0700 Really fix source term copying Tools/GNUMake/Make.rules commit e5cde30f59c4e060077b9e0897fb6a50b11c2391 Author: Max Katz Date: Sun Jun 24 22:39:08 2018 -0700 Fix source file copying Tools/GNUMake/Make.rules commit e88588e5fb51a330c981e742efd4730cac820421 Author: Max Katz Date: Sun Jun 24 16:19:57 2018 -0700 Use the srcTempDir for the dependency generation Tools/GNUMake/Make.rules commit 121bd385ccb9d57a4106772b0830686406a1ab61 Author: Max Katz Date: Sun Jun 24 16:03:43 2018 -0700 Fix tmpbuilddir logic Tools/GNUMake/Make.rules commit 9406ac004c610c7d732fd27c629b8622c0a1a6b3 Author: Max Katz Date: Sun Jun 24 16:00:32 2018 -0700 Add a missing @ Tools/GNUMake/Make.rules commit ba483a6ac97f7cef6f519d19d96529d5693d8c87 Author: Max Katz Date: Sun Jun 24 15:17:27 2018 -0700 Always include the temp build directory first Tools/GNUMake/Make.defs commit e1aa87114abe50d4ad1a39bdb9f3480a08641020 Author: Max Katz Date: Sun Jun 24 15:02:59 2018 -0700 Reverse order so that source copies occur first Tools/GNUMake/Make.rules commit 69bf42190ccb725ac26b33e1f036d658c6063763 Author: Max Katz Date: Sun Jun 24 14:20:48 2018 -0700 Copy all source files to a temp build directory before compilation Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 7c70d8d29d6f30688808c3f00cab4f67652987ba Author: Max Katz Date: Sat Jun 23 21:21:03 2018 -0700 [WIP] Update the CUDA script description Tools/F_scripts/write_cuda_headers.py commit 64dfddba06ed20d4a9d4bd02827008155b31595c Author: Max Katz Date: Sat Jun 23 21:19:21 2018 -0700 [WIP] Update the CUDA script description Tools/F_scripts/write_cuda_headers.py commit c8c36717097b95d6a53f85722c7457ec66a0dc91 Author: Max Katz Date: Sat Jun 23 21:14:37 2018 -0700 Replace AMREX_DEVICE with !$gpu Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit d4bcc41b0b070404ae7a9b9ebf7bad01d2542f71 Author: Max Katz Date: Sat Jun 23 20:28:24 2018 -0700 Add some more GPU defines Tools/GNUMake/Make.defs commit a702c708071cc8b600e7cfa2124ca51397ffc38f Merge: b41bec709 b02764fdb Author: Max Katz Date: Sat Jun 23 14:45:39 2018 -0700 Merge branch 'development' into gpu Conflicts: Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Tools/GNUMake/sites/Make.olcf commit b02764fdb7c19739f9bc2129b012b0afba5f0a50 Author: Max Katz Date: Sat Jun 23 14:38:28 2018 -0700 Add reduction macros Src/Base/AMReX_BLFort.H commit b41bec709cfd7c6fcb3cac1e38989805f9ed4ae3 Author: Max Katz Date: Sat Jun 23 14:13:48 2018 -0700 Fix logic on the nvcc version check Src/Base/AMReX_BLFort.H commit 976b61db32359ab9d662516d8d08b7639fafe2ef Author: Max Katz Date: Sat Jun 23 15:36:18 2018 -0400 Remove legacy non-CUDA 8 code Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.cpp Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.olcf commit d765df200c7dc7f7e059a9d42f15519cb8b57899 Author: Max Katz Date: Sat Jun 23 12:16:01 2018 -0700 Disallow CUDA toolkit versions <= 8.0 Tools/GNUMake/comps/nvcc.mak commit ad68aa1bbb697aed6846808a1a59aa2ef0640672 Author: Max Katz Date: Sat Jun 23 12:12:01 2018 -0700 bl_error -> amrex_error for CUDA Src/Base/AMReX_CUDA.F90 commit 568d8ad9f0c75e86ff56af90646f31fa7b5f4c43 Author: Max Katz Date: Sat Jun 23 14:20:59 2018 -0400 Capture NVCC version Tools/GNUMake/comps/nvcc.mak commit cd50afa43ea0bd80afbdceb5ee381ecf2d85a69c Author: Michele Rosso Date: Fri Jun 22 18:15:30 2018 -0700 CMake: start transition to 'modern CMake' Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/EB/CMakeLists.txt Src/EB2/CMakeLists.txt Src/Extern/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/GeometryShop/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/CMakeLists.txt commit f11605d0f58061cf79b32ec5ac38c45db6c9de61 Author: Lawrence Minion Date: Fri Jun 22 18:05:33 2018 -0700 Getting implicit example in SDC tutorials Tutorials/SDC/HeatEquation_EX3_C/GNUmakefile Tutorials/SDC/HeatEquation_EX3_C/Make.package Tutorials/SDC/HeatEquation_EX3_C/advance.cpp Tutorials/SDC/HeatEquation_EX3_C/advance_2d.f90 Tutorials/SDC/HeatEquation_EX3_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX3_C/init_phi_3d.f90 Tutorials/SDC/HeatEquation_EX3_C/inputs_2d Tutorials/SDC/HeatEquation_EX3_C/inputs_3d Tutorials/SDC/HeatEquation_EX3_C/main.cpp Tutorials/SDC/HeatEquation_EX3_C/myfunc.H Tutorials/SDC/HeatEquation_EX3_C/myfunc_F.H Tutorials/SDC/HeatEquation_EX3_C/pf_quadrature.f90 commit 5784a293b03ea40adfe1a7bb515803c1ef72e7cd Author: Andrew Myers Date: Fri Jun 22 16:55:58 2018 -0700 use std::memcpy here instead of reinterpret_cast Src/Particle/AMReX_ParticleContainerI.H commit f6b1ebb041503825e26bf3baf86aaeda791648de Author: Andrew Myers Date: Fri Jun 22 16:15:08 2018 -0700 simplify timers Src/Particle/AMReX_ParticleContainerI.H commit d4bb40e66c98a186fcdbcabe535f9a6d991f6cf2 Author: Andrew Myers Date: Fri Jun 22 16:11:40 2018 -0700 remove code that isn't needed any more Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 0e3e68fcfb487d85c145d1ac0193b0dabb0934d5 Author: Andrew Myers Date: Fri Jun 22 16:09:32 2018 -0700 remove an un-needed copy Src/Particle/AMReX_ParticleContainerI.H commit 6f9629d47e78df1afd64d3a73d38d7f2b88f8de6 Author: Andrew Myers Date: Fri Jun 22 13:48:20 2018 -0700 Some systems require flush calls here for the particle io to work correctly. There is a similar work-around in AMReX_FArrayBox.cpp. Src/Particle/AMReX_ParticleContainerI.H commit 76b3e77c63bea2b6f70142bcf5648d15c4bdb9e1 Merge: 2aa1ecfdd a66a2676f Author: Andrew Myers Date: Fri Jun 22 13:04:24 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2aa1ecfdd97334d555ecce10b903fbd09cb98d18 Author: Andrew Myers Date: Fri Jun 22 12:01:57 2018 -0700 try threading only the locate Src/Particle/AMReX_ParticleContainerI.H commit 782048a5b102a4be24be363de9db6bf7e00cef73 Author: Andrew Myers Date: Fri Jun 22 11:43:27 2018 -0700 add some more timers Src/Particle/AMReX_ParticleContainerI.H commit 2bd98e48e6ec3d896c832679caafbeb626219137 Author: Andrew Myers Date: Fri Jun 22 11:32:25 2018 -0700 adding threading to the unpack Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit a66a2676fce13e0062aab9ce18a3836c54f261e0 Author: Weiqun Zhang Date: Fri Jun 22 07:15:47 2018 -0700 need to test the fortran function ptr in interp hook Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp commit e10441995db13a801a0c809264d7b1000492ddc7 Merge: bfef39ebf f8ec4d84d Author: Weiqun Zhang Date: Thu Jun 21 18:13:40 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bfef39ebf3d201f6b75a5956149153ba7fb1e9b8 Author: Weiqun Zhang Date: Thu Jun 21 18:13:28 2018 -0700 minor Src/AmrCore/AMReX_FillPatchUtil.H commit 6d86765ecbe95ea5d01d2b8ce1ba3d25253ff571 Author: Weiqun Zhang Date: Thu Jun 21 18:06:15 2018 -0700 show how to use interploation hooks in tutorial Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/Amr/Advection_octree_F/Source/fillpatch_mod.F90 commit ac6d7b00245ba7746af8fe9cdda68fb75b80ab96 Author: Weiqun Zhang Date: Thu Jun 21 17:50:41 2018 -0700 add pre- and post-interp hooks in fillpatch for flash Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 commit 6eebf3fecf862845345948e8a7628e6b5161b2d3 Author: Andrew Myers Date: Thu Jun 21 17:41:50 2018 -0700 update test Tests/Particles/test.py commit 58b37604ab7e3e54fd7498415f5d8836db3ad895 Author: Andrew Myers Date: Thu Jun 21 17:41:36 2018 -0700 start threading unpacking the particle data in RedistributeMPI Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 95b6697e6f41cb075d20858a811b124d4b660fc0 Author: Michael Zingale Date: Thu Jun 21 18:38:16 2018 -0400 remove duplicate signatures from the list of targets Tools/F_scripts/write_cuda_headers.py commit f8ec4d84d6d93aef06815ed55914f6bc1cb59bf5 Author: Johannes Blaschke Date: Thu Jun 21 10:54:39 2018 -0700 Avoid FillBoundary in recursive step Src/EB/AMReX_EB_levelset.cpp commit eb264040b9a59299c3b3cf16cb33be2fcee6c2e3 Merge: ed5173526 0c90ce2bc Author: Michele Rosso Date: Thu Jun 21 09:57:21 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ed5173526c190fe8c277e81f796442622fdd8f1e Author: Michele Rosso Date: Thu Jun 21 09:57:12 2018 -0700 CMake: add NDEBUG only in non-XSDK mode Tools/CMake/AMReX_Defines.cmake commit 39de63a406a32cfe3217e7ec367c7f8118ed1ac0 Author: Max Katz Date: Thu Jun 21 09:36:09 2018 -0700 Do reductions on host when not offloading Src/Base/AMReX_BaseFab.cpp commit 7e13fddd461cb70ac5ce3b5b5ecd531d5da5a146 Author: Max Katz Date: Thu Jun 21 08:00:46 2018 -0700 Add flag to disable device offload Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 0c90ce2bc44433a845655738c4937d80d538dbb6 Author: Weiqun Zhang Date: Wed Jun 20 21:54:44 2018 -0700 NDEBUG -> AMREX_DEBUG Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/Base/AMReX.H Src/Base/AMReX_BLassert.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_IArrayBox.cpp Src/Boundary/AMReX_LO_UTIL.F90 Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Convergence/RichardsonConvergenceTest.cpp Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp Tools/GNUMake/Make.defs commit 0911eed7a39394dbd4a45c873c2248934e041784 Author: Weiqun Zhang Date: Wed Jun 20 17:59:48 2018 -0700 compiles Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit d5c9a32aec89834d201f724a39e7e482568630aa Author: Kevin Gott Date: Wed Jun 20 20:39:05 2018 -0400 Broken Arena Change Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BArena.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CArena.H commit 0a81f14094d90d5646c300419f70cd724002d770 Author: sireeveslbl Date: Wed Jun 20 17:09:12 2018 -0700 Ramp written for EB2, with both regular plane arguments and slope-point args. tested with Sod, will test Shock Reflection Tutorials/EB/CNS/Exec/Sod/inputs Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/CNS_init_eb2.cpp commit 25b770c5438993fbc8b5de304f48f52b2eb2c488 Author: Johannes Blaschke Date: Wed Jun 20 17:02:00 2018 -0700 change the way `valid` is populated... this should perform better if n_pad is large Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 303b6319fc67d01dfd25ecb2fabe2bfbcac136d2 Author: Kevin Gott Date: Wed Jun 20 18:41:11 2018 -0400 Update inputs files. Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d commit 8cf5b25c9060a050e6f95e429b3c0e6ada3e8e34 Author: Kevin Gott Date: Wed Jun 20 17:52:52 2018 -0400 Addition of Device & CUDA from Max's branch. Devices initialize & finalize added to AMReX.cpp. Arenas adjusted to work with multiple MPI ranks. Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_Managed.H Src/Base/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HelloWorld_C/main.cpp commit 79650123e53095383ef0eb381299100e94bcad42 Author: Minion Date: Wed Jun 20 12:34:08 2018 -0700 moving SDC tutorials into separate directory Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile Tutorials/SDC/HeatEquation_EX1_C/Make.package Tutorials/SDC/HeatEquation_EX1_C/advance.cpp Tutorials/SDC/HeatEquation_EX1_C/advance_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/advance_3d.f90 Tutorials/SDC/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/SDC/HeatEquation_EX1_C/inputs_2d Tutorials/SDC/HeatEquation_EX1_C/inputs_3d Tutorials/SDC/HeatEquation_EX1_C/main.cpp Tutorials/SDC/HeatEquation_EX1_C/myfunc.H Tutorials/SDC/HeatEquation_EX1_C/myfunc_F.H Tutorials/SDC/HeatEquation_EX1_C/pf_quadrature.f90 commit 723e167a45164f32ea03a96cf1a51d9415fd52a0 Merge: 7983a86d0 d3a127c70 Author: Minion Date: Wed Jun 20 12:29:11 2018 -0700 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit 7983a86d014f5505ffcfcee146a33fb64bc98c9f Author: Minion Date: Wed Jun 20 12:28:28 2018 -0700 starting to clean up SDC structures Tutorials/Basic/SDCHeat_Equation_EX1_C/GNUmakefile Tutorials/Basic/SDCHeat_Equation_EX1_C/Make.package Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H Tutorials/Basic/SDCHeat_Equation_EX1_C/pf_quadrature.f90 commit 3766d6a8bab33c0320e4acaae80edfed0e9994ea Author: Johannes Blaschke Date: Wed Jun 20 11:41:51 2018 -0700 fix naming convention for fortran module Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset_F.F90 commit a83507a0e26add9ca3248a50a2ce3c833e62d897 Author: Weiqun Zhang Date: Wed Jun 20 09:52:11 2018 -0700 add an argument to makeSFC to limit the maximal number of boxes a process can get Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit a86326cc5dda3be186bb756e8da3cfb7036b199c Author: Michael Zingale Date: Wed Jun 20 12:13:01 2018 -0400 fix the ability to compile normal after CUDA w/o headers getting in the way Tools/GNUMake/Make.rules commit 08307bb0c1f8a48573f81eff22aac5a4deceff5b Author: Weiqun Zhang Date: Wed Jun 20 07:59:21 2018 -0700 update make Src/EB2/CMakeLists.txt Src/EB2/Make.package commit a8421ed87904f2869578e2f2bf8f0a94dd9d8450 Author: Max Katz Date: Tue Jun 19 19:53:30 2018 -0700 Generalize the IBM config so it is not OLCF specific Tools/GNUMake/comps/ibm.mak Tools/GNUMake/sites/Make.olcf commit 2f2acc311d50c8fb9ccb69f1d1140831894267fc Author: Max Katz Date: Tue Jun 19 19:51:16 2018 -0700 Update LLNL MPI setup Tools/GNUMake/sites/Make.llnl commit 34e39cbec74f61bc5d231a19b69fb76ee4ecc131 Author: Weiqun Zhang Date: Tue Jun 19 18:07:48 2018 -0700 RotationIF: fix 2d compilation; add std:: to cos and sin for portability; fix the sign in rotation matrix because we are rotating the object. Src/EB2/AMReX_EB2_IF_Rotation.H commit 26f4d00baf6abc2ffc6cf8de3e8138ec6c4c8253 Author: Weiqun Zhang Date: Tue Jun 19 17:27:45 2018 -0700 fix typo Src/AmrCore/AMReX_INTERP_2D.F90 commit 3e180e08588d7faa535834bd3b9e8727f87cc266 Merge: 2f83e472e 954ed5f2c Author: Weiqun Zhang Date: Tue Jun 19 17:15:42 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2f83e472e16903334fa3f7f16084cdf41563a19c Author: Weiqun Zhang Date: Tue Jun 19 17:15:29 2018 -0700 xSDK: fix some Fortran print Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/EB2/AMReX_eb2_3d.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 commit d3a127c70971be6fbcb82356a1e51be283aa7d9a Author: Weiqun Zhang Date: Tue Jun 19 17:03:47 2018 -0700 typo Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H commit f1bc3faa6eeb6618b5234c2ecc924e7d53e8d7b8 Author: Weiqun Zhang Date: Tue Jun 19 16:38:09 2018 -0700 xSDK: print Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrCore.H Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/EB2/AMReX_EB2_GeometryShop.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 4356487b7ccc0ffcb9a54cc432e19937d826885f Author: sireeveslbl Date: Tue Jun 19 16:24:22 2018 -0700 Rotation about the origin axes Src/EB2/AMReX_EB2_IF_Rotation.H commit 954ed5f2c9368dd088a4f1aeab5c480f7550284c Merge: 792a904ee bd5477a9c Author: Johannes Blaschke Date: Tue Jun 19 16:08:45 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 792a904eec1ae9ca2ac55a51a710f5d8f61565ea Author: Johannes Blaschke Date: Tue Jun 19 16:08:42 2018 -0700 update EB level-set to reflect recent changes in mfix Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 Src/EB/AMReX_compute_normals.F90 commit bd5477a9c3262d59c2cbd04d78201658a440a8dc Author: Weiqun Zhang Date: Tue Jun 19 15:17:42 2018 -0700 turn off print unless verbose is true Src/Base/AMReX_Utility.cpp commit 19313a92be69c4178ba1023c309e1e741a33021c Author: Weiqun Zhang Date: Tue Jun 19 15:17:02 2018 -0700 add amrex::RuntimeError and amrex.throw_exception ParmParse parameter Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Exception.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 5f6d498fb63cfe2c6fc849f291b81ad6dc77a4de Author: Andrew Myers Date: Tue Jun 19 12:26:45 2018 -0700 some clean up / comments Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 3f569b5497139cca5a1a76a09078df45ab060ffa Author: Andrew Myers Date: Tue Jun 19 12:20:51 2018 -0700 store vectors directly instead of unique_ptr to vectors Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 9f650ea0c0c8a8812b62da95b8f1055657774662 Merge: 4f0d546f2 37afd673f Author: Andrew Myers Date: Tue Jun 19 10:52:02 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4f0d546f221b1f98b5e045f640923d18f641eac7 Author: Andrew Myers Date: Tue Jun 19 10:51:45 2018 -0700 remove another unused variable. Src/Base/AMReX_NFiles.cpp commit 67f56724ea1789403ba77ff17f1362add1f22fc0 Author: Andrew Myers Date: Tue Jun 19 10:47:31 2018 -0700 remove unused variables. Src/Base/AMReX_MultiFabUtil_nd.F90 commit 37afd673f9947b093bab463e59b664a91963abff Author: Andrew Myers Date: Tue Jun 19 09:50:10 2018 -0700 adding an additional Timer to RedistributeMPI Src/Particle/AMReX_ParticleContainerI.H commit 2a4efea2f1dfd6cfecf75c8386a3c557755e680e Author: Andrew Myers Date: Mon Jun 18 16:33:31 2018 -0700 remove need to explicitly update the structure of the cell vectors. Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/main.cpp commit cbdbee6b74908a400083ff011a4d9018f1740ea2 Merge: d987660f4 b88cd73a8 Author: Andrew Myers Date: Mon Jun 18 15:40:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d987660f41e89e832799c3fe2a70efe2242a1f41 Author: Andrew Myers Date: Mon Jun 18 15:40:41 2018 -0700 starting to track to the ref of the BA and DM that the cell vectors are defined on. Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit ce50a3fa1b0117b9b37c349ccdd912485f9094b1 Author: Michael Zingale Date: Mon Jun 18 10:21:50 2018 -0400 have the python preprocessor remove unwanted preprocessor directives Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit c63f46ff65e7dd1b2067da31dab97d88bf18e608 Author: Michael Zingale Date: Mon Jun 18 10:09:11 2018 -0400 fix CUDA flags Tools/GNUMake/Make.rules commit b88cd73a8e9c0a3efa709baffac6849f1c016816 Author: Michael Zingale Date: Sun Jun 17 22:18:47 2018 -0400 add some macros to sync with what is happening on the gpu branch this gives us CPU compatibility Src/Base/AMReX_ArrayLim.H commit 7e7c4122c55572d237df83947d6f16548468660a Author: Max Katz Date: Sun Jun 17 13:03:24 2018 -0400 Handle MPICH with CUDA Tools/GNUMake/Make.defs commit 3342dbe48c805496e2712811fabbb8c862456662 Author: Michael Zingale Date: Sun Jun 17 11:41:01 2018 -0400 don't pass the MPI preprocessor directives into the CUDA stuff Tools/GNUMake/Make.rules commit 3613075489a2a3b2c6023085e5304b8f0d435c21 Author: Lawrence Minion Date: Sat Jun 16 19:24:44 2018 -0700 optimal SDC order for heat equation Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H Tutorials/Basic/SDCHeat_Equation_EX1_C/pf_quadrature.f90 commit 4c83d6724037f90c699872662ed7b024d635ed8e Author: Andrew Myers Date: Fri Jun 15 16:52:42 2018 -0700 enable OpenMP in some loops Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit ba0a78a0f77d719d523cdc392a1821d9dc1da437 Author: Andrew Myers Date: Fri Jun 15 16:45:54 2018 -0700 turn on mpi Tutorials/Particles/CellSortedParticles/GNUmakefile commit 5d32eb88bc423a85fdf44e43a69198a9c8e50df8 Author: Andrew Myers Date: Fri Jun 15 16:44:28 2018 -0700 keeping track of which particle in which cell as they move around. Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Particles/CellSortedParticles/cell_sorted_F.H Tutorials/Particles/CellSortedParticles/main.cpp commit 94f69a9eb9e523b1560efe4f0a34140f813e5342 Author: Andrew Myers Date: Fri Jun 15 14:57:56 2018 -0700 use the fortran to link when using intel with a Fortran main. Tools/GNUMake/comps/intel.mak Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/GNUmakefile Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile Tutorials/Basic/HelloWorld_F/GNUmakefile Tutorials/Basic/main_F/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile commit 482ba98598fd25f612661fd409c2ef82057f854a Author: Andrew Myers Date: Fri Jun 15 12:52:04 2018 -0700 start working on cell-sorted particles for DSMC Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/GNUmakefile Tutorials/Particles/CellSortedParticles/Make.package Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Particles/CellSortedParticles/cell_sorted_F.H Tutorials/Particles/CellSortedParticles/inputs Tutorials/Particles/CellSortedParticles/main.cpp commit f34caa7547b10445639b1fa4a78b8993fda93ad4 Author: Andrew Myers Date: Fri Jun 15 12:50:58 2018 -0700 give ParticleContainer a virtual destructor. Src/Particle/AMReX_Particles.H commit 2e0797832067d4a2f2bdb2beecf61108e0154ffd Author: Michael Zingale Date: Thu Jun 14 19:47:10 2018 -0400 add back in the c99 standard Tools/GNUMake/Make.rules commit 5dbb67046ca257762b1dd0149bb72c0c81a028f6 Author: Weiqun Zhang Date: Thu Jun 14 16:05:24 2018 -0700 EB MLMG: add interp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 075ce237d62f559a2163360235123e7369d6e4db Author: Kevin Gott Date: Thu Jun 14 18:29:50 2018 -0400 Redesign GeometryData object and data function to prevent caching. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit f581cddacbd4871acf13a00b1f847667c0d304f8 Author: Michael Zingale Date: Thu Jun 14 18:17:16 2018 -0400 remove the check on the gcc return code for now it works for gcc > 6.4.0 but not earlier Tools/F_scripts/preprocess.py commit ffedf72ed7165d940840245007d6608e1e8b83a3 Author: Weiqun Zhang Date: Thu Jun 14 14:57:39 2018 -0700 EB MLMG: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit b47e76f8c91edfa449a46165e33699765f2e4790 Author: Weiqun Zhang Date: Thu Jun 14 14:22:43 2018 -0700 EB MLMG: interp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H commit be3e7f91c490e273dd6e9d177125db6d9e9cdea6 Author: Michael Zingale Date: Thu Jun 14 17:08:31 2018 -0400 don't restrict to python3 Tools/F_scripts/write_cuda_headers.py commit 72b3d2c04a9aca3a0ab2ea8af576c4cdd504bf80 Author: Max Katz Date: Thu Jun 14 16:11:05 2018 -0400 Fix IBM MPI library Tools/GNUMake/sites/Make.olcf commit 3223c783811cec73a1c1622b95ebf60115827948 Author: Michael Zingale Date: Thu Jun 14 16:03:22 2018 -0400 this works Tools/F_scripts/write_cuda_headers.py commit 743ca37eb884392a124b7b2a5388dd6e055805b4 Author: Michael Zingale Date: Thu Jun 14 15:07:55 2018 -0400 this is mostly right, but somewhat wrong Tools/F_scripts/write_cuda_headers.py commit 8a8bc7fa123fa9481ce411c0a549a862508df393 Author: Weiqun Zhang Date: Thu Jun 14 11:22:02 2018 -0700 add a new eb_average_down Src/Base/AMReX_FabArray.H Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 516dc6a0f7032ef8d38d7903b37e3bb7286d98a2 Author: Michael Zingale Date: Thu Jun 14 13:24:49 2018 -0400 fix the case where a sig is on a line to itself Tools/F_scripts/write_cuda_headers.py commit 268e92831173e3268506c3c7fc0619e04357e080 Author: Weiqun Zhang Date: Thu Jun 14 10:10:32 2018 -0700 EB MLMG: normalize Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 2a4ad73dc5a337bec67c0be0a02c3cc5e27f076d Author: Michael Zingale Date: Thu Jun 14 11:53:48 2018 -0400 restore file that my script overwrote :( Src/Base/AMReX_BaseFab_f.H commit 9e435207d11d7a24ae7a310355b63dc84786ba5c Author: Michael Zingale Date: Thu Jun 14 11:50:25 2018 -0400 weren't storing preprocessed headers Src/Base/AMReX_BaseFab_f.H Tools/F_scripts/write_cuda_headers.py commit dcf863bc97661b6fd24ed7e0432f816d7f939b16 Author: Michael Zingale Date: Thu Jun 14 10:27:18 2018 -0400 fix the preprocessing Tools/F_scripts/preprocess.py Tools/GNUMake/Make.rules commit 07e5de83cfcf8baa32bf03cb8d284f25cd1f4565 Author: Michael Zingale Date: Wed Jun 13 21:49:08 2018 -0400 the new preprocess version of the script. Doesn't work yet Tools/F_scripts/preprocess.py Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit aec591bd6001ceca4d6a69e870deedcde9b25cd9 Merge: 50996d279 de5346057 Author: Andrew Myers Date: Wed Jun 13 17:32:50 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 50996d2791ce72a7fc2aba01631d88feb3bca788 Author: Andrew Myers Date: Wed Jun 13 17:32:38 2018 -0700 update NeighborList Tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 0e4369c3f8d1f3c67c1577c0fca552eceb47d982 Author: Andrew Myers Date: Wed Jun 13 17:32:18 2018 -0700 use a template rather than a virtual function for checking particle pairs. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 89a5e9ba71a5526d23dbcddba3a1a424eb133084 Author: Weiqun Zhang Date: Wed Jun 13 17:03:37 2018 -0700 EB MLMG: gsrb Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 75a026b586a7c2cbba6e3707d88282a5a136b416 Author: Kevin Gott Date: Wed Jun 13 19:06:56 2018 -0400 HeatEquation_EX_1 works with USE_CUDA=FALSE in 2D and 3D, with global kernels in C and passing by value. Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit ceac75dd2739c6df561f507fb24a033adf739d47 Author: Kevin Gott Date: Wed Jun 13 19:02:37 2018 -0400 Remove unnecessary #ifdefs around GeometryData object. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit e4edbe75625b99cd96eb61c2e2a2bc459117f1d9 Author: Kevin Gott Date: Wed Jun 13 19:01:34 2018 -0400 CUDA function wrappers for USE_CUDA=FALSE. Src/Base/AMReX_Managed.H commit 5984d25757d21d253d3f9b2a715c64f2c74ecfb1 Author: Kevin Gott Date: Wed Jun 13 19:00:57 2018 -0400 Creation and implementation of amrex_simpleArray to allow HOST DEVICE function declaration on macros. Src/Base/AMReX_ArrayLim.H commit 96ec006c4ef30a083dad04c616f0de9bda0a51e2 Author: Weiqun Zhang Date: Wed Jun 13 13:59:01 2018 -0700 EB MLMG: adotx and factories Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 465eb90970c44b4aa17f59d2ffb7e52b1937ba23 Author: Michael Zingale Date: Wed Jun 13 15:48:06 2018 -0400 split the preprocessor out for reuse Tools/F_scripts/dep.py Tools/F_scripts/preprocess.py commit de53460570e500b22bc27b85bd5de795294728bd Author: Weiqun Zhang Date: Wed Jun 13 12:20:10 2018 -0700 eb/cns: more udpates of inputs Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Exec/Sod/inputs commit 2310e83a5d55a6c81e1ac2c23353b6cc7e210424 Merge: 90071dd9a 1b34a9329 Author: Weiqun Zhang Date: Wed Jun 13 11:21:28 2018 -0700 Merge branch 'eb2' into weiqun/mlmg commit 1b34a93290c068d38a8f2f9541a9404c5606bc78 Author: Weiqun Zhang Date: Wed Jun 13 11:20:22 2018 -0700 eb/cns: update inputs Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Combustor/inputs.testing Tutorials/EB/CNS/Exec/Combustor/inputs_combustor Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.amr Tutorials/EB/CNS/Exec/ShockRef/inputs.regt commit 8c32a704fd0cf6495d4b17065907e4336e6def03 Author: Weiqun Zhang Date: Wed Jun 13 09:55:26 2018 -0700 Fortran: add max_coarsening_level Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 33e205d0861d2349f2d58792b2f8007a78965ec9 Author: Weiqun Zhang Date: Wed Jun 13 09:45:34 2018 -0700 Fortran: add multigrid % set_bottom_solver Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 90071dd9ad8bb70214eba4977ac802a16c26f2e3 Merge: ebb6a2e00 07d886939 Author: Weiqun Zhang Date: Wed Jun 13 08:59:22 2018 -0700 Merge branch 'eb2' into weiqun/mlmg commit 07d886939fc07a772ae930d9a7922989993a353a Author: Weiqun Zhang Date: Wed Jun 13 08:58:49 2018 -0700 fix typo Src/AmrTask/tutorials/MiniApps/HeatEquation/myfunc_F.H Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc_F.H Tests/ProfTests/ThirdParty/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc_F.H Tutorials/CVODE/EX1/myfunc_F.H Tutorials/CVODE/EX2/myfunc_F.H commit 0e82dff8192b475419933ba0bb611a762c7302ee Author: Weiqun Zhang Date: Wed Jun 13 08:54:36 2018 -0700 add init eb2 in a new file Tutorials/EB/CNS/Source/CNS_init_eb2.cpp commit ebb6a2e00a3c7c829469cb78cafb45add563465e Merge: 8dde62c18 4b47bab38 Author: Weiqun Zhang Date: Tue Jun 12 20:49:41 2018 -0700 Merge branch 'eb2' into weiqun/mlmg commit 4b47bab38fb1bfbaf6c4369ed00b13ff9f06ba41 Author: Weiqun Zhang Date: Tue Jun 12 20:49:09 2018 -0700 add required coarsening level Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Tests/EBEB2/MyTest.cpp Tutorials/EB/CNS/Source/main.cpp commit 0fa5fd0dc369ed3075bb4997fa418696c9f93693 Merge: 75721da5a 70deacbc5 Author: Max Katz Date: Tue Jun 12 20:12:43 2018 -0700 Merge branch 'development' into gpu commit 75721da5a7ea9cd151bdc57bc4bb014ff4c75b93 Author: Michael Zingale Date: Tue Jun 12 22:53:40 2018 -0400 can't have CPP_sources be a dependency for write_cuda_headers.py since it now writes the CPP sources in a new location Tools/GNUMake/Make.rules commit e67debb704b4415822b4f9d175fd1f60870ff2f1 Author: Michael Zingale Date: Tue Jun 12 21:42:26 2018 -0400 this does the C++ #pragma expansion still need to hook it into the vpath Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit 8dde62c180453857d60a83ad5ff4a8cbc3c0b29d Author: Weiqun Zhang Date: Tue Jun 12 17:13:05 2018 -0700 EBABecLap: start adotx Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 26ac13a69c08a7dc79738853d87a894d686f9855 Author: Max Katz Date: Tue Jun 12 15:41:50 2018 -0700 Use #pragma gpu Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BaseFab.cpp Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit 2419f72a3138ddbfb642fe794e8d0c77279cf430 Author: Weiqun Zhang Date: Tue Jun 12 14:56:50 2018 -0700 EBABecLap: prepare for solve Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 255fe9213e3192990fef4b820dbc09fb6596c024 Author: Weiqun Zhang Date: Tue Jun 12 13:58:43 2018 -0700 stubs Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 3da6218309759ae76eaee1c7eb5a94ef63cdd5e3 Author: Kevin Gott Date: Tue Jun 12 16:26:54 2018 -0400 Pass GeometryData by class. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit bda53b3d0cafacab01b629fbb6a23b107f1f19f5 Author: Kevin Gott Date: Tue Jun 12 16:13:19 2018 -0400 Add Pinned version of memory for passing small constant objects to kernels. Used on GeometryData. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Managed.H commit cb48bc55fa1c0011780211f6641b72d4a91fb31f Author: Weiqun Zhang Date: Tue Jun 12 13:04:08 2018 -0700 it's possible to have only one cut Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit e8f07076a3cc7262a459e459dddaf48c6a96f284 Author: Weiqun Zhang Date: Tue Jun 12 13:04:08 2018 -0700 it's possible to have only one cut Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 53bac3ee7e13540326aea905949300cefe00ac74 Merge: 58a5eb84b 3dcf1ce1a Author: Weiqun Zhang Date: Tue Jun 12 12:27:51 2018 -0700 Merge branch 'weiqun/eb2' into weiqun/mlmg commit 58a5eb84b13bf029ddb6929c86959c23739ab822 Merge: f5a88d9f3 70deacbc5 Author: Weiqun Zhang Date: Tue Jun 12 12:27:35 2018 -0700 Merge branch 'development' into weiqun/mlmg commit 6cfb6bcd8386cee33df4ab253d3241b08a7d7ba9 Author: Kevin Gott Date: Tue Jun 12 15:20:17 2018 -0400 Change HeatEquation_EX1 to pass Box by class to C++ based wrapper kernel. Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit b204c08f0fbf58e585b6b6d57e379ec4260ede27 Author: Kevin Gott Date: Tue Jun 12 15:18:30 2018 -0400 Testing passing Box into kernel by class. Tutorials/GPU/HelloWorld_C/main.cpp commit 3dcf1ce1ab9c3f5fdab1f7e8db1cdd5b9e4babc6 Author: Weiqun Zhang Date: Tue Jun 12 12:18:14 2018 -0700 EB/CNS: set support level before initializing EB2 Tutorials/EB/CNS/Exec/Sod/inputs Tutorials/EB/CNS/Source/main.cpp commit aafc649ada86c079bf14caf485bc3ebe6d4aad6a Author: Kevin Gott Date: Tue Jun 12 15:17:43 2018 -0400 Declaring a few more function __host__ __device__. Src/Base/AMReX_Geometry.H Src/Base/AMReX_RealBox.H commit 5fa5a121c7163b2c4602a1d5d42ccd89b397dd19 Author: Max Katz Date: Tue Jun 12 14:27:15 2018 -0400 AMREX_ARLIM_VAL is no longer required Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_filcc_f.H Tools/F_scripts/write_cuda_headers.py Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit 70deacbc592f6bf4ab00da083431674e3e4bdf1d Merge: ea2f56096 ea6d89f90 Author: Weiqun Zhang Date: Tue Jun 12 10:42:36 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ea6d89f9052b755fb44bd007d13209c840ae380b Merge: d4848b6c5 5ffb39150 Author: Andrew Myers Date: Tue Jun 12 10:27:30 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d4848b6c55da179745dfae45bc9b059f111ba3fc Author: Andrew Myers Date: Tue Jun 12 10:27:12 2018 -0700 just have Make.ccse refer to Make.unknown - should work on both updgraded and non-updated ccse machines. Tools/GNUMake/sites/Make.ccse commit ea2f56096c0c808addfaf903cecf73b184b90d5f Author: Weiqun Zhang Date: Tue Jun 12 10:15:54 2018 -0700 fix make of the eb levelset test Tutorials/EB/LevelSet/Exec/GNUmakefile commit 5812441de9d619762c2e5aee42d3615ce5bffd6c Author: Weiqun Zhang Date: Tue Jun 12 09:48:20 2018 -0700 no need to have USE_EB2 Tools/GNUMake/Make.defs commit 03ffa38390c0762949ddb4e6fde67934934d8dab Author: Weiqun Zhang Date: Tue Jun 12 09:39:38 2018 -0700 add EB2 to cmake Src/CMakeLists.txt Src/EB2/CMakeLists.txt commit c7f6b57e8fe6587e2526bf59d95783612d196964 Author: Max Katz Date: Tue Jun 12 12:24:19 2018 -0400 Move a device sync to the right place Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit 69033e9a701a8a9db92892181ac166ed8aae3d35 Merge: 32f7dc170 5ffb39150 Author: Weiqun Zhang Date: Tue Jun 12 09:19:07 2018 -0700 Merge branch 'development' into weiqun/eb2 commit e366079e90abc501f68f70f62f638890f810a661 Author: Max Katz Date: Tue Jun 12 11:57:58 2018 -0400 Cover some more Box functions, for safety Src/Base/AMReX_Box.H commit c7fccf4622043bafd5648935e0dfb618192cead5 Author: Max Katz Date: Tue Jun 12 11:48:12 2018 -0400 Use the FA arena Src/Base/AMReX_FabArrayCommI.H commit 5ec60a3f65d8f9ea87acfd13c0976fef4c57d414 Author: Max Katz Date: Mon Jun 11 20:38:33 2018 -0400 Fix indexing issue in copyfrommem Src/Base/AMReX_BaseFab_nd.F90 commit 32f7dc170a53d4536f0de51b7527a39fb23b8471 Author: Weiqun Zhang Date: Mon Jun 11 17:28:13 2018 -0700 add all_regular Src/AmrCore/AMReX_AmrMesh.cpp Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_AllRegular.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/Make.package Tutorials/EB/CNS/Exec/Sod/inputs Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/main.cpp commit b8af3d7ef1736706438adf49bb9597dbadfc678a Author: Max Katz Date: Mon Jun 11 18:28:05 2018 -0400 Fix offsets in copytomem/copyfrommem Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 5dc795bb8db6e2522d9e7b3d900986f5d89c5234 Merge: 5cc607a7c 09265f80a Author: Weiqun Zhang Date: Mon Jun 11 15:47:41 2018 -0700 Merge branch 'development' into weiqun/eb2 commit 8519ea6b10ce533e90e29af4e37552405b2c501a Author: Max Katz Date: Mon Jun 11 17:14:27 2018 -0400 Use AMREX_ARLIM_3D Src/Base/AMReX_ArrayLim.H commit 5ffb39150a7a850a744853a8e6613d240b816cab Merge: 09265f80a 5132e9b24 Author: WeiqunZhang Date: Mon Jun 11 13:39:54 2018 -0700 Merge pull request #274 from jaharris87/development Add interface for character bcast to F_BaseLib commit 998114d796ebf08512b511e2f1d72bda51050ff7 Merge: 97bc4282a 1f86292f0 Author: Max Katz Date: Mon Jun 11 16:26:50 2018 -0400 Merge branch 'development' into gpu commit 5cc607a7caa089cd3161bbf482684f8d48f11696 Author: Weiqun Zhang Date: Mon Jun 11 13:20:41 2018 -0700 coarsen valid cells only Src/EB/AMReX_EBCellFlag.H Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/inputs commit 09265f80a8469d50490d231792f78a9f8950c061 Merge: 3ec893519 1f86292f0 Author: Andrew Myers Date: Mon Jun 11 13:14:03 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3ec89351911c8e532ed80faf0fb281ff0eb2b1c4 Author: Andrew Myers Date: Mon Jun 11 13:13:52 2018 -0700 clean up CreateGhost and CreateVirtualParticles Src/Particle/AMReX_ParticleContainerI.H commit 1a8164e2b2b190a832936c97a9143024f8519c44 Author: Andrew Myers Date: Mon Jun 11 13:11:15 2018 -0700 remove unused static member of RealVect Src/Base/AMReX_RealVect.H commit 5ff8a9bd5049864f7381107fff4f3bd8382f2e5c Author: Andrew Myers Date: Mon Jun 11 13:01:10 2018 -0700 silence another warning Src/Particle/AMReX_ParticleContainerI.H commit aad7b52712d92e1c8f50b4ce3a6643c1848a005f Author: Andrew Myers Date: Mon Jun 11 12:58:14 2018 -0700 silence unused variable compiler warning Src/Particle/AMReX_ParticleContainerI.H commit 5132e9b244089ed2a64a633e9fe03d4c68308f46 Author: Harris, James Austin Date: Mon Jun 11 15:25:22 2018 -0400 Add interface for character bcast to F_BaseLib Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 1f86292f0c372875b3fcd1eb54f2c3d655b2c1ff Merge: f0cd1e531 0e3370dd4 Author: Daniel Ladiges Date: Mon Jun 11 10:36:05 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f0cd1e531f065c860e4120196a861726cd82eed8 Author: Daniel Ladiges Date: Mon Jun 11 10:30:45 2018 -0700 Added bl_random_.f90 bl_random_c.cpp bl_random_c.H to make package Src/F_BaseLib/FParallelMG.mak commit 766ab53894dc6281390d2685ff6b5284cb9f7597 Author: Kevin Gott Date: Mon Jun 11 00:37:42 2018 -0400 GeomData into all kernels. Requires non-const Geometry in advance.cpp function call in current form. Src/Base/AMReX_Geometry.H Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H commit 97bc4282a2cae52ee7b48c5b564fdacb69d108f8 Author: Max Katz Date: Sun Jun 10 21:48:45 2018 -0400 Sync up with the original heat equation example Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/physbc.cpp commit 9ce350b75d245a437b0992a44bec254eeaa97c56 Author: Max Katz Date: Sun Jun 10 21:43:27 2018 -0400 Complete removal of amrex_fort_launch (except PIC) Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit a1208681c95bcf960e3a02fcc81a4b4ab6d934c5 Author: Max Katz Date: Sun Jun 10 21:17:19 2018 -0400 Finish BaseFab Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 40d5e4486cc37bda433237120ea1788c75614b27 Author: Max Katz Date: Sun Jun 10 20:49:33 2018 -0400 Convert more BaseFab to new launch mechanism Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 8d8d982bb41fb75da8cf60bd41392a4b6d0a0ec6 Author: Weiqun Zhang Date: Sat Jun 9 13:58:44 2018 -0700 fix bug in 3d cell flag Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.cpp commit 1925d35f47071c688db39f5d7949b28cffd16268 Author: Weiqun Zhang Date: Sat Jun 9 13:16:56 2018 -0700 ignore cells outside domain for cellflagfab type Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/GNUmakefile commit 0e3370dd4f32cd3a8611eace966ecac4055d76dc Merge: de6893069 9f62a0347 Author: WeiqunZhang Date: Sat Jun 9 12:24:21 2018 -0700 Merge pull request #266 from AMReX-Codes/f_interfaces_particles Adding some particle support to the F_Interfaces commit 8acd7254a9cfaa84681cf6817ceaeb89a81cf627 Author: Weiqun Zhang Date: Fri Jun 8 22:53:05 2018 -0700 typo Tests/EBEB2/GNUmakefile Tests/EBEB2/initEB.cpp commit 80ce3d192addd63ce7149f6d3740dff4a530355b Author: Weiqun Zhang Date: Fri Jun 8 22:10:08 2018 -0700 set default value fo boundary centroid to -1 for consistence with the old implementation Tests/EBEB2/MyTest.cpp Tests/EBEB2/inputs commit 9f62a03475bf480810256eb18dad83e9e6369ce1 Merge: c230aa78a 986710c5c Author: Andrew Myers Date: Fri Jun 8 21:54:10 2018 -0700 Merge branch 'f_interfaces_particles' of github.com:AMReX-Codes/amrex into f_interfaces_particles commit c230aa78a2f2af896091f27e726ceeff055ba156 Author: Andrew Myers Date: Fri Jun 8 21:53:00 2018 -0700 simplify logic in advection kernels Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 commit 8c758e6a979d346c3e1ab1147fe0be24f7821c14 Author: Weiqun Zhang Date: Fri Jun 8 21:49:06 2018 -0700 zero out neighbors for covered cells Src/EB/AMReX_EBCellFlag.H commit 14e1f010bccadae0c2b6babde00a771b9b096720 Author: Cyrus Harrison Date: Fri Jun 8 17:07:17 2018 -0700 initial ascent integration Src/Base/AMReX_Conduit_Blueprint.cpp Tests/Blueprint/AssignMultiLevelDensity/GNUmakefile Tests/Blueprint/AssignMultiLevelDensity/main.cpp Tests/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile Tests/Blueprint/HeatEquation_EX1_C/Source/main.cpp commit 18069131a39cbbf6b982ddd51b30c1a4f868dc4d Author: Weiqun Zhang Date: Fri Jun 8 17:06:28 2018 -0700 fix the check for multi-cuts Src/EB2/AMReX_eb2_2d.F90 commit 147c015f35d848a7ac68bfa55b8c0b128130c8b5 Author: Weiqun Zhang Date: Fri Jun 8 16:33:45 2018 -0700 add plane to test Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs commit 59c4ecec293caf43defdca8aab585c595fdeddb0 Author: Weiqun Zhang Date: Fri Jun 8 16:08:44 2018 -0700 buid cell flags from aperture Src/EB/AMReX_ebcellflag_mod.F90 Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.cpp commit 3dafa8bfe38dcbabcc9f080d96aa6d2dd6d6c56b Author: Weiqun Zhang Date: Fri Jun 8 14:30:14 2018 -0700 fix coarsening Src/EB2/AMReX_eb2_2d.F90 commit 7cb390864011623c8ce615d8d988e53fb30b9bb9 Author: Weiqun Zhang Date: Fri Jun 8 14:20:19 2018 -0700 bug fix Src/EB/AMReX_EBTower.cpp Src/EB2/AMReX_eb2_2d.F90 Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs commit 7f612820518f6a0818e30662eb96aebd7d9c2c1e Author: Andrew Myers Date: Fri Jun 8 12:32:15 2018 -0700 convert this logical to a c_int Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit 92947f6cd9f81614bf8b3fbf6b00de6f7e3481c8 Author: Andrew Myers Date: Fri Jun 8 12:26:48 2018 -0700 use nullptr instead of NULL Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp commit f5472ac8d38738e03107899775d853c7cb308706 Author: Andrew Myers Date: Fri Jun 8 12:24:34 2018 -0700 this doesn't need to be a target Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit 1af7dc1c69080e09d3b78cdc18b852bbc65f528b Author: Andrew Myers Date: Fri Jun 8 12:21:15 2018 -0700 change name of these variables so as not to clash with Fortran built-ins Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit 9f5e9061de9d0f39588ac1bc4a6582af6cdad053 Author: Weiqun Zhang Date: Fri Jun 8 11:13:05 2018 -0700 avoid comparing domain boundary cells Src/EB2/AMReX_eb2_2d.F90 Tests/EBEB2/MyTest.cpp commit 686c3888affebe67d703323809416519a4c800c4 Author: Max Katz Date: Fri Jun 8 11:02:46 2018 -0700 Start porting BaseFab to use the new launch mechanism Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 5f69b6949f137b782376e11870d9df081bccfbb8 Author: Weiqun Zhang Date: Fri Jun 8 10:51:03 2018 -0700 zero out number of vofs for covered cell Src/EB/AMReX_ebcellflag_mod.F90 commit e1e0393f5712df19eec331b3ba8161843fa31dd9 Author: Weiqun Zhang Date: Fri Jun 8 10:40:04 2018 -0700 change the default value of EBCellFlag in 2d for comparison Src/EB/AMReX_EBCellFlag.H commit 260c9246ab11fdf3e4d4510c15c439dad520fec3 Author: Cyrus Harrison Date: Fri Jun 8 10:34:19 2018 -0700 initial blueprint support Src/Base/AMReX_Conduit_Blueprint.H Src/Base/AMReX_Conduit_Blueprint.cpp Src/Base/Make.package Tests/Blueprint/AssignMultiLevelDensity/GNUmakefile Tests/Blueprint/AssignMultiLevelDensity/Make.package Tests/Blueprint/AssignMultiLevelDensity/inputs Tests/Blueprint/AssignMultiLevelDensity/main.cpp Tests/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile Tests/Blueprint/HeatEquation_EX1_C/Exec/inputs_2d Tests/Blueprint/HeatEquation_EX1_C/Exec/inputs_3d Tests/Blueprint/HeatEquation_EX1_C/Source/Make.package Tests/Blueprint/HeatEquation_EX1_C/Source/advance.cpp Tests/Blueprint/HeatEquation_EX1_C/Source/advance_2d.f90 Tests/Blueprint/HeatEquation_EX1_C/Source/advance_3d.f90 Tests/Blueprint/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tests/Blueprint/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tests/Blueprint/HeatEquation_EX1_C/Source/main.cpp Tests/Blueprint/HeatEquation_EX1_C/Source/myfunc.H Tests/Blueprint/HeatEquation_EX1_C/Source/myfunc_F.H Tests/Blueprint/README.txt Tools/GNUMake/Make.defs commit 2179be3f7e4ab8dd9f81ccf71dd6956b8c4f6c0c Author: Weiqun Zhang Date: Fri Jun 8 10:32:39 2018 -0700 fix bug Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 commit 6529aa2716309566b4f8f1a5e6359a97261ae41a Author: Max Katz Date: Fri Jun 8 10:23:05 2018 -0700 16x16 seems to be better Src/Base/AMReX_Device.cpp commit 368569661f28ac073b77f41ecc5acd61baba4a27 Author: Kevin Gott Date: Fri Jun 8 13:21:55 2018 -0400 Initial GeometryData tests and implementation in HeatEquation_EX_1. Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HelloWorld_C/GNUmakefile Tutorials/GPU/HelloWorld_C/inputs_geometry Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/run.script Tutorials/GPU/run.script commit 6d8eb3cff52b703e4f006326d9b7df3e12f1e1c8 Author: Kevin Gott Date: Fri Jun 8 13:19:56 2018 -0400 GeometryData object for CUDA managed memory. Src/Base/AMReX_Box.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_RealBox.H commit 9b9283b7d67f2248344cbb6185c547b95bf38aa3 Author: Max Katz Date: Fri Jun 8 09:47:37 2018 -0700 Switch to 32x8 thread layout Src/Base/AMReX_Device.cpp commit 39eafc15440bad0dec60b6308c757b83668a3432 Author: Weiqun Zhang Date: Fri Jun 8 09:46:08 2018 -0700 for consistence, set boundary centroid to -1 for regular and cover cells Src/EB/AMReX_EBTower.cpp Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs commit 0e8e28b16ebb9bdfb5da2195fdedb2afba4b2fe0 Author: Max Katz Date: Thu Jun 7 20:33:20 2018 -0400 Need to pass an int by value Src/Base/AMReX_BaseFab_nd.F90 commit 091b2e9b5a14e040058e80aaec8294e5dc66ffa1 Author: Weiqun Zhang Date: Thu Jun 7 17:11:06 2018 -0700 parameter eb2.use_eb2 and function makeEBFabFactory Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Tutorials/EB/CNS/Exec/Make.CNS commit de689306973c625683999b18087ae74c1ce08a52 Merge: bf1e68108 6aaacfeac Author: Michele Rosso Date: Thu Jun 7 16:27:51 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit bf1e6810819faeac2e97609ff5dfa8a95c353706 Author: Michele Rosso Date: Thu Jun 7 16:27:45 2018 -0700 Add C++ versions of fcompare and fextract Tools/Postprocessing/C_Src/fcompare.cpp Tools/Postprocessing/C_Src/fextract.cpp commit f571114d6acc9cee1f44fbc859c6fc7a8ebba37a Author: John Wakefield Date: Thu Jun 7 16:19:00 2018 -0700 Changed SWFFT max_sizes to be at least as large as inputs. Tutorials/SWFFT/inputs.128 commit fce0b488d07ff9117d44790716ff0c936a7ea5fe Author: John Wakefield Date: Thu Jun 7 16:18:39 2018 -0700 Changed SWFFT max_sizes to be at least as large as inputs. Tools/C_util/AugmentPlotfile/AugFolder.sh Tools/C_util/AugmentPlotfile/GNUmakefile Tutorials/SWFFT/inputs.32 Tutorials/SWFFT/inputs.64 Tutorials/SWFFT/swfft_solver.cpp commit 8c3722f84bebfc6d389e78753fdd5dfc6268a8f5 Author: Max Katz Date: Thu Jun 7 19:12:31 2018 -0400 Fix the block/thread override Src/Base/AMReX_Device.cpp commit 95a4bf23650aaebd8ef29055d0eb362554fd1720 Author: Weiqun Zhang Date: Thu Jun 7 15:52:03 2018 -0700 scale Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Scale.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp commit d76d18d5fdc723b60901d01f00cdafff150b06da Author: Weiqun Zhang Date: Thu Jun 7 15:09:02 2018 -0700 add ellipsoid Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Ellipsoid.H Src/EB2/Make.package commit 6aaacfeac9eb39a383b5468bcead61e9abf90f9e Author: Ann Almgren Date: Thu Jun 7 14:45:11 2018 -0700 Moved files from amrex/Tools/Postprocessing/F_Src/MAESTRO* into MAESTRO/Diagnostics. Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra.f90 Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_tests/fgaussianpulse.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlcompare.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlconverge.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fnorm.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo_driver.py Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_xrb/fad_excess.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fbuoyancy.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fconv_slopes.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/frates.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspec_total_mass.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspeciesmass.f90 commit bf0678e5b06b0a37fcd45b4bc1ae6ccdfa33c138 Merge: cd2b8773f d8b647d08 Author: Ann Almgren Date: Thu Jun 7 14:37:22 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit cd2b8773faa6aa941b144d70315a046e2779fd7a Author: Ann Almgren Date: Thu Jun 7 14:36:49 2018 -0700 Moved amrex/Tools/Postprocessing/F_Src/CASTRO_radiation files out of amrex and into Castro itself Tools/Postprocessing/F_Src/CASTRO_radiation/GNUmakefile Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsource.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/frhdshocktube.f90 commit 53fad007f43b90672d598063a7eed73457d0304a Author: Weiqun Zhang Date: Thu Jun 7 14:29:27 2018 -0700 some modification for comparison of the two implementations Src/EB/AMReX_EBTower.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/EBEB2/inputs commit e19e5dd3b7fcc345df11b9de1a8f9a74cfd26132 Author: Weiqun Zhang Date: Thu Jun 7 13:56:00 2018 -0700 function to covert MultiCutFab to MultiFab Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp Tests/EBEB2/MyTest.cpp commit c0d75ea730364967313e3d0bb11576dc0ad98beb Author: Weiqun Zhang Date: Thu Jun 7 13:27:45 2018 -0700 fix return type Src/EB/AMReX_EBCellFlag.cpp Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp commit 13e166fe7593321a6ae27a14175bf9f91209cddd Author: Weiqun Zhang Date: Thu Jun 7 13:25:40 2018 -0700 fill boundary centroid, area fraction and face centtroid Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_WrappedGShop.cpp Tests/EBEB2/MyTest.cpp commit 564ab0f5478f83643fdc9f2451fd245bd258efd9 Author: Max Katz Date: Thu Jun 7 12:48:15 2018 -0700 Handle the OpenMPI + CUDA case generally, not just for CORAL Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit fff2d838c8f38f5866b7caac9ca4da3b605f3156 Author: Weiqun Zhang Date: Thu Jun 7 12:38:36 2018 -0700 fix # of components for face centroid Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 90a22fe43cc80c2d5efd2903e947f4fec751d855 Author: Weiqun Zhang Date: Thu Jun 7 12:01:31 2018 -0700 fix # of components Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBTower.cpp commit ad7e7aec4b1b07296d4e9b6f59fe4fc60d3946b3 Author: Weiqun Zhang Date: Thu Jun 7 11:59:00 2018 -0700 fill centroid Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp commit f4980e5c1d604220f9f0f9964b3539216c55f5bd Author: Max Katz Date: Thu Jun 7 14:07:41 2018 -0400 Fix capitalization in a macro Src/Base/AMReX_Device.cpp commit 628a7836f4addb92c386514c0522d5ae9d0f7ce4 Author: Weiqun Zhang Date: Thu Jun 7 10:35:18 2018 -0700 fill cell flags Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBDataCollection.cpp Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/MyTest.cpp commit d8b647d08e1123b6718163134ffae657aff00403 Merge: 8b532f089 745221393 Author: Brandon Runnels Date: Thu Jun 7 11:17:49 2018 -0600 Merge pull request #271 from AMReX-Codes/corner-fill-update updated corner fill for non-cross stencil to work in 3D as well as 2D commit 7452213930935a7595e3ae958fa73de901434c79 Author: Brandon Runnels Date: Thu Jun 7 12:08:19 2018 -0500 updated corner fill for non-cross stencil to work in 3D as well as 2D Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit af001afecea0d97b30d191711e3912a9e4583d01 Author: Weiqun Zhang Date: Thu Jun 7 09:11:47 2018 -0700 make EB2:max_grid_size a ParmParse parameter Src/Base/AMReX.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Tests/EBEB2/MyTest.cpp commit e03f69128fc45031c0b7493eff73aa3979f4f45e Author: Max Katz Date: Thu Jun 7 08:52:31 2018 -0700 Disable calls to memadvise for unsupported GPUs Src/Base/AMReX_Device.cpp commit 434362f5eaba5ae90480549be36331438955adbf Author: Max Katz Date: Thu Jun 7 08:52:17 2018 -0700 Collect the CUDA device properties in C++ Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 40b20bb66a30adeef9008bee490765599949397f Author: Max Katz Date: Wed Jun 6 23:42:58 2018 -0400 Remove some more dependences on the tile box Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 3cfa4c02778039528620c76314af8f0f684f6721 Author: Max Katz Date: Wed Jun 6 23:23:23 2018 -0400 Rewrite fab copy to avoid dependence on lo Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 49023d75d109bef14dc5b051258d4411d16602b7 Merge: a26f64254 8b532f089 Author: Max Katz Date: Wed Jun 6 20:49:19 2018 -0400 Merge branch 'development' into gpu commit a26f642548aaacca901ec9bfccabe6884f5378f6 Merge: 2c34d881a 82f7a2c35 Author: Max Katz Date: Wed Jun 6 20:40:36 2018 -0400 Merge commit '82f7a2c35a68e74bc12a7058d5d09d790031973c' into gpu commit 0a051a46909a72b60fccda30b5e20f0b934736f7 Author: Weiqun Zhang Date: Wed Jun 6 17:40:11 2018 -0700 new EB factory Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs commit 6d60470feffd45b28418f6c94042871f1a8ff634 Author: Weiqun Zhang Date: Wed Jun 6 17:07:26 2018 -0700 move initEB to a new file Tests/EBEB2/Make.package Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp commit 618980c66537ecd653730e4b65e66914e46db069 Author: Weiqun Zhang Date: Wed Jun 6 16:15:27 2018 -0700 2d compiles Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp commit 9ed72258180c50a1d26bf5ff9325c5db54de874a Author: Weiqun Zhang Date: Wed Jun 6 15:18:39 2018 -0700 coarsen geometry Src/EB/AMReX_ebcellflag_mod.F90 Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_EB2_MultiGFab.cpp Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/inputs commit 4dd1cf4d80babd04cd7c9b5f9755ca2a8e5616db Author: Kevin Gott Date: Wed Jun 6 17:58:48 2018 -0400 Turn on advance and change bc vector to HostAllocator. Tutorials/GPU/HeatEquation_EX2_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc.H commit 9a386ab25b2a3d2aa26dbe9f1e423057dc47ac89 Author: Kevin Gott Date: Wed Jun 6 17:58:10 2018 -0400 Add CudaHostAllocator for cudaMallocHost based Vectors. Src/Base/AMReX_BCRec.H Src/Base/AMReX_CudaAllocators.H commit 2c34d881ae644fd670d4ff973bf9273b4c831dce Author: Max Katz Date: Wed Jun 6 14:47:24 2018 -0700 Add a registerBox hook for new growntilebox Src/Base/AMReX_MFIter.cpp commit fa9866d6c1001beb169b0da1afec36cd53d9c4fc Author: Kevin Gott Date: Wed Jun 6 17:03:22 2018 -0400 HeatEquation_EX2_C with BCs and managed vector running with small problem. Also awaiting features for further improvement. Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Tutorials/GPU/HeatEquation_EX2_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX2_C/Source/Make.package Tutorials/GPU/HeatEquation_EX2_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc_F.H commit fe056487f92dd48820c3974dac096d1706bed838 Author: Max Katz Date: Wed Jun 6 14:01:21 2018 -0700 Avoid non amrex-prefixed macros Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_FILCC_1D.F90 Tools/F_scripts/write_cuda_headers.py commit 59b9b5748c43faa969728801b26e7df963e7fa70 Author: Kevin Gott Date: Wed Jun 6 16:59:49 2018 -0400 CudaAllocators for Vector CUDA memory management. Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Vector.H Src/Base/Make.package commit 32a0c1720bb12b89a104c755deecc0d2a8499588 Author: Kevin Gott Date: Wed Jun 6 16:56:56 2018 -0400 Improved HeatEquation_EX_1 for larger problem. Awaiting features for further improvement. Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 9ce0e74bbf8b7ea241a3742c895cd9f4b0241fd6 Author: Max Katz Date: Wed Jun 6 10:36:44 2018 -0700 Correct summitdev MPI setup in F_mk Tools/F_mk/GMakeMPI.mak commit 0301b2d09031bd98597feaa46b8b1f68b18c4081 Author: Max Katz Date: Wed Jun 6 10:35:38 2018 -0700 Update LLNL MPI setup Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit 96ac0345fd3b699cea840d705ce06243f31ac78a Author: Kevin Gott Date: Wed Jun 6 13:02:07 2018 -0400 Clean up Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit b387c1ae3740f9e54ee785993f3c930ecf574850 Author: Weiqun Zhang Date: Wed Jun 6 08:43:31 2018 -0700 eb cell flags Src/EB/AMReX_ebcellflag_mod.F90 Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.cpp commit d9f60b318b6ad0999b59ec5302e715884cbc3672 Author: Kevin Gott Date: Wed Jun 6 11:40:09 2018 -0400 HeatEquation_EX1 first draft. Running with kernels. Needs threads and blocks setup. Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit 53e170aa0e75ee2cda044bcde2a8e78f0e84ce2b Author: Max Katz Date: Tue Jun 5 19:31:57 2018 -0400 Include amrex_ macros Tools/F_scripts/write_cuda_headers.py commit d90a3ad5f4aaa0581bf6d97dccbe38e8fda3daa0 Author: Max Katz Date: Tue Jun 5 19:31:37 2018 -0400 Use basename to avoid bug in find_files_vpath Tools/F_scripts/find_files_vpath.py commit f980914dd2b09eb22d2c813dd9503f20ffeb7373 Author: Max Katz Date: Tue Jun 5 19:00:54 2018 -0400 Catch amrex_arlim_val too Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit d4ac06eb75a6a20d47c597a56803a322f2d99e85 Author: Max Katz Date: Tue Jun 5 18:57:35 2018 -0400 Fix the header class for basefab Src/Base/Make.package commit 5ba258140121177ff606e6b8c3f488580e1220c1 Author: Max Katz Date: Tue Jun 5 18:57:11 2018 -0400 Add amrex_arlim_rep Src/Base/AMReX_ArrayLim.H commit 1d1059682776bacef7ad55773c86e205f4b43add Author: dwillcox Date: Tue Jun 5 18:31:28 2018 -0400 Pass IFABs by value in write_cuda_headers.py Tools/F_scripts/write_cuda_headers.py commit 5cd55908ecb8485b1d0e3003a9e49ac32bbf2f2a Merge: 4f514f8ce 29f51056c Author: dwillcox Date: Tue Jun 5 18:17:58 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 4f514f8ce708d36472c942f9ea7f04f065a5a6f9 Author: dwillcox Date: Tue Jun 5 18:17:53 2018 -0400 Fix bound subroutine searching in write_cuda_headers.py Tools/F_scripts/write_cuda_headers.py commit 8b532f089a284bf01676bdedbd9b74979534aaa2 Merge: b83be4151 dd4b70f4f Author: Weiqun Zhang Date: Tue Jun 5 15:12:45 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b83be41512858dfa2598ad02bbb1fa1772e33192 Author: Weiqun Zhang Date: Tue Jun 5 15:11:36 2018 -0700 fix a new bug in amrex_pd_bcast Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 commit 1b09bdfb2834058f2e4effbad85bbb0d80cbbfba Author: Weiqun Zhang Date: Tue Jun 5 15:11:36 2018 -0700 fix a new bug in amrex_pd_bcast Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 commit 29f51056ccf50beb7b90aec6f192f0ff08f51fce Merge: 23d70a5ad bba9bef8b Author: Max Katz Date: Tue Jun 5 17:58:11 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit bba9bef8b77cf47063c54c8fb2a7af864721d26b Author: dwillcox Date: Tue Jun 5 17:19:38 2018 -0400 Fix target finding bug in write_cuda_headers.py Tools/F_scripts/write_cuda_headers.py commit 14f5fcc708ddfd8466b256af8ebefc2bccf280f4 Author: dwillcox Date: Tue Jun 5 17:17:28 2018 -0400 Make the function signature error verbose for write_cuda_headers.py Tools/F_scripts/write_cuda_headers.py commit 23d70a5ad7eb8f9340128106192ed63477d12abf Merge: be2997909 4a706af6b Author: Max Katz Date: Tue Jun 5 15:34:29 2018 -0400 Merge commit '4a706af6b9899688636480ed77e34b0b8972cea7' into gpu commit be2997909d328c6755a910273f022c3f906d77e4 Merge: dd8dc11c0 a292478ca Author: Max Katz Date: Tue Jun 5 15:25:04 2018 -0400 Merge commit 'a292478ca0999bdcf6281e467e77f838ae9750dc' into gpu commit d766396ed3541f0a0fa294106ae2b23ab0177f7f Merge: 026f0b3a9 dd4b70f4f Author: Cy Chan Date: Tue Jun 5 12:19:55 2018 -0700 Merge branch 'development' into forkjoin commit 026f0b3a9518c668c5c1a1c011c0d829cb71e18d Author: Cy Chan Date: Mon May 14 15:56:40 2018 -0700 forkjoin: modify Print.H to redirect task output to files default behavior unchanged added ParallelContext frame ID, IO filename, and ostream pointer OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_Print.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit dd4b70f4f56a647fc569a5713fef48979e5f07c8 Author: Ann Almgren Date: Tue Jun 5 11:43:34 2018 -0700 1) Replace . by --> (gnu allowed this but pgi caught it) 2) remove unused variable Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_WrappedGShop.cpp commit a7fac48147db7ffffa935326fc070d8eba0f92c5 Author: Kevin Gott Date: Tue Jun 5 14:26:48 2018 -0400 HeatEqu cleanup Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit dd8dc11c07d0202c115ff11980141056c4264737 Author: Max Katz Date: Tue Jun 5 13:00:54 2018 -0400 Temp headers depend on all Fortran sources Tools/GNUMake/Make.rules commit ecc933f15f0d948aa0e340435263f3dd5e091dc7 Author: Kevin Gott Date: Tue Jun 5 12:16:48 2018 -0400 First draft of kernel in HeatConduction Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Tools/GNUMake/Make.defs Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/GPU/HelloWorld_C/main.cpp commit 47179f6ab6c0324d67382299326d29394a4cac42 Author: Max Katz Date: Tue Jun 5 10:59:52 2018 -0400 Really always re-execute the temp CUDA header rule, and also avoid infinite loops Tools/GNUMake/Make.rules commit a7836daaa3a879160f6dc33d116c78c70df3f265 Author: Max Katz Date: Tue Jun 5 10:50:44 2018 -0400 Revert "Always re-execute the temp CUDA header rule" This reverts commit 0ce010e325c028348bb2c83a750e9f93a1d963ec. Tools/GNUMake/Make.rules commit 0ce010e325c028348bb2c83a750e9f93a1d963ec Author: Max Katz Date: Tue Jun 5 10:33:50 2018 -0400 Always re-execute the temp CUDA header rule Tools/GNUMake/Make.rules commit 856ea01ba556d1bb8956e2dd84c85e3268f81843 Author: Max Katz Date: Tue Jun 5 00:05:44 2018 -0400 Fix the device launch macro token concatenation Src/Base/AMReX_BLFort.H commit b519ce3a06405be06cba0fe15cbb093eba045ba7 Author: Weiqun Zhang Date: Mon Jun 4 17:08:03 2018 -0700 combustor Src/EB2/AMReX_EB2_IF_Intersection.H Src/EB2/AMReX_EB2_IF_Union.H Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.cpp commit 57647a5cda2aa7ab5bfcc00b2078d79c846f0048 Author: Weiqun Zhang Date: Mon Jun 4 16:34:18 2018 -0700 lathe and translate Src/EB2/AMReX_EB2_IF_Lathe.H Src/EB2/AMReX_EB2_IF_Translation.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp Tests/EBEB2/inputs commit 664041f430966d62ad657d36117d1f96451275d3 Author: Max Katz Date: Mon Jun 4 18:25:11 2018 -0400 Fix the macros so CPU code works Src/Base/AMReX_ArrayLim.H commit 0958929c12027533686a3dac94bbb8c222b6e5e8 Author: Weiqun Zhang Date: Mon Jun 4 15:22:59 2018 -0700 translation Src/EB2/AMReX_EB2_IF_Box.H Src/EB2/AMReX_EB2_IF_Complement.H Src/EB2/AMReX_EB2_IF_Translation.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp commit 07de7089d018957569b893c6eb56855a44ce6079 Author: Max Katz Date: Mon Jun 4 18:16:03 2018 -0400 Fix up the CUdA header generation Tools/F_scripts/find_files_vpath.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 68f5d95a057b93ac1dcaeea02b314a4c8d4ed1c6 Author: Weiqun Zhang Date: Mon Jun 4 15:10:25 2018 -0700 add Complement Src/EB2/AMReX_EB2_IF_Box.H Src/EB2/AMReX_EB2_IF_Complement.H Src/EB2/AMReX_EB2_IF_Cylinder.H Src/EB2/AMReX_EB2_IF_Plane.H Src/EB2/AMReX_EB2_IF_Sphere.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp commit f4b99639424f94533910d04b779f8014756a4ea6 Author: Weiqun Zhang Date: Mon Jun 4 13:22:48 2018 -0700 add two arguments versions of amrex_error Src/Base/AMReX_error_mod.F90 commit 1a77d25dffb8a0826933e8ed9f84f8f2e3cfb685 Merge: 303523c11 624e31102 Author: Weiqun Zhang Date: Mon Jun 4 12:22:05 2018 -0700 Merge branch 'development' into weiqun/eb2 commit 624e3110215692c614628bbc244d357b8bbf9e11 Author: Weiqun Zhang Date: Mon Jun 4 12:05:33 2018 -0700 add amrex_io_module Src/Base/AMReX_io_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit 104ce7ffe2134f2a22334fabec12b901fad4d3ec Author: Weiqun Zhang Date: Mon Jun 4 11:59:50 2018 -0700 add amrex_pd_wtime Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 commit 5a6a455fa7ff496d401bc2979ce62d632ffc5a13 Author: Max Katz Date: Mon Jun 4 14:26:18 2018 -0400 Move CUDA header script over from StarLord Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit a61f1fa46be1a92e9f2def7ca97d143cc179ea88 Author: Max Katz Date: Mon Jun 4 13:40:21 2018 -0400 Add an apparently necessary device synchronize Src/Base/AMReX_FabArray.H commit 303523c11e64a901e766cb53b8da45d4f462e577 Author: Weiqun Zhang Date: Sun Jun 3 16:50:05 2018 -0700 Union and intersection Src/Base/AMReX_IndexSequence.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_IF_Intersection.H Src/EB2/AMReX_EB2_IF_Union.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp commit 14efdc35d03668ceb818bb26dc50663deccd54b9 Author: Weiqun Zhang Date: Sun Jun 3 07:35:35 2018 -0700 clean up Src/EB2/AMReX_EB2.cpp commit 1288283430b8b99c08d2cdaa1f6d74eccff5be06 Author: Weiqun Zhang Date: Sun Jun 3 07:32:46 2018 -0700 add PlaneIF Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Box.H Src/EB2/AMReX_EB2_IF_Cylinder.H Src/EB2/AMReX_EB2_IF_Plane.H Src/EB2/Make.package commit 709189f3070a70f96ed1e64e7023168c3fea80e7 Author: Ann Almgren Date: Sat Jun 2 17:53:53 2018 -0700 Replace dp_t by rt Tools/F_scripts/write_probin.py commit 6cd3ed1738a046c2e83ea2288b37c24a6bff0d37 Author: Weiqun Zhang Date: Sat Jun 2 16:36:47 2018 -0700 add Box Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Box.H Src/EB2/AMReX_EB2_IF_Cylinder.H Src/EB2/Make.package commit 15bfee6dceb5ce4bf82fc78227709364dd6d0a86 Author: Weiqun Zhang Date: Sat Jun 2 15:50:39 2018 -0700 rename so that all implicit function files start with AMReX_EB2_IF_ Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Cylinder.H Src/EB2/AMReX_EB2_IF_Sphere.H Src/EB2/Make.package commit 17b8e4fc10366e0128974e55f08b79d0a39ceb08 Author: Weiqun Zhang Date: Sat Jun 2 15:23:07 2018 -0700 function to fill volume fraction Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/MyTest.cpp commit 986710c5ce8baf16961158726f3489bf7bab0148 Author: Weiqun Zhang Date: Sat Jun 2 14:05:19 2018 -0700 fix omp compilation Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 6b93ba7ad8759d24d55b9c4902a69e0e7dd8191c Author: Weiqun Zhang Date: Sat Jun 2 08:56:19 2018 -0700 add getLevel Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Tests/EBEB2/MyTest.cpp commit 4e3b5a6529e8004c0fdac8e03f7141c7487fbede Author: Weiqun Zhang Date: Sat Jun 2 08:38:49 2018 -0700 cleanup Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H commit 3ddd681d7c598d473a5415292e40dd40f4a84d9a Author: Weiqun Zhang Date: Sat Jun 2 08:03:00 2018 -0700 add base Level class Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/Make.package commit 6af8cf48117cd41b7cb1ffbb82a9ecfd65f750a8 Author: Weiqun Zhang Date: Sat Jun 2 07:31:33 2018 -0700 add a new test Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_ISLevel.H Tests/EBEB2/GNUmakefile Tests/EBEB2/Make.package Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/inputs Tests/EBEB2/main.cpp commit 8433e94744e62be608a95b7ba35eaed3dfc9b976 Author: Kevin Gott Date: Sat Jun 2 00:01:34 2018 -0400 BaseFab buildable on GPU with all constructors except copy. Test included. Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_Managed.H Tutorials/GPU/HelloWorld_C/main.cpp commit 3831810d8b55412fb0087721e266a8a713a7e470 Merge: 30818a9fe f699c21d1 Author: Weiqun Zhang Date: Fri Jun 1 17:06:44 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 30818a9fe888c7c89b57f4cc01ff25ca3909e5d6 Author: Weiqun Zhang Date: Fri Jun 1 17:06:15 2018 -0700 add bast to amrex_paralleldescriptor_module Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 commit 3e2c5e607ce228d1606e43c95bcc3c8e5db64f09 Author: Weiqun Zhang Date: Fri Jun 1 14:47:23 2018 -0700 finish 2d cells Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_2d.F90 commit 246cac80d5d91ab391f9e61ec68b996bc9e10285 Author: Weiqun Zhang Date: Fri Jun 1 13:13:30 2018 -0700 assert there are no multiple cuts in 2d Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_2d.F90 commit f699c21d1c97e12bafd042d3f12884b8a63f567e Merge: 774210498 bad02aacf Author: Andrew Myers Date: Fri Jun 1 10:39:17 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 77421049828386291150be68b3cff98a3330fded Author: Andrew Myers Date: Fri Jun 1 10:38:53 2018 -0700 adding an Electromagnetic PIC tutorial to development Tutorials/Particles/ElectromagneticPIC/Constants.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/IO.H Tutorials/Particles/ElectromagneticPIC/IO.cpp Tutorials/Particles/ElectromagneticPIC/Make.package Tutorials/Particles/ElectromagneticPIC/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/main.cpp commit bad02aacf581aff5483552911f81bbe1b3291f74 Merge: 69c7ea2b9 73475491a Author: WeiqunZhang Date: Fri Jun 1 09:50:17 2018 -0700 Merge pull request #267 from cgilet/master Fix --ghost option. Do not advance farg in case(--ghost) section bec… commit 73475491a28f0ef6569a92f44d9da5c25d3b15f8 Author: cgilet Date: Fri Jun 1 12:40:08 2018 -0400 Fix --ghost option. Do not advance farg in case(--ghost) section because --ghost does not take any arguments. Tools/Postprocessing/F_Src/fcompare.f90 commit 69c7ea2b9ecdff7deba1360bc48ef059ed192276 Author: Weiqun Zhang Date: Fri Jun 1 09:33:11 2018 -0700 remove some old Fortran BoxLib tutorials OldTutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile OldTutorials/AMR_Adv_F/Exec/SingleVortex/GPackage.mak OldTutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 OldTutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d OldTutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d OldTutorials/AMR_Adv_F/Exec/SingleVortex/set_velocity.f90 OldTutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile OldTutorials/AMR_Adv_F/Exec/UniformVelocity/GPackage.mak OldTutorials/AMR_Adv_F/Exec/UniformVelocity/init_phi.f90 OldTutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_2d OldTutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_3d OldTutorials/AMR_Adv_F/Exec/UniformVelocity/set_velocity.f90 OldTutorials/AMR_Adv_F/Source/GPackage.mak OldTutorials/AMR_Adv_F/Source/advance.f90 OldTutorials/AMR_Adv_F/Source/compute_flux.f90 OldTutorials/AMR_Adv_F/Source/main.f90 OldTutorials/AMR_Adv_F/Source/slope.f90 OldTutorials/AMR_Adv_F/Source/tag_boxes.f90 OldTutorials/AMR_Adv_F/Source/update_phi.f90 OldTutorials/AMR_Adv_F/Source/write_plotfile.f90 OldTutorials/Exp_CNS_NoSpec_F/CNSEquations.tex OldTutorials/Exp_CNS_NoSpec_F/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/GPackage.mak OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/bench.c OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.h OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.x86.c OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/Make.package OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/Make.package OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/README OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/advance.f90 OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/main.f90 OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/README OldTutorials/Exp_CNS_NoSpec_F/README OldTutorials/Exp_CNS_NoSpec_F/advance.f90 OldTutorials/Exp_CNS_NoSpec_F/init_data.f90 OldTutorials/Exp_CNS_NoSpec_F/inputs.jbb OldTutorials/Exp_CNS_NoSpec_F/inputs_3d OldTutorials/Exp_CNS_NoSpec_F/main.f90 OldTutorials/Exp_CNS_NoSpec_F/write_plotfile.f90 OldTutorials/GettingStarted_F/GNUmakefile OldTutorials/GettingStarted_F/GPackage.mak OldTutorials/GettingStarted_F/main.f90 OldTutorials/GettingStarted_F/work_on_data.f90 OldTutorials/HeatEquation_EX1_F/GNUmakefile OldTutorials/HeatEquation_EX1_F/GPackage.mak OldTutorials/HeatEquation_EX1_F/advance.f90 OldTutorials/HeatEquation_EX1_F/init_phi.f90 OldTutorials/HeatEquation_EX1_F/inputs_2d OldTutorials/HeatEquation_EX1_F/inputs_3d OldTutorials/HeatEquation_EX1_F/main.f90 OldTutorials/HeatEquation_EX1_F/write_plotfile.f90 OldTutorials/HeatEquation_EX2_F/GNUmakefile OldTutorials/HeatEquation_EX2_F/GPackage.mak OldTutorials/HeatEquation_EX2_F/advance.f90 OldTutorials/HeatEquation_EX2_F/define_bc_tower.f90 OldTutorials/HeatEquation_EX2_F/init_phi.f90 OldTutorials/HeatEquation_EX2_F/inputs_2d OldTutorials/HeatEquation_EX2_F/inputs_3d OldTutorials/HeatEquation_EX2_F/main.f90 OldTutorials/HeatEquation_EX2_F/multifab_physbc.f90 OldTutorials/HeatEquation_EX2_F/write_plotfile.f90 OldTutorials/HeatEquation_EX3_F/GNUmakefile OldTutorials/HeatEquation_EX3_F/GPackage.mak OldTutorials/HeatEquation_EX3_F/advance.f90 OldTutorials/HeatEquation_EX3_F/define_bc_tower.f90 OldTutorials/HeatEquation_EX3_F/init_phi.f90 OldTutorials/HeatEquation_EX3_F/inputs_2d OldTutorials/HeatEquation_EX3_F/inputs_3d OldTutorials/HeatEquation_EX3_F/main.f90 OldTutorials/HeatEquation_EX3_F/multifab_physbc.f90 OldTutorials/HeatEquation_EX3_F/write_plotfile.f90 OldTutorials/HeatEquation_EX4_F/GNUmakefile OldTutorials/HeatEquation_EX4_F/GPackage.mak OldTutorials/HeatEquation_EX4_F/advance.f90 OldTutorials/HeatEquation_EX4_F/define_bc_tower.f90 OldTutorials/HeatEquation_EX4_F/init_phi.f90 OldTutorials/HeatEquation_EX4_F/inputs_2d OldTutorials/HeatEquation_EX4_F/inputs_3d OldTutorials/HeatEquation_EX4_F/main.f90 OldTutorials/HeatEquation_EX4_F/multifab_physbc.f90 OldTutorials/HeatEquation_EX4_F/write_plotfile.f90 OldTutorials/HeatEquation_EX5_F/GNUmakefile OldTutorials/HeatEquation_EX5_F/GPackage.mak OldTutorials/HeatEquation_EX5_F/advance.f90 OldTutorials/HeatEquation_EX5_F/define_bc_tower.f90 OldTutorials/HeatEquation_EX5_F/init_phi.f90 OldTutorials/HeatEquation_EX5_F/inputs-rt OldTutorials/HeatEquation_EX5_F/inputs-rt-expl OldTutorials/HeatEquation_EX5_F/inputs-rt-impl OldTutorials/HeatEquation_EX5_F/inputs_2d OldTutorials/HeatEquation_EX5_F/inputs_3d OldTutorials/HeatEquation_EX5_F/main.f90 OldTutorials/HeatEquation_EX5_F/multifab_physbc.f90 OldTutorials/HeatEquation_EX5_F/write_plotfile.f90 OldTutorials/MultiGrid_F/GNUmakefile OldTutorials/MultiGrid_F/README OldTutorials/MultiGrid_F/constants.f90 OldTutorials/MultiGrid_F/cycle_tower.f90 OldTutorials/MultiGrid_F/fmg_cycle.f90 OldTutorials/MultiGrid_F/init_coeffs.f90 OldTutorials/MultiGrid_F/init_rhs.f90 OldTutorials/MultiGrid_F/inputs_fmg_lin_2d OldTutorials/MultiGrid_F/inputs_fmg_lin_3d OldTutorials/MultiGrid_F/inputs_fmg_pc_2d OldTutorials/MultiGrid_F/inputs_fmg_pc_3d OldTutorials/MultiGrid_F/inputs_v_lin_2d OldTutorials/MultiGrid_F/inputs_v_lin_3d OldTutorials/MultiGrid_F/inputs_v_pc_2d OldTutorials/MultiGrid_F/inputs_v_pc_3d OldTutorials/MultiGrid_F/main.f90 OldTutorials/MultiGrid_F/solve.f90 OldTutorials/MultiGrid_F/traverse.f90 OldTutorials/MultiGrid_F/v_cycle.f90 OldTutorials/Random_F/GNUmakefile OldTutorials/Random_F/GPackage.mak OldTutorials/Random_F/main.f90 OldTutorials/Tiling_Heat_F/GNUmakefile OldTutorials/Tiling_Heat_F/GPackage.mak OldTutorials/Tiling_Heat_F/advance.f90 OldTutorials/Tiling_Heat_F/init_phi.f90 OldTutorials/Tiling_Heat_F/inputs_3d OldTutorials/Tiling_Heat_F/main.f90 OldTutorials/Tiling_Heat_F/results.txt OldTutorials/Tiling_Heat_F/results/babbage_omp.run OldTutorials/Tiling_Heat_F/results/results.txt OldTutorials/Tiling_Heat_F/results/t1a.txt OldTutorials/Tiling_Heat_F/results/t1b.txt OldTutorials/Tiling_Heat_F/results/t2a.txt OldTutorials/Tiling_Heat_F/results/t2b.txt OldTutorials/Tiling_Heat_F/results/t3a.txt OldTutorials/Tiling_Heat_F/results/t3b.txt OldTutorials/Tiling_Heat_F/results/t4a.txt OldTutorials/Tiling_Heat_F/results/t4b.txt OldTutorials/Tiling_Heat_F/results/t5a.txt OldTutorials/Tiling_Heat_F/results/t5b.txt OldTutorials/Tiling_Heat_F/results/t6a.txt OldTutorials/Tiling_Heat_F/results/t6b.txt OldTutorials/Tiling_Heat_F/results/t7a.txt OldTutorials/Tiling_Heat_F/results/t7b.txt OldTutorials/Tiling_Heat_F/write_plotfile.f90 OldTutorials/WaveEquation_F/GNUmakefile OldTutorials/WaveEquation_F/GPackage.mak OldTutorials/WaveEquation_F/advance.f90 OldTutorials/WaveEquation_F/init_data.f90 OldTutorials/WaveEquation_F/inputs_2d OldTutorials/WaveEquation_F/inputs_3d OldTutorials/WaveEquation_F/main.f90 OldTutorials/WaveEquation_F/write_plotfile.f90 commit f3a0691f3aee87830c3d76a66a217c11428896db Author: Weiqun Zhang Date: Fri Jun 1 09:31:23 2018 -0700 rename OldMiniApps/FillBoundary/GNUmakefile OldMiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp OldMiniApps/FillBoundary/README OldMiniApps/FillBoundary/qsub.ipm.bat OldMiniApps/MultiGrid_C/COEF_3D.F OldMiniApps/MultiGrid_C/COEF_F.H OldMiniApps/MultiGrid_C/GNUmakefile OldMiniApps/MultiGrid_C/Make.package OldMiniApps/MultiGrid_C/README OldMiniApps/MultiGrid_C/RHS_3D.F OldMiniApps/MultiGrid_C/RHS_F.H OldMiniApps/MultiGrid_C/main.cpp OldMiniApps/MultiGrid_C/qsub.ipm.bat Tools/CompileTesting/compiletesting.py commit a85f24130fe6e1b4663c5b43813654af0a8d08d9 Author: Weiqun Zhang Date: Fri Jun 1 09:21:52 2018 -0700 remove some old mini apps MiniApps/PGAS_SMC/GNUmakefile MiniApps/PGAS_SMC/LiDryer.c MiniApps/PGAS_SMC/Make.package MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_F.H MiniApps/PGAS_SMC/SMC_advance.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/chemistry_module.f90 MiniApps/PGAS_SMC/derivative_stencil.f90 MiniApps/PGAS_SMC/init_data.f90 MiniApps/PGAS_SMC/kernels.f90 MiniApps/PGAS_SMC/main.cpp MiniApps/PGAS_SMC/make_plot.f90 MiniApps/PGAS_SMC/transport_properties.f90 MiniApps/PGAS_SMC/variables.f90 MiniApps/SMC/GNUmakefile MiniApps/SMC/GPackage.mak MiniApps/SMC/LiDryer.c MiniApps/SMC/_parameters MiniApps/SMC/advance.f90 MiniApps/SMC/chemistry_module.f90 MiniApps/SMC/derivative_stencil.f90 MiniApps/SMC/init_data.f90 MiniApps/SMC/initialize.f90 MiniApps/SMC/inputs_SMC MiniApps/SMC/kernels.f90 MiniApps/SMC/main.f90 MiniApps/SMC/make_plotfile.f90 MiniApps/SMC/probin.template MiniApps/SMC/smc.f90 MiniApps/SMC/smcdata.f90 MiniApps/SMC/time.f90 MiniApps/SMC/transport_properties.f90 MiniApps/SMC/variables.f90 commit c2da595466d4ff2a4db229aed31730b5e393fdd9 Merge: 2f38bb77a e767cd1a9 Author: Weiqun Zhang Date: Fri Jun 1 08:49:25 2018 -0700 Merge branch 'development' into weiqun/eb1 commit e767cd1a9e7a7ec78bd99da4afa9021c3129a8b5 Author: Weiqun Zhang Date: Fri Jun 1 08:47:53 2018 -0700 update CHANGES CHANGES commit 2f38bb77abed4827800c41723739579e9ccf0f43 Author: Weiqun Zhang Date: Thu May 31 17:32:11 2018 -0700 more on 2d Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 738a906cf017c5d4e05ed89707db5dc0f0d54011 Author: Weiqun Zhang Date: Thu May 31 14:44:28 2018 -0700 add a new EB2::Initialize with simple geometries Src/Base/AMReX_Array.H Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp commit 9cfae8839c4df3d57120e3905ec4009c503fc2ac Author: Weiqun Zhang Date: Thu May 31 14:04:25 2018 -0700 no need to use least square in 2d Src/EB2/AMReX_eb2_3d.F90 commit 040c5b71fa80397bcc65130a933e9b80ff33e5c1 Author: Kevin Gott Date: Thu May 31 15:46:19 2018 -0400 BaseFab::copy, copyToMem and copyFromMem tested and working. std::min and std::max in IntVect written out to avoid namespace conflict. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H Tutorials/GPU/HelloWorld_C/main.cpp commit 9ab8bc0df885d155c4718724c1c9349cade24199 Author: Andrew Myers Date: Thu May 31 11:31:59 2018 -0700 move the if np == 0 checks to inside the fortran subroutines. Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 7a4158984319f06aca4c0a31eff332a2412db5c9 Author: Andrew Myers Date: Thu May 31 11:19:08 2018 -0700 make this a bit less hard-coded for tracers Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit b5b3d966019a8b68ef1cb8e46e81c184b47e7bad Author: Andrew Myers Date: Thu May 31 11:08:53 2018 -0700 rename particle container module files Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Src/F_Interfaces/Particle/Make.package commit fa610dcf504865987a6cac9cb1746827384f0d0a Author: Andrew Myers Date: Thu May 31 10:57:35 2018 -0700 implement 3d Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 commit 16f0ae1369814d7233afa4674c11a1daaa10c8bd Author: Andrew Myers Date: Thu May 31 10:30:42 2018 -0700 refactor advect_particles into a loop over spacedim Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 commit 181a13d1f0754104aeab8592a38940d4a2d4a9f2 Author: Andrew Myers Date: Thu May 31 10:07:09 2018 -0700 advection tutorial working with particles Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 commit baf2029ea6d69101c8b584e90cb96f50cbc61ed7 Author: Weiqun Zhang Date: Thu May 31 09:33:29 2018 -0700 compute centroid Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit 12f4422adfa25b5b22e47e04861914579edfa998 Author: Andrew Myers Date: Thu May 31 09:28:56 2018 -0700 some bug fixes Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 commit f89b34026b31efe964f829af3758ddd2da74a5a5 Merge: 763c59107 fdb98cac9 Author: WeiqunZhang Date: Thu May 31 08:47:23 2018 -0700 Merge pull request #265 from jameslehoux/patch-1 Updated SingleVortex GNUmakefile commit fdb98cac93944b13d1647247738766239c8f1f46 Author: jameslehoux <37665786+jameslehoux@users.noreply.github.com> Date: Thu May 31 14:49:27 2018 +0100 Updated SingleVortex GNUmakefile Corrected AMREX_HOME to allow it to be built (should be 5 levels up, was 4 levels) Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile commit 53a3755e5d561636351f4dd0ad273a42a71bf441 Author: Andrew Myers Date: Wed May 30 20:58:10 2018 -0700 implement advect_particles in 2D Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit 9bbbaafc6dd6d38a72abf0ee5ec361735d1ce1e1 Author: Andrew Myers Date: Wed May 30 18:21:21 2018 -0700 3D version of advect particles Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 3a0b7fb4bbc99a88db15bafb266a319e8c743d10 Author: Andrew Myers Date: Wed May 30 18:11:56 2018 -0700 wrap the call to c_to_f_pointer in amrex_get_particles Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 460764ff0bb6971aa9a8974271213f341a711b1d Author: Andrew Myers Date: Wed May 30 17:51:03 2018 -0700 also pass the velocity data into advect_particles Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 763c591077dee3f682e5e666d5f8dcea0c568894 Author: Weiqun Zhang Date: Wed May 30 16:26:57 2018 -0700 MFIter dynamic scheduling: must call barrier before setting the staic variable Src/Base/AMReX_MFIter.cpp commit ef0deaf54d2c8d9fe1e1861e8b802fa228930797 Author: John Wakefield Date: Wed May 30 15:49:12 2018 -0700 Added skipping of existing components. Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp Tools/C_util/AugmentPlotfile/inputs commit 5822e63da0b9810bbcd668c64ff5ae1d0b1f4a68 Author: Kevin Gott Date: Wed May 30 16:23:26 2018 -0400 Fix fortran bind name. Src/Base/AMReX_BaseFab_nd.F90 commit ca9ff4e0559b3812d127247a3582021f0d44c320 Author: Kevin Gott Date: Wed May 30 13:41:30 2018 -0400 Intermediate commit before working on std::min and std::max. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Tutorials/GPU/HelloWorld_C/main.cpp commit 81f8f32a4b6f79143728bc5c788225d4fde8916c Author: Andrew Myers Date: Tue May 29 20:07:46 2018 -0700 starting to implement advection kernel for tracer particles in Fortran Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 010853e190750f6659b1daadf44848a084824fa0 Author: Weiqun Zhang Date: Tue May 29 15:52:54 2018 -0700 compute 2nd moments on faces Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit e66b015d0275d598cc53fcbd4d2cdaa4d2e4b111 Author: Kevin Gott Date: Tue May 29 19:26:02 2018 -0400 BaseFab setval tests. Working fine. Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Tutorials/GPU/HelloWorld_C/main.cpp commit d575b853e0a00192ab60082282acf12fb51017ba Author: atmyers Date: Tue May 29 16:14:30 2018 -0700 add routine to recalculate superparticle size Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit b7fd3d380622ca026b97000fa5188d893aafa628 Author: Kevin Gott Date: Tue May 29 18:53:55 2018 -0400 Change macros to have prefix AMREX_CUDA_ Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Managed.H Tutorials/GPU/HelloWorld_C/main.cpp commit 46810f576f04947b869bcbcb7503d9805289f72b Author: John Wakefield Date: Tue May 29 14:02:22 2018 -0700 Augmentplotfile working in parallel Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp Tools/C_util/AugmentPlotfile/GNUmakefile commit deb9a496e3898198cd61b5ef470aaf132e4d8216 Author: Kevin Gott Date: Tue May 29 16:34:27 2018 -0400 BaseFab setVal running on both host and device. Small make system tweak for OpenMP. Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Tools/GNUMake/sites/Make.olcf Tutorials/GPU/HelloWorld_C/main.cpp commit 1ab91232105d9f9323db0b8aa7163f6cb2c3a30d Author: John Wakefield Date: Tue May 29 13:29:01 2018 -0700 Augment plotfile functional in serial. Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp Tools/C_util/AugmentPlotfile/AugmentPlotfile_F.H Tools/C_util/AugmentPlotfile/AugmentPlotfile_F.f90 Tools/C_util/AugmentPlotfile/GNUmakefile Tools/C_util/AugmentPlotfile/inputs commit eb8168b6c52720ab033f2ab6d5a6c38e2b74da35 Author: John Wakefield Date: Tue May 29 13:26:58 2018 -0700 Added cell size getter. Src/Extern/amrdata/AMReX_AmrData.H commit 0e31e57ffcba528906bcdfe39de63d37cde582d3 Author: Andrew Myers Date: Tue May 29 11:33:38 2018 -0700 fix amrex_get_particles and add a function for returning the number of particles in a tile. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 5877d820f3506c759cd330da780f40663ffd2d27 Author: Andrew Myers Date: Tue May 29 10:51:58 2018 -0700 initialize the tracer particle velocities to zero instead of the weird thing it was doing before Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 038263c0dffd8bde49c27c7a26eb40baf2d10190 Author: Andrew Myers Date: Tue May 29 10:47:13 2018 -0700 add a function for getting the particls on a tile in fortran. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 1da64057ab0655fcc9b67c6d0ebc728b1feda647 Author: Weiqun Zhang Date: Tue May 29 10:24:11 2018 -0700 add cylinder Src/EB2/AMReX_EB2_CylinderIF.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_SphereIF.H Src/EB2/AMReX_eb2_3d.F90 Src/EB2/Make.package commit e07ee4f0bb5b723c174497417c7cc347e607f3fb Author: Kevin Gott Date: Mon May 28 20:17:53 2018 -0400 First edit of BArena to allocate BaseFab data. Need to edit CArena as well for COALESCE_FABS. Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_Managed.H Tools/GNUMake/Make.defs Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/outline.cpp commit a2649a7ee31498190fa8ea08127e9e1585df9fdb Author: Weiqun Zhang Date: Sat May 26 18:55:44 2018 -0700 compute volume fraction, and boundary norm, centrold and area Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit 7f123f5d5abeff713ed5377b3e3e28aefcff5258 Author: Weiqun Zhang Date: Sat May 26 17:34:07 2018 -0700 fix small cells and almost regular cells Src/EB2/AMReX_eb2_3d.F90 commit 55bf91ae14942a1681e9c6d928963d1ba9a406e8 Author: Andrew Myers Date: Fri May 25 16:46:42 2018 -0700 some bug fixes. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 commit a6df1f1a5d63e67b718eddc4e52dffa581afed9f Author: Andrew Myers Date: Fri May 25 16:46:26 2018 -0700 put the calls to amrex_particle_redistribute in the right place in the update loop. Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit d61fb18cbc9f2c19023d9dc5b64fcc2d9076f2e6 Author: Andrew Myers Date: Fri May 25 16:01:42 2018 -0700 wrap Redistribute. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 commit bd870dfcc50acb7a43151ae74236dd95efda1f5b Author: Andrew Myers Date: Fri May 25 15:27:18 2018 -0700 writing plot files. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/fmain.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit 9b4bfe153f691ef5e344cfda9a1b5584ea912bf5 Author: Andrew Myers Date: Fri May 25 14:07:23 2018 -0700 also wrap InitOnePerCell Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/fmain.F90 commit 09086ec9eaf8fbf6af263e65bc14e610b9542769 Author: Andrew Myers Date: Fri May 25 13:48:23 2018 -0700 showing that I can initialize a tracer particle container from Fortran Src/AmrCore/AMReX_AmrCore.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/fmain.F90 commit 266b4fbf88cc88ca03dd836481d8e6cedebc20e0 Author: Weiqun Zhang Date: Fri May 25 13:42:31 2018 -0700 compute area fraction and face centroids for y and z-faces Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit 9545ed179a5983291cd62af652e89ddb787a3104 Author: Weiqun Zhang Date: Fri May 25 12:42:41 2018 -0700 compute area fraction and face centroids for x-faces Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit 15ac433de5ba2800da822e9a37ac27658c41ca4b Author: Andrew Myers Date: Fri May 25 11:46:56 2018 -0700 first attempt at wrapping the AmrTracerParticleContainer for use with the Fortran interfaces. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Exec/Make.Adv Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile commit 2846a0133ec2d7715cbcdd3d85fe291dd25d8f0e Merge: 7dcf984cc 52de4f292 Author: Andrew Myers Date: Thu May 24 11:00:09 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7dcf984cc92acfa97ddbc776261aa21614073d8f Author: Andrew Myers Date: Thu May 24 10:59:51 2018 -0700 fix timer name Src/Particle/AMReX_ParticleContainerI.H commit a8e0523b8a50e2d1d6d3bfabc28d8b3021938a68 Author: Weiqun Zhang Date: Thu May 24 10:25:41 2018 -0700 3d build_types Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_EB2_MultiGFab.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 5ea7c58c387f909c5272dc508ae72f1e55473d46 Merge: 8ac55fed9 52de4f292 Author: Weiqun Zhang Date: Wed May 23 12:38:28 2018 -0700 Merge branch 'development' into weiqun/eb2 commit 8ac55fed954cf1483e689d51ba82c90633fd59ef Author: Weiqun Zhang Date: Wed May 23 12:38:22 2018 -0700 fix typo and add an alias IntVect::hasher Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H Src/EB2/AMReX_EB2_Graph.H commit 52de4f2921781f0d4ad61b8e2d6aaa7157028154 Author: Weiqun Zhang Date: Wed May 23 10:51:15 2018 -0700 fix non-mpi build Src/Base/AMReX_FabArrayCommI.H commit c28695be42ec42b98a3e01996f7ccc57167d992d Author: Weiqun Zhang Date: Wed May 23 10:38:52 2018 -0700 non-blocking parallel copy Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit be5059853e42d18f1c8c13eab06331724848ba40 Author: Kevin Gott Date: Wed May 23 12:53:29 2018 -0400 Test update. Tutorials/GPU/HelloWorld_C/GNUmakefile Tutorials/GPU/HelloWorld_C/main.cpp commit 8358df65874c44da760f04392b2b6191525edeb4 Author: Kevin Gott Date: Tue May 22 21:52:47 2018 -0400 compiler no longer complaining Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/HelloWorld_C/main.cpp commit 149791101ceb74a6e4801fa3891d7f8424f57ee5 Merge: 5afe1ad18 6fa2d2118 Author: Weiqun Zhang Date: Tue May 22 11:15:07 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5afe1ad18c5544169802304a2d396d9f62ee47ef Author: Weiqun Zhang Date: Tue May 22 11:15:00 2018 -0700 rm a profiler Src/Particle/AMReX_ParticleContainerI.H commit ba41ec3d12276e5330253beabbf448ff7103f233 Author: Kevin Gott Date: Tue May 22 10:59:23 2018 -0400 setVal working. Src/Base/AMReX_BaseFab.H Tools/GNUMake/comps/nvcc.mak commit 6fa2d2118e714bfc03298ba8f8698b36f8b25d73 Author: Andy Nonaka Date: Mon May 21 17:20:22 2018 -0700 endl -> std::endl so this compiles Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit 7658742c039d2982c8c3e921d7a252c5a98eb7c2 Author: Weiqun Zhang Date: Mon May 21 17:04:48 2018 -0700 SumBoundary: use IntVect version of Copy Src/Base/AMReX_MultiFab.cpp commit e65dda013f81a471ccb6cda33128e605d4615d07 Author: Max Katz Date: Mon May 21 16:14:02 2018 -0700 Fix MPI compilation at LLNL Tools/GNUMake/sites/Make.llnl commit 39274912b315948f460c45f804c5094a07e61810 Author: Weiqun Zhang Date: Mon May 21 16:11:06 2018 -0700 fix tiling bug in nodal linear solver Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit d871892461863f8cf0e159ebc3c796d8f83f1925 Author: Kevin Gott Date: Mon May 21 17:21:24 2018 -0400 BaseFab::setVal prepped except for 'ForEach' Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Managed.H Tutorials/GPU/HelloWorld_C/main.cpp commit 5104ebe7158e75231f9064c58be4b7247932d89b Merge: a443a8be0 6c7df835b Author: Weiqun Zhang Date: Mon May 21 13:04:33 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6c7df835bbada0c2d0c1b68b3686f8ee86d3eb94 Merge: a768d074e b44bdba71 Author: Marc Day Date: Mon May 21 11:45:46 2018 -0700 Merge pull request #263 from knutsvk/development add pp.query for unstable_criterion commit b44bdba71da8dec464416c92ed9507cb2e637938 Author: knutsvk Date: Mon May 21 13:35:43 2018 +0100 add pp.query for unstable_criterion Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp commit a443a8be0d8e96cc5411e734b946ae7e27c586a3 Author: Weiqun Zhang Date: Sat May 19 17:20:29 2018 -0700 fix single precision for 2d too Src/AmrCore/AMReX_FillPatchUtil_2d.F90 commit a768d074e7d718f96828913124bd11aefc713ad2 Author: Michele Rosso Date: Fri May 18 16:11:27 2018 -0700 Fix single precision issue in AmrCore Src/AmrCore/AMReX_FillPatchUtil_3d.F90 commit c873d381969951d991e2b76e66403ac84c505edf Author: Max Katz Date: Fri May 18 18:26:53 2018 -0400 FORT_LAUNCH -> AMREX_FORT_LAUNCH, DEVICE_LAUNCH -> AMREX_DEVICE_LAUNCH Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_filcc_f.H Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit f5e87387312d6f717caeb1e2a32fddecd2fbecd9 Merge: 5d617c468 e9366d8f0 Author: Max Katz Date: Fri May 18 17:50:50 2018 -0400 Merge commit 'e9366d8f02bc9ebab7e1defe4f5cdc0f55fcb67b' into gpu commit 5d617c46874f3613be8eab5d8534b00b5747bcd9 Merge: 0ffe665fc 9e3ed0489 Author: Max Katz Date: Thu May 17 22:19:20 2018 -0400 Merge commit '9e3ed04897fb938e5e474aa870307badc52f71e1' into gpu commit 0ffe665fc71049445a6194a7a4e9e0f1a57508bf Merge: 6abff4bc5 652a065d4 Author: Max Katz Date: Thu May 17 21:39:01 2018 -0400 Merge commit '652a065d4545bb442325f2a8fd2403f809e457cb' into gpu commit 6abff4bc57e2b039a209593c9a50c8c324525156 Merge: f1bec191a 184fba026 Author: Max Katz Date: Thu May 17 21:38:44 2018 -0400 Merge commit '184fba0260e4b067bec73f28d9422e5837bb5ef5' into gpu commit 52469100477a5b379b4990682f8368578786a4e6 Author: Weiqun Zhang Date: Thu May 17 14:00:16 2018 -0700 ignore .nfs* files .gitignore commit a29524c51e7e3f7f0e7105e27488511b646d7438 Author: Weiqun Zhang Date: Thu May 17 13:56:49 2018 -0700 rm .nfs file Tutorials/GPU/HelloWorld_C/.nfs0000000002226f1d00001727.REMOVED.git-id commit fcd70e9a1bcc3b426eec0b3bf505c6997cae111b Merge: 1ad83b522 fc00f4451 Author: Weiqun Zhang Date: Thu May 17 09:52:18 2018 -0700 Merge branch 'development' into weiqun/eb1 commit f1bec191aa148d928b8889c83d326ef6aef72004 Merge: 70657f5f0 51452f005 Author: Max Katz Date: Thu May 17 11:50:38 2018 -0400 Merge commit '51452f005e31fe1479fdc50c2a3deee9e0e262e1' into gpu commit 70657f5f049ddff15354afe506069c7a44d7ba4b Merge: 16dc17dcc 84603a9fb Author: Max Katz Date: Thu May 17 11:47:30 2018 -0400 Merge commit '84603a9fbf1a7bfd1ec8da77edae3e9c007fb61f' into gpu commit 16dc17dcc35bbe03b71cf67e8d551d402d83472a Merge: 405aaa9f8 8e47f3e29 Author: Max Katz Date: Thu May 17 11:43:09 2018 -0400 Merge commit '8e47f3e29251589312e5185c9d3046264de328d6' into gpu commit 405aaa9f8028b40ac5e24ed663fd78275a5490bf Merge: b4d34fa47 b033d37ee Author: Max Katz Date: Thu May 17 11:42:55 2018 -0400 Merge commit 'b033d37eec1bf75f2aafe7de98d14a9cab1a4ddf' into gpu commit b4d34fa4776688a274a52846814f0c0028afbd6a Merge: 3d4af98db db34ed33d Author: Max Katz Date: Thu May 17 11:32:11 2018 -0400 Merge commit 'db34ed33d6fa36e354a89f06aa19866051a8ca55' into gpu commit 3d4af98dbc001e9f713357d7ffc3e0f3e18ea2d6 Merge: 9ebb799a1 4e8451c56 Author: Max Katz Date: Thu May 17 11:28:39 2018 -0400 Merge commit '4e8451c562ea5f04f149552f8aa0b1dcae651b2c' into gpu commit 9ebb799a1e736ecf12d4ac36a8185ee0d537bc1b Merge: bcba864c8 52a2e1b04 Author: Max Katz Date: Thu May 17 11:17:34 2018 -0400 Merge commit '52a2e1b04801e71b7282069ad26a0997c199b30c' into gpu commit bcba864c8c4eca59ec8f3d62436060872de696c8 Merge: d025614f8 8cd48768f Author: Max Katz Date: Thu May 17 11:16:10 2018 -0400 Merge commit '8cd48768ff841c33e83cefd74a78d14f5abca79e' into gpu commit d025614f85c2bb6a2407b6353362721d64ac3b8a Merge: 40bbc9bef 8e103b621 Author: Max Katz Date: Thu May 17 10:51:27 2018 -0400 Merge commit '8e103b621daa6f34b4f5cef43b07869f873b7c2c' into gpu commit 40bbc9befcaa60bb3d55f74c0ea8cdd9e0f79b06 Author: Max Katz Date: Wed May 16 20:56:23 2018 -0400 Allow runtime overriding of strided grid/block size Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 5c414492140573da4b90d34f820c36f4c9b53315 Author: Max Katz Date: Wed May 16 16:09:32 2018 -0400 sharedmemcarveout is only in 9.1+ Src/Base/AMReX_BLFort.H commit 6ed070e2ce9003085bd46f64f233f8f81b6e7b69 Author: Max Katz Date: Wed May 16 11:38:15 2018 -0400 Set the default register count to 255 Tools/GNUMake/Make.defs commit b72f93a03f1de8eecf94e8e7922901b81827528f Author: Max Katz Date: Wed May 16 11:37:45 2018 -0400 Cap filcc at 128 registers Src/Base/Make.package commit 8ceaac49d2c7190aeeb018f4996b5775b698619f Author: Max Katz Date: Wed May 16 11:36:44 2018 -0400 Add the ability to do a file-specific register maximum Tools/GNUMake/Make.rules commit a38a5646eed0b9ede1875559334318a56da055da Author: Max Katz Date: Wed May 16 07:21:13 2018 -0400 Compare correct y and z dimensions Src/Base/AMReX_CUDA.F90 commit 7f355cc7c5aaaa054c1ba68af49215b37a6c190d Author: Max Katz Date: Wed May 16 07:19:37 2018 -0400 Correct the sanity check on too many threads Src/Base/AMReX_CUDA.F90 commit 1566090f0b482abdfdd5ce5190fa4e704245f649 Author: Max Katz Date: Wed May 16 05:27:22 2018 -0400 Limit to 256 threads per block Tools/GNUMake/Make.defs commit f4f509048b2a40a8a6836886636e3741404d4ff7 Author: Max Katz Date: Tue May 15 20:12:26 2018 -0400 Add more macros for the GPU script Src/Base/AMReX_ArrayLim.H commit fc00f4451bd88eb0fcf47f589352a35911b8d7d4 Merge: 77b71f411 df739c5c2 Author: Michael Zingale Date: Tue May 15 20:06:40 2018 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit 77b71f4113296962339b741f1e6c93586c27182b Author: Michael Zingale Date: Tue May 15 20:06:13 2018 -0400 make this importable Tools/F_scripts/find_files_vpath.py commit 4315cfc91a2e92f8297a5fa48e2542f23c8e1a45 Author: Kevin Gott Date: Tue May 15 17:11:29 2018 -0400 IntVect managed memory start. Need AMReX_Vector to keep going. Src/Base/AMReX_IntVect.H commit c10e1f16b72b9d94e28d5d53bc6556f6c2678ed3 Author: Kevin Gott Date: Tue May 15 17:10:42 2018 -0400 First outline of managed memory class and macros. Src/Base/AMReX_Managed.H Src/Base/Make.package Tutorials/GPU/HelloWorld_C/.nfs0000000002226f1d00001727.REMOVED.git-id Tutorials/GPU/HelloWorld_C/GNUmakefile Tutorials/GPU/HelloWorld_C/Make.package Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/outline.cpp commit 19b2cf825523016a62858acbc307b2e5995e70b6 Author: Kevin Gott Date: Tue May 15 17:09:57 2018 -0400 Copy of GPU build system from gpu branch. Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.defs Tools/GNUMake/Make.local.template Tools/GNUMake/Make.machines Tools/GNUMake/Make.rules Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak Tools/GNUMake/packages/Make.cvode Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf Tools/GNUMake/tools/Make.craypat Tools/GNUMake/tools/Make.vtune commit df739c5c275a4226a26835f32ce01170354322a3 Merge: cddc70570 fd2120bde Author: Andrew Myers Date: Tue May 15 13:08:21 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cddc70570b1370ba21e2aec3c4e2567d75895509 Author: Andrew Myers Date: Tue May 15 13:08:08 2018 -0700 add option to interpolate in space when using amrex::get_slice_data Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 commit 1ad83b522ec1d01f779ad2d414f2366cf6841728 Author: Weiqun Zhang Date: Tue May 15 12:23:09 2018 -0700 find intercept using Brent method Src/Base/AMReX_Box.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_Graph.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_2d.F90 commit ae0bbda0a85d3f1072e251a8ed6c62869cbe1e6f Author: Weiqun Zhang Date: Mon May 14 10:10:35 2018 -0700 build types Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_EB2_MultiGFab.cpp Src/EB2/AMReX_EB2_SphereIF.H Src/EB2/AMReX_eb2_2d.F90 commit 1f47eda8346d11531a210321fafb66ecbe74c3e8 Author: Weiqun Zhang Date: Sun May 13 07:29:09 2018 -0700 add fortran function stub for building types Src/Base/AMReX_LayoutData.H Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_Graph.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_EB2_MultiGFab.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/Make.package commit 7da568f9f6261170a796852cbd9b60eb3aca24a8 Author: Weiqun Zhang Date: Sat May 12 08:26:04 2018 -0700 keep cut boxes only Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_Graph.H Src/EB2/AMReX_EB2_ISLevel.H commit 279ab03af29c7ba0b556ed251c776f87576b7bcd Author: Weiqun Zhang Date: Fri May 11 18:32:38 2018 -0700 start EB2:Graph Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_Graph.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_SphereIF.H Src/EB2/Make.package commit fd2120bdefd88564b1863090fbd15b7576ff23e3 Merge: 18787cf7c 2e22862f5 Author: Michele Rosso Date: Fri May 11 15:07:24 2018 -0700 Merge branch 'mr/cmake' into development commit 18787cf7c657bda4ebe6caeba07b47784d8eae82 Author: Marc Day Date: Fri May 11 14:42:52 2018 -0700 Remove debugging output. Src/GeometryShop/AMReX_EBISLevel.cpp commit 4ffd20ff728b9218323691be55f99aac63d5304b Author: Cy Chan Date: Fri May 11 13:46:31 2018 -0700 ForkJoin: remove task_rank_n member field since split_bounds duplicates information add forkjoin.verbose input parameter make MyTask and NTasks public OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit 1bfeffd59271809501005d58e1adc07adf9c0814 Author: Cy Chan Date: Fri May 11 13:06:07 2018 -0700 some clean up OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.cpp commit b115882bbe0d7f34bda546f4d85f86370d49cd66 Merge: 12a046bfd f86b0149e Author: Andrew Myers Date: Fri May 11 12:45:04 2018 -0700 Merge pull request #260 from nataraj2/master Advection_F generalized to 2d and 3d commit c83b89e23dcee82225720ec288a5b8ab3a75f972 Author: Cy Chan Date: Fri May 11 12:36:45 2018 -0700 changed MultiFab collectives to use ParallelContext subcommunicator instead of ParallelDescriptor added Parallel(All)Reduce Or and And added ParallelAllGather and ParallelGather functions updates to MultiFab::(min/max)Index() remove broadcast, replace with allgather, everyone does reduction OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelReduce.H commit 2e22862f55a19435902a338c6f10a4ef0ed8e466 Author: Michele Rosso Date: Fri May 11 11:58:40 2018 -0700 Fix namespace in export file Tools/CMake/AMReXConfig.cmake.in commit aad0b8bbaf42909958a88d5d199f70c41aa41e63 Author: Michele Rosso Date: Fri May 11 11:55:52 2018 -0700 Disable linear solver legacy components by default Docs/sphinx_documentation/source/BuildingAMReX.rst Src/LinearSolvers/CMakeLists.txt Tools/CMake/AMReX_Options.cmake commit 12a046bfdb93fcf806150312e327e0f1d41545d9 Author: Andrew Myers Date: Fri May 11 11:05:12 2018 -0700 make this link go directly to the issues page. Docs/sphinx_documentation/source/index.rst commit 51f3854e879106097d5a932903ed05b68d7c2abc Author: Andrew Myers Date: Fri May 11 11:03:49 2018 -0700 remove duplicated link Docs/sphinx_documentation/source/Introduction.rst commit 12344faee0196c521d00dd656b5bca30f6d288ba Author: Andrew Myers Date: Fri May 11 11:02:39 2018 -0700 remove duplicated information between the introduction and main landing page for the docs. Docs/sphinx_documentation/source/Introduction.rst Docs/sphinx_documentation/source/index.rst commit 43808b82be81ef8fa023ec73c0dd7ea557b67eeb Author: Andrew Myers Date: Fri May 11 11:00:49 2018 -0700 use hyperlink targets instead of including the entire test of links in the text. Docs/sphinx_documentation/source/index.rst commit 645cabd979f563cbff56638e668ff5331e7bd30f Author: Andrew Myers Date: Fri May 11 10:49:03 2018 -0700 include a link to the Doxygen API docs on the main page for the long-form documentation. Docs/sphinx_documentation/source/index.rst commit 6eea5ddc85a5aa062887e6cb186143d74d68759e Author: Andrew Myers Date: Fri May 11 10:47:03 2018 -0700 some clarifying remarks in the documenation Docs/sphinx_documentation/source/Introduction.rst Docs/sphinx_documentation/source/index.rst commit db48ae55ae984f892f1a3f625d544a45a67bc8f3 Author: Weiqun Zhang Date: Thu May 10 21:02:35 2018 -0700 fix MLMG nodal solver in case there is no coarsening at all Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 755cb02715eaba2b320a7aa9ea64589c6cfb777c Author: Weiqun Zhang Date: Thu May 10 17:28:26 2018 -0700 start EB2 and set up IndexSpace Src/Base/AMReX_Array.H Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_SphereIF.H Src/EB2/Make.package Tools/GNUMake/Make.defs commit fd8b91f14e2d28ce5a28d4599c77efaa6b5ff69a Merge: 49a24be88 013c2b562 Author: Michael Zingale Date: Thu May 10 16:44:32 2018 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit 49a24be88174c88198ac39ed3e1545b7913f1b92 Author: Michael Zingale Date: Thu May 10 16:44:17 2018 -0400 allow for multiple specific variables to be output Tools/Postprocessing/F_Src/fextrema.f90 commit ebd458199d1669b317e9a85b4ff808e121fe4688 Author: Cy Chan Date: Thu May 10 11:47:48 2018 -0700 add support for custom MultiFab component split across tasks OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit 013c2b5625641fe91c1fcc1be23f02afeabb7978 Author: Ann Almgren Date: Thu May 10 11:30:38 2018 -0700 Remove ifdef from around void setCoarseningStrategy so that we can call it even with EB defined. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit a570caf8595f571247b5954002d17e10643a6af8 Author: Michael Zingale Date: Thu May 10 12:28:52 2018 -0400 GCC 8.x introduces more options for the sanitizers -- enable them is we are building with GCC >= 8 Tools/GNUMake/comps/gnu.mak commit 83a920e397ccf91ee5b2c2538c685f09f08e26ad Author: Weiqun Zhang Date: Thu May 10 08:45:14 2018 -0700 makeFineMask works for any index types as long as they are consistent Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 6df45d6e5b3959e8095c350e0d32139e4ae66f2b Merge: 29a641163 a4dfe07f3 Author: Andrew Myers Date: Wed May 9 17:38:42 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 29a6411632701722978d6e38208dcfd07f1a2994 Author: Andrew Myers Date: Wed May 9 17:38:27 2018 -0700 add a function to test for the intersection of two RealBoxes Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 9b6e9b86e743bf9e7926d356a4ca59dd356e0756 Author: Cy Chan Date: Wed May 9 15:41:40 2018 -0700 forkjoin: add some error checking OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit a4dfe07f39f1b748055d8547a0bad3a04a868ce1 Author: Weiqun Zhang Date: Wed May 9 14:46:56 2018 -0700 makeFineMask function Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 3fe4edb5a96c1a272745d63d5196ae561aa460e7 Author: Weiqun Zhang Date: Wed May 9 14:45:44 2018 -0700 enable iMultiFab operator= for rvalue rhs Src/Base/AMReX_iMultiFab.H commit f5a88d9f3250796279400e38217fa86ef468e9dc Merge: 2ec5aadd0 6046ef355 Author: Weiqun Zhang Date: Wed May 9 10:02:26 2018 -0700 Merge branch 'development' into weiqun/mlmg commit 6046ef3554d21ed839ca2c0adec06a2fc8540cab Author: Weiqun Zhang Date: Wed May 9 09:24:04 2018 -0700 ParmParse: support FILE=probin where probin is a Fortran namelist file Src/Base/AMReX_parmparse_mod.F90 commit b005675fffcff4474b639a44a86f81d3d81372ee Author: Ann Almgren Date: Tue May 8 17:32:05 2018 -0700 Add AMReX_CoveredSlabs* to CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit 3c8230d127dadac9cd8424705078e8207c08a6e7 Author: Weiqun Zhang Date: Tue May 8 17:24:57 2018 -0700 amrex namespace and prefix Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 Src/EB/AMReX_compute_normals.F90 Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 208805189c899d0d6ff1e31de46a1921ca048858 Author: Weiqun Zhang Date: Tue May 8 16:58:54 2018 -0700 EB levelset: make 2d compile Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/main.cpp commit 7ff11b56b58875b0a12b37fcfc646c12d4d36d8d Merge: 82bf80056 af18bac57 Author: Weiqun Zhang Date: Tue May 8 15:37:13 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 82bf800566ad26007d0e04f247ed424f9d256659 Author: Weiqun Zhang Date: Tue May 8 15:37:04 2018 -0700 define USE_EB=TRUE and simplify GNUmakefile Tutorials/EB/LevelSet/Exec/GNUmakefile commit af18bac57acbfa00f181f3b9390cab330c279d04 Merge: 7a25adc22 900892ef8 Author: Johannes Blaschke Date: Tue May 8 15:31:02 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7a25adc223ce9f33a60d32496523757c36abcb06 Author: Johannes Blaschke Date: Tue May 8 15:30:55 2018 -0700 cleanup Tutorials/EB/LevelSet/Src/Make.package commit 900892ef89c6c4d26c8423789c8f13db11ef1077 Merge: 9c7f0aba1 93daf0ebb Author: Weiqun Zhang Date: Tue May 8 15:06:17 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9c7f0aba14f1b29dac50c8bfeec79266764de811 Author: Weiqun Zhang Date: Tue May 8 15:06:13 2018 -0700 ParmParse now reads Fortran namelist blocks in inputs file and saves them in amrex_namelist in amrex_parmparse_module. This allows mixing ParmParse parameters and Fortran namelist parameters in a single inputs file. Note that namelist is not stored in ParmParse database. Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_parmparse_mod.F90 commit f1a954bd0a94533ba9716764407376f6c5c03a4e Author: Max Katz Date: Tue May 8 17:43:28 2018 -0400 Remove a stray variadic arg Src/Base/AMReX_BLFort.H commit 93daf0ebb8c7ff4824daeb6ff8b3310dc8efe221 Author: Johannes Blaschke Date: Tue May 8 14:19:32 2018 -0700 moved level-set source into AMReX Src/EB Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 Src/EB/AMReX_compute_normals.F90 Src/EB/CMakeLists.txt Src/EB/Make.package Tutorials/EB/LevelSet/Src/Make.package Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 389bc79f5d9365a5dbfa64465905454502e9ac3f Merge: 0ffdba5f8 8ba1deff4 Author: Johannes Blaschke Date: Tue May 8 13:35:42 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0ffdba5f897686c171267cd01267c81fbeb6b9c0 Author: Johannes Blaschke Date: Tue May 8 13:35:26 2018 -0700 Fix level-set tutorial Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 8ba1deff4f04a58fc0c79b0e635deb902df50dd6 Merge: 175f9b823 2fccc5260 Author: dtgraves Date: Tue May 8 13:15:25 2018 -0700 Merge pull request #259 from AMReX-Codes/dtg_branch added CoveredSlab geometry generation per Marc's request so we can ha… commit 10f0ea652380891d438cd13ececa981f99adb019 Author: Michael Zingale Date: Thu Apr 26 15:45:29 2018 -0400 fix PGI compilation PGI complains that with the 'pure' keyword here: PGF90-S-0074-Illegal number or type of arguments to heapsort_indirect_d - arguments of greater_d and cmp do not agree (/home/zingale/development/AMReX//Src/F_BaseLib/knapsack.f90: 85) Src/F_BaseLib/knapsack.f90 commit 6679b4500420fbebe030fe80d1fa7ada9e79dee4 Author: Max Katz Date: Tue May 8 16:14:06 2018 -0400 PGI now uses a different variable for the CUDA toolkit Tools/GNUMake/comps/pgi.mak commit 2fccc5260d87b302b53c28968d89ba05dae351d2 Author: dtgraves Date: Tue May 8 13:13:22 2018 -0700 added CoveredSlab geometry generation per Marc's request so we can have geometries with sharp corners. Src/GeometryShop/AMReX_CoveredSlabs.H Src/GeometryShop/AMReX_CoveredSlabs.cpp Src/GeometryShop/Make.package Tutorials/EB/GeometryGeneration/exec/GNUmakefile Tutorials/EB/GeometryGeneration/exec/coveredSlabs.cpp Tutorials/EB/GeometryGeneration/exec/coveredslabs.inputs commit 175f9b823c1ee095826070693968465b8fe3f291 Merge: 252ab0f93 c9c052edc Author: Weiqun Zhang Date: Tue May 8 10:45:38 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 252ab0f93ccaa8df63c82b13b645e74ac353842c Author: Weiqun Zhang Date: Tue May 8 10:45:30 2018 -0700 MLMG: refactor grids agglomeration so that it works even if the argument grids is not directly coarsenable. Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit c9c052edc1dd6c250d98c98bc0c8deb239b4be84 Author: Ann Almgren Date: Tue May 8 10:37:02 2018 -0700 Add Tutorials/EB/LevelSet to demonstrate how to generate level set from EB specification. Tutorials/EB/LevelSet/Exec/GNUmakefile Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/Make.package Tutorials/EB/LevelSet/Src/compute_normals.f90 Tutorials/EB/LevelSet/Src/eb_F.H Tutorials/EB/LevelSet/Src/eb_geometry.f90 Tutorials/EB/LevelSet/Src/eb_levelset.H Tutorials/EB/LevelSet/Src/eb_levelset.cpp Tutorials/EB/LevelSet/Src/eb_levelset_f.f90 Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 07cb7e86bd5a51028c56d0657bd55ebba83a19c4 Author: Weiqun Zhang Date: Mon May 7 17:34:18 2018 -0700 MLMG: assert grids are coarsenable Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit a7a282dfecb1d607d5398f2a8a2d3c59ed8b15b3 Merge: fac7b019c a245bde43 Author: Ann Almgren Date: Mon May 7 17:18:43 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit fac7b019ce141ea0d51b57806df8f841dd0f9ad7 Author: Ann Almgren Date: Mon May 7 17:18:37 2018 -0700 Revert "Allow face-based arrays to coarsen even if the boxes don't quite line up right (eg if a fine" This reverts commit 4c81fbb2ed12307fb765f124b0c3f38657a481f6. Src/Base/AMReX_MultiFabUtil.cpp commit a245bde43a760f7c6d08e4dd2b725026cabea901 Merge: 40e833a9e 4c81fbb2e Author: Weiqun Zhang Date: Mon May 7 17:10:40 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 40e833a9e74313024032e6fa352853724f70be07 Author: Weiqun Zhang Date: Mon May 7 17:10:36 2018 -0700 fix print in TinyProfiler Src/Base/AMReX_TinyProfiler.cpp commit 4c81fbb2ed12307fb765f124b0c3f38657a481f6 Author: Ann Almgren Date: Mon May 7 16:56:03 2018 -0700 Allow face-based arrays to coarsen even if the boxes don't quite line up right (eg if a fine 32x32 domain is broken into boxes 15-wide and 17-wide but the coarse boxes are 8x8) Src/Base/AMReX_MultiFabUtil.cpp commit 214757a5ab381090e428c73186850f0e1d128078 Author: Weiqun Zhang Date: Mon May 7 16:49:42 2018 -0700 avoid using cout and cerr directly Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_TracerParticles.cpp commit 2adf9dd7cc46d921021ce3aa62510f35ca3cffa2 Author: Weiqun Zhang Date: Mon May 7 15:37:23 2018 -0700 avoid using cout and cerr directly in Base/ Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp commit afdaca4e920bddcf42db232be358b120595493a8 Author: Max Katz Date: Mon May 7 18:07:45 2018 -0400 Indent make.olcf for clarity Tools/GNUMake/sites/Make.olcf commit f0377862bf479d0aa866f307d668bbd22bcb867f Author: Weiqun Zhang Date: Mon May 7 15:01:05 2018 -0700 add amrex::ErrorStream and remove cout and cerr from Amr/ Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX.H Src/Base/AMReX.cpp commit f86b0149eda5243a5e731396a31f6dd2e7936911 Author: Mahesh Natarajan Date: Mon May 7 17:46:46 2018 -0400 Advection_F generalized to 2d and 3d Tutorials/Amr/Advection_F/Exec/SingleVortex/movie.visit commit 9fd6972b0ffab513abee24afb2bc86a11e79b58d Author: Mahesh Natarajan Date: Mon May 7 17:44:57 2018 -0400 Advection_F generalized to 2d and 3d Tutorials/Amr/Advection_F/Exec/SingleVortex/.GNUmakefile.swp commit ba1605f5d0ea57e22e0ae51d7b933465eea4c525 Author: Mahesh Natarajan Date: Mon May 7 17:44:37 2018 -0400 Advection_F generalized to 2d and 3d Tutorials/Amr/Advection_F/Exec/SingleVortex/.inputs.swp commit d9e1683d7ecdd9f3f19fec80935f0eb25022d028 Author: Mahesh Natarajan Date: Mon May 7 17:43:32 2018 -0400 Advection_F generalized to 2d and 3d Tutorials/Amr/Advection_F/Exec/SingleVortex/.GNUmakefile.swp Tutorials/Amr/Advection_F/Exec/SingleVortex/.inputs.swp Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_F/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_2d.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_3d.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/face_velocity_3d.F90 Tutorials/Amr/Advection_F/Exec/SingleVortex/movie.visit Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_F/Source/Src_3d/Make.package Tutorials/Amr/Advection_F/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_F/Source/Src_3d/slope_3d.f90 commit 3b4c41d86d7265402a3b52458cc46de005c4d8e1 Author: Max Katz Date: Mon May 7 16:30:37 2018 -0400 Fix MPI compilation on summitdev Tools/GNUMake/sites/Make.olcf commit 1587672584592402f47dd9877a1e0f4bd37eda6b Author: dtgraves Date: Mon May 7 11:51:17 2018 -0700 added a bit about using WrappedGShop for generating higher order EB moments. Docs/sphinx_documentation/source/EB.rst commit 3c88047259978c0fd5481d1c1ff8fd56910c63bb Author: dtgraves Date: Mon May 7 10:32:20 2018 -0700 added derivative functions for Union, Intersection and Complement implicit functions. Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp commit 3537b101576e21020e25bc20657ed2e759c801e9 Author: Weiqun Zhang Date: Mon May 7 09:45:25 2018 -0700 add geom_type box to Tests/EBbcent Tests/EBbcent/main.cpp commit 8eda5e5aecafff79f17889316ab183ba0469bd51 Author: Max Katz Date: Sun May 6 17:49:57 2018 -0400 Use the new shared mem carveout attribute for CUDA 9 Src/Base/AMReX_BLFort.H commit 50aa4a0f86345d68dac4165b581d4e79c27b1267 Author: Max Katz Date: Sun May 6 17:27:48 2018 -0400 Always do strided DEVICE_LAUNCH Src/Base/AMReX_BLFort.H commit e2c2dfbaea29139d4aa569a4a6f2173813294f3e Author: Max Katz Date: Sun May 6 17:27:38 2018 -0400 Note minimum number of threads Src/Base/AMReX_Device.cpp commit 59e682ed779d4572b13b6aa3c4db8d9d37a0a4a8 Author: Max Katz Date: Sun May 6 16:35:40 2018 -0400 Update the grid strided loop layout Src/Base/AMReX_Device.cpp commit b9ed0f31ef33730dbc36a5608cd7313190cb09b9 Author: Max Katz Date: Sun May 6 15:12:43 2018 -0400 Add a grid-strided device launch macro Src/Base/AMReX_BLFort.H commit bcdc08e86ad5080ff4f9d657e6311504355e83c6 Author: Max Katz Date: Sun May 6 07:06:24 2018 -0400 Add a function for doing a grid-stride kernel Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 7ce13c146c633316fc9fed7677119863b4fd641d Author: Max Katz Date: Sun May 6 07:05:11 2018 -0400 Add function to return number of device SMs Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 010142c31722ad00e386afa3e8ca79a6c39238e0 Author: Max Katz Date: Sat May 5 20:08:15 2018 -0400 Add a DEVICE_LAUNCH macro Src/Base/AMReX_BLFort.H commit 58cba37c40c961e54b56a0428190d2200244790f Author: Max Katz Date: Sat May 5 19:37:32 2018 -0400 Move nvcc code to a unique file Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit ca4684a3a503c903388b356ecf4e290a29119ffe Author: Max Katz Date: Sat May 5 19:31:13 2018 -0400 Sync up IBM compile flags with PGI Tools/GNUMake/comps/ibm.mak commit 3b0a16b8b6f42cb048750c159534c96a171913e3 Author: Max Katz Date: Sat May 5 17:14:42 2018 -0400 Nullify a function template for CUDA Src/Base/AMReX_BLFort.H commit e7208abe149cbe00a046a968bdaecbc2d3211c8f Merge: fb6c45e05 955e63d37 Author: Max Katz Date: Sat May 5 16:36:30 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit fb6c45e05ac460ebdf36d4f47ab9b58e93be96fd Author: Max Katz Date: Sat May 5 16:36:25 2018 -0400 Do not link device code until final link Src/Base/AMReX_BLFort.H Tools/GNUMake/comps/pgi.mak commit 1a05cf9f239be4d9ae3db2a9b05ec0a74efb7bc2 Author: Max Katz Date: Sat May 5 16:36:08 2018 -0400 get_loop_bounds is a device call Src/Base/AMReX_Device.H commit e66fce7c78536057efbd628951982008e4df77e1 Merge: 129c879cd dc3725379 Author: WeiqunZhang Date: Fri May 4 16:07:08 2018 -0700 Merge pull request #256 from AMReX-Codes/cg-mulicomponent updated CG solver for multicomponent solves commit dc3725379e2b183fbf07bd8b1e57fd75fb7cdb3c Author: Brandon Runnels Date: Fri May 4 17:04:33 2018 -0600 updated CG solver for multicomponent solves Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 129c879cde5c9b4c029128dfdb05496d3e5dc552 Author: Weiqun Zhang Date: Fri May 4 15:37:02 2018 -0700 add FabArray::Redistribute function that redistributes FabArray data from one to another with the same BoxArray but different DistributionMapping Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit 955e63d37eca618391dcb0ef3bc2a6e8d9ca664a Merge: 0d80eb045 ee42ed839 Author: Andrew Myers Date: Fri May 4 17:16:21 2018 -0400 Merge branch 'gpu' of https://github.com/AMReX-Codes/amrex into gpu commit 0d80eb045e3502837206c9fe03439709a44f72c0 Author: Andrew Myers Date: Fri May 4 17:15:44 2018 -0400 pass the allocator template parameter in to all uses of the base class in Vector. Src/Base/AMReX_Vector.H commit 0558b5020d440c5c619c98b60753bafd9b6b7410 Author: Andrew Myers Date: Fri May 4 16:17:32 2018 -0400 make swapBytes a regular, non-template function. Src/Base/AMReX_IntConv.H Src/Base/AMReX_IntConv.cpp commit fc3bf820520e4f6feaff6c72948c711a927cd9f9 Merge: 3e526a4fb 79d17e376 Author: Andrew Myers Date: Fri May 4 12:18:38 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3e526a4fb8f8f6df36dd8fb7f75a476d40bbe9d4 Author: Andrew Myers Date: Fri May 4 12:18:09 2018 -0700 merging. Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IrregNode.cpp Tests/EBbcent/GNUmakefile Tests/EBbcent/Make.package Tests/EBbcent/main.cpp commit 9f899a9015cba1673d27336553c31d3142d74b4b Author: Andrew Myers Date: Fri May 4 12:14:00 2018 -0700 make the swapBytes function templated on size rather than type to make it work on Titan with cce Src/Base/AMReX_IntConv.H Src/Base/AMReX_IntConv.cpp commit 79d17e376e936d4077488e99297e6b62de727bee Merge: f5e53e40a eef19594d Author: dtgraves Date: Fri May 4 11:00:15 2018 -0700 Merge pull request #255 from AMReX-Codes/eb-bcent bug fix in higher order moments commit eef19594d717edba31d165236223b52be36fbdee Author: dtgraves Date: Fri May 4 10:57:53 2018 -0700 added fix for where EBMoments get the wrong sign Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IrregNode.cpp Tests/EBbcent/main.cpp commit f5e53e40ac1f6cbfd2909467ca132aea985eeea6 Author: Andrew Myers Date: Fri May 4 10:13:34 2018 -0700 fix loop bounds problem in BndryRegister. Src/Boundary/AMReX_BndryRegister.cpp commit 95556263dcf414d9dd3e598d6f4fabd75de9ef7b Author: Andrew Myers Date: Fri May 4 10:04:52 2018 -0700 simplify the logic here a bit. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 55ee4050e9bd0da8addb10eee37aa3b810a38d94 Author: Weiqun Zhang Date: Fri May 4 09:56:47 2018 -0700 test for debugging Tests/EBbcent/GNUmakefile Tests/EBbcent/Make.package Tests/EBbcent/main.cpp commit d0c0dea66053d254b3ab8caf6bcebdd98f18534c Merge: d01c55c55 ad6834c48 Author: atmyers Date: Thu May 3 21:00:51 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d01c55c55932ab777a67c24bea6f484d6e2c34c0 Author: atmyers Date: Thu May 3 21:00:28 2018 -0700 remove the version of amrex::ResetRandomSeed that set all the threads to have the same seed. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit ad6834c48c7dd369499e42750387d3822bb0b122 Merge: 89bc7f12c 1d4340f60 Author: Weiqun Zhang Date: Thu May 3 15:00:47 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 89bc7f12ccd0543e51cc64d9664dc4d3f2478a3a Author: Weiqun Zhang Date: Thu May 3 14:57:36 2018 -0700 add cg to MLMG Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 4f994875f50d6f07bf40dfdcd4791520ee1d5741 Author: Weiqun Zhang Date: Thu May 3 13:50:28 2018 -0700 clean up SPMD.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMD.cpp Src/Base/AMReX_SPMDI.H Src/Base/AMReX_parstream.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/levelRedistTest.cpp commit 1d4340f6037a3b1520814872789d94bbb3dfbf56 Author: Andy Nonaka Date: Thu May 3 13:49:05 2018 -0700 MultiFab is_nodal test for a single direction Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit ee42ed8398e4adbe0b72ebc202927a446085add6 Author: Max Katz Date: Thu May 3 13:34:35 2018 -0700 Update to new SMPI at LLNL Tools/GNUMake/sites/Make.llnl commit ce295fb000c67a8fab8d2fcb33314876095da7fa Author: Weiqun Zhang Date: Thu May 3 13:24:00 2018 -0700 change pout basename to amrex_pout and use ParmParse instead of environment variable for specifying output interval Src/Base/AMReX_parstream.H Src/Base/AMReX_parstream.cpp commit eeacd27936e5a8a5bff9511c70419055789b2aa7 Author: Weiqun Zhang Date: Thu May 3 12:47:11 2018 -0700 amrex::Initialize can now take an std::ostream argument for amrex::Print() to use Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Print.H commit 84c26d118f7186013814a068817e9bc68927cb1a Author: Max Katz Date: Thu May 3 11:59:52 2018 -0700 Sync up LLNL build system Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit 929d2ca2ef3450995a2ae3c23c42613bfbbcc1de Merge: 4e4750071 b875ca3c4 Author: Max Katz Date: Thu May 3 11:59:19 2018 -0700 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 9ddcca20bbe8da7bddc7443f07d34736d585ce0c Author: Weiqun Zhang Date: Wed May 2 16:14:45 2018 -0700 rm EBAMRElliptic Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H Src/EBAMRElliptic/AMReX_BiCGStabSolver.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/AMReX_EBMultiGrid.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp Src/EBAMRElliptic/AMReX_LinearSolver.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_NoOpSolver.H Src/EBAMRElliptic/AMReX_VCAggStencil.H Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Src/EBAMRElliptic/Make.package Tests/EBAMRElliptic/exec/GNUmakefile Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 54debc4c8152b02e0c6170077c21a1d6c4ae567e Author: Weiqun Zhang Date: Tue May 1 11:23:39 2018 -0700 minor update INSTALL commit 82f7a2c35a68e74bc12a7058d5d09d790031973c Author: Weiqun Zhang Date: Tue May 1 09:32:44 2018 -0700 update CHANGES CHANGES commit 3ce7d61f3844f72e9fc6b61e6ed87ec3d252dde7 Author: Kevin Gott Date: Fri Apr 27 17:39:20 2018 -0700 MemCheck versions of flush for testing after timeSteps. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp commit 7d6cfcfed083736e726c3c18992f1896b9bc8d70 Author: Kevin Gott Date: Fri Apr 27 14:45:35 2018 -0700 BL_PROFILE_FLUSH() allows user-specified profiling database writes. input flag 'blprofiler.prof_flushprint' can be set to false to remove intermediate std::cout outputs. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Tests/ProfTests/HeatEquation_EX1_C/Exec/GNUmakefile Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_2d Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_3d Tests/ProfTests/HeatEquation_EX1_C/Source/Make.package Tests/ProfTests/HeatEquation_EX1_C/Source/advance.cpp Tests/ProfTests/HeatEquation_EX1_C/Source/advance_2d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/advance_3d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/main.cpp Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc.H Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc_F.H commit 755a2637590dd5d0b2611d49e26334373d424143 Merge: ab5bad3e6 3bb9120db Author: Michael Zingale Date: Fri Apr 27 08:39:20 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ab5bad3e69ec6ef5a91cfda217df77c448e633db Author: Michael Zingale Date: Fri Apr 27 08:38:45 2018 -0400 only warn if not all variables are present still send a success code so tests pass when we add new variables Tools/Postprocessing/F_Src/fcompare.f90 commit 3bb9120dbab77e93383b1762721a0f3049fa2bd6 Author: Weiqun Zhang Date: Thu Apr 26 22:33:15 2018 -0700 get aroung a compiler bug? Src/Base/AMReX_Box.H commit 883cab78c619664885888cd00eaedea433166691 Author: Weiqun Zhang Date: Thu Apr 26 15:57:04 2018 -0700 remove a number of function level static variables that may not be thread safe Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit 0ca446f913b0c6e725f8998accc894248e40a533 Author: Weiqun Zhang Date: Thu Apr 26 15:33:13 2018 -0700 tidy Src/Base/AMReX_Box.H commit 01bfe7fee7e04e7861e37ed43314b02fd8e02ba6 Author: Weiqun Zhang Date: Thu Apr 26 13:36:27 2018 -0700 fix new Box bug and revert my revert Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 6e621c09f11242996d0abfe18f27dd77c3f63694 Author: Weiqun Zhang Date: Thu Apr 26 13:31:26 2018 -0700 fix omp compilation Src/Boundary/AMReX_YAFluxRegister.cpp commit 410e0180ef09703129f798f42bc3ecdd9f2e1742 Author: Weiqun Zhang Date: Thu Apr 26 13:22:36 2018 -0700 revert my change in Box due to a bug Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 11ea492c399264c45c31dc0bd20b302c9dc3ad9e Merge: 241477379 84c26c314 Author: Weiqun Zhang Date: Thu Apr 26 13:00:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 24147737936fe8a1ebb24dbf43d69d47c0c17b37 Author: Weiqun Zhang Date: Thu Apr 26 13:00:43 2018 -0700 omp in in YAFluxRegister::define Src/Boundary/AMReX_YAFluxRegister.cpp commit 84c26c3146fbf38b19b0546c0660505823f99f81 Merge: 8f33aaeb1 4e284a627 Author: WeiqunZhang Date: Thu Apr 26 12:54:12 2018 -0700 Merge pull request #252 from AMReX-Codes/pgi fix PGI compilation commit 4e284a6272eabb85b7f3d67f20b4ba6eeeda0fa1 Author: Michael Zingale Date: Thu Apr 26 15:45:29 2018 -0400 fix PGI compilation PGI complains that with the 'pure' keyword here: PGF90-S-0074-Illegal number or type of arguments to heapsort_indirect_d - arguments of greater_d and cmp do not agree (/home/zingale/development/AMReX//Src/F_BaseLib/knapsack.f90: 85) Src/F_BaseLib/knapsack.f90 commit 8f33aaeb1c01bcb33e4c95065cc84a0b16f66955 Merge: c593af9bc 4a706af6b Author: Ann Almgren Date: Thu Apr 26 12:16:23 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit c593af9bc91ebe072c50b87f7fa9f6d72fd317e5 Author: Ann Almgren Date: Thu Apr 26 12:14:48 2018 -0700 Remove unused variables Src/GeometryShop/AMReX_GeometryShop.cpp commit 0f00c9297ba46a38ed5279281142c6198d7b31f1 Author: Weiqun Zhang Date: Thu Apr 26 11:12:28 2018 -0700 optimization in YAFluxRegister::define Src/Boundary/AMReX_YAFluxRegister.cpp commit 55ffef4deec4abdbece86282e488d2060fc1c7c9 Author: Weiqun Zhang Date: Thu Apr 26 11:10:04 2018 -0700 inline most of IntVect and Box functions Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit 4a706af6b9899688636480ed77e34b0b8972cea7 Author: Weiqun Zhang Date: Wed Apr 25 22:13:20 2018 -0700 when BoxArray is cell-centered and its coarse ratio is 1, use the internal Box data directly Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H commit 6e49518b33a37173710dc20673a2b4b5ba08014a Author: Weiqun Zhang Date: Wed Apr 25 16:41:46 2018 -0700 add Tests/complementIn Src/Base/AMReX_VisMF.cpp Tests/complementIn/GNUmakefile Tests/complementIn/Make.package Tests/complementIn/grids/grids_1 Tests/complementIn/grids/grids_10.REMOVED.git-id Tests/complementIn/grids/grids_2 Tests/complementIn/grids/grids_3.REMOVED.git-id Tests/complementIn/grids/grids_4.REMOVED.git-id Tests/complementIn/grids/grids_5.REMOVED.git-id Tests/complementIn/grids/grids_6 Tests/complementIn/grids/grids_7 Tests/complementIn/grids/grids_8.REMOVED.git-id Tests/complementIn/grids/grids_9.REMOVED.git-id Tests/complementIn/main.cpp commit 1f0eaa1e02265c7de5c81e3ea450e845c838408e Author: Andrew Myers Date: Wed Apr 25 16:09:07 2018 -0700 replace sed with perl here. Tools/GNUMake/Make.rules commit be745eae5ad103f0962d994f61fae1298af791f8 Merge: 5c480e9bf 24172ad26 Author: atmyers Date: Wed Apr 25 15:40:19 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5c480e9bfc838413f349ecd95730d084acc264a3 Author: atmyers Date: Wed Apr 25 15:40:08 2018 -0700 add this newline in a way that works with OS X sed. Tools/GNUMake/Make.rules commit 24172ad260b8507804d0ab7f38f4fb8160f39087 Merge: 5c4dd86bc 2be6da208 Author: Weiqun Zhang Date: Wed Apr 25 15:13:08 2018 -0700 Merge branch 'development' into weiqun/complementIn commit 5c4dd86bcf16d6d438b376ea12822abb4238615a Author: Weiqun Zhang Date: Wed Apr 25 13:53:42 2018 -0700 fix assertion Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit e72d4948e6c8c6142551a24b599dc70bf0f83589 Author: Weiqun Zhang Date: Wed Apr 25 13:37:22 2018 -0700 more optimization on using complementIn Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.cpp Src/Particle/AMReX_ParticleContainerI.H commit 2249ef43881df679098a6170fc8ecbc9eb810b26 Author: Weiqun Zhang Date: Wed Apr 25 13:03:30 2018 -0700 optimization of BoxList::complementIn Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit 2be6da2084ffdbd57bdb92b367a87025a1a4e2bf Merge: 3f165e315 51b00bfce Author: Michele Rosso Date: Wed Apr 25 11:23:47 2018 -0700 Merge branch 'mr/cmake' into development commit 3f165e3155585a9ca0e766f0a7546f536eccc9b2 Author: atmyers Date: Wed Apr 25 10:39:51 2018 -0700 remove the newline here, as Mac's sed doesn't like it. Tools/GNUMake/Make.rules commit 46bec5fdc3bcdcb844e73ff493fb68ab15c59887 Author: atmyers Date: Wed Apr 25 10:22:48 2018 -0700 include missing header in AMReX_IntVect.H Src/Base/AMReX_IntVect.H commit 4f057ac5e202c8474400f95feb6749d7cb8346a5 Author: Weiqun Zhang Date: Tue Apr 24 14:57:10 2018 -0700 profiling BoxList::complementIn Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BoxList.cpp commit 51b00bfcec6a3c75d43ae65a735f060f2419c057 Merge: d7d43c81b 84cf40057 Author: Michele Rosso Date: Tue Apr 24 11:35:28 2018 -0700 Merge branch 'development' into mr/cmake commit d7d43c81bdc4a0471c8b8e6a83fd590e01761611 Author: Michele Rosso Date: Tue Apr 24 11:30:27 2018 -0700 CMake:update docs Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_Config.cmake commit f3a40411c6b22891c8505f769ca44ea2e758dad9 Author: Weiqun Zhang Date: Tue Apr 24 11:06:51 2018 -0700 BoxList::complementIn calls BoxArray::complementIn Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 84cf40057d4823790728b61067f78e5714038194 Author: Weiqun Zhang Date: Tue Apr 24 07:46:49 2018 -0700 fix typos Src/Base/AMReX_MultiFab.cpp commit cbd493790f09f43482a7809d33220528ecd779c0 Author: Marc Day Date: Mon Apr 23 22:04:56 2018 -0700 Initialize fab ptr array with nullptr, allowing safe call to delete whether or not data allocated, then remove FabArray::ok() test in AmrData::FlushGrids, allowing FlushGrids to clear fabs even if not allocated. Add AmrData::FlushGrids() function to clear all variables. Src/Base/AMReX_FabArray.H Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp commit c4acf5c4eaeb68266e84716c17c93821a39784f2 Author: Weiqun Zhang Date: Mon Apr 23 17:08:30 2018 -0700 add some functions in MultiFab to deal with IntVect ghost cells Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit b37309aa6c4f7e1a16029ca83c2ce2260407ebf9 Author: Weiqun Zhang Date: Mon Apr 23 13:24:23 2018 -0700 add some profilers Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 91c2de675846b5c07d1a73936f04bce76f15538e Merge: 7dceef395 cc8ff1541 Author: Weiqun Zhang Date: Mon Apr 23 13:21:14 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7dceef395e96001d4041a882cc354a2ac9b7c7b3 Author: Weiqun Zhang Date: Mon Apr 23 13:20:50 2018 -0700 BoxList::reserve is bad if it is used in a loop! Src/Base/AMReX_BoxList.cpp commit cc8ff1541f7c1db41f2ce99c9ad2bc3d8c959d68 Merge: bfb64b22d b6152ed6e Author: Andrew Myers Date: Mon Apr 23 11:27:39 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bfb64b22d5bb4abf1a6d98b22f3ad79011eb9f58 Author: Andrew Myers Date: Mon Apr 23 11:23:16 2018 -0700 refactor the CreateVirtualParticles code so that we don't create the buffer if we're not doing Cell aggregation. Src/Particle/AMReX_ParticleContainerI.H commit 20cf608bdf77d92b01e6c7d0daf8dabf494dd5c9 Author: Andrew Myers Date: Mon Apr 23 10:53:52 2018 -0700 use a C++-style cast here. Src/Particle/AMReX_ParticleContainerI.H commit b6152ed6ec2fcfbce1f7b20b7b09a035f6fe793b Author: Weiqun Zhang Date: Sat Apr 21 18:38:47 2018 -0700 add --enable-xsdk-defaults to configure Tools/GNUMake/Make.defs Tools/libamrex/configure.py commit cca6e695d7e8da8da0eb2242bfdd051cbce7362e Author: Weiqun Zhang Date: Sat Apr 21 18:02:08 2018 -0700 some amrex prefix in EB Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_TransformIF.cpp Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90 Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/fortran/bc_fill_nd.F90 commit e5612a8b5b78580d87c92f7b857b4c3ba3d3735e Author: Weiqun Zhang Date: Sat Apr 21 17:37:13 2018 -0700 do not build with unused old particles fortran routines Src/Particle/AMReX_Particles_1D.F Src/Particle/AMReX_Particles_2D.F Src/Particle/AMReX_Particles_3D.F Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 0dca11b1eaec148a7360fd5635638590b3930abc Author: Weiqun Zhang Date: Sat Apr 21 17:25:59 2018 -0700 AMREX_XSDK: Particle/ Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_Particles_F.H commit aec8f767eccdcb41402fafbe9a18ef04ce1be6f0 Author: Weiqun Zhang Date: Sat Apr 21 15:55:03 2018 -0700 AMREX_XSDK: C_CellMG/ Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit 3426ac8a55aa09f6eea912d879c5fef251e34f41 Author: Weiqun Zhang Date: Sat Apr 21 15:31:29 2018 -0700 some amrex_ in LinearSovlers/ Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit d60e747c946a165524eb2e32567d3499d999e012 Author: Weiqun Zhang Date: Sat Apr 21 14:34:52 2018 -0700 AMREX_XSDK: Boundary/ Src/Base/AMReX_BaseFab.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_YAFluxRegister.H commit 5aa658395d43cebd624b9f5a3a902920de9dca01 Author: Weiqun Zhang Date: Sat Apr 21 14:04:54 2018 -0700 amrex prefix in Amr/ Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 commit 50d17203ec9f3ac59125862d5fab3b6af985af24 Merge: a292478ca 998fa4b8f Author: Weiqun Zhang Date: Sat Apr 21 10:48:48 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a292478ca0999bdcf6281e467e77f838ae9750dc Author: Weiqun Zhang Date: Sat Apr 21 10:47:09 2018 -0700 Merge branch 'weiqun/ng' into development Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_TagBox.cpp Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Tools/CompileTesting/compiletesting.py commit d5941f43735ff34105493a1177171c4baf3f643e Author: Michele Rosso Date: Fri Apr 20 17:37:41 2018 -0700 CMake:generate AMReX_BuildInfo.cpp and include it in the build Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake commit b9fe4044cf2f5dd37bedb19bc5aab28f7daf2fbc Author: Michele Rosso Date: Fri Apr 20 15:56:04 2018 -0700 CMake:fix CMakeLists bugs Src/LinearSolvers/CMakeLists.txt commit b875ca3c4e1e2ec6167d7b1ec0d71d351d55188e Author: Max Katz Date: Fri Apr 20 18:46:10 2018 -0400 Sync up Titan build properties for CUDA Tools/GNUMake/sites/Make.olcf commit 684a5c976a1cc2335df457c590f04287f4aa495e Author: Max Katz Date: Fri Apr 20 18:45:52 2018 -0400 Guard against using CUDA 8 when unavailable Src/Base/AMReX_Device.cpp commit 998fa4b8fe7af1e19cf907e0694d27c47613b954 Merge: 278372d20 be65e9bca Author: atmyers Date: Fri Apr 20 15:27:17 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 278372d204fe28309c873f9444466a2338e12e18 Author: atmyers Date: Fri Apr 20 15:09:47 2018 -0700 be more conservative with writing output files in this tutorial by default. Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit be65e9bcab84d79bbe90fe5cbd1440772230e258 Author: Weiqun Zhang Date: Fri Apr 20 14:53:46 2018 -0700 for typecheck Src/Boundary/AMReX_INTERPBNDRYDATA_F.H commit 0c23a180e0bbeca75e7efada8be885fb38c33303 Merge: b74bf24b5 d06d4d5d8 Author: Ann Almgren Date: Fri Apr 20 14:00:41 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit b74bf24b5eef19b2168420b588c17706b3b11b93 Author: Ann Almgren Date: Fri Apr 20 14:00:12 2018 -0700 Move distribution.h to distribution_c.h Src/Extern/SWFFT/Distribution.H Src/Extern/SWFFT/Make.package Src/Extern/SWFFT/distribution.c Src/Extern/SWFFT/distribution_c.h commit 2ec5aadd06d0e05b09b11dd33e5ed9d3dc1d2881 Author: Weiqun Zhang Date: Fri Apr 20 11:14:43 2018 -0700 fix makefile Src/LinearSolvers/MLMG/Make.package commit eed135499fca90721a8fa016b46b419ad37084ed Merge: cb4eefd2b d06d4d5d8 Author: Weiqun Zhang Date: Fri Apr 20 11:11:22 2018 -0700 Merge branch 'development' into weiqun/mlmg commit d06d4d5d8ac92626d122f75ee1a52986be5942d8 Author: Weiqun Zhang Date: Fri Apr 20 11:04:03 2018 -0700 AMREX_CRSEGRNDOMP Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Tutorials/EB/CNS/Exec/Make.CNS commit 06d1947aa2736d08be7bf43319eb0a347be0c18b Author: Weiqun Zhang Date: Fri Apr 20 10:54:11 2018 -0700 minor Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_StateData.cpp commit 6a74d10946aa6f6e694d436f56b6f3f7109b9509 Author: Michele Rosso Date: Fri Apr 20 10:44:39 2018 -0700 CMake:more xSDK stuff Src/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 75f3354c4eacbd313970d272c1f163f2ca1efb09 Author: Weiqun Zhang Date: Fri Apr 20 10:30:34 2018 -0700 add anonymous namespace to some file scope classes Src/AmrCore/AMReX_Cluster.cpp commit 3462a70a2079f6eacfabe38066b2bae6afee365d Author: Weiqun Zhang Date: Fri Apr 20 09:57:53 2018 -0700 use amrex_bc_types_module instead of AMReX_bc_types.fi Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 commit bbc2443ec55722d9498e32d5ea6a2f8281efbfdc Author: Weiqun Zhang Date: Fri Apr 20 09:35:51 2018 -0700 remove some old tutorials OldTutorials/GettingStarted_C/GNUmakefile OldTutorials/GettingStarted_C/Make.package OldTutorials/GettingStarted_C/main.cpp OldTutorials/GettingStarted_C/work_on_data_2d.f90 OldTutorials/GettingStarted_C/work_on_data_3d.f90 OldTutorials/HeatEquation_EX2_C/FILCC_2D.F OldTutorials/HeatEquation_EX2_C/FILCC_3D.F OldTutorials/HeatEquation_EX2_C/GNUmakefile OldTutorials/HeatEquation_EX2_C/Make.package OldTutorials/HeatEquation_EX2_C/advance_2d.f90 OldTutorials/HeatEquation_EX2_C/advance_3d.f90 OldTutorials/HeatEquation_EX2_C/bc_fill_nd.F90 OldTutorials/HeatEquation_EX2_C/init_phi_2d.f90 OldTutorials/HeatEquation_EX2_C/init_phi_3d.f90 OldTutorials/HeatEquation_EX2_C/inputs_2d OldTutorials/HeatEquation_EX2_C/inputs_3d OldTutorials/HeatEquation_EX2_C/main.cpp OldTutorials/HeatEquation_EX2_C/myfunc_F.H OldTutorials/HeatEquation_EX2_C/writePlotFile.H OldTutorials/HeatEquation_EX2_C/writePlotFile.cpp commit 3b36d61676bab94bdaa9a7959479377b4c5f2d49 Author: Weiqun Zhang Date: Fri Apr 20 09:30:42 2018 -0700 add AMREX_ Src/Extern/ProfParser/AMReX_AVGDOWN_2D.F Src/Extern/ProfParser/AMReX_AVGDOWN_3D.F Src/Extern/amrdata/AMReX_FABUTIL_1D.F Src/Extern/amrdata/AMReX_FABUTIL_2D.F Src/Extern/amrdata/AMReX_FABUTIL_3D.F Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit cb4eefd2b2e52a2104bbc0013999e07e2d0dbacc Author: Weiqun Zhang Date: Fri Apr 20 09:04:17 2018 -0700 start MLEBABecLap Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/Make.package commit e3fce29b7f13caad9bbb4999ae0210de360d6575 Author: Marc Day Date: Thu Apr 19 18:00:42 2018 -0700 Add a simple AmrData-based function to computer (weighted) horizontal averages of plotfile variables. Tools/Postprocessing/C_Src/HorizontalAvg.cpp commit fec4515b9c3babfa149f3978b02193c656701e75 Author: Michele Rosso Date: Thu Apr 19 15:03:14 2018 -0700 CMake:one step closer to xSDK compliance Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_CompilersFlags.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake commit e247eeeec946b305dcd6cd98131c0a71c4d0db1e Merge: 798053448 ec82972ee Author: atmyers Date: Thu Apr 19 12:40:49 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 79805344862e09165aafe965d9c9caf0a0fe75f0 Author: atmyers Date: Thu Apr 19 12:40:37 2018 -0700 move these function out of an anonymous namepsace and into a separate file to avoid compiler warnings. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleMPIUtil.H Src/Particle/AMReX_ParticleMPIUtil.cpp Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 9871bc976c10640cb3a493d421e7482cd9296748 Merge: 50370618e ec82972ee Author: Weiqun Zhang Date: Thu Apr 19 11:36:23 2018 -0700 Merge branch 'development' into weiqun/mlmg commit e40b77fd8758312dcf685244079e5ccb86562c97 Author: atmyers Date: Thu Apr 19 11:23:06 2018 -0700 remove some unused variables from the ElectrostaticPIC particle container Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/main.cpp commit ec82972ee8637038d4363088726b2c0f2cdc7f0f Author: Weiqun Zhang Date: Thu Apr 19 11:08:07 2018 -0700 amrex prefix in LinearSolver/ Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit dbe0a8054b7ca2ec561af7d81e5c3999a17f384c Author: Weiqun Zhang Date: Thu Apr 19 10:49:44 2018 -0700 amrex prefix in Amr/ and Particle/ etc. Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_StateDescriptor.cpp Src/Extern/ProfParser/AMReX_AVGDOWN_F.H Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/BLProfParser.y Src/Extern/amrdata/AMReX_AmrData.cpp Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/Particle/AMReX_ParticleContainerI.H Tests/C_BaseLib/tUMap.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit f6305f00de331a7f20df05244e721c716bb84767 Merge: efed842b8 e757418ce Author: atmyers Date: Thu Apr 19 10:42:31 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit efed842b845a5a6cceeed66cc16c8e290b0fbff8 Author: atmyers Date: Thu Apr 19 10:42:19 2018 -0700 remove the ShortRangeParticles tutorial, as that stuff is all included in the NeighborList tutorial now. Tutorials/Particles/ShortRangeParticles/GNUmakefile Tutorials/Particles/ShortRangeParticles/Make.package Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/inputs Tutorials/Particles/ShortRangeParticles/main.cpp Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 Tutorials/Particles/ShortRangeParticles/short_range_F.H commit 642918e862c6db52b6fca298d7e6235fdc6e69be Author: atmyers Date: Thu Apr 19 10:40:46 2018 -0700 some minor tweaks to the particle documentation. Docs/sphinx_documentation/source/Chapter8.rst Docs/sphinx_documentation/source/Particle.rst commit 3b27adfa731e33e72810a83b7d477dae8369aa9f Author: atmyers Date: Thu Apr 19 10:40:11 2018 -0700 add some info about the particle tutorials Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit 5b1f39705c11388d3e1d676b59447945bc5fd1ed Author: atmyers Date: Thu Apr 19 10:39:44 2018 -0700 fix typo Docs/sphinx_tutorials/source/Basic_Tutorial.rst commit 50370618ea1d6eed1bd5dfb6822298ad8d31750a Merge: 15ef44292 e757418ce Author: Weiqun Zhang Date: Thu Apr 19 10:15:27 2018 -0700 Merge branch 'development' into weiqun/mlmg commit e757418cef312638abde00af6d57a82f20eadc12 Author: Weiqun Zhang Date: Thu Apr 19 09:05:20 2018 -0700 fix the conflict between macro and enum type Src/Base/AMReX_BC_TYPES.H Src/Boundary/AMReX_MacBndry.cpp commit f09f08278b8be9b6e8715084746c3768a786c437 Author: Weiqun Zhang Date: Thu Apr 19 08:56:19 2018 -0700 remove preprocessor directive form AMReX_bc_types.fi Src/Base/AMReX_bc_types.fi commit a3864b1c8fdd4fe035318cf0f01e45ed6fb8174c Author: Weiqun Zhang Date: Wed Apr 18 22:03:50 2018 -0700 amrex prefix in AmrCore and Boundary Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/bc_fill_nd.F90 commit 41a963791bf27fa6307eb24259d4cbf4a004dcda Author: Weiqun Zhang Date: Wed Apr 18 17:02:23 2018 -0700 D_DECL --> AMREX_D_DECL Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp commit 1fb41c58b5dea58bb122a01e4dd653eb9a401d13 Author: Weiqun Zhang Date: Wed Apr 18 16:57:23 2018 -0700 AMREX_XSDK: bc types and filcc Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit 36a726cd6e9d367431db17e871d52af32f136bc7 Author: Weiqun Zhang Date: Wed Apr 18 14:56:52 2018 -0700 make sure enum base type is int in BC_TYPES.H Src/Base/AMReX_BC_TYPES.H commit 7e0630d3996de76c6bedd4cf231dbec4c60eda15 Author: Weiqun Zhang Date: Wed Apr 18 14:31:30 2018 -0700 AMREX_XSDK: BC_TYPES.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_bc_types_mod.F90 commit 7d9cdcc1617d420264693f9826aa029f4a9eb92a Author: Weiqun Zhang Date: Wed Apr 18 14:06:10 2018 -0700 add amrex_random and amrex_random_int and AMREX_XSDK old fortran interface to amrex::Random Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_fort_mod.F90 commit 6b3ee0ea7cc5bdc0cb839f9c8b2a02fdce40c515 Author: Michele Rosso Date: Wed Apr 18 15:31:52 2018 -0700 CMake:fix tutorials link issue Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt commit f5825a8301498230824012f366cca12bf28ec3bf Author: Michele Rosso Date: Wed Apr 18 13:05:17 2018 -0700 CMake:forgot to include Fortran-only defines Tools/CMake/AMReX_CompilersFlags.cmake commit 89ab5c57da2594458bf1164b5deed4a483cc38ba Author: dtgraves Date: Wed Apr 18 11:33:05 2018 -0700 added some const_cast calls so that ParallelContext will continue to compile with old versions of MPI. Src/Base/AMReX_ParallelContext.cpp commit 2e4e2f35c23dbdfd24e95ea8c89fa75de501d5e8 Merge: 1e38ab0d4 fe83b6596 Author: dtgraves Date: Wed Apr 18 11:16:16 2018 -0700 Merge pull request #249 from AMReX-Codes/dtg_branch moment convergence test good to go. commit fe83b6596b372a752674409632959abe926cc7bb Author: dtgraves Date: Wed Apr 18 11:14:56 2018 -0700 fixed another test that got broken by an interface change. Moment convergence test works fine. Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/simplemomentexample.inputs commit af265ab15b2aa1c4c8e97849348278d8fed6f5d2 Author: Michele Rosso Date: Wed Apr 18 11:11:41 2018 -0700 CMake: modify how compiler flags are handled Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_CompilersFlags.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 1e38ab0d4245b33f4734e953675654923dae58d1 Author: Weiqun Zhang Date: Wed Apr 18 11:03:41 2018 -0700 fix a test Tests/C_BaseLib/tUMap.cpp commit 71bed02cf854d6b3a75de1ff49d302bd0212151f Merge: f505226e8 41ec5f363 Author: dtgraves Date: Wed Apr 18 10:54:49 2018 -0700 Merge branch 'development' into dtg_branch commit 41ec5f3634ebe7f849077b723f4785d5158fd307 Author: Weiqun Zhang Date: Wed Apr 18 10:27:17 2018 -0700 mempool_module --> amrex_mempool_module Docs/sphinx_documentation/source/Basics.rst Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Src/Base/AMReX_mempool_f.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/vector_i.f90 Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90 Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit 5e61d7726d5a3138778cb7f27d031db1086a83c4 Author: Weiqun Zhang Date: Wed Apr 18 10:00:24 2018 -0700 AMREX_XSDK: filcc Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_2D.F Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_3D.F commit e9366d8f02bc9ebab7e1defe4f5cdc0f55fcb67b Author: Weiqun Zhang Date: Tue Apr 17 14:48:01 2018 -0700 use new ArrayLim macros in Base Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp commit 9e3ed04897fb938e5e474aa870307badc52f71e1 Author: Weiqun Zhang Date: Tue Apr 17 14:34:55 2018 -0700 FORTRAN_BOXLIB --> AMREX_FORTRAN_BOXLIB; add amrex prefix a BaseFab Fortran functions; add amrex prefix to macros in AMReX_ArrayLim.H. Src/Base/AMReX_Array.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLassert.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_MemPool.cpp Src/F_BaseLib/backtrace_c.cpp Tools/F_mk/GMakedefs.mak commit 520cdbb549e69a683a5cd6a2cf7a45cf3e33d235 Author: Weiqun Zhang Date: Tue Apr 17 17:28:26 2018 -0700 put subroutine filcc inside #ifndef AMREX_XSDK Src/Base/AMReX_BLBoxLib_F.F90 Src/Base/AMReX_BLProfiler_F.F90 Src/Base/AMReX_BLutil_F.F90 Src/Base/AMReX_BaseUmap_f.H Src/Base/AMReX_BaseUmap_nd.f90 Src/Base/AMReX_FILCC_1D.F90 commit 07cacb033b6be749d5e5a33d8c18ff11a4d6e9aa Author: Weiqun Zhang Date: Tue Apr 17 17:08:19 2018 -0700 add missing std:: Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 64e3f3a858a3935f0ed236dafb3c555acfa8e26b Author: Weiqun Zhang Date: Tue Apr 17 16:23:10 2018 -0700 D_* -> AMREX_D_* macros in Base/ Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_SPACE.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMDI.H Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 663add137c7d93aee146020cb9262dd38d8a9331 Author: Weiqun Zhang Date: Tue Apr 17 15:54:43 2018 -0700 put some variables inside #ifndef AMREX_XSDK Src/Base/AMReX_CONSTANTS.H Src/Base/AMReX_REAL.H Src/Base/AMReX_bc_types.fi Src/Base/AMReX_bc_types_mod.F90 commit e5ae46f10b158f9b2ebcbcbbf43509fea25fb287 Author: Weiqun Zhang Date: Tue Apr 17 15:43:12 2018 -0700 more namespace/prefix changes in Base/ Src/Base/AMReX_BLFort.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BaseUmap_f.H Src/Base/AMReX_PhysBCFunct.H Tests/ProfTests/ThirdParty/Source/main.cpp commit 7b23a2b540e1ebf563fd74cef785189974a0e3dd Author: Johannes Blaschke Date: Tue Apr 17 17:13:41 2018 -0700 fillNodalMultifab: allignment factor could be ratio => int -> Real Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp commit f505226e86d597891c25998672077c2a05f02a03 Author: dtgraves Date: Tue Apr 17 17:04:03 2018 -0700 added moment convergence test. Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/momentConvTest.cpp Tests/GeometryShop/regression/momentconvtest.inputs commit 45b42236b2713e8baef0dde9f4d5d24e6ee65777 Author: Weiqun Zhang Date: Tue Apr 17 11:09:47 2018 -0700 amrex prefix for include guards Src/AmrCore/AMReX_AmrParGDB.H Src/Boundary/AMReX_InterpBndryData.H Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_AnisotropicIF.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_CH_EBIS_ORDER.H Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ConstrainedLS.H Src/GeometryShop/AMReX_CoordinateSystem.H Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CutCellMoments.H Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinement.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_ExtrudeIF.H Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_FixedRefinement.H Src/GeometryShop/AMReX_FixedRefinementImplem.H Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_GenericArithmetic.H Src/GeometryShop/AMReX_GenericArithmeticI.H Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_IFData.H Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_KDTree.H Src/GeometryShop/AMReX_LSProblem.H Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LoHiSide.H Src/GeometryShop/AMReX_MetaPrograms.H Src/GeometryShop/AMReX_MinimalCCCM.H Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MomentIteratorImplem.H Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_MonomialPowers.H Src/GeometryShop/AMReX_MultiIndex.H Src/GeometryShop/AMReX_MultiIndexImplem.H Src/GeometryShop/AMReX_NoRefinement.H Src/GeometryShop/AMReX_NoRefinementImplem.H Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_Notation.H Src/GeometryShop/AMReX_PXStuff.H Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.H Src/GeometryShop/AMReX_SmoothIntersection.H Src/GeometryShop/AMReX_SmoothUnion.H Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_ZCylinder.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H Tools/GNUMake/Make.defs commit 04a5ec117c6d019c97a86ed5149b424576b17a58 Merge: 58007fb15 bdd541481 Author: dtgraves Date: Tue Apr 17 12:36:51 2018 -0700 Merge pull request #248 from AMReX-Codes/dtg_branch adding simple higher order moments example commit bdd541481d2fddfaecdb0cb81fb19e0b124dba83 Author: dtgraves Date: Tue Apr 17 12:34:43 2018 -0700 added simple example that illustrates moment stuff. I also fixed a test whose interface had moved out from under it. Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/momentConvTest.cpp Tests/GeometryShop/regression/simpleMomentExample.cpp Tests/GeometryShop/regression/simplemomentexample.inputs Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit 383e49af11616262120f7c8b9d459e207c73a1cb Author: Michele Rosso Date: Tue Apr 17 11:48:06 2018 -0700 CMake:start implementation of xSDK guidelines Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 58007fb1590a4607d25a911890145a3d655f44a3 Author: atmyers Date: Tue Apr 17 11:40:52 2018 -0700 allow the passing of a number of ghost cells when constructing the redistribute mask Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 652a065d4545bb442325f2a8fd2403f809e457cb Merge: 8ff0aa628 bc6f821d1 Author: Johannes Blaschke Date: Mon Apr 16 18:03:48 2018 -0700 Merge remote-tracking branch 'origin/development' into jpb/fill-nodal commit 8ff0aa628c7ac6441ca2e96eec5441890643a459 Author: Johannes Blaschke Date: Mon Apr 16 18:03:14 2018 -0700 allow filling nodal MF with different refinement than EBIndexSpace's dx Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 75d157ac30833ef9719105cc668abd6477f875e8 Author: shashankNREL Date: Mon Apr 16 14:05:12 2018 -0600 Modification of MLMG to use IJ matrix interface Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit bc6f821d1e7d89e324cfcc965a85d7b514930ab8 Author: Weiqun Zhang Date: Mon Apr 16 10:25:01 2018 -0700 restore previous exception trap status in amrex::Finalize Src/Base/AMReX.cpp commit 8cbe08bcc99b67b5bfad0004c4ffe56381556e93 Author: Weiqun Zhang Date: Mon Apr 16 09:51:09 2018 -0700 add amrex.call_addr2line parameter so that the call to add2rline can be skipped Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit 71f9c712640e142d1eba2559f7b05d8ae4ed851a Author: Weiqun Zhang Date: Mon Apr 16 09:15:07 2018 -0700 move SIG_DFL to the beginning of handler Src/Base/AMReX_BLBackTrace.cpp commit 184fba0260e4b067bec73f28d9422e5837bb5ef5 Author: Weiqun Zhang Date: Sun Apr 15 13:31:41 2018 -0700 add a Fortran module for ParallelDescriptor Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit 6a3d6c1a211ea794b777b681e9723c1225539d33 Author: Michael Zingale Date: Sat Apr 14 13:15:23 2018 -0400 simple script to report git describe/hashes Tools/C_scripts/describe_sources.py commit 51452f005e31fe1479fdc50c2a3deee9e0e262e1 Author: Weiqun Zhang Date: Thu Apr 12 17:58:13 2018 -0700 This is weird. GCC 7 with certain combination of flags requires explicitly defining these std::allocator's otherwise it fails at link time. Note that we have seen this before. Src/Base/AMReX.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_ParallelReduce.H Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp commit 28579a4768cfc6c7eb4bd9f0d0d49023b7a21d83 Author: Weiqun Zhang Date: Thu Apr 12 17:38:01 2018 -0700 Comment out everything in Make.local.template. It was meant just to show things that can be done in Make.local, not meant for people to simply copy it to Make.local Tools/GNUMake/Make.local.template commit 71d0fcd2cde8d32e3e731b0fc5e2754c26cdaf54 Author: Michele Rosso Date: Thu Apr 12 17:06:21 2018 -0700 CMake: fix bug in site recognition Tools/CMake/AMReX_Machines.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake commit 500da205bde2914564c0b359b543acf797074b65 Author: Michele Rosso Date: Thu Apr 12 15:41:10 2018 -0700 CMake: add support for third party profiler tools Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Machines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake commit 0e9e805bf66f1be4222c242a1ae110afddfe5211 Author: Michele Rosso Date: Thu Apr 12 14:22:23 2018 -0700 CMake: add host infos and third party profiling options Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Machines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake commit 4e750b6e89620f34ca96206fe88b1cd95381d321 Merge: 1f1f3033a b3569b6ca Author: Michele Rosso Date: Thu Apr 12 10:41:56 2018 -0700 Merge branch 'development' into mr-cmake commit 1f1f3033aa1a217a4d164491e81f79460bdac02f Author: Michele Rosso Date: Thu Apr 12 10:40:10 2018 -0700 CMake: turn off verbosity by default CMakeLists.txt commit 61b2b7ef745645f642342c0c0254a0a1983fdaef Author: Michele Rosso Date: Thu Apr 12 10:30:37 2018 -0700 CMake: slightly modify setup CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/AMReX_Version.cmake commit 4d494f132f175e23434692118778cdb916ea8a69 Author: shashankNREL Date: Thu Apr 12 10:44:23 2018 -0600 Removed some additional unused variables Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 93c38f58cc43736d8fec7331edae99e6acb326fd Author: shashankNREL Date: Thu Apr 12 10:39:48 2018 -0600 Optimized the IJ matrix interface Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit b3569b6ca8c956562bfc94cf154c6badb545a685 Author: Weiqun Zhang Date: Thu Apr 12 08:36:26 2018 -0700 fix AMREX_DIMENSION_AGNOSTIC Tools/GNUMake/Make.defs commit e655c8853aaa3ee890a3a90b3bc8f8807d52c8e3 Author: Weiqun Zhang Date: Wed Apr 11 16:53:23 2018 -0700 add AMREX_NO_STRICT_PREFIX Tools/CMake/AMReX_Defines.cmake Tools/GNUMake/Make.defs commit 84603a9fbf1a7bfd1ec8da77edae3e9c007fb61f Author: Weiqun Zhang Date: Wed Apr 11 16:05:27 2018 -0700 update cmake for AMREX_DEBUG and AMREX_PARTICLES Tools/CMake/AMReX_Defines.cmake commit 2ea89c5fad5110be8c52f17b3e6828fb1240bd72 Author: Weiqun Zhang Date: Wed Apr 11 15:41:07 2018 -0700 DEBUG --> AMREX_DEBUG Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_NFiles.cpp Src/Extern/ProfParser/AMReX_BLProfStats.cpp Tools/GNUMake/Make.defs commit c4657f5c16db2baf4d430a704d691fe52a003b15 Author: Weiqun Zhang Date: Wed Apr 11 13:37:03 2018 -0700 DIMENSION_AGNOSTIC --> AMREX_DIMENSION_AGNOSTIC Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Tools/GNUMake/Make.defs commit fda52fd558d9057946c05662cbf8df7cb52590c5 Author: Weiqun Zhang Date: Wed Apr 11 13:32:27 2018 -0700 add AMREX_ version of BL_* definitions Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 7bb879c66325d7587a0543c10865bddd7f1bc6d6 Author: Weiqun Zhang Date: Wed Apr 11 12:59:39 2018 -0700 USE_CVODE --> AMREX_USE_CVODE Tools/GNUMake/packages/Make.cvode commit 2a07007b783479e7eb667e020eb446b85bd6ef2b Author: Weiqun Zhang Date: Wed Apr 11 11:38:29 2018 -0700 PARTICLES and USE_PARTICLES --> AMREX_PARTICLES Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp Src/Particle/AMReX_NeighborParticles.H Tools/GNUMake/Make.defs Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit e998f2c3335072c70b97d703b5d8278e9c71ea5a Author: kngott Date: Wed Apr 11 14:23:15 2018 -0700 Adjust third party profiling macros to 'AMREX_name'. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_ThirdPartyProfiling.H Tools/GNUMake/Make.defs Tools/GNUMake/tools/Make.craypat Tools/GNUMake/tools/Make.forge Tools/GNUMake/tools/Make.vtune commit 75a2ed4332947a199c40c4a0719d09455ca27d53 Author: Ann Almgren Date: Mon Apr 9 17:54:33 2018 -0700 Add link to original SWFFT source code Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst commit 4c2aee4f01bf9f1010dbcdd967ceef902fa29f9c Author: Ann Almgren Date: Mon Apr 9 17:50:44 2018 -0700 Update the sample inputs files in Tutorials/SWFFT. Tutorials/SWFFT/inputs.128 Tutorials/SWFFT/inputs.32 Tutorials/SWFFT/inputs.64 Tutorials/SWFFT/run_me Tutorials/SWFFT/swfft_solver.cpp commit 711267d4fd57e5dc420a4aff3cb9efc39a64fbe9 Author: Ann Almgren Date: Mon Apr 9 17:19:04 2018 -0700 Adding source code for SWFFT so that the Tutorial can run. Src/Extern/SWFFT/AlignedAllocator.h Src/Extern/SWFFT/COPYING Src/Extern/SWFFT/CheckDecomposition.c Src/Extern/SWFFT/Dfft.H Src/Extern/SWFFT/DfftC.cpp Src/Extern/SWFFT/Distribution.H Src/Extern/SWFFT/DistributionC.cpp Src/Extern/SWFFT/Error.h Src/Extern/SWFFT/Make.package Src/Extern/SWFFT/README Src/Extern/SWFFT/TimingStats.h Src/Extern/SWFFT/complex-type.h Src/Extern/SWFFT/distribution.c Src/Extern/SWFFT/distribution.h commit 9bfb66072250f7d4437f1837c802c1d6b2a5a86c Author: Ann Almgren Date: Mon Apr 9 16:54:21 2018 -0700 Update SWFFT Tutorial. Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst commit d67d9b553e9a58c4ba97856fce051fef00704fe1 Merge: ad727db71 9aa110e60 Author: Michael Zingale Date: Mon Apr 9 16:16:30 2018 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit ad727db71dc2ad40b587fb93401c2f3594e3421e Author: Michael Zingale Date: Mon Apr 9 16:16:03 2018 -0400 fextrema was a little misleading, since it was not giving the extrema over the whole domain. Now it does by looping over all levels Tools/Postprocessing/F_Src/fextrema.f90 commit d86b7cda29ac456b6fc9c3a7a8489cff490c4f26 Merge: 2760c709c 8ad6f6d2b Author: shashankNREL Date: Mon Apr 9 12:52:08 2018 -0600 Added the IJ solver call to amrex_hypre.cpp commit 9aa110e601dc8c801467eb666f497013a4554ed7 Author: Andrew Myers Date: Mon Apr 9 11:33:43 2018 -0700 Remove FORTH from AMReX_CONSTANTS.H as well. Src/Base/AMReX_CONSTANTS.H commit 2760c709ce4fc13158dbb157f548efe2b8539349 Author: shashankNREL Date: Mon Apr 9 12:02:02 2018 -0600 Moved the HYPRE IJ calls to Fortran; Works well on the HYPRE tutorial case and compares well against the SStruct interface Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/HYPRE/Make.package commit 980bd79270be24ecfbc8afb1083a8e42ef15aef8 Author: Andrew Myers Date: Mon Apr 9 10:33:48 2018 -0700 replace 'forth' with 'fourth' Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 commit 18a4daea42fc1e2e8bca80dffd770ea5e1d64152 Author: Andrew Myers Date: Mon Apr 9 10:25:27 2018 -0700 remove redundant definition of 1/4 in AMReX_constants_mod.f90 Src/Base/AMReX_constants_mod.f90 commit 1e4671e2d8df61a4fbb1a8ad65e18cdcda2fc1da Author: Weiqun Zhang Date: Sun Apr 8 18:29:20 2018 -0700 add Fortran interface to FluxRegister::OverwriteFlux Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit 4c7886bca1bc998858068c57f90cae279b9ada3e Author: Weiqun Zhang Date: Sun Apr 8 18:00:20 2018 -0700 add FluxRegister::OverwriteFlux Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FLUXREG_nd.F90 Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit ef7d5306e4f401345e6d24fb6e967e0e12544506 Author: Ann Almgren Date: Sun Apr 8 09:00:37 2018 -0700 Link back to documentation Docs/sphinx_tutorials/source/CVODE_Tutorial.rst commit 09c908cf7cd511d65e0c7e3a4d73224d9ef629c0 Author: Ann Almgren Date: Sun Apr 8 08:42:05 2018 -0700 Try to fix link. Docs/sphinx_documentation/source/CVODE.rst commit 567f6224a46834805ec3ec6e156f29c77f3175a6 Author: Ann Almgren Date: Sun Apr 8 08:14:17 2018 -0700 update link Docs/sphinx_documentation/source/CVODE.rst commit ed9d3c6b3e0c22277f681af2e3cb2f70518a8771 Author: Ann Almgren Date: Sun Apr 8 08:06:27 2018 -0700 Move the CVODE Tutorial description into the Tutorials section Docs/sphinx_documentation/source/CVODE.rst Docs/sphinx_tutorials/source/CVODE_Tutorial.rst commit 5e0903d1e97968c5f9b6aa3d6356b4074d43d5e7 Author: Ann Almgren Date: Sun Apr 8 07:54:56 2018 -0700 Update Basics_Tutorials page Docs/sphinx_tutorials/source/Basic_Tutorial.rst commit 53f1cba2d3ebd75842e7705befc3ea8fadbddeb8 Author: Ann Almgren Date: Sat Apr 7 18:05:15 2018 -0700 Start to fill in the Tutorials documentation. Docs/sphinx_tutorials/source/Basic_Tutorial.rst Docs/sphinx_tutorials/source/index.rst commit 52a0e790ef2b65a6e6cdafdad95a4da0e6d907da Author: Weiqun Zhang Date: Sat Apr 7 16:55:03 2018 -0700 add mising conf.py Docs/sphinx_tutorials/source/conf.py commit 8918e33b1c160de4473e4836477324e7ae75be8f Author: Weiqun Zhang Date: Sat Apr 7 16:38:20 2018 -0700 rm old ParmParse Fortran Src/Base/AMReX_BLParmParse_F.F90 Src/Base/AMReX_ParmParse.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 868637034f053480144e04c424fbf88f330db3d6 Author: Weiqun Zhang Date: Sat Apr 7 16:32:58 2018 -0700 rm AMReX_bl_flush.f Src/Base/AMReX_bl_flush.f commit 6c26cbcb3e007ab3c29db805bb7bedba2f43be57 Author: Weiqun Zhang Date: Sat Apr 7 16:29:38 2018 -0700 rm AMReX_SPACE_F.H Src/Base/AMReX_SPACE_F.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 8a2f08ae5e1bb82a232f5bc5686c7c5978ea9d24 Author: Weiqun Zhang Date: Sat Apr 7 16:20:35 2018 -0700 add a wrapper to polyintercoeff for tensormg Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F Src/LinearSolvers/C_TensorMG/Make.package Src/LinearSolvers/C_TensorMG/amrex_tmg_util.F90 commit 479b9ec61988ece342f93ccf07d817b933df0817 Author: Weiqun Zhang Date: Sat Apr 7 14:11:21 2018 -0700 C_CellMG4: .F files to .F90 files OldTutorials/MultiGrid_C/GNUmakefile Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H Src/LinearSolvers/C_CellMG4/Make.package commit 873b3c8981fcc68313e4bbe723b15169f1145a3e Author: Weiqun Zhang Date: Sat Apr 7 10:44:46 2018 -0700 remove AMREX_REAL.H from Fortran 90 files Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_LO_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 61d5e2762ace8a40821696b3f6b8faf1864129a9 Merge: 76fcd0ec6 bc2e80885 Author: Marc Day Date: Sat Apr 7 15:40:37 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 76fcd0ec64e045f006063e6ac71414ea924d1c83 Author: Marc Day Date: Sat Apr 7 15:40:25 2018 -0700 Fix bugs in postprocessing codes, add matlab .m script files that can read the output generated by PlotfileToMatLab.cpp Tools/C_util/WritePlotFile.cpp Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/PtwisePltTransform.cpp Tools/Postprocessing/C_Src/binread.m Tools/Postprocessing/C_Src/mk2d.m commit bc2e808856eade1af6c0fb8610441bb4c8bc8c14 Author: Ann Almgren Date: Sat Apr 7 15:18:47 2018 -0700 Move tutorials.rst to index.rst Docs/sphinx_tutorials/source/index.rst commit ecd1c0df870a8c4cd5a35d81a34ce3a3e7e90e6a Author: Ann Almgren Date: Sat Apr 7 15:09:13 2018 -0700 Try to build tutorials_html separately from docs_html Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/AmrCore/figs/Adv1.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv1.png Docs/sphinx_documentation/source/AmrCore/figs/Adv2.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv2.png 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Author: Weiqun Zhang Date: Fri Apr 6 18:00:36 2018 -0700 expand typedef for typecheck and fix type problems Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_F.H commit 0577bc9d03bb44bfafa9d31c730b1e5c475bc58a Author: Weiqun Zhang Date: Fri Apr 6 17:56:35 2018 -0700 rename for typecheck Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 94a8064e3d74fe5df78254016c0c44bdac2debce Author: Weiqun Zhang Date: Fri Apr 6 17:38:59 2018 -0700 break up some really long lines Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 commit 66ade5775fbb04aa959a213b2f5058e2da671033 Author: Weiqun Zhang Date: Fri Apr 6 17:19:01 2018 -0700 filcc: remove AMReX_REAL.H Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 commit d2199e44b782787e5ab6da9bc8076bd30bd635d0 Author: Weiqun Zhang Date: Fri Apr 6 17:03:46 2018 -0700 linear solver routines: module and c binding Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG/AMReX_lo_bctypes.fi Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 8139e209124dbd44355ac65711a20ce2a1ec097c Merge: 42aa36b7a 79991da77 Author: Marc Day Date: Fri Apr 6 16:44:57 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 42aa36b7a592c48e7c9100a786590706c01bb61a Author: Marc Day Date: Fri Apr 6 16:44:49 2018 -0700 Add a simple AmrData-based post-processing function Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/Make.package Tools/Postprocessing/C_Src/PtwisePltTransform.cpp Tools/Postprocessing/C_Src/PtwisePltTransform_nd.f90 commit 0a26f4eb1457bc19ca9de9c2ad1b5c35a5481541 Author: Weiqun Zhang Date: Fri Apr 6 16:02:03 2018 -0700 put interpbndrydata routine into module and add c binding Src/Base/AMReX_constants_mod.f90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.cpp commit d96918b892e552e584ee11c8d899d80bba8c4cfa Author: Weiqun Zhang Date: Fri Apr 6 14:44:23 2018 -0700 put coordsys routines into module Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.cpp commit af412264f1b6693b1d7fae3ba93429bd25fa2c39 Author: Weiqun Zhang Date: Fri Apr 6 14:25:20 2018 -0700 put interpolation routines into module Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp commit 79991da772b94b7b98ab61c9597fa1708163d826 Author: Andrew Myers Date: Fri Apr 6 14:13:16 2018 -0700 fix the ParticleContainer::Restart routine to work when levels are lost on restart.' Src/Particle/AMReX_ParticleContainerI.H commit b94c0a0b42e6620b6f56b8008bea93c019df8b83 Author: Weiqun Zhang Date: Fri Apr 6 13:37:17 2018 -0700 put flux register fortran code into module Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FluxRegister.cpp commit 813e23da8c13d02ec9418dfd4538562910d9ad81 Author: Weiqun Zhang Date: Fri Apr 6 12:50:42 2018 -0700 replace DIM[123] Src/AmrCore/AMReX_INTERP_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 commit f6f9ed6e439b4b3d9c548bcbce660e23e68576d9 Author: Weiqun Zhang Date: Fri Apr 6 12:48:00 2018 -0700 move ARRAYLIM_?D.F90 to IAMR Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/Amr/CMakeLists.txt Src/Amr/Make.package commit ed14f486efd4126b8c76ce13b1f2bf4809e5cfa7 Author: Weiqun Zhang Date: Fri Apr 6 11:17:44 2018 -0700 remove AMReX_ArrayLim.H from F90 files Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 commit e6b6ef5fd918f6ec1da00017a48c469abd2dbe06 Author: Weiqun Zhang Date: Fri Apr 6 11:10:21 2018 -0700 replace ARG_L1, ARG_L2, ... etc. Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 commit 05d0e691479316e3c1bd33a511373d41d9b2911b Author: Weiqun Zhang Date: Fri Apr 6 11:04:39 2018 -0700 replace DIM1, DIM2 and DIM3 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 commit c32a81f00ead4d405fde7d1b577dcccfb152f5a9 Author: Weiqun Zhang Date: Fri Apr 6 11:00:10 2018 -0700 replace DIMV Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 commit e98d6972faf07cfed70bbfd1701ce3362861b299 Author: Weiqun Zhang Date: Fri Apr 6 10:55:55 2018 -0700 replace DIMDEC in F90 files Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 commit 92fa0eddca9fed3901354eb41b7ed28a6d48d461 Author: Weiqun Zhang Date: Fri Apr 6 10:53:39 2018 -0700 replace DIMS in F90 files Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 commit 87388019d5d85eccaa83accf6150a7fa80fb26e6 Author: Marc Day Date: Fri Apr 6 10:52:19 2018 -0700 Remove commented out code, clean up slightly. Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp commit b033d37eec1bf75f2aafe7de98d14a9cab1a4ddf Author: Weiqun Zhang Date: Thu Apr 5 14:18:25 2018 -0700 add AMREX prefix to some include guards Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Extrapolater.H Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateDescriptor.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_TagBox.H Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/Amr/AMReX_AmrLevelTask.H Src/AmrTask/AmrCore/AMReX_FillPatchUtil.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseIndex.H Src/Base/AMReX_BaseUmap_f.H Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_Periodicity.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMDI.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_parstream.H Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_MultiMask.H Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particles.H commit d73c54f48e0b20ff7ae56c7733bb00b3dbbcbcc8 Merge: 521912070 f4043b49e Author: asalmgren Date: Wed Apr 4 14:21:27 2018 -0700 Merge pull request #240 from AMReX-Codes/add_matlab_conv Add plotfile-to-Matlab converter. commit 521912070ce405e331f1e4c7820e4393624e55c3 Author: kngott Date: Wed Apr 4 12:06:13 2018 -0700 Adjustment to RStartStop profiling object to reomve padding and eliminate valgrind warning message. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp commit 8ad6f6d2bcdd6db43c2d1b7bcf9584fe6216ef3e Author: shashankNREL Date: Wed Apr 4 12:56:17 2018 -0600 Added call to the IJ solver in the hypre solver constructor Src/Extern/HYPRE/AMReX_Hypre.cpp commit 15ef4429275075c1baf93dca131e434101745583 Merge: e5a862513 9c021357a Author: Weiqun Zhang Date: Wed Apr 4 09:24:03 2018 -0700 Merge branch 'development' into weiqun/mlmg commit f4043b49e564891ac32c60f64b0613579b8335cb Author: Marc Day Date: Tue Apr 3 11:25:43 2018 -0700 Add plotfile-to-Matlab converter. Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/Make.package Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp commit 9c021357ab2b68d0646325f66452d049c9cb7c43 Author: Johannes Blaschke Date: Tue Apr 3 11:19:21 2018 -0700 just to be _really_ clear about how to open flow fields with paraview Docs/sphinx/source/Visualization.rst commit f04a8b1668c8d1e360d58352b02f913853038ccb Author: Johannes Blaschke Date: Tue Apr 3 11:16:50 2018 -0700 Fix some small problems with the documentation Docs/sphinx/source/Basics.rst Docs/sphinx/source/Visualization.rst commit db34ed33d6fa36e354a89f06aa19866051a8ca55 Author: Weiqun Zhang Date: Tue Apr 3 10:56:19 2018 -0700 fix a typo Src/Base/AMReX_ParallelContext.H commit 9831a9b2d9edf9edf5cccd653cb09fa1cd314919 Author: Weiqun Zhang Date: Tue Apr 3 10:06:57 2018 -0700 Make amrex::Array an alias of std::array instead of amrex::Vector. This may break some codes. But warning was given 4 months ago. Src/Base/AMReX_Array.H commit cc3afa8a49377c6ff8a5d31c32e23c40f17636d0 Author: Andrew Myers Date: Tue Apr 3 09:40:35 2018 -0700 remove a debug print statement from ParticleContainer::Checkpoint Src/Particle/AMReX_ParticleContainerI.H commit d6f6adb5e4f690c3d1d627d67117a03359185032 Merge: 6bb31258b 834553d7f Author: Weiqun Zhang Date: Mon Apr 2 18:57:56 2018 -0700 Merge branch 'forkjoin' into development commit 834553d7f03391d78c69a1ce6279f281585c4d30 Author: Weiqun Zhang Date: Mon Apr 2 18:40:45 2018 -0700 Merge branch 'development' into forkjoin Docs/sphinx/source/EB.rst Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ThirdPartyProfiling.H Src/Base/Make.package Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Tests/ProfTests/ThirdParty/Exec/GNUmakefile Tests/ProfTests/ThirdParty/Exec/inputs_2d Tests/ProfTests/ThirdParty/Exec/inputs_3d Tests/ProfTests/ThirdParty/Source/Make.package Tests/ProfTests/ThirdParty/Source/advance.cpp Tests/ProfTests/ThirdParty/Source/advance_2d.f90 Tests/ProfTests/ThirdParty/Source/advance_3d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_2d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_3d.f90 Tests/ProfTests/ThirdParty/Source/main.cpp Tests/ProfTests/ThirdParty/Source/myfunc.H Tests/ProfTests/ThirdParty/Source/myfunc_F.H Tools/GNUMake/Make.defs Tools/GNUMake/tools/Make.forge Tools/GNUMake/tools/Make.vtune commit 6bb31258b0ceb06d23ed267828de99e450ce4687 Merge: 0e1a31b9b b94ed2b6a Author: Johannes Blaschke Date: Mon Apr 2 17:30:05 2018 -0700 Merge branch 'development' into jpb/fill-nodal commit 0e1a31b9b48c430155caf5a887ddac2acebb9096 Author: Johannes Blaschke Date: Mon Apr 2 17:21:10 2018 -0700 fix double-scaling if fillNodalArrays from AnisotropicIF Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp commit b94ed2b6af36141e6334a324168347ae720fc1f3 Merge: 22331f5a1 e38db4fcb Author: kngott Date: Mon Apr 2 16:07:07 2018 -0700 Merge branch 'kngott_tpp' into development commit e38db4fcbeef6b83f30e2930171373a6649b599d Merge: a3616cd09 212af5064 Author: kngott Date: Mon Apr 2 16:03:46 2018 -0700 Merge branch 'development' into kngott_tpp commit a3616cd091dda8b8b8e5a4efc9c661b620252712 Author: kngott Date: Mon Apr 2 15:56:06 2018 -0700 Final Third Party Version Src/Base/AMReX_BLProfiler.H Tests/ProfTests/ThirdParty/Exec/GNUmakefile Tests/ProfTests/ThirdParty/Exec/inputs_2d Tests/ProfTests/ThirdParty/Exec/inputs_3d Tests/ProfTests/ThirdParty/Source/Make.package Tests/ProfTests/ThirdParty/Source/advance.cpp Tests/ProfTests/ThirdParty/Source/advance_2d.f90 Tests/ProfTests/ThirdParty/Source/advance_3d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_2d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_3d.f90 Tests/ProfTests/ThirdParty/Source/main.cpp Tests/ProfTests/ThirdParty/Source/myfunc.H Tests/ProfTests/ThirdParty/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp commit 22331f5a12eec954ce27b862443e3d35d1465cd6 Merge: 4cc12b30a 212af5064 Author: dtgraves Date: Mon Apr 2 15:14:15 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4cc12b30a9bc76004c519cc6d98401a89048b55d Author: dtgraves Date: Mon Apr 2 15:13:55 2018 -0700 added a bit about EBIndexSpace::read and EBIndexSpace::write into the User's guide. Docs/sphinx/source/EB.rst commit 212af506478499fed116751ac1083f0515c51fd9 Author: kngott Date: Mon Apr 2 15:13:19 2018 -0700 Eliminate extra padding in ReadAndBcastFile. Src/Base/AMReX_ParallelDescriptor.cpp commit 41456520f67b46effb9e06dba3abe1fa441372ef Author: shashankNREL Date: Mon Apr 2 13:44:01 2018 -0600 Added HYPRE Matrix IJ Interface Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit c0fa861fdd9f9bb24666568eeac0a1ae1901f23b Merge: 4e8451c56 9f1d24e84 Author: Weiqun Zhang Date: Mon Apr 2 09:40:32 2018 -0700 Merge branch 'development' into forkjoin commit 9f1d24e84a4263bb74abe7f12703715de3dd54f3 Author: Weiqun Zhang Date: Mon Apr 2 09:38:03 2018 -0700 update changes CHANGES commit 35ec89c33c3f78054d970e191a2cacfe2f8767c9 Author: Ann Almgren Date: Sun Apr 1 09:32:02 2018 -0700 Add pointers to individual files Docs/sphinx/source/tutorials.rst commit 2488c06213511d4354ea6a0b8de7668233f8ce24 Author: Ann Almgren Date: Sun Apr 1 09:31:47 2018 -0700 Add file for each Tutorial directory Docs/sphinx/source/AMR_Tutorial.rst Docs/sphinx/source/Basic_Tutorial.rst Docs/sphinx/source/CVODE_Tutorial.rst Docs/sphinx/source/EB_Tutorial.rst Docs/sphinx/source/HYPRE_Tutorial.rst Docs/sphinx/source/LinearSolvers_Tutorial.rst Docs/sphinx/source/Particles_Tutorial.rst Docs/sphinx/source/SWFFT_Tutorial.rst commit 514ed9eb6a17737c36552fe96c4a115510d52e72 Author: Ann Almgren Date: Sun Apr 1 09:18:49 2018 -0700 Trying to set up tutorals link Docs/sphinx/source/tutorials.rst commit e1f90415471db1586c7718047a3633ce75ed7d05 Author: Ann Almgren Date: Sun Apr 1 09:09:32 2018 -0700 Add Tutorials.rst for first start at Tutorials link from amrex io page. Docs/sphinx/source/Tutorials/Tutorials.rst commit fcdb2bba62412c87a35d5c31aab803d59e4522c2 Author: Weiqun Zhang Date: Sat Mar 31 14:32:00 2018 -0700 replace HUGE with numeric_limits constexpr functions Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_LSProblemImplem.H commit c19a9dfe9267da884c36ef0a7cb9edfc51f5da04 Merge: 424b25bff 0846a94e6 Author: Andrew Myers Date: Fri Mar 30 16:32:07 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 424b25bffa218566ba9f13abcf1787c2cf1ad447 Author: Andrew Myers Date: Fri Mar 30 16:31:57 2018 -0700 add some parentheses here to silence compiler warnings. Src/Base/AMReX_MultiFabUtil.cpp commit 0846a94e604b9137a255f6d0d6c19f35c24712f3 Author: Ann Almgren Date: Fri Mar 30 14:51:37 2018 -0700 Modify the AssignDensity routine here (and the interfaces and calling routines in Nyx) so that we can pass in the number of grow cells used to define the array that will hold the particle deposition. Some previous calls defaulted to 1 ghost cell which is not big enough if valid particles live in ghost cells themselves (eg if starting the second level 1 solve of a subcycled level 0-1-2 simulation.) Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ac4333e1ba7cba11a30083840833287c95930531 Author: Andrew Myers Date: Fri Mar 30 14:18:17 2018 -0700 Removing RegressionTesting from the amrex repo. These live at https://github.com/AMReX-Codes/regression_testing now. Tools/RegressionTesting/AMReX-tests.ini Tools/RegressionTesting/README Tools/RegressionTesting/example-tests.ini Tools/RegressionTesting/gen_compile_test.sh Tools/RegressionTesting/params.py Tools/RegressionTesting/reg_test_gc.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/repo.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit a8745d4785328e6457021dcd19602ed4ea683ccf Merge: d7c93cbc8 79666bdee Author: Andrew Myers Date: Thu Mar 29 16:43:14 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d7c93cbc861e4c203b952dfdf2551342adc1a885 Author: Andrew Myers Date: Thu Mar 29 16:42:22 2018 -0700 improve omp scaling of CacheNeighborInfo Src/Particle/AMReX_NeighborParticlesI.H commit 79666bdee0bde8ca86895c28b35340f2366b4a18 Author: Ann Almgren Date: Thu Mar 29 16:06:09 2018 -0700 Fix typo in init_rhs and make sure the rhs sums to 0 Tutorials/SWFFT/SWFFT_Test.cpp Tutorials/SWFFT/SWFFT_Test_F.F90 Tutorials/SWFFT/swfft_solver.cpp commit 4e8451c562ea5f04f149552f8aa0b1dcae651b2c Author: Weiqun Zhang Date: Thu Mar 29 14:42:11 2018 -0700 split some FabArray communciation functions into a separate file Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 52a2e1b04801e71b7282069ad26a0997c199b30c Author: Weiqun Zhang Date: Thu Mar 29 13:53:40 2018 -0700 use move when possible OldTutorials/MultiFabTests_C/MultiFabFillBoundary.cpp OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_VisMF.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 9a24f1571826b562692d149eb152ddc50c5ee985 Author: Weiqun Zhang Date: Thu Mar 29 13:05:48 2018 -0700 add new constructor that moves Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp commit b6af6fd0c87ff1ec0d66749399532b078dd3b92c Author: Weiqun Zhang Date: Thu Mar 29 12:56:06 2018 -0700 MLMG: fix subcommunicator Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit e0cab03fa249839ae16ed46bfb384977f22a798c Author: Weiqun Zhang Date: Thu Mar 29 12:34:01 2018 -0700 MLMG: update for fork/join Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 8cd48768ff841c33e83cefd74a78d14f5abca79e Author: Weiqun Zhang Date: Thu Mar 29 11:23:59 2018 -0700 add ParallelReduce, rename some functions and use MLMG in MultiColor_C OldTutorials/MultiColor_C/GNUmakefile OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelReduce.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 81e1b5c20f5e07b4688bf1629b62352469a7d210 Merge: 316504ac4 9d84a39a4 Author: Weiqun Zhang Date: Thu Mar 29 10:09:20 2018 -0700 Merge branch 'development' into forkjoin Conflicts: Src/Amr/AMReX_AmrLevel.cpp commit 316504ac4afca41b1cbf20dfbc6b67dabe1c6c46 Author: Weiqun Zhang Date: Thu Mar 29 10:07:21 2018 -0700 store groups to avoid repeatedly creating groups in rank translation Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp commit b6abe60314b0f04de317d85a8ee553df46f284cf Author: Weiqun Zhang Date: Thu Mar 29 09:34:29 2018 -0700 fix MultiColor_C Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.cpp commit 01f1c89d4e8fab674e7f836c493183ad5fe18666 Author: Weiqun Zhang Date: Thu Mar 29 08:52:19 2018 -0700 rename Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp commit 9d84a39a4dacaab3aec2a357c4e30b84b08e7ce6 Author: Ann Almgren Date: Thu Mar 29 08:28:33 2018 -0700 Change name from solver_itself to swfft_solver Tutorials/SWFFT/SWFFT_Test.cpp Tutorials/SWFFT/swfft_solver.cpp commit c1adb53c4dbe8ef86f35af383ce8f4475378eb64 Author: Ann Almgren Date: Thu Mar 29 08:02:44 2018 -0700 Modify so that the interface to the solver isn't part of the testing class, but a stand alone routine that takes the rhs multifab and geometry and returns the soln multifab. Tutorials/SWFFT/Make.package Tutorials/SWFFT/SWFFT_Test.H Tutorials/SWFFT/SWFFT_Test.cpp Tutorials/SWFFT/SWFFT_Test_F.F90 Tutorials/SWFFT/SWFFT_Test_F.H Tutorials/SWFFT/main.cpp Tutorials/SWFFT/swfft_solver.cpp commit 0473face11f676988a65d1234a18756cefa4c974 Author: Ann Almgren Date: Wed Mar 28 21:22:21 2018 -0700 Update the call to the solver so it correctly handles the case where we decompose a cubic grid into different numbers of grids in each direction, eg a 32^3 grid decomposed into 32x16x16 boxes. Tutorials/SWFFT/SWFFT_Solver.cpp Tutorials/SWFFT/SWFFT_Solver_F.F90 Tutorials/SWFFT/SWFFT_Solver_F.H Tutorials/SWFFT/inputs.32 commit 622003b1e361fb8954538962b34911704aec7642 Merge: 06fb8a43d 0591e30b8 Author: Ann Almgren Date: Wed Mar 28 20:36:15 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 06fb8a43d378833e6383ebde58fa239b40fe23e6 Author: Ann Almgren Date: Wed Mar 28 20:35:23 2018 -0700 Change the user interface so that for both max_grid_size and n_cell you can enter one value, which would set the values in all directions to that value, or it can take in 3 values, one for each direction (in 3d) Tutorials/SWFFT/SWFFT_Solver.H Tutorials/SWFFT/SWFFT_Solver.cpp commit 0591e30b836fe8451c1b2462d7e610dc365f62b7 Merge: 5b2f40d9c 0b5a226e5 Author: Brandon Runnels Date: Wed Mar 28 17:39:56 2018 -0700 Merge pull request #235 from AMReX-Codes/MLLinOp_Fix MLLinop Corner Fix commit 0b5a226e580c25dd711273be6658133c5a4009a4 Author: Brandon Runnels Date: Wed Mar 28 19:27:39 2018 -0500 removed mask condition and added support for mixed bcs Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 5b7594f32901603a3ab78df50db9a76a0b219ed3 Author: Weiqun Zhang Date: Wed Mar 28 17:00:06 2018 -0700 update DistributionMapping for fork/join Src/Base/AMReX_DistributionMapping.cpp commit dcbc97f351559175c70c53c3eb3a33038188dc88 Author: Weiqun Zhang Date: Wed Mar 28 12:41:42 2018 -0700 update FabArray communication for fork/join Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelReduce.H commit 5b2f40d9cefe97e31102d1f0a2b7f99028527659 Author: Weiqun Zhang Date: Wed Mar 28 10:58:52 2018 -0700 add Sod test to EB/CNS Tutorials/EB/CNS/Exec/Sod/GNUmakefile Tutorials/EB/CNS/Exec/Sod/Make.package Tutorials/EB/CNS/Exec/Sod/cns_prob.F90 Tutorials/EB/CNS/Exec/Sod/inputs commit e640bfff93483ae61bca8a9c5fca529def5ac248 Author: Weiqun Zhang Date: Wed Mar 28 09:32:36 2018 -0700 use the global communicator in ParallelDescriptor Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_Print.H commit ffd031139a5a74ebd97fee8c978a02bde151607e Merge: a6e0d6bf7 58f493f91 Author: Andrew Myers Date: Wed Mar 28 09:51:38 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a6e0d6bf7d3b5f1374cc2fe13c0769db99929b15 Author: Andrew Myers Date: Wed Mar 28 09:51:22 2018 -0700 remove AllReduce from RedistributeMPI Src/Particle/AMReX_ParticleContainerI.H commit cbb769576554242a08b33346c9035279b92ac23d Author: Weiqun Zhang Date: Wed Mar 28 09:21:38 2018 -0700 MLMG bottom: use ParallelContext Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 58f493f9186b1725bf07050238e0c8bbe73bf7fd Merge: 394d6d9f2 566a30e5d Author: WeiqunZhang Date: Wed Mar 28 08:59:23 2018 -0700 Merge pull request #234 from AMReX-Codes/MLCellLinOp_NCompFix Enable multicomponent flux registers commit 566a30e5d3e06813398a9e338e7de3ec19ec89db Author: Brandon Runnels Date: Wed Mar 28 11:28:40 2018 -0400 removed extra comment Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 52fefb47153e7712f08eccd86b59cfff40a403ce Author: Brandon Runnels Date: Wed Mar 28 11:27:23 2018 -0400 fixed bug caused by assuming single component flux registers Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit d2d7cce46327f962287908d06921d422896863d2 Author: Weiqun Zhang Date: Tue Mar 27 16:27:29 2018 -0700 simplify SeqNum() Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 0f924fda42acc39d479fcf6c064fb6936666b92c Author: Weiqun Zhang Date: Tue Mar 27 14:48:38 2018 -0700 fix a new bug Src/Base/AMReX_ParallelDescriptor.cpp commit f39b46c9b8e561c7add10234e37069256fff5ea7 Merge: 094db81a2 394d6d9f2 Author: Max Katz Date: Tue Mar 27 16:54:25 2018 -0400 Merge branch 'development' into gpu commit 4333b017fe7c7b14dd0bf63f114c0df1fbe25895 Author: Weiqun Zhang Date: Tue Mar 27 13:54:01 2018 -0700 fix non-MPI Src/Base/AMReX_ParallelDescriptor.cpp commit 394d6d9f2187dd5335968071d4bc83ec1e01fadd Author: Max Katz Date: Tue Mar 27 16:29:45 2018 -0400 Add IBM MPI lib for Fortran on Summit Tools/GNUMake/sites/Make.olcf commit 515a5b0b10a35f3a063ceb3e63581d070c8cfb3b Author: Weiqun Zhang Date: Tue Mar 27 11:56:38 2018 -0700 rm BroadCast DistributionMapping and BoxArray Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 2baeac6e02b02b85e60de1b5b4b33d4e4a0f93ac Author: Weiqun Zhang Date: Tue Mar 27 11:51:52 2018 -0700 rm PFC Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 8e103b621daa6f34b4f5cef43b07869f873b7c2c Author: Weiqun Zhang Date: Tue Mar 27 11:36:51 2018 -0700 rm FAPId Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 1aab47864030a14164f416202a5392362b41ece2 Author: Weiqun Zhang Date: Tue Mar 27 11:25:27 2018 -0700 rm FAPointers Src/Base/AMReX_FabArray.H commit 03216dad6667eebf0194e11ce8b71bb6671d9dda Author: Weiqun Zhang Date: Tue Mar 27 11:16:32 2018 -0700 rm MoveFabs OldTutorials/MultiFabTests_C/GNUmakefile OldTutorials/MultiFabTests_C/GridMoveTest.cpp OldTutorials/MultiFabTests_C/Make.package OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H commit 2616290db559025e871c4ad7863f1437d1a9a191 Author: Weiqun Zhang Date: Tue Mar 27 11:05:43 2018 -0700 rm AddProcsToComp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H commit dfe15ac19c592ff10d1831a074703be39b057ba0 Author: Weiqun Zhang Date: Tue Mar 27 10:57:48 2018 -0700 rm more sidecar stuff OldTutorials/DataServicesTest0/GNUmakefile Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_MemProfiler.H Src/Base/AMReX_MemProfiler.cpp Tests/IOBenchmark/GNUmakefile commit 70b098c021b0b90de6d727e540182552da801445 Author: Weiqun Zhang Date: Tue Mar 27 10:29:23 2018 -0700 first pass of removing sidecar Docs/Readme.sidecars OldTutorials/Sidecar_EX1/DestMFTest.cpp OldTutorials/Sidecar_EX1/GNUmakefile OldTutorials/Sidecar_EX1/GridMoveTest.cpp OldTutorials/Sidecar_EX1/InTransitAnalysis.H OldTutorials/Sidecar_EX1/InTransitAnalysis.cpp OldTutorials/Sidecar_EX1/Make.package OldTutorials/Sidecar_EX1/NSidecarsTest.cpp OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp OldTutorials/Sidecar_EX1/TestRankSets.cpp OldTutorials/Sidecar_EX1/inputs_3d OldTutorials/Sidecar_EX1/inputs_sc OldTutorials/Sidecar_EX1/run.sh Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Print.H Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 Tests/C_BaseLib/BcastClasses/BcastClasses.cpp Tests/C_BaseLib/BcastClasses/GNUmakefile Tools/CompileTesting/compiletesting.py commit ee95e75e97f2fec1cece588871dce76d479f6d50 Author: Ann Almgren Date: Tue Mar 27 09:16:25 2018 -0700 Get rid of more IOIOIO:CD writes Src/Amr/AMReX_AmrLevel.cpp commit d3010f90a8b6fdbc1729d5e42170579ad2f9d801 Author: Ann Almgren Date: Tue Mar 27 09:15:19 2018 -0700 Get rid of all those IOIOIOI write statements Src/Amr/AMReX_Amr.cpp commit e5dd1086dcdbc309a16ebc541af0d7737ee87a72 Author: Weiqun Zhang Date: Mon Mar 26 15:52:44 2018 -0700 c bind for hoextraptocc Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 commit 5b989f4be165ae6f8caaac0c5afa482a819fde93 Author: Ann Almgren Date: Mon Mar 26 13:22:40 2018 -0700 Remove the IOIOIOIO print statements Src/Particle/AMReX_ParticleContainerI.H commit 40c4dd225bc6fdf0333586d3bd87e41fe34a3cf4 Merge: 099a99897 e608757a0 Author: Weiqun Zhang Date: Mon Mar 26 12:26:38 2018 -0700 Merge branch 'development' into forkjoin Conflicts: Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.cpp commit e608757a0716994636bc2001a5a4607d731cc798 Author: dtgraves Date: Mon Mar 26 10:53:44 2018 -0700 removed slabservice-- an unused geometry service. Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp Src/GeometryShop/CMakeLists.txt commit ffb6a9eb20819d2ad0ea2eee9bc51ddea50b9689 Merge: a4044a7ec 4d324a835 Author: dtgraves Date: Mon Mar 26 10:43:35 2018 -0700 merging stuff commit 4d324a835733f996c9311905d2845e08c58273a0 Author: dtgraves Date: Mon Mar 26 10:36:59 2018 -0700 updated CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit a4044a7ec6da04488c6b3752f606825ab2556de9 Author: Weiqun Zhang Date: Mon Mar 26 10:24:39 2018 -0700 nodal solvability: fix a bug Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit fd3833b2cb6ac947f1defed7bcb76ac2292c9a3a Merge: d66cdbc1c 0362f0600 Author: Weiqun Zhang Date: Mon Mar 26 09:05:27 2018 -0700 Merge branch 'development' into nd_solvability commit 0362f0600d969afdfabccbd4f1d75b9b814f79e5 Author: Ann Almgren Date: Mon Mar 26 07:26:43 2018 -0700 Missed another one Src/GeometryShop/CMakeLists.txt commit ccef59b93960ab0efdc32995042b421cadffdf8d Author: Ann Almgren Date: Mon Mar 26 07:22:43 2018 -0700 Fix typo Src/GeometryShop/CMakeLists.txt commit bbbd4b30c78ff5f0b1f9ab327e363cd1e56c3958 Author: Ann Almgren Date: Mon Mar 26 07:18:21 2018 -0700 Missed another one... Src/GeometryShop/CMakeLists.txt commit 084bda0ba8c58483fca7b8c6c864c7dd3f6a1daa Author: Ann Almgren Date: Mon Mar 26 07:14:52 2018 -0700 Fix typo Src/GeometryShop/CMakeLists.txt commit a947fa0a3aa38052fc5b56a963dea83bca38f69b Author: Ann Almgren Date: Mon Mar 26 07:12:26 2018 -0700 I think I got the rest of them... Src/GeometryShop/CMakeLists.txt commit 0aa9f24e0cd31ad35f165052ada18a8af8a6fe2d Author: Ann Almgren Date: Mon Mar 26 07:04:02 2018 -0700 Add AMReX_IndexedMoments.H to CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit 65edfc2d8dd551a6844d90a16e00b0adddcf9406 Author: Weiqun Zhang Date: Sun Mar 25 16:19:47 2018 -0700 some minor additions to Finalize Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.cpp commit 068d07bb5a9364ad0713471a1955c42d1b993366 Author: Weiqun Zhang Date: Sun Mar 25 15:09:14 2018 -0700 Tests/ThirdPartiLib: solve Poisson GNUmakefile.in Src/Base/AMReX_ParallelDescriptor.cpp Tests/ThirdPartyLib/bar.F90 Tests/ThirdPartyLib/foo.cpp commit af08aeb5facd74c9873e930497a574f23a3a08fc Author: Weiqun Zhang Date: Sat Mar 24 23:57:38 2018 -0700 reentrant: AMReX.cpp Src/Base/AMReX.cpp Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MemProfiler.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_ParmParse.cpp commit 7c301e84e30d20f63a42ed09861208a80e09e419 Author: Weiqun Zhang Date: Sat Mar 24 21:38:34 2018 -0700 add a test for using amrex as a third-party library Tests/ThirdPartyLib/GNUmakefile Tests/ThirdPartyLib/Readme Tests/ThirdPartyLib/bar.F90 Tests/ThirdPartyLib/foo.cpp Tests/ThirdPartyLib/main.c commit 2ac7f2a03bc153aee6cdd3492e6ad1ff2ba66913 Author: Weiqun Zhang Date: Sat Mar 24 19:58:30 2018 -0700 no longer print # of MPI processes and OMP threads if verbose is not on Src/Base/AMReX.cpp commit a19a8fad9763875f727a4b00de0f2fdf9e3b09d7 Author: Weiqun Zhang Date: Sat Mar 24 19:43:51 2018 -0700 MPI_Comm is now safe if AMReX is initialized and then finalized repeated Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit d3271447c9da0667b891c4aaa36704d73c99c784 Author: Weiqun Zhang Date: Sat Mar 24 19:36:00 2018 -0700 rm F_BaseLib and F_MG from libamrex GNUmakefile.in commit bbb54fbe8a925bdda4c97249af44eb32b1183275 Author: Weiqun Zhang Date: Sat Mar 24 14:52:29 2018 -0700 amrex::Initialize is now OK with argc=0. do not stop if get_command fails Src/Base/AMReX.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 commit 449d64649f5f0164c678d770cccfffc55be26d35 Author: Weiqun Zhang Date: Sat Mar 24 13:09:20 2018 -0700 if the communicator given is MPI_COMM_WORLD, we should go ahead calling MPI_Init Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 094db81a263ed2de59303bae406f847282a89479 Merge: 1558c461d 05b79343e Author: Max Katz Date: Sun Mar 25 13:17:36 2018 -0400 Merge branch 'development' into gpu commit 1558c461d233d728143a11b9ab9eca3ddf3a3c2c Author: Max Katz Date: Sun Mar 25 12:57:33 2018 -0400 Use built-in F90 link when compiling with CUDA Tools/GNUMake/Make.rules Tools/GNUMake/comps/pgi.mak commit 05b79343e77c7a79f1a9213ea18a892ab4169f87 Author: Ann Almgren Date: Sat Mar 24 11:21:10 2018 -0700 Updated the SWFFT Tutorial so 1) It correctly solves the Poisson equation on a single grid, 2) it creates a version of the DistributionMapping to pass to dfft. Tutorials/SWFFT/README Tutorials/SWFFT/SWFFT_Solver.H Tutorials/SWFFT/SWFFT_Solver.cpp Tutorials/SWFFT/SWFFT_Solver_F.F90 Tutorials/SWFFT/SWFFT_Solver_F.H Tutorials/SWFFT/inputs.128 Tutorials/SWFFT/inputs.32 Tutorials/SWFFT/inputs.64 commit d66cdbc1ca0067206ede589732d45e51559b1ce0 Author: Weiqun Zhang Date: Fri Mar 23 20:36:59 2018 -0700 merge two mfiter loops Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 60b02681b583a3ca2e4238f7891b59244d35c19b Author: Weiqun Zhang Date: Fri Mar 23 18:05:16 2018 -0700 solve nodal solvability Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit 16ddf9bd30d61e1795b126c6ee9a6867cb9058b9 Author: Ann Almgren Date: Fri Mar 23 16:44:42 2018 -0700 This version seems to work. Tutorials/SWFFT/SWFFT_Solver.H Tutorials/SWFFT/SWFFT_Solver.cpp commit 7dad5979ca9567ce8a7c7d71ad4c01434688aded Merge: e92ed6fc1 0ef49dabe Author: Ann Almgren Date: Fri Mar 23 15:49:51 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit e92ed6fc15da735bd8c30315db742ef9e215289f Author: Ann Almgren Date: Fri Mar 23 15:49:40 2018 -0700 Save this before I accidentally delete it Tutorials/SWFFT/SWFFT_Solver.cpp commit 0ef49dabe81a476b9e01124934684a04f108e341 Merge: e7a1e67f4 6ef68a97d Author: dtgraves Date: Fri Mar 23 13:54:12 2018 -0700 Merge pull request #232 from AMReX-Codes/dtg/high_order_moments added higher order moment infrastructure commit 6ef68a97db813cce11772c76854745addc2f9bff Merge: 3b9fcc260 e7a1e67f4 Author: dtgraves Date: Fri Mar 23 13:51:48 2018 -0700 Merge branch 'development' into dtg/high_order_moments commit 3b9fcc26078c99d65068bd55af2f78f8cc1c8caf Author: dtgraves Date: Fri Mar 23 13:50:42 2018 -0700 geometry generation with higher order moments now passes all the regression tests. Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp Tests/GeometryShop/regression/ebio.cpp commit 43395ead1570c9e32525cac83e5c7c73988fb4f4 Author: dtgraves Date: Fri Mar 23 10:38:36 2018 -0700 fixed eb data serialization. all serial regression tests pass now. on to mpi testing Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/serialization.cpp commit e7a1e67f44a14365956070d0c3442b279e1853dd Author: Weiqun Zhang Date: Fri Mar 23 09:01:19 2018 -0700 fix non-mpi build Src/Base/AMReX_ParallelDescriptor.cpp commit 099a99897456895a914964627852f015e61bbdaa Author: Weiqun Zhang Date: Fri Mar 23 08:55:41 2018 -0700 array version of rank translation Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp commit 7287e8113025ed99c789b58b963780192abe95ab Author: Kevin Gott Date: Thu Mar 22 16:27:25 2018 -0700 Fix ParallelDescriptor::Waitany and update all other MPI_Wait calls to use the ParallelDescriptor versions. Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp commit a5a11964a968901ea360e1be76a04717d8b33726 Author: Andrew Myers Date: Thu Mar 22 15:56:22 2018 -0700 use the ParallelDescriptor version of Waitall in the particle communication routines. Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit 47f8837fd99aef576ebcff4a552ed796316099c0 Merge: 6a679202f 6caf213d8 Author: Andrew Myers Date: Thu Mar 22 14:49:04 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6a679202f2fed46acc7f08c506d364835e162fe9 Author: Andrew Myers Date: Thu Mar 22 14:48:55 2018 -0700 fix omp shared variable list in plt_compare_diff_grids Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit ecc33e176607fe0b25eb58fdcfa9a76be88df86b Author: Weiqun Zhang Date: Thu Mar 22 14:44:58 2018 -0700 use MyProcAll instead of MyProc in some places; if the current context is the global communicator, no need to call translate Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_Print.H commit 6caf213d835da64f482510a30955a5db3d669dbd Author: Kevin Gott Date: Thu Mar 22 14:21:47 2018 -0700 Profiling added to the MPI Wait call wrappers. Simple test case also included. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelDescriptor.cpp Tools/AMRProfParser/TestCodes/GNUmakefile Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp commit fd30f89e03d7712ffe2a0685c2a65ce19c6f19fd Author: Andrew Myers Date: Thu Mar 22 13:28:04 2018 -0700 add extra newline Tools/RegressionTesting/test_report.py commit 66f30833ac52b0cfa369c88a8e47229c97d1df06 Author: Andrew Myers Date: Thu Mar 22 12:50:16 2018 -0700 protect against pcomp_line being None. Tools/RegressionTesting/test_report.py commit acf4a415149d96c894f633e270cb0d7837688a51 Author: Weiqun Zhang Date: Thu Mar 22 12:44:41 2018 -0700 use ParallelContext in ParallelDescriptor Src/Base/AMReX.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 88ef1f83bf0e041df00d346637b68a9b402912c2 Merge: 94aea4f56 ccc6f02fb Author: Andrew Myers Date: Thu Mar 22 12:09:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 94aea4f568352b11b374766cef99be7aab7d0e4d Author: Andrew Myers Date: Thu Mar 22 12:09:44 2018 -0700 hack the test suite to print out the particle comparison command. Tools/RegressionTesting/test_report.py commit 8f275717dfbd8056bb692f95f6c6620c0fdc0c2e Merge: be0dcd1d8 ccc6f02fb Author: Weiqun Zhang Date: Thu Mar 22 09:43:34 2018 -0700 Merge branch 'development' into forkjoin commit ccc6f02fbac7e01ed15d40488565d7f012e04ccd Author: Kevin Gott Date: Wed Mar 21 19:41:07 2018 -0700 Add empty Wait wrappers for cases without MPI. Src/Base/AMReX_ParallelDescriptor.cpp commit b691dc884247abe94608f9357732a42523822e3a Author: Weiqun Zhang Date: Wed Mar 21 17:18:35 2018 -0700 need to call MPI_Comm_free even wehn bl_fortran_mpi_comm_free has been called because the one in Fortran is a duplicate Src/Base/AMReX_ParallelDescriptor.cpp commit 03b96602c66c751421fa457d29ff7de2aac05eea Author: kngott Date: Wed Mar 21 16:21:48 2018 -0700 AMReX wrappers for all MPI Wait functions. Profiling to be added and tested. Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tools/AMRProfParser/TestCodes/GNUmakefile Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp commit c6372a1b3caf15efa6f3329fbbff3aaff42a7fd9 Author: kngott Date: Wed Mar 21 16:10:13 2018 -0700 Make.allinea file rename to Make.forge Tools/GNUMake/tools/Make.forge commit 2ec36bac92175513e787baf6915a5b239115c9b5 Author: kngott Date: Wed Mar 21 16:08:33 2018 -0700 TPP header file Src/Base/AMReX_ThirdPartyProfiling.H commit cf0c8e6e72ac600d72d760180d320b1ae3b46d49 Author: kngott Date: Wed Mar 21 16:05:51 2018 -0700 Third Party Profiling First Attempt Src/Base/AMReX_BLProfiler.H Src/Base/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/tools/Make.vtune Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp commit bc57cfce59a1115c878d955b253d7c8bf8868b47 Author: dtgraves Date: Wed Mar 21 14:51:46 2018 -0700 serialization still broken for higher order but all the other tests pass Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_PlaneIF.cpp Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/levelRedistTest.cpp Tests/GeometryShop/regression/multicelllev.cpp Tests/GeometryShop/regression/multicelllev.inputs Tests/GeometryShop/regression/runalltests.serial.sh commit c17687132baf4da0c7f058d080fa2347de11dc52 Author: Johannes Blaschke Date: Wed Mar 21 13:30:48 2018 -0700 fix over-zealous deletions build_and_deploy.sh commit e5f901fa4d28168dde8362fcf32549742821cf25 Author: dtgraves Date: Wed Mar 21 11:57:53 2018 -0700 fixed more tests so they also run with WrappedGShop. Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebnormalizeTest.cpp Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/serialization.cpp commit b4f9fc4f0692f77597f375f975419eb3bfa26f45 Author: Johannes Blaschke Date: Wed Mar 21 11:48:41 2018 -0700 fix broken link in the docs (to Amrvis profiling) Docs/sphinx/source/AMReX_Profiling_Tools.rst Docs/sphinx/source/GettingStarted.rst commit 394bb421e50420a6a5e81b58e4904ac4291b8d53 Author: Johannes Blaschke Date: Wed Mar 21 11:06:26 2018 -0700 debugging travis script build_and_deploy.sh commit e6ca34ca9ab76a4d2758e47d5cbc94c38f953e48 Author: Johannes Blaschke Date: Wed Mar 21 10:52:32 2018 -0700 update travis to reflect new web root for docs build_and_deploy.sh commit 6274575ebceb4f979f76c94ee08dbc161053e44c Author: dtgraves Date: Tue Mar 20 16:28:40 2018 -0700 More tests are passing. Higher order stuff coming along. Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ramp/main.cpp commit d9583b50c4f9cf00dfaf1e52f6e19d19ee4bfa87 Author: Weiqun Zhang Date: Tue Mar 20 13:32:38 2018 -0700 EBFluxRegister: fix a bug when tile size is odd Src/EB/AMReX_EBFluxRegister.cpp commit cc3118699a0c94f244a56690632c435a70c7ddd9 Author: dtgraves Date: Tue Mar 20 10:58:21 2018 -0700 first higher order test passed. I still have to put in the new bits that fix regular next to covered and add more derivative methods to the implicit function classes. Src/Base/AMReX_IntVect.H Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/AMReX_WrappedGShop.cpp commit 92863545c869bc88716ef6cf882b9bc87c899466 Merge: 67c324137 418931cd4 Author: Andrew Myers Date: Tue Mar 20 10:20:34 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 67c32413744ec0b9c6fe0ced52381a5e24b72f66 Author: Andrew Myers Date: Tue Mar 20 10:20:22 2018 -0700 wrap this variable in a BL_USE_MPI ifdef Src/Base/AMReX_ParallelDescriptor.cpp commit 418931cd4b41a1c31ec83aeb7f13d30a003a50cc Merge: 7f7b39be9 b1c768804 Author: WeiqunZhang Date: Tue Mar 20 09:20:22 2018 -0700 Merge pull request #229 from JBlaschke/development GNUMake used by Tools/F_mk and Tools/Postprocessing/C_Src should respect settings in Make.local commit 42a34e8d0586271f2787916abdc8b757ec709ebe Merge: b6088f279 7f7b39be9 Author: dtgraves Date: Mon Mar 19 15:46:24 2018 -0700 merging with dev branch commit b6088f27927d498f9045d49fedc407f1b6dac392 Author: dtgraves Date: Mon Mar 19 15:44:03 2018 -0700 more fixes. I am not sure how to get Marc's intersection information in the new context. Still need to fix a bunch of implicit function so they produce their derivatives. Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp commit 7f7b39be9a529ff390532872625bb61828554c7a Author: Weiqun Zhang Date: Mon Mar 19 15:39:26 2018 -0700 move amrex_malloc and amrex_free to cpp file so that linker can find them for Fortran code Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit a6fd1c3c31984f8dc0c02bfa7c22145b6a1b437e Author: dtgraves Date: Mon Mar 19 15:01:39 2018 -0700 Serialization of higher order moments is written and compiles. On to testing. Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFAB.cpp Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp commit c248b8802de3febe60064606d914fc6458f86245 Author: dtgraves Date: Mon Mar 19 11:33:35 2018 -0700 put Weiqun's isnan code into a template specialization so BaseIFFAB can work with other data types Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFAB.cpp Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/Make.package commit b1c768804c23d5c7bd69e39416ce793d87a408ab Author: Johannes Blaschke Date: Sun Mar 18 21:39:25 2018 -0700 fix typo in docs Docs/sphinx/source/BuildingAMReX.rst commit 6cf86e038a69deb511314627db26da86cd3dcf00 Author: Johannes Blaschke Date: Sun Mar 18 21:30:45 2018 -0700 GNUMake used by Tools/F_mk and Tools/Postprocessing/C_Src now respects compiler options in Make.local Tools/F_mk/comps/gfortran.mak Tools/Postprocessing/C_Src/GNUmakefile commit a21e66edfbcf2f3b3d759c0756f510a73e4afb9e Merge: 95a61482a 0bb22d0a5 Author: WeiqunZhang Date: Fri Mar 16 17:25:42 2018 -0700 Merge pull request #227 from AMReX-Codes/MultiComponentMLMG Multi component mlmg commit 0bb22d0a5d515e539fa3b1e52f2ea1bcf91f6dc2 Author: Weiqun Zhang Date: Fri Mar 16 16:38:07 2018 -0700 multi-component solvability fix for cell-centered solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f50b256481629e2660afafa8808cc93859862315 Author: dtgraves Date: Fri Mar 16 16:15:55 2018 -0700 integration with EBIS is complete except for the serialization stuff. This is very much like saying that except for the hundred year war, it was a heck of a century. Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp commit 70b6feaca9d199a5298d9a348436a96c841dbc61 Merge: 23ae3f7de 23eddc916 Author: Brandon Runnels Date: Fri Mar 16 15:47:15 2018 -0700 Merge pull request #228 from AMReX-Codes/MCMLMG_bc Add isCrossStencil virtual function to MLCellLinOp. For non-cross st… commit 95a61482af81aad71b33587835431c3a9e90eecc Author: Andrew Myers Date: Fri Mar 16 14:28:17 2018 -0700 grow by an additional cell here (can be needed even if all particles are in the right place due to roundoff errors). Src/Particle/AMReX_NeighborParticlesI.H commit 7a11bb16fa68472e431fb4a6310447556a602471 Author: Andrew Myers Date: Fri Mar 16 14:26:50 2018 -0700 add some debug-mode asserts to help catch problems earlier. Src/Particle/AMReX_NeighborParticlesI.H commit ac153521567b6ab07b381404a766dd3469d70d37 Author: Andrew Myers Date: Fri Mar 16 14:06:15 2018 -0700 use an explicit cast here to shut up compiler warnings. Src/Particle/AMReX_ParticleContainerI.H commit 23eddc91615b135a6c02b60aba6f2feb28ae52eb Author: Weiqun Zhang Date: Fri Mar 16 12:23:58 2018 -0700 Add isCrossStencil virtual function to MLCellLinOp. For non-cross stencil, extend mask to corners and extrpolation is done only for non-covered corner cells. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 23ae3f7de65d7962199b134ccec4ebab59b76cbd Author: Weiqun Zhang Date: Fri Mar 16 11:03:38 2018 -0700 use double precision Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 754aa6c9064c98d23796f56a3852cd351202e3d6 Author: Weiqun Zhang Date: Fri Mar 16 10:26:58 2018 -0700 no need to have overriding virtual function getNComp in MLCellLinop because a default implementation already exists in its base class MLLinOp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 1d82268888a15d958e36d8522d1b58a470cce6b1 Author: Weiqun Zhang Date: Fri Mar 16 10:16:11 2018 -0700 minor Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 2f6fed098efcca599d7e5d7a52fcf85aca4ca674 Author: Weiqun Zhang Date: Fri Mar 16 10:05:24 2018 -0700 no need to call linop.prepareForSolve in cases it has been called Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7817506a6c9affd2aa9744009342e77b54a97001 Author: Weiqun Zhang Date: Fri Mar 16 09:37:34 2018 -0700 fix type mismatch Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 48cba9f1cb5fe0899061e458f3578abb1e3fcaf6 Author: Weiqun Zhang Date: Fri Mar 16 09:30:14 2018 -0700 fix typos in 1d Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 commit 3a1ce445ea98b04416b33c0bb69969036349e3c6 Author: Brandon Runnels Date: Thu Mar 15 17:59:24 2018 -0600 reverted bndrydata Src/Boundary/AMReX_BndryData.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit f6ae7f8e7e83f5db37367da4407a67fd99630290 Author: Brandon Runnels Date: Thu Mar 15 17:49:01 2018 -0600 reverted ncomp changes Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit fa972fadf50ec4905f8b93309006815df38996d5 Author: Brandon Runnels Date: Thu Mar 15 16:39:37 2018 -0600 fixed 3d error Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit 96d2bc45678e39268868187c80c5c87e397b465b Author: Brandon Runnels Date: Thu Mar 15 16:14:09 2018 -0600 minor fixes to MLCG norm and to the number of components for masks in MLCellLinOp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit f75c4a7c483b07ce01aa1ce4c092b0465c17b8a4 Merge: 099cdaa96 06fbde903 Author: Brandon Runnels Date: Thu Mar 15 15:55:57 2018 -0600 Merge branch 'development' into MultiComponentMLMG commit 099cdaa965dd2c5f8448bdb7b0fd4c9355e877a8 Author: Brandon Runnels Date: Thu Mar 15 15:47:19 2018 -0600 removed printout statement Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit be0dcd1d8912e85d1901a575786ea855734ecbdc Author: Weiqun Zhang Date: Thu Mar 15 14:22:37 2018 -0700 move task splitting stuff from ParallelContext into ForkJoin Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ccse-mpi.H commit 50cbb3cd3354842a92aafefbc1ead8a03efb63c8 Author: dtgraves Date: Thu Mar 15 11:10:16 2018 -0700 port of higher order moment infrastructure is complete. Now I need to integrate it into EBIndexSpace and all that. Src/GeometryShop/AMReX_IFData.cpp Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_MetaPrograms.H Src/GeometryShop/AMReX_MonomialPowers.H Src/GeometryShop/Make.package commit c9ef4a2913e4830e88cef21d083d76826150825f Author: Weiqun Zhang Date: Thu Mar 15 10:24:57 2018 -0700 include ParallelContext in ParallelDescriptor header Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ccse-mpi.H commit 3942512a6a2d3851f1f90fad8880c089891c2807 Author: Weiqun Zhang Date: Thu Mar 15 09:00:46 2018 -0700 more to private of ForkJoin Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit 06fbde90310426eaec0f65217d86a16bcc926b3b Merge: 1e2b733d8 4851bf754 Author: Andrew Myers Date: Wed Mar 14 23:15:12 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1e2b733d800c6f3a31cecc7c092a22ce288664c1 Author: Andrew Myers Date: Wed Mar 14 23:14:48 2018 -0700 some changes needed in the test suite for SedonaBox Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit 63c84f95fa27499ec59817c4aec88b97f9776a38 Author: dtgraves Date: Wed Mar 14 15:58:42 2018 -0700 lots of progress made in the big slog. Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_WrappedGShop.cpp commit 17d1a391bbdc5fd3a6e766e42b0bb094702c1e70 Author: Weiqun Zhang Date: Wed Mar 14 14:42:10 2018 -0700 move MFFork to private and other minor changes Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit c6e0eba32eeea98e201fb16d34712fe28f037b68 Author: Weiqun Zhang Date: Wed Mar 14 14:00:50 2018 -0700 make MultiColor_C compile again OldTutorials/MultiColor_C/GNUmakefile OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp commit ff460b4e442904e1b67027a68394428da9b64177 Author: Weiqun Zhang Date: Wed Mar 14 12:36:23 2018 -0700 remove Color Src/Base/AMReX.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 23b16f48a0e2c438f1161e16afa816928f5d13d0 Author: dtgraves Date: Wed Mar 14 11:53:24 2018 -0700 waist deep in the big muddy Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MomentIteratorImplem.H Src/GeometryShop/AMReX_MonomialPowers.H Src/GeometryShop/Make.package commit e4fc09febed54534243c8d4a41c771dbc92534c2 Author: Weiqun Zhang Date: Wed Mar 14 09:42:51 2018 -0700 add ParallelContex::init and finalize to amrex::Initialize and Finalize OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX.cpp commit 8c9d43820ed88b2b3a0b2a4a92652f0f3b3df49e Author: Weiqun Zhang Date: Wed Mar 14 09:35:00 2018 -0700 move AMReX_ForkJoin and AMReX_ParallelContext to Base/ OldTutorials/MultiColor_C/GNUmakefile Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 4851bf7543950f4acc4136f011742f0387dd5dc0 Author: Michele Rosso Date: Tue Mar 13 16:27:56 2018 -0700 CMake:start setup for profiling improvements Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit a3e1be703d47860da329bf488c02719b2344b2eb Author: dtgraves Date: Tue Mar 13 15:34:16 2018 -0700 templates and namespaces are really not fond of one another Src/Base/AMReX_IntVect.H Src/GeometryShop/AMReX_ConstrainedLS.H Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CoordinateSystem.H Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CutCellMoments.H Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinement.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBGeomDebugDump.H Src/GeometryShop/AMReX_EBGeomDebugOut.H Src/GeometryShop/AMReX_EBGeomDebugOut.cpp Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_GenericArithmetic.H Src/GeometryShop/AMReX_GenericArithmeticI.H Src/GeometryShop/AMReX_IFData.H Src/GeometryShop/AMReX_IFData.cpp Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicer.cpp Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_LSProblem.H Src/GeometryShop/AMReX_LSProblem.cpp Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_MinimalCCCM.H Src/GeometryShop/AMReX_MinimalCCCM.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MultiIndex.H Src/GeometryShop/AMReX_MultiIndexImplem.H Src/GeometryShop/AMReX_NoRefinement.H Src/GeometryShop/AMReX_NoRefinementImplem.H Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_NormalDerivativeImplem.H Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_NormalDerivativeNewImplem.H Src/GeometryShop/AMReX_Notation.H Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.cpp Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Src/GeometryShop/Make.package commit 09005870ec480b3fe785b2362d2f3013e240e3a6 Author: dtgraves Date: Mon Mar 12 16:34:47 2018 -0700 more slogging through the vast amount of code needed to get higher order geometric information. Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBGeomDebugOut.H Src/GeometryShop/AMReX_EBGeomDebugOut.cpp Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_MinimalCCCM.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Src/GeometryShop/Make.package commit 41306e00d9a46d6abd85a58836a187377ba0cdcf Author: dtgraves Date: Mon Mar 12 12:31:43 2018 -0700 the slog continues Src/Base/AMReX_IntVect.H Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicer.cpp Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_LSProblem.cpp Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_SmoothAbsoluteValue.H Src/GeometryShop/AMReX_SmoothIntersection.H Src/GeometryShop/AMReX_SmoothUnion.H Src/GeometryShop/AMReX_SmoothUnion.cpp commit 9f0695b565ffa011a535b949c73e5efdcde31b02 Author: Weiqun Zhang Date: Sun Mar 11 18:27:34 2018 -0700 move public apply from MLLinOp to MLMG Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit efe9926c8a6397ae1a1fa153e8ce11bb664f9119 Author: Weiqun Zhang Date: Sun Mar 11 16:18:28 2018 -0700 add public apply function to MLLinOp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 71436fbe29f1c28ac08e55e4375510694f0fad87 Author: Weiqun Zhang Date: Sun Mar 11 14:07:09 2018 -0700 MLMG: option to set max coarsening level Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 0b4cdc82ee82148b5d58d41eb617b5e0e92fd8cf Author: Weiqun Zhang Date: Fri Mar 9 17:12:49 2018 -0800 add amrex_malloc and amrex_free to Fortran module amrex_fort_module Src/Base/AMReX_Utility.H Src/Base/AMReX_fort_mod.F90 commit d5f6ad1b2819519758075c2e9fd44a0d352085c4 Author: dtgraves Date: Fri Mar 9 15:57:30 2018 -0800 slogging through the vast amount of code needed to get higher order geometric information. Src/GeometryShop/AMReX_CH_EBIS_ORDER.H Src/GeometryShop/AMReX_ConstrainedLS.H Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CoordinateSystem.H Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CutCellMoments.H Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinement.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBGeomDebugDump.H Src/GeometryShop/AMReX_EBGeomDebugOut.H Src/GeometryShop/AMReX_EBGeomDebugOut.cpp Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_FixedRefinement.H Src/GeometryShop/AMReX_FixedRefinementImplem.H Src/GeometryShop/AMReX_GenericArithmetic.H Src/GeometryShop/AMReX_GenericArithmeticI.H Src/GeometryShop/AMReX_IFData.H Src/GeometryShop/AMReX_IFData.cpp Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicer.cpp Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_LSProblem.H Src/GeometryShop/AMReX_LSProblem.cpp Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_MetaPrograms.H Src/GeometryShop/AMReX_MinimalCCCM.H Src/GeometryShop/AMReX_MinimalCCCM.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MultiIndex.H Src/GeometryShop/AMReX_MultiIndexImplem.H Src/GeometryShop/AMReX_NoRefinement.H Src/GeometryShop/AMReX_NoRefinementImplem.H Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_NormalDerivativeImplem.H Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_NormalDerivativeNewImplem.H Src/GeometryShop/AMReX_Notation.H Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.cpp Src/GeometryShop/AMReX_SmoothIntersection.H Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_SmoothUnion.H Src/GeometryShop/AMReX_SmoothUnion.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Src/GeometryShop/Make.package commit b70c2fa2edc7a8184cd67d7ab4dd6942cd9d7da6 Author: dtgraves Date: Fri Mar 9 15:56:28 2018 -0800 slogging through the vast amount of code needed to get higher order geometric information. Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit 0833f02f7ebad6191f8084e7c9d70485e7d9a10d Author: Cy Chan Date: Thu Mar 8 20:35:20 2018 -0800 bunch of small updates to fork-join follow some of weiqun's suggestions trying to follow existing AMReX conventions put mpi_tag back as frame member so each frame has its own copy OldTutorials/MultiColor_C/AMReX_ForkJoin.H OldTutorials/MultiColor_C/AMReX_ForkJoin.cpp OldTutorials/MultiColor_C/AMReX_ParallelContext.H OldTutorials/MultiColor_C/AMReX_ParallelContext.cpp OldTutorials/MultiColor_C/main.cpp commit 9a4b88f89a8ce8547966bcbbd826325dec5b2ce3 Author: Weiqun Zhang Date: Thu Mar 8 16:04:00 2018 -0800 don't use MPI_COMM_WORLD directly Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp commit 7896ed75bfae2392b09ad1bda36b06557b520098 Author: Andrew Myers Date: Thu Mar 8 14:14:47 2018 -0800 improve profiling in Neighbor Particles. Src/Particle/AMReX_NeighborParticlesI.H commit dadca42e369721f3d3c3309823cfcdf420343fe3 Author: Weiqun Zhang Date: Thu Mar 8 11:32:01 2018 -0800 a bunch of small changes OldTutorials/MultiColor_C/AMReX_ForkJoin.H OldTutorials/MultiColor_C/AMReX_ForkJoin.cpp OldTutorials/MultiColor_C/AMReX_ParallelContext.H OldTutorials/MultiColor_C/AMReX_ParallelContext.cpp OldTutorials/MultiColor_C/main.cpp commit b333e5107963aab01339cfc84bc04bc335588ad1 Merge: 91e93a1c7 eef719e51 Author: Weiqun Zhang Date: Thu Mar 8 08:56:09 2018 -0800 Merge branch 'development' into forkjoin commit e5a862513ca7ebf3f9ade5c3e7c2ab25bcf63d98 Author: Weiqun Zhang Date: Wed Mar 7 17:13:03 2018 -0800 nodal projection: bug fix in restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 91e93a1c75c2c1fdfd5f5e027d3c73b576eb6e02 Author: Cy Chan Date: Wed Mar 7 16:14:01 2018 -0800 moved ParallelContext and ForkJoin into separate files OldTutorials/MultiColor_C/AMReX_ForkJoin.H OldTutorials/MultiColor_C/AMReX_ForkJoin.cpp OldTutorials/MultiColor_C/AMReX_ParallelContext.H OldTutorials/MultiColor_C/AMReX_ParallelContext.cpp OldTutorials/MultiColor_C/GNUmakefile OldTutorials/MultiColor_C/main.cpp commit 3b4aa8d220e385d9873c13ed918d930c721a0e52 Author: Cy Chan Date: Wed Mar 7 15:37:56 2018 -0800 fork join can be invoked multiple times using same ForkJoin object reuses forked multifabs and distribution maps across invocations added distribution map cache member added verbose debugging information OldTutorials/MultiColor_C/main.cpp commit 9eb5075c0c4f7aff6ad6f42ea2654000487c6138 Merge: 5d5fb8472 eef719e51 Author: Weiqun Zhang Date: Wed Mar 7 14:47:16 2018 -0800 Merge branch 'development' into weiqun/mlmg commit eef719e51d051f567f881d40a3b0a65e050a61bd Author: Weiqun Zhang Date: Wed Mar 7 14:44:09 2018 -0800 mlmg: print the correct residual for vebose>=4 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5d5fb8472069c4ad73a87d37a799acb9d8d634dd Author: Weiqun Zhang Date: Wed Mar 7 13:52:57 2018 -0800 nodal projection: allow coarsening strategy be sigma for all regular eb Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit 50277b148f35658256da1561ebe7481331b5bf57 Author: Weiqun Zhang Date: Wed Mar 7 13:34:16 2018 -0800 nodal projection: in restriction and interpolation, if both weights are zero, take average Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit d3b77e1b17d62c0fbef20ab0cdeb06de07049c77 Author: Weiqun Zhang Date: Wed Mar 7 12:58:44 2018 -0800 nodal projection: fix bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 697fa1c51152add37a57c27eb09fb1f85cb157a3 Author: Weiqun Zhang Date: Wed Mar 7 12:52:30 2018 -0800 nodal projection: fix array bound and index bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 0b2beeaf21d0201146ccf353582bbb4413e7119f Author: Weiqun Zhang Date: Wed Mar 7 12:50:55 2018 -0800 nodal projection: fix array bound Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 95805cbf7cf80bfe7160a21d9a9b742efe84c09e Author: Weiqun Zhang Date: Wed Mar 7 12:49:22 2018 -0800 nodal projection: fix divide by zero and change some parameters back to default Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit b813065eee6ef8c199793727446577dc7777c10c Author: Weiqun Zhang Date: Wed Mar 7 09:57:03 2018 -0800 WIP: RAP stencil for testing constant sigma Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 39949bac97468583f2dbefcdd1cd5a831a08990f Author: Weiqun Zhang Date: Wed Mar 7 09:50:44 2018 -0800 3d nodal projection: RAP version of restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 94719de7b9dddfef01594c0c791127d2be32a9f7 Author: Weiqun Zhang Date: Tue Mar 6 17:32:04 2018 -0800 remove _images/ from top directory because the only figure there has a copy already in Docs/ as it should be _images/ParaView_filegroup.png commit 0778227cf9bbfab34a7aac0fba479a34aa81d09f Author: Weiqun Zhang Date: Tue Mar 6 17:07:21 2018 -0800 WIP: RAP version of restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit e633e791b3e2394abe3127c0cc17d2377b07f7ba Author: Cy Chan Date: Tue Mar 6 16:26:46 2018 -0800 only create distribution mapping object once per (box array, task) pair multiple multifabs accessed by each task may share the same boxarray they need to have same distribution mapping OldTutorials/MultiColor_C/main.cpp commit dca5d8d1ad137dbfb5000ed0038d5c92180b09c2 Author: Weiqun Zhang Date: Tue Mar 6 14:33:44 2018 -0800 3d nodal projection: RAP version of interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 3d03bedf29b8e5a2c74b309ffa6d3e2087676ed9 Author: Cy Chan Date: Tue Mar 6 14:14:39 2018 -0800 more work on fork join and parallel context frames: updated local/global rank translation added mpi tag getter/incrementer with wrap-around init first frame to ParallelDescriptor::Communicator update asserts to AMREX_ style update enum to enum class OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ParallelDescriptor.H commit b51d4969607f8cd40400d362651bd411f5a1efad Merge: e3285d7fe e9746fd49 Author: Weiqun Zhang Date: Tue Mar 6 13:14:52 2018 -0800 Merge branch 'development' into weiqun/mlmg commit 346dd5ecb000d0f922293f3c75b417d225e7d74b Author: Brandon Runnels Date: Tue Mar 6 10:21:08 2018 -0700 added update for ghost corners (2D only) Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit e9746fd49dcebd96886e07c39902483c6847e0bf Author: Andrew Myers Date: Tue Mar 6 09:04:50 2018 -0800 put this preprocessor macro back. Src/GeometryShop/AMReX_EBFluxFAB.H commit c342b9780da37b12754f73c7658bb85cb7406d7a Author: Ann Almgren Date: Mon Mar 5 16:29:42 2018 -0800 Update the multifab norms to use versions in Src/Base instead of local definitions. Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit e3285d7fee0e51fa840fe2de9a473fe4c3206b4b Merge: 736ea1c12 d38afdc30 Author: Weiqun Zhang Date: Mon Mar 5 16:17:11 2018 -0800 Merge branch 'development' into weiqun/mlmg commit d38afdc30c809a0b24673420a90c3900b56bbfaf Merge: 5a32e6056 14618f725 Author: Weiqun Zhang Date: Mon Mar 5 16:16:15 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5a32e605658428987b7ba55399e172c7b14ce5f5 Author: Weiqun Zhang Date: Mon Mar 5 16:08:19 2018 -0800 update CHANGES CHANGES commit 223639fc5f63fae860dbfa5b0837a2e1771015ad Author: Brandon Runnels Date: Mon Mar 5 17:00:10 2018 -0700 removed comment Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5e481b2f3719fb0822334db94328457404486331 Author: Cy Chan Date: Mon Mar 5 12:13:21 2018 -0800 added single mode for MF access in fork-join added task bound split calculation misc. clean up OldTutorials/MultiColor_C/main.cpp commit 14618f7253b7dcec48b2916f7505784be367b832 Author: Ann Almgren Date: Mon Mar 5 09:36:45 2018 -0800 Cleaning out more headings for consistency Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H Src/EBAMRElliptic/AMReX_BiCGStabSolver.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBMultiGrid.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp Src/EBAMRElliptic/AMReX_LinearSolver.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_NoOpSolver.H Src/EBAMRElliptic/AMReX_VCAggStencil.H Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp commit bd1ffca734663cca65becd2800f8284a35f22429 Author: Ann Almgren Date: Mon Mar 5 09:30:43 2018 -0800 More consistency fixes. Src/GeometryShop/AMReX_ZCylinder.H Src/GeometryShop/AMReX_ZCylinder.cpp commit be1b3293546291d67b9be72d46ea954adb0c9d40 Author: Ann Almgren Date: Mon Mar 5 09:28:45 2018 -0800 For consistency, remove logo at top of files. If we decide on a common header later we can then add it to all files uniformly Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseIndex.H Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxIterator.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMD.cpp Src/Base/AMReX_SPMDI.H Src/Base/AMReX_parstream.H Src/Base/AMReX_parstream.cpp Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_AnisotropicIF.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIFFactory.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBFluxFAB.cpp Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBFluxFactory.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/AMReX_Ellipsoid.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_ExtrudeIF.H Src/GeometryShop/AMReX_ExtrudeIF.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregFAB.cpp Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_LoHiSide.H Src/GeometryShop/AMReX_LoHiSide.cpp Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PXStuff.H Src/GeometryShop/AMReX_PXStuff.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_PolynomialIF.cpp Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLBox.cpp Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLIF.cpp Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLMesh.cpp Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_STLUtil.cpp Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_Stencils.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp commit c884ae8b39ffe062ac7951c06edfa43cfb4942cc Merge: b1141c379 77b41c8c0 Author: dtgraves Date: Mon Mar 5 08:55:37 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b1141c37903dea1e54c6bcd7f12032aaf9226254 Author: dtgraves Date: Mon Mar 5 08:55:21 2018 -0800 fixed a bug in ZCylinder Src/GeometryShop/AMReX_ZCylinder.cpp commit 77b41c8c0b2dd35c7cb4b30614cd4504f7b39641 Merge: 9be5d5c21 ec28cce9f Author: Andrew Myers Date: Sat Mar 3 22:32:28 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9be5d5c21598baacc3d1d014ce02f8196fc8e7cd Author: Andrew Myers Date: Sat Mar 3 22:30:23 2018 -0800 improving the scaling of particle redistribute when the changes are known to be local. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ec28cce9f3cf297f400e46908c29a37c4b39a017 Author: dtgraves Date: Fri Mar 2 16:13:53 2018 -0800 added simple cylinder geometry Src/GeometryShop/AMReX_ZCylinder.H Src/GeometryShop/AMReX_ZCylinder.cpp Src/GeometryShop/Make.package commit e847daf41defdca24ff68f4b54efd925a65e4922 Author: Cy Chan Date: Fri Mar 2 15:41:42 2018 -0800 working on test implementation of fork-join OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp commit 65365bfc2c01814adcc98d84cc2be28d068368a6 Author: Weiqun Zhang Date: Fri Mar 2 10:48:16 2018 -0800 new BoxList constructor making n Boxes by chopping a given Box in a given direction Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 50fff4d78925e696f447695b401b09bd3c8eab7d Author: Weiqun Zhang Date: Fri Mar 2 10:46:42 2018 -0800 add enum class Direction Src/Base/AMReX_Orientation.H commit b23830bf83ba1195c17a1d75e125c038b2c3f28c Author: Weiqun Zhang Date: Fri Mar 2 10:04:19 2018 -0800 more flush fixed MiniApps/SMC/main.f90 MiniApps/SMC/smc.f90 OldTutorials/AMR_Adv_F/Source/main.f90 OldTutorials/Random_F/main.f90 commit ad7612d53c6127b6b24341cf49ab46afaf15976d Merge: edc840b8b 657ea8953 Author: WeiqunZhang Date: Fri Mar 2 09:56:12 2018 -0800 Merge pull request #219 from AMReX-Codes/flush Use Fortran intrinsic flush instead of call flush commit edc840b8bba48d1194a1f7b6dc217f3be4b11a7c Author: Weiqun Zhang Date: Fri Mar 2 09:53:08 2018 -0800 new BoxList constructor that makes n Boxes from a single Box where n is an argument to the constructor Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 0aa64f454154462dbb4bc2575ac2606a13632645 Author: Ann Almgren Date: Thu Mar 1 19:10:31 2018 -0800 Add README for Tutorials/SWFFT Tutorials/SWFFT/README commit 38aac2164fbb7c62f9f24fc3413602220294169a Author: Ann Almgren Date: Thu Mar 1 19:04:39 2018 -0800 Change in comment only. Src/Base/AMReX_parstream.H Src/Base/AMReX_parstream.cpp commit 736ea1c12a6671898b59f0f5fca47ad21d92297e Author: Weiqun Zhang Date: Thu Mar 1 17:17:33 2018 -0800 WIP nodal projection Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit b3f5199f311950c2cf15100f7118f9fa4776099d Author: Brandon Runnels Date: Thu Mar 1 17:45:47 2018 -0700 Basic multicomponent MLMG solves working in 2D. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H commit ed3caea3dd6e09931f9a07ba75839fb643196ec4 Merge: 1c96a5dc8 5dead2f82 Author: Andrew Myers Date: Thu Mar 1 15:36:41 2018 -0800 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 1c96a5dc890fee30353fac07c6c5e93aaab01c9a Author: Andrew Myers Date: Thu Mar 1 15:36:30 2018 -0800 update AMReX_BCUtil.cpp to reflect recent API change to the wrapper around cudaMemcpyAsync. Src/Base/AMReX_BCUtil.cpp commit efd18d378bf41a6ebe6d11847ab8c0af878b6aef Author: Andrew Myers Date: Thu Mar 1 15:34:50 2018 -0800 remove use of 'ParticleVector', which doesn't exist on the gpu branch anymore Src/Particle/AMReX_Particles.H commit 17695c10fed47f2b7049ef73aba32fa7984c87a8 Author: Ann Almgren Date: Thu Mar 1 13:18:22 2018 -0800 Remove unused MyProc and quiet some gnu compiler warnings. Src/Particle/AMReX_ParticleContainerI.H commit 66b35f1562bbd67e1e5e0bce0fcfe3046759f548 Author: Michael Zingale Date: Thu Mar 1 13:01:50 2018 -0500 add an option to specific the height (in 2-d) for a slice Tools/Postprocessing/F_Src/fextract.f90 commit 36a225792114c7b424a7a72a2bed10d004988a94 Author: Weiqun Zhang Date: Thu Mar 1 08:47:24 2018 -0800 update CHANGES CHANGES commit 7ac4a5f608e33cd5301df1d14a6825cc12f88119 Author: Weiqun Zhang Date: Thu Mar 1 08:45:32 2018 -0800 update CHNAGES CHANGES commit 87c7fe6daf22076c2321921911858ad340706cc0 Author: Brandon Runnels Date: Wed Feb 28 16:46:27 2018 -0700 Began update for MLMG, MLCG, MLLinop, MLCellLinop for multicomponent. Src/Base/AMReX_DistributionMapping.cpp Src/Boundary/AMReX_BndryData.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5180b0d7e21a21f08341c5361b88a5373fca57e4 Author: Weiqun Zhang Date: Wed Feb 28 15:12:25 2018 -0800 nodal projection: allow rhnd for rap if it's zero Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b75aef02f7ac9770033bb991a2e78cdbfe700961 Author: Weiqun Zhang Date: Wed Feb 28 14:45:51 2018 -0800 nodal projection: clean up the simple rap Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b34a4d2c36f44731132a1895929f385bf3a265ac Author: Weiqun Zhang Date: Wed Feb 28 14:36:25 2018 -0800 3d eb nodal projection: smoothers Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 7591f704a9f63b6a6f66428aaa89ec2c5eaf8fe9 Author: Weiqun Zhang Date: Wed Feb 28 14:08:46 2018 -0800 3d eb nodal projection: stencil verion of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 4e4750071a51c6ed288513101f75eaec73c26a18 Author: Max Katz Date: Wed Feb 28 12:43:45 2018 -0800 Fix comments Tools/GNUMake/sites/Make.olcf commit 957bb4799f1b94bf74c6655a707349bdd28632ef Author: Ann Almgren Date: Wed Feb 28 11:54:23 2018 -0800 Add README and clean up GNUmakefile Tutorials/SWFFT/GNUmakefile Tutorials/SWFFT/inputs commit 8906e0b6edc4bc84767e8e532829f2e29660f071 Author: Ann Almgren Date: Wed Feb 28 11:35:24 2018 -0800 Slight tweaks Tutorials/SWFFT/SWFFT_Solver.cpp Tutorials/SWFFT/main.cpp commit ccc5b95fda7c08777b1a400e9936b9b1c78a7298 Author: Ann Almgren Date: Wed Feb 28 11:18:51 2018 -0800 Add Tutorial demonstrating how to call the SWFFT wrapper for the fftw3 solver. Tutorials/SWFFT/GNUmakefile Tutorials/SWFFT/Make.package Tutorials/SWFFT/SWFFT_Solver.H Tutorials/SWFFT/SWFFT_Solver.cpp Tutorials/SWFFT/SWFFT_Solver_F.F90 Tutorials/SWFFT/SWFFT_Solver_F.H Tutorials/SWFFT/inputs Tutorials/SWFFT/main.cpp commit 0d77ae144421eb461bf42ade2ed6cf0557248a11 Author: Michael Zingale Date: Wed Feb 28 09:07:01 2018 -0500 fix typo to make things compile Src/Amr/AMReX_extrapolater_2d.f90 commit dea01be4a4c2ade864a347028f7ecdd6199a98ff Author: Ann Almgren Date: Tue Feb 27 17:27:54 2018 -0800 BL_SPACEDIM --> AMREX_SPACEDIM Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.cpp Src/Amr/AMReX_extrapolater_2d.f90 commit 82f31414e847bce472f92d27a6d317ab93a427ef Author: Ann Almgren Date: Tue Feb 27 17:25:41 2018 -0800 BL_SPACEDIM --> AMREX_SPACEDIM Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.cpp commit d53ae887137cc7fdd765dbe2d66e5e65acea2730 Author: Ann Almgren Date: Tue Feb 27 17:23:08 2018 -0800 BL_SPACEDIM --> AMREX_SPACEDIM Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Src/GeometryShop/AMReX_ExtrudeIF.cpp Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_VolIndex.cpp commit a0acf94ef5e1294aca268e395c69809e97522299 Author: Ann Almgren Date: Tue Feb 27 17:17:24 2018 -0800 Change BL_SPACEDIM --> AMREX_SPACEDIM Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/AMReX_TracerParticles.H Src/Particle/AMReX_TracerParticles.cpp commit 2ab1c6c5bdaca7c6a473f9f41bef8d2e4f8c9683 Author: Weiqun Zhang Date: Tue Feb 27 17:02:24 2018 -0800 3d eb nodal projection: set integral and connection Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 028c3da1b7b7d7e281a5195418fe39ac877651f4 Author: Michael Zingale Date: Tue Feb 27 20:00:34 2018 -0500 fix spelling of AMREX_SPACEDIM Src/Base/AMReX_DistributionMapping.cpp commit cc7fadc99473554106605c998dbd9dd22b5c2c66 Author: Ann Almgren Date: Tue Feb 27 16:01:06 2018 -0800 Replace BL_SPACEDIM by AMREX_SPACEDIM Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_F.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp commit 38229c41f84d353e20a88c88c1528877a9da4693 Author: Ann Almgren Date: Tue Feb 27 15:57:43 2018 -0800 Replace BL_SPACEDIM by AMREX_SPACEDIM. Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_Orientation.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_SPACE_F.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_iMultiFab.cpp commit 57309720ba4d406024b2250334192d63d6a99fc0 Author: Ann Almgren Date: Tue Feb 27 14:55:17 2018 -0800 Update with 3rd and 4th slide decks Docs/sphinx/source/Chapter12.rst commit 5dead2f8232fd2abf3190de102e54fbf3ab3bc1d Author: Max Katz Date: Mon Feb 26 13:11:05 2018 -0500 Hook in register capping to IBM compiler Tools/GNUMake/comps/ibm.mak commit ab9529cd42f6fde3106f82dfa49c304c05b9dc86 Author: Max Katz Date: Sat Feb 24 20:55:46 2018 -0500 Do cudaMemcpyAsync in C++, not Fortran Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_MFIter.cpp commit 43f46d9a3941630f5c69266cf00f888b658f564c Author: Max Katz Date: Sat Feb 24 19:52:11 2018 -0500 Handle maximum register counts Tools/GNUMake/Make.defs Tools/GNUMake/comps/pgi.mak commit 7e364b327c650139c1a6da03e9c4aec67e571e2f Author: Max Katz Date: Sat Feb 24 19:14:59 2018 -0500 Avoid unnecessary MPI linking for non-MPI code with IBM Tools/GNUMake/comps/ibm.mak commit b96bc6bab0f0fd99c62f8fa4947077bb35bf4030 Author: Max Katz Date: Sat Feb 24 16:49:36 2018 -0500 Generalize CUDA version/compute capabilities Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak commit 3573919681cf6a85759b521341b4dfb239b7c6a4 Author: Max Katz Date: Sat Feb 24 16:33:06 2018 -0500 Fix preprocessing issues on summit Tools/F_mk/GMakedefs.mak commit f195760b543870c32f7aae0ac44d6b62058722c0 Author: Max Katz Date: Fri Feb 23 20:45:45 2018 -0500 Specify a default maximum of 512 threads per CUDA threadblock This is because we usually need 8 threads to handle ghost zones in a FillPatch, and in a corner this could require 8x8x8 = 512 threads, so the default maximum should allowe for this case. Tools/GNUMake/Make.defs commit 8788b19401638e9b843859b8ae5278019875ae68 Author: Max Katz Date: Fri Feb 23 20:45:36 2018 -0500 Specify CUDA/compute capabilities for summit/summitdev Tools/GNUMake/sites/Make.olcf commit ed75545e90a25f820c90a4ebef2e51c3a040d301 Author: Max Katz Date: Fri Feb 23 20:45:09 2018 -0500 Allow for a more general selection of CUDA version Tools/GNUMake/Make.defs Tools/GNUMake/comps/pgi.mak commit 5f016bff214b2990f877078a180c2d5fd5447d00 Author: Max Katz Date: Fri Feb 23 18:42:08 2018 -0500 Remove unnecessary CUDA specification Tools/GNUMake/comps/pgi.mak commit 32728af90fd47324cbaf76fe0ed1a9f789bcc4f0 Author: Max Katz Date: Fri Feb 23 18:33:42 2018 -0500 Disable NVML on Summit since it's not working right now Tools/GNUMake/sites/Make.olcf commit bf193fbca005bc85e84e1546c7db46590014df19 Author: Max Katz Date: Fri Feb 23 18:32:50 2018 -0500 Only do immediate gcc_version expansion for CUDA Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/pgi.mak commit f57c584067a2048258c808378dbc49a016530ee3 Author: Weiqun Zhang Date: Fri Feb 23 14:06:02 2018 -0800 mlmg: add assertions to some untested functions Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ca336b11febce1ec122815c5cae6cd05d64e52e7 Author: Weiqun Zhang Date: Fri Feb 23 13:56:42 2018 -0800 mlmg: MLALaplacian Src/LinearSolvers/MLMG/AMReX_MLALap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_F.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp commit bcf9afa014a4314ce080223a91a384ea1a0a895a Author: Weiqun Zhang Date: Fri Feb 23 13:43:45 2018 -0800 mlmg: rescale 1d & 2d MLPoisson for bicgstab Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H commit 12c0d85eed3d9ff9c386d65fed55d07355ac0034 Author: Weiqun Zhang Date: Fri Feb 23 13:03:25 2018 -0800 mlmg: rescale MLABecLaplacian for bicgstab Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 4c4f445125fa31f891c0ea901ef8ca0af58716a2 Author: Michele Rosso Date: Fri Feb 23 10:24:19 2018 -0800 CMake: update source list for C_CellMG folder Src/LinearSolvers/CMakeLists.txt commit b61d124098cac6c9d38a77122d81ee2b7d7fd482 Author: Brian Friesen Date: Thu Feb 22 22:52:27 2018 -0800 Update XL flags (#186) * Tools: move common XL Fortran compiler flags to GENERIC_IBM_FLAGS * Tools: add flag to enforce fixed form format in XL FORTRAN 77 compiler This compiler makes assumptions about the source code format based on file suffixes, which leads to errors when compiling some AMReX files. Fix this by explicitly stating the source code style with this flag. * Tools: change XL MPI compiler wrappers on summitdev to "mpifort" The OpenMPI man page for "mpif90" and "mpif77" notes that these wrappers are deprecated, and that one should instead use "mpifort" for all Fortran files, both free and fixed format. The observant user will note also that all three wrappers point to the same file ("opal_wrapper"). This change is currently in contradiction with the documentation on the OLCF summitdev website, which recommends continued use of "mpif77" and "mpif90". Tools/GNUMake/comps/ibm.mak Tools/GNUMake/sites/Make.olcf commit 67e8009776db0db6ebd53cb6b51a9d3de195b473 Merge: bfc22c0d5 946016376 Author: Andrew Myers Date: Thu Feb 22 17:12:15 2018 -0800 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 167afe92688b906ed4af26321033276b75bf60d6 Author: Weiqun Zhang Date: Thu Feb 22 16:30:09 2018 -0800 nd mlmg: rescale the problem in bicgstab Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 272f98b948cef9c413bd72e1d1796bb957091433 Author: Weiqun Zhang Date: Thu Feb 22 14:01:45 2018 -0800 use local parameter Src/Base/AMReX_constants_mod.f90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit d255390457da0848e3f2a8807687f8e60ef7c013 Merge: 25eee949b 54ad68433 Author: Weiqun Zhang Date: Thu Feb 22 13:56:48 2018 -0800 Merge branch 'development' into weiqun/mlmg commit 25eee949b3ec32d9d99d49b3dacc6af38ac9ad11 Author: Weiqun Zhang Date: Thu Feb 22 13:40:35 2018 -0800 rm centroid from EBTower Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp commit 54b2d16dc8517843d24a95399033b0635edf478d Author: Weiqun Zhang Date: Thu Feb 22 13:34:56 2018 -0800 nodal projection: stub for 1d and 3d Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit aaeeed173412ec122d1804e2c4df8f967628603f Author: Weiqun Zhang Date: Thu Feb 22 11:57:01 2018 -0800 nodal projection: clean up Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 946016376c16d231cd85fdd8a161075d852391f8 Author: Max Katz Date: Thu Feb 22 03:35:44 2018 -0500 Switch to C++ for UM hints Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit fd727ab3094711fd60cee1d2c7e5560902e702dc Author: Donald E. Willcox Date: Thu Feb 22 01:12:30 2018 -0500 Change default CUDA_VERSION to 9.0 in Fortran build system. (#220) This changes the default CUDA version in the Fortran build system back to 9.0 instead of 8.0. CUDA 9.0 was formerly (cf. commit 23486c8) the default version of CUDA in the Fortran build system. Tools/F_mk/GMakedefs.mak commit ae42480af6c257c4a7bb9aeda3159ae2501387f7 Merge: 9369c0212 54ad68433 Author: Max Katz Date: Thu Feb 22 00:18:39 2018 -0500 Merge branch 'development' into gpu commit 54ad684337aa3de8e5e967e172582338eb66fe91 Author: Max Katz Date: Thu Feb 22 00:05:38 2018 -0500 Use the correct flag for enabling OpenMP in XL Tools/GNUMake/comps/ibm.mak commit 657ea89535450161bf706d421524f71e40d9b4b0 Author: Max Katz Date: Wed Feb 21 23:30:51 2018 -0500 call flush -> flush Src/F_BaseLib/multifab_physbc_edgevel.f90 commit ccb5e0f20ef2f270b076a3cd7248d9a8681a1861 Author: Max Katz Date: Wed Feb 21 23:29:57 2018 -0500 call flush -> flush Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit f69591db1fcf9f138a6740632fcd62f585e1b918 Author: Max Katz Date: Wed Feb 21 23:24:31 2018 -0500 Move more F77 to F90 to please XL Src/Amr/AMReX_ARRAYLIM_1D.F Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/Amr/CMakeLists.txt Src/Amr/Make.package Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Boundary/AMReX_LO_UTIL.F90 Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 Src/LinearSolvers/C_CellMG/Make.package commit 9369c0212d0138749fd677da16ad350ae94ab8f4 Author: Andrew Myers Date: Wed Feb 21 18:45:38 2018 -0800 enforce max thread count in each direction (#218) Sometimes the current code create blocks that have too many threads in the z-direction. Src/Base/AMReX_CUDA.F90 commit bfc22c0d510041bad5f862e5b9314d7266e13fe9 Author: Andrew Myers Date: Wed Feb 21 17:01:01 2018 -0800 enforce max thread count in each direction Src/Base/AMReX_CUDA.F90 commit ecab00c52f1c3b75007a8efc5f91f56f0b394f88 Author: Andrew Myers Date: Wed Feb 21 16:03:41 2018 -0800 re-add this figure. Docs/sphinx/source/Visualization/ParaView_filegroup.png commit 02f8955f8834e0fed3e60ca0102aed5d12d1a0e6 Author: Utkarsh Ayachit Date: Wed Feb 21 15:22:19 2018 -0500 update docs for ParaView viz. Updated docs to reflect the new workflow for reading particles in ParaView 5.5. Docs/sphinx/source/Visualization.rst _images/ParaView_filegroup.png commit 795968f9dc65738d32bcf30d5960af60b5d86684 Author: Ann Almgren Date: Wed Feb 21 15:16:56 2018 -0800 Have the default be to build the optimized version Tests/GeometryShop/STLGeom/GNUmakefile commit 564bc61f6b285d929215fbf940a4ddb438c6498b Merge: 222a163a6 14c34c32a Author: Max Katz Date: Wed Feb 21 17:19:56 2018 -0500 Merge branch 'development' into gpu commit 14c34c32aa1ef18f262b4982533c66e88ddbd523 Author: Max Katz Date: Wed Feb 21 17:19:19 2018 -0500 Restore coalesced fabs option Src/Base/AMReX_BaseFab.cpp commit 222a163a6e885e12632caec7cc3de5aeac25f8d2 Merge: 67786385f 0b0b1a192 Author: Max Katz Date: Wed Feb 21 15:42:33 2018 -0500 Merge branch 'development' into gpu commit 0b0b1a1922eba589ed7f6714c578d8703dc1a521 Author: Max Katz Date: Wed Feb 21 14:55:22 2018 -0500 Make XLF compiler accept C-style comments Tools/GNUMake/comps/ibm.mak commit 9fa9ae65b89afe66ffc629e209db004ecdca78cc Author: Max Katz Date: Wed Feb 21 14:32:20 2018 -0500 Convert some F77 files to F90 This is mainly done to make the IBM compiler happy Src/Base/AMReX_BLBoxLib_F.F90 Src/Base/AMReX_BLBoxLib_F.f Src/Base/AMReX_BLParmParse_F.F90 Src/Base/AMReX_BLParmParse_F.f Src/Base/AMReX_BLProfiler_F.F90 Src/Base/AMReX_BLProfiler_F.f Src/Base/AMReX_BLutil_F.F90 Src/Base/AMReX_BLutil_F.f Src/Base/AMReX_COORDSYS_1D.F Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F Src/Base/AMReX_COORDSYS_3D.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit 5e21d7f1c163675f50ed58c7af7fbf8ac080124d Author: Weiqun Zhang Date: Wed Feb 21 10:55:09 2018 -0800 nodal projection: flag to use simple interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 27646d6fd8a4950f975c6f4eefc843ddece9a72b Author: Weiqun Zhang Date: Tue Feb 20 16:58:27 2018 -0800 nodal projection: 2d rap for eb Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a82a2f97c423ed264ffdfd6dca3b550e07c72648 Merge: 4585db76f 4dac05918 Author: WeiqunZhang Date: Tue Feb 20 14:57:02 2018 -0800 Merge pull request #215 from bcfriesen/update_CCE_flags Tools: update Cray compiler flags commit 4dac05918d02d6ebc775f1ee05dcc34f38b4556f Author: Brian Friesen Date: Tue Feb 20 14:11:25 2018 -0800 Tools: make Cray compiler trap floating point exceptions when DEBUG=TRUE Tools/GNUMake/comps/cray.mak commit a068bd8b16788a49f6507d68a610554540918207 Author: Brian Friesen Date: Tue Feb 20 14:10:31 2018 -0800 Tools: make Cray compiler print opt report only if building optimized code There is no reason to save the opt report for debug (non-optimized) code. Tools/GNUMake/comps/cray.mak commit 1a5e2a5b92dd6eccc92e9acdf4aa54aae976bd75 Author: Weiqun Zhang Date: Tue Feb 20 12:59:32 2018 -0800 nodal projection: rap works in 2d now Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 86fd12409c5b8abc430c5f4d2967ce9335834450 Author: Weiqun Zhang Date: Tue Feb 20 12:24:05 2018 -0800 comment out print in VisMF Src/Base/AMReX_VisMF.cpp commit ac6dc358a56ff5a7c2e2ec59c3837f252ace43b0 Author: Weiqun Zhang Date: Mon Feb 19 14:23:23 2018 -0800 nodal projection: remove scaling at Neumann boundary for RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 4585db76f21f75e1f2afe4914a35a0e660dd557f Author: Ann Almgren Date: Mon Feb 19 12:18:08 2018 -0800 Add AMReX_KDStruct.H to Make.package and CMakeLists.txt Src/GeometryShop/CMakeLists.txt Src/GeometryShop/Make.package commit 1075f3071fdd9747d844dfecd966927435a7771b Author: Ann Almgren Date: Mon Feb 19 12:09:08 2018 -0800 Add the same files to CMakeLists.txt that we add to Make.package Src/GeometryShop/CMakeLists.txt commit 2f916454332b9df8df1035db2f2673958968707f Author: Weiqun Zhang Date: Sun Feb 18 18:29:08 2018 -0800 nodal projection: first pass of RAP Fortran routines; still need work at boundaries Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 19af9662a350c61b404549a47361daa9c47dfb8b Author: Weiqun Zhang Date: Sun Feb 18 12:00:55 2018 -0800 nodal projection: R in RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit d5aefc2a770c6bba0e837e47e09b98a3e8ef32c2 Author: Weiqun Zhang Date: Sun Feb 18 08:22:19 2018 -0800 nodal projection: p in rap Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 0c2b985b7b6e82e5eb9a8dc812655d88a06398e3 Author: Weiqun Zhang Date: Sun Feb 18 07:45:39 2018 -0800 mlmg nodal: start RAP Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit fb39c721835af9a38716f0cd1c080c34fb891e07 Merge: 449a8a9ae 2b6f03afe Author: Marc Day Date: Sat Feb 17 11:26:19 2018 -0800 Merge pull request #212 from JBlaschke/development Overlooked this in GNUMake. AMReX should build fine now... commit 2b6f03afe83949422fc8a56c3fa3ab4c2d18ce6b Author: Johannes Blaschke Date: Sat Feb 17 11:16:51 2018 -0800 Overlooked this in GNUMake. AMReX should build fine now... Tools/GNUMake/Make.defs commit 449a8a9ae10be5b753b9d664de41719b897b220a Author: dtgraves Date: Fri Feb 16 15:07:00 2018 -0800 added some files that had been neglected. Tests/GeometryShop/STLGeom/GNUmakefile Tests/GeometryShop/STLGeom/stlgeom.cpp commit fefef566282e312be4af2fd1cdc720afb27dad31 Merge: d74f5089c b87802084 Author: dtgraves Date: Fri Feb 16 13:26:04 2018 -0800 Merge pull request #211 from AMReX-Codes/dtg_branch merging STL capability into GeometryShop commit b878020842eae5ed09f533903ad1d791c400e82d Author: dtgraves Date: Fri Feb 16 13:21:14 2018 -0800 finished integrating STL geometry capability. Caveat emptor. If you can manage it, you are far better off using analytic geometric descriptions. Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLExplorer.cpp Tests/GeometryShop/STLGeom/bad.cylinder.inputs Tests/GeometryShop/STLGeom/bad.reactor.inputs Tests/GeometryShop/STLGeom/good.cylinder.inputs Tests/GeometryShop/STLGeom/good.reactor.inputs Tests/GeometryShop/STLGeom/good.sphere.inputs Tests/GeometryShop/STLGeom/stl.inputs commit d74f5089caeef87f48a310d89265daf66387fc05 Merge: a197e15a2 927f38104 Author: WeiqunZhang Date: Fri Feb 16 09:02:34 2018 -0800 Merge pull request #210 from JBlaschke/development GNUMake respects Make.local's compile commands commit 927f38104a8d219be1e9f051152c13707109f761 Author: Johannes Blaschke Date: Fri Feb 16 08:52:01 2018 -0800 gnu.mak warns user if system's default gcc is outdated (<4.8), and reminds the user to specify a Make.local. Tools/GNUMake/comps/gnu.mak commit 3dc191e052c0a2d366761bd955d21f06a8020f12 Merge: a914868de a197e15a2 Author: Johannes Blaschke Date: Thu Feb 15 22:28:14 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a914868de76d038288da000f6e07d80d29969cf8 Author: Johannes Blaschke Date: Thu Feb 15 22:27:43 2018 -0800 WIP clean up documentation formatting Docs/sphinx/source/Chapter5.rst commit e5775454991e9b0cbc6674d67944cf21b35fefe7 Author: Johannes Blaschke Date: Thu Feb 15 22:24:54 2018 -0800 WIP: clean up formatting (including table captions) Docs/sphinx/source/Basics.rst Docs/sphinx/source/Chapter4.rst commit c03f5724642ce0fecce83b7c796ff43e28493afa Author: Johannes Blaschke Date: Thu Feb 15 20:57:40 2018 -0800 WIP: clean up formatting of docs Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter2.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Introduction.rst Docs/sphinx/source/index.rst commit a1cdf60a692b627f5cfc86639816d24c5b0a9803 Author: Johannes Blaschke Date: Thu Feb 15 20:38:14 2018 -0800 Document new Make.local behaviour Docs/sphinx/source/BuildingAMReX.rst commit 1c8c8c4c65d8ff1a0cbfbb598072e968cef8a4b2 Author: Johannes Blaschke Date: Thu Feb 15 20:10:40 2018 -0800 GNUMake compiler settings can be overwritten by Make.local (ie. introduce lazy evaluation to `comps/*.mak`). In order to work, compiler version checking for gnu had to be disabled (it makes little sense nowdays anyway). Tools/GNUMake/Make.defs Tools/GNUMake/comps/cray.mak Tools/GNUMake/comps/gnu-7.mak Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/intel.mak Tools/GNUMake/comps/llvm.mak Tools/GNUMake/comps/nag.mak Tools/GNUMake/comps/pgi.mak commit 0420f943e56d5f7e2bb9cd62a84f47aa688a9a9c Author: dtgraves Date: Thu Feb 15 16:20:32 2018 -0800 all the stl code is in geometryshop and it compiles. not tested yet. Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit a197e15a2ea1aaa53325b0d457944bf7deb862e9 Author: Max Katz Date: Thu Feb 15 19:09:40 2018 -0500 Add Summit to machine list Tools/GNUMake/Make.machines Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.olcf commit 8ea1cb59fc2dc235fb778ca2953d51c050326298 Merge: f6edc51a2 8fa37b8c0 Author: asalmgren Date: Thu Feb 15 15:57:29 2018 -0800 Merge pull request #209 from JBlaschke/development Forgot to add this file commit 8fa37b8c0f0786abc99159a2061264da531ff583 Author: Johannes Blaschke Date: Thu Feb 15 15:52:18 2018 -0800 Forgot to add this file Tools/GNUMake/comps/gnu-7.mak commit f6edc51a27eab70d8bfbf7e0797a8cd09e3e7bff Merge: 908570755 94b360fea Author: asalmgren Date: Thu Feb 15 15:37:21 2018 -0800 Merge pull request #208 from JBlaschke/development Development, added gnu-7 compiler definition commit 94b360fea9f10f506d8ddafb76aeff0ae05d63d2 Merge: 494af9acc 908570755 Author: Johannes Blaschke Date: Thu Feb 15 15:33:31 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 494af9acc0b8727ce391370c2a27ead84d79bee5 Author: Johannes Blaschke Date: Thu Feb 15 15:32:19 2018 -0800 added gnu-7 build target for gcc-7.x.x compilers. Needed, for example, for macOS where gcc links to gcc 4.2 Tools/GNUMake/Make.defs commit 1fcf31367bd2a5bb9564d0080e5d40755b7b99ce Author: dtgraves Date: Thu Feb 15 15:04:09 2018 -0800 note to self: never volunteer to port code before looking it over first. Src/GeometryShop/#AMReX_STLExplorer.H# Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_KDTree.H Src/GeometryShop/AMReX_KDTree.cpp Src/GeometryShop/AMReX_PXStuff.H Src/GeometryShop/AMReX_PXStuff.cpp Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLBox.cpp Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLIF.cpp Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLMesh.cpp Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_STLUtil.cpp Src/GeometryShop/Make.package Tests/GeometryShop/STLGeom/cylinder.stl Tests/GeometryShop/STLGeom/reactor.stl Tests/GeometryShop/STLGeom/sphere.stl commit 908570755bafa00fa86b5b1d11e97e8504ed6a77 Author: Ann Almgren Date: Thu Feb 15 14:47:30 2018 -0800 Add additional print statements for the MultiGrid Vcycle when verbose > 1 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 2f459c323b5b09dcd0d329a2e73f70dc105d6c3a Author: dtgraves Date: Wed Feb 14 16:24:43 2018 -0800 slogging through Issac Asher's code to get STL files into EBIndexSpace. Src/GeometryShop/#AMReX_STLExplorer.H# Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_Ellipsoid.cpp Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_KDTree.H Src/GeometryShop/AMReX_KDTree.cpp Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLBox.cpp Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLIF.cpp Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLMesh.cpp Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_STLUtil.cpp commit 627ed5272d465165da9440bcd35e6b8657102b4f Merge: 212ed7da4 eeb8a5eb2 Author: dtgraves Date: Wed Feb 14 12:58:56 2018 -0800 merging with dev branch commit 57e72351a876c201ffe9d253591c4813d4a15c8d Author: Weiqun Zhang Date: Tue Feb 13 17:09:25 2018 -0800 eb nodal projection: gauss seidel Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 08df0969bff13623e38fb2a550d74fdb24069afa Author: Weiqun Zhang Date: Tue Feb 13 16:37:57 2018 -0800 mlmg: harmonic average for jacobi Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 15bd63570e1e4f0068579b15d8e03a29437d5e8d Author: Weiqun Zhang Date: Tue Feb 13 16:06:26 2018 -0800 mlmg: enable eb on coarse mg levels Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 36741fb1d6eb15f158593f56b56a00ddc863a55c Author: Weiqun Zhang Date: Tue Feb 13 15:58:14 2018 -0800 EBTower: add function testing if the domain is valid Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp commit 7a4d8e89a3d600feaf94c846c8bb5922ca851a5f Merge: 232066016 eeb8a5eb2 Author: Weiqun Zhang Date: Tue Feb 13 15:18:56 2018 -0800 Merge branch 'development' into weiqun/mlmg commit 232066016877196d083029fd9018062580b36396 Author: Weiqun Zhang Date: Tue Feb 13 14:52:01 2018 -0800 mlmg: store factory as base class pointers Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit eeb8a5eb2d5ef2ec7222366b7492bfcb04469ae7 Author: Andy Nonaka Date: Tue Feb 13 12:53:42 2018 -0800 in the F_MG cell-centered solver, if the user tries to use the fancy bottom solver and the grid structure can't be re-arranged for further coarsening, use fancy_bottom_type in (if it was passed in) before resorting to the default BiCGStab Src/LinearSolvers/F_MG/mg.f90 commit b2a13fff595765541476779df7db71e4c7d3f433 Author: Weiqun Zhang Date: Tue Feb 13 09:58:27 2018 -0800 wip: eb nodal projection: fix rhs Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 9d42a576b48488962750ca6bda04981d8da185e1 Merge: 91a4156d3 898e4fdfb Author: Marc Day Date: Mon Feb 12 12:56:06 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 91a4156d31f82e41c6942f1ba45ae460f396bde9 Author: Marc Day Date: Mon Feb 12 12:55:14 2018 -0800 Fix code to predict data filename Tools/EBSurfaceTools/ConvertEBSurface.cpp commit 212ed7da4744cc2ea98d4b52166c957927dbeb31 Merge: 90938a5d5 898e4fdfb Author: dtgraves Date: Mon Feb 12 09:32:34 2018 -0800 merging with dev branch commit 898e4fdfbc77f83a3a92fa13152adf3b229eceed Merge: db406968d a98bd95be Author: dtgraves Date: Mon Feb 12 09:31:28 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit db406968dbfb543673639d0052ade60a54a4152e Author: dtgraves Date: Mon Feb 12 09:31:09 2018 -0800 added destructor fix that was found by Johannes Src/EB/AMReX_EBTower.cpp commit 90938a5d52f12a45e3b565621c27f5093eaf552f Author: dtgraves Date: Mon Feb 12 09:26:42 2018 -0800 tweaked inputs Tests/GeometryShop/regression/multicelllev.inputs commit a98bd95be97e30c7e807e491ed2287c34e30bb26 Merge: ada2cde0f 2c5ad4656 Author: Ann Almgren Date: Sun Feb 11 09:11:17 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ada2cde0f7a5a08d92777025f4b871a99fe3d759 Author: Ann Almgren Date: Sun Feb 11 09:10:58 2018 -0800 Updated default DATA_Digits_Read from 4 to 5. Tools/Postprocessing/C_Src/particle_compare.cpp commit 42d4a3654f03967ff007b32185ab67fe1593e043 Author: Weiqun Zhang Date: Thu Feb 8 13:24:31 2018 -0800 wip: eb nodal projection: update velocity at centroids Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e26ae8fc7bf2a78f077844199bf9aff68e680e71 Author: Weiqun Zhang Date: Thu Feb 8 11:23:26 2018 -0800 wip: eb nodal projection jacobi smoother Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 39e76dde9bc12c9f1af57c4d83bb100dc45892d2 Author: Weiqun Zhang Date: Thu Feb 8 09:46:47 2018 -0800 wip: eb node projection: a dot x Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 6825c5b2e55b64ef620c63b80d72192e2da29968 Author: Johannes Blaschke Date: Thu Feb 8 10:24:09 2018 -0500 Updated build instructions for source (sphinx -> latex) Docs/Readme.sphinx commit dce8c45ae43082923e50b3f7a4fd916e4e6c54ff Author: Weiqun Zhang Date: Wed Feb 7 17:00:41 2018 -0800 wip: compute the connections Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 16f4848c7b7e9713fe77ec1cafe087c36d396381 Author: Weiqun Zhang Date: Wed Feb 7 15:04:53 2018 -0800 wip: add stencil connection Src/Base/AMReX_constants_mod.f90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a9036a0bbf088bed3ae563f63e7823fee5a7a483 Author: Weiqun Zhang Date: Tue Feb 6 15:24:37 2018 -0800 2d mlmg: another way of interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 7137530e7e60c237be28a20d69f4768e9d152ef1 Author: Weiqun Zhang Date: Tue Feb 6 15:08:18 2018 -0800 2d mlmg: interpolate velocity from cell centers to centroids Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2c5ad4656e9b89f9d0150008d1208649680dc13a Author: Andy Nonaka Date: Tue Feb 6 14:39:52 2018 -0800 put IO in its own chapter Docs/sphinx/source/Basics.rst Docs/sphinx/source/Chapter6a.rst Docs/sphinx/source/IO.rst Docs/sphinx/source/index.rst commit abd91d4b90fd3981af2e732cc8fe5e06ee894302 Author: Andy Nonaka Date: Tue Feb 6 14:33:28 2018 -0800 wrote documentation for how to do checkpoint/restart Docs/sphinx/source/Basics.rst Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 7a6d1644faf3ccb562e3f55dfc66631546c06cc1 Author: Andy Nonaka Date: Tue Feb 6 14:02:56 2018 -0800 implemented checkpoint-restart in Tutorials/Amr/Advection_AmrCore Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit 4ff2747ceed26a2985336101a173e4e02f457a89 Author: Weiqun Zhang Date: Tue Feb 6 13:31:03 2018 -0800 add centroid to EBTower Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp commit 2f7db7cf2e8a1a02f5af6d057081e6e96653ee82 Author: Weiqun Zhang Date: Tue Feb 6 11:17:36 2018 -0800 mlmg: refactor Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b70560fc75002568004211eb9901f481a6e4ef11 Author: Weiqun Zhang Date: Tue Feb 6 09:52:32 2018 -0800 mlmg: using FactoryType Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit e9fd98e1e504f6e230782c02fd26f9fd72bde6d6 Merge: 005945c38 8e8d4e6a3 Author: dtgraves Date: Mon Feb 5 15:39:43 2018 -0800 Merge pull request #207 from AMReX-Codes/dtg_branch ebindexspace now can tell you where multi-valued cells start commit 8e8d4e6a38e7ed804a9c8481317e8d5765834cf6 Author: dtgraves Date: Mon Feb 5 15:37:34 2018 -0800 added functionality to EBIndexSpace which allows the user to find out the finest level where the graph is multivalued in a cell. The test works in serial and in parallel. Also I added an ellipsoid implicit function. Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/Make.package Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/multicelllev.cpp Tests/GeometryShop/regression/multicelllev.inputs commit 30e88d1e691b39c590e6c4ee21e90f00262c2d2c Author: Weiqun Zhang Date: Mon Feb 5 15:31:55 2018 -0800 mlmg: turn off harmonic average for now because there seems to be a bug; set velocity in covered cells to zero before computing rhs Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 44edec51352ca45bbfa3d5fa28fb6f7e0ac1b5d3 Author: Weiqun Zhang Date: Mon Feb 5 13:41:09 2018 -0800 mlmg: always use harmonic average for eb and make sure no divided-by-zero Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5c38e6d61c149e7c0d306a8859da631c69a3c675 Author: Weiqun Zhang Date: Mon Feb 5 12:29:02 2018 -0800 mlmg: make factory argument to be vector of ptrs Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit ca0ea4278696ed554e49ed1f2ba35c81ad2b19f8 Author: Weiqun Zhang Date: Mon Feb 5 11:20:52 2018 -0800 rm EBNodalProjection tutorial Tutorials/LinearSolvers/EBNodalProjection/GNUmakefile Tutorials/LinearSolvers/EBNodalProjection/Make.package Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp Tutorials/LinearSolvers/EBNodalProjection/initEB.cpp Tutorials/LinearSolvers/EBNodalProjection/main.cpp commit a015d7b34702ef648b97bebdadc3afdbd87849e1 Author: Weiqun Zhang Date: Mon Feb 5 11:18:43 2018 -0800 minor Tools/GNUMake/comps/gnu.mak commit 005945c38173d9486a30da4b57747bfa9d1bc4ff Author: Ann Almgren Date: Sat Feb 3 11:19:16 2018 -0800 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit ddc22772debc4cef821cb08efbd543b59592ab83 Author: Ann Almgren Date: Fri Feb 2 20:10:37 2018 -0800 Add line break between Lecture1 and Lecture2 Docs/sphinx/source/Chapter12.rst commit e968523f9bb06669da071ec5fe9e5c17ee35311e Author: Ann Almgren Date: Fri Feb 2 19:17:13 2018 -0800 Add link to 2nd week of profiling tutorial Docs/sphinx/source/Chapter12.rst commit a87c5ef08e0f7769bb44d05cee04b6fbfd278edd Author: Ann Almgren Date: Fri Feb 2 16:09:07 2018 -0800 Add pointer to Amrvis/Docs/Amrvis.tex Docs/sphinx/source/Visualization.rst commit 60c8d493ddb74de5e2985932f5f988b8487ae1e5 Author: Ann Almgren Date: Fri Feb 2 15:48:43 2018 -0800 Update link to amrvis Docs/sphinx/source/Visualization.rst commit fbb4c43079d76ed45a3b2a84bf6a69548c326050 Author: Minion Date: Fri Feb 2 15:48:40 2018 -0800 adding quadrature terms in sweeper Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H commit 7775775abcc3d9da93267e17cf9ff7a97d089e14 Merge: 269580f68 659770f35 Author: dtgraves Date: Fri Feb 2 15:38:50 2018 -0800 Merge pull request #205 from AMReX-Codes/dtg_branch fixing a bunch of small stuff with EB commit 659770f35be8478214263663333152d9f5d9d036 Author: dtgraves Date: Fri Feb 2 15:28:53 2018 -0800 fixed a bunch of tests that were broken because of interface changes. Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/ramp/main.cpp Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphereEBISBox/GNUmakefile commit 3f51924544ea0a1d6d610a19495e14142e04dcab Author: Minion Date: Thu Feb 1 17:42:40 2018 -0800 Using Vector correctly for SDC arrays and saxpy in C++ Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H commit db1b6289e363d73a31ef60a9d2db6d49dddc0e64 Author: Weiqun Zhang Date: Thu Feb 1 17:05:10 2018 -0800 MLMG: add factory as optional argument Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 1e337c92ea92bd824718c4681504ac9669c6c6a3 Author: dtgraves Date: Thu Feb 1 16:52:44 2018 -0800 think I have the serialization issue beat but I need to test it more before I put it into dev branch. Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs Tests/GeometryShop/regression/serialization.cpp commit 55fc6b8540a0de40648cedca2bb1f7326b5b9ba1 Author: Weiqun Zhang Date: Thu Feb 1 15:09:21 2018 -0800 EBNodalProjection test: build factories Tutorials/LinearSolvers/EBNodalProjection/Make.package Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp Tutorials/LinearSolvers/EBNodalProjection/initEB.cpp commit 56a6a2186c87a90d2a8f136b97dafc7ef45657c7 Author: Weiqun Zhang Date: Thu Feb 1 13:33:19 2018 -0800 mlmg: make sure the corners do not trigger floating point exception and remove fillSolutionBC function because we always fill bc to compute residuals Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit b82e24bf798073529910e96b03d3fd3bf07a37d5 Author: Weiqun Zhang Date: Thu Feb 1 10:32:10 2018 -0800 EBNodalProjection test: setup with eb is done Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp commit 269580f688eaaf15d062ed47ac1d5ffd6b33c5ad Merge: 69797e5c4 f0528bad8 Author: WeiqunZhang Date: Thu Feb 1 10:15:28 2018 -0800 Merge pull request #203 from hsitaram/haribranch Extrude IF utility commit 6e21d139351a0f15cfb4f00bf6638e11cc273f8b Merge: 49acc1d95 69797e5c4 Author: Weiqun Zhang Date: Thu Feb 1 08:52:20 2018 -0800 Merge branch 'development' into weiqun/dev commit fcc6ab09c3b5501661b900cf04fa078517bf5441 Author: dtgraves Date: Wed Jan 31 16:24:50 2018 -0800 took out some directory thrashing. Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs commit 30b2c206eaa3b03697a200dddf6f62e4ef53250c Author: dtgraves Date: Wed Jan 31 16:00:26 2018 -0800 made ebgraph serialization a bit more consistent. Src/GeometryShop/AMReX_EBGraph.cpp commit 0577d411d6637cc899cd91f3eeffdf582ba4781b Author: dtgraves Date: Wed Jan 31 15:58:01 2018 -0800 some bugs had crept into EBIndexSpace linearization. this fixes some of them Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/ebio.cpp commit f0528bad8efb622c3bfb70c327b526e0b483dd57 Author: hari Date: Wed Jan 31 14:58:27 2018 -0700 leaving 2D extruded surface as is Src/GeometryShop/AMReX_ExtrudeIF.H Src/GeometryShop/AMReX_ExtrudeIF.cpp Src/GeometryShop/CMakeLists.txt Src/GeometryShop/Make.package commit 69797e5c4b0af436fe29a42b5e10971d1eac2aea Merge: 75a0263a3 a7c9e7532 Author: dtgraves Date: Wed Jan 31 12:01:01 2018 -0800 Merge pull request #201 from AMReX-Codes/dtg_branch added ability to fill Node-centered FArrayBox from implicit function … commit a7c9e7532dfbbbde4f1ca8b369452e7579eda9a0 Author: dtgraves Date: Wed Jan 31 11:59:57 2018 -0800 added ability to fill Node-centered FArrayBox from implicit function values. Test lives in Tests/GeometryShop/regression Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.H Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/fabfromif.cpp commit 49acc1d9509fe01e342987a0178d7ed61613d865 Author: Weiqun Zhang Date: Wed Jan 31 10:45:06 2018 -0800 add a profiler to GeometryShop::fillGraph Src/GeometryShop/AMReX_GeometryShop.cpp commit bf342f25ab7b873858c6ca338967823445da8046 Author: Weiqun Zhang Date: Wed Jan 31 10:02:34 2018 -0800 mlmg: if the solution multifab argument does not have exactly one ghost cell, make a local copy Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 75a0263a38ee6778367b46c8c0d104b629bf4fc9 Author: Andy Nonaka Date: Tue Jan 30 17:37:40 2018 -0800 expanded on the Basics of the HeatEquation_EX1_C tutorial Docs/sphinx/source/Basics.rst Docs/sphinx/source/Basics/figs/flowchart.odg Docs/sphinx/source/Basics/figs/flowchart.pdf Docs/sphinx/source/Basics/figs/flowchart.png Docs/sphinx/source/GettingStarted.rst Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp commit 651ea123bd6e022722508685b20059de7048329e Author: Andy Nonaka Date: Tue Jan 30 17:01:23 2018 -0800 re-org tutorials Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/Basic/HeatEquation_EX1_C/Source/Make.package Tutorials/Basic/HeatEquation_EX1_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX2_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_3d Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_2D.F Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_3D.F Tutorials/Basic/HeatEquation_EX2_C/Source/Make.package Tutorials/Basic/HeatEquation_EX2_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/advance_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/Source/advance_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/Source/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/Source/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX3_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX3_C/Source/Make.package Tutorials/Basic/HeatEquation_EX3_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX3_C/Source/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX3_C/Source/inputs_3d Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc_F.H commit b4548c4d6b4a31fb012d9668887cbb6bf4b5633f Author: Weiqun Zhang Date: Tue Jan 30 16:29:17 2018 -0800 added amrex_multifab_build_alias and amrex_imultifab_build_alias to Fortran interface CHANGES Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 75bd0b7e39d2109cc4b3bb524957fde27b373b7b Author: Weiqun Zhang Date: Tue Jan 30 15:42:22 2018 -0800 WIP: nodal projection tutorial Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp commit 42526dd45f0c3dbe716310a94965495bc4734d77 Author: Weiqun Zhang Date: Tue Jan 30 15:08:32 2018 -0800 writeFabs function that writes out each individual fab Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit d656c4548677e548c181aebac3402d7fa83f7170 Author: Weiqun Zhang Date: Tue Jan 30 14:20:58 2018 -0800 add non-const version of BaseFab::ForEachIV Src/Base/AMReX_BaseFab.H commit acf94542b423d5fe35c3337a1e0d1f11212783c8 Author: Weiqun Zhang Date: Tue Jan 30 14:20:22 2018 -0800 start eb nodal projection test Tutorials/LinearSolvers/EBNodalProjection/GNUmakefile Tutorials/LinearSolvers/EBNodalProjection/Make.package Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp Tutorials/LinearSolvers/EBNodalProjection/main.cpp commit 33281777d045992f2406d37dae79aa855a2c4135 Author: Andy Nonaka Date: Tue Jan 30 15:29:40 2018 -0800 pass in basic data types (int, real) into fortran using pointers, not pass-by-reference Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrLevel/Source/Adv_F.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Basic/HeatEquation_EX1_C/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H Tutorials/Basic/HeatEquation_EX2_C/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/myfunc_F.H commit d81a349d56f563cd9a57d341be11081a3fc40542 Author: Lawrence Minion Date: Tue Jan 30 14:29:28 2018 -0800 adding quadrature routines and SDC arrays Tutorials/Basic/SDCHeat_Equation_EX1_C/Make.package Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_3d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H Tutorials/Basic/SDCHeat_Equation_EX1_C/pf_quadrature.f90 commit 79488d511f0210a0e4078caf0ea23895d0019b90 Author: Weiqun Zhang Date: Tue Jan 30 10:12:51 2018 -0800 EB: make sure the BoxArray is cell-centered Src/EB/AMReX_EBDataCollection.cpp commit 21051ed97549c5539d45679c93dc16ff090b72b7 Merge: 1d1067abf 2497b19df Author: Andrew Myers Date: Tue Jan 30 09:53:43 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1d1067abfdc112d3d8c479eed4c320b29d3a09db Author: Andrew Myers Date: Tue Jan 30 09:53:33 2018 -0800 wrap these MPI helper functions in #ifdef BL_USE_MPI Src/Particle/AMReX_ParticleContainerI.H commit 2497b19dfdec11d6de0491a1a1ebe9e5f2a4d2be Merge: 52a8d0718 f574cd5af Author: Andy Nonaka Date: Mon Jan 29 14:09:38 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 52a8d0718a15b48a011eef2bab28c64bab12934d Author: Andy Nonaka Date: Mon Jan 29 14:09:18 2018 -0800 profiling lecture notes Docs/sphinx/source/Chapter12.rst commit f574cd5afa62db7e78b7e2395593f17cda1a13e0 Author: Andrew Myers Date: Mon Jan 29 12:14:04 2018 -0800 fix a couple of bugs in assert statements that broke compilation in DEBUG. Src/Particle/AMReX_ParticleContainerI.H commit 9c9506614eb42ab4044cb092940918dcd1e2505a Merge: 4ece270d7 39f89a3de Author: Andrew Myers Date: Mon Jan 29 12:04:54 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4ece270d770ad8c8fd15a7b919f40b62f15d4740 Author: Andrew Myers Date: Mon Jan 29 12:04:10 2018 -0800 FabArray > -> iMultiFab Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 53ec6356fdda9f8cdc8a10499cfe3a75a811ad66 Author: Andrew Myers Date: Mon Jan 29 11:59:49 2018 -0800 A version of Redistribute for particles that have only moved a certain amount (typically one cell) since the last Redistibute() call. This version does not need to do All-to-all communication. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 39f89a3de70a1da19e4489c505a2f182f91a61f7 Author: Kevin Gott Date: Mon Jan 29 11:18:53 2018 -0800 Docs update: BL_PROFILE_TINY_FLUSH Docs/sphinx/source/AMReX_Profiling_Tools.rst commit 5f31e89dba38d9f492a7ac72f73f28add6335f23 Author: Andrew Myers Date: Mon Jan 29 10:42:21 2018 -0800 move Redistribute handshake stuff into helper function. Src/Particle/AMReX_ParticleContainerI.H commit 3b4d10a0847e7bdf487f6710cbfd018bc905c418 Author: Andrew Myers Date: Fri Jan 26 21:10:30 2018 -0800 remove now unused template parameter Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit 0f3f8bfe21f0a569da35e10b4e1650ea5f45024f Author: Andrew Myers Date: Fri Jan 26 20:53:06 2018 -0800 Don't require users to call BuildLevelMask - just build it the first time it's needed. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 581bfd935bfe4de8a53c0e1b1096f65ce10dce8b Author: Weiqun Zhang Date: Fri Jan 26 19:45:09 2018 -0800 fix a bug recently introduced by me Src/Base/AMReX_BaseFab.H commit 105cec5b028e2ea77b9878dcdb40c8229cfdd0d5 Author: Ann Almgren Date: Fri Jan 26 17:12:22 2018 -0800 Add link to sample output Docs/sphinx/source/AMReX_Profiling_Tools.rst commit d12ab9626692a42d5bc38c185d60e8126db37c99 Author: Ann Almgren Date: Fri Jan 26 17:05:40 2018 -0800 Update to include cmake flags as well as GNU make flags Docs/sphinx/source/AMReX_Profiling_Tools.rst commit 5430e758d0f10782bc2ff3faab1168a3f3c4fc9c Author: Ann Almgren Date: Fri Jan 26 16:59:01 2018 -0800 Update sample output Docs/sphinx/source/AMReX_Profiling_Tools.rst commit 0e4967661c52b706d9ef39a47570ba65ebe571f9 Author: Ann Almgren Date: Fri Jan 26 16:53:03 2018 -0800 This copy of Readme.profiling only contains information that has not been migrated to the online documentation. Docs/Readme.profiling commit a46ba7267e7c0453d27f75dc59b14555e53e34fb Merge: 675b65634 dcd526cce Author: Ann Almgren Date: Fri Jan 26 16:45:37 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 675b65634aab924fb98cf867525671b084243c39 Author: Ann Almgren Date: Fri Jan 26 16:45:15 2018 -0800 Break profiling into two parts Docs/sphinx/source/AMReX_Profiling_Tools.rst Docs/sphinx/source/Chapter12.rst Docs/sphinx/source/Chapter13.rst Docs/sphinx/source/Chapter14.rst Docs/sphinx/source/External_Profiling_Tools.rst Docs/sphinx/source/index.rst commit dcd526ccec39fff970660fc29c5a11c23f6ec2d9 Merge: d607ea0ac 345515a09 Author: Andrew Myers Date: Fri Jan 26 16:25:10 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d607ea0acd84395bdfd4c49e7d85692866b8f2e4 Author: Andrew Myers Date: Fri Jan 26 16:25:01 2018 -0800 use BL_PROFILE_VAR instead of BL_PROFILE here Src/Particle/AMReX_ParticleContainerI.H commit 345515a098c8316cf38abff4d10b09ce05068532 Author: kngott Date: Fri Jan 26 15:54:01 2018 -0800 Addition of BL_PROFILE_TINY_FLUSH() to allow the user to flush the TINYPROFILER results to stdout whenever they like. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 72807d73ecbc7bd4c7a62e9cbb625ff0be71b1dc Merge: 079d67237 9b34e0efa Author: Weiqun Zhang Date: Fri Jan 26 12:42:34 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 079d672379c57cea7daaed693bc215714211877c Author: Weiqun Zhang Date: Fri Jan 26 12:41:24 2018 -0800 hypre add amrex_ prefix to some fortran functions Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 9b34e0efabc11ef269ae133a6a00eda666127a82 Merge: 4b44036c4 94931b014 Author: Andrew Myers Date: Fri Jan 26 11:16:07 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4b44036c49ec0d725893fc06e7dbe854d648a191 Author: Andrew Myers Date: Fri Jan 26 11:15:57 2018 -0800 Real -> ParticleType::Real Src/Particle/AMReX_NeighborParticlesI.H commit 94931b0146bc00997ee80505ffcd33e4b71ab4a9 Author: Weiqun Zhang Date: Fri Jan 26 10:33:27 2018 -0800 hypre: rm duplicated calls to assemble vectors Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp commit a6c852bb1507772ac1937d35883518af62fb38b1 Merge: 94f7fb421 71fccde16 Author: Weiqun Zhang Date: Fri Jan 26 09:01:40 2018 -0800 Merge branch 'hypre' into development commit 94f7fb42188a230dbd6698f43950c6ee88d186b4 Merge: 9d53b14e7 fb93d0ba8 Author: Weiqun Zhang Date: Thu Jan 25 18:07:24 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9d53b14e7e7d7aa92f495643b96bf6a74987bccc Merge: 9ea7ef0c6 b1439903f Author: Weiqun Zhang Date: Thu Jan 25 18:07:18 2018 -0800 Merge branch 'weiqun/looping' into development commit 71fccde16be0fce137782e3cd0d0e2784e060a4e Author: Weiqun Zhang Date: Thu Jan 25 16:08:08 2018 -0800 mlmg: set hypre verbosity Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e3345fc9ee7a1d73e9fe02d74d3f7e128e61d6a2 Author: Weiqun Zhang Date: Thu Jan 25 15:40:58 2018 -0800 MLMG: use hypre as bottom solver for cell-centered solve Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit fb93d0ba84c5f05f6a0ae82e660c1b7d92fae7fb Merge: 779e00524 9ea7ef0c6 Author: Ann Almgren Date: Thu Jan 25 13:05:46 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 779e005245934372a4f52f83814ae3f58106d55a Author: Ann Almgren Date: Thu Jan 25 12:10:25 2018 -0800 Change the default for probin_natonce from 32 to 512 since 32 reads at a time is way too few when running with many ranks. Src/Amr/AMReX_Amr.cpp commit b1439903f23cd1429fdd917b06e3e4cc1029558c Author: Weiqun Zhang Date: Thu Jan 25 10:28:47 2018 -0800 add BaseFab::Transform Src/Base/AMReX_BaseFab.H commit 02330497517485a0b91d5a6dec2368154369ec88 Author: Weiqun Zhang Date: Thu Jan 25 10:06:05 2018 -0800 make sure box passed to setVal is ok Src/Base/AMReX_BaseFab.H Src/Boundary/AMReX_MultiMask.cpp commit 9ea7ef0c6fb6c7d9686bff13e50241acf1a9a594 Author: Andy Nonaka Date: Thu Jan 25 09:17:52 2018 -0800 updates Docs/sphinx/source/Introduction.rst Docs/sphinx/source/index.rst commit 48c0145ee0c23efcbf13379836cd5e876b5cc260 Author: Weiqun Zhang Date: Wed Jan 24 17:20:24 2018 -0800 bug fixes Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Boundary/AMReX_Mask.cpp commit e3b6f8175b88ad203724f03926079e1e43c5ddab Author: Weiqun Zhang Date: Wed Jan 24 15:49:09 2018 -0800 rm AMReX_Looping.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseUmap.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_Looping.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/Boundary/AMReX_Mask.cpp commit d69165d1fa0809437030d4110216c4b11dae0ca7 Merge: 74870d51a 829e68df6 Author: Lawrence Minion Date: Wed Jan 24 13:50:51 2018 -0800 Fixing double naming. Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit 74870d51abb00c4e99e5eb9c8a4e16e06d7483b5 Author: Andy Nonaka Date: Wed Jan 24 11:22:04 2018 -0800 User's Guide -> Documentation Docs/sphinx/source/Chapter9.rst Docs/sphinx/source/Introduction.rst Docs/sphinx/source/index.rst commit 68114f84eb556cc3be9c880afb8c72e1b32949ee Author: Weiqun Zhang Date: Wed Jan 24 10:34:00 2018 -0800 rm ForAllThisBNNXC Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Looping.H Src/Boundary/AMReX_Mask.cpp commit c71b0abe3cdaeb9c8d32eb8c6a7e0e673ef608fc Author: Weiqun Zhang Date: Wed Jan 24 10:14:48 2018 -0800 rm ForAllThisBNNXCBN Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Looping.H Src/Boundary/AMReX_Mask.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 9b4ea8a14462c5e77a0b24a0d015b2b261440484 Merge: d76c7a650 4e2f7fa24 Author: Andy Nonaka Date: Tue Jan 23 19:00:37 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d76c7a65013ebab5e8a07b491e3ba6a9b4a0530a Author: Andy Nonaka Date: Tue Jan 23 19:00:24 2018 -0800 update intro Docs/sphinx/source/Introduction.rst commit 4e2f7fa2452fc38776841e9790747eb26061c86b Merge: daf6c6c87 81529a663 Author: Andrew Myers Date: Tue Jan 23 18:02:21 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit daf6c6c87a2d865d088973c1a2ad150137278243 Author: Andrew Myers Date: Tue Jan 23 18:02:03 2018 -0800 add note about minimum version of yt needed for AMReX Datasets Docs/sphinx/source/Visualization.rst commit 80cb4968c2bb9986aea967ee69f18dd648277a2d Author: Weiqun Zhang Date: Tue Jan 23 17:15:16 2018 -0800 ForAllThisBNNXCBNYCBN is gone Src/Base/AMReX_Looping.H commit 81529a66387fd8e45dd6d784f322456e3d5e1078 Author: Andy Nonaka Date: Tue Jan 23 17:13:35 2018 -0800 switch chapters Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/Chapter7.rst commit 04434a199b854e131d50a2dc9aaccf0e6e69465d Author: Weiqun Zhang Date: Tue Jan 23 17:13:31 2018 -0800 rm linComb for non-Real type Src/Base/AMReX_BaseFab.H commit 49b15aeec17699a2c0db287b5f304a073d99ccdd Author: Andy Nonaka Date: Tue Jan 23 17:11:13 2018 -0800 linear solver placeholder Docs/sphinx/source/Basics.rst Docs/sphinx/source/Chapter5.rst Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/LinearSolvers.rst Docs/sphinx/source/index.rst commit 2bb0c0a12adf10724c4c91de9e987002f2a5b48b Author: Weiqun Zhang Date: Tue Jan 23 16:58:14 2018 -0800 use Accumulate; rm ForAllRevXBNYCBNNN and BaseFab::copyRev Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Looping.H commit f033f6ca8a705d5a247ca0d00dd5fdd5f4fefd72 Author: Weiqun Zhang Date: Tue Jan 23 16:47:53 2018 -0800 ForAllThisBNN is gone Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Looping.H commit 7e3e27d4f0320dc0ac70c6a82a13e8c8ec2cde29 Author: Weiqun Zhang Date: Tue Jan 23 16:31:55 2018 -0800 BaseFab: add ForEach and Accumulate Src/Base/AMReX_BaseFab.H commit 58cda74a7c64fe8939c4fea6f74ee10ecec65c23 Author: Andy Nonaka Date: Tue Jan 23 16:00:04 2018 -0800 teaching myself sphinx. cleaning up user's guide Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/AmrLevel.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Boundary.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/index.rst commit 829e68df6d3e313057ccf9831274f4087efeaa96 Author: Minion Date: Tue Jan 23 15:37:21 2018 -0800 Framework for SDC Heat Example Tutorials/Basic/SDCHeat_Equation_EX1_C/GNUmakefile Tutorials/Basic/SDCHeat_Equation_EX1_C/Make.package Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_3d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_3d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_3d Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H commit 1d218918d4663d17c3efd962bbddaf401c68ce7d Author: Weiqun Zhang Date: Tue Jan 23 14:41:11 2018 -0800 ForAllThisCPencil is gone Src/Base/AMReX_BaseFab.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_Looping.H commit e237e4982c5300dab5a37d04c5d60283fd87eea4 Author: Weiqun Zhang Date: Tue Jan 23 14:12:01 2018 -0800 add some functions to BaseFab in order to eliminate looping macros Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H commit 416db144ca58a9dad9b0727b25c593739e9dbcce Author: Weiqun Zhang Date: Tue Jan 23 12:29:29 2018 -0800 rm unused macros for looping over BaseFabs Src/Base/AMReX_Looping.H commit b4a1235934b609fd5b018cb241e01a9cd79dd6b4 Author: Weiqun Zhang Date: Tue Jan 23 12:04:53 2018 -0800 update CHANGES CHANGES commit 906e31c02b2d9fa84240ab709defc2e69e2c5f48 Author: Ann Almgren Date: Tue Jan 23 10:33:47 2018 -0800 Remove the latex source for the users guide -- we now use the .rst files in sphinx as the primary source for the documentation. Docs/AMReXUsersGuide/.gitignore Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/Adv1.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv2.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv3.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv4.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv5.pdf Docs/AMReXUsersGuide/AmrCore/figs/flowchart.odg Docs/AMReXUsersGuide/AmrCore/figs/flowchart.pdf Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf Docs/AMReXUsersGuide/AmrCore/figs/subcycling.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.odg Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.pdf Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/amrgrids.pdf Docs/AMReXUsersGuide/Basics/cc_growbox.pdf Docs/AMReXUsersGuide/Basics/cc_tilebox.pdf Docs/AMReXUsersGuide/Basics/cc_validbox.pdf Docs/AMReXUsersGuide/Basics/ec_growbox.pdf Docs/AMReXUsersGuide/Basics/ec_tilebox.pdf Docs/AMReXUsersGuide/Basics/ec_validbox.pdf Docs/AMReXUsersGuide/Basics/figs/flowchart.odg Docs/AMReXUsersGuide/Basics/figs/flowchart.pdf Docs/AMReXUsersGuide/Basics/indextypes.pdf Docs/AMReXUsersGuide/Boundary/Boundary.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/CVODE/CVODE.tex Docs/AMReXUsersGuide/Debugging/Debugging.tex Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/EB/EB_example.eps Docs/AMReXUsersGuide/EB/EB_example.fig Docs/AMReXUsersGuide/EB/EB_example.fig.bak Docs/AMReXUsersGuide/EB/EB_example.pdf Docs/AMReXUsersGuide/EB/areas_and_volumes.eps Docs/AMReXUsersGuide/EB/areas_and_volumes.fig Docs/AMReXUsersGuide/EB/areas_and_volumes.pdf Docs/AMReXUsersGuide/EB/eb_fluxes.eps Docs/AMReXUsersGuide/EB/eb_fluxes.fig Docs/AMReXUsersGuide/EB/eb_fluxes.fig.bak Docs/AMReXUsersGuide/EB/eb_fluxes.pdf Docs/AMReXUsersGuide/EB/graph.pdf Docs/AMReXUsersGuide/EB/multidivide.pdf Docs/AMReXUsersGuide/EB/parabsphere.pdf Docs/AMReXUsersGuide/EB/parabsphere.ps.REMOVED.git-id Docs/AMReXUsersGuide/EB/redist.eps Docs/AMReXUsersGuide/EB/redist.fig Docs/AMReXUsersGuide/EB/redist.pdf Docs/AMReXUsersGuide/EB/revolution.pdf Docs/AMReXUsersGuide/EB/revolution.ps.REMOVED.git-id Docs/AMReXUsersGuide/EB/volume.pdf Docs/AMReXUsersGuide/Fortran/Fortran.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Particle/neighbor_list.pdf Docs/AMReXUsersGuide/Particle/neighbor_list.tex Docs/AMReXUsersGuide/Particle/neighbor_particles.pdf Docs/AMReXUsersGuide/Particle/neighbor_particles.tex Docs/AMReXUsersGuide/Particle/particle_arrays.pdf Docs/AMReXUsersGuide/Particle/particle_arrays.tex Docs/AMReXUsersGuide/Preface/Preface.tex Docs/AMReXUsersGuide/Profiling/Profiling.tex Docs/AMReXUsersGuide/Profiling/figs/commtopo.png Docs/AMReXUsersGuide/Profiling/figs/mpi.png Docs/AMReXUsersGuide/Profiling/figs/msgsizes.png Docs/AMReXUsersGuide/Profiling/figs/papi.png Docs/AMReXUsersGuide/Profiling/figs/summary.png Docs/AMReXUsersGuide/Profiling/figs/timings.png Docs/AMReXUsersGuide/README.md Docs/AMReXUsersGuide/Visualization/Amrvis_2d.eps Docs/AMReXUsersGuide/Visualization/Amrvis_3d.eps Docs/AMReXUsersGuide/Visualization/ParaView.eps Docs/AMReXUsersGuide/Visualization/ParaView_particles.eps.REMOVED.git-id Docs/AMReXUsersGuide/Visualization/VisIt_2D.eps Docs/AMReXUsersGuide/Visualization/VisIt_3D.eps Docs/AMReXUsersGuide/Visualization/Visualization.tex Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_slice.png Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_vol_rend.png Docs/AMReXUsersGuide/amrexsymbols.tex commit 5ceace152c091d701cf0063d5b80275942e6cdca Author: Weiqun Zhang Date: Tue Jan 23 09:25:43 2018 -0800 rm oboslete macros Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_ccse-mpi.H Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F Src/Boundary/AMReX_LO_UTIL.F Src/LinearSolvers/F_MG/FParallelMG.mak commit 402dd7538865b50b21f16a8f0766de99455828a1 Author: Ann Almgren Date: Tue Jan 23 09:54:32 2018 -0800 Fixed the centering commands. Docs/sphinx/source/CVODE.rst Docs/sphinx/source/EB.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/Visualization.rst commit cac220b5cbed24c2adfffa6e2805c639bc03a473 Author: Weiqun Zhang Date: Tue Jan 23 09:20:53 2018 -0800 finally fixed 1d node based bilinear interpolation Src/AmrCore/AMReX_INTERP_1D.F commit 4acbf3c064e4f7381629fa38021cd194f4cab5ad Merge: 1f066afcb 3ba8fd87a Author: Andrew Myers Date: Mon Jan 22 17:15:31 2018 -0800 merging. commit 1f066afcb0f4e64bde706f44bbb2b6c08f1556d0 Author: Andrew Myers Date: Mon Jan 22 17:13:49 2018 -0800 clarify doc building instructions slightly Docs/Readme.sphinx commit 3ba8fd87ad0a17befab11ecfb317c30431672008 Author: Ann Almgren Date: Mon Jan 22 16:37:19 2018 -0800 Add details about "make latexpdf" Docs/Readme.sphinx commit 5b371b915ae371e57bcee46925f43d25e03bfafb Merge: 4af3e755c b41660a9a Author: Ann Almgren Date: Mon Jan 22 16:36:08 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4af3e755cce1d65d15f9a9bf3656843b9431726d Author: Ann Almgren Date: Mon Jan 22 16:35:48 2018 -0800 Replace some centering commands so they work correctly for make latexpdf Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Profiling.rst commit b41660a9aff1578dee49f2bdff5e79d48e23cfd4 Author: Michele Rosso Date: Mon Jan 22 16:27:24 2018 -0800 CMake:do not retrieve git hash if git not installed or .git not present Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Utils.cmake commit c465ead19d1da1b7eec3467f6d49912bf815de73 Author: Andrew Myers Date: Mon Jan 22 15:59:31 2018 -0800 fix the centering of the tables when building using latexpdf Docs/sphinx/source/BuildingAMReX.rst commit 140ac5b4287841db4c226ef9431fdd4a3a3f063f Merge: e797758f6 3df686d34 Author: Ann Almgren Date: Mon Jan 22 15:23:54 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e797758f68fdcf786064d149b2f0551795b0606b Author: Ann Almgren Date: Mon Jan 22 15:23:47 2018 -0800 Update rst files Docs/sphinx/source/Basics.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/Visualization.rst commit 3df686d34b23cfa876305ad0b038fae896e33ba0 Author: Andrew Myers Date: Mon Jan 22 15:03:22 2018 -0800 add a few comments. build_and_deploy.sh commit 5c79bcb9fc9d545f3cb20aee00a83885191eb6fe Author: Andrew Myers Date: Mon Jan 22 14:58:24 2018 -0800 minor Docs/sphinx/source/BuildingAMReX.rst commit 6fdeffd34911b7c1e19de0cde6c79f59ca45f749 Author: Andrew Myers Date: Mon Jan 22 14:54:41 2018 -0800 update deploy script to compile libamrex before exiting early if not on development build_and_deploy.sh commit 2fc8c6b4474282e643964b7e751e7e4492570ce6 Author: Andrew Myers Date: Mon Jan 22 14:37:38 2018 -0800 override the default page width for the read the docs theme, which is optimized for mobile. Docs/sphinx/source/conf.py commit 2ef04933c7f7071a62bc2caaa6f92eecc9854b47 Author: Andrew Myers Date: Mon Jan 22 14:31:03 2018 -0800 update the AMReX version every time the docs are built. Docs/sphinx/source/conf.py commit 8a0e6ec1d4073f24ad2663be67bb3fe97f924f6b Merge: 389b0c586 787af403a Author: Andrew Myers Date: Mon Jan 22 13:44:51 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 389b0c5861cbb61a4448dc014b8c63c3274ba508 Author: Andrew Myers Date: Mon Jan 22 13:44:41 2018 -0800 updates to the sphinx installation instructions. Docs/Readme.sphinx commit 787af403a7acd0b1bb6c4e0597a9869fcfdd71d6 Author: Weiqun Zhang Date: Mon Jan 22 13:28:27 2018 -0800 Array --> Vector Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/Amr/AMReX_AmrLevelTask.H Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 32dc2019bd1bd8a84936bbd70638d64d1a903454 Author: Ann Almgren Date: Mon Jan 22 13:00:15 2018 -0800 More path highlighting Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/AmrLevel.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Boundary.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/Chapter7.rst Docs/sphinx/source/Fortran.rst Docs/sphinx/source/Particle.rst commit c2866e949581d93aca01be309804d01e89382f5e Author: Ann Almgren Date: Mon Jan 22 12:54:17 2018 -0800 More path names Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/CVODE.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/Chapter7.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/Visualization.rst commit 7754851b06168692f9402a17525b01512b8a8ea2 Author: Ann Almgren Date: Mon Jan 22 12:49:50 2018 -0800 All path names should be highlighted Docs/sphinx/source/Boundary.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/EB.rst Docs/sphinx/source/Fortran.rst commit 7e4f13fe2d671429f2d8143bd65f73d85c8dd655 Author: Ann Almgren Date: Mon Jan 22 12:46:42 2018 -0800 formatting Docs/sphinx/source/Chapter6.rst commit 61a6f693b83c48c259de6dac458bb7d5443af4ee Author: Weiqun Zhang Date: Mon Jan 22 10:39:09 2018 -0800 MLMG N-Solve: refactor making grids Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit b075130f36ea330260f077112512ddac862e5a8a Author: Weiqun Zhang Date: Mon Jan 22 09:23:36 2018 -0800 MLMG N-Solve: add paramter controlling grid size Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 8b46b285e104d895746d4aeadaa194cfced10d7d Merge: d2f932189 7292d5db0 Author: Andrew Myers Date: Mon Jan 22 12:09:38 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d2f9321890bccade2821de70fc7afe460192332f Author: Andrew Myers Date: Mon Jan 22 12:09:28 2018 -0800 update sphinx instructions. Docs/Readme.sphinx commit 7292d5db082fb9cd1509ee7028a633d42113fe23 Author: Ann Almgren Date: Mon Jan 22 12:07:48 2018 -0800 Update highlighting Docs/sphinx/source/AmrCore.rst commit 431c7bee83ec4035b27fc194374d19e7c6e37c68 Author: Ann Almgren Date: Mon Jan 22 12:05:11 2018 -0800 Highlight path names Docs/sphinx/source/AmrCore.rst commit f3f5c417df84dc1293e7864d515c6a31c56a6fba Merge: 9c053344e 3402c4c4c Author: Ann Almgren Date: Mon Jan 22 12:01:18 2018 -0800 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit 3402c4c4c127ff6e3ae03d8032c5bd01663c4514 Author: Andrew Myers Date: Mon Jan 22 11:56:27 2018 -0800 fix c++ syntax highlighting for this snippet. Docs/sphinx/source/Particle.rst commit 9c053344edbc6f2e3825eded303e3d9655114560 Merge: be53d6b19 953fd4360 Author: Ann Almgren Date: Mon Jan 22 11:50:53 2018 -0800 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit be53d6b199bee6d788fb597703b017372302650b Author: Ann Almgren Date: Mon Jan 22 11:44:01 2018 -0800 1) updated BuildingAMReX.rst 2) Added notes for how to update AMReX documentation in Readme.sphinx Docs/Readme.sphinx Docs/sphinx/source/BuildingAMReX.rst commit 953fd4360f70fc9f03738c55ce8b5d82f66ee3da Author: Andrew Myers Date: Mon Jan 22 11:39:07 2018 -0800 minor docs typo fix Docs/sphinx/source/Particle.rst commit dc77f1f55578454db00fd10fd418b047ce62620e Merge: ed48539bc f5471062e Author: Ann Almgren Date: Mon Jan 22 11:26:17 2018 -0800 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit f5471062e7a98a0525f0b95b0ae7b35aaec5fe61 Author: Andrew Myers Date: Mon Jan 22 11:21:47 2018 -0800 remove reference to non-existent section. Docs/sphinx/source/EB.rst commit d6cfc45486f4c4bcc0b29ef6d726f5a49494cb18 Merge: aaf35f97e c3b727505 Author: Andrew Myers Date: Mon Jan 22 11:16:28 2018 -0800 Merge pull request #199 from JBlaschke/development Fix figure in EB section commit c3b7275054f0bd53dc87ca7d14ec640c66ee2330 Merge: 86ac72df8 aaf35f97e Author: Johannes Blaschke Date: Mon Jan 22 11:10:09 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 86ac72df88af63981c80a4545ceee39d458ecac4 Author: Johannes Blaschke Date: Mon Jan 22 11:09:30 2018 -0800 fix .pdf->.png for figure Docs/sphinx/source/EB.rst Docs/sphinx/source/EB/areas_and_volumes.png Docs/sphinx/source/EB/eb_fluxes.png commit aaf35f97e2f6c5e542230ad02552b5510ab2cd10 Author: Weiqun Zhang Date: Mon Jan 22 10:37:40 2018 -0800 comparison operators for Box Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H commit ed48539bcf16e829590e5853eb1057cf79b5b858 Author: Ann Almgren Date: Mon Jan 22 10:33:24 2018 -0800 Update several rst files Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/GettingStarted.rst commit 93704c83f077818047fa039d3481f5049139fe0d Merge: 7b1a7ef07 c65b2f4e2 Author: asalmgren Date: Mon Jan 22 08:00:36 2018 -0800 Merge pull request #198 from JBlaschke/development Update Docs commit c65b2f4e2c829f95a05cc34dcc4b93ba349ac474 Merge: c184500f1 7b1a7ef07 Author: Johannes Blaschke Date: Sun Jan 21 22:52:45 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit c184500f1cd78f62b45d8d91761318fc3796b60c Author: Johannes Blaschke Date: Sun Jan 21 22:51:57 2018 -0800 fix label issue Docs/sphinx/source/Basics.rst commit aeb96cd15fd4c3a14d99ac1412ee9e2bb000f8fd Author: Johannes Blaschke Date: Sun Jan 21 22:47:39 2018 -0800 clean up some rst errors Docs/sphinx/source/Basics.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/CVODE.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/intro.rst commit 17dc1485ebe1513f89673ac8e9640cbddefbb701 Author: Johannes Blaschke Date: Sun Jan 21 22:32:15 2018 -0800 Finished formatting CVODE section Docs/sphinx/source/CVODE.rst Docs/sphinx/source/Chapter13.rst Docs/sphinx/source/index.rst commit 586c244a825b3863c89dd688c197b08d16167ab4 Author: Johannes Blaschke Date: Sun Jan 21 22:09:22 2018 -0800 Finished converting Profiling section Docs/sphinx/source/Profiling.rst commit dd25d511b6a0f88c5f57b4e4a31d012c84fb806a Author: Johannes Blaschke Date: Sun Jan 21 21:37:16 2018 -0800 Begin converting section on profiling Docs/sphinx/source/Chapter12.rst Docs/sphinx/source/Profiling.rst Docs/sphinx/source/Profiling/figs/commtopo.png Docs/sphinx/source/Profiling/figs/mpi.png Docs/sphinx/source/Profiling/figs/msgsizes.png Docs/sphinx/source/Profiling/figs/papi.png Docs/sphinx/source/Profiling/figs/summary.png Docs/sphinx/source/Profiling/figs/timings.png commit adb04523ae488747d0d71414352e278b29e788fb Author: Johannes Blaschke Date: Sun Jan 21 21:31:23 2018 -0800 finished reformatting visualization section Docs/sphinx/source/Chapter11.rst Docs/sphinx/source/Visualization.rst Docs/sphinx/source/Visualization/Amrvis_2d.png Docs/sphinx/source/Visualization/Amrvis_3d.png Docs/sphinx/source/Visualization/ParaView.png.REMOVED.git-id Docs/sphinx/source/Visualization/ParaView_particles.png.REMOVED.git-id Docs/sphinx/source/Visualization/VisIt_2D.png Docs/sphinx/source/Visualization/VisIt_3D.png Docs/sphinx/source/index.rst commit 06e19d936b32f7fe062d2112175ac1c5c9d688c7 Author: Johannes Blaschke Date: Sun Jan 21 20:05:29 2018 -0800 Finished converting EB chapter Docs/sphinx/source/Chapter10.rst Docs/sphinx/source/Chapter11.rst Docs/sphinx/source/EB.rst Docs/sphinx/source/EB/EB_example.eps Docs/sphinx/source/EB/EB_example.fig Docs/sphinx/source/EB/EB_example.fig.bak Docs/sphinx/source/EB/EB_example.pdf Docs/sphinx/source/EB/EB_example.png 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Docs/sphinx/source/Fortran.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/index.rst commit 03a9a115c0cbc4c607b263061549800255ecd9c5 Author: Johannes Blaschke Date: Sat Jan 20 14:04:28 2018 -0800 Add particle figures to docs Docs/sphinx/source/Particle/neighbor_list.pdf Docs/sphinx/source/Particle/neighbor_list.png Docs/sphinx/source/Particle/neighbor_list.tex Docs/sphinx/source/Particle/neighbor_particles.pdf Docs/sphinx/source/Particle/neighbor_particles.png Docs/sphinx/source/Particle/neighbor_particles.tex Docs/sphinx/source/Particle/particle_arrays.pdf Docs/sphinx/source/Particle/particle_arrays.png Docs/sphinx/source/Particle/particle_arrays.tex commit 338e6be3c8f86a4c3d4cdffbe181252f2993b26c Merge: fd6a402cc c4873c7dc Author: Johannes Blaschke Date: Sat Jan 20 14:00:36 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit fd6a402cc90c41bb33c321c17787272da719009d Author: Johannes Blaschke Date: Sat Jan 20 13:59:47 2018 -0800 Finished fromatting particles section Docs/sphinx/source/Amr.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/Particles.rst Docs/sphinx/source/conf.py commit c4873c7dc336f5d85e7bc9812a0e3df0258d656f Author: Weiqun Zhang Date: Fri Jan 19 16:36:52 2018 -0800 less verbose Src/Amr/AMReX_Amr.cpp commit 6e84e5cf7c88519ce39ada659ce257ee8b4e25cd Author: Weiqun Zhang Date: Fri Jan 19 16:33:31 2018 -0800 MLMG: clean up M-Solve because it has been replaced by nsolve Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 4738a00352c1cc001ac19e8382cd15cbd34ed2f6 Author: kngott Date: Fri Jan 19 15:57:16 2018 -0800 Fix for SparseIO file number calculations. Src/Base/AMReX_VisMF.cpp commit 5c1b898f4cd139103bb328318b96b4354c4aa681 Author: Weiqun Zhang Date: Fri Jan 19 13:30:39 2018 -0800 MLMG: use SFC in N-Solve Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 4b4840b01397a904bcdd9c2f5438d60897b85c22 Author: Weiqun Zhang Date: Fri Jan 19 13:15:29 2018 -0800 MLMG: N-Solve Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 309bdcaf938df5f67dfb91b6c4554cda523b0256 Author: Ann Almgren Date: Fri Jan 19 12:59:36 2018 -0800 Fix to formatting Docs/sphinx/source/GettingStarted.rst commit 069a4ae794db621c3f897e903b6c2d411b36b1e3 Merge: 8cc17ae6c 2fd6ed138 Author: dtgraves Date: Fri Jan 19 09:09:45 2018 -0800 Merge pull request #195 from AMReX-Codes/dtg_branch bug fix push commit 2fd6ed1383f447a290ab1dd224d41bcce6c3993f Author: dtgraves Date: Fri Jan 19 09:08:39 2018 -0800 fixed issue with regression test. The ghost routine was being called where there were no ghost cells. Src/EB/AMReX_EBTower.cpp commit 8cc17ae6ce3938a66c6597dda82edcb7c2ec599b Merge: 18992267d 72a627886 Author: WeiqunZhang Date: Fri Jan 19 08:43:40 2018 -0800 Merge pull request #168 from bcfriesen/IOBenchmark_OpenMP IOBenchmark: make only master thread flush and close file in thread-shared IO commit c500710168c0c25d8ca9afaf69789ece8c516143 Author: Johannes Blaschke Date: Fri Jan 19 00:21:07 2018 -0800 Fix some typos Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Basics.rst commit 0491a64c30a00124cda96a65055a13063b4de415 Author: Johannes Blaschke Date: Fri Jan 19 00:13:36 2018 -0800 reformatted Amr Source Code section Docs/sphinx/source/AmrCore/figs/Adv1.pdf Docs/sphinx/source/AmrCore/figs/Adv1.png Docs/sphinx/source/AmrCore/figs/Adv2.pdf Docs/sphinx/source/AmrCore/figs/Adv2.png Docs/sphinx/source/AmrCore/figs/Adv3.pdf Docs/sphinx/source/AmrCore/figs/Adv3.png Docs/sphinx/source/AmrCore/figs/Adv4.pdf Docs/sphinx/source/AmrCore/figs/Adv4.png Docs/sphinx/source/AmrCore/figs/Adv5.pdf Docs/sphinx/source/AmrCore/figs/Adv5.png Docs/sphinx/source/AmrCore/figs/flowchart.odg Docs/sphinx/source/AmrCore/figs/flowchart.pdf Docs/sphinx/source/AmrCore/figs/flowchart.png Docs/sphinx/source/AmrCore/figs/subcycling.pdf Docs/sphinx/source/AmrCore/figs/subcycling.png Docs/sphinx/source/AmrCore/figs/subcycling.tex Docs/sphinx/source/AmrLevel.rst Docs/sphinx/source/AmrLevel/figs/flowchart.odg Docs/sphinx/source/AmrLevel/figs/flowchart.pdf Docs/sphinx/source/AmrLevel/figs/flowchart.png Docs/sphinx/source/Chapter7.rst Docs/sphinx/source/Chapter8.rst commit 18992267d33d06cd05e6a932afdc612a17d8b9f4 Merge: ce91cce95 2d5c1fc11 Author: asalmgren Date: Thu Jan 18 19:32:26 2018 -0800 Merge pull request #193 from JBlaschke/development Development commit 2d5c1fc11148a410ddf3b0065ffc76f2231b5b98 Merge: 35aca3c6e ce91cce95 Author: Johannes Blaschke Date: Thu Jan 18 18:10:57 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 35aca3c6e80cf92c7775dafcec0b7f132a970bd2 Author: Johannes Blaschke Date: Thu Jan 18 18:05:37 2018 -0800 finished converting AmrCore Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Chapter6.rst commit ce91cce95175b59176c28b3f8815d4afb5f2b5f6 Author: Weiqun Zhang Date: Thu Jan 18 14:59:27 2018 -0800 msolve: a different approach to make new BoxArray Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 12cab9e90723184dd11670d3d6c6a227ac142235 Author: dtgraves Date: Thu Jan 18 14:48:38 2018 -0800 took print statements out of CNS.cpp Tutorials/EB/CNS/Source/CNS.cpp commit ff0f63f0c0d739ae585c5eaf7dc88b558eebc376 Merge: 509e51bfd be79f1526 Author: dtgraves Date: Thu Jan 18 13:48:02 2018 -0800 Merge pull request #192 from AMReX-Codes/dtg_branch bug fixes to the bug fixes to the ... commit be79f1526a0dc3f7fa60cc96a6869f41c00510d4 Author: dtgraves Date: Thu Jan 18 13:46:05 2018 -0800 more bug fixes for periodic stuff. now the corner cells seem to be correct Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Source/CNS.cpp commit 509e51bfd7f85d6890dc25d03c5d5eacb5426d67 Merge: 5a7d6217e abc8a75bd Author: Andy Nonaka Date: Thu Jan 18 13:31:30 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5a7d6217e56725072fe42fd09d48b60863d67621 Author: Andy Nonaka Date: Thu Jan 18 13:31:20 2018 -0800 comments only Tutorials/Basic/HeatEquation_EX3_C/advance.cpp commit abc8a75bde7506ea319f442e618427d526793d4d Merge: 27f8c1bc8 baf2125a8 Author: dtgraves Date: Thu Jan 18 11:48:14 2018 -0800 Merge pull request #191 from AMReX-Codes/dtg_branch bug fixes to periodic EBTower commit baf2125a87a5fa22beec89031cf819842d4d0090 Author: dtgraves Date: Thu Jan 18 11:46:14 2018 -0800 bug fixes for periodic stuff. seems to do the right thing for Ann's case now. Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 9c1249192644233c8f6add69ec267ea1576d14fb Author: Johannes Blaschke Date: Thu Jan 18 11:18:51 2018 -0800 finished formatting Boundary.rst Docs/sphinx/source/AmrLevel.rst Docs/sphinx/source/Basics/amrgrids.pdf Docs/sphinx/source/Basics/amrgrids.png Docs/sphinx/source/Basics/cc_growbox.pdf Docs/sphinx/source/Basics/cc_growbox.png Docs/sphinx/source/Basics/cc_tilebox.pdf Docs/sphinx/source/Basics/cc_tilebox.png Docs/sphinx/source/Basics/cc_validbox.pdf Docs/sphinx/source/Basics/cc_validbox.png Docs/sphinx/source/Basics/ec_growbox.pdf Docs/sphinx/source/Basics/ec_growbox.png Docs/sphinx/source/Basics/ec_tilebox.pdf Docs/sphinx/source/Basics/ec_tilebox.png Docs/sphinx/source/Basics/ec_validbox.pdf Docs/sphinx/source/Basics/ec_validbox.png Docs/sphinx/source/Basics/figs/flowchart.odg Docs/sphinx/source/Basics/figs/flowchart.pdf Docs/sphinx/source/Basics/figs/flowchart.png Docs/sphinx/source/Basics/indextypes.pdf Docs/sphinx/source/Basics/indextypes.png Docs/sphinx/source/Boundary.rst Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/Chapter7.rst Docs/sphinx/source/Chapter8.rst Docs/sphinx/source/Particle.rst commit 38558a4449b1638c4f15397a131835fd94730fa3 Author: Johannes Blaschke Date: Thu Jan 18 11:03:21 2018 -0800 finished Basics.rst, added relevant links Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Boundary.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Visualization.rst Docs/sphinx/source/index.rst commit 27f8c1bc82af91f24d43b943be6d532eee974e2e Author: Weiqun Zhang Date: Thu Jan 18 10:50:22 2018 -0800 To placate gcc-7 Src/Base/AMReX_ParallelReduce.H Src/Base/AMReX_Vector.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 67786385fd48690f5b571ff8b2afa9ae904199dd Author: Max Katz Date: Thu Jan 18 13:27:20 2018 -0500 Update to CUDA 9.0 by default Tools/GNUMake/Make.defs commit 54f6ed221f7c680e54275433f9463318a5fd5d90 Author: Weiqun Zhang Date: Thu Jan 18 10:00:12 2018 -0800 msolve: add parameter for grid size Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 692c48902cc640ef82a0070cd78c1d938a1a44e6 Author: Weiqun Zhang Date: Thu Jan 18 09:36:33 2018 -0800 msolve: minor optimization Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 4af1a7363dec22bb33260907d1f83f432c920a9c Merge: 1e19e4152 da215a32f Author: dtgraves Date: Wed Jan 17 16:06:16 2018 -0800 Merge pull request #189 from AMReX-Codes/dtg_branch merging support for periodic EBTower into dev branch commit da215a32f70987459c0a2b3149e77d8ef25b1206 Author: dtgraves Date: Wed Jan 17 16:04:45 2018 -0800 added support for periodic to EBTower. For the tests that I ran, it does the right thing. I offer no guarantees for implicit functions which are not periodic. Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Exec/Pulse/GNUmakefile Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 1e19e415224fba014d712b2d7fe2c40329cf3213 Author: Weiqun Zhang Date: Wed Jan 17 15:00:30 2018 -0800 remove mlcg Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 54e0873637bed67e9435db5b4fe3aca8ad85690e Author: Weiqun Zhang Date: Wed Jan 17 10:42:39 2018 -0800 use MLALaplacian for M-Solve Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 2da11d45606d01400a445c4884bef00fd5383fe4 Author: Weiqun Zhang Date: Wed Jan 17 10:41:47 2018 -0800 mlmg: add MLALaplacian Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLALap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_F.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit 682aca8d9320d5df54dd7c38112d2cc35b2f313c Author: Weiqun Zhang Date: Wed Jan 17 09:35:31 2018 -0800 M-Solve: support for ref ratio of 4 Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 754f023d34ba3ff15ca37aa077a1fef4ec71ec2c Author: Johannes Blaschke Date: Tue Jan 16 23:20:53 2018 -0800 finished convering section on MFIter and Tiling Docs/sphinx/source/Basics.rst commit 857033dc7744edb988e2a19c1a33e8063167c4de Author: Johannes Blaschke Date: Tue Jan 16 18:09:02 2018 -0800 finished FABs documentation Docs/sphinx/source/Basics.rst commit 91ed36efa41cea683d694382eb19720537a69c01 Author: Max Katz Date: Tue Jan 16 20:40:19 2018 -0500 Add Summit Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.olcf commit e163bb342adab9a464d9c52cdb5584a8d6035f15 Author: Weiqun Zhang Date: Tue Jan 16 16:59:17 2018 -0800 msolve: clean up Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 5ae9f1b3a3411d207761d7c06858921da71f85f2 Author: Doreen Fan Date: Tue Jan 16 16:27:08 2018 -0800 Added implicit heat equation solver in Tutorials/Basic/HeatEquation_EX3_C/ Tutorials/Basic/HeatEquation_EX3_C/GNUmakefile Tutorials/Basic/HeatEquation_EX3_C/Make.package Tutorials/Basic/HeatEquation_EX3_C/advance.cpp Tutorials/Basic/HeatEquation_EX3_C/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX3_C/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX3_C/inputs_2d Tutorials/Basic/HeatEquation_EX3_C/inputs_3d Tutorials/Basic/HeatEquation_EX3_C/main.cpp Tutorials/Basic/HeatEquation_EX3_C/myfunc.H Tutorials/Basic/HeatEquation_EX3_C/myfunc_F.H commit beca7fdff05932235bbb7f9448c8e2c4cac14e00 Author: Weiqun Zhang Date: Tue Jan 16 16:00:57 2018 -0800 msolve works for at least one example Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 6646c823ddcf55415152a063bd25a5e76ea474ba Author: Johannes Blaschke Date: Tue Jan 16 16:12:08 2018 -0800 work on basics Docs/sphinx/source/Basics.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/GettingStarted.rst commit aaa63601c8a38aae93e72802c319cde30cb29fb4 Author: Weiqun Zhang Date: Tue Jan 16 13:37:40 2018 -0800 firs pass of msolve Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit bce55e63d6c06d0263efc6631ea09b2a48619d21 Author: Weiqun Zhang Date: Tue Jan 16 09:12:51 2018 -0800 make this regression test much smaller Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-poisson-com commit 15283e1301836903e16f336bf65040e2d68f2a3b Merge: 7043a286f 5b6586c92 Author: Johannes Blaschke Date: Mon Jan 15 10:53:11 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7043a286fb1d65ebf72424b429bb5bb66d53cc9f Author: Johannes Blaschke Date: Mon Jan 15 10:52:46 2018 -0800 completed the Building AMReX section Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter3.rst commit 82984b07953403124e20880ebae31db7209231a3 Author: Johannes Blaschke Date: Sun Jan 14 12:54:56 2018 -0800 finished GettingStarted section Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Visualization.rst commit d8f7a43158b5c48eddf6dfdabd0056a6a31f475f Author: Johannes Blaschke Date: Sun Jan 14 12:45:00 2018 -0800 almost done with GettingStarted Docs/sphinx/source/Basics.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/GettingStarted.rst commit 4937591baba2f347e0f020eb30b85c2e9ff3c340 Author: Johannes Blaschke Date: Sun Jan 14 12:21:15 2018 -0800 find a good comprimize solution for typesetting small fraction Docs/sphinx/source/GettingStarted.rst commit 1ae4b8951ab2e592170221d5345b76a7bf7a0e65 Author: Johannes Blaschke Date: Sun Jan 14 11:53:39 2018 -0800 working on `GettingStarted` section of the sphinx docs. Note: changing LaTeX references to sphinx rst references for cross-referencing different sections Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter2.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/GettingStarted.rst commit 93f3939bc7ae85771fede43634d3b6fc9a03ee64 Author: Johannes Blaschke Date: Sun Jan 14 11:12:32 2018 -0800 added preamble to doc index Docs/sphinx/source/index.rst commit 5b6586c92c11360608aad835260a14217694af2c Author: Ann Almgren Date: Sun Jan 14 09:52:55 2018 -0800 Replace FillBoundary by EnforcePeriodicity since the interior ghost cells are filled by the loop above Src/EB/AMReX_EBTower.cpp commit a28ebf5a4f0cb4f1ad62b71668212a53ad8cd194 Author: Ann Almgren Date: Sat Jan 13 18:17:58 2018 -0800 No longer have a FillBoundary call for MultiCutFabs Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit de67b5c3e6520f9867ccd5bdac2f740d05b6f24a Author: Johannes Blaschke Date: Sat Jan 13 17:27:07 2018 -0800 ingore sphinx build dir .gitignore commit 19925b583ea9113d455d2227494564d72a4d4f8c Author: Johannes Blaschke Date: Sat Jan 13 17:25:45 2018 -0800 LaTeX Introduction -> rst Docs/sphinx/source/Introduction.rst commit 4cdf808fbf96d86755ea71cb1dc05821f5ac9529 Merge: 9eeb1d676 d84491612 Author: Johannes Blaschke Date: Sat Jan 13 16:49:44 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9eeb1d6763e7ec105c22d452e6cda4ffb8977c29 Author: Johannes Blaschke Date: Sat Jan 13 16:49:10 2018 -0800 tweak: avoid picking up on temporary files generated when making docs .gitignore commit d8449161266d64ec2186a6a5c2e6cb7988bb4a98 Author: Ann Almgren Date: Sat Jan 13 15:23:46 2018 -0800 Add FillBoundary call when filling flag and other geometric info so that we can correctly fill periodic ghost cells. (Had to add interface for MultiCutFab) Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit b6f792be861030a06b48c93959104c7316eafec8 Author: Ann Almgren Date: Sat Jan 13 10:14:27 2018 -0800 Modify parallel copy in the EBTower stuff to include the periodicity flag so it will fill periodic ghost cells correctly. Had to modify an interface for MultiCutFabs. Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit d1e0b99872133ce46df52de32c963d42a0325d87 Merge: 3fc53c191 da997167f Author: WeiqunZhang Date: Fri Jan 12 12:47:40 2018 -0800 Merge pull request #188 from JBlaschke/development Documentation commit 3fc53c191218daead6fb573420f14cf85d872723 Merge: d65705cec cebb5ee84 Author: Marc Day Date: Fri Jan 12 12:44:27 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d65705cecf93a25dc0d0708e2979180e47e0b8d2 Author: Marc Day Date: Fri Jan 12 12:44:19 2018 -0800 Fix typ Docs/AMReXUsersGuide/Particle/Particle.tex commit da997167fc10afb7bf37680fe29decdaf086448a Merge: cebb5ee84 c8271c7b8 Author: Johannes Blaschke Date: Fri Jan 12 12:39:31 2018 -0800 Merge branch 'jpb/ug/fix-typos' into development commit cebb5ee8457037731ba2273432e0d0b3981aa7de Author: jbb Date: Fri Jan 12 12:24:07 2018 -0800 added more infomration Tools/Postprocessing/F_Src/faverplot.f90 commit 1c3c3c244a70dc8694a2d832704fb3d47dcc3ea5 Author: jbb Date: Fri Jan 12 11:59:22 2018 -0800 cleanup Tools/Postprocessing/F_Src/faverplot.f90 commit 92a5d491fd1682b86969f20e645409e0178fa396 Author: jbb Date: Fri Jan 12 11:54:59 2018 -0800 added build to makefile Tools/Postprocessing/F_Src/GNUmakefile commit 2b05b75d0a442330d38c89fd5972571c83b0b50c Merge: 99034427f 85f83e705 Author: jbb Date: Fri Jan 12 11:52:23 2018 -0800 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit 99034427fc6b6452a7727a2813c17ee4d2e724b8 Author: jbb Date: Fri Jan 12 11:51:42 2018 -0800 added code to average a collection of plotfiles Tools/Postprocessing/F_Src/faverplot.f90 commit 85f83e70568e97ec4e712f5820decf5b98b43853 Author: Weiqun Zhang Date: Fri Jan 12 09:28:07 2018 -0800 add some profilers Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 17746a7e06901700c643af8c76e59da0e434757b Author: Weiqun Zhang Date: Fri Jan 12 09:14:51 2018 -0800 nodal projection in 2d rz: turn on correction by default Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 3b0266274538e32866536f5e5cc2f9c089264237 Author: Weiqun Zhang Date: Thu Jan 11 17:34:06 2018 -0800 nodal projection: fix rz Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit fe08cb9a41ce71447e940a77b07ef989787d8a65 Author: Andrew Myers Date: Thu Jan 11 16:42:04 2018 -0800 Fix bug affecting the particle container when tiling is off but non-zero tile size is set. Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit 93e9719e9238b3a350c85368077654824ddb2843 Author: Weiqun Zhang Date: Thu Jan 11 13:42:02 2018 -0800 nodal projection: some support for rz correction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 94681e4166f21bdb7a064d47cd0ba8841fafbfaa Author: Weiqun Zhang Date: Thu Jan 11 12:56:11 2018 -0800 remove some const so that MPI 2 is happy Src/Base/AMReX_ParallelReduce.H commit 22d7b68de64c2d8168273854c11d889f616fe218 Author: Weiqun Zhang Date: Thu Jan 11 10:19:54 2018 -0800 fix a bug in my last commit Src/F_Interfaces/Base/AMReX_FPhysBC.cpp commit de00a420dfa1e399e23ac3c29afb741220bf96db Author: Weiqun Zhang Date: Thu Jan 11 09:02:30 2018 -0800 Fortran module AMReX_fillpatch_module takes a user provided callback function for filling physical boundary conditions. That function used to use 0-based index for component (i.e., the last index). For consistence with 1-based index for component in other Fortran modules, this has been changed to 1-based index for component. CHANGES Src/F_Interfaces/Base/AMReX_FPhysBC.cpp commit f02d850a0ffac7e3eab3e9112d568d89ea701771 Merge: 56a073bb5 bbd507e5e Author: Weiqun Zhang Date: Wed Jan 10 17:37:56 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 56a073bb5a7beaee46029fd0b2dfc2a7934ba9d6 Author: Weiqun Zhang Date: Wed Jan 10 17:15:26 2018 -0800 nodal projection: no neumann bc doubling for fine sync residual because how SyncRegister works Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit bbd507e5ede1656bc2c85d50ac7c2d98b291986e Merge: 2712df36f 902840d23 Author: vince Date: Wed Jan 10 16:03:05 2018 -0800 Merge branch 'profvis' into development commit 2712df36f9f2e870f5a965f762b09705a3d8c544 Merge: 237debfff 75c1004f9 Author: vince Date: Wed Jan 10 16:02:57 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 75c1004f915e74104486de3534c54b68033c77fd Author: Weiqun Zhang Date: Wed Jan 10 14:51:04 2018 -0800 nodal projection: add support for cc rhs Src/Base/AMReX_ArrayLim.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 902840d235f1f5e12d3ba1a29452698beb45e3be Author: kngott Date: Wed Jan 10 12:44:12 2018 -0800 Addition of sends plotfile dispatch feature. Also includes filtering if using serial amrvis. Src/Extern/amrdata/AMReX_DataServices.cpp commit c21ce86c1fbcd80da04faad6ebdb16b1fe44285f Merge: 8d71bff61 237debfff Author: kngott Date: Wed Jan 10 12:40:59 2018 -0800 Merge branch 'profvis' of https://github.com/AMReX-Codes/amrex into profvis commit 8d71bff614f900dd78f1906b0a5881610a486097 Author: kngott Date: Wed Jan 10 12:40:23 2018 -0800 Addition of a BroadcastBool class and appropriate test code. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp commit 237debfff6289fcd1f9239e349bfce6a39473b34 Merge: dcd62d278 02da3a220 Author: vince Date: Wed Jan 10 11:57:46 2018 -0800 Merge branch 'development' into profvis commit dcd62d278fff1e04fa3f80aa015c29f65791c37e Author: vince Date: Wed Jan 10 11:56:55 2018 -0800 add time range file for timelines. Src/Extern/amrdata/AMReX_DataServices.cpp commit 02da3a2200985913f73674003c4bbf5d86fd2d5e Author: Weiqun Zhang Date: Tue Jan 9 15:40:18 2018 -0800 fix a bug in 3d nodal projection Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit dc72f408acd68255d4d6abc46894e592dc177132 Merge: 68f69effc 815093d2c Author: Andrew Myers Date: Tue Jan 9 12:45:37 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 68f69effcb6e6c0d8cefc830f8cd934286955c85 Author: Andrew Myers Date: Tue Jan 9 12:45:18 2018 -0800 bugfix for neighbor particle container when tiling is turned off. Src/Particle/AMReX_NeighborParticlesI.H commit 815093d2c3d945135ac901eaae25a7d9efea36ad Author: Weiqun Zhang Date: Tue Jan 9 10:03:18 2018 -0800 fix fmg for nodal solver Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 3a0278ce0e4b2b5230f2a8a6b79a6e5adbdeeaa2 Author: Weiqun Zhang Date: Tue Jan 9 09:43:54 2018 -0800 nodal projection: finish inflow Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e4d9d7783afba2ed742f1f030e4e44d7372c5400 Author: Weiqun Zhang Date: Mon Jan 8 15:50:57 2018 -0800 Fortran: add function for testing boxarray box intersection Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 commit 38dfbd0a3ab25007dcfee805b19cd3dd3f92c086 Author: Weiqun Zhang Date: Mon Jan 8 11:10:53 2018 -0800 minor optimization Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 12c2c575cb8609a639f9ceeb03bf06c3f1c27f5b Author: Weiqun Zhang Date: Mon Jan 8 11:06:32 2018 -0800 nodal projection: fix sync residual mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 248b313f6afb54eea8ba3a4cff85542548179f42 Author: Weiqun Zhang Date: Mon Jan 8 10:17:30 2018 -0800 nodal projection: when fine boxes touch the symmetry axis Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e1027f7c73eaee860d3d92e78407307674ea2cb2 Author: Weiqun Zhang Date: Mon Jan 8 09:14:55 2018 -0800 no need to apply metric term to coarse mg levels because they get coefficients from average down Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 5b0978c49ab630551d6ed883e975c58ec6bfa023 Author: Weiqun Zhang Date: Sat Jan 6 13:28:10 2018 -0800 fix crse/fine residual at Neumann boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ad14218ca90719843926a4f982123b0b65fa15f3 Author: Weiqun Zhang Date: Fri Jan 5 17:46:44 2018 -0800 when fine boxes touch Neumann boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 0d3c61785ac2ef0fad9fb7d22e37c4b3b208df10 Author: Weiqun Zhang Date: Fri Jan 5 10:46:15 2018 -0800 nodal projection: be explicit on the number of components when calling FillBoundary on velocity because IAMR may pass a MulitFab with more components Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit eec6f91b9f1f99d896d2157f7327ddc792a7220b Merge: d8efb00a1 f0879f59a Author: vince Date: Thu Jan 4 14:34:34 2018 -0800 merge fix Merge branch 'development' into profvis commit f0879f59af2838114a31a57f1d0c9b485c0b19d1 Author: Weiqun Zhang Date: Wed Jan 3 13:40:30 2018 -0800 nodal projection: start support for inflow Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit e9e8cb3bdad9cf3debffbbaa0359a9ff3a7c0ffa Author: Weiqun Zhang Date: Wed Jan 3 12:47:12 2018 -0800 nodal projection: clean up Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 596820b5d5016f67ddaa257b335de07f9594fdfb Author: Weiqun Zhang Date: Wed Jan 3 12:44:15 2018 -0800 nodal projection: sync solutions after each iteration Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit c5689483572128598d7920942b6a2560d3422443 Author: Weiqun Zhang Date: Wed Jan 3 10:45:59 2018 -0800 fix mask in fine sync residual Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 151ee89ac63f5f43cd8fe15e6e4c084ff76bb588 Author: Weiqun Zhang Date: Wed Jan 3 09:25:24 2018 -0800 3d nodal projection: fix a bug in crse/fine residual Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit e7fcd9b7d8ab65264567192dbc4a715829b0a087 Author: Weiqun Zhang Date: Tue Jan 2 14:52:02 2018 -0800 fix cmake Src/LinearSolvers/CMakeLists.txt commit a46ea95241de25c2ee196839c42b280a7873dc83 Author: Weiqun Zhang Date: Tue Jan 2 13:29:13 2018 -0800 nodal projection: fix tiling bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e554c64f26e20c7e789971c2db5f9b873ecf118e Merge: fc2a247a6 f295bc8fa Author: Weiqun Zhang Date: Tue Jan 2 09:59:06 2018 -0800 Merge branch 'development' into weiqun/mlmg commit fc2a247a6ec966b62f5a601401a605e841e7d89a Author: Weiqun Zhang Date: Tue Jan 2 09:44:07 2018 -0800 nodal projection: fix solvability for bottom solver Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H commit f295bc8fa660d2851b8ee212df3bd9e34eb30fc8 Author: Weiqun Zhang Date: Tue Jan 2 08:30:37 2018 -0800 update CHANGES CHANGES commit dad37957e87ea8e53f432b45879a0fcac185d9df Author: Weiqun Zhang Date: Sat Dec 30 21:11:59 2017 -0800 3d nodal projection: bug fixes Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 6976f0d400946cca2c6c69e93fe9fabbc211fdd9 Author: Weiqun Zhang Date: Sat Dec 30 13:29:39 2017 -0800 3d nodal projection: bug fix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 89db38650d317105d9755c8ae45700a7b56ee7b7 Author: Weiqun Zhang Date: Sat Dec 30 13:13:38 2017 -0800 3d nodal projection: bug fixes Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 304df1dfd8841027c92a0e47b3c5c72a8cb6c735 Author: Weiqun Zhang Date: Sat Dec 30 12:32:07 2017 -0800 3d nodal projection: bug fix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 3ef0c9e9500bac1aca9df8ebe8cd0d0845f74d00 Author: Weiqun Zhang Date: Sat Dec 30 12:26:44 2017 -0800 3d nodal projection: bug fix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit b8ab950671bb6d97c1c5f2996adaaa5b9d8263ef Author: Weiqun Zhang Date: Sat Dec 30 11:49:55 2017 -0800 3d nodal projection: bug fix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 6ad0d39e84a11df0906ac65c06fbaca24ecfd2d6 Author: Weiqun Zhang Date: Sat Dec 30 11:14:32 2017 -0800 3d nodal projection: bug fixes Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 8d4339e0d86e20d51167e2d9d0826b7fccc4fd34 Author: Weiqun Zhang Date: Fri Dec 29 21:38:27 2017 -0800 3d nodal projection: first pass Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 48a947145ee6da3ad248ffbf8700082b44e9cc24 Author: Weiqun Zhang Date: Fri Dec 29 18:01:58 2017 -0800 3d nodal projection: fine contribution of residual Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 3e0f0bc186df5efc5a556e49b7483d3dc90fa160 Author: Weiqun Zhang Date: Fri Dec 29 17:29:07 2017 -0800 nodal projection: refactor crse/fine residual Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 05905c0f3dca4ed2f7874da1fb147f49a32c4144 Author: Weiqun Zhang Date: Fri Dec 29 15:44:45 2017 -0800 3d nodal projection: crse/fine divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit ec293c45f75d3102c38d6e9a281458215d5bb920 Author: Weiqun Zhang Date: Fri Dec 29 15:28:15 2017 -0800 nodal projection: refactor fine contribution of divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 01adc278398cc66a2c6c2705e2f43e3b365b6439 Author: Weiqun Zhang Date: Thu Dec 28 19:20:29 2017 -0800 3d nodal projection: fine contribution of divu WIP Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 9c7840effa975b337b71cf41463a8d885418f7c2 Author: Weiqun Zhang Date: Tue Dec 26 16:20:28 2017 -0800 3d nodal projetion: add cell-centered rhs and make new u Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 7f1b15ea277a5207e1b9233ec1c82234791bc7c7 Author: Weiqun Zhang Date: Tue Dec 26 13:21:42 2017 -0800 3d nodal projection: divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 575b961316bbc27f2a4ab4b3b41a060f6fb38149 Author: Weiqun Zhang Date: Tue Dec 26 13:07:49 2017 -0800 3d nodal projection: arithmetic average version of interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit e9ec2a2e547622063a5e1c71ca0ba1ba0979d96f Author: Weiqun Zhang Date: Tue Dec 26 11:45:29 2017 -0800 3d nodal projection: harmonic average version of interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 99cf609df32578c35887fe4006867407de85593e Author: Weiqun Zhang Date: Tue Dec 26 10:20:17 2017 -0800 3d nodal projection: restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 7a4b4d56f5f3b74c6ee0e82f5f374db020ee8e12 Author: Weiqun Zhang Date: Mon Dec 25 17:18:37 2017 -0800 nodal projectoin: minor Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 5263ee231923765cbda4ed380ed585e834734cbb Author: Weiqun Zhang Date: Mon Dec 25 17:16:15 2017 -0800 3d nodal projectoin: Gauss-Seidel smoother Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit d057608cb8e49c2ee6f3df58f422272df7bad23f Author: Weiqun Zhang Date: Mon Dec 25 16:49:53 2017 -0800 3d nodal projectoin: Jacobi smoother Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit eefc50e3336bf011a013561dbe833bda4805da2a Author: Weiqun Zhang Date: Mon Dec 25 16:22:27 2017 -0800 3d nodal projectoin: arithmetic average version of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 87e834943a182ba50aee6dc633fe080793a6ef16 Author: Weiqun Zhang Date: Mon Dec 25 11:16:19 2017 -0800 3d nodal projection: refactor harmonic average version of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 21a1157fe59b8e4b2a6c68d2c01e73ba7fe3a6a5 Author: Weiqun Zhang Date: Sun Dec 24 16:48:53 2017 -0800 nodal projection: optimization of smoother Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 10e841e4f91b21d4700d804c067284d46204c6e8 Author: Weiqun Zhang Date: Sun Dec 24 16:33:22 2017 -0800 nodal projection: optimization of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2d02b16be177dbd39a5d57ba54903114503c1043 Author: Weiqun Zhang Date: Sun Dec 24 14:22:01 2017 -0800 3d nodal projection: harmonic average version of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 610e839535d3125383914f47a2951e849ae3eb9d Author: Weiqun Zhang Date: Sun Dec 24 12:51:04 2017 -0800 3d nodal projection: bc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit c8271c7b86a28fda26583ea6d061f14876640b0f Author: Johannes Blaschke Date: Sat Dec 23 09:50:10 2017 -0800 Typo in description of ghost cells (in MultiFab). This way makes more sense now Docs/AMReXUsersGuide/Basics/Basics.tex commit fc55407de2686edb8805a8114375d89390c2eac4 Author: Weiqun Zhang Date: Fri Dec 22 21:32:30 2017 -0800 3d nodal projection: average down coefficients Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit eb97d86f5731fd1db9f19fb0be36901e4483d95e Author: Weiqun Zhang Date: Fri Dec 22 21:20:40 2017 -0800 3d nodal projection: masks Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 7d2c4922375191c4ee56a2117b568cd2409e3ee4 Author: Weiqun Zhang Date: Fri Dec 22 21:00:11 2017 -0800 3d nodal projection: linear interpolation Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit 24312396987fc2b0651bcefa021a25be3f1addee Author: Weiqun Zhang Date: Fri Dec 22 18:05:49 2017 -0800 nodal projection: add stub functions so that 1d and 3d can compile Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit ff56827d4e82355a99fbc38d8d16398ff8bde0c2 Author: Weiqun Zhang Date: Fri Dec 22 17:34:06 2017 -0800 nodal projection: organization Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H commit 7e8c436b5a4b737a36fbbed39c3e81afefd23d18 Author: Weiqun Zhang Date: Fri Dec 22 17:03:54 2017 -0800 nodal projection: clean up Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 9636dcf14be5c9bb40d2efd2934d71bf021e767e Author: Weiqun Zhang Date: Fri Dec 22 17:01:11 2017 -0800 nodal projection: cleanup Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit fbb074ed0bacdbef9a996e0cbd6674b3782dbc91 Author: Weiqun Zhang Date: Fri Dec 22 16:44:42 2017 -0800 nodal projection: add nodal mask in addition to cell mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 00881ad8389c1c417b300ff9eba35da2f26a84be Author: Weiqun Zhang Date: Fri Dec 22 16:17:07 2017 -0800 nodal projection: use parameter instead of hardwired number for dirichlet mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit c7063a996668b7de35465491c8df5ed4b9d47392 Author: Weiqun Zhang Date: Fri Dec 22 15:40:16 2017 -0800 nodal projection: clean up overlap mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 5b2e01c5426b43702478c1bda1dce3759379c154 Author: Weiqun Zhang Date: Fri Dec 22 15:36:59 2017 -0800 nodal projection: clean up weight Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit eb35e3f3a2608d5dc68f1614c87bbb9d00f3c050 Merge: 5dde12800 2751b4199 Author: Tan Nguyen Date: Fri Dec 22 13:37:52 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5dde12800102c597d44ef2911ecb2a765cdf55d2 Author: Tan Nguyen Date: Fri Dec 22 13:37:39 2017 -0800 transform recursive timesteps into iterative tasks Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/graph/AMReX_AbstractTask.H Src/Base/AMReX_FabArray.H commit b3d602d720bf254f2adb6214b2032fb17480f90b Author: Max Katz Date: Fri Dec 22 14:54:02 2017 -0500 Remove -lcudart for OpenACC Tools/GNUMake/comps/pgi.mak commit 31b5c63bc22fddceccfea977dfe2bac6b79830b9 Author: Max Katz Date: Fri Dec 22 14:45:51 2017 -0500 Add .ACC to exe name when USE_ACC=TRUE Tools/GNUMake/Make.defs commit b729a7978d9f7d575ef3990a66bd2063b5e172c5 Author: Andrew Myers Date: Fri Dec 22 10:53:50 2017 -0800 Some fixes to the dot, sum, and norm routines of BaseFab. (#184) These routines were not correctly accessing device data on the return value, and were also inadvertently having each thread zero out the stored sum. Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_nd.F90 commit 409e7a4734380890e3cd7d73cc04ac3640bcc275 Author: Weiqun Zhang Date: Thu Dec 21 16:21:36 2017 -0800 f90 nodal solver: the initial residual is now computed as composite residual Src/LinearSolvers/F_MG/ml_nd.f90 commit ab03f83dd4172ffd09525d073501e6234cfb3e1b Author: Weiqun Zhang Date: Thu Dec 21 15:55:32 2017 -0800 fix up residual mask Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2751b41992829567f4dbebb03993bc6ace474aec Merge: 69c5a4066 5a9912051 Author: dtgraves Date: Thu Dec 21 15:21:42 2017 -0800 Merge pull request #185 from AMReX-Codes/dtg_branch moving document and bug fixes to dev branch. commit 5a9912051bffdf6b0e04f82e1228f8022c2e63b0 Author: dtgraves Date: Thu Dec 21 15:20:21 2017 -0800 added section to tutorial document explaining derivation of time interpolation formulae Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit 11c41cb874f67b9c611dc76599dcd2f253ee3517 Author: dtgraves Date: Thu Dec 21 15:19:52 2017 -0800 bug fix and took out unused functions Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit bd964211a636ebac49b74d40a793a1d575d5f4f8 Author: Weiqun Zhang Date: Thu Dec 21 15:19:13 2017 -0800 fix a bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit d8efb00a174f349acd74ac1c74992c7acd5b05be Author: vince Date: Thu Dec 21 15:06:48 2017 -0800 precreate update for nyx support. Src/Amr/AMReX_Amr.cpp commit 7650a500cd6dafdbd9c7c653a6965d1b39b951b7 Merge: 9d2100e3e d7872c272 Author: vince Date: Thu Dec 21 15:05:22 2017 -0800 merge fix. commit 980ef629cb150358a5170e9dfdfe483b792ba45e Author: Weiqun Zhang Date: Thu Dec 21 13:46:41 2017 -0800 use the restricted rhs for reflux Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7a4b6519f988c465585c7a9fcb340c2918f26877 Author: Weiqun Zhang Date: Thu Dec 21 12:39:59 2017 -0800 nodal project: full weight restriction of rhs Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 69c5a4066ecdec61317c34635c12f2beb2f90f07 Author: Andrew Myers Date: Thu Dec 21 12:16:26 2017 -0800 patch fcompare to not choke on plotfiles that only have particle data. Tools/Postprocessing/F_Src/fcompare.f90 commit c9ae9f5b4cba68b76084b8046723d818a0b1ab88 Author: Andrew Myers Date: Thu Dec 21 12:15:30 2017 -0800 initialize these pointers to Null() Src/F_BaseLib/plotfile.f90 commit d3bcd85458a1d08b1b9f518b38c112a678c52c39 Author: Max Katz Date: Wed Dec 20 23:32:40 2017 -0500 Do not compile in the old filcc when using CUDA Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 Src/Base/Make.package commit 646442b86bdc766b9b1e0c39deadb990232d6549 Author: Andrew Myers Date: Wed Dec 20 17:55:50 2017 -0800 Removing the particle stuff from the GPU branch (will add again on a separate branch) (#158) Src/Particle/AMReX_CudaManagedAllocator.H Src/Particle/AMReX_Particles.H Src/Particle/Make.package Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp Tests/Particles/ManagedCUDADeposition/GNUmakefile Tests/Particles/ManagedCUDADeposition/Make.package Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/inputs Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp commit d7872c2723eb52fee85de7d292ba3453e083301e Merge: 38629f10c b03bb7969 Author: WeiqunZhang Date: Wed Dec 20 17:07:53 2017 -0800 Merge pull request #183 from AMReX-Codes/marc/allow_strict_mode Marc/allow strict mode commit 10b55525de429a19fe70b006e746d91b901320e5 Author: Weiqun Zhang Date: Wed Dec 20 16:58:05 2017 -0800 fix weight Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 77f3bc0f7e8a492bd68e74d415ce5c77cd5fa06d Author: Max Katz Date: Wed Dec 20 19:10:19 2017 -0500 Make NVML support be opt-in Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Tools/GNUMake/Make.defs commit a7c3fe92f0022a12ecbdd8434666a987089af078 Author: Weiqun Zhang Date: Wed Dec 20 15:38:46 2017 -0800 average down nodal rhs and solution Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit ba6265fe670f2f42ffe77a2e4849059cfd07f315 Author: dtgraves Date: Wed Dec 20 15:14:57 2017 -0800 finished the parts ScalarAdvection Tutorial that anyone ought to care about. I will also add an appendix explaining where the formulae come from. Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex commit 7f5cbe0c4ea05caf11f523a9be49bbd4f743eccd Author: Weiqun Zhang Date: Wed Dec 20 14:42:53 2017 -0800 fix assertion Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 996847863e8b079e135c276b9606145d08860452 Author: Weiqun Zhang Date: Wed Dec 20 14:36:56 2017 -0800 minor optimization Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b03bb796936a255f1db1a60d5ed8cfb764e4c1a2 Author: Marc Day Date: Wed Dec 20 14:23:46 2017 -0800 Minor changes to satisfy compilation under AMREX_STRICT_MODE Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.cpp commit 0b4412dae4a45c986c5a92acdffdb92c3127bec3 Author: Weiqun Zhang Date: Wed Dec 20 14:09:13 2017 -0800 average down of solution is only needed for cell-centered solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a841ab9f2b836811c4c78e29bb0ae3b3b3d3db9d Author: Weiqun Zhang Date: Wed Dec 20 14:03:19 2017 -0800 nodal interpolation of correction between amr levels Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H commit 38629f10c640b177cce6b8327bfa61ee06c24cd9 Author: Andrew Myers Date: Wed Dec 20 13:54:52 2017 -0800 allow fcompare to work with plotfiles that only have particle data (for the regression testing suite) Src/F_BaseLib/plotfile.f90 commit 9b5e524db11f4b27604fcede811d0f82b3803634 Author: Weiqun Zhang Date: Wed Dec 20 11:10:37 2017 -0800 use the correct rhs Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 20a281dc65dcc57199cd86f928444ac409b9fc98 Author: dtgraves Date: Tue Dec 19 18:29:05 2017 -0800 added a bunch to document for this tutorial Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 6759b6dae2531cb0cbb1bd6e8956f8eae83e7e45 Author: Weiqun Zhang Date: Tue Dec 19 17:27:23 2017 -0800 restriction of residual Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 53624ebdf5f438f084c86499faea64b2846a9220 Author: Weiqun Zhang Date: Tue Dec 19 12:44:21 2017 -0800 pass fine residual to reflux too Src/Base/AMReX_MultiFabUtil.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit aef7b501d2d53addfa6e8047680ab59312f1674f Author: Weiqun Zhang Date: Tue Dec 19 12:03:03 2017 -0800 make average_down work for nodal too Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit c6632bbfb5493ffb3e593e22833efc00ef2888f2 Author: Weiqun Zhang Date: Tue Dec 19 12:01:22 2017 -0800 add MultiFab::is_cell_centered function Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit b4550409be044543ccde044a1b5b53969d921566 Author: Weiqun Zhang Date: Tue Dec 19 10:25:05 2017 -0800 fine contribution of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5817701afd93ab5c94ad62b07f0e0f9c5ff79129 Author: Weiqun Zhang Date: Mon Dec 18 17:41:28 2017 -0800 WIP: fine contribution of A dot x Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8174d57b7d18b1a7ae4b72c675d97cc91e65a67a Author: Andrew Myers Date: Mon Dec 18 17:18:05 2017 -0800 pass the pld by value instead of by reference. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 474039c9769b01cf5fee43637ae5559f277c9b46 Author: Andrew Myers Date: Mon Dec 18 17:12:33 2017 -0800 allow caching of the particle location between calls to Reset() Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 19d9fac628db4821a2292e092324b5966e59273b Author: Weiqun Zhang Date: Mon Dec 18 15:24:02 2017 -0800 rework the weight Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 19f519feadaa61a96b8051b3ed7e8fbe9c38ff0b Author: Andrew Myers Date: Mon Dec 18 12:39:36 2017 -0800 fix bad merge. Src/Particle/AMReX_ParticleContainerI.H commit 7ec8d63b730dfa6177d3207b988427a4e5c4ce03 Merge: e94a9ab28 8eb0af9be Author: Andrew Myers Date: Mon Dec 18 12:36:58 2017 -0800 merging. commit e94a9ab28f0b9f11c87a74c9fe1deae83357afbf Author: Andrew Myers Date: Mon Dec 18 12:34:35 2017 -0800 don't profile this funtion - it gets called too many times and skews results. Src/Particle/AMReX_ParticleContainerI.H commit 900328db4d36e8a69abe389921374675745eb03e Author: Weiqun Zhang Date: Sat Dec 16 14:56:19 2017 -0800 nodal projection: fix fine contribution Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 647d5034d314edcbbaa2d0c6408bc5427dce070c Author: Weiqun Zhang Date: Fri Dec 15 14:53:59 2017 -0800 add FabArray::ParallelAdd; coarse contribution in nodal projection Src/Base/AMReX_FabArray.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 9d2100e3e1033f20bd907c016b366a509d0a2906 Author: kngott Date: Fri Dec 15 17:35:30 2017 -0800 BroadcastString and BroadcastStringArray functions, plus corresponding test. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp commit e9919bb4d848003123b088e05eb787cf5cfe050c Author: Weiqun Zhang Date: Fri Dec 15 13:10:23 2017 -0800 WIP: compute fine contribution Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 071d8292b164dc65ee1838d9e827f1a05db47b5b Author: kngott Date: Fri Dec 15 12:05:18 2017 -0800 Improved RemovePiece fix. Src/Extern/ProfParser/AMReX_BLProfStats.cpp commit 4f76a92c7b5206188a0df38e8dae9466dcb3d558 Author: kngott Date: Fri Dec 15 12:02:02 2017 -0800 BLProfStats::RemovePiece now successfully removes equal TimeRanges. Src/Extern/ProfParser/AMReX_BLProfStats.cpp commit 5e40c6f617da6d319b922060fc6d0cac17690e96 Merge: 001693af5 8eb0af9be Author: Klaus Weide Date: Thu Dec 14 19:24:08 2017 -0600 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8eb0af9be2098fdeb85f7abe5c685e5e60ef97ea Author: kngott Date: Thu Dec 14 16:52:25 2017 -0800 Additional profiler flags. Src/Amr/AMReX_AmrLevel.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit c4faaa8504cf867eafcc2249a5743c14a8b0e547 Author: Weiqun Zhang Date: Thu Dec 14 14:47:32 2017 -0800 add rhcc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 62bf092e5727e1a5c809ba51ac6a4f73098d78f6 Merge: 8a2dc84ce ec1dce22e Author: WeiqunZhang Date: Thu Dec 14 13:02:52 2017 -0800 Merge pull request #178 from bcfriesen/update_CVODE_build CVODE, Tools: use Cray version of SUNDIALS if module is loaded commit 8a2dc84ce91973aefe5b9b5f3a3553fa37dea176 Merge: c9a4973de e4a611ee4 Author: WeiqunZhang Date: Thu Dec 14 13:01:58 2017 -0800 Merge pull request #179 from AMReX-Codes/fextract Enable coarse and fine level selection in fextract commit c9a4973defaeae11d812a96a7f658da6d2a677b9 Author: Andy Nonaka Date: Thu Dec 14 12:43:03 2017 -0800 note about PhysBCFunct class Docs/AMReXUsersGuide/Boundary/Boundary.tex Src/Base/AMReX_PhysBCFunct.H commit d2de2978b7cbe354d7b8cac34f98ab5fa6b39ec7 Author: Weiqun Zhang Date: Wed Dec 13 21:23:48 2017 -0800 save the number of iterations Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 3d905dbab2f464c044b73cd1ffaeb73f5505deca Merge: d5d9677d5 bc0c9b817 Author: vince Date: Wed Dec 13 18:13:46 2017 -0800 merge fixes. commit bc0c9b817a0cbbc12aa72b527febdad9b6c927ab Author: vince Date: Wed Dec 13 17:56:49 2017 -0800 added option to set size of DATA_nnnnn digits. Src/Particle/AMReX_ParticleContainerI.H commit 6517e242901c5fc291ecde40ad1d87d7364b0b2c Author: kngott Date: Wed Dec 13 17:40:42 2017 -0800 Timeline in GUI now runs in parallel. Src/Extern/amrdata/AMReX_DataServices.cpp commit d5d9677d578628ca85146f8c31e8043f0ef87b8b Merge: 7ed9c9319 6d7f34542 Author: vince Date: Wed Dec 13 16:29:14 2017 -0800 Merge branch 'development' into partio commit 6d7f345426c2eb1c040eb024ec14084cbd514d11 Merge: ad9129a0d 91aa886f4 Author: dtgraves Date: Wed Dec 13 14:52:46 2017 -0800 Merge pull request #180 from AMReX-Codes/dtg_branch merging in some small bug fixes and other sundries commit ec1dce22e2765392660d7f0753647e6d37be8513 Author: Brian Friesen Date: Wed Dec 13 14:10:38 2017 -0800 CVODE: Update user guide with instructions for linking SUNDIALS on Crays Docs/AMReXUsersGuide/CVODE/CVODE.tex commit 47719094f89bcfe344974cef453a0356306b756f Author: Weiqun Zhang Date: Wed Dec 13 14:05:10 2017 -0800 compute fine sync residual Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 91aa886f47e476c08883e363c6954da129cf0b31 Author: dtgraves Date: Wed Dec 13 14:01:07 2017 -0800 scalar advection tests passing showing correct covergence 2d/3d, with and without limiting. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_mpi_driver.py commit e4a611ee4cd42795b878c2515e086b5364682b9a Author: Max Katz Date: Wed Dec 13 16:44:06 2017 -0500 Enable coarse and fine level selection in fextract fextract previously would extract data on all levels by default. This adds options to select a different set of levels; for example, a use case might be to only see the data on the finest level so you can examine where the refined regions are. The new options are -c/--coarse_level and -f/--fine_level. Tools/Postprocessing/F_Src/fextract.f90 commit f27f0e96b41330e02178092398bad6b8d4fdb8cb Author: Brian Friesen Date: Wed Dec 13 12:52:19 2017 -0800 CVODE, Tools: use Cray version of SUNDIALS if module is loaded Cray includes SUNDIALS in the "cray-tpsl" module. Use that if the module is loaded. If the module is not loaded, then look for the home-cooked version. Tools/GNUMake/packages/Make.cvode commit 7ed9c9319bb1a2d5c70d9c5395ef47c55c02d325 Merge: ce513d046 ad9129a0d Author: vince Date: Wed Dec 13 12:22:36 2017 -0800 Merge branch 'development' into partio commit 5184ded536405a0a97334afbe190a483ceda7b24 Merge: 7b7d3baf8 ad9129a0d Author: vince Date: Wed Dec 13 12:20:29 2017 -0800 merge fixes. commit 601ba2e72aabb8fe666c4e84cdf02bda7e9334b2 Author: Weiqun Zhang Date: Wed Dec 13 12:12:51 2017 -0800 do not touch dirichlet boundary cells in applybc Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e5ecf02a73d0a1ff433e837ff0a1f903cf34cb8f Author: Weiqun Zhang Date: Wed Dec 13 10:55:48 2017 -0800 build dirichlet mask if it hasn't been built when compRHS is called Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 85070fe8ff35877ddd619b65c61bafdc35dfa1ad Author: Weiqun Zhang Date: Tue Dec 12 17:12:47 2017 -0800 WIP: add nodal mask for inhomogeneous Dirichlet Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 0dec7cb3d74937065c4bfdcfcffb123eac053346 Author: dtgraves Date: Tue Dec 12 15:48:56 2017 -0800 added mpi-driven convergence utility Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_mpi_driver.py commit 3dcd25b0574aa41bf5b20573018eec4934e8c224 Author: dtgraves Date: Tue Dec 12 15:14:11 2017 -0800 found declaration bug that was causing code to act differently with chopped-up boxes Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit ad9129a0db96754f41c050a707d1518e6417d634 Author: Weiqun Zhang Date: Tue Dec 12 15:10:57 2017 -0800 fix FillCoarsePatch as well Src/Amr/AMReX_AmrLevel.cpp commit b5a548664c806b30049b42b14fdb3d11453b3d78 Merge: 77807cbe3 1e51a0729 Author: Weiqun Zhang Date: Tue Dec 12 15:07:12 2017 -0800 Merge branch 'development' into weiqun/mlmg commit 1e51a07292b94e0e030fae880b21693c53592f63 Author: Weiqun Zhang Date: Tue Dec 12 15:02:44 2017 -0800 fix the old fillpath too Src/Amr/AMReX_AmrLevel.cpp commit 8f238dfeee507263fdf8e6cf7f08e8f1855068f0 Author: Weiqun Zhang Date: Tue Dec 12 14:53:57 2017 -0800 need to set ghost cells for temp mfs in FillPatch too Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArray.H commit 77807cbe341b221279c73f3e17171510c17b0538 Merge: 2635b1a7d 4745e153b Author: Weiqun Zhang Date: Tue Dec 12 14:10:45 2017 -0800 Merge branch 'development' into weiqun/mlmg commit 4745e153b535c3837b8282f4558c774dcccaa3f2 Author: Weiqun Zhang Date: Tue Dec 12 13:20:19 2017 -0800 FillPatch: initialize the initial data outside physical domain to quiet nan otherwise in some corner cases floating point exception could happen Src/Amr/AMReX_AmrLevel.cpp commit af55c38a01f4983db700805b482a83d51b7c4c21 Author: Marc Day Date: Tue Dec 12 12:44:16 2017 -0800 Quiet the compiler in DEBUG mode by avoiding shadowed and unused variables. Src/F_BaseLib/box_f.f90 Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp commit 86b01a7a70591c7e6e1a04701b427afb92c5a3a9 Merge: 488a65162 2b722ac77 Author: Marc Day Date: Tue Dec 12 11:12:26 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2b722ac774f7c5a31a52bb07d77d6a522afcdae2 Merge: c33dfb008 744341ecb Author: atmyers Date: Tue Dec 12 10:41:24 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c33dfb0086152c82fa196d9303cc9673a47a4195 Author: atmyers Date: Tue Dec 12 10:41:07 2017 -0800 use the VectorIO stuff in particel checkpoint / restart (again) Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 744341ecb14ef4292ecf6bbbda740b45bf647b3d Author: Michele Rosso Date: Tue Dec 12 10:25:06 2017 -0800 CMake: add new sources Src/GeometryShop/CMakeLists.txt commit 808abbc3b011a757033d8dfe26bd7733e7becd59 Author: atmyers Date: Tue Dec 12 09:37:33 2017 -0800 add functions to write Vectors of float data when Real is double precision and vice versa. Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_VectorIO.H Src/Base/AMReX_VectorIO.cpp Tests/Particles/TypeDescriptor/main.cpp commit 2635b1a7da87ac4f433fe7669f442b7a3dbb1dc2 Author: Weiqun Zhang Date: Tue Dec 12 09:32:54 2017 -0800 nodal projection: make sync residual consistent with F90 solver Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5d6e3a053a0dec5db4e8594107595cc4d5b40ab2 Author: dtgraves Date: Mon Dec 11 16:17:45 2017 -0800 4th order with limiting has good convergence in the simplest case. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/debug.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit c2db3b4e79169ea2d6964e8c167aba0f926ba663 Author: Michele Rosso Date: Mon Dec 11 16:12:11 2017 -0800 Remove assertion from norm1() Src/Base/AMReX_MultiFab.cpp commit ce513d046e2a8659e6cc789405e4a689f01d6799 Author: vince Date: Mon Dec 11 13:52:20 2017 -0800 remove diagnostics. Src/Amr/AMReX_AmrLevel.cpp Src/Particle/AMReX_ParticleContainerI.H commit 70bcf5f94cb0942ced4fc29e1073fb50a49c1da1 Author: Weiqun Zhang Date: Mon Dec 11 13:34:56 2017 -0800 nodal projection: coarse sync residual Src/Base/AMReX_MultiFab.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f841eb9209a04bc5e7e8eae99e389a9b9214d184 Author: Weiqun Zhang Date: Mon Dec 11 09:04:26 2017 -0800 mlmg: assertions for periodic boundary Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit e208e7a725e092a7168d7f1969cdd443bbe636ea Author: Weiqun Zhang Date: Sun Dec 10 21:06:47 2017 -0800 fix a compiler warning Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f9fffaf963495bfc42fa7f1189ba3fc9428ddb0f Author: Weiqun Zhang Date: Sun Dec 10 21:03:04 2017 -0800 nodal projection: use arithmetic average Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit e4853ed87076ad5b2ba5b83e7fc046b7eb5e2f20 Author: Weiqun Zhang Date: Sun Dec 10 20:48:24 2017 -0800 nodal projection: fix coefficent at periodic boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit bc84f146a1e571849cbb69b5b8037b9e2670740f Author: Weiqun Zhang Date: Sun Dec 10 11:35:21 2017 -0800 add MLNodeLinOp::nodalSync function Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit cb29b071413a9bdf11400690dda5334e16f78351 Author: Weiqun Zhang Date: Sat Dec 9 22:20:17 2017 -0800 nodal projection: add arithemic average in addition to harmonic average Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 959ec49a385a049251ab2ed43747453fc85ade88 Author: Weiqun Zhang Date: Fri Dec 8 23:11:57 2017 -0800 nodal projection: fix periodici boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit a6c5f2da8dc0ca31e618a8236af10727076aa5a9 Author: Weiqun Zhang Date: Fri Dec 8 17:52:05 2017 -0800 For Gauss Seidel, we need to sync Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit addabf461b2c4a358270ed36c2667cb851266cc9 Author: Weiqun Zhang Date: Fri Dec 8 15:57:03 2017 -0800 mlmg: print more information Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 1b9ad44fbb67bd407651fa28b14d44f99ee1f2f0 Author: Weiqun Zhang Date: Fri Dec 8 15:33:34 2017 -0800 nodal projection: make new u Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ca25ccf1932b8e614a0e60b568fb6641436e4fe2 Merge: 9139a01b7 1074e82d7 Author: atmyers Date: Fri Dec 8 14:10:16 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9139a01b7a65d722ff14433d814f9451f16e90de Author: atmyers Date: Fri Dec 8 14:09:25 2017 -0800 have AmrMesh abort if it gets a problem domain with zero volume. Src/AmrCore/AMReX_AmrMesh.cpp commit 9ed12f8f82f184c4ad5e2052c79d3553504b9efe Author: atmyers Date: Fri Dec 8 14:04:38 2017 -0800 add function returning the volume of the RealBox. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 66c7edf032ea30d6df5856637c3d57b5f63d50df Author: atmyers Date: Fri Dec 8 14:00:22 2017 -0800 make the RealBox documentation consistent with its actual behavior. Src/Base/AMReX_RealBox.H commit 1074e82d7146685b3a6a975019f1b7c07b18828e Merge: 8a13188cb 010a0f21d Author: dtgraves Date: Fri Dec 8 12:45:19 2017 -0800 Merge pull request #177 from AMReX-Codes/dtg_branch merging in corrected rk time interpolators and geometry generation examples commit 010a0f21d57e754b7a697bf454d669c5c86f9d52 Author: dtgraves Date: Fri Dec 8 12:43:25 2017 -0800 fixed the same bugs in the pwm versions, even though they are not called. Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 2f90476afe8295d617fc3baa26b2de7db1c6c252 Author: vince Date: Fri Dec 8 12:40:56 2017 -0800 more precreate directory support. Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp commit e6795a9db69a66fd0ac2dc5d49010df44828278b Author: dtgraves Date: Fri Dec 8 12:35:49 2017 -0800 fixed bug in time interpolation (you have to be very careful which dt you use). both rk3 and rk4 get good convergence numbers. and there was much rejoicing. Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 7b7d3baf80ee8c7e96489ab09ddb35acd58810e7 Author: kngott Date: Fri Dec 8 12:10:22 2017 -0800 RunTimeline error with va when using multiple procs in GUI. Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 7e188c6065d76d4eff0969e9bc63631916cad960 Author: Weiqun Zhang Date: Fri Dec 8 11:08:41 2017 -0800 nodal projection: fixed jacobi and added gauss seidel Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 488a651620f0b37f3c784c75b49da8c285edef43 Merge: a82870e14 8a13188cb Author: Marc Day Date: Fri Dec 8 11:01:21 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8a13188cb643775cbff88f0a94c7d001df5570cb Merge: 746e975ff e31cc27cf Author: Marc Day Date: Fri Dec 8 10:26:55 2017 -0800 Merge branch 'marc/geom_surface' into development This commit adds a capability to write out the intersection points between the fine mesh and the embedded boundary geometry, and is triggered if the ParmParse option ebis.eb_surface_filename is set. By default it is not set. Since a surface is not a standard AMReX data structure (yet), a custom IO format was created for it. The surface is created and written in parallel, and written in a binary format. The amrex folder, Tools/EBSurfaceTools, contains some code to interact with this format. In particular, the files can be read and the surface merged to a single surface on a single processor, and written to a simple text file of node and element data (polylines in 2D, triangles in 3D). A Python script is provided there to convert the output to a VTK format that can be read natively in Paraview. The format of the surface files will be documented elsewhere, but can be used, e.g., to store isosurfaces/contours. It may also become useful for interacting with computed/fixed boundary data at the eb. commit e31cc27cfe028a22f9da6fa2000468a301d9f531 Author: Marc Day Date: Thu Dec 7 19:48:30 2017 -0800 Make compiler happier. Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryService.cpp Tools/EBSurfaceTools/ConvertEBSurface.cpp commit 45e0cebcc66a2153c600527fb0855cee3e1fc6d5 Author: Marc Day Date: Thu Dec 7 19:38:09 2017 -0800 Make 2D version of eb surface stuff compatible with the 3D approach. Src/GeometryShop/AMReX_EBISLevel.cpp Tools/EBSurfaceTools/ConvertEBSurface.cpp commit 7ed5428fb25ca40fac099bf9741daf8ec70878ec Author: Marc Day Date: Thu Dec 7 18:11:49 2017 -0800 whoops! Gotta make the dir before writing to it. Src/GeometryShop/AMReX_EBISLevel.cpp commit a5f0446e8b50df68afbf6db6cbc9664e2ca205f0 Author: Marc Day Date: Thu Dec 7 18:00:55 2017 -0800 Move some code around. Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeomIntersectUtils.cpp commit bbcf653f9f31c7374509553ddb91e0c30852f12a Author: Marc Day Date: Thu Dec 7 17:40:20 2017 -0800 Make 3D output write to a folder+header and use binary IO. Add EBSurfaceTools folder with code to read surface out, and reduce the surface across boxes and write a simple ASCII text file. Include a python script to convert this to VTK-compatible format for viewing in Paraview. Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeomIntersectUtils.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tools/EBSurfaceTools/ConvertEBSurface.cpp Tools/EBSurfaceTools/GNUmakefile Tools/EBSurfaceTools/isoToVTK.py commit ea18c12d9a16eba76a3bce359692ed8bb97c42b8 Merge: b421f22f3 746e975ff Author: vince Date: Thu Dec 7 17:12:55 2017 -0800 merge fix. commit bcce7915bbcc7250bbc8902064ebfccfdf755f0e Author: Weiqun Zhang Date: Thu Dec 7 16:31:23 2017 -0800 nodal projection: clean up Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 3e3fbeceb41aeeb1cb818d878f09b0f83bf81cc8 Author: Weiqun Zhang Date: Thu Dec 7 15:55:12 2017 -0800 nodal projection: zero out dirichlet boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b421f22f389fb0bee052243f8310c13f9c43a4c3 Author: vince Date: Thu Dec 7 15:50:03 2017 -0800 fix warning. Src/Base/AMReX_FACopyDescriptor.H commit 1183af431d1c6d25095b7a491b6110330545db6f Author: vince Date: Thu Dec 7 15:14:22 2017 -0800 prepost updates for plotfiles. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 841884a8186fcc0022518138d2695d36dd08d665 Author: vince Date: Thu Dec 7 15:11:57 2017 -0800 prepost updates for plotfiles. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit 8377b337e28561a9da7df5ad64915cf3d44ba62e Author: Weiqun Zhang Date: Thu Dec 7 14:23:23 2017 -0800 nodal projection: fix a bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit a189955131e44701e729b5f379ae4396188e63b5 Author: Weiqun Zhang Date: Thu Dec 7 13:41:13 2017 -0800 nodal projection: interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5871d31efd561b20799e545201e4a00fdc889be7 Author: dtgraves Date: Thu Dec 7 12:49:51 2017 -0800 more examples of geometries Tutorials/EB/GeometryGeneration/exec/GNUmakefile Tutorials/EB/GeometryGeneration/exec/parabolaWithSphere.cpp Tutorials/EB/GeometryGeneration/exec/parabolaWithSphere.inputs Tutorials/EB/GeometryGeneration/exec/surfaceOfRevolution.cpp Tutorials/EB/GeometryGeneration/exec/surfaceOfRevolution.inputs commit 6e193e1c55ca5e11c0a995fccc5b3cd68ce91af4 Author: kngott Date: Thu Dec 7 12:22:29 2017 -0800 Addition of regions data checks to -check batch function. Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 65fbebb92d5c454aee7f7f837fe41283046c6c82 Author: Weiqun Zhang Date: Thu Dec 7 12:17:10 2017 -0800 add virtual MLLinOp::interpolation Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 02c504212cdf00337e03baf5a41b44f51d0459e7 Author: Weiqun Zhang Date: Thu Dec 7 11:20:17 2017 -0800 nodal projection: add nodal owner mask Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit f6f38ea7027dfe0e4e7f8eef22f1d8e82d8d8468 Merge: 9fa65935e 746e975ff Author: Marc Day Date: Thu Dec 7 11:17:25 2017 -0800 Merge remote-tracking branch 'origin/development' into marc/geom_surface commit 9fa65935e2578af43ab994dd91f886a7f72adc0c Merge: aeb83d730 a0db3f296 Author: Marc Day Date: Thu Dec 7 11:15:54 2017 -0800 Merge remote-tracking branch 'origin/development' into marc/geom_surface commit c694cc2946df0fe080a04d4b23f97eee4e8ffada Author: Weiqun Zhang Date: Thu Dec 7 11:15:41 2017 -0800 add MultiFab::Dot for nodal with mask Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 128a4dbb7992547d657b671ea0495845365751b8 Author: Weiqun Zhang Date: Thu Dec 7 10:17:54 2017 -0800 nodal projection: restriction Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 21d4d950441a1cd5b42510b2ac94f5735d4843e2 Author: Weiqun Zhang Date: Thu Dec 7 10:16:34 2017 -0800 add free function coarsen for BoxArray Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 746e975ff3954eeefde79e0e735a8fd610651b2d Author: Weiqun Zhang Date: Thu Dec 7 08:45:54 2017 -0800 update CHANGES CHANGES commit ede5cec780c2d072a4d52ce04a4ec9cd7ac57eeb Author: Andrew Myers Date: Thu Dec 7 06:33:17 2017 -0800 update LoadBalance tutorial Tutorials/Particles/LoadBalance/main.cpp commit d1e2b573aab9f2e942d1ab464eae6f360a886190 Author: Andrew Myers Date: Thu Dec 7 06:32:45 2017 -0800 add lo-dim versions of these functions too Src/Particle/AMReX_KDTree_1d.F90 Src/Particle/AMReX_KDTree_2d.F90 commit e378d696a107823355974dcd32ca4c04c85e4dcc Author: Andrew Myers Date: Thu Dec 7 06:24:23 2017 -0800 also add 1D and 2D versions of this function. Src/Particle/AMReX_KDTree_1d.F90 Src/Particle/AMReX_KDTree_2d.F90 commit c7209aa8e0c4a642a7295421425124fa68649312 Author: Andrew Myers Date: Wed Dec 6 20:01:08 2017 -0800 don't let the KD-tree create 0 cost boxes. Src/Particle/AMReX_KDTree_3d.F90 Src/Particle/AMReX_KDTree_F.H Src/Particle/AMReX_LoadBalanceKD.cpp commit 9f7d73014b9bff79622a6af38488ab58708c0606 Author: Weiqun Zhang Date: Wed Dec 6 16:58:29 2017 -0800 nodal projection: add virtual restriction method Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 28a1e34bfdf018de69f3749caec8c080865c4108 Author: Weiqun Zhang Date: Wed Dec 6 16:21:09 2017 -0800 nodal projection: applybc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 13aa60c6ce9ab685022b4c80157436690254ec69 Author: dtgraves Date: Wed Dec 6 16:00:25 2017 -0800 more examples of geometry generation Tutorials/EB/GeometryGeneration/exec/GNUmakefile Tutorials/EB/GeometryGeneration/exec/sphere.cpp Tutorials/EB/GeometryGeneration/exec/sphere.inputs Tutorials/EB/GeometryGeneration/src/CommonCode.cpp Tutorials/EB/GeometryGeneration/src/Make.package Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.H Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.cpp commit 52c99014d0cb3293d0e382dde9a137d7c828769d Author: Weiqun Zhang Date: Wed Dec 6 15:32:47 2017 -0800 nodal projection: fillbc for sigma Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit aeb83d730bf31b1ff3096369e21fe51e98942ec1 Author: Marc Day Date: Wed Dec 6 13:04:05 2017 -0800 Separate out the IO of the eb surface file in order to better manage writes in parallel Src/GeometryShop/AMReX_EBISLevel.cpp commit 76719409abe8ff83230077a31f244033f405d0ad Author: Weiqun Zhang Date: Wed Dec 6 10:43:48 2017 -0800 nodal projection: 2d Jacobi smoothing Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 0a6d58ef417c4d587682d310a4b8d102bcedd00b Author: Weiqun Zhang Date: Wed Dec 6 10:18:23 2017 -0800 fix a minor bug Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 04681b615d48bec594d88461625e21507eaf91af Author: Weiqun Zhang Date: Wed Dec 6 10:18:23 2017 -0800 fix a minor bug Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 012d0577db9fffb530ca2807a91bc2dcc289f379 Author: Weiqun Zhang Date: Wed Dec 6 09:45:28 2017 -0800 nodal projection: 2d A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5506aba529d74fde55dd363a5695aee2d2307ed0 Author: dtgraves Date: Tue Dec 5 16:38:10 2017 -0800 starting on tutorial where I show how to make a bunch of different geometries. Tools/C_util/Convergence/GNUmakefile Tutorials/EB/GeometryGeneration/exec/GNUmakefile Tutorials/EB/GeometryGeneration/exec/sphere.cpp Tutorials/EB/GeometryGeneration/exec/sphere.inputs Tutorials/EB/GeometryGeneration/src/CommonCode.H Tutorials/EB/GeometryGeneration/src/CommonCode.cpp Tutorials/EB/GeometryGeneration/src/Make.package Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.H Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.cpp commit df6d1c3a5ea7ff7b9adefb5029a44101e0a5babf Author: Tan Nguyen Date: Tue Dec 5 15:31:37 2017 -0800 build the body of an AMR task hierarchy Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/main.cpp Src/Base/AMReX_FabArrayBase.H commit b859895909b70d4d83f598cbb23705d337c93d0c Merge: 1dfc44c80 59a354728 Author: dtgraves Date: Tue Dec 5 14:03:00 2017 -0800 merging with dev branch commit 59a35472825a77155ae0b9bfd6a21dc67f75cdaf Author: Weiqun Zhang Date: Tue Dec 5 09:51:51 2017 -0800 stdint.h -> cstdint because this is C++ Src/Base/AMReX_IntConv.H commit 130775c9412cc19c8cedaab44c71e3bf00497aad Author: Weiqun Zhang Date: Tue Dec 5 09:43:59 2017 -0800 fix template specialization Src/Base/AMReX_IntConv.cpp commit 56c05b67a18adeb2fc0bc67688da6bafd909d446 Author: Weiqun Zhang Date: Tue Dec 5 09:38:37 2017 -0800 Revert "use the new VectorIO routines in the particle checkpoint and restart routines." This reverts commit 3c44f13d61ff821c8a21e6058feeaf2a3322fdf5. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit b66f3b17af3739c4dee4ef36cfe0519fe804a292 Merge: 53df579af 548e4c314 Author: WeiqunZhang Date: Tue Dec 5 09:08:27 2017 -0800 Merge pull request #176 from AMReX-Codes/portable_particle_io Functions for writing Vectors of ints, longs, and Reals to disk in a portable manner. commit 548e4c31484b9c666484e8d187c8b2e855415013 Author: atmyers Date: Mon Dec 4 22:43:53 2017 -0800 clean up endianness macros Src/Base/AMReX_FPC.cpp commit 9ac178350bb20f5fda6486e920a086de437d1cce Author: kngott Date: Mon Dec 4 18:06:33 2017 -0800 ClickHistory and Send/Recv List Button. Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 1dfc44c80ff23328a191685670f42328df574643 Author: dtgraves Date: Mon Dec 4 17:20:38 2017 -0800 redid the math for rk3 case---still not stable. Maybe I need to do something leastsquares-ish or add higher order terms. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 3c44f13d61ff821c8a21e6058feeaf2a3322fdf5 Author: atmyers Date: Mon Dec 4 16:49:35 2017 -0800 use the new VectorIO routines in the particle checkpoint and restart routines. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 53df579af7b8b3f2506f2f9fd404ee67082f90eb Merge: ffd2e6e44 1d6531c89 Author: Andrew Myers Date: Mon Dec 4 16:45:47 2017 -0800 Merge pull request #175 from JBlaschke/development fix macros leading to incorrec endianness in fab io commit 1d6531c8948c18b3d4e12c5f5f9225f40ee5cf2c Author: Johannes Blaschke Date: Mon Dec 4 16:28:08 2017 -0800 fix macros leading to incorrec endian-ness in fab io Src/F_BaseLib/fabio_c.c commit f797650fe4c6b18838209dd65f4f949ba1b3691a Author: atmyers Date: Mon Dec 4 13:25:07 2017 -0800 consolidate the vector IO functions into a file. Src/Base/AMReX_IntConv.H Src/Base/AMReX_IntConv.cpp Src/Base/AMReX_VectorIO.H Src/Base/AMReX_VectorIO.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Tests/Particles/TypeDescriptor/main.cpp commit 9deadc73846007838f6ddab9f51cfd8f39b3836d Author: atmyers Date: Mon Dec 4 13:12:22 2017 -0800 also testing real data. Tests/Particles/TypeDescriptor/main.cpp commit 6f31e4149950117e644cf14305d56ee187d0d7bf Author: atmyers Date: Mon Dec 4 12:37:29 2017 -0800 typo fix in comment. Src/Base/AMReX_FabConv.H commit ec87ebdba7ddc3df173e3d2c8887a1a2e7b2cf71 Author: atmyers Date: Mon Dec 4 12:32:14 2017 -0800 include negatives in test. Tests/Particles/TypeDescriptor/main.cpp commit 3e2fb6e004cd6633004846f89c5a74f24b9c9ca7 Author: atmyers Date: Mon Dec 4 12:23:33 2017 -0800 also support long data; some reorganization. Src/Base/AMReX_IntConv.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/Particles/TypeDescriptor/main.cpp commit ffd2e6e44ad58fe87b4a189d06ff5b06ba7e257c Author: Weiqun Zhang Date: Mon Dec 4 10:30:23 2017 -0800 Fortran octree: add support for amr.max_grid_size_x, _y and _z Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit ff52c7c5eb7d87dbbe3eac9bd11dd851e92f2486 Author: atmyers Date: Mon Dec 4 10:28:22 2017 -0800 also read/write the IntDescriptor to a header file. Tests/Particles/TypeDescriptor/main.cpp commit 438c463e9c529f5b2575ea2bc596605b9af8473b Author: Weiqun Zhang Date: Sat Dec 2 13:42:40 2017 -0800 WIP: nodal projection Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 704b2092f407b74ce7c9eb90967f476c6cc5abfa Author: atmyers Date: Sat Dec 2 12:55:45 2017 -0800 move the int conversion stuff to Base and install the header Src/Base/AMReX_IntConv.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/Particles/TypeDescriptor/Make.package Tests/Particles/TypeDescriptor/main.cpp commit 78690bd1678eac2b0f9a2da9fbca661838b24363 Author: atmyers Date: Sat Dec 2 12:48:20 2017 -0800 swap bytes for unsigned as well. Tests/Particles/TypeDescriptor/Convert.H commit 3633a3c8cdb63b3703c96cd49c8c1b89f992a0bd Author: atmyers Date: Sat Dec 2 12:42:08 2017 -0800 handle short Tests/Particles/TypeDescriptor/main.cpp commit 8b264bc66a7210928a3cd1f1cd6f7d13ae0eb173 Author: atmyers Date: Sat Dec 2 12:39:02 2017 -0800 handle endianness Tests/Particles/TypeDescriptor/Convert.H Tests/Particles/TypeDescriptor/main.cpp commit 6f0c80aec159dee02a291d255f80a02b98bbe0cc Author: atmyers Date: Sat Dec 2 12:28:36 2017 -0800 add a test for the more portable io stuff Tests/Particles/TypeDescriptor/Convert.H Tests/Particles/TypeDescriptor/GNUmakefile Tests/Particles/TypeDescriptor/Make.package Tests/Particles/TypeDescriptor/main.cpp commit 8ef30bfc0744ee5cd7c5768f8c83aa1dfd077ac4 Author: atmyers Date: Sat Dec 2 12:27:44 2017 -0800 some BoxLib -> AMReX Src/Base/AMReX_FabConv.H commit 27b004984bdfb39230032954eddd6ff4aa54b0b6 Author: Andrew Myers Date: Sat Dec 2 10:07:55 2017 -0800 fix bug with rcv count caching in the neighbor particle code. Src/Particle/AMReX_NeighborParticlesI.H commit 01f7ad64a46f9fff0d998e907c83c082019cb537 Author: Ann Almgren Date: Fri Dec 1 18:23:46 2017 -0800 Protect against negative grid ID in BuildLevelMask Src/Particle/AMReX_NeighborParticlesI.H commit c44c338c8acc6de06e143e6f89f3be04dd2ab761 Author: atmyers Date: Fri Dec 1 13:50:35 2017 -0800 implement io operators for the IntDescriptor Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp commit b13a356ad17120ab39d38424bbcfcf6e09a24dbe Author: atmyers Date: Fri Dec 1 13:05:05 2017 -0800 adding a NativeIntDescriptor. Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabConv.H commit 57c73b8a146415433e37f0e1a7b34eb4c5198b0a Author: Weiqun Zhang Date: Fri Dec 1 10:48:58 2017 -0800 average down edge coefficients Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 90a16a8cbc4573576d02145fa929d66c16df635a Author: Marc Day Date: Fri Dec 1 09:09:36 2017 -0800 WIP: collect intersections from geo server into distributed data structure, connect up contour lines or triangulated surface patches, and write...if ebis.build_eb_surface=true Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeomIntersectUtils.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/Make.package commit 031881908216b2226d9e8831896e6002bbb9b4d6 Merge: 2e48372f3 1b9f11d96 Author: Weiqun Zhang Date: Fri Dec 1 08:40:29 2017 -0800 Merge branch 'development' commit 1b9f11d969b59f686b5f2f7288e372e7405b5d7a Author: Ann Almgren Date: Thu Nov 30 17:30:58 2017 -0800 Add more missing files to CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit 108cf2ae7068da33c410c4fa3a1d65514c0039e0 Author: kngott Date: Thu Nov 30 17:18:45 2017 -0800 Comment distinguishing backtrace options. Src/Base/AMReX_BLBackTrace.H commit b3ed443c5c4cc06cb9c2382d670674844689eeeb Author: Weiqun Zhang Date: Thu Nov 30 16:58:15 2017 -0800 add index type Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit fabd348388b632ab049a7acc25bcbfd5ecf03599 Merge: 40c595ee5 e2557be8c Author: Ann Almgren Date: Thu Nov 30 16:52:42 2017 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 40c595ee5bb416f5be40f6d207063288ed1b2d0b Author: Ann Almgren Date: Thu Nov 30 16:52:34 2017 -0800 Add missing .H file Src/GeometryShop/CMakeLists.txt commit 8ab4852c02f1890aeccb2d81f585af34924342bd Author: dtgraves Date: Thu Nov 30 16:30:04 2017 -0800 redid the calculations for rk4. still not showing the right convergence. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 9f52734e24e5c725fec217f0d5ea4834c76ab8d5 Author: Weiqun Zhang Date: Thu Nov 30 16:23:51 2017 -0800 move MLCellLinOp specific stuff from base class MLLinOp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit d93a7d3b7f933bc90eef4bfe2ab2eb8013a01a4a Author: Weiqun Zhang Date: Thu Nov 30 14:38:35 2017 -0800 nodal projection: compute divu Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_lo_bctypes_mod.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e2557be8c3ff77b12b6f84297e6fbff572833999 Merge: 756870317 db024ced3 Author: Andrew Myers Date: Thu Nov 30 13:44:43 2017 -0800 Merge pull request #174 from emotheau/master update commit db024ced3e685ea7cc64035e5c03d1605d603d90 Author: Emmanuel Motheau Date: Thu Nov 30 13:41:59 2017 -0800 move file Tools/C_util/Convergence/AVGDOWN_1D.F commit cdf57746f077a9bcde4ae31a6836cab4af910665 Merge: 716456a53 cd31e1451 Author: Emmanuel Motheau Date: Thu Nov 30 13:29:24 2017 -0800 Merge pull request #1 from emotheau/emotheau-patch-1 Add missing file for 1D convergence test commit cd31e145164a8deb3990d36f42f99c4a79db5316 Author: Emmanuel Motheau Date: Thu Nov 30 13:28:31 2017 -0800 Add missing file for 1D convergence test AVGDOWN_1D.F commit 7568703173fc607e0403b5f4b96769d94b0b7769 Author: Ann Almgren Date: Thu Nov 30 12:57:18 2017 -0800 Add AMReX_AnisotropicIF.H to the CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit 0651232b15c53443e1794945b91f987af10888bb Author: Weiqun Zhang Date: Thu Nov 30 10:01:43 2017 -0800 split MLLinOp into MLCellLinOp and MLNodeLinOp Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/Make.package commit d2be80bac77cde2da2d403163772eb1888f3c5ac Author: Andrew Myers Date: Thu Nov 30 06:15:26 2017 -0800 fix assertion. Src/Particle/AMReX_NeighborParticlesI.H commit d5fc770aae596a2b4643164a205931f73862e9ed Author: Weiqun Zhang Date: Wed Nov 29 17:15:27 2017 -0800 average nodal coefficients from cell centers to edges Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 56b56bb68b4b33c0aae27fc4a2e1f4802ed4b704 Author: Weiqun Zhang Date: Wed Nov 29 15:07:33 2017 -0800 start nodal projection Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit ecd3e1dc81119c774158cc154b0f7f732a513ca1 Author: dtgraves Date: Wed Nov 29 09:56:59 2017 -0800 put back in abort message in CNS that disallows ansiotropic dx Tutorials/EB/CNS/Source/CNS.cpp commit 28c2e679e28025c82758070223f43314429d0918 Author: dtgraves Date: Wed Nov 29 09:55:54 2017 -0800 added general anisotropic dx implicit function (along with an example in CNS that calls it) Src/GeometryShop/AMReX_AnisotropicIF.H Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 654d0d8b8d029c064e9d817890a5e6fe47d3eeeb Merge: 024bc0414 669721809 Author: dtgraves Date: Wed Nov 29 09:36:28 2017 -0800 Merge branch 'development' into dtg_branch commit 669721809c2b5a6dde5ab3d36efe338e61565a07 Author: Weiqun Zhang Date: Wed Nov 29 09:25:37 2017 -0800 add amrex::second() that calls C++ clock. use it in TinyProfiler Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit a22364564bb47eacca8548bd43924510cd922acc Author: Ann Almgren Date: Tue Nov 28 16:15:10 2017 -0800 Don't need prob_domain in that routine Src/Particle/AMReX_NeighborParticlesI.H commit 024bc0414f37e7e71e81d98b19c43355fea94492 Author: dtgraves Date: Tue Nov 28 12:30:52 2017 -0800 found a bug in jbb version of time interpolation. rk3 looks very good. have to check math for rk4 again. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit df61cbb63bc1ad68c974f41a9e9ba016d60182da Author: Weiqun Zhang Date: Tue Nov 28 09:04:32 2017 -0800 TinyProfiler: disable BL_PROFILE_REGION_START and STOP so that the output is smaller Src/Base/AMReX_BLProfiler.H commit 76b8cb95a0ec3ed15e18a706571c56bfaf472b39 Author: Marc Day Date: Mon Nov 27 18:59:01 2017 -0800 Add 3D code to dump triangulated surface. Src/GeometryShop/AMReX_GeometryShop.cpp commit 76887cd60ce6e5990ccc84926e0b2cc37e947667 Author: Tan Nguyen Date: Mon Nov 27 18:03:11 2017 -0800 reuse some original Amr code Src/AmrTask/Amr/AMReX_AmrLevelTask.H Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/AmrTask/Amr/Make.package Src/AmrTask/Amr/Makefile Src/AmrTask/AmrCore/AMReX_FillPatchUtil.H Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp commit 3bf78515fc16708a455a256836db20359c5ec062 Merge: 57e70699a 4799d37c9 Author: Tan Nguyen Date: Mon Nov 27 17:56:16 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 57e70699a57d842b70ec75b9d49ab5d907f23a42 Author: Tan Nguyen Date: Mon Nov 27 17:56:05 2017 -0800 writing a fully asynchronous version of the Advection code Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/CMakeLists.txt Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/Make.Adv Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Prob.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/probin Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probin Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/README Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Adv_F.H Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/LevelBldAdv.cpp Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/main.cpp commit 4799d37c95385e20fb8719a34830e9840c898e80 Author: Weiqun Zhang Date: Mon Nov 27 17:53:08 2017 -0800 add some regional profilers to MLMG Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit 3a77463784a08a646b9f344309a8f87b5c70b69c Merge: ac1bd0420 4f89f4f92 Author: Tan Nguyen Date: Mon Nov 27 17:51:29 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ac1bd042083545d2166e1952973bfc365508abe6 Author: Tan Nguyen Date: Mon Nov 27 17:51:17 2017 -0800 add AmrTask support Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AmrLevel.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/AMFIter/Makefile Src/AmrTask/Makefile Src/AmrTask/arch/arch.mpi.generic Src/AmrTask/graph/AMReX_AbstractTask.H commit 4f89f4f92ee09a11443b7a3cd8fae8c651e0653f Merge: 020a0623a bcff6c682 Author: Weiqun Zhang Date: Mon Nov 27 17:39:43 2017 -0800 Merge branch 'tprof-region' into development commit 8264aadcf52a5fddf490ba95cbd88cf0c2488383 Author: Marc Day Date: Mon Nov 27 16:35:55 2017 -0800 Fix scaling of intercept points. Src/GeometryShop/AMReX_GeometryShop.cpp commit 020a0623a65f12ff908120c7f9a5c7d508146d0b Author: Michele Rosso Date: Mon Nov 27 15:49:23 2017 -0800 CMake: include MLMG in build Src/LinearSolvers/CMakeLists.txt commit a82870e14dbdd33181603f9b6d9ff1510d0a589d Merge: 4abf1dc03 a0db3f296 Author: Marc Day Date: Mon Nov 27 15:40:48 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d5c7d14693b8db3b5be442084439f6ec21abf9bd Author: dtgraves Date: Mon Nov 27 15:40:30 2017 -0800 coded yet another version of time interpolation. the simple polynomial version seems to work best. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 6ab3ed65b8e71667293d85d3d911a16043784476 Author: Marc Day Date: Mon Nov 27 15:39:52 2017 -0800 WIP: Extracting intersections Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit bcff6c6826a73587684f8798c702498ddcf457bc Author: Weiqun Zhang Date: Mon Nov 27 10:53:29 2017 -0800 add TinyProfileRegion class Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit a0db3f296dd98b1b7bd2729772ee878d7cd9e505 Author: Weiqun Zhang Date: Sun Nov 26 20:07:38 2017 -0800 put a global variable into anonymous namespace Src/Base/AMReX_Utility.cpp commit 6dcedf4316930939cea468e211f8e3079614ca23 Author: Weiqun Zhang Date: Sun Nov 26 15:12:15 2017 -0800 Regional profiling support in TinyProfiler Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Particle/AMReX_ParticleContainerI.H commit 571d6268141964c48a96ad506cef400e08997fc1 Author: Weiqun Zhang Date: Sun Nov 26 12:08:15 2017 -0800 TinyProfiler ctor optimization Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit eeb628c1149a2fc48c37b495e8bbfa45a5534bc5 Author: Max Katz Date: Sun Nov 26 13:45:16 2017 -0500 Add method to swap old/new data with another StateData Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit eb6d6567928f4209252acff0f5304f866bbfefe2 Merge: 709c3375f f48d503d7 Author: Tan Nguyen Date: Fri Nov 24 17:04:11 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 709c3375f0e1c74df384166a857f1c9ab4040339 Author: Tan Nguyen Date: Fri Nov 24 17:03:47 2017 -0800 remove an anonymous namespace Src/Amr/AMReX_Amr.cpp commit f48d503d79fb593a4648e3ab51fdd991ae222263 Author: Weiqun Zhang Date: Fri Nov 24 16:50:44 2017 -0800 make: if AMREX_HOME string contains ~, replace it because make won't like it and the error message cannot be easily understood. Tools/GNUMake/Make.defs commit 6018be5399320ddb82468a1e46b6f5d971cbf634 Author: Max Katz Date: Fri Nov 24 13:20:05 2017 -0500 Ensure uniform gcc version number reporting with -dumpfullversion Tools/F_mk/comps/gfortran.mak Tools/GNUMake/comps/gnu.mak commit 306d63ab5d491925cb8cac927875f475f83a09c1 Author: Max Katz Date: Fri Nov 24 13:14:23 2017 -0500 Throw error if gcc < 4.8 (F_mk) Tools/F_mk/comps/gfortran.mak commit 2d9a952ca9d13f7941c03822aae026bba9b6291d Author: Weiqun Zhang Date: Fri Nov 24 08:40:25 2017 -0800 throw error if gcc < 4.8 Tools/GNUMake/comps/gnu.mak commit 4abf1dc03f130f2bd67cee7b7b00d282c11efbec Merge: d5c9e4828 1a00814ec Author: Marc Day Date: Wed Nov 22 14:36:34 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 22b62209a9bd0125a7e324e24efe3a6f30fa3d44 Author: dtgraves Date: Wed Nov 22 13:48:32 2017 -0800 we now have three versions of time interpolation. for super smooth problems, the simply polynomial seems to work best. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 1a00814ec3856d41880d4dfe55543004ae7cb953 Author: Tan Nguyen Date: Wed Nov 22 13:04:33 2017 -0800 add a function that returns the number of data states Src/Amr/AMReX_AmrLevel.H commit 95755b87e46a1fbda5ef45eabae95247e37e3caa Merge: 2b4070db9 2d891c709 Author: Andrew Myers Date: Wed Nov 22 11:51:38 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2b4070db918915fe66be2bdd76eabdfe0746db73 Author: Andrew Myers Date: Wed Nov 22 11:51:28 2017 -0800 functions for growing all the boxes in a BoxArray in a given direction on only the lo / hi side. Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 2d891c70997a0407b883fe7f2b25d650f49fe4db Author: Weiqun Zhang Date: Wed Nov 22 11:30:07 2017 -0800 fix thread id Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit ac781886570ac32b95fcefd9437d4e40a644e732 Author: Weiqun Zhang Date: Wed Nov 22 11:20:14 2017 -0800 hopefully I fixed it this time. Shouldn't have done this before going out shopping Src/Base/AMReX_BoxArray.cpp commit 583ed71182b7ad8cb801064081e22de05b5d277c Author: Weiqun Zhang Date: Wed Nov 22 11:12:10 2017 -0800 fix a bug Src/Base/AMReX_BoxArray.cpp commit 5ea41e9c788c80da049c2b9987652062f1ffb502 Author: Weiqun Zhang Date: Wed Nov 22 11:06:16 2017 -0800 fix a typo Src/Base/AMReX_BoxArray.cpp commit 1b616d4829fe00f624e4e6afd3546c07c79f4e8a Author: Weiqun Zhang Date: Wed Nov 22 11:02:27 2017 -0800 optimizatin of BoxList::complementIn Src/Base/AMReX_BoxList.cpp commit 27010e10ba9f80568df50782378f619562b6a929 Author: Weiqun Zhang Date: Wed Nov 22 11:02:00 2017 -0800 OMP BoxArray::minimalBox() Src/Base/AMReX_BoxArray.cpp commit 3f2118a29236e187d7c439f4b5eccc2fe5eccac0 Author: Weiqun Zhang Date: Wed Nov 22 07:46:29 2017 -0800 added BoxList::swap and some minor changes Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit fd2590dadea5ceb42e4acced3249ae1c13ef83f3 Author: Weiqun Zhang Date: Wed Nov 22 07:33:47 2017 -0800 OMP BoxList::complementIn Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit ac8964896c1fb1ebaf83ce8158c077d4443392ba Author: Weiqun Zhang Date: Wed Nov 22 07:21:19 2017 -0800 A faster way of removing dupliates (which may break some regression tests). Added BoxList::reserve Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BoxList.H commit 2062722db8d7f7310ca4c7ea2b6ec41f25c1425e Author: Weiqun Zhang Date: Wed Nov 22 07:06:00 2017 -0800 fix typos Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp commit 0152dbf6c3067e859a1b6716614b280dda4bb39a Author: dtgraves Date: Tue Nov 21 15:53:40 2017 -0800 redid the math and recoded time interpolation for rk3/4. I am still losing an order in solution error but it looks pretty good. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit d891f85135cf1745a87ebe1b2011cdbb675a3da1 Merge: f528f097e 66407a7a8 Author: Andrew Myers Date: Tue Nov 21 14:56:18 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f528f097ec8019e8a991714bb62a79b6861f2ecb Author: Andrew Myers Date: Tue Nov 21 14:56:06 2017 -0800 enable users to turn off the MPI communication of certain particle components when filling ghost particles. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 66407a7a8fc4c81d51024ccc12b6da3fd5c4232c Author: Weiqun Zhang Date: Tue Nov 21 14:54:10 2017 -0800 Tutorials/LinearSolvers/ABecLaplacian_C Tools/RegressionTesting/AMReX-tests.ini Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/Make.package Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTestPlotfile.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest_F.H Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp Tutorials/LinearSolvers/ABecLaplacian_C/init_prob.F90 Tutorials/LinearSolvers/ABecLaplacian_C/inputs Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-abeclap-com Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-poisson-lev Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit 9169e44a90c19ab1ff8aa6d49530c3186d1f910a Merge: 73a469c04 312c9a460 Author: kngott Date: Tue Nov 21 13:17:08 2017 -0800 Merge branch 'profvis' of https://github.com/AMReX-codes/amrex into profvis commit ec1329f5f55161f6695b374f6337a89880e10b83 Author: Weiqun Zhang Date: Tue Nov 21 08:49:35 2017 -0800 add amrex:: Src/Base/AMReX_ParallelDescriptor.H commit 38d453427b3a1c0a5d677e7edd9c4d8fbdd9ef5c Author: dtgraves Date: Mon Nov 20 16:46:27 2017 -0800 more debugging hooks. new time interpolation not there yet. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit d27a90ff44b9640e180b12841ed761f4e8510186 Author: vince Date: Mon Nov 20 13:14:08 2017 -0800 use 5 digits in DATA_ string. we need to sync thses sizes. Src/Particle/AMReX_ParticleContainerI.H commit 98bf4e1532ea6d30fc2a01bef70985bb1c7616b0 Merge: 6db2b7ba4 896a2aa4a Author: WeiqunZhang Date: Fri Nov 17 20:44:59 2017 -0800 Merge pull request #165 from bcfriesen/EB_updates EB updates commit 6db2b7ba4d52006616667ca700edc699a70036ec Author: Weiqun Zhang Date: Fri Nov 17 20:42:35 2017 -0800 add README to the Fortran linear solver tutorial Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Tutorials/LinearSolvers/ABecLaplacian_F/README commit 5227757747c5b159c1efd561f6849fe014a6a41c Author: vince Date: Fri Nov 17 18:16:46 2017 -0800 remove diagnostic. Src/Base/AMReX_NFiles.cpp commit fd64246b2b1e091dc113cfe79620eb300d9fb33a Author: Weiqun Zhang Date: Fri Nov 17 17:00:54 2017 -0800 update regression tests Tools/RegressionTesting/AMReX-tests.ini Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-abeclap-lev Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-poisson-com commit 43aa6c6929536ade9c252ed4eb357c92b7f99f4f Author: dtgraves Date: Fri Nov 17 15:57:13 2017 -0800 have rk3 and rk4 time interpolation coded in john's new way. Now I Have to figure out whether my algebra or my coding (or both) are incorrect Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit 01477544ef432da90c2d37977fe23a8a98978b1a Author: Weiqun Zhang Date: Fri Nov 17 15:48:01 2017 -0800 Fixed a bug that causes segfault when making alias FabArray of alias. The bug was introduced 3 days in a255e56940fbf57 by me. Src/Base/AMReX_FabArray.H commit 43dace8bd4baf1649e3fcd1fe668f31c03ee55f0 Author: Andrew Myers Date: Fri Nov 17 15:20:15 2017 -0800 don't need to do this intersection any more. Src/Particle/AMReX_NeighborParticlesI.H commit 7e39e6f2eddffa31f7c769666a730a243daa15a3 Author: Weiqun Zhang Date: Fri Nov 17 15:19:08 2017 -0800 finished Fortran linear solver tutorial Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit ccdb0141f2247c3d967e138ec68273fe8cd02af8 Author: Weiqun Zhang Date: Fri Nov 17 13:04:41 2017 -0800 implement amrex_abeclaplacian_module Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linear_solver_mod.F90 commit f8d735915992f10ffddc6a2506ba049faef4a677 Author: Andrew Myers Date: Fri Nov 17 14:04:33 2017 -0800 this loop only needs to go over the real particles, not the real + neighbors. Src/Particle/AMReX_NeighborParticlesI.H commit af0c7e9350f65274dd4c5fb2cb98166ae49e2be3 Merge: f319ddeb4 18cee043e Author: vince Date: Fri Nov 17 13:33:48 2017 -0800 merge fixes. commit f319ddeb43f76a3c488276da95a15f67839eec4c Author: vince Date: Fri Nov 17 13:21:47 2017 -0800 use dss from nfilesiter. Src/Base/AMReX_NFiles.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 92ef11309d72453cd9316638dd61f6c3ce80f1aa Author: dtgraves Date: Fri Nov 17 12:55:08 2017 -0800 added in new style fourth-order limiting Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 285b10a86168a316e2b51b01b8102a14d8e2fb09 Merge: 81abe9f17 0cda1c36d Author: vince Date: Fri Nov 17 12:35:42 2017 -0800 Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio commit 0cda1c36da278f9c33382b2c1c913ef4342310cd Author: vince Date: Fri Nov 17 12:35:20 2017 -0800 use long. Src/Extern/ProfParser/AMReX_CommProfStats.cpp commit 81abe9f17987d4323eb830807375d2a5b3aad75a Merge: 83c6c4c74 c181bb6d8 Author: vince Date: Fri Nov 17 12:25:06 2017 -0800 merge fix. commit 83c6c4c7428ba2a22f06ab930200630a71bf9f51 Author: vince Date: Fri Nov 17 12:23:45 2017 -0800 init value. Src/Particle/AMReX_ParticleContainerI.H commit e91469f63543cbe9576f91a9f1e9be8695c4d242 Author: vince Date: Fri Nov 17 12:23:14 2017 -0800 parser fixes. Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit bf086cb8ec3e9047b782aca90182ef425ea5b76e Author: vince Date: Fri Nov 17 12:20:30 2017 -0800 fix comment. Src/Base/AMReX_NFiles.H Src/Base/AMReX_VisMF.cpp commit c181bb6d88bacdf3159dbc4744160b5c2ff64c93 Author: vince Date: Fri Nov 17 12:15:47 2017 -0800 use rank for sparse file number. Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_VisMF.cpp commit 18cee043e05fa5338db7cd88eb9994ef0f4870f0 Merge: e1a858220 7ce6a4548 Author: Andrew Myers Date: Fri Nov 17 11:06:46 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e1a858220bab450533684019e4752f766aa45d85 Author: Andrew Myers Date: Fri Nov 17 10:57:04 2017 -0800 removing a couple of now un-needed functions. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 7ce6a45484395a3803aa9dabe64b62f869404ed9 Author: Weiqun Zhang Date: Fri Nov 17 10:56:04 2017 -0800 add amrex_average_cellcenter_to_face to amrex_multifabutil_module Src/F_Interfaces/Base/AMReX_multifabutil_fi.cpp Src/F_Interfaces/Base/AMReX_multifabutil_mod.F90 Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit dc30bacc6132435781f30090e4d15ade2831fd6f Merge: d3f65bab6 9b74a8305 Author: Andrew Myers Date: Fri Nov 17 10:39:52 2017 -0800 merging. commit d3f65bab68e3d6cb9f7d42df3cfdda74ee0c0f58 Author: Andrew Myers Date: Fri Nov 17 10:33:43 2017 -0800 reduce temporary copies in the neighbor particle code. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 48413f69cada425f28c435005a55731e43425cb4 Author: Andrew Myers Date: Fri Nov 17 10:33:06 2017 -0800 more efficient to insert these at the end, rather than the beginning. Src/Particle/AMReX_ParticleContainerI.H commit 9b74a83053f5e74b8d26cb3a39f5fb8071ef1db9 Author: Weiqun Zhang Date: Fri Nov 17 10:14:40 2017 -0800 port more features of MFIter from C++ to Fortran CHANGES Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 24f8e11af67dad62e49efee627ee636e9d2e73ea Merge: 5fd547e94 e5af0134f Author: vince Date: Thu Nov 16 17:54:09 2017 -0800 Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio commit e5af0134f78a2dc10e4b0cd12246046de7f11a49 Author: vince Date: Thu Nov 16 17:52:55 2017 -0800 header diagnostics for sparse fabarray writes. Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 9176ca9099da3801cf7b240bc9415692f40a0765 Author: vince Date: Thu Nov 16 17:50:21 2017 -0800 temp flush fix. Src/Amr/AMReX_Amr.cpp commit 263a73e28b7230f6e29b60d82dfa3b3dd83df089 Author: Weiqun Zhang Date: Thu Nov 16 17:11:43 2017 -0800 Fortran linear solver tutorial: init abeclapacian coefficients Tests/LinearSolvers/MLMG/fort_3d.F90 Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 5b0fa5675d5efe2dc8dd976d3d454afc491f085a Author: Weiqun Zhang Date: Thu Nov 16 16:45:11 2017 -0800 Fortran linear solver tutorial: level by level poisson solve works Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 609a17077141c675c67c52e05c8ceb7de37f2b60 Author: Weiqun Zhang Date: Thu Nov 16 15:03:57 2017 -0800 rename setBCWithCoarseData to setCoarseFineBC Src/F_Interfaces/LinearSolvers/AMReX_linop_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 7b63c32b65698544f114102a82260af55f582c16 Author: Weiqun Zhang Date: Thu Nov 16 14:31:51 2017 -0800 Fortran linear sovler tutorial works for compsite Poisson Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 77126202317d23dcc4774dbf89e5f3fe27c8de75 Author: Weiqun Zhang Date: Thu Nov 16 14:25:23 2017 -0800 add more functions to Fortran amrex_multifab_module CHANGES Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit d5c9e482836b59717245d0fcac0ca0624af32094 Merge: a7024ad0c 15db38af6 Author: Marc Day Date: Thu Nov 16 14:20:49 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 15db38af63a46440a4e356a6648a826fea254b48 Author: Weiqun Zhang Date: Thu Nov 16 13:10:03 2017 -0800 fix typo in amrex_multigrid_module Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 commit ff7b3f55f8ae7be16ae89785a8362f8a5c5805c9 Author: Weiqun Zhang Date: Thu Nov 16 12:05:37 2017 -0800 fix omp bug in amrex_geometry_module; more on the linear solver tutorial Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 commit 35866fe0668082eb70823ce01a74687cf4f25876 Author: Weiqun Zhang Date: Thu Nov 16 12:03:29 2017 -0800 fix omp bug in amrex_geometry_module; more on the linear solver tutorial Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 commit 0efcc01d92b1c955cf5780494274402e9cfcd33f Author: Weiqun Zhang Date: Thu Nov 16 12:02:21 2017 -0800 fix omp bug in amrex_geometry_module Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Tutorials/Basic/HeatEquation_EX1_F/init_phi.f90 Tutorials/LinearSolvers/ABecLaplacian_F/Make.package Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 84e1d694df425f34daad112697df0ce1703b13dc Author: Weiqun Zhang Date: Thu Nov 16 10:30:11 2017 -0800 amrex_box_module: add coarsen and refine Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 78051c2ed5c13b2b22030895f30e6daab7725563 Author: Weiqun Zhang Date: Thu Nov 16 09:34:31 2017 -0800 add some functions to amrex_geometry_module for setting coordinates, problem domain and periodicity through funcitons instead of inputs Src/F_Interfaces/Base/AMReX_geometry_mod.F90 commit a2a86b437d8a201b746f22538466d43db04e2f7a Author: Weiqun Zhang Date: Thu Nov 16 08:55:06 2017 -0800 MLMG: test singularity on the bottom instead because it's cheaper Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit c517c5959ca53429bd881146c16ba9073740d423 Author: dtgraves Date: Thu Nov 16 08:50:09 2017 -0800 bug fixes in 4th order limiting. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit 2fd71f2228bd25ea66c6da69afee5b1476d162c1 Author: Weiqun Zhang Date: Wed Nov 15 18:09:11 2017 -0800 F_Interfaces/LinearSolvers: finished amrex_multigrid_module Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 commit 7ced2c8ce73e481fa64638115efaac622f3ce3e0 Author: dtgraves Date: Wed Nov 15 16:30:00 2017 -0800 slogged my way through writing the limiting code a la mccorquodale. The limiting versions still untested. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit 72a6278864ec4bbf0580ba83aaad6981cf79cd61 Author: Brian Friesen Date: Wed Nov 15 14:56:40 2017 -0800 IOBenchmark: make only master thread flush and close file in thread-shared IO Tests/IOBenchmark/IOTestDriver.cpp commit 902435948747cf50fddb54a0c572386cd943a41b Author: Weiqun Zhang Date: Wed Nov 15 14:28:31 2017 -0800 F_Interfaces/LinearSolvers: wip Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linear_solver_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 Src/F_Interfaces/LinearSolvers/Make.package Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit b6e09aa1ab794b50fb64f6b560ce320d013c2610 Author: Weiqun Zhang Date: Wed Nov 15 13:14:25 2017 -0800 F_Interfaces/LinearSolvers: WIP Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_linop_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 Src/F_Interfaces/LinearSolvers/Make.package Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 3efacbb06ef95101622f8e524de5428a0c3cae1e Author: Weiqun Zhang Date: Wed Nov 15 09:40:56 2017 -0800 start F_Interfaces/LinearSolvers Src/Base/AMReX_string_mod.F90 Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_lo_bctypes_mod.F90 Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linear_solver_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 Src/F_Interfaces/LinearSolvers/Make.package Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/Make.package Tutorials/LinearSolvers/ABecLaplacian_F/inputs Tutorials/LinearSolvers/ABecLaplacian_F/main.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 3eeeb89db8f401093820df4b0eee5edd75622b84 Author: Michael Zingale Date: Wed Nov 15 13:57:03 2017 -0500 add the total time to the summary page Tools/RegressionTesting/regtest.py Tools/RegressionTesting/test_report.py commit ad6616dacc116cbb1e70db271dccc7867a635f48 Merge: 4d4d4fa19 b2d4214db Author: Michael Zingale Date: Wed Nov 15 13:38:51 2017 -0500 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit 4d4d4fa19e318a7d33f30f0b5d0118e8ab1b161e Author: Michael Zingale Date: Wed Nov 15 13:38:41 2017 -0500 quote slack posts Tools/RegressionTesting/regtest.py commit b2d4214db788e2a1293c2a83d38c8273b65b84a2 Merge: 3ffe320c9 b443b6f50 Author: WeiqunZhang Date: Wed Nov 15 08:09:03 2017 -0800 Merge pull request #167 from AMReX-Codes/fillpatchadd Add a FillPatch that adds, not copies commit b443b6f5027273844d5a5d275dc0ed3982e36506 Author: Max Katz Date: Wed Nov 15 01:59:44 2017 -0500 Add a FillPatch that adds, not copies Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit eaf87c41596d4fc59d6f079b5a92b184d8941b84 Author: dtgraves Date: Tue Nov 14 16:07:00 2017 -0800 put in hooks and started code for fourth order limiting. This stuff is complex. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 3ffe320c9a67c374e0d97716975bdc601c903da3 Author: Weiqun Zhang Date: Tue Nov 14 15:49:10 2017 -0800 MLMG: make some changes so that Cy can put in his mapping Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 5fd547e942a2552624feb818dcc85abf82795dae Merge: 581231929 6e277ef9c Author: vince Date: Tue Nov 14 13:46:09 2017 -0800 Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio commit 6824aa2be64a1a14ea61601e10306004fac7c316 Author: Weiqun Zhang Date: Tue Nov 14 13:42:20 2017 -0800 update CHANGES CHANGES commit f0d03f16b365994e90255fba3c354005d4160484 Author: Weiqun Zhang Date: Tue Nov 14 13:21:51 2017 -0800 Tutorials/Amr/Advection_AmrCore: add memory log Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 839cbf6a99c85c8e9d5ba0e551a3a6b0745af45f Author: Weiqun Zhang Date: Tue Nov 14 13:20:26 2017 -0800 manually write MultiFab move ctor so that build can be logged Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit a255e56940fbf57b75683c4f236d03b1b2bff645 Author: Weiqun Zhang Date: Tue Nov 14 12:48:05 2017 -0800 FabArray: clear before define; Tutorials/Amr/Advection_AmrCore: use Vector Src/Base/AMReX_FabArray.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 2b858dda315c969cb447c60fe63e463fff0b4f14 Author: Weiqun Zhang Date: Tue Nov 14 11:45:10 2017 -0800 add clear() to FluxRegister Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp commit 6b7df9a9b50c7a425ccf00eb282c1cd106375375 Author: Weiqun Zhang Date: Tue Nov 14 11:22:44 2017 -0800 implement move assignment operator for FabArray Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_iMultiFab.H commit 736829d5382596454ef846c6b3c3e18156f38adc Merge: 1844db91f bea583464 Author: Weiqun Zhang Date: Tue Nov 14 09:14:04 2017 -0800 Merge branch 'development' into moveassign commit bea583464af6d06e2ac09e09d992ad5a213f18d2 Author: Weiqun Zhang Date: Tue Nov 14 09:13:22 2017 -0800 add GetVecOfPtrs again for FabArray types only Src/Base/AMReX_Vector.H commit 93b2b2eadd9b5fd89dcb14ebb06e91cd66d4fa9a Author: Weiqun Zhang Date: Mon Nov 13 20:49:05 2017 -0800 revert Src/Base/AMReX_Vector.H commit 1844db91fc7526b3e58895bdf5f6d5cb4c185156 Author: Weiqun Zhang Date: Mon Nov 13 17:35:31 2017 -0800 start writing move assignment for MultiFab and FabArray Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H commit 6c7b3162e8347142749c179b569fa1caa0759b78 Author: Weiqun Zhang Date: Mon Nov 13 17:34:12 2017 -0800 add GetVecOfPtrs Src/Base/AMReX_Vector.H commit 6e277ef9c1a80baf89a88784834099cf24552087 Author: vince Date: Mon Nov 13 17:31:46 2017 -0800 remove flush. Src/Amr/AMReX_Amr.cpp commit 5812319295280292890b6ee5d707c35abda62ff2 Merge: f6732ebc5 ddadcab92 Author: vince Date: Mon Nov 13 16:28:29 2017 -0800 Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio commit ddadcab9232f9c1c2559e77894989b32cd408df6 Author: vince Date: Mon Nov 13 16:19:13 2017 -0800 additions for pre and post checkpoint functions for i/o optimization. Src/Base/AMReX_NFiles.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 0039b3b0a6ba896cdb37ee68e3f547e3b78c6c1c Merge: 8a7a43eaf ec0eb76a8 Author: dtgraves Date: Mon Nov 13 15:54:37 2017 -0800 merging with dev commit 8a7a43eaf07e9b698eeb584ec9d77ab2dbe45acd Author: dtgraves Date: Mon Nov 13 15:52:34 2017 -0800 added the hooks in the fortran to make limiting optional Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90 commit ec0eb76a8174e352e08d593e4071de753e89ec02 Merge: 7fcd29430 4f87f1010 Author: Andy Nonaka Date: Mon Nov 13 14:32:17 2017 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7fcd29430ce25aff458bff267e4317f8e91ea162 Author: Andy Nonaka Date: Mon Nov 13 14:32:02 2017 -0800 add a CountCells function Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit ebfac58b1bb6cb9bab1a2250d3fb1150a6a0b387 Author: dtgraves Date: Mon Nov 13 14:11:45 2017 -0800 cleaned up code--can now switch algorithm choice via the input file Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 4f87f10102033b3709ef3e4b43e738f662423cb8 Author: Weiqun Zhang Date: Mon Nov 13 13:21:14 2017 -0800 add MLMG to libamrex GNUmakefile.in Tools/libamrex/configure.py commit 12f13ece08e31e9e78ad79908776e6bfae1a698c Merge: 45e0c71de a7923daf3 Author: Andrew Myers Date: Mon Nov 13 13:23:28 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2b625353c2cc6e4df1d48d1cb43bdb46a92a8456 Author: vince Date: Mon Nov 13 13:00:09 2017 -0800 additions for pre and post checkpoint functions for i/o optimization. Src/Particle/AMReX_Particles.H commit 9e4ef2f3f77ecc732fe775b743f7a2d25a3136c0 Author: vince Date: Mon Nov 13 12:59:13 2017 -0800 added particle nfiles. Docs/Readme.io commit b03d1b24f632169b2b7d6ef4835f35dfa7d3f328 Author: vince Date: Mon Nov 13 12:52:00 2017 -0800 additions for pre and post checkpoint functions for i/o optimization. Src/Particle/AMReX_ParticleContainerI.H commit fca80946282c6c83563fb9aaf4fd5f3001882e73 Author: vince Date: Mon Nov 13 12:51:10 2017 -0800 increase default nfiles. Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_VisMF.cpp commit 7323cd6e3345fcbb0a25f8c23b9e32e37ee15203 Author: vince Date: Mon Nov 13 12:49:27 2017 -0800 additions for pre and post checkpoint functions for i/o optimization. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit c53f60503806118693a73ef0fb4a967856c796c7 Author: dtgraves Date: Mon Nov 13 12:01:09 2017 -0800 made progress on algorithm document Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Doc/references.bib commit a7923daf30310a6be28917083b15975e9a1bac3e Author: Weiqun Zhang Date: Mon Nov 13 11:00:18 2017 -0800 MLMG: some experimental approaches in consolidation Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 45e0c71de17f9acbff8ba31d2b03e8f3dfab15b8 Author: Andrew Myers Date: Mon Nov 13 10:38:23 2017 -0800 exit early from Redistribute if particle is invalidated. Src/Particle/AMReX_ParticleContainerI.H commit a54a1c1292f0e8341f0e1bc4e506d415861f0fb0 Author: Weiqun Zhang Date: Sat Nov 11 20:39:39 2017 -0800 add some profilers Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a049f7deff2314ba007e2ea9eede013cd989146b Author: Weiqun Zhang Date: Sat Nov 11 12:09:51 2017 -0800 fix a new bug in MLMGBndry Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit da8312a8a9ba375a0c8fe729c676813301fcb093 Author: Weiqun Zhang Date: Sat Nov 11 10:48:04 2017 -0800 omp parallel Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit 2d0d0e2d248ea16bdc35a4d2d9e0a85c0b8c23e7 Author: Weiqun Zhang Date: Sat Nov 11 10:30:52 2017 -0800 add MLMGBndry Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_LO_BCTYPES.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Src/LinearSolvers/MLMG/Make.package commit 2089f4f6b92115163d9e3c8371d1fcfc5099385b Merge: f39f47096 d789da394 Author: Max Katz Date: Sat Nov 11 01:42:45 2017 -0500 Merge branch 'development' into gpu commit d789da39407902d684bb6b6e3ad195839cde847b Author: Weiqun Zhang Date: Fri Nov 10 17:52:14 2017 -0800 MLMG: add ReflectOdd and divide flux by beta Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H commit 312c9a4604af3f6c7faa965f6be3956f3741f059 Author: kngott Date: Fri Nov 10 14:53:38 2017 -0800 Optimization tweaks. Src/Extern/amrdata/AMReX_DataServices.cpp commit 2b71112585323ba25ab05384221be6dcd15b928a Merge: 973281396 650b8c04c Author: Andrew Myers Date: Fri Nov 10 14:20:10 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 973281396cda107ff214b54da265fc1e1b92845b Author: Andrew Myers Date: Fri Nov 10 14:19:49 2017 -0800 some optimizations for neighbor particle finding and updating. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 650b8c04c9dd4a001b7f8720e0a01a54e49a411e Author: Weiqun Zhang Date: Fri Nov 10 12:00:15 2017 -0800 MLMG: fix 2d Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 780458f37412f83dd84def7305150b2e4b95108a Author: Weiqun Zhang Date: Fri Nov 10 11:51:42 2017 -0800 MLMG: remove static memebers Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit b8fc8db9028d57f13abc2877bb1ad89046861095 Author: Weiqun Zhang Date: Fri Nov 10 10:26:26 2017 -0800 MLMG: option to disable metric terms Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 73a469c041f0bcde2f0dc5b1b152ec93b6fb63c3 Merge: febfc2b63 085004c86 Author: kngott Date: Thu Nov 9 18:09:04 2017 -0800 Merge branch 'partio' into profvis Conflicts: Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit febfc2b63a1ffe2404b2ed19b575561e10ffd73c Author: kngott Date: Thu Nov 9 17:31:45 2017 -0800 One more adjustment. Src/Extern/ProfParser/AMReX_CommProfStats.cpp commit 377a54534cf7ab2d1128753120621caeb1d5924d Author: kngott Date: Thu Nov 9 17:27:29 2017 -0800 OpenStreams adjustment. Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit 7c437eae5d103343b8d0dd75956edfaea7f12a72 Author: Weiqun Zhang Date: Thu Nov 9 16:44:15 2017 -0800 MLMG: option to fill final bc Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 979ea8c53ba5920b258af925c12d0132575d135f Author: kngott Date: Thu Nov 9 16:26:20 2017 -0800 bl_profprof Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp commit c317be1565c7078fcb829e847f7a3b2759d9f860 Author: dtgraves Date: Thu Nov 9 16:06:37 2017 -0800 working on more detailed document for this tutorial Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Doc/references.bib Tutorials/Amr/ScalarAdvectionDiffusion/Doc/working_notes.tex commit db78cafabd41d218098679bbd217ea91110a8601 Author: kngott Date: Thu Nov 9 15:41:36 2017 -0800 Additional/Corrected profiling flags in profiler. Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 7b6b5093b49b848c49c29dcd4d8c4223c9242bc0 Author: Weiqun Zhang Date: Thu Nov 9 14:50:40 2017 -0800 MLMG: fix periodic boundary Src/Base/AMReX_Geometry.H Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 62059c1cb79cd2d60de31848e98878b930a63006 Merge: 17ea691dc 4e9d84d14 Author: dtgraves Date: Thu Nov 9 13:50:36 2017 -0800 merging with dev branch commit 4e9d84d1405b880b8cdac5528c55f6107357cc1b Author: kngott Date: Thu Nov 9 12:41:28 2017 -0800 Fixed incorrect bool. proxMap -> statsCollected Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 17ea691dc7e59843bc680acc2cd5b0e697f45b7e Author: dtgraves Date: Thu Nov 9 12:39:54 2017 -0800 fixed time interpolation for TVD RK3 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit fc290d8d358581a9c88905e54b50bc47abe3e8a5 Author: Weiqun Zhang Date: Thu Nov 9 11:15:42 2017 -0800 MLMG: fix the special case of alpha is zero Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 00799f9ccaf30bba79e3a47408ea7253cbde4a97 Author: Weiqun Zhang Date: Thu Nov 9 10:54:32 2017 -0800 MLMG: fix spherical Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit cb53b2160cb878b3159d666a5c2c9d7db5991562 Author: Weiqun Zhang Date: Thu Nov 9 10:49:22 2017 -0800 MLMG: skip applying metric terms in Cartesian Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 085004c861884a5d8158e05b765b144684b6b0f9 Author: vince Date: Wed Nov 8 17:57:57 2017 -0800 add sparse vismf write for fabarrays with data on fewer mpi procs than nfiles. Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_VisMF.cpp commit f97ef7d806351c3ed5640ed3a69843a3c28a0e8d Author: Weiqun Zhang Date: Wed Nov 8 17:39:18 2017 -0800 MLMG test: option to do fine level solve only Tests/LinearSolvers/MLMG/inputs.boxes Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 7b253814ef83f7b7ee209c70c2a2970d2a63603f Author: Weiqun Zhang Date: Wed Nov 8 17:29:27 2017 -0800 MLMG test: option to read grids Tests/LinearSolvers/MLMG/grids/gr.3_128cubed Tests/LinearSolvers/MLMG/grids/gr.3_256cubed Tests/LinearSolvers/MLMG/grids/gr.3_2boxes_a Tests/LinearSolvers/MLMG/grids/gr.3_2x3x4 Tests/LinearSolvers/MLMG/grids/gr.3_512cubed Tests/LinearSolvers/MLMG/grids/gr.3_big Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_a Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_b Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_c Tests/LinearSolvers/MLMG/grids/gr.3_mac_tst Tests/LinearSolvers/MLMG/grids/gr.3_shiftedUp Tests/LinearSolvers/MLMG/grids/gr.3_small_a Tests/LinearSolvers/MLMG/grids/gr.3_stack_a Tests/LinearSolvers/MLMG/grids/grids.15456.REMOVED.git-id Tests/LinearSolvers/MLMG/grids/grids.213 Tests/LinearSolvers/MLMG/grids/grids.25600.REMOVED.git-id Tests/LinearSolvers/MLMG/grids/grids.5034 Tests/LinearSolvers/MLMG/inputs.boxes Tests/LinearSolvers/MLMG/main.cpp commit fa99de392d90827ea580526d2024fc419b55b30c Author: dtgraves Date: Wed Nov 8 16:58:32 2017 -0800 fixed loop bound bug in 3d fortran Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 496b09ca925fcee7b9cf21f3f65cc5bff8586f1f Author: Weiqun Zhang Date: Wed Nov 8 16:24:15 2017 -0800 MLMG: if scalar a is zero, we can simply set coefficient to zero Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 550b0f395d53d018d01608b38875fc345bf226b0 Author: kngott Date: Wed Nov 8 14:09:38 2017 -0800 Testing and turning off of persistent streams for profparser when number of files is extremely large. Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit e027b66a1b4ba761a05fcb98751390d4f7027362 Author: kngott Date: Wed Nov 8 13:56:49 2017 -0800 Output cleanup for MoveAllFabs and MoveFabs. Src/Base/AMReX_FabArray.H commit 4e707546b2af7a6e7fc1283387e19de4ab95b159 Author: kngott Date: Wed Nov 8 13:45:26 2017 -0800 MoveAllFabs adjustment to allow testing at any number of procs. OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp commit cd5ebbd1571457a5a318a216da49d413e20ff528 Author: dtgraves Date: Wed Nov 8 13:37:17 2017 -0800 convergence results look pretty good Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit d10e8470208a1d76b444edb9583c5e0404d3b308 Author: dtgraves Date: Wed Nov 8 13:20:41 2017 -0800 finished coding time interpolation for TVD rk3 scheme. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 41566c1f9f47082f3da7aebc930286de914ba96b Author: Weiqun Zhang Date: Wed Nov 8 09:36:53 2017 -0800 MLMG test: add option to do level by level solve Tests/LinearSolvers/MLMG/inputs Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit a2538e19815c237825fc4926bbef1d48a5722400 Author: Weiqun Zhang Date: Wed Nov 8 09:36:21 2017 -0800 MLMG: agglomeration and consolidation flags need to be static because they are used by the constructor Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit c81eba6fa74fb73e5fe3291a42178befb414422d Author: Weiqun Zhang Date: Tue Nov 7 16:55:12 2017 -0800 MLMG: 1d implemented but not tested Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 0ad3ad6dc2e888e7ece7d58a814190c23d45fd1a Author: Weiqun Zhang Date: Tue Nov 7 16:39:59 2017 -0800 MLMG: 1d Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 commit 78979b7305bc92d97a4d4eed7b78f0bcc6ed4b33 Author: Weiqun Zhang Date: Tue Nov 7 15:59:29 2017 -0800 MLMG: add getGradSolution function Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/Make.package commit cbe027384af687c83dd68cbed0c729bdc9978cc5 Author: vince Date: Tue Nov 7 15:52:05 2017 -0800 more information for errors. Src/Extern/amrdata/AMReX_DataServices.cpp commit ff8c0751f321975fbbaea9dd0495c107b2878d04 Author: Weiqun Zhang Date: Tue Nov 7 15:22:42 2017 -0800 MLMG: metric terms for ABecLaplacian Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 850adf15363ee50e0267abac1bc99f5b6bd017c7 Author: Weiqun Zhang Date: Tue Nov 7 13:56:44 2017 -0800 MLMG: 2d and cylindrical coordinates Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H commit 896a2aa4ac6b4329da493b9f461b64cea6d5aff8 Author: Brian Friesen Date: Tue Nov 7 14:16:08 2017 -0800 EB: change type of get_neighbor_cells_int_single() function from PURE to ELEMENTAL ELEMENTAL is a stronger statement about the function's behavior, and implies PURE anyway. Src/EB/AMReX_ebcellflag_mod.F90 commit c310946090f2b27113312d1777630f53807f5e02 Author: dtgraves Date: Tue Nov 7 14:08:47 2017 -0800 now seeing third order solution error with AMR Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 4474ad6259312e9bcece9040f8b4f698a6f1a367 Author: Brian Friesen Date: Tue Nov 7 12:58:54 2017 -0800 EB, Combustor: add function get_neighbor_cells_int_single() This function behaves similarly to get_neighbor_cells_int(), except it returns a single value for the requested neighbor cell, rather than returning a 3x3x3 array containing values for all neighbors. This single-value approach is friendlier to function inlining and vectorization, and also yields better memory access patterns because a compiler attempting to vectorize a loop which calls this function need not generate private 3x3x3 arrays for each lane of a vector processing unit. Src/EB/AMReX_ebcellflag_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 commit 68e96074df6e8716f6ac61a92214929cb16299c3 Author: Andrew Myers Date: Tue Nov 7 12:40:41 2017 -0800 also cache the grown_gridbox in EnforcePeriodicWhere. Src/Particle/AMReX_ParticleContainerI.H commit a4ed403519a45d0d6cd7bc75e360dfefe265427a Author: dtgraves Date: Tue Nov 7 12:31:29 2017 -0800 now getting fourth order truncation error with AMR Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/fourthOrderCFInterpTest.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/test.inputs commit 6192580e7b8c1529b5bad9679c40baf579f4c933 Merge: ff6173777 ae8d7ea1c Author: Andrew Myers Date: Tue Nov 7 11:26:08 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ff61737775b2c3b9f02074fd22f86ad00065f880 Author: Andrew Myers Date: Tue Nov 7 11:25:57 2017 -0800 reset the pld cache after trying the grown particle locate (the next one might not have the same nGrow) Src/Particle/AMReX_ParticleContainerI.H commit ae8d7ea1c76494e7b30f3fdee1fcd53cb39cbc94 Author: Weiqun Zhang Date: Tue Nov 7 10:16:29 2017 -0800 PlotFileUtil: option to pre-build extra directories in plotfile Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit 1b478778da7e95ce970a5c251d3635625cf2e243 Author: Weiqun Zhang Date: Tue Nov 7 09:37:30 2017 -0800 PlotFileUtil: use default in VisMF Src/Base/AMReX_PlotFileUtil.cpp commit f39f4709642a8331f9b83f9bb2f6fa53d245d69d Author: Max Katz Date: Mon Nov 6 21:34:22 2017 -0500 Add C binding to get_loop_bounds Src/Base/AMReX_Device.H Src/Base/AMReX_fort_mod.F90 commit a7024ad0cfeabb9566cdf0b0fc0a2215c8577ad0 Author: Marc Day Date: Mon Nov 6 18:22:35 2017 -0800 Lower limit error mag for computing order Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit 7d6fab52063b6b9a4443085f737301c3c79c9d04 Author: Andrew Myers Date: Mon Nov 6 17:43:26 2017 -0800 try four. build_and_deploy.sh commit 5d4b2e4899741d27d664ef20e869f7dffbcfb9f2 Author: Andrew Myers Date: Mon Nov 6 17:37:56 2017 -0800 try two make jobs build_and_deploy.sh commit cf29cf52eda2dccd328453587cf482dc00fa0dc0 Author: Andrew Myers Date: Mon Nov 6 17:31:18 2017 -0800 do serial build. build_and_deploy.sh commit 5472034128a5d7e6e33159e95a40a468734f5fac Author: Andrew Myers Date: Mon Nov 6 17:25:23 2017 -0800 have travis build libamrex on each push. .travis.yml build_and_deploy.sh commit 72110d805a00b6cd7ae13281f3d2c2beee7bd08f Merge: 2b373b845 cb6b1ab7e Author: Max Katz Date: Mon Nov 6 20:23:55 2017 -0500 Merge branch 'development' into gpu commit cb6b1ab7e578dc529bf33b74e7941749bf7965e1 Author: Andrew Myers Date: Mon Nov 6 16:45:37 2017 -0800 another Redistribute optimization. Src/Particle/AMReX_ParticleContainerI.H commit 8896ca2c14963003854bd2de255adac0ceced00e Author: dtgraves Date: Mon Nov 6 16:17:38 2017 -0800 added test for coarse-fine interpolation. FillPatchUtil with quartic_interp is indeed fourth order Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/fourthOrderCFInterpTest.cpp commit ec981019492f6c73fd07cd324b60069806e74ea1 Author: Andrew Myers Date: Mon Nov 6 16:14:47 2017 -0800 an optmization for ParticleContainer::Redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 08215dad8381537a48fcca632760ccf3bb5dfdd0 Merge: b3befde03 a2963d91e Author: Andrew Myers Date: Mon Nov 6 12:10:43 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a2963d91ed59bae3e40c23cfd2046ffa44466ef5 Author: Weiqun Zhang Date: Sun Nov 5 12:46:41 2017 -0800 MLMG make applybc work for any d Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/Make.package commit 3ba47937101ce88c1170ac43d06e1843a8237fa1 Author: Weiqun Zhang Date: Sun Nov 5 12:23:50 2017 -0800 MLMG: implement 2D version of some funcitons Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 commit 40cacbba99d1bafb1c321a4c18531124f116642e Author: Weiqun Zhang Date: Fri Nov 3 09:08:05 2017 -0700 fix for the most vexing parse in C++ Src/F_Interfaces/Base/AMReX_geometry_fi.cpp commit 4bf59972097749a540528d7bee0e2727ce380b98 Author: Weiqun Zhang Date: Fri Nov 3 09:05:28 2017 -0700 fix particle module for 1d Src/Particle/AMReX_Particle_mod_1d.F90 commit 5dc6ec5b0fc641ec56d1b4a4822ac1bb1dd05d87 Author: Michael Zingale Date: Fri Nov 3 11:43:11 2017 -0400 warn if analysis failed and store analysis output Tools/RegressionTesting/regtest.py commit b410e11279c3063a81287e8085ae80fb8469eb88 Author: Michael Zingale Date: Thu Nov 2 20:03:16 2017 -0400 quote slack posts Tools/RegressionTesting/regtest.py commit 2e48372f3271dbefb95e12bd79b1ab90ca714147 Author: Neil Carlson Date: Thu Nov 2 12:55:13 2017 -0600 Use amrex_constants_module in amrex_filcc_2d Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 commit 19807295d3d4dd637a7d986f732191d0680470ef Author: Max Katz Date: Thu Nov 2 14:09:41 2017 -0400 Add protections against accessing invalid dimensions Src/Base/AMReX_filcc_mod.F90 commit 929b4d6362a1d7dcfa35dffff6b932223ab6db65 Author: Neil Carlson Date: Thu Nov 2 10:41:13 2017 -0600 Use amrex_constants_module in amrex_filcc_3d; trivial nag fix Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit 6f01652b4c44f523e984f2cca34f2853d3d434d8 Author: Weiqun Zhang Date: Wed Nov 1 17:23:50 2017 -0700 use amrex_constants_module in amrex_filcc_module Src/Base/AMReX_filcc_mod.F90 commit 4af830ad50d04d634a46a4bbeaa2d60d095ed82b Author: Weiqun Zhang Date: Wed Nov 1 17:20:25 2017 -0700 add amrex_constants_module and make bl_constants_module use it Src/Base/AMReX_constants_mod.f90 Src/Base/CMakeLists.txt Src/Base/GPackage.mak Src/Base/Make.package Src/F_BaseLib/bl_constants.f90 commit 77691daf7dcc00e0db09cec4e2b5ccfc32f3f049 Merge: c1cc71bf7 520fc965d Author: Weiqun Zhang Date: Thu Nov 2 12:52:03 2017 -0700 Merge branch 'weiqun/mlmg' into development commit 520fc965d9a84099893d62d508ae125d39aa35c3 Author: Weiqun Zhang Date: Thu Nov 2 12:51:22 2017 -0700 MLMG: must use the fine dx for bc location on coarse MG levels Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit c1cc71bf72064d4f6a12f46f1673d296b6813363 Merge: cddd586d7 be53255a3 Author: WeiqunZhang Date: Thu Nov 2 11:59:51 2017 -0700 Merge pull request #163 from nncarlson/constants-fix Use amrex_constants_module in amrex_filcc_2d commit be53255a3ed57f024ad259198a8b81a64bb99101 Author: Neil Carlson Date: Thu Nov 2 12:55:13 2017 -0600 Use amrex_constants_module in amrex_filcc_2d Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 commit cddd586d7f1c9fc9064f79d119eaf59c7ae6b532 Author: Max Katz Date: Thu Nov 2 14:09:41 2017 -0400 Add protections against accessing invalid dimensions Src/Base/AMReX_filcc_mod.F90 commit b3befde0304276200a0db6b1a11787573e11dea2 Merge: b395f0b6c 5dc0a3e70 Author: Andrew Myers Date: Thu Nov 2 10:05:04 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 63759e3ef979b1f5214013e44ddafbe1a1897998 Author: Weiqun Zhang Date: Thu Nov 2 10:02:44 2017 -0700 MLMG: simplify norm_inf calls Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 5dc0a3e704ccd79bddafc8648bf7b37f3595032a Merge: 114ccf19f cbc8b284b Author: WeiqunZhang Date: Thu Nov 2 09:47:49 2017 -0700 Merge pull request #161 from nncarlson/nag-fixes Use amrex_constants_module in amrex_filcc_3d; trivial nag fix commit cbc8b284b267a7e08f1f7ab20f3cfad3d47eddc4 Author: Neil Carlson Date: Thu Nov 2 10:41:13 2017 -0600 Use amrex_constants_module in amrex_filcc_3d; trivial nag fix Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit 81c763f1b3a75a30c82032fee6df725b35a853fd Merge: 8d239421c 114ccf19f Author: Weiqun Zhang Date: Thu Nov 2 08:48:00 2017 -0700 Merge branch 'development' into weiqun/mlmg commit 8d239421cce7dfcd63baf69c94718d5cb9883540 Author: Weiqun Zhang Date: Thu Nov 2 08:47:56 2017 -0700 minor Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit bb10dc27368452c1b564f11f63d007e4bdece9ef Author: Brian Friesen Date: Thu Nov 2 08:40:48 2017 -0700 EB: change INTENT of neighbor lists in get_neighbor_cells() to OUT Src/EB/AMReX_ebcellflag_mod.F90 commit 114ccf19f9ff2790345212bff201b1d36083d906 Author: atmyers Date: Wed Nov 1 18:12:34 2017 -0700 revert testing stuff for now. .travis.yml build_and_deploy.sh commit 2b762c52fdd139c16f5eca68119d1f0291cfc22d Author: atmyers Date: Wed Nov 1 18:02:39 2017 -0700 try openmpi and gfortran .travis.yml commit 57e997bf4dfab94e46bd823d5fd496dafee87dca Author: atmyers Date: Wed Nov 1 17:55:12 2017 -0700 add mpich to the packages to install .travis.yml commit cf76d815920c1f42c03507fbf73597ead13ece79 Author: atmyers Date: Wed Nov 1 17:36:24 2017 -0700 also test whether we can build libamrex in travis. build_and_deploy.sh commit 1ada4807558c72eb6a47324646244e3f99c19e5d Author: Weiqun Zhang Date: Wed Nov 1 17:23:50 2017 -0700 use amrex_constants_module in amrex_filcc_module Src/Base/AMReX_filcc_mod.F90 commit 49a1cb8943feef3f85cfdfb47eaa7cf75477d2f5 Author: Weiqun Zhang Date: Wed Nov 1 17:20:25 2017 -0700 add amrex_constants_module and make bl_constants_module use it Src/Base/AMReX_constants_mod.f90 Src/Base/CMakeLists.txt Src/Base/GPackage.mak Src/Base/Make.package Src/F_BaseLib/bl_constants.f90 commit c41595104c57a2d4a4e44b4ce5d82f9c3e6cf2d1 Author: atmyers Date: Wed Nov 1 17:03:27 2017 -0700 always return true from both git commit and git push. build_and_deploy.sh commit ce609c69963f43997c9e0897615b9bc9b48c6ee7 Author: dtgraves Date: Wed Nov 1 16:28:16 2017 -0700 bug fix in time interpolation Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 117d5f84788482c765fd13f7a94dfb04a31700c8 Author: atmyers Date: Wed Nov 1 16:26:06 2017 -0700 exit successfully if there are no changes. build_and_deploy.sh commit c17a6e7d170fdd38b6cf809b280788e20023557c Author: Weiqun Zhang Date: Wed Nov 1 16:08:01 2017 -0700 MLMG: fix bugs Src/Base/AMReX_ParallelDescriptor.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 6e6ca6ab64f5675b833bd106d9a920d9b4be2178 Author: atmyers Date: Wed Nov 1 15:58:06 2017 -0700 always return true from git push build_and_deploy.sh commit 1e07ff7f52eb221845f1399ad29c4028c56f75c7 Merge: 5b921ffee c9043b6db Author: WeiqunZhang Date: Wed Nov 1 15:47:11 2017 -0700 Merge pull request #160 from nncarlson/F2003-pure-fix Add argument intent for pure subroutine required by F2003 commit c9043b6dbd08ab3bb03c750ec8c18a5545837a8c Author: Neil Carlson Date: Wed Nov 1 16:17:31 2017 -0600 Add argument intent for pure subroutine required by F2003 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 commit 7a0b52263d280004104b28d81eabdcd4bbe51fe6 Author: Weiqun Zhang Date: Wed Nov 1 15:01:38 2017 -0700 MLMG: distribution map consolidation Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 2156567cb3d6deee8a1bcc19523040ec594a5fdf Merge: fd9053f10 5b921ffee Author: dtgraves Date: Wed Nov 1 14:15:30 2017 -0700 keeping up with dev branch commit fd9053f10c9784c8631b04a8a2e97912759308a6 Author: dtgraves Date: Wed Nov 1 14:15:17 2017 -0700 added some small debugging hooks Tools/C_util/Convergence/DebugDump.H Tools/C_util/Convergence/DebugOut.H Tools/C_util/Convergence/DebugOut.cpp Tools/C_util/Convergence/Make.package Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit 387d95c85655924ae6af71142fb0ce8a5232a565 Author: dtgraves Date: Wed Nov 1 14:09:24 2017 -0700 now have fourth order interpolation running without NaN's---on to testing Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 062f29e1cc18f2f3be54872c4b6c3eedf10ac466 Author: dtgraves Date: Wed Nov 1 14:03:39 2017 -0700 added a hook to avoid dividing by zero in BaseFab::linInterp Src/Base/AMReX_BaseFab.H commit 64fdbb8898d629481cca5dd22f627d3c05de2004 Author: Weiqun Zhang Date: Wed Nov 1 13:42:05 2017 -0700 MLMG: jump the sequence number before bottom solve and and then reset afterwards Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5432c777e6e8956cabfc9b0f71b860a4226edf0b Author: Weiqun Zhang Date: Wed Nov 1 13:29:35 2017 -0700 MLMG: fix bug Src/Base/AMReX_ParallelReduce.H commit 501b3fa8fcdfbc1baf237e91dc227782eebe2f58 Author: Weiqun Zhang Date: Wed Nov 1 11:34:58 2017 -0700 minor Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 7f1b52c79acf7adaf5a1a35e1618c8baf68603f3 Author: Weiqun Zhang Date: Wed Nov 1 11:23:57 2017 -0700 MLMG::bottomSolve: use subcommunicator for allreaduce of sum Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 00ac2b2a5477e297fc6fe8da84b052b6d6eac6b0 Author: Weiqun Zhang Date: Wed Nov 1 11:16:39 2017 -0700 MLMG: build subcommunicator for bottom Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 1a9ba2fecaa0aecdb6a7fb2576cce219e3b943e4 Author: Weiqun Zhang Date: Wed Nov 1 09:27:14 2017 -0700 MLMG: only bottom needs a subcommunicator Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5b921ffee623c74f0a5d2c981012320d02c90a73 Author: Weiqun Zhang Date: Wed Nov 1 08:48:03 2017 -0700 add 17.11 to CHANGES CHANGES commit 08a0fc9a68babd9b0fd9d4c69f513268275884fa Author: vince Date: Tue Oct 31 17:42:00 2017 -0700 fix for alternate bl_prof directory names. Src/Base/AMReX_BLProfiler.cpp commit a23edc28a04822c7a68f96bec672334659ce16f1 Author: Weiqun Zhang Date: Tue Oct 31 16:51:48 2017 -0700 MLMG: use sub communicator Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_ParallelReduce.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit f993ac382ade5af515118139cd761372d176f2f2 Author: dtgraves Date: Tue Oct 31 16:53:41 2017 -0700 added rk4 time interpolation Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit b395f0b6ce69314e0f063989a3fc83aa9b4e7bea Merge: a86145b67 db8b99896 Author: Andrew Myers Date: Tue Oct 31 16:09:30 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit db8b998966db1a061724a740c3e78426359168b7 Author: atmyers Date: Tue Oct 31 15:41:37 2017 -0700 helps if you use the right format so Doxygen can parse it. Src/Particle/AMReX_Particles.H commit 736bf63ec115dd347abffa6fd8ded729c76ec0cd Author: Weiqun Zhang Date: Tue Oct 31 15:11:54 2017 -0700 MLMG: store communicators Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit ffd29fa4a859157e16a3476756b41f1bf855ed81 Author: Weiqun Zhang Date: Tue Oct 31 14:40:02 2017 -0700 MLMG: build special distributionmapping Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H commit 68104f056c12bc252c621290d6c786f6743f7333 Author: atmyers Date: Tue Oct 31 14:37:01 2017 -0700 don't need to remove this here. build_and_deploy.sh commit f1f0c7dde9cfe938bc892f6ebb9368b8d08b2c20 Author: atmyers Date: Tue Oct 31 14:36:01 2017 -0700 only make new directories if they don't already exist. build_and_deploy.sh commit 85b0495c23d3d39f803ba3a4a021024349700902 Author: atmyers Date: Tue Oct 31 14:27:08 2017 -0700 add a doxygen-formated brief for ParticleContainer to test the Travis CI stuff. Src/Particle/AMReX_Particles.H commit 710a4ce1bf82efb47f0443ab0c6d858389e9748c Author: dtgraves Date: Tue Oct 31 14:13:05 2017 -0700 diffusion convergence rates are now correct, as well. On to time interpolation for AMR Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 30aaccfe83ce51f5c66ac9cb9a4bac3853160e31 Author: atmyers Date: Tue Oct 31 14:09:59 2017 -0700 adding deploy script and configuration for Travis CI .travis.yml build_and_deploy.sh id_rsa_travis.enc commit f4f7358def9951658520c2a6b4eadde616cf16d1 Author: atmyers Date: Tue Oct 31 14:01:25 2017 -0700 remove ystatic from html_static_path entry. Docs/sphinx/source/conf.py commit e47d58e050f360250ff1b9e20ce955af618d6053 Author: atmyers Date: Tue Oct 31 13:58:13 2017 -0700 update link location for the doxygen documentation. Docs/sphinx/source/intro.rst commit c27666d4da14bad759210d0b0883f5199f1eab45 Author: atmyers Date: Tue Oct 31 12:06:45 2017 -0700 turn off latex in the doxygen build. Docs/Doxygen/doxygen.conf commit cf7bb88fbd14c19b3db7531a0a553f337897526b Author: dtgraves Date: Tue Oct 31 11:43:37 2017 -0700 bug fix Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit f8d1b8a43572d2a8415c4ba24f2b41941349eec4 Author: dtgraves Date: Tue Oct 31 11:31:31 2017 -0700 bug fix in diffusion flux stencil Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit 2b373b8454ca1554db028f3de65da8a701175c8f Author: Max Katz Date: Tue Oct 31 13:28:48 2017 -0400 Restore device copy of nvar Src/Base/AMReX_BaseFab.H commit 545fc98640ce8efa02142bb512580ed0216b32db Author: Max Katz Date: Tue Oct 31 13:00:15 2017 -0400 Update to use cellsize again Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit ce7505c03209a0f28ecfdb49abda2ee1e4c3c1f8 Author: Max Katz Date: Tue Oct 31 12:59:51 2017 -0400 Add device notation to dimensional filcc Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 commit 0d2a8f3cbfb4797c6a532cb301325ddaed422522 Merge: d838d490a 1ce310701 Author: Max Katz Date: Tue Oct 31 12:49:38 2017 -0400 Merge branch 'development' into gpu commit 1ce31070154e8da0edbd6c791d8d552c509f6ffd Merge: 1de358b03 dedf46cde Author: WeiqunZhang Date: Tue Oct 31 09:38:40 2017 -0700 Merge pull request #154 from AMReX-Codes/filcc Have old filcc's call new filccn commit 1de358b039ed26e7e8cbe4c44ad6788408e16745 Author: Weiqun Zhang Date: Tue Oct 31 09:08:27 2017 -0700 F_Interfaces: add nodal_type function to multifab, imultifab and boxarray Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit d124e1c7b156782b0eb6e0c563c6c7c80b372f9c Merge: 0bc29ba36 20938ba48 Author: Weiqun Zhang Date: Mon Oct 30 17:54:35 2017 -0700 Merge branch 'development' into weiqun/mlmg commit 0bc29ba36aeaf60e187a6e8b25ed53d6825bbe45 Author: Weiqun Zhang Date: Mon Oct 30 17:54:07 2017 -0700 MLMG: fix bugs in agglomeration Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 4d7838dc5768b8d995217a1160fa5c90e68e938f Author: Weiqun Zhang Date: Mon Oct 30 17:37:02 2017 -0700 MLMG: build bc conditions and locations for each MG level Src/Base/AMReX_LayoutData.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit a9f02a4d2c5f7c2effbcca590675016d8d6eda42 Author: dtgraves Date: Mon Oct 30 17:03:47 2017 -0700 Apparently, using pi=4.0d0*atan(1.0d0) is not an accurate enough representation of pi to avoid RK integrators producing bogus results at periodic boundaries (using this, I was getting sin(2.0d0*pi*1.0d0) = O(10^-7) instead of something near roundoff). Who knew? Now all looks correct in the convergence universe. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 commit bb1f3ccfeac4b3e8d57de8bad7303f53a2ce5c17 Author: Weiqun Zhang Date: Mon Oct 30 15:24:12 2017 -0700 MLMG: use the new applybc Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 9b03c17984cd0e72de0c05494b22e6fe679c8c4b Author: dtgraves Date: Mon Oct 30 13:41:50 2017 -0700 bug fixes for rk4 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit a86145b67e7d07abf5396eae2915122f92a22407 Merge: 3dd5c8a5b 20938ba48 Author: Andrew Myers Date: Mon Oct 30 10:43:29 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 20938ba48c43d98a828cf4e339dd1de8fe0b49dd Merge: aa26fd407 a4da1d763 Author: Max Katz Date: Mon Oct 30 09:23:33 2017 -0700 Merge pull request #156 from zingale/development if we are doing `print-`, then don't do dependency checking commit a4da1d763f0d87edc513fd197aa54c9c25a8f6a8 Author: Michael Zingale Date: Mon Oct 30 12:08:19 2017 -0400 if we are doing `print-`, then don't do dependency checking Tools/GNUMake/Make.rules commit a1e346574c88f9737965d5b2f115e9f443ee0c8f Author: Weiqun Zhang Date: Sun Oct 29 16:00:32 2017 -0700 WIP MLMG: more on applybc Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H commit f905946b976b46e273c5ac16b0b38b7e23274749 Author: Weiqun Zhang Date: Sun Oct 29 11:32:32 2017 -0700 MLMG: wip Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 14ca211234a769dce627a492d825876057137e2d Author: Weiqun Zhang Date: Sun Oct 29 08:16:20 2017 -0700 MLMG: add some fortran files in preparation for rewriting applybc Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/Make.package commit 2ffa3ed3e34b50caeac7b1f5dec3e79d4d19cfb7 Author: Weiqun Zhang Date: Sat Oct 28 21:28:16 2017 -0700 MLMG: finish first pass of agglomeration without consolidation Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit b6097f97fd49081510cd7448ced67a729acf2766 Author: Weiqun Zhang Date: Sat Oct 28 15:42:17 2017 -0700 make averag_down_faces more general Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit cde0c9ec7dbd36d80ce8938263a439f62ae602f2 Author: Weiqun Zhang Date: Sat Oct 28 14:09:53 2017 -0700 MLMG: agglomeration WIP Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 12986d5567d12964117e4c4ffc2428de27c7705c Author: Weiqun Zhang Date: Sat Oct 28 13:21:22 2017 -0700 min width argument for coarsenable function Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit d838d490a4be0aac48a2bd85f2d6637375e3f6e5 Merge: d86564079 aa26fd407 Author: Max Katz Date: Sat Oct 28 14:45:17 2017 -0400 Merge branch 'development' into gpu commit aa26fd407eff9fe9df2fb37085b1b7566cd42013 Author: Weiqun Zhang Date: Fri Oct 27 19:37:42 2017 -0400 fix omp atomic form Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 319941aa7558fd5809db163a5b7b7b0991efe92a Author: dtgraves Date: Fri Oct 27 16:06:18 2017 -0700 more hooks and options Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugDump.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit 6712330a0284df0c379bab9257575da920221bb0 Author: kngott Date: Fri Oct 27 15:53:45 2017 -0700 Making it run again. Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H commit af56c14de92f5be252fa7fb9111d4f458ace5b07 Author: kngott Date: Fri Oct 27 15:25:24 2017 -0700 Removal of proximity mapping options. Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_DistributionMapping.H commit 07461bb4a6c068c6428a4c404f5a6c444647eaa5 Author: kngott Date: Fri Oct 27 14:58:15 2017 -0700 Constant reference adjustment. Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp commit f593d88598a44784c6d69019df24bc6dd32534aa Author: kngott Date: Fri Oct 27 14:46:19 2017 -0700 Addition of BoxArray and DistributionMapping hashing functions for comparison across MPI. Also, adjustment of BroadcastDistributionMapping to include color. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 951a7c425f668b5868519e2f50c7122f07d0e7c2 Author: kngott Date: Fri Oct 27 14:43:52 2017 -0700 Function that outputs a backtrace but does not abort. Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp commit 800930247b77f0994ec67c307669b00467da36c0 Author: Ann Almgren Date: Fri Oct 27 12:48:37 2017 -0700 Need to reflect FILCC change in the CMakeLists.txt Src/Base/CMakeLists.txt commit e04186e9bb19fb7af4d6afc8af95d7c80773e938 Merge: 78af29598 8b8a91189 Author: Ann Almgren Date: Fri Oct 27 12:47:19 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 78af29598be35d55ff7d44eb4946284e05451e14 Author: Ann Almgren Date: Fri Oct 27 12:47:14 2017 -0700 Fix typo Docs/AMReXUsersGuide/EB/EB.tex commit f6732ebc5a4e3f081943bb07ba1690fbcffddf33 Merge: fa12fcb8f 8b8a91189 Author: vince Date: Fri Oct 27 11:57:53 2017 -0700 Merge branch 'development' into partio commit dedf46cde76b2bb6f77288d073b5bd4dff197edd Author: Max Katz Date: Fri Oct 27 11:16:32 2017 -0400 Have old filcc's call new filccn Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 commit 8b8a91189d721125c2236e211307a3676cdf1a01 Author: Max Katz Date: Fri Oct 27 02:57:46 2017 -0400 Move the FILCC functions to F90 files Src/Base/AMReX_FILCC_1D.F Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F Src/Base/AMReX_FILCC_3D.F90 Src/Base/Make.package commit d86564079b72809952d0bcd79a6fffb760f1c5bd Author: Max Katz Date: Fri Oct 27 02:05:19 2017 -0400 Wrap a CUDA-only parameter in an ifdef Src/Base/AMReX_FabArrayBase.cpp commit 07674bbd15ddac2a0e4938a44f2e12e236ae2055 Author: Max Katz Date: Fri Oct 27 01:55:04 2017 -0400 Move .F90 FILCC files back to .F Src/Base/AMReX_FILCC_1D.F Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F Src/Base/AMReX_FILCC_3D.F90 Src/Base/Make.package commit b063eda1d5a35e7baf6d795d5b25c24aa606b1a9 Author: Max Katz Date: Fri Oct 27 01:33:13 2017 -0400 Use a larger string size for bl_error/warning Src/Base/AMReX_BLBoxLib_F.f commit 93daa461b18f0959b17271ab0a626882d4712c2f Author: Max Katz Date: Fri Oct 27 01:28:00 2017 -0400 Sync up heat equation with development Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit 4400397b595cd587a90819033099ce8ea835c541 Author: Max Katz Date: Fri Oct 27 01:16:33 2017 -0400 Update sites for CORAL early access systems Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf Tools/GNUMake/sites/Make.unknown commit a2e1f642f1af2f03a0e835eebed11fc8ac440bac Author: Max Katz Date: Fri Oct 27 01:24:37 2017 -0400 summit -> summitdev Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak commit c9534a554c5fb62fb31fd960fc4b887121957d3b Merge: fb02ada5a 216a6b1f9 Author: Max Katz Date: Fri Oct 27 00:57:22 2017 -0400 Merge branch 'development' into gpu commit 216a6b1f9a3891b2c925010e0d701576dec355a8 Merge: 0e80fb68b dd94eebcb Author: WeiqunZhang Date: Thu Oct 26 16:18:35 2017 -0700 Merge pull request #152 from AMReX-Codes/filcc Create a dimension agnostic, multi-component filcc commit dd94eebcb660c3342daa5f8d77e73248f17f185e Merge: e9dd8330a 79b5b0100 Author: Max Katz Date: Thu Oct 26 16:04:39 2017 -0700 Merge pull request #153 from AMReX-Codes/fillcc2 move some if tests out of nested i-j-k loops commit 0e80fb68b47816d78cc264c99f06e4c0557977ac Merge: 4edd05624 0402d624e Author: vince Date: Thu Oct 26 15:58:10 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4edd05624d7577d4a4607d1b7533e8950c183bf7 Author: vince Date: Thu Oct 26 15:57:46 2017 -0700 added 1-e/i percent time to html output. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit 0402d624eb4e943c00a150e613e3fdd173929c80 Author: Weiqun Zhang Date: Thu Oct 26 13:34:31 2017 -0700 MLMG: fix ref ratio of 4 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit 79b5b0100bfa49936a8250ef19277f465642dab6 Author: Weiqun Zhang Date: Thu Oct 26 13:19:04 2017 -0700 move some if tests out of nested i-j-k loops Src/Base/AMReX_filcc_mod.F90 commit fb02ada5a1ecfcec87a1a34fdc56a44c16246b96 Author: Max Katz Date: Thu Oct 26 12:11:01 2017 -0400 Revert to CUDA 8 default Tools/F_mk/GMakedefs.mak Tools/GNUMake/Make.defs commit 44568675f717308699bd1b6881eeb4706102e503 Author: Max Katz Date: Thu Oct 26 12:10:22 2017 -0400 Specify CUDA_VERSION at compile time for the PGI compiler Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.defs Tools/GNUMake/comps/pgi.mak commit 9b27d62538ec9cc893e6440c9289d1af59c83693 Author: Weiqun Zhang Date: Wed Oct 25 17:56:33 2017 -0700 make sure relative tolerance is not less than 1.e-13 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6ea2bab5aa01869cd44d7ed51b02398ff74b8e31 Author: Weiqun Zhang Date: Wed Oct 25 17:35:08 2017 -0700 MLMG: in case crse bc data is not provides, use zero Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit fef809999bcca3bc1f136a887148d27382843ea6 Author: vince Date: Wed Oct 25 16:51:35 2017 -0700 work on the profiler flush interval. Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp commit 614262db02dceb4ed7fb18a7a0a0af19681b5417 Author: Weiqun Zhang Date: Wed Oct 25 16:48:39 2017 -0700 fix assertion Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EBFluxRegister.cpp commit 9b9b6325943791827f8dfd3f74ad66c0da8fb93b Author: Weiqun Zhang Date: Wed Oct 25 16:47:05 2017 -0700 fix bug in YAFluxRegister Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1d.F90 Src/Boundary/AMReX_YAFluxRegister_2d.F90 Src/Boundary/AMReX_YAFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 47f01cb94fbb572099527fe8b550ef7460f74688 Author: dtgraves Date: Wed Oct 25 16:07:37 2017 -0700 fillboundary needs to know about periodicity Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 commit 4c43c187c41fa6f79242ea4dbfd8d4a1ac1c5e18 Author: dtgraves Date: Wed Oct 25 15:51:52 2017 -0700 ScalarAdvectionDiffusion now fourth order for non-AMR calcs. Now on the hard part. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit e9dd8330a1caa2e6706ddba5fa0875d89cc59a28 Author: Max Katz Date: Wed Oct 25 17:17:57 2017 -0400 Create a dimension agnostic, multi-component filcc This version of filcc is both dimension agnostic, and works over an arbitrary number of components. It gives the same results as the dimensionful versions of filcc. It will be necessary for performance reasons to use a version like this on the GPU. This also applies the new filcc to amrex_fab_filcc. Src/Base/AMReX_filcc_mod.F90 commit 3dd5c8a5b1e164824ac8062b37503f76f54d7677 Author: Andrew Myers Date: Wed Oct 25 14:17:28 2017 -0700 remove unused variable. Src/Particle/AMReX_NeighborParticlesI.H commit 5d832b5b9cf00b43fed24a57a47e731dce3f6c9d Merge: 0c83d0ce7 295b479de Author: Max Katz Date: Wed Oct 25 17:16:57 2017 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0c83d0ce7abcffee5c15f8e39971b8a3f8a7bdef Author: Max Katz Date: Wed Oct 25 16:54:10 2017 -0400 Bring over a few stub functions from gpu branch Src/Base/AMReX_BLFort.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs commit aa76a4b59b6447c8fc362acbcb969a17778083c5 Author: Andrew Myers Date: Wed Oct 25 14:16:07 2017 -0700 add profiling to amrex::get_slice_data Src/Base/AMReX_MultiFabUtil.cpp commit 295b479de94e29cbb79836bfaf12ea16ec8794bf Author: Weiqun Zhang Date: Wed Oct 25 13:53:25 2017 -0700 MLMG: add getFluxes and compResidual Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 6a0c2a5ff9e7d7ade521481a2c6a6e7e239e13c3 Author: Max Katz Date: Wed Oct 25 16:44:57 2017 -0400 Compile fix for ppc64le Src/Base/AMReX_FPC.cpp commit c399423ba612f63dbfe95c8a39ab4fe5396a1943 Author: Max Katz Date: Wed Oct 25 15:42:49 2017 -0400 Simplify logic for copying Box data Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_RealBox.H commit 2cea01808d8893eb18e31e10fd172ea00827e892 Author: Max Katz Date: Wed Oct 25 14:42:50 2017 -0400 CUDA-awareness in MPI is now a runtime option Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Tools/GNUMake/Make.defs commit dede1487697b003c279860d2881dd2171a3fb35c Author: Max Katz Date: Wed Oct 25 14:29:41 2017 -0400 Remove unnecessary device synchronizations Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.cpp commit d9903f823ab152e3056aaaf8d6afaa09a09a74b9 Author: Max Katz Date: Wed Oct 25 14:14:07 2017 -0400 Reduce more diffs with development Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit 5b7e23595589db907b6c7353c98667a4f95c3495 Author: Weiqun Zhang Date: Wed Oct 25 11:02:46 2017 -0700 update Users Guide for Array -> Vector Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/amrexsymbols.tex commit 4655eba643ad0945a6917280690490a4b62badf8 Author: Max Katz Date: Wed Oct 25 13:56:48 2017 -0400 Remove functionality to have device data in Fab's/MF's/StateData This may be introduced in a future GPU release, but is currently unnecessary. Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit f33851033635b3e399c5a67862587f7a3ec29459 Author: Weiqun Zhang Date: Wed Oct 25 10:46:39 2017 -0700 add macros AMREX_ASSERT_WITH_MESSAGE and AMREX_ALWAYS_ASSERT_WITH_MESSAGE CHANGES Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BLassert.H commit 810367b513e6f91b119c2975ce22f216454deb2a Author: dtgraves Date: Wed Oct 25 10:44:50 2017 -0700 put check for isotropic dx back into CNS Tutorials/EB/CNS/Source/CNS.cpp commit e5c7d3d8d8d4f3c3309513850ba1327367cbd1b0 Author: Max Katz Date: Wed Oct 25 13:29:56 2017 -0400 Reduce some diffs with development Src/Amr/AMReX_StateData.cpp commit e091e5030f62c1fb54271036b41bc48e933c1806 Author: Weiqun Zhang Date: Wed Oct 25 09:57:59 2017 -0700 MLPoisson: fix bug Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 commit 35144dd3714e4f5ea8a9c340946368b7244ff977 Author: Weiqun Zhang Date: Tue Oct 24 17:20:10 2017 -0700 minor typo Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 03818260ce790373c10fe5166eb9524e23e55ea2 Author: Max Katz Date: Wed Oct 25 12:43:20 2017 -0400 No longer need a special gcc configuration for PGI on summitdev Tools/GNUMake/comps/pgi.mak commit b0ba9646420d56b163cfc14b2e43898c384ea0f1 Merge: 04f8c26f4 aba804ad0 Author: Ann Almgren Date: Wed Oct 25 09:17:52 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 04f8c26f44dd52078b2247e28f51273d62708798 Author: Ann Almgren Date: Wed Oct 25 09:17:07 2017 -0700 Update BuildingAMReX chapter of the sphinx docs Docs/sphinx/source/BuildingAMReX.rst commit aba804ad00e8096274e130619bfe2690bc94dd71 Author: dtgraves Date: Wed Oct 25 09:09:18 2017 -0700 added new header to CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit d0ba79a5ddd8d300d6d8ac49b2322d255e1a4f1d Merge: 915e6a47e fa36fbbfe Author: dtgraves Date: Wed Oct 25 09:06:37 2017 -0700 Merge branch 'dtg_branch' into development commit fa36fbbfe11f139edd218a6638c7668bab5b43a3 Author: dtgraves Date: Wed Oct 25 09:05:52 2017 -0700 bug fix (needed to also add new factory function) Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_PlaneIF.H commit 915e6a47ebc91bd0b4614f7924a887ba90bce077 Merge: 17a79637b b06bc2025 Author: dtgraves Date: Wed Oct 25 08:50:20 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 17a79637b43bd9846acc649512d3add9a55cb1f9 Author: dtgraves Date: Wed Oct 25 08:49:24 2017 -0700 adding missing file Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H commit b06bc2025d752c6c440b07848add15aa742e369a Author: Weiqun Zhang Date: Tue Oct 24 16:58:06 2017 -0700 MLPoisson: rm member m_Anorm Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit a60f5e31155297b76b699903a1ca270ee025c8d5 Author: Weiqun Zhang Date: Tue Oct 24 16:31:44 2017 -0700 add MLPoisson::Anorm Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 35aee01c061060750b378e5e32cc61a0771444e7 Author: Weiqun Zhang Date: Tue Oct 24 16:21:59 2017 -0700 add amrex_mlpoisson_gsrb Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H commit 517c283dc9274b658cb295d3436cc9d8c0756c30 Author: Max Katz Date: Tue Oct 24 19:14:09 2017 -0400 Remove remaining calls to get_host_pointer Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H commit 8f79e5e20320b2e52195f9b20ec50c910a47f190 Merge: 04b4fec26 8c1f6819f Author: dtgraves Date: Tue Oct 24 16:11:39 2017 -0700 Merge pull request #151 from AMReX-Codes/dtg_branch merging with dev so Jordan can get implicit function for plane with anistropic dx. commit 8c1f6819fd59be79cf75aaa38f366439d796e279 Merge: 78e6f0357 04b4fec26 Author: dtgraves Date: Tue Oct 24 16:09:32 2017 -0700 Merge branch 'development' into dtg_branch commit 78e6f0357506fda57f249d89b440ef9f8a64f6a7 Author: dtgraves Date: Tue Oct 24 16:08:45 2017 -0700 added Plane geometry for anistropic dx. I tested it on CNS and it seems to give the right geometry Tools/C_util/TV_TempWrite.H Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 611bbb99de8e8e9293d57bbe3dabac91d8e8bc5c Author: Max Katz Date: Tue Oct 24 18:54:33 2017 -0400 Remove RealBox::loF/hiF Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 7ea77a1a5117db2ff85d8e62cf99c0773ef2d050 Author: dtgraves Date: Tue Oct 24 15:45:30 2017 -0700 more debugging hooks Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 2b31264b98a928cb8dca959c2c45031b4b146caa Author: Max Katz Date: Tue Oct 24 18:40:33 2017 -0400 Remove Geometry::CellSizeF() Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_CoordSys.H commit b8aa8f007f166b6b42384905e1896c8798586821 Author: Max Katz Date: Tue Oct 24 18:39:23 2017 -0400 Avoid using write-combined pinned memory This can in theory provide a performance benefit, but in practice it probably never will matter, and we want to switch to using a uniform pointer for pinned memory between the host and device, which means we need to avoid WC memory if we want to skip the use of cudaHostGetDevicePointer(). Src/Base/AMReX_CUDA.F90 commit 04b4fec2643e73bf33c8baf2654d80d08bc22484 Author: Weiqun Zhang Date: Tue Oct 24 15:31:22 2017 -0700 start MLPoisson Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H Src/LinearSolvers/MLMG/Make.package commit 0ba63bf6fa1454ad241f9ac5912a7d05bd427f0e Author: Weiqun Zhang Date: Tue Oct 24 13:41:27 2017 -0700 minor tweak of amrex_array_to_vector.sh Tools/Migration/amrex_array_to_vector.sh commit f3e10c4939b1f1bc012b330a51fcc19ba3119af6 Author: dtgraves Date: Tue Oct 24 13:10:59 2017 -0700 added a pile of debugging hooks. fluxes are fourth order. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py commit b0d71a3887ade6fd473bf6f2b0145939cb6ee62e Author: Weiqun Zhang Date: Tue Oct 24 13:03:05 2017 -0700 MLMG: use more restrictive convergence criteria for CG Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 4b4c0e25e4fb3701f60551897dcb9dd09e64b476 Author: Weiqun Zhang Date: Tue Oct 24 11:12:31 2017 -0700 MLMG: need to apply bc before reflux Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit b8cc03559a9dc0eee80847161a2ba090dac8ca9b Merge: 0901389ea a0b6c9db3 Author: WeiqunZhang Date: Tue Oct 24 09:24:21 2017 -0700 Merge pull request #150 from bcfriesen/update_F_mk_for_intel F_mk: add support for compiling with Intel v17 and v18 commit a0b6c9db31f90255f39f380223e82ff82569ad66 Author: Brian Friesen Date: Tue Oct 24 09:01:42 2017 -0700 F_mk: add support for compiling with Intel v17 and v18 Tools/F_mk/comps/Linux_intel.mak commit 0901389eaff285e284fd7103d0c176c8a0f4c165 Author: Weiqun Zhang Date: Tue Oct 24 08:58:53 2017 -0700 MLMG: isSingular virtual function Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 8056ce9b452f205764070d7fe2983b8dfeb76606 Author: Weiqun Zhang Date: Mon Oct 23 17:04:11 2017 -0700 MLMG: solvability WIP Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 85b06d9de1c196f2a630cce59620b4a9e4e33f32 Author: Weiqun Zhang Date: Mon Oct 23 15:16:44 2017 -0700 MLMG: enforce solvability Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/main.cpp commit 71e0b3fe43ebaa31ef5d698b879bb1370e76d12a Author: Weiqun Zhang Date: Mon Oct 23 11:16:13 2017 -0700 MLMG: add m_singular vector Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 2e38c1b1177ae767e54304bf0c7d0c4e5adfe42b Author: Weiqun Zhang Date: Mon Oct 23 10:41:59 2017 -0700 MLMG test: set up periodic and Neumann Tests/LinearSolvers/MLMG/fort.H Tests/LinearSolvers/MLMG/fort_3d.F90 Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/inputs Tests/LinearSolvers/MLMG/prob_par.H Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 88149ddd29158d374afe72dcfb773a3aa8d21c6e Merge: 11daa8a9b 2157ae2df Author: Andrew Myers Date: Mon Oct 23 17:02:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 11daa8a9b8a3241b19d2feb35caeb90ed9a03cad Author: Andrew Myers Date: Mon Oct 23 17:02:29 2017 -0700 add a version of MakeMFIter that overrides the default tiling setting. Src/Particle/AMReX_Particles.H commit 2157ae2df397bc6c95bceeaa072b3adf39e9e914 Author: Ann Almgren Date: Mon Oct 23 16:45:39 2017 -0700 Default for ENABLE_EB should be off. Tools/CMake/AMReX_Options.cmake commit 835290342df36420cd345c3c22ea8af51d565d89 Author: Ann Almgren Date: Mon Oct 23 16:44:44 2017 -0700 Fix bug where there were 0 neighbors and we were trying to fill an array with zero values. Src/Particle/AMReX_NeighborParticlesI.H commit c1eace42e12b15bda80282db2f98d0ba27374184 Author: dtgraves Date: Mon Oct 23 16:36:20 2017 -0700 added interior box option as an example Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 3087bd06491c2a7fa1487d7791447d5583ce138c Author: Max Katz Date: Mon Oct 23 18:09:55 2017 -0400 Add CUDA suffix for F90 builds Tools/F_mk/GMakedefs.mak commit b547111dbe55a2b681db9db87df2e1c4d309be83 Author: dtgraves Date: Mon Oct 23 14:42:26 2017 -0700 some bug fixes. dphi/dt for MOL code still only second order. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py commit 724375bb085e9883efe9b462c38d3e188555caf5 Author: Max Katz Date: Mon Oct 23 17:13:19 2017 -0400 Update to CUDA 9 in F90 build system Tools/F_mk/comps/Linux_pgi.mak commit 8b2e0c1402adc0829ed6054a1c14f39d6b2113b7 Author: Max Katz Date: Mon Oct 23 16:28:30 2017 -0400 Support CUDA module in F90 build Src/Base/AMReX_CUDA.F90 Tools/F_mk/GMakedefs.mak commit 8f09a3022ee683c96a18cdbc235994907c5918a7 Author: Weiqun Zhang Date: Mon Oct 23 10:06:06 2017 -0700 MLMG: no longer requires AmrCore Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile commit a3ee38c5622faace0b3eb49ed9b107ce56d71d13 Author: Weiqun Zhang Date: Mon Oct 23 10:03:54 2017 -0700 MLMG: cleanup Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 08fbe3ca18c9dee7735333b3c78320e1ec9677fd Author: Weiqun Zhang Date: Sun Oct 22 12:26:03 2017 -0700 MLMG: set bc interface Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 6897a5d99083d56446aed440b23a7988e57e29b3 Author: Ann Almgren Date: Sun Oct 22 17:08:27 2017 -0700 Update the EBParticles Tutorial with 1) 3d bounce routine , 2) replace 0.0005 by dt in bounce. Tutorials/Particles/EBParticles/EBParticleContainer.H Tutorials/Particles/EBParticles/EBParticleContainer.cpp Tutorials/Particles/EBParticles/GNUmakefile Tutorials/Particles/EBParticles/ebparticles_2d.f90 Tutorials/Particles/EBParticles/ebparticles_3d.f90 Tutorials/Particles/EBParticles/ebparticles_F.H Tutorials/Particles/EBParticles/main.cpp commit b2cd6bcf5bae1ad70095c20e102224114127e7ec Author: Ann Almgren Date: Sat Oct 21 18:12:01 2017 -0700 Fix some typos Docs/AMReXUsersGuide/EB/EB.tex commit ac427e54c207c0e178a1223abfa2da837e0594df Author: dtgraves Date: Sat Oct 21 14:47:25 2017 -0700 added fixed_dt option so I can do proper convergence tests Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 5cf3b28e559b758d3ab1b2b6a9f1ad310fe6e325 Author: dtgraves Date: Sat Oct 21 13:31:17 2017 -0700 added a python utility for convergence tests Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py commit d2b1b9d6afcc396c78afec0adf280bf890d105d1 Author: Michele Rosso Date: Fri Oct 20 17:42:43 2017 -0700 CMake: fix few bugs Src/Boundary/CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit cc2b5fd0ce6a54e6f41095679d319e6c9707f224 Author: Ann Almgren Date: Fri Oct 20 17:14:01 2017 -0700 Fix another typo Src/GeometryShop/CMakeLists.txt commit acb1c6024103bfaac55a2142524d9f89dd0800ac Author: Ann Almgren Date: Fri Oct 20 17:13:07 2017 -0700 Fix typo Src/GeometryShop/CMakeLists.txt commit 1d11389f8049f2190303055afbfa3bbc6d20c28c Author: Ann Almgren Date: Fri Oct 20 17:11:50 2017 -0700 Fix typos Src/EB/CMakeLists.txt commit 07998f9d11acf840706ee312e875b999c7e0628b Author: Ann Almgren Date: Fri Oct 20 16:58:48 2017 -0700 Adding more cmake support for using EB Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 3497a01f6f465efd3ef4789f25f2674fcd9f34ae Author: Ann Almgren Date: Fri Oct 20 16:50:49 2017 -0700 Adding CMakeLists.txt for EB and GeometryShop Src/EB/CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit 709bbc49208aa9eaa125c8c8690d900cecb8daa6 Author: Weiqun Zhang Date: Fri Oct 20 16:34:18 2017 -0700 improve amrex_array_to_vector.sh Tools/Migration/amrex_array_to_vector.sh commit fa12fcb8f3943d1f21cf94a9cd44a33af76ab43d Author: vince Date: Fri Oct 20 15:55:18 2017 -0700 more support for precreate directories and particle io. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Particle/AMReX_ParticleContainerI.H commit 8375fab5df2ee3935ac920b3b3e27ac2f5cb175e Author: Weiqun Zhang Date: Fri Oct 20 15:07:51 2017 -0700 MLMG: use linear interp for amr level prolongation Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 41400efb2e9839d40771da6f3ebbc1d8df54c63f Merge: ef990f1ba b43ab36b5 Author: Andrew Myers Date: Fri Oct 20 15:11:38 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ef990f1ba10eb71578468b9007b86337fcfc99f4 Author: Andrew Myers Date: Fri Oct 20 15:09:13 2017 -0700 add utility functions for filling slices of data from a Multifab. Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 commit b43ab36b50a80fab45166c03597cc500c9660ec7 Author: Weiqun Zhang Date: Fri Oct 20 15:00:41 2017 -0700 MLMG: fix linear interp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H Src/LinearSolvers/MLMG/Make.package commit f454ea63fffaec61da2977188331a5c3d0927c62 Author: Weiqun Zhang Date: Fri Oct 20 13:59:05 2017 -0700 move heap allocation out of mfiiter Src/AmrCore/AMReX_FillPatchUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a3a3b0d72f9895f273454d017eff16793cee2ff2 Author: vince Date: Fri Oct 20 13:35:42 2017 -0700 more support for precreate directories. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Particle/AMReX_Particles.H commit 7ac36b0726de377d218f7549b9bcc89d4c4a02b8 Author: dtgraves Date: Fri Oct 20 13:13:41 2017 -0700 some bug fixes Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.2d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.3d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit 1cb4e5a485947d4162b0f87330ccd60fae18640c Author: dtgraves Date: Fri Oct 20 11:49:27 2017 -0700 added (exact) smooth initial condition, confirmed via convergence test Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/debug.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.2d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.3d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probdata.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probin Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit add92f07a71d74770536f0fdefdbfa9960bf5b79 Author: vince Date: Fri Oct 20 11:36:26 2017 -0700 shorten profiling names. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 35383e945ff938206e8a74d41d292cac6628aa5c Merge: 36004bb31 3356b77ff Author: vince Date: Fri Oct 20 10:32:51 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3356b77ffb2e32fc7527db080d18c93495dd8950 Author: Weiqun Zhang Date: Fri Oct 20 10:31:22 2017 -0700 MLMG: remove nu0 and fix mini-cycle Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a244adb70185c9ff01e6af8643406499a23184c2 Merge: 243601df9 165250c37 Author: Michele Rosso Date: Fri Oct 20 09:51:39 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 243601df9c6f815b1287aa269df6afe622cbbd1a Author: Michele Rosso Date: Fri Oct 20 09:51:24 2017 -0700 CMake: add header to cmake list Src/Base/CMakeLists.txt commit 165250c37b8ec2a20e269bcadb2971ae97a2446d Author: Weiqun Zhang Date: Fri Oct 20 09:41:55 2017 -0700 MLMG: fix a minor bug Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 06331c176f762a31f05710daf3f7ada6836e6a3f Author: Weiqun Zhang Date: Fri Oct 20 09:32:48 2017 -0700 MLMG:: add profilers Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit b37f7493768e6fa4137f498b1f3338c51b9e7cb0 Author: Weiqun Zhang Date: Fri Oct 20 09:07:05 2017 -0700 MLMG test: add inputs Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/inputs Tests/LinearSolvers/MLMG/prob_par.H commit 001693af5f833ce111d704652f685698eb51a1f0 Merge: 3531a2da4 1783235eb Author: Klaus Weide Date: Fri Oct 20 10:36:58 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1783235eb6fce8af3c326149fd6eecbab7c5824d Author: Ann Almgren Date: Thu Oct 19 18:26:11 2017 -0700 Add rst files for the rest of the user guide chapters. Docs/sphinx/source/Amr.rst Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Boundary.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/CVODE.rst Docs/sphinx/source/Chapter2.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/EB.rst Docs/sphinx/source/Fortran.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Particles.rst Docs/sphinx/source/Profiling.rst Docs/sphinx/source/Visualization.rst Docs/sphinx/source/index.rst Docs/sphinx/source/intro.rst commit c5e94f640482263a06c10efade1c5ff01d382698 Merge: 5866e8876 e94ac4743 Author: Max Katz Date: Thu Oct 19 20:52:42 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 5866e8876c95b85d728ae279b55b382b27c8b115 Author: Max Katz Date: Thu Oct 19 19:55:14 2017 -0400 Correct the reporting of how many total GPUs are available Src/Base/AMReX_Device.cpp commit ffb8ac25363202e10449530c628d483b4d437c57 Author: Max Katz Date: Thu Oct 19 19:22:19 2017 -0400 Use the same CPU-GPU matching algorithm without MPI Src/Base/AMReX_Device.cpp commit 489a05b2c6f6542fb4db908d99d250f9a84004ad Author: Ann Almgren Date: Thu Oct 19 16:11:02 2017 -0700 Fix subsections Docs/sphinx/source/Basics.rst commit 81d24557b52d24fff2e4b1a23c30f915a73d0e97 Author: Ann Almgren Date: Thu Oct 19 16:03:57 2017 -0700 Fix the index Docs/sphinx/source/index.rst commit ef470f7b3c4fbb6710a31cd22473923381f0717f Author: Ann Almgren Date: Thu Oct 19 15:59:29 2017 -0700 Add Basics/Basics.tex Docs/sphinx/source/Basics.rst Docs/sphinx/source/index.rst commit e5fcc1605905faa45cdca7697170694fa313fd97 Merge: b84c96233 afe5db5e0 Author: Ann Almgren Date: Thu Oct 19 15:55:03 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b84c962338f70017fad238c021268d7f237443ab Author: Ann Almgren Date: Thu Oct 19 15:54:48 2017 -0700 Missing curly brackets in emph lines Docs/AMReXUsersGuide/Basics/Basics.tex commit c35f2c3b10b73e364ea3c25c1a522185abab651e Author: dtgraves Date: Thu Oct 19 15:46:47 2017 -0700 added an algorithm description to the notes Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit afe5db5e048e4d7558d2478d1f68cde85c425d9f Author: Weiqun Zhang Date: Thu Oct 19 15:37:13 2017 -0700 MLMG: remove unnecessary fillboundary Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6657db1d047c1bd642dd902bbadcf159b9997ca7 Author: Ann Almgren Date: Thu Oct 19 15:17:28 2017 -0700 sphinx for github.io pages Docs/sphinx/Makefile Docs/sphinx/source/conf.py Docs/sphinx/source/index.rst Docs/sphinx/source/intro.rst commit 55be57f368ac947af7e8da423281609fb0cec85a Author: Weiqun Zhang Date: Thu Oct 19 14:36:58 2017 -0700 MLMG: fix bug Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 8041ec23e0edad724943c54f3586e161a0038108 Author: Weiqun Zhang Date: Thu Oct 19 14:23:05 2017 -0700 MLMG: refactor and comments Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit b20e34c373d2b7ea03939c9c912615f39c062490 Author: dtgraves Date: Thu Oct 19 14:19:36 2017 -0700 added fourth order fortran routines. On to testing. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit e94ac4743a1901d6899858b450f5a4e7f2275def Author: dwillcox Date: Thu Oct 19 17:09:38 2017 -0400 Add BL_USE_F_BASELIB as a preprocessor variable for F90 build system. This fixes CUDA compilation for the Microphysics test_react unit test. Tools/F_mk/GMakedefs.mak commit 7b7f6c6644d318aefc03fcbd27149025e7cb39bc Author: Weiqun Zhang Date: Thu Oct 19 10:52:21 2017 -0700 MLMG: avoid recursive function Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 94c695a1c42cd97bff666674e9121d86c54543e2 Author: Weiqun Zhang Date: Thu Oct 19 10:40:31 2017 -0700 MLMG test: add max_fmg_iter parameter Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 5e1e8870dadf9ef7eb4471b6c129c70568229804 Author: Weiqun Zhang Date: Thu Oct 19 10:20:27 2017 -0700 MLMG: add linear interpolation Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 28f3f6c6956e0a98fcf17015912cf6a40f86f585 Author: Max Katz Date: Thu Oct 19 06:17:10 2017 -0400 Make NVML mandatory Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Tools/GNUMake/Make.defs commit b42918cc086a6cb691484f6f92f49da8ccfd945e Author: Max Katz Date: Thu Oct 19 06:05:09 2017 -0400 Clean up the code for assigning ranks to GPUs Src/Base/AMReX_Device.cpp commit 01f6eb80941e09f30b436172ac0f3ee56dc55bb8 Author: Max Katz Date: Thu Oct 19 06:04:33 2017 -0400 Add an NVML error check macro Src/Base/AMReX_Device.H commit 7653d72bc54430ed67d03e6637d08e4264fd5dd3 Author: Max Katz Date: Thu Oct 19 05:14:33 2017 -0400 Do not divide up GPUs that are not visible to CUDA Src/Base/AMReX_Device.cpp commit d6277acb8907b112edd5cc2b91e1f30d4177429e Merge: cdf41e262 9db5c57a8 Author: Max Katz Date: Thu Oct 19 05:13:45 2017 -0400 Merge branch 'development' into gpu commit cdf41e262e3cc5cb52ac371c933677a26ef54704 Author: Max Katz Date: Thu Oct 19 02:07:35 2017 -0400 Allow disabling of CUDA-aware MPI at compile time Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Tools/GNUMake/Make.defs commit 094afe6dbd17c116cb4373a29286e97bdf65b144 Author: Weiqun Zhang Date: Wed Oct 18 21:57:42 2017 -0700 MLMG: use swap Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit af9c9822ca94e392fe344c6d0ef5b61558a463f3 Author: Weiqun Zhang Date: Wed Oct 18 21:51:02 2017 -0700 MLMG: remove a temp mf Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 8f05cf9f7af8678570b7fa0823d2d8b17d718653 Author: Max Katz Date: Wed Oct 18 23:19:46 2017 -0400 Only link in NVTX if profiling Tools/GNUMake/Make.defs commit c0ead92e8989237dd9b228af83987bd1c3ea2784 Author: Max Katz Date: Wed Oct 18 23:06:58 2017 -0400 Update to CUDA 9 (requires PGI 17.9+) Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.olcf commit 9db5c57a8bc2a1793864ce10b0e1a476b6e8f126 Author: Weiqun Zhang Date: Wed Oct 18 17:39:14 2017 -0700 MLMG: better name Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 2ba2f09bdd47f119ca2ca93f4700a19c0aca8140 Author: Weiqun Zhang Date: Wed Oct 18 17:35:23 2017 -0700 MLMG: implement FMG cycle Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 8ab5878a4e7dc09aa8c5ca7b897c978e45de3d15 Author: Weiqun Zhang Date: Wed Oct 18 12:13:07 2017 -0700 MLMG: some timers Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 4bf4df2f4f2470d5d52ceb708fad60f893bec58f Author: Weiqun Zhang Date: Wed Oct 18 11:02:28 2017 -0700 MLMG: some cleanup Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/MLMG/GNUmakefile commit 7b406ce1c7342f160853b2c3c616030d80fb0058 Merge: bbd321df6 884ecf5f7 Author: Andrew Myers Date: Wed Oct 18 16:37:50 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bbd321df631458bceab8ef3e71d6eb0ba3c42abc Author: Andrew Myers Date: Wed Oct 18 16:28:43 2017 -0700 change the value of insideRegular to be consistent with the above example, which has the solution domain on the inside of the sphere. Docs/AMReXUsersGuide/EB/EB.tex commit 0814e362b7c8e16d46ad1ad1f94cd458b3d20f52 Author: dtgraves Date: Wed Oct 18 15:19:24 2017 -0700 added in fortran framework Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 884ecf5f79c1330991f31dac6f8148b92b8c084e Merge: 09a3e78ad 1d4a618d9 Author: Michele Rosso Date: Wed Oct 18 14:41:29 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 09a3e78ad7ff40409f47f68a66a6acc91650b65f Author: Michele Rosso Date: Wed Oct 18 14:40:40 2017 -0700 CMake: add support for Cray compiler Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake commit c12b6682fbeac7ccc17572ea59d487081eef9b3f Author: dtgraves Date: Wed Oct 18 14:05:55 2017 -0700 added some more notes and put in 4th order framework for advance Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 33b23537d92fbff26683e3c6a2c14e9829e48d8b Author: Michele Rosso Date: Wed Oct 18 14:00:11 2017 -0700 CMake: remove cmake file copied by mistake in Tutorials/ScalarAdvectionDiffusion Tutorials/Amr/ScalarAdvectionDiffusion/CMakeLists.txt commit 1d4a618d9fc8a2ffe5eba91e84e4d91798beacb9 Merge: 603280d1f 96d26fa5d Author: Andrew Myers Date: Wed Oct 18 12:17:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 603280d1f42b1ba3b78118a028531576b266358d Author: Andrew Myers Date: Wed Oct 18 12:17:15 2017 -0700 clean up main. Tutorials/Particles/EBParticles/main.cpp commit 6d366d29cca7537695e514de25fe0e051422ae99 Author: Andrew Myers Date: Wed Oct 18 12:16:20 2017 -0700 clean up inputs file. Tutorials/Particles/EBParticles/inputs commit 73c8043a65108c0e61e9272e273ba7d08adbe132 Author: Andrew Myers Date: Wed Oct 18 12:09:41 2017 -0700 Tutorial for particles that interact with embedded boundaries. Tutorials/Particles/EBParticles/EBParticleContainer.H Tutorials/Particles/EBParticles/EBParticleContainer.cpp Tutorials/Particles/EBParticles/GNUmakefile Tutorials/Particles/EBParticles/Make.package Tutorials/Particles/EBParticles/ebparticles_2d.f90 Tutorials/Particles/EBParticles/ebparticles_3d.f90 Tutorials/Particles/EBParticles/ebparticles_F.H Tutorials/Particles/EBParticles/inputs Tutorials/Particles/EBParticles/main.cpp commit 96d26fa5d0b9b8103306cea53e0ac1a8d170102b Merge: 9ebec95a8 d81e4b85c Author: dtgraves Date: Wed Oct 18 11:37:44 2017 -0700 Merge pull request #148 from AMReX-Codes/dtg_branch moving a couple of things to dev so Marc can get the convergence test utility commit d81e4b85c79bbb01463382ab709d07f2a234e909 Author: dtgraves Date: Wed Oct 18 11:36:20 2017 -0700 added full Richardson convergence test utility to save some of the manual labor of convergence tests Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit 9ebec95a8b3827742e07d1613583a57bf59ddfb0 Author: Weiqun Zhang Date: Wed Oct 18 08:54:41 2017 -0700 add inputs for regression only Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt commit f2d4f20fcec0236ffadc982a5fbe6279349fb684 Author: Max Katz Date: Wed Oct 18 04:31:28 2017 -0700 Correctly handle the case with fully interior boxes Src/Amr/AMReX_StateData.cpp commit b12244f8897309d732bbfa2a996b5c08690f01fe Author: Max Katz Date: Wed Oct 18 04:31:10 2017 -0700 Insert sanity check: positive number of CUDA threads/blocks Src/Base/AMReX_CUDA.F90 commit dbf11c9bb3d8200defae2c17a29e599bda2be913 Author: Max Katz Date: Wed Oct 18 03:46:56 2017 -0700 Add CORAL EA systems at LLNL Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit fcd99f8270bdff91763fbbda12121af0f41e7168 Author: Weiqun Zhang Date: Tue Oct 17 18:08:39 2017 -0700 MLMG: fix mask for compute residual Src/Base/AMReX_BaseFab_nd.f90 Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 9a567a316dbf49aea6452df7a9f0f7b569d6e6cb Author: Max Katz Date: Tue Oct 17 17:49:17 2017 -0700 Add a second sanity check on number of threads Src/Base/AMReX_CUDA.F90 commit 9f5438a48ba2a5a8c01ebecd1b84ea157eb563f2 Author: Weiqun Zhang Date: Tue Oct 17 17:42:20 2017 -0700 add a new function to compute masked inf norm Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Print.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 31db08adc4cc44015e3db8dea02236e41e471c93 Author: dtgraves Date: Tue Oct 17 16:33:58 2017 -0700 added some working notes Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit a90c09d424e6b1059d772c5e2094d655e14e6906 Author: Max Katz Date: Tue Oct 17 15:48:18 2017 -0700 Use the C++ CUDA error checker Src/Base/AMReX_Device.cpp commit e7035c31b874d30395cc738aaf9b29269bf2156b Merge: 6cd14f429 a8fa411f2 Author: dtgraves Date: Tue Oct 17 15:47:35 2017 -0700 Merge pull request #146 from AMReX-Codes/dtg_branch bringing convergence tool fixes over to dev branch commit a8fa411f22d48e01e115f4539863b8c2c24e73a9 Author: dtgraves Date: Tue Oct 17 15:45:13 2017 -0700 all the tools except for ComputeAmrNorms compile. ComputeAmrNorms has no main. Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNormB.cpp commit 19995b3461327d379a413c8cf009d0f6ef7ec360 Author: Max Katz Date: Tue Oct 17 15:44:42 2017 -0700 Error check routines do not need to be on a single line Src/Base/AMReX_Device.H commit fd408c9bfd17f5aacc90f00e6022e57e347557d5 Author: Max Katz Date: Tue Oct 17 15:44:24 2017 -0700 Add Spectrum MPI to list of known implementations Tools/GNUMake/sites/Make.unknown commit 6cd14f429ffc8b43f9c4241adb484865b060c29a Author: Weiqun Zhang Date: Tue Oct 17 14:11:03 2017 -0700 MLMG: need to update coarse level solution bc Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 62c609f5c8ed1e2610d51611abb26424bb4c09e0 Author: dtgraves Date: Tue Oct 17 13:44:51 2017 -0700 more progress toward getting these tools working again. On a bunch of them, the MultiFab declarations need to be reworked Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp commit 689e694e9a8be90816c208b5059cd209b6409b7f Author: Weiqun Zhang Date: Tue Oct 17 12:58:17 2017 -0700 take out wrong assertion Src/Boundary/AMReX_YAFluxRegister.cpp commit 187bef0f999bc85115f520374d71a87630a86220 Author: Weiqun Zhang Date: Tue Oct 17 12:41:27 2017 -0700 Revert "tiling: make sure tile boxes are generally coarsenable" This reverts commit 616c5b59e8a4338147ba398a386833100c1da61d. Src/Base/AMReX_FabArrayBase.cpp commit 14f7e82b0f74f4030ac286cbe8efa38243e27249 Author: Marc Day Date: Tue Oct 17 12:41:52 2017 -0700 Add dest_comp argument to YAFluxRegister::Reflux Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp commit ebd5c2198b14fa5b17bfcfd2c634a6ba3a9a221b Merge: a5215de5c a9e81e7b7 Author: dtgraves Date: Tue Oct 17 11:13:43 2017 -0700 merging with dev to get convergence tools commit a9e81e7b7b299070b86f59db720af6d1adef0710 Merge: 616c5b59e 738a1a696 Author: Marc Day Date: Tue Oct 17 10:58:33 2017 -0700 Merge pull request #143 from AMReX-Codes/migrate_Convergence_util Migrate convergence util commit 616c5b59e8a4338147ba398a386833100c1da61d Author: Weiqun Zhang Date: Tue Oct 17 09:28:10 2017 -0700 tiling: make sure tile boxes are generally coarsenable Src/Base/AMReX_FabArrayBase.cpp commit a5215de5c616bbec708585633d1cd95461d843f9 Author: dtgraves Date: Mon Oct 16 14:19:05 2017 -0700 MOL2nd order now seems to work even with AMR. YAFluxRegister makes more sense in this context than FluxRegister. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 4551e3404a306fa4c8014d8c91a8830ba290b6d4 Author: dtgraves Date: Mon Oct 16 12:00:45 2017 -0700 added some debugging tools and I got MOL to work without AMR. Still something off with AMR, however. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugDump.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp commit 6eb1c642f02f44522a087dba62da2541ebc70bbf Author: dtgraves Date: Sun Oct 15 12:51:27 2017 -0700 godunov version works fine. MOL version needs work. Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 2263a1b4685c3b5bb42fe0c679f77f9983e8b9ba Author: dtgraves Date: Sat Oct 14 21:39:37 2017 -0700 couple of dimension-specific bug fixes Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit 0e6602b9fc4ea2097c250f49afaf8dadffef88ec Author: dtgraves Date: Sat Oct 14 21:36:49 2017 -0700 bunch of bug fixes Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv.Diff Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 417a3c272be94b1c1a7beacb0a104b8f47d323c2 Author: dtgraves Date: Fri Oct 13 20:54:47 2017 -0700 changed adv diff integrator to 2nd Order MOL. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 8997f302d77da01febbb11f867c3fba63abdd7e1 Author: Weiqun Zhang Date: Fri Oct 13 18:05:29 2017 -0700 MLMG test: add more parameters Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 4a9dc2e528583c28e567a61a5fff3f88895c7bed Author: Weiqun Zhang Date: Fri Oct 13 17:41:55 2017 -0700 MLMG: fix data type Src/LinearSolvers/MLMG/AMReX_MLMG.H commit b0bd068ded9a880473b36f228570a29517a60b90 Author: Weiqun Zhang Date: Fri Oct 13 17:36:04 2017 -0700 MLMG: set cg parameters Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit b9edf16acb9fba677bd989665e182cd59cb5dc10 Author: Weiqun Zhang Date: Fri Oct 13 17:32:58 2017 -0700 MLMG: fix cg tolerance Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5d0af86864f5a3723fe223aecc28a62a1e6d1b63 Author: Weiqun Zhang Date: Fri Oct 13 17:19:02 2017 -0700 CG for MLMG Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/Make.package commit bca731ab245f644a2ca3a9162037f3ae75ef838d Author: Weiqun Zhang Date: Fri Oct 13 14:14:34 2017 -0700 add anonymous namespace aroung some functions in CGSolver Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit aa3d3df67fd417072447752188f892d17d7e5c40 Author: Weiqun Zhang Date: Fri Oct 13 12:16:40 2017 -0700 MLLinOp::setMaxOrder Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 3348b9f66ac494c3185e1589f5e4d708bf3c0447 Merge: 04dbce1b0 50639530a Author: Andrew Myers Date: Fri Oct 13 14:54:16 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 04dbce1b025d91b575ea7c3bb90c6845d291d662 Author: Andrew Myers Date: Fri Oct 13 14:54:04 2017 -0700 clarify comment. Docs/AMReXUsersGuide/EB/EB.tex commit b4e5e4a1cf729c4bd90a1ace83b512619e8cd756 Author: dtgraves Date: Fri Oct 13 14:29:00 2017 -0700 advection/diffusion (in Godunov mode) reproduces advection tutorial. Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/README Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 50639530a7cedf3acc28990dfe3dd8641f07067b Author: Weiqun Zhang Date: Fri Oct 13 11:16:32 2017 -0700 MLMG: bottomSolve Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit c281ee7826c8bf1ddbd81e707022a779ce756fd9 Author: Andrew Myers Date: Fri Oct 13 11:19:33 2017 -0700 handle low dimensionality in the neighbor particle finding. Src/Particle/AMReX_NeighborParticlesI.H commit 81f5dbe0fc2fdd31ca7a4245077a8ac282599ec1 Author: Andrew Myers Date: Fri Oct 13 10:59:21 2017 -0700 fix a couple more typos. Docs/AMReXUsersGuide/EB/EB.tex commit 1329352b58835d75ca3d8344a084669aa1ae3176 Merge: 357b28e65 a5fcb9fad Author: Max Katz Date: Fri Oct 13 13:36:12 2017 -0400 Merge branch 'development' into gpu commit a5fcb9fad10d0a9351851d526fedb6f2fa2d7d69 Merge: 43b6f3a8f 310fb01ef Author: Andrew Myers Date: Fri Oct 13 10:28:13 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 43b6f3a8f6cb2943c9bb4dc7eecc180935a4cff8 Author: Andrew Myers Date: Fri Oct 13 10:27:57 2017 -0700 fix minor formatting issue. Docs/AMReXUsersGuide/EB/EB.tex commit 310fb01efa72f75d48a850e285d19d5421f620f5 Author: Weiqun Zhang Date: Fri Oct 13 10:24:23 2017 -0700 MLMG: add more set methods Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 357b28e65463535b15a6be7892265eea070b8412 Author: Max Katz Date: Fri Oct 13 13:14:59 2017 -0400 Add sanity check on total number of CUDA threads Src/Base/AMReX_CUDA.F90 commit 55e641dbbd8551976a5a99499f0633a91e381846 Author: Andrew Myers Date: Fri Oct 13 10:14:11 2017 -0700 fix typo in EB docs. Docs/AMReXUsersGuide/EB/EB.tex commit cf32ab2d0c5f28da240b7e0b4261763b7b2c4827 Author: Max Katz Date: Fri Oct 13 13:06:40 2017 -0400 Deal appropriately with varying box sizes in FillBoundary Src/Amr/AMReX_StateData.cpp commit 244ed5b5f06ac8f298fdf238d8fcdc272ce92b05 Author: Ann Almgren Date: Thu Oct 12 18:39:44 2017 -0700 Changes to be compatible with Sam's latest changes to HPGMG for Nyx. Src/Extern/hpgmg/BL_HPGMG.H Tools/GNUMake/packages/Make.hpgmg commit d9035a577093b617376fbe175d195966c3486af3 Author: Weiqun Zhang Date: Thu Oct 12 17:10:53 2017 -0700 MLMG test: add some runtime parameters Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 2f3a3e1fa4eb90eedb0f099a64aae4ad119c8233 Author: Weiqun Zhang Date: Thu Oct 12 16:37:13 2017 -0700 MLMG: mgCycle Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 117ba8be282ab1246fb00772e5ca4601d592c7ea Author: Weiqun Zhang Date: Thu Oct 12 15:09:16 2017 -0700 MLMG: up the amr v-cycle Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 9636228613e36d39ae00d385b4dbc467a36df523 Author: Weiqun Zhang Date: Thu Oct 12 13:35:32 2017 -0700 MLMG: save BndryRegister used in updating bc Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit cc68406f85a08f08f911e3908fbc0ededa669ec0 Author: Max Katz Date: Thu Oct 12 19:41:58 2017 -0400 Set a minimum threadblock size for StateData::FillBoundary Src/Amr/AMReX_StateData.cpp commit c49ab6bb2822aedfe431b14bd166dcfd2cade63b Author: Max Katz Date: Thu Oct 12 19:12:19 2017 -0400 Sync threads in between BC fill dimensions Src/Base/AMReX_filcc_mod.F90 commit 56cf18cf099bc47479beb3692cd7ed61bf34eaff Author: Max Katz Date: Thu Oct 12 19:11:55 2017 -0400 Add capability to set minimum number of CUDA threads Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit fbda66160467ecd75051ed8d5f6a2c1d222b69a9 Author: dtgraves Date: Thu Oct 12 15:34:36 2017 -0700 added advection-(explicit)diffusion example. Just starting to get this organized. Tutorials/Amr/ScalarAdvectionDiffusion/CMakeLists.txt Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs.tracers Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/probin Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probdata.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probin Tutorials/Amr/ScalarAdvectionDiffusion/README Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/LevelBldAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Adv_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/tagging_params.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp commit ccc4acfa770ed9b687244a4120e87f9718f1694f Merge: 832162f68 6bd9f1a2a Author: Andrew Myers Date: Thu Oct 12 15:26:45 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 832162f686d0fdf8f344a7fb2a706d1fedf1c429 Author: Andrew Myers Date: Thu Oct 12 15:26:33 2017 -0700 avoid allocating memory for temporaries in threaded regions. Src/Particle/AMReX_NeighborParticlesI.H commit 6bd9f1a2a4bac46c452d818f4b04dfcacdd90f5b Author: Weiqun Zhang Date: Thu Oct 12 13:13:39 2017 -0700 MLMG: updateSolBC Src/Base/AMReX_IntVect.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit c6b08523bc8901cda26860d1374d4b31532692a7 Author: Andrew Myers Date: Thu Oct 12 12:42:43 2017 -0700 constructing a ParIter with an MFItInfo should not imply tiling=true. Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParIterI.H commit 0dfa00600f5d0f1fe8c7fcab5e801e1efe4f81f1 Author: Andrew Myers Date: Thu Oct 12 11:07:48 2017 -0700 use async MPI communication in the particle neighbor fill Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 957aacfc3c6e41cdcf7381c71f0b24a843aaa606 Author: Andrew Myers Date: Thu Oct 12 11:07:14 2017 -0700 move the duplicate helper function to AMReX_Vector.H so it can be used elsewhere as well. Src/Base/AMReX_Vector.H commit 2d6a3290751c3a34667c3f0aca38bf55218d29b3 Author: Andrew Myers Date: Thu Oct 12 09:59:03 2017 -0700 std::vector -> amrex::Vector Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit d56131a803f1a00a9dba1de9b6b845fc580818eb Author: Andrew Myers Date: Thu Oct 12 09:56:41 2017 -0700 encapsulate remove duplicates from a vector into a function. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit a040ce97258312011566652dbed951f92bb6d40b Author: Weiqun Zhang Date: Thu Oct 12 08:58:51 2017 -0700 MLMG: clean up the interface and fix dx in reflux Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a5b7eb48635a6c54079b44fa0d9b9def91a80325 Author: Max Katz Date: Thu Oct 12 06:20:19 2017 -0400 Wrap CUDA launch in its own block Src/Base/AMReX_BLFort.H commit 6f171b160b11e51ac813b24c4edac1a0e6287ffd Author: Max Katz Date: Thu Oct 12 04:31:30 2017 -0400 Unify on a single filccn Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit 317f43b4f05b8493fd02270c3816da11d0516577 Author: Max Katz Date: Thu Oct 12 03:58:44 2017 -0400 Decrease default number of max CUDA threads Src/Base/AMReX_CUDA.F90 Tools/GNUMake/Make.defs commit 568dfbb218402f8a6f7a94cb0db35f7e2a62e7d9 Author: Max Katz Date: Thu Oct 12 03:46:43 2017 -0400 Update heat equation GPU test Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit 9990f28a0d4a13fc885d44b7b49d0569b057932f Author: Max Katz Date: Thu Oct 12 03:38:56 2017 -0400 Remove SUBROUTINE from macro names Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs commit 2d779c24a32f76c2498b81a8c147088d80f24bf0 Author: Max Katz Date: Thu Oct 12 03:31:02 2017 -0400 Use device subroutine macro Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs commit 95b012686d5f6f9d2822014c28104b8d2ce0026c Author: Max Katz Date: Thu Oct 12 03:22:39 2017 -0400 Call filcc directly from C++ Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 commit 007af5f0dcb16c4c723f66922992039a22865324 Merge: a6438f466 c2cae79dd Author: Tan Nguyen Date: Thu Oct 12 00:19:20 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a6438f466d4b0fa6977eaffa76044f045df6febf Author: Tan Nguyen Date: Thu Oct 12 00:19:08 2017 -0700 add SMC code Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/GNUmakefile Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/LiDryer.c Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/Make.package Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC.H Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_F.H Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_advance.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_init.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_io.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/chemistry_module.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/derivative_stencil.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/init_data.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/inputs_SMC Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/kernels.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/main.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/make_plot.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/transport_properties.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/variables.f90 commit c2cae79ddb6869525f4777e779cc89b056224a5e Merge: 92caaad3b 8bbdbb188 Author: WeiqunZhang Date: Wed Oct 11 16:45:38 2017 -0700 Merge pull request #145 from bcfriesen/pmi_fixes PMI: change computation of unique groups/chassis/slots from unordered_set to vector commit 8bbdbb188f49195b4c7baed0d279b8d786f9469e Author: Brian Friesen Date: Wed Oct 11 16:39:55 2017 -0700 PMI: change computation of unique groups/chassis/slots from unordered_set to vector This has better performance for large arrays. Src/Base/AMReX_ParallelDescriptor.cpp commit 92caaad3bbffb9e9be187ab5ced736c5c1083cbd Author: Weiqun Zhang Date: Wed Oct 11 16:22:47 2017 -0700 MLMG: prolongation of correction from coarse to fine amr level Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile commit bf6f597a523d57a7fbcba424bcf4118f0f672817 Author: Weiqun Zhang Date: Wed Oct 11 15:35:38 2017 -0700 MLMG: Reflux Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 2d36421cc8a3a899ce8dcf0b55036d1fcb6e8e00 Merge: 76cac72c0 3057a29ba Author: Weiqun Zhang Date: Wed Oct 11 15:10:35 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 76cac72c03a072b3596c14650cabea25b13062d2 Author: Weiqun Zhang Date: Wed Oct 11 15:09:10 2017 -0700 MLMG: coarse part of reflux Src/Boundary/AMReX_YAFluxRegister.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 3057a29baba50b5fd2825b19fea5213d29505a89 Merge: 4b3f2fe17 a972c2553 Author: WeiqunZhang Date: Wed Oct 11 13:59:55 2017 -0700 Merge pull request #144 from bcfriesen/add_pmi_support Base: add support for querying Process Management Interface (PMI) commit a972c2553b921d3a082d70b5b12f482479a9694c Author: Brian Friesen Date: Wed Oct 11 13:36:07 2017 -0700 Base: print simple header to STDOUT before PMI statistics Src/Base/AMReX_ParallelDescriptor.cpp commit 01a0eff33beefedd8b2ed18eaef91fe1db596c4a Author: Brian Friesen Date: Wed Oct 11 13:35:53 2017 -0700 Base: "PMI" -> "AMREX_PMI" Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tools/GNUMake/Make.defs commit 4b3f2fe17bb1c98d07862906772adfc3f2ac1e9a Author: kngott Date: Wed Oct 11 13:19:38 2017 -0700 Adjustments to test output and general cleanup of MoveAllFabs. Src/Base/AMReX_FabArray.H commit 9ab7fe886949599e65f9df8969bedd94ca53acbf Author: kngott Date: Wed Oct 11 13:10:18 2017 -0700 Change AddCompsToProc in FabSet to properly allocate FluxRegister FabArrays Src/Boundary/AMReX_FabSet.H commit 4bf5d960e8b54515b40fa5a7f86e19bc67b04d88 Author: kngott Date: Wed Oct 11 13:07:46 2017 -0700 Rewrite a comment from Array to Vector Src/Amr/AMReX_Amr.H commit b6073af307442cac501c0370e1baac83e7d41c68 Author: Brian Friesen Date: Fri Oct 6 13:17:33 2017 -0700 Base: add support for querying Process Management Interface (PMI) PMI is available on Cray systems and provides information about the topology of the job on the network. One can use this information to apply optimizations at run time which exploit higher bandwidth, lower-latency connections between particular groups of processes on the network. PMI support is disabled by default, and can be activated by setting USE_PMI=TRUE in the makefile. Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tools/GNUMake/Make.defs commit c761748c12167e88ac21c1206b0df3c113b734f5 Author: Weiqun Zhang Date: Wed Oct 11 12:25:29 2017 -0700 move YAFluxRegister to Boundary/ Src/AmrCore/Make.package Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1d.F90 Src/Boundary/AMReX_YAFluxRegister_2d.F90 Src/Boundary/AMReX_YAFluxRegister_3d.F90 Src/Boundary/AMReX_YAFluxRegister_F.H Src/Boundary/AMReX_YAFluxRegister_nd.F90 Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/write_plotfile.cpp commit 7889d091d00817d3223de9d56198f887a5808f3b Author: Weiqun Zhang Date: Wed Oct 11 10:37:39 2017 -0700 MLMG: smooth Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 36004bb31b4a7b5aaeeba4168eccdc406b8de66f Merge: 1e51f8610 1596e8c24 Author: vince Date: Wed Oct 11 10:23:07 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1596e8c248726c18c19537690e011adf7d9ec64f Author: Weiqun Zhang Date: Wed Oct 11 09:36:38 2017 -0700 MLMG: finish applyBC Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 86599d1e04b90ca04848dc203c8cc3b1257504ea Author: Weiqun Zhang Date: Wed Oct 11 07:46:24 2017 -0700 Array is used by Fortran BoxLib and in that case cannot include AMReX_SPACE.H Src/Base/AMReX_Array.H commit ac6a8b5685031bc456311d121ce30eab2164a282 Author: Weiqun Zhang Date: Tue Oct 10 16:55:52 2017 -0700 MLMG: applyBC WIP Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_LayoutData.H Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 1e51f8610899ba8eb721a29d915cabbdcf752994 Merge: 038539afd fcdefa3f2 Author: vince Date: Tue Oct 10 15:03:46 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b0112558b9e52a0fe81e9be7c7c7ee5acd3ee616 Author: Weiqun Zhang Date: Tue Oct 10 13:31:17 2017 -0700 MLMG: wip Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 1a352f817fa16e7d881785e35433da9ddadf8842 Author: Max Katz Date: Tue Oct 10 15:59:35 2017 -0400 Fix rank <-> GPU identification for MPS case Src/Base/AMReX_Device.cpp commit fcdefa3f29d83d0f2a92c649b3d92b4a0df5f180 Author: Weiqun Zhang Date: Tue Oct 10 12:41:26 2017 -0700 MLMG: add A dot x Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit 9e5efc7b8e3086988c387d834e0193b6ea7df30d Author: Weiqun Zhang Date: Tue Oct 10 11:06:45 2017 -0700 add a few virtual function stubs to MLLinOp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit acfe5325ec8009b6cbec25ff1bd0e2af41ca5de4 Merge: 57b41fc69 58e4fd369 Author: Weiqun Zhang Date: Tue Oct 10 10:31:15 2017 -0700 Merge branch 'weiqun/mlmg' into development commit 58e4fd369ef05d76f1354ddce14236dcf1b6ca1b Author: Weiqun Zhang Date: Tue Oct 10 10:30:35 2017 -0700 MLMG: WIP Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit bad73ccc91f23a36da4bb49598136c8c8a7d09cb Author: Weiqun Zhang Date: Mon Oct 9 17:23:58 2017 -0700 WIP Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp commit 57b41fc69d53db2ab4ca371e187415b8ccdeae12 Merge: ae90dbfd4 ec3110776 Author: Andrew Myers Date: Mon Oct 9 16:36:50 2017 -0700 fixing merge conflict commit 5e53b9f733bd31af429f355731d9bbeb99dcbe0c Author: Weiqun Zhang Date: Sun Oct 8 12:06:21 2017 -0700 MLMG: notes Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 14bbb92b548bab77c9ec9f9545177b68b7ad843e Author: Max Katz Date: Sun Oct 8 06:39:10 2017 -0400 Fix a compile fail without MPI Src/Base/AMReX_Device.cpp commit a55517b78527f0414d940fd4e14ed291d600b04a Author: Max Katz Date: Sun Oct 8 01:51:32 2017 -0400 Use 512 threads per block Note that for Pascal, this means you need to limit the number of registers per function to 128. Src/Base/AMReX_CUDA.F90 commit 04e77cc5d5db4d90cc960d512944728923e1d154 Author: Max Katz Date: Sun Oct 8 01:19:50 2017 -0400 Do not tile threadblock size; this hurts performance Src/Base/AMReX_CUDA.F90 commit 1897612dd67748378d6fc1d980dd683edc23678c Author: Max Katz Date: Sat Oct 7 22:00:51 2017 -0400 Move the loop over components to the top level Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 commit d914d5f7afced9efb110596863ec1d5da3a81747 Author: Max Katz Date: Sat Oct 7 21:02:32 2017 -0400 filccn loops over all n variables Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit d67523c9358a704f04526144ad8e83aa613dc251 Author: Weiqun Zhang Date: Sat Oct 7 15:48:43 2017 -0700 WIP: MLMG Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp commit 36520d83b07f435a81b9b24b15ac84b5deea881b Author: Weiqun Zhang Date: Sat Oct 7 13:30:40 2017 -0700 MLMG: prepare for solve Src/Base/AMReX_Array.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit d3fcbb948196f1d3eed0708c159898e0ba3c20b9 Author: Weiqun Zhang Date: Fri Oct 6 17:12:30 2017 -0700 MLMG::solve WIP Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit d98329a3bedf1513a95db42471d851c4143673f6 Author: Weiqun Zhang Date: Fri Oct 6 16:49:18 2017 -0700 MLMG constructor Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit e24efe2f04270851132dfefe908d0e11719f6469 Author: Weiqun Zhang Date: Fri Oct 6 16:36:51 2017 -0700 set ABecLaplacian coefficients Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 96c3a8cd7eb50a8aac07e426966c9c2811a86c39 Author: Weiqun Zhang Date: Fri Oct 6 15:08:44 2017 -0700 MLLinOp and MLABecLaplacian constructors Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 038539afd3b72d98099235c45dff2c6fda61905b Author: vince Date: Fri Oct 6 14:41:02 2017 -0700 remove debug diagnostic. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit ea61045fe1534a75304786b6b60f87d6e1bd477b Author: Weiqun Zhang Date: Fri Oct 6 12:35:15 2017 -0700 Array --> Vector in mlmg test Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp Tests/LinearSolvers/MLMG/write_plotfile.cpp commit 3d8be64878ab61817a88ddea2381be417aca6a09 Merge: e7c5b1dcf ec3110776 Author: Weiqun Zhang Date: Fri Oct 6 12:32:19 2017 -0700 Merge branch 'development' into weiqun/mlmg Conflicts: Src/Base/AMReX_Array.H commit 738a1a696824d80e16f9110368fbe917b229e961 Merge: 7feb1c361 ec3110776 Author: rgrout Date: Fri Oct 6 13:20:28 2017 -0600 Merge branch 'development' into migrate_Convergence_util commit 7feb1c361398ac55b1cbef73289e5f920c3bcb5c Author: Ray Grout Date: Fri Oct 6 09:30:05 2017 -0700 Updates to track AMReX development Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/Make.package Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp commit ec31107762d7ed12e82d49d6a0d7d1c4cb8064a0 Author: Weiqun Zhang Date: Fri Oct 6 08:53:01 2017 -0700 Array --> Vector in Tools Tools/AMRProfParser/TestCodes/BLProfCallTimes.cpp Tools/AMRProfParser/TestCodes/Pieces.cpp Tools/AMRProfParser/TestCodes/SendTest0.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/PltFileFluxAve.H Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.H Tools/C_util/Statistics/PltFileXAve.cpp Tools/C_util/ViewMF/mfMinMax.cpp Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp commit 68544a54fa5cbe5fcf7c62e271d421f0ee15c226 Merge: a274becd1 945759d46 Author: Tan Nguyen Date: Fri Oct 6 01:15:39 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a274becd1542d5f383c8212a7c67609b477fb015 Author: Tan Nguyen Date: Fri Oct 6 01:15:30 2017 -0700 fix a memory leak bug Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H commit e2d9950f1860ad21bebedfef5087d13773aaf1e0 Merge: 669a6a9ba 945759d46 Author: Max Katz Date: Fri Oct 6 03:11:53 2017 -0400 Merge branch 'development' into gpu commit 669a6a9badc2a3ba62fc3a5a9ee669a1557395e9 Author: Max Katz Date: Fri Oct 6 02:07:33 2017 -0400 Give simplified initial output if device is not verbose Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 537f635792e5e264fbff6fd72f60905b343c8395 Author: Max Katz Date: Thu Oct 5 22:01:58 2017 -0400 Add device.verbose output parameter Src/Base/AMReX.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 945759d46ba1bd3a0e00b1b125fc703966afad5a Author: Weiqun Zhang Date: Thu Oct 5 17:48:51 2017 -0700 update CHANGES CHANGES commit faa0d57083c3abee8c1b659b8fc90b793cc063dc Merge: d6785a628 bb60bc275 Author: Tan Nguyen Date: Thu Oct 5 17:39:25 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d6785a6281e56a28811ba62cb305b39a769f3b2d Author: Tan Nguyen Date: Thu Oct 5 17:39:04 2017 -0700 grant friend access to MFGraph and Action classes Src/Base/AMReX_FabArray.H commit e65447ec7130090d5045e4d2cd5da1363d4888f7 Author: Tan Nguyen Date: Thu Oct 5 17:36:45 2017 -0700 runtime support for AMFIter Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.cpp Src/AmrTask/AMFIter/AMReX_Connections.H Src/AmrTask/AMFIter/Makefile Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/rts_impls/MPI_Generic/Makefile Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/tutorials/MiniApps/HeatEquation/advance.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/inputs_3d commit bb60bc275816f0ad98a63f0426c8aff2f82251d3 Author: Weiqun Zhang Date: Thu Oct 5 17:35:05 2017 -0700 Array --> Vector in Docs Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Boundary/Boundary.tex Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/Particle/Particle.tex Docs/Readme.sidecars Tools/Migration/amrex_array_to_vector.sh commit f19ceb6d5d36ad99b55c5ae8aadfb4e8a62bb59f Author: Weiqun Zhang Date: Thu Oct 5 17:29:43 2017 -0700 a script for Array --> Vector Tools/Migration/amrex_array_to_vector.sh commit 67db2c14fcf8daa675bc44d26efbe608007e38ff Author: Weiqun Zhang Date: Thu Oct 5 17:27:21 2017 -0700 Array --> Vector in Tutorials Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX2_C/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/main.cpp Tutorials/Basic/HeatEquation_EX2_C/myfunc.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/main.cpp Tutorials/Particles/LoadBalance/main.cpp commit 8dac4ff5ca7c480c38d9f602bef37150276ccb4e Author: Weiqun Zhang Date: Thu Oct 5 17:26:31 2017 -0700 Array --> Vector in Tests Tests/BBIOBenchmark/BBIOTest.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tRABcast.cpp Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/divergenceOpTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/gradientOpTest.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp Tests/EBAMRTools/regression/simpleMeshRefine.cpp Tests/FillBoundaryComparison/main.cpp Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/ramp/main.cpp Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/GeometryShop/vofStructures/umapTest.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/Particles/AssignMultiLevelDensity/main.cpp Tests/Particles/ParticleIterator/main.cpp Tests/Particles/main.cpp commit 205418320396c9d6172b9acfe08c2c5bc2f4cf2c Author: Weiqun Zhang Date: Thu Oct 5 17:25:01 2017 -0700 Array --> Vector in OldTutorials OldTutorials/DataServicesTest0/DataServicesTest0.cpp OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp OldTutorials/GettingStarted_C/main.cpp OldTutorials/HeatEquation_EX2_C/main.cpp OldTutorials/MeshRefinement/MyAmr.H OldTutorials/MeshRefinement/MyAmr.cpp OldTutorials/MeshRefinement/main.cpp OldTutorials/MultiColor_C/main.cpp OldTutorials/MultiFabTests_C/GridMoveTest.cpp OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp OldTutorials/MultiFabTests_C/MultiFabFillBoundary.cpp OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp OldTutorials/MultiGrid_C/main.cpp OldTutorials/PGAS_HEAT/main.cpp OldTutorials/PIC_C/single_level.cpp OldTutorials/PIC_C/solve_for_accel.cpp OldTutorials/PIC_C/solve_with_f90.cpp OldTutorials/PIC_C/two_level.cpp OldTutorials/Sidecar_EX1/DestMFTest.cpp OldTutorials/Sidecar_EX1/NSidecarsTest.cpp OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp OldTutorials/Sidecar_EX1/TestRankSets.cpp OldTutorials/Tiling_Heat_C/main.cpp OldTutorials/TwoGrid_PIC_C/main.cpp OldTutorials/TwoGrid_PIC_C/solve_for_accel.cpp OldTutorials/TwoGrid_PIC_C/solve_with_f90.cpp OldTutorials/TwoGrid_PIC_C/split_boxes.cpp OldTutorials/libamrex_C/MyAmr.H OldTutorials/libamrex_C/MyAmr.cpp OldTutorials/libamrex_C/main.cpp commit c02d0ca36b8e247696f7c635acd9b33a28bc88bd Author: Weiqun Zhang Date: Thu Oct 5 17:21:44 2017 -0700 Array --> Vector in MiniApps MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_init.cpp commit 5fecfa6e986de5dbfbf0c26ec39c504b4acd4a04 Author: Weiqun Zhang Date: Thu Oct 5 16:20:21 2017 -0700 Array --> Vector in Src/ Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/AmrCore/AMReX_YAFluxRegister.H Src/AmrCore/AMReX_YAFluxRegister.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/main.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/physbc.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_LayoutData.H Src/Base/AMReX_MFCopyDescriptor.H Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Src/Base/AMReX_parmparse_fi.cpp Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_MultiMask.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBInterpolater.H Src/EB/AMReX_EBInterpolater.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.H Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_BLWritePlotFile.H Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/amrdata/AMReX_XYPlotDataList.H Src/Extern/amrdata/AMReX_XYPlotDataList.cpp Src/F_BaseLib/MultiFab_C_F.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_PolynomialIF.cpp Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit dd050be633bce59c18e65e24e39c6e6a0023c8aa Author: Weiqun Zhang Date: Thu Oct 5 16:12:14 2017 -0700 include AMReX_Vector.H in addition to AMReX_Array.H Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateDescriptor.H Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxList.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabConv.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_Utility.H Src/Base/AMReX_parmparse_fi.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.H Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_XYPlotDataList.H Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particles.H commit e7c5b1dcf8998f9b819363153bc7cbf6b5703ccf Merge: 94a465e2f 5a6178be9 Author: Weiqun Zhang Date: Thu Oct 5 15:57:43 2017 -0700 Merge branch 'development' into weiqun/mlmg commit 5a6178be9654b662d3bd30244e28ee406e89d501 Author: Weiqun Zhang Date: Thu Oct 5 15:57:14 2017 -0700 add amrex::Vector Src/Base/AMReX_Vector.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 94a465e2f83782694c950dfa9eafb79b3e3d27bb Author: Weiqun Zhang Date: Thu Oct 5 15:47:48 2017 -0700 MLMG test: wip Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/prob_par.H Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit b306d7d96d1447adc1e726b1323269d4002deaf7 Author: Weiqun Zhang Date: Thu Oct 5 14:42:03 2017 -0700 set up a test problem for MLMG Src/Base/AMReX_Array.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/fort.H Tests/LinearSolvers/MLMG/fort_3d.F90 Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp Tests/LinearSolvers/MLMG/write_plotfile.cpp commit dc1e602b560ecfeb825da5b2607445a9b203c442 Merge: 85d76e883 cbb336a40 Author: Michele Rosso Date: Thu Oct 5 11:21:41 2017 -0700 Merge branch 'development' into mr-cmake commit cbb336a4012b027b75bd8b76aa5a6b3576e56453 Merge: 36ac652b6 3441bfde2 Author: WeiqunZhang Date: Thu Oct 5 10:44:24 2017 -0700 Merge pull request #142 from zingale/development sync up with fcompare commit 36ac652b627d61050f7a694c8981996e194c624a Author: Andrew Myers Date: Thu Oct 5 10:22:50 2017 -0700 update changelog CHANGES commit bd0179deb38c4943ee6d2080e822de0aa75e4966 Author: Weiqun Zhang Date: Thu Oct 5 10:20:33 2017 -0700 start MLMG Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/main.cpp commit d6df9c293b057db4e473e3785372d40574f77c2f Author: Max Katz Date: Thu Oct 5 05:01:55 2017 -0400 Fix an error testing against a possibly empty vector Src/Base/AMReX_MFIter.cpp commit d1722ed0697e437609bc910eb06faa3351c5c166 Author: Max Katz Date: Thu Oct 5 05:01:33 2017 -0400 Allow for multi-node CPU<->GPU mappings Src/Base/AMReX_Device.cpp commit 3531a2da499f929cc620fc766e10c564e8711ee0 Merge: d7ca2bc19 74aa06398 Author: Klaus Weide Date: Thu Oct 5 01:38:33 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 85e3ea22d2ff90973862621d84e4af9cee739585 Author: Max Katz Date: Thu Oct 5 02:10:54 2017 -0400 Use a distinct (non-coalesced) memory arena for FabArray Src/Base/AMReX_Arena.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 74aa06398304e0f2cf71cfeb9d1e1c6c3b61cab4 Merge: 7a060dfbd 95ed12916 Author: Andy Nonaka Date: Wed Oct 4 18:32:57 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7a060dfbd23fdd3ed7c2a44916e50ecd4c97104c Author: Andy Nonaka Date: Wed Oct 4 18:31:48 2017 -0700 add sort=.false. to the boxarray constructor for the diff multifab it fixes problems with this utility when the input plotfile boxarray are not in the "sorted" order Tools/Postprocessing/F_Src/fcompare.f90 commit 3441bfde27d002247cd8fc96231d377430d50cff Author: Michael Zingale Date: Wed Oct 4 20:43:08 2017 -0400 sync up with fcompare you now don't need to use --infile1 and --infile2, just list the plot files after the command the 2 features it doesn't do that fcompare does is compare ghost cells (not sure if it makes sense with different boxes) and output a plotfile with the difference between plotfiles Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit 95ed12916155eb12a072544c660a9d0fc545f854 Merge: 9593e9577 9e9865508 Author: WeiqunZhang Date: Wed Oct 4 17:34:27 2017 -0700 Merge pull request #141 from AMReX-Codes/parallel_print_to_file Parallel print to file commit 9e9865508d2041b5319a05b9448f11be68cc2ac0 Author: Andrew Myers Date: Wed Oct 4 16:58:48 2017 -0700 trading some code duplication for some clarity. Src/Base/AMReX_Print.H Tests/Particles/ParticleIterator/main.cpp commit efedbbe60f3a3dc9874e3577a61656004eeb1eb5 Author: Max Katz Date: Wed Oct 4 19:50:40 2017 -0400 Add C++ CUDA error checking Src/Base/AMReX_BLFort.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 25b862b52fb84cc0e076b4f615392433140ad9b8 Author: Andrew Myers Date: Wed Oct 4 15:31:58 2017 -0700 update this test to demonstrate the new amrex::Print() capability Tests/Particles/ParticleIterator/GNUmakefile Tests/Particles/ParticleIterator/main.cpp commit f19c64a8e8e194a9619686eeb22b61879862dc9d Author: Andrew Myers Date: Wed Oct 4 15:31:21 2017 -0700 new versions of amrex::Print() that send the output to a different file for each proc (and for each thread if called inside a parallel region). Src/Base/AMReX_Print.H commit 85d76e88359e9fd8e3a88db80025b17b70ccda72 Author: Michele Rosso Date: Wed Oct 4 15:29:53 2017 -0700 Remove garbage Tutorials/Amr/Advection_octree_F/CMakeLists.txt commit 9593e9577645d26ae2b767556bc953532ff0af94 Merge: 1a9dcfe79 6e5eda778 Author: vince Date: Wed Oct 4 15:12:02 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5c222f5eaeb3ed998c607edc91e67f8ae8086b58 Merge: 45c70be70 6e5eda778 Author: Michele Rosso Date: Wed Oct 4 13:55:04 2017 -0700 Merge branch 'development' into mr-cmake Conflicts: Src/AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrCore/CMakeLists.txt commit 6e5eda7789de63c1e3d3bbe9bab0b31afff33173 Author: Weiqun Zhang Date: Wed Oct 4 08:50:41 2017 -0700 clean up old files Src/EB/AMReX_EBFaceFlag.H Src/EB/AMReX_EBFaceFlag.cpp Src/EB/AMReX_EBLevel.H Src/EB/AMReX_EBLevel.cpp Src/EB/Make.package commit eaaeca7a11d30a1545c557ad5fec201584302927 Author: Weiqun Zhang Date: Tue Oct 3 17:50:46 2017 -0700 EB/CNS: tagging on density gradient Tutorials/EB/CNS/Exec/ShockRef/inputs.amr Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/fortran/CNS_tagging.F90 Tutorials/EB/CNS/Source/fortran/Make.package commit 1a9dcfe7912dcfeba5ebbabfd6ae55ebffc8a18c Author: vince Date: Tue Oct 3 16:09:03 2017 -0700 fix comments. Src/Base/AMReX.H commit 3e7487ca9ddc2f96e091389c2d2d28593d4de060 Merge: 0cd099cf4 3e44cf771 Author: Michele Rosso Date: Tue Oct 3 15:53:47 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0cd099cf436a4c5f989c60b8a2c16be38c459878 Author: Michele Rosso Date: Tue Oct 3 15:53:27 2017 -0700 CMake: update CMakeLists.txt in Tutorials Tutorials/Amr/Advection_AmrCore/CMakeLists.txt commit 3e44cf771a2472917a3bc82e511d54a33b06e1bb Merge: 35691dd7e 32a121d8e Author: Weiqun Zhang Date: Tue Oct 3 15:41:34 2017 -0700 Merge branch 'weiqun/eb' into development commit 35691dd7edfd00900277494e9694ee554bf13121 Merge: 7f47b5442 39aa4f48f Author: dtgraves Date: Tue Oct 3 15:27:43 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7f47b5442c0e603eb21dca5d105a609ddf0df659 Author: dtgraves Date: Tue Oct 3 15:26:50 2017 -0700 added some timers Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 commit f634d9b94cf47683622034aafdfee235ca7e5663 Author: vince Date: Tue Oct 3 14:42:50 2017 -0700 move file into Extern/ProfParser. Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/ProfParser/Make.package Tools/AMRProfParser/GNUmakefile commit d0b7cfabb9b662771ac441297b403ce3920560eb Author: vince Date: Tue Oct 3 14:22:56 2017 -0700 move the amrprofparser into amrex tools. the parser functionality will be replaced by amrvis. Tools/AMRProfParser/AMReX_ProfParserBatch.cpp Tools/AMRProfParser/BLProfParser.cpp Tools/AMRProfParser/GNUmakefile Tools/AMRProfParser/TestCodes/AMRProfTest0.cpp Tools/AMRProfParser/TestCodes/BLProfCallTimes.cpp Tools/AMRProfParser/TestCodes/GNUmakefile Tools/AMRProfParser/TestCodes/Pieces.cpp Tools/AMRProfParser/TestCodes/SendTest0.cpp Tools/AMRProfParser/TestCodes/TokenizeTest.cpp commit 8d9338393645477c8c169819a5d98c09fdb2b7ac Merge: 2a2cb9403 39aa4f48f Author: vince Date: Tue Oct 3 14:07:30 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 2a2cb9403840f64008cdc2517ece55afde05284a Merge: e3441f0cd 0f51486ef Author: vince Date: Tue Oct 3 14:07:28 2017 -0700 merge fix. commit 39aa4f48f9d8e8ccb55ef615438bd64c4b245655 Merge: 6b68a5271 0f51486ef Author: Andrew Myers Date: Tue Oct 3 13:28:41 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6b68a52713d904b810576652e85171e8cb746d14 Author: Andrew Myers Date: Tue Oct 3 13:28:25 2017 -0700 add ability to load balance based on the square of the particle count. Src/Particle/AMReX_KDTree_3d.F90 Src/Particle/AMReX_KDTree_F.H Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp commit 32a121d8ed48268b03bb1f70907f9141bef9a5ff Merge: f44c383ee 0f51486ef Author: Weiqun Zhang Date: Tue Oct 3 12:50:06 2017 -0700 Merge branch 'development' into weiqun/eb commit f44c383ee8b9d6cbbb544729b24f0b45a7b71a92 Author: Weiqun Zhang Date: Tue Oct 3 12:48:43 2017 -0700 fine tune # of ghost cells Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/main.cpp commit e3441f0cdf84fb801f3107dcc165fc9346317a67 Author: vince Date: Tue Oct 3 12:19:22 2017 -0700 update for amrex. OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp commit e550df3759446a23e2fdb2d927fc1e07cbae942f Author: vince Date: Tue Oct 3 12:17:22 2017 -0700 fix comment. Src/Base/AMReX_ParallelDescriptor.H commit 0f51486ef8dd1ea3bfe96f70de10fb5abecb7e1e Author: Weiqun Zhang Date: Tue Oct 3 10:05:29 2017 -0700 Revert "simplify overloaded calls to InterpFromCoarseLevel and FillPatchTwoLevels" This reverts commit b984bd551bb96802bb0896d63e4ca7ca8132955f. Src/AmrCore/AMReX_FillPatchUtil.cpp commit b747bf33304a8cecaf267110a6309d3a3844cb94 Merge: 3aa540ff8 fa6163cb4 Author: Weiqun Zhang Date: Tue Oct 3 09:43:38 2017 -0700 Merge branch 'development' into weiqun/eb commit 3aa540ff8faa25c7461510156a083767961065b5 Author: Weiqun Zhang Date: Tue Oct 3 09:43:26 2017 -0700 more clean up of EBMultiFabUtil Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Tutorials/EB/CNS/Source/CNS.cpp commit 1122ee807e939c04b7264d249f511a27c732c879 Author: Weiqun Zhang Date: Tue Oct 3 09:30:54 2017 -0700 EBTower: bug fix Src/EB/AMReX_EBTower.cpp commit f81e3c6165170b47d514f7994decbcbf2e70a38c Author: Weiqun Zhang Date: Tue Oct 3 09:18:32 2017 -0700 clean up Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit fa6163cb4e3b27e7e1ea3c3b8ca0ce712a385b2b Merge: 914a64625 b984bd551 Author: Andrew Myers Date: Mon Oct 2 23:31:39 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 914a646257466ee306ba038af78bbe2693816c48 Author: Andrew Myers Date: Mon Oct 2 23:31:15 2017 -0700 handle case where a level is lost on restart in Particle::Redistribute() Src/Particle/AMReX_ParticleContainerI.H commit b984bd551bb96802bb0896d63e4ca7ca8132955f Author: Andy Nonaka Date: Mon Oct 2 17:42:51 2017 -0700 simplify overloaded calls to InterpFromCoarseLevel and FillPatchTwoLevels Src/AmrCore/AMReX_FillPatchUtil.cpp commit 61b5aefd418faf1e4d7fa9df5603a8081423eae6 Author: Weiqun Zhang Date: Mon Oct 2 17:32:16 2017 -0700 fix no-mpi Src/Base/AMReX_Box.cpp commit 65198ccbfbe35c0f39e2770c1a021bfe9e2ffd51 Author: Weiqun Zhang Date: Mon Oct 2 17:10:06 2017 -0700 update EB average down and fix local copy of CutFab Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 6349b636f83e393c505324e7441c1f82477d1d41 Author: Andy Nonaka Date: Mon Oct 2 17:00:40 2017 -0700 boundary condition documentation, example cleanup Docs/AMReXUsersGuide/Boundary/Boundary.tex Src/Base/AMReX_PhysBCFunct.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 5a36ae5a4aab19dbf3a63d1ab5fd5107c69ec6a2 Merge: cca88eb0d 5760d5a78 Author: Weiqun Zhang Date: Mon Oct 2 16:29:08 2017 -0700 Merge branch 'development' into weiqun/eb commit cca88eb0d0316e1faad6c72831661f548b8a289f Author: Weiqun Zhang Date: Mon Oct 2 16:28:54 2017 -0700 ParallelCopy for MultiCutFab Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_FabArray.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 7da89b98d0403c2272e5043f538ff5c37d438794 Merge: 73cac8afe c79b8f8f7 Author: Andy Nonaka Date: Mon Oct 2 13:52:42 2017 -0700 removing this file Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development Conflicts: Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt commit 73cac8afe29c62459a44a785b32ce5537684bb68 Author: Andy Nonaka Date: Mon Oct 2 13:50:47 2017 -0700 greatly cleaned up the Advection_AmrCore example so now it includes physical boundary conditions removed the derived AmrAdvPhysBC.H class, it wasn't needed and now uses PhysBCFunct class in amrex/Src/Base so there are less local files/classes Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore/Source/Make.package Tutorials/Amr/Advection_AmrCore/Source/bc_fill_nd.F90 Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt Tutorials/Amr/Advection_AmrCore_Boundary/Exec/Make.Adv Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore_Boundary/README Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/main.cpp commit 4fe6565fb6cdce54af4d306722d8a1351ea99f00 Author: Andy Nonaka Date: Mon Oct 2 13:39:52 2017 -0700 further simplification of this tutorial to rely on amrex-native classes Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/bc_fill_nd.F90 commit 8ee6aa8f330f468a92ac75e1096ddc3f402755c1 Author: Andy Nonaka Date: Mon Oct 2 13:38:49 2017 -0700 overloaded FillPatchTwoLevels and InterpFromCoarseLevel to allow const BCRec& bcs as an option for input instead of const Array& bcs Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit e022a2bf28f38e35af701cf2bc8650949197e034 Author: Andy Nonaka Date: Mon Oct 2 13:16:15 2017 -0700 boundary condition work in progress Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp commit c79b8f8f739f58d6a1d204214b28888c0975e06a Author: Andrew Myers Date: Mon Oct 2 12:43:56 2017 -0700 give this executable a different name so the cmake install will work. Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt commit 1124a21ca4358b33c8404aeef73701b815814521 Author: Andy Nonaka Date: Mon Oct 2 12:35:54 2017 -0700 start of expanded documenation on domain boundary conditions Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Boundary/Boundary.tex Docs/AMReXUsersGuide/GNUmakefile Tutorials/Basic/HeatEquation_EX2_C/advance.cpp commit 5760d5a780fbe44d6c8d61ce6a76ed04dfe6fc79 Merge: 2bc3b4ddf f47d9cbaa Author: Weiqun Zhang Date: Mon Oct 2 08:29:44 2017 -0700 Merge branch 'development' commit f47d9cbaada52932155596a0a4e194a9b9146f45 Author: kngott Date: Sun Oct 1 16:52:44 2017 -0700 Fix some OldTutorials/MultiFabTests_C and OldTutorials/Sidecar_EX1 to function again. OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp OldTutorials/Sidecar_EX1/DestMFTest.cpp OldTutorials/Sidecar_EX1/GNUmakefile OldTutorials/Sidecar_EX1/GridMoveTest.cpp OldTutorials/Sidecar_EX1/InTransitAnalysis.H OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp commit f9d5c866ca5352e9b4a008a87920f17b91930d35 Author: Weiqun Zhang Date: Sun Oct 1 16:09:31 2017 -0700 update EB/CNS to use cached geometry data Src/EB/AMReX_EBFabFactory.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit db5571b31376c99d0a961f04cd9902eb9ce01c45 Author: Weiqun Zhang Date: Sun Oct 1 15:55:15 2017 -0700 fill bndrycent, areafrac and facecent Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit cc57b80dff8c73f4aba2c1e40157cc77e0301345 Author: Weiqun Zhang Date: Sun Oct 1 15:08:43 2017 -0700 MultiCutFab: remove regular and covered fabs Src/Base/AMReX_FabArray.H Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 9126e3f35589307e4af20ebffb3fecff598afb84 Author: Weiqun Zhang Date: Sun Oct 1 14:56:49 2017 -0700 EBDataCollection: define bndrycent, areafrac and facecent Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 8f70156b2cfb06ad2bf85c3ef859e979d4ba1fc6 Author: Weiqun Zhang Date: Sun Oct 1 12:55:24 2017 -0700 EBTower: added bndrycent, areafrac and facecent Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp Src/EB/Make.package commit 4f265ca8ee53ebb2bb889bfdfcc133046f256c6a Author: Max Katz Date: Sat Sep 30 19:24:56 2017 -0400 Broadcast plot_and_continue to all processors Src/Amr/AMReX_Amr.cpp commit da101cb65518d9ba4fc40cfb93f87bd2b5519e03 Author: Max Katz Date: Sat Sep 30 18:38:44 2017 -0400 Add small_plot_and_continue file checker Src/Amr/AMReX_Amr.cpp commit ae185e2f97db3dab24e0552586416a08cb59ba18 Author: Max Katz Date: Sat Sep 30 18:38:21 2017 -0400 Add a level option to fdump Tools/Postprocessing/F_Src/fdump.f90 commit dd7145c62c144cf36080b89fbabf7f720c5a4afb Author: Weiqun Zhang Date: Sat Sep 30 13:23:45 2017 -0700 function to delete the EBIndexSpace singleton Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Tutorials/EB/CNS/Source/main.cpp commit 4e33c7289bcce57378eb2e869bd30641bc6cec06 Author: Weiqun Zhang Date: Fri Sep 29 18:05:56 2017 -0700 WIP: get volume fraction Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit 9b503de64e4a1839059d4fba065892803d76b33f Merge: 9674d2e24 c9abf710c Author: Andy Nonaka Date: Fri Sep 29 19:21:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9674d2e24f35215099e62ece45da3e0bc95a7d43 Author: Andy Nonaka Date: Fri Sep 29 19:21:26 2017 -0700 comments Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp commit c9abf710c458a8d470ab8f30dffa64ead45ad987 Author: Weiqun Zhang Date: Fri Sep 29 18:05:19 2017 -0700 EB/CNS: fix RK2 Tutorials/EB/CNS/Source/CNS_advance.cpp commit 4fb0028b716100e7c4f138ed96796059c58a394e Author: Andy Nonaka Date: Fri Sep 29 17:20:59 2017 -0700 new Tutorial showing how to do walls (homogeneous Neumann) scalar bc's in the AmrCore framework Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt Tutorials/Amr/Advection_AmrCore_Boundary/Exec/Make.Adv Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore_Boundary/README Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/main.cpp commit ec0a3f441c6aa012b3603a65b233cc18d88e5680 Author: Weiqun Zhang Date: Fri Sep 29 16:50:01 2017 -0700 WIP: EBTower: volume fraction Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBSupport.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/main.cpp commit a9f214e2067033311519366a93193c45e9c87556 Author: Weiqun Zhang Date: Fri Sep 29 14:26:12 2017 -0700 WIP: EBTower: fill cell flags for EBDataCollection Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_MultiFab.H Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBSupport.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/Make.package Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit 59aaa3aa9033d727118e0c9e658c4a76d71af86f Merge: 90b62388d d791f53cf Author: vince Date: Fri Sep 29 11:14:42 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d791f53cf230c43d0e044fb317d3ed88ded6865c Author: Weiqun Zhang Date: Fri Sep 29 10:40:57 2017 -0700 add ostream& operator<< for BoxArray::RefID, DistributionMapping::RefID and FabArrayBase::BDKey Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit bb73713264704d76da109d27e8a04ca166d4eb85 Author: Ann Almgren Date: Thu Sep 28 19:09:41 2017 -0700 Fix Oops in AMReX_DistributionMapping.cpp Src/Base/AMReX_DistributionMapping.cpp commit 6943a9aa980bc22e3c896226793d1062886000ff Merge: fada55b92 ebeafa803 Author: Ann Almgren Date: Thu Sep 28 19:04:27 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development Conflicts: Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit fada55b92c6692a2eb0412006d4f9410d714240e Author: Ann Almgren Date: Thu Sep 28 19:02:00 2017 -0700 Add the ability to call makeKnapsack with a list of weights rather than the boxes themselves -- this is what we want to do within the KD Load Balancing algorithm Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Particle/AMReX_LoadBalanceKD.H commit 90b62388d6f139816e1afbada3323a825ab3b79a Author: vince Date: Thu Sep 28 18:11:05 2017 -0700 make html headers consistent with output. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit b42d19524c324687c6b846be554212ab45c95e4a Author: vince Date: Thu Sep 28 17:27:03 2017 -0700 some cleanup. Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit cfb5bd8e4519bb651833e5c448bb4c7d7bc755a1 Author: vince Date: Thu Sep 28 17:14:02 2017 -0700 fix compiler warnings. Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit ebeafa80315b361a7629117baaf5a9202925149f Merge: d5da75fad 4bc1cd000 Author: vince Date: Thu Sep 28 14:50:36 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d5da75fadcfd7dff874c4178430f3d7cdec14c4a Author: vince Date: Thu Sep 28 14:37:17 2017 -0700 fix compiler warnings. Src/Extern/amrdata/AMReX_AmrData.cpp commit edc20dd682da2eec9f4773e1d9db6bbbd6d77ee1 Author: vince Date: Thu Sep 28 14:24:04 2017 -0700 fix compiler warning. Src/Extern/ProfParser/AMReX_CommProfStats.H commit 4bc1cd0004a20ab66a6e210d9f120b32f2848988 Author: Weiqun Zhang Date: Thu Sep 28 13:45:27 2017 -0700 parameter to limit the number of boxes can be assigned to a single process in load balance Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 0bb7117f0d5eeb9a32fb56bdc1203e976e918ccc Author: vince Date: Thu Sep 28 14:14:30 2017 -0700 fix compiler warning. Src/Base/AMReX_BLProfiler.H commit 000350842fb103cb49260571a8f55a9ae8bcf374 Merge: 7a3277b19 6a0551057 Author: vince Date: Thu Sep 28 14:05:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7a3277b194766aede5782cd50c784f0dab50ffa5 Author: vince Date: Thu Sep 28 14:03:05 2017 -0700 added show body flag for eb. Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp commit 6a0551057e7b658da5384bd11e6ce7a33e64c643 Author: Andrew Myers Date: Thu Sep 28 13:09:28 2017 -0700 fix cmake install Src/AmrCore/CMakeLists.txt commit c2e41219618cdabf5d087a2091924e7016f44ce9 Author: Weiqun Zhang Date: Wed Sep 27 17:30:44 2017 -0700 added EBDataCollection Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBTower.H Src/EB/Make.package commit 104438a509d17c4bb0894a68ab571808b1c60cb2 Author: Andy Nonaka Date: Wed Sep 27 16:55:18 2017 -0700 add Dirichlet boundary conditions Tutorials/Basic/HeatEquation_EX2_C/AMReX_FILCC_2D.F Tutorials/Basic/HeatEquation_EX2_C/AMReX_FILCC_3D.F commit 44be6cfbf1855a07cb09211de27eab89abf32ec8 Author: Weiqun Zhang Date: Wed Sep 27 16:21:50 2017 -0700 cache EBCellFlags Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp commit 45c70be70d318fdf072f890fa37e9c9539d3feff Merge: 17029dee6 ac86317c5 Author: Michele Rosso Date: Wed Sep 27 15:31:49 2017 -0700 Merge branch 'development' into mr-cmake Conflicts: Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Particle/CMakeLists.txt commit 32af9438456346ea5309679594ce7f8ae5371086 Author: Weiqun Zhang Date: Wed Sep 27 15:25:24 2017 -0700 started EBTower Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/Make.package Tutorials/EB/CNS/Source/main.cpp commit 95bb13388d31417e97583a8b5cfaab0d5b70ca59 Author: Weiqun Zhang Date: Wed Sep 27 15:23:57 2017 -0700 access to some EB internal data Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBIndexSpace.H commit d462b5bf16706a2db4adfd80f6a1d6edd098110c Author: Weiqun Zhang Date: Wed Sep 27 15:23:02 2017 -0700 added a new BoxList constructor that takes rvalue Array Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit effe379bbd459f9c3c6631987add8782a83ba017 Author: Weiqun Zhang Date: Wed Sep 27 15:22:16 2017 -0700 added amrex::AllGatherBoxes Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit ac86317c5ff9057ce47f31b4cd68f5a87ee0fb1b Author: Weiqun Zhang Date: Wed Sep 27 10:31:45 2017 -0700 EB/CNS: update plotfile Tutorials/EB/CNS/Source/CNS_io.cpp commit 26c49a90c6e7cc37c7f9b762621ff810b3bd1012 Author: Weiqun Zhang Date: Wed Sep 27 10:12:58 2017 -0700 add CartGrid-V2.0 to plotfile types Src/F_BaseLib/fabio.f90 Src/F_BaseLib/plotfile.f90 commit b203331883deedb53fd93b83ff3c57cc7de44701 Merge: adf127359 d2d923298 Author: WeiqunZhang Date: Wed Sep 27 09:00:45 2017 -0700 Merge pull request #140 from bcfriesen/cvode_docs_fix Docs: add note to CVODE compilation about the examples linking dynamically commit d2d92329806df5bf4837eefa528785efac22c876 Author: Brian Friesen Date: Tue Sep 26 21:12:34 2017 -0700 Docs: add note to CVODE compilation about the examples linking dynamically Docs/AMReXUsersGuide/CVODE/CVODE.tex commit adf127359acc07aeafcd6d53371d46565df2fbf2 Author: Andrew Myers Date: Tue Sep 26 17:20:47 2017 -0700 don't profile this function - called too many times. Src/Particle/AMReX_ParticleContainerI.H commit 281435ab09c3f47232c1b68d4669be8ed9370ccf Author: Andrew Myers Date: Tue Sep 26 17:20:15 2017 -0700 fix some parameters shadowings. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit c066df38544070ae3349f7e881e32149841b3e35 Author: Weiqun Zhang Date: Tue Sep 26 16:39:08 2017 -0700 EB/CNS: use Amr's load balance approach Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Combustor/inputs.testing Tutorials/EB/CNS/Exec/Combustor/inputs_combustor Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.regt Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/main.cpp commit a3582a42b3ebb72d8317ddafa9d4f348b6d2eabf Author: Weiqun Zhang Date: Tue Sep 26 16:21:10 2017 -0700 update CHANGES CHANGES commit 3bdb7d118cbb22ed2bebd25fb42cccd4583b0032 Author: Weiqun Zhang Date: Tue Sep 26 16:14:41 2017 -0700 add amr.loadbalance_with_workestimates and amr.loadbalance_level0_int Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H commit 321e416282eb5bcccbee99a162f1056661750a84 Author: Ann Almgren Date: Tue Sep 26 15:33:23 2017 -0700 Tweaks to some of the text in the User Guide Docs/AMReXUsersGuide/EB/EB.tex commit ae90dbfd4d517d8300a6f81377c4c15eb516a85f Author: Andrew Myers Date: Tue Sep 26 13:12:45 2017 -0700 also turn it on for building the neighbor list. Src/Particle/AMReX_NeighborParticlesI.H commit a7cbcc8b194b1695bb660ac05efaa27e5874f5a0 Author: Weiqun Zhang Date: Tue Sep 26 12:20:50 2017 -0700 EB/CNS: update plotfile to CartGrid-V2.0 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS_io.cpp commit 7e4caedb99a85b24fb365427bdf622c1142188f2 Author: Andy Nonaka Date: Mon Sep 25 17:24:44 2017 -0700 implemented periodic, zero-flux, and Dirichlet options Tutorials/Basic/HeatEquation_EX2_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/inputs_2d Tutorials/Basic/HeatEquation_EX2_C/inputs_3d Tutorials/Basic/HeatEquation_EX2_C/main.cpp commit c483132e6c4d4fde05003d1c9d3080b260b5b619 Merge: c46db98b8 8128fa703 Author: dtgraves Date: Mon Sep 25 15:27:29 2017 -0700 merging with dtg_branch to get documentation changes over commit 8128fa7034c8ba7aca0ec780c48d047f7e701d0a Author: dtgraves Date: Mon Sep 25 15:25:46 2017 -0700 added more geometry examples Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/EB/EB_example.fig.bak Docs/AMReXUsersGuide/EB/eb_fluxes.fig.bak Docs/AMReXUsersGuide/EB/parabsphere.pdf Docs/AMReXUsersGuide/EB/parabsphere.ps.REMOVED.git-id Docs/AMReXUsersGuide/EB/revolution.pdf Docs/AMReXUsersGuide/EB/revolution.ps.REMOVED.git-id commit 9daf62c8ba9e3468906ce3974988c38ad69d16da Author: dtgraves Date: Mon Sep 25 15:09:07 2017 -0700 added polynomial geometry Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_PolynomialIF.cpp Src/GeometryShop/Make.package commit 40f405c2c1224524d3371900e11143fc9f3235bb Author: dtgraves Date: Mon Sep 25 15:08:48 2017 -0700 added a couple more geometry options Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit c46db98b874513a64399996a093c7615649c1a6f Merge: ef626dd22 6d919a782 Author: Andy Nonaka Date: Mon Sep 25 15:01:12 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ef626dd22195a672a7bb58a75bf3f4146d327b64 Author: Andy Nonaka Date: Mon Sep 25 15:00:02 2017 -0700 split the Basic/HeatEquation_EX1_C into EX1 and EX2. EX1 is periodic, EX2 will support Neumann and Dirichlet conditions eventually (WIP) Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/inputs_2d Tutorials/Basic/HeatEquation_EX1_C/inputs_3d Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc.H Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H Tutorials/Basic/HeatEquation_EX1_C/physbc.cpp Tutorials/Basic/HeatEquation_EX2_C/GNUmakefile Tutorials/Basic/HeatEquation_EX2_C/Make.package Tutorials/Basic/HeatEquation_EX2_C/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/inputs_2d Tutorials/Basic/HeatEquation_EX2_C/inputs_3d Tutorials/Basic/HeatEquation_EX2_C/main.cpp Tutorials/Basic/HeatEquation_EX2_C/myfunc.H Tutorials/Basic/HeatEquation_EX2_C/myfunc_F.H commit 6d919a7821c8117459d51dfb39f701a4adb0ed01 Merge: ab0f44f07 c0dd93eae Author: WeiqunZhang Date: Mon Sep 25 13:16:05 2017 -0700 Merge pull request #139 from zingale/development add stub versions of the new broadcasts commit c0dd93eae18f98677f6f444398a69cf69aba4c27 Author: Michael Zingale Date: Mon Sep 25 16:11:58 2017 -0400 add stub versions of the new broadcasts Src/F_BaseLib/parallel_stubs.f90 commit eb6e1823af64a065914de277dab6ec1e38d5151d Author: Andrew Myers Date: Mon Sep 25 13:05:42 2017 -0700 fix some dynamic scheduling bugs. Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit ab0f44f0745bc37adc7bdacc2184f15e37f27243 Author: Weiqun Zhang Date: Mon Sep 25 12:55:54 2017 -0700 VisMF::Exist(const std::string&) returns ture iff a MultiFab with such name exists Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit d530a2cabaaea7d70c4af6e86753e2955715638c Author: Weiqun Zhang Date: Mon Sep 25 09:16:48 2017 -0700 update EB regression test to include amr Tutorials/EB/CNS/Exec/Pulse/inputs.regt commit eeb265b083a80758bb0dd8608f822d7b8ba457da Merge: 3d469e562 4598e9253 Author: WeiqunZhang Date: Mon Sep 25 08:48:03 2017 -0700 Merge pull request #138 from AMReX-Codes/multid_bcast Add 2D, 3D, 4D parallel_bcast commit 3d469e56245aa61ad225dba009a7b0c73d678a2d Author: Max Katz Date: Mon Sep 25 01:37:52 2017 -0400 Add index options to fdump Tools/Postprocessing/F_Src/fdump.f90 commit 208e72e458a29e510eb9147154337f38830033b1 Author: Max Katz Date: Mon Sep 25 01:14:32 2017 -0400 Add minimum and maximum value options to fdump Tools/Postprocessing/F_Src/fdump.f90 commit 4598e9253b4d1f5e5558445a7ac0ffc0cfb79939 Author: Max Katz Date: Sun Sep 24 23:26:20 2017 -0400 Add 2D, 3D, 4D parallel_bcast Src/F_BaseLib/parallel.f90 commit f3843a48e3ab88eb2684c8d07d50ef263b37cd5e Author: Max Katz Date: Sun Sep 24 20:00:28 2017 -0400 Default last_smallplotfile to -1 This allows for a quick test to see if the user has requested any small plot files at all; the number will end up >= 0 if so, and stay negative if not. Src/Amr/AMReX_Amr.cpp commit cb9d9e95bacafa3f542f8413b3410d067268d444 Author: Max Katz Date: Sun Sep 24 07:48:41 2017 -0400 Add function to set level_count Src/Amr/AMReX_Amr.H commit fe85124be95b26dede0906fcf9e4209163343501 Author: Weiqun Zhang Date: Sat Sep 23 13:13:47 2017 -0700 EB/CNS: turn off various profiling Src/Base/AMReX_BoxArray.cpp Tutorials/EB/CNS/Exec/Combustor/GNUmakefile commit 57dfc3335aa0bb1b67371111d4cb870dbf976085 Author: Weiqun Zhang Date: Sat Sep 23 12:17:28 2017 -0700 fix 2d Src/EB/AMReX_EBFluxRegister_2d.F90 commit 1271f3b23049ffb7d74a9be23e2680a617289a50 Merge: 3b9a6cc0e 02a84a62a Author: Weiqun Zhang Date: Sat Sep 23 12:14:42 2017 -0700 Merge branch 'weiqun/eb' into development commit 02a84a62a3a62bff6d39a5e73dc3c499bbd4b121 Author: Weiqun Zhang Date: Sat Sep 23 12:14:22 2017 -0700 Merge branch 'development' into weiqun/eb Docs/AMReXUsersGuide/EB/EB.tex commit 14b635b5942fc69cb8e92658b7e80385e44a285c Author: Weiqun Zhang Date: Sat Sep 23 12:13:40 2017 -0700 refactor EBFluxRegister Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Exec/Pulse/inputs.debug commit 3b9a6cc0e2e8efaab28e601122893ae098412bfa Author: Marc Day Date: Fri Sep 22 20:15:14 2017 -0700 Work the EB section of the doc a bit Docs/AMReXUsersGuide/EB/EB.tex commit fb6273f4cc016210f1dd1b213c2f203b03ca812b Author: Weiqun Zhang Date: Fri Sep 22 17:30:47 2017 -0700 re-re-redistribution Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 commit 584a8361fcbef100ef6a84a2a6da22de0392c913 Author: Weiqun Zhang Date: Fri Sep 22 17:06:55 2017 -0700 WIP: Re-reflux Src/AmrCore/AMReX_YAFluxRegister.H Src/AmrCore/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS.cpp commit 331da41f6cd57c11818eeaf5f28c20de7a406410 Author: vince Date: Fri Sep 22 15:38:39 2017 -0700 fixed error messages. Src/Extern/amrdata/AMReX_DataServices.cpp commit 711a729c7f7eada8938a5704ebb07a4529508602 Merge: 7f8e6b8c2 0eb10b979 Author: dtgraves Date: Fri Sep 22 09:46:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7f8e6b8c2a8803c5d97ebfed52f298a27e2669dc Author: dtgraves Date: Fri Sep 22 09:45:49 2017 -0700 bug fixes in EB.tex Docs/AMReXUsersGuide/EB/EB.tex commit 0eb10b979666ae8934c44eb4a1d18fd44c603a8d Author: Weiqun Zhang Date: Fri Sep 22 09:41:29 2017 -0700 YAFluxRegister: update comment Src/AmrCore/AMReX_YAFluxRegister.cpp commit 4ba8e0d03aa6f3fc0c5fcf6b74e79820abffe083 Merge: 31bb27991 bda96126b Author: dtgraves Date: Fri Sep 22 09:27:43 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 31bb2799128c04370f0178311551e7c9a6d05563 Author: dtgraves Date: Fri Sep 22 09:26:07 2017 -0700 added surface of revolution section Docs/AMReXUsersGuide/EB/EB.tex commit bda96126bf2006527a63507fd46ef8b146edf12a Author: Weiqun Zhang Date: Fri Sep 22 09:21:19 2017 -0700 EB/CNS: add cns.do_reflux Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_io.cpp commit 51c928fcb35c77dc4ff1c1c08a518341b89cb58b Author: Weiqun Zhang Date: Fri Sep 22 09:11:43 2017 -0700 option to disable reredistribution for testing Src/EB/AMReX_EBFluxRegister_nd.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 commit 3bec2a3ed99624d4215dcf0b75f54d9a041db129 Author: Weiqun Zhang Date: Thu Sep 21 17:56:11 2017 -0700 inputs for John to hack Tutorials/EB/CNS/Exec/Pulse/inputs.debug commit 3e99b9ea51ebc6346e0b61e8cb46f8342a056085 Author: Weiqun Zhang Date: Thu Sep 21 17:47:46 2017 -0700 yet another flux register Src/AmrCore/AMReX_FillPatchUtil_1d.F90 Src/AmrCore/AMReX_YAFluxRegister.H Src/AmrCore/AMReX_YAFluxRegister.cpp Src/AmrCore/AMReX_YAFluxRegister_1d.F90 Src/AmrCore/AMReX_YAFluxRegister_2d.F90 Src/AmrCore/AMReX_YAFluxRegister_3d.F90 Src/AmrCore/AMReX_YAFluxRegister_F.H Src/AmrCore/AMReX_YAFluxRegister_nd.F90 Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Src/EB/AMReX_EBFluxRegister_nd.F90 commit 4f673b6f4021a4dd14e1e9a0ae66d9b4fc0443d4 Author: Weiqun Zhang Date: Thu Sep 21 13:12:33 2017 -0700 add re-redistribution threshold Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_nd.F90 Src/EB/Make.package Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit 08c2aafabf0fd003525b471d7bc549cb20fca78e Author: Weiqun Zhang Date: Thu Sep 21 10:05:11 2017 -0700 EBFluxRegister: fix periodic boundary Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp commit 75cd1b21ec40370d94f7d3ecf75c7620be8585e2 Author: Weiqun Zhang Date: Thu Sep 21 10:03:16 2017 -0700 add a free function converting iMultiFab to MultiFab Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit ac6f7631a75d912a54200fa569a175d975c0f533 Merge: 65f093b90 6b37c2125 Author: dtgraves Date: Thu Sep 21 16:29:29 2017 -0700 merging documentation changes over to dev so others can see them commit 6b37c21251ed03dd249e71d8a7ae0ee64c3a01dc Author: dtgraves Date: Thu Sep 21 16:27:34 2017 -0700 some missing files Docs/AMReXUsersGuide/EB/redist.eps Docs/AMReXUsersGuide/EB/redist.fig Docs/AMReXUsersGuide/EB/redist.pdf commit 096535a23d09c417d328c133093646887bee9b66 Author: dtgraves Date: Thu Sep 21 16:27:12 2017 -0700 started on documentation revisions of EB stuff per John and Marc's recommendations Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/EB/EB_example.eps Docs/AMReXUsersGuide/EB/EB_example.fig Docs/AMReXUsersGuide/EB/EB_example.pdf Docs/AMReXUsersGuide/EB/areas_and_volumes.eps Docs/AMReXUsersGuide/EB/areas_and_volumes.fig Docs/AMReXUsersGuide/EB/areas_and_volumes.pdf Docs/AMReXUsersGuide/EB/eb_fluxes.eps Docs/AMReXUsersGuide/EB/eb_fluxes.fig Docs/AMReXUsersGuide/EB/eb_fluxes.pdf commit 65f093b9061c50ccef0dd06da6ae5067d2bfd3e0 Author: Ann Almgren Date: Thu Sep 21 14:26:12 2017 -0700 Fix the flags getting passed to HPGMG Tools/GNUMake/packages/Make.hpgmg commit 1c0abd4a9d6ecf3ae4e5ee8c88b831c126ed9e2e Author: Andrew Myers Date: Thu Sep 21 14:19:44 2017 -0700 First stab at making the particle iterator able to use dynamic scheduling with OpenMP. Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp commit 2f3c976249f6291d57199f67a71133d0881ed220 Author: Ann Almgren Date: Thu Sep 21 11:57:34 2017 -0700 John's which --> that corrections. Docs/AMReXUsersGuide/CVODE/CVODE.tex commit b51a66addedc244f996ed8f8d8453e6b115e4848 Merge: 3e49497ed 65e58ca25 Author: WeiqunZhang Date: Thu Sep 21 09:03:32 2017 -0700 Merge pull request #137 from bcfriesen/update_cvode_docs Docs: update CVODE docs commit e08851e43c184ba50012010bebe60cab85827212 Author: Max Katz Date: Thu Sep 21 03:57:02 2017 -0400 Move BaseFab kernels to FORT_LAUNCH Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit c7273b65ba3dc759a58a5bd0ebe4fd35b2c4f8b2 Author: Max Katz Date: Thu Sep 21 03:56:46 2017 -0400 Do not pass MFIter to FORT_LAUNCH Src/Base/AMReX_BLFort.H Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit 6d3762f6b9d8d5dafdef5b04c90bd1da480fc042 Author: Max Katz Date: Thu Sep 21 03:56:19 2017 -0400 Add static current CUDA stream Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit e9b44e2a98140e72bd98bf7461fdb16398456c2d Author: Max Katz Date: Thu Sep 21 03:08:10 2017 -0400 Fix non-GPU compilation of heat equation Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit bb860b5ab5dbcf0d67349791855d8dcc34a41af6 Author: Max Katz Date: Thu Sep 21 03:04:18 2017 -0400 Use subroutine defines in heat equation example Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 commit 8607140cf87bf220f1bdf632cd6dcee4d8fe2d4a Author: Max Katz Date: Thu Sep 21 03:04:01 2017 -0400 Rename CUDA defines to all caps Tools/GNUMake/Make.defs commit d58ec09f4bd49de2b9a43cf8fa67f9910d107c25 Author: Max Katz Date: Thu Sep 21 02:58:01 2017 -0400 Launch heat equation kernels from C++ Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit 7f8997df8c2d5bae79bd4ac090411ede77d498e9 Author: Max Katz Date: Thu Sep 21 02:52:07 2017 -0400 Add FORT_LAUNCH and FORT_LAUNCHABLE macros for CUDA kernels Src/Base/AMReX_BLFort.H commit c1b4ee9e99ec7c50c8db7b987446e5ec1e936c9e Author: Max Katz Date: Thu Sep 21 02:51:37 2017 -0400 Add helper routines for launching kernels from C++ Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 65e58ca25af4f4f5aaff1585ee7db5bbc7b22f69 Author: Brian Friesen Date: Wed Sep 20 22:30:18 2017 -0700 Docs: add a new section describing the CVODE Tutorials Docs/AMReXUsersGuide/CVODE/CVODE.tex commit 2e8cbf25c1e73b776c1b1e79cda10c45b06690af Author: Brian Friesen Date: Wed Sep 20 22:29:47 2017 -0700 Docs: revise the wording of the CVODE Fortran 2003 interface description Docs/AMReXUsersGuide/CVODE/CVODE.tex commit 569acbbde053531f304d2fb096f1ffc240ec7ef3 Author: Brian Friesen Date: Wed Sep 20 22:28:54 2017 -0700 Docs: add note discouraging FCVODE in favor of the Fortran 2003 interface Docs/AMReXUsersGuide/CVODE/CVODE.tex commit 454bf7a1be9fee46f5ba564251e348d9985db7d2 Author: Max Katz Date: Thu Sep 21 01:01:37 2017 -0400 Handle the bl_error difference between the C++ and F90 build systems Src/Base/AMReX_CUDA.F90 commit ef077c76ac761c73e4d97074dcefbdc773827e56 Merge: 0c5f20049 3e49497ed Author: Max Katz Date: Thu Sep 21 00:51:52 2017 -0400 Merge branch 'development' into gpu commit 3e49497ed702495ef141ea0de11928de24c94952 Merge: 9e78f21e0 762fd0f5d Author: Andrew Myers Date: Wed Sep 20 14:59:33 2017 -0700 Merge branch 'development' into threaded_neighbor_particles commit 762fd0f5d3fcfb490798f3efa18893d02de20b91 Author: Andy Nonaka Date: Wed Sep 20 14:26:44 2017 -0700 fix errors in comments Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 2bc3b4ddf1aea4c54fb9fdc36d812165a73ad118 Author: Andy Nonaka Date: Wed Sep 20 14:18:51 2017 -0700 Revert "fix comments regarding regridding functions" This reverts commit 3dfec1d7158bc40188427d88c8bc2a900291907f. Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 3dfec1d7158bc40188427d88c8bc2a900291907f Author: Andy Nonaka Date: Wed Sep 20 14:11:38 2017 -0700 fix comments regarding regridding functions Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit b9e92afa0c4fafa4694a9448037657809dc80209 Author: Weiqun Zhang Date: Wed Sep 20 13:13:19 2017 -0700 check signal_handling for F_BaseLib too CHANGES Src/F_BaseLib/backtrace_c.cpp commit 9e78f21e0f5e27ddd1736a4e85e6e5b4c1b125df Author: Andrew Myers Date: Wed Sep 20 13:12:50 2017 -0700 avoid rellocating this vector repeatedly in parallel region. Src/Particle/AMReX_NeighborParticlesI.H commit d4ea49ddd688d107292bcbc58ed831f6b95922e3 Author: Weiqun Zhang Date: Wed Sep 20 13:05:15 2017 -0700 runtime parameter amrex.signal_handling for disabling signal handling Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.cpp commit 864fe23295896a08ea8b8c2adbb28ba8b7987b3b Author: Andrew Myers Date: Wed Sep 20 12:25:01 2017 -0700 just use regular parallel for regions here. Src/Particle/AMReX_NeighborParticlesI.H commit 974ccdb4f263e81c2a7e0646b49893ca72e30c66 Merge: 1020dc1cf 99ea7a69b Author: dtgraves Date: Wed Sep 20 12:03:12 2017 -0700 Merge pull request #136 from AMReX-Codes/dtg_branch with these fixes, I was able to run Pele with threads commit 99ea7a69b380339475ec21bca06583e013bf0a33 Author: dtgraves Date: Wed Sep 20 11:59:40 2017 -0700 took out some debugging statements Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit ca44e491657f840b8811905c3e1ecede1f9911ba Author: dtgraves Date: Wed Sep 20 11:57:19 2017 -0700 I added some return values to AMReX_RegionsProfStats.cpp for cases where it is being called incorrectly just to shut up the compiler. I also fixed EBGraph::fillIntMask to make it thread safe Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit 9e340d0e526b72e1f5dd95ce3a3bcff38efac31e Author: Andrew Myers Date: Wed Sep 20 11:08:01 2017 -0700 the local temporaries need entries for the neighboring tiles, too. Src/Particle/AMReX_NeighborParticlesI.H commit 84810a96158ab75738e019a9ef25d35018147eae Author: Andrew Myers Date: Wed Sep 20 10:45:49 2017 -0700 correctly build map for remote particles in serial to allow for multithreaded processing. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 1020dc1cf209f3dd0ffadab13358d638abe43b71 Merge: 8bb972a61 d9c5cfe39 Author: dtgraves Date: Wed Sep 20 09:14:48 2017 -0700 Merge pull request #134 from AMReX-Codes/dtg_branch missed one commit d9c5cfe39248d13b745befbe004d095a46ff34d4 Author: dtgraves Date: Wed Sep 20 09:13:31 2017 -0700 translation amount in ebinit was wrong if maxlev > 0 Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 8bb972a612d72fbb9be5060d5d31a77b0ab3c8d0 Merge: 8644824c8 10c0e13f1 Author: dtgraves Date: Wed Sep 20 09:07:15 2017 -0700 Merge pull request #133 from AMReX-Codes/dtg_branch minor bug fix commit 10c0e13f191f9e90781b7c5ca9796b9cf1d0ae4c Author: dtgraves Date: Wed Sep 20 09:05:44 2017 -0700 volume fraction variable has to be named vfrac in order for visit to work Tutorials/EB/CNS/Source/CNS_io.cpp commit 8644824c847d497a10ca1557597974fc3cccd116 Author: Ann Almgren Date: Tue Sep 19 16:38:51 2017 -0700 We now pass in "cell_weight" as the initialization for the weight of each cell. To this we will add the number of particles in that cell. Src/Particle/AMReX_LoadBalanceKD.H commit c69e7fea037aaacf6e1a09df66400861dd57b815 Author: Ann Almgren Date: Tue Sep 19 16:38:28 2017 -0700 Remove write statement "actually rebuilding" Src/Particle/AMReX_NeighborParticlesI.H commit a551b8584b0027cfa53419fae4cfad1beb1525b1 Author: Andrew Myers Date: Tue Sep 19 16:22:31 2017 -0700 remove some more debugging crap Src/Particle/AMReX_NeighborParticlesI.H commit c3d64fff7ac5e0a1687b82df990cbbc2ea42b923 Author: Andrew Myers Date: Tue Sep 19 16:21:57 2017 -0700 handle update neighbors too. Src/Particle/AMReX_NeighborParticlesI.H commit 7796d91cf3d73d7d5b005205e2500245cf1b697c Author: Andrew Myers Date: Tue Sep 19 16:13:41 2017 -0700 handle threading for the local neighbor particles in fillNeighbors. Src/Particle/AMReX_NeighborParticlesI.H commit a148a7405d92df57e726ad8d24dc89ddffbb8283 Author: Weiqun Zhang Date: Tue Sep 19 15:48:17 2017 -0700 EB/CNS: inputs parameters for fine level grids placement Src/Base/AMReX_RealBox.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit b0e9d196f892a3be38c8e6f46447788702bb20d7 Merge: ee69438fb 55606925d Author: WeiqunZhang Date: Tue Sep 19 15:41:50 2017 -0700 Merge pull request #132 from cmsquared/osx_fix add missing library to link line for gfortran in osx commit 55606925de8a4f2b93723ed1a63c09563d481fd3 Author: Chris Malone Date: Tue Sep 19 16:27:11 2017 -0600 add missing library to link line for gfortran in osx Tools/F_mk/comps/gfortran.mak commit 3fb94bd4c78dac745d7ad3f62fdc622cc66632df Author: Andrew Myers Date: Tue Sep 19 15:21:38 2017 -0700 handle threading for the remote neighbor particles. Src/Particle/AMReX_NeighborParticlesI.H commit ee69438fbdd16f654a18dc86de00adb597eaad94 Author: Weiqun Zhang Date: Tue Sep 19 14:54:41 2017 -0700 #if 0 some debug code Tutorials/EB/CNS/Source/CNS.cpp commit e4ee971c763c8cd711966a4234884383e7efee51 Author: Weiqun Zhang Date: Tue Sep 19 14:52:09 2017 -0700 EB/CNS: minor tweak Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 1c405bb2f1cc55b9e5a09efe506e4166672d0dea Author: dtgraves Date: Tue Sep 19 13:24:58 2017 -0700 added some timers Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp commit 5a5d94573a876ddfef700ac27df51ad3a0acab6d Author: Andrew Myers Date: Tue Sep 19 12:41:36 2017 -0700 remove some debugging junk. Src/Particle/AMReX_NeighborParticlesI.H commit d3416799245751667d0dec419ff1d94f4329c8af Author: Andrew Myers Date: Tue Sep 19 12:40:32 2017 -0700 refactor the neighbor particle code to make it easier to thread. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 63e513836cc4c9435b01c2802b9002db465e9b58 Merge: e04d0d974 b5f6e9b4f Author: dtgraves Date: Tue Sep 19 10:32:26 2017 -0700 Merge pull request #131 from AMReX-Codes/dtg_branch merging with development to get EBCellFlagFab caching in place commit b5f6e9b4ffca7ccf5df4a716c221704c81d8a5ea Author: dtgraves Date: Tue Sep 19 10:31:07 2017 -0700 took out some debugging statements Src/EB/AMReX_EBLevel.cpp commit 882e3fb4d8e0d84d218532a87de53b85b3ad52f8 Author: dtgraves Date: Tue Sep 19 10:26:20 2017 -0700 added cache of EBCellFlagFab inside EBGraph. For the CNS benchmark problem, this appears to speed things up quite a lot. Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBLevel.cpp Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp commit e04d0d974c9af64535933c657b6689e563d7e842 Author: Weiqun Zhang Date: Tue Sep 19 10:16:51 2017 -0700 add CHANGES CHANGES commit f3e29086fc21483a5aad7f9f18448b50362c11b4 Merge: 3910d99c3 84e8516eb Author: Weiqun Zhang Date: Tue Sep 19 10:08:59 2017 -0700 Merge branch 'development' into weiqun/eb Conflicts: Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit 3910d99c39e7dabdca5e627bc5ad4bbc7884276b Author: Weiqun Zhang Date: Tue Sep 19 10:07:33 2017 -0700 EBFluxRegister: finish 2D Src/EB/AMReX_EBFluxRegister_2d.F90 commit 77980206952d232b2d10dde97ff6d07807ef0d49 Author: Weiqun Zhang Date: Tue Sep 19 09:44:56 2017 -0700 add some comments to EBFluxRegister Src/EB/AMReX_EBFluxRegister.H commit 84e8516ebe32fe2826824c8984e29a3fb8d4f409 Author: Max Katz Date: Tue Sep 19 04:29:17 2017 -0400 Allow small plotfile to have derived variables Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp commit dab85aaf63d26e3c8de7b524c7d6c2a0eeb0baba Author: Tan Nguyen Date: Mon Sep 18 17:41:44 2017 -0700 remove an app Src/AmrTask/tutorials/AMReXApps/3DJacobi/3DJacobi.C Src/AmrTask/tutorials/AMReXApps/3DJacobi/Makefile commit b54d07134a97045a3abbabb59b5e36965651f3c4 Author: Tan Nguyen Date: Mon Sep 18 17:37:57 2017 -0700 add heat solver Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/graph/AMReX_WorkerThread.H Src/AmrTask/graph/AMReX_WorkerThread.cpp Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/tutorials/MiniApps/HeatEquation/.DS_Store Src/AmrTask/tutorials/MiniApps/HeatEquation/GNUmakefile Src/AmrTask/tutorials/MiniApps/HeatEquation/Make.package Src/AmrTask/tutorials/MiniApps/HeatEquation/advance.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/advance_2d.f90 Src/AmrTask/tutorials/MiniApps/HeatEquation/advance_3d.f90 Src/AmrTask/tutorials/MiniApps/HeatEquation/init_phi_2d.f90 Src/AmrTask/tutorials/MiniApps/HeatEquation/init_phi_3d.f90 Src/AmrTask/tutorials/MiniApps/HeatEquation/inputs_2d Src/AmrTask/tutorials/MiniApps/HeatEquation/inputs_3d Src/AmrTask/tutorials/MiniApps/HeatEquation/main.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/myfunc.H Src/AmrTask/tutorials/MiniApps/HeatEquation/myfunc_F.H Src/AmrTask/tutorials/MiniApps/HeatEquation/physbc.cpp commit 9c6347ad1dcb7d704b2c34f9b03bb632d33b0c21 Author: Tan Nguyen Date: Mon Sep 18 16:50:46 2017 -0700 relocate files Src/AmrTask/graph/AMReX_AsyncMFIter.H Src/AmrTask/graph/AMReX_AsyncMFIter.cpp commit 30a4434bd9fdfbee6410d1a333020ac4f28d6930 Author: Tan Nguyen Date: Mon Sep 18 16:47:26 2017 -0700 async MFIter interface Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.cpp Src/AmrTask/AMFIter/Makefile Src/AmrTask/Makefile Src/AmrTask/arch/arch.mpi.generic Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C commit bb8670270a0fd99dab7342061f78e51de213e008 Merge: 32466a1de 00a90a9aa Author: Andy Nonaka Date: Mon Sep 18 16:36:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 32466a1ded09f391583e8293a97d4f07b0b81c95 Author: Andy Nonaka Date: Mon Sep 18 16:36:01 2017 -0700 fix comment Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 0bbeb22c6272930defb5718df6527363c148138f Author: Weiqun Zhang Date: Mon Sep 18 16:01:42 2017 -0700 fix octree tutorial Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 commit 00a90a9aa0933008ba320b1d9a856b3756770b49 Author: Weiqun Zhang Date: Mon Sep 18 16:01:42 2017 -0700 fix octree tutorial Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 commit 9ef77637302f285b91e26b1a5767e76e9b8a1603 Author: Brian Friesen Date: Mon Sep 18 15:57:46 2017 -0700 CVODE: "CVODE" -> "\cvode" Docs/AMReXUsersGuide/CVODE/CVODE.tex commit f2d70e7001ffea40c0aeec61f3428764c1da8678 Author: Brian Friesen Date: Mon Sep 18 15:27:32 2017 -0700 CVODE: Move FCVODE doc cite from inline to a footnote Docs/AMReXUsersGuide/CVODE/CVODE.tex commit a3ab937e6c2bcc2869a889b00c492ac0ec51c99a Author: Weiqun Zhang Date: Mon Sep 18 13:26:09 2017 -0700 fix more gcc shadow warnings Src/Amr/AMReX_Amr.cpp Src/EB/AMReX_EBFArrayBox.cpp Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_Stencils.cpp Src/GeometryShop/AMReX_TransformIF.cpp Tutorials/EB/CNS/Source/CNS_io.cpp commit 623b7194670d7219a243eaf30148dffe9c9a9e40 Author: Weiqun Zhang Date: Mon Sep 18 13:03:15 2017 -0700 fixed some gcc -Wshadow warnings Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_Mask.cpp Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp commit c219b596a0cc6763a9b9f31d65f206021574be38 Author: Weiqun Zhang Date: Mon Sep 18 12:40:22 2017 -0700 for gcc >= 6, add -Wnull-dereference in DEBUG mode Tools/GNUMake/comps/gnu.mak commit ed8c1bec1ab2a06b515a564dff92a76e90efe139 Author: dtgraves Date: Mon Sep 18 11:46:50 2017 -0700 added volume mask to GeometryShop--on to testing it. Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H commit 60a644c79f5b90bc07852e90ed6b77421653cde5 Merge: d05a04fb1 a0f804794 Author: Andrew Myers Date: Mon Sep 18 11:02:05 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d05a04fb168d71846add91cf5effa863e6cd8f17 Author: Andrew Myers Date: Mon Sep 18 11:01:46 2017 -0700 Give the NeighborParticleContainer a regrid method and update the necessary internal data structures. Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit a0f80479472bfe2441bc003e2035f160c67f21bd Author: Weiqun Zhang Date: Mon Sep 18 09:16:20 2017 -0700 add -Wshadow to gcc flags in DEBUG Tools/GNUMake/comps/gnu.mak commit c206280f9c3b7f207b2ffe43f4a6a1be10ef9378 Author: Weiqun Zhang Date: Mon Sep 18 09:01:40 2017 -0700 tidy Src/EB/AMReX_EBFluxRegister.cpp commit d6824375683f7b000ca62135e46f7a2d1c9bab6d Author: Weiqun Zhang Date: Sat Sep 16 21:36:59 2017 -0700 EBFluxRegister: omp atomic Src/EB/AMReX_EBFluxRegister_3d.F90 commit 9b43b9507993d6f95a677f4ee0778fe5aace2195 Author: Weiqun Zhang Date: Sat Sep 16 21:18:46 2017 -0700 EB/CNS: fix re-redistribution scaling and cleanup Src/EB/AMReX_EBFluxRegister.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit c878f7f7b1b3d04ea31454d9b6ab01472fa2fca2 Author: Weiqun Zhang Date: Sat Sep 16 14:51:41 2017 -0700 EB/CNS: minor change for clarity Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit b1ddb21395616573a325a6d1f4d22c8f2693d683 Merge: d9a675afb 06734196f Author: dtgraves Date: Sat Sep 16 13:53:43 2017 -0700 moving minor optimiizations over to development commit 06734196fec15c96c41252ab7dc81c206ea77827 Author: dtgraves Date: Sat Sep 16 13:41:24 2017 -0700 Some clean up and optimization of EBLevel::defineDoIt. It did not speed stuff up as much as I had hoped (amounted to 20 seconds off a 500 second run). Src/EB/AMReX_EBLevel.H Src/EB/AMReX_EBLevel.cpp commit caa8ecbceda956440e6516d7dff3ce6c7f1e116f Author: Weiqun Zhang Date: Sat Sep 16 12:51:31 2017 -0700 EB/CNS: rename some variables Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit d9a675afbd29d07dc77c170a73ca50e6e4557c1c Author: Max Katz Date: Fri Jul 7 01:28:08 2017 -0700 Fix Intel Fortran compiler preprocessing of AMReX_REAL.H Src/Base/AMReX_REAL.H commit 274f409965b514ab94eddfbe02e5b2f43b044986 Author: Weiqun Zhang Date: Fri Sep 15 17:19:02 2017 -0700 EB Re-redistribution: fix scaling Src/EB/AMReX_EBFluxRegister_3d.F90 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 67f2f797fc9c58ceb6772358c4dff1ed0c4d1e06 Author: Ann Almgren Date: Fri Sep 15 18:02:10 2017 -0700 Fix oops in last commit Tools/Postprocessing/F_Src/GNUmakefile commit 3563e1a9a3a5be8a9b586561f66005914a62f1df Author: Ann Almgren Date: Fri Sep 15 17:41:14 2017 -0700 Update plt_compare_diff_grids so that it measures the relative error the same as fcompare does -- instead of dividing error by value pointwise it sums the error and sums the values and divides the sums. Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit 1437e3b1952bb55ed01f4bec5e14cc338db12cb8 Merge: cf0633d1c b55839956 Author: Ann Almgren Date: Fri Sep 15 17:20:00 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit cf0633d1cedbaa5c5e36ad842a217feb21a04a68 Author: Ann Almgren Date: Fri Sep 15 17:19:47 2017 -0700 File should be fcompare not fcompareFinest Tools/Postprocessing/F_Src/GNUmakefile commit e0e68e7c329e3e34f05bf575603e818bf3ba59b0 Author: Weiqun Zhang Date: Fri Sep 15 16:05:11 2017 -0700 EB/CNS: pass level to fortran just in case Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit b558399561e067acece29b938ab90dd86e98f822 Author: John Bell Date: Fri Sep 15 15:23:37 2017 -0700 added new options for eb redsitribution weighting Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 commit 22101c638f74a8fede638c050212786110c57491 Author: Weiqun Zhang Date: Fri Sep 15 14:44:59 2017 -0700 EB/CNS: add level mask Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 commit f5875b18d1112a1d4a9ca52f7cdd0cc78bcae9ac Author: Weiqun Zhang Date: Fri Sep 15 13:10:44 2017 -0700 EB/CNS: fix bug Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit 2499be719cbb358a9a9552a830bfc856ff24d137 Author: Weiqun Zhang Date: Fri Sep 15 13:10:44 2017 -0700 EB/CNS: fix bug Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit 073d8862d949d325ef812c10f917470ddc5047f2 Author: dtgraves Date: Fri Sep 15 13:02:31 2017 -0700 turned on all the profiling flags I could find and I added some refinements on the benchmark inputs Tutorials/EB/CNS/Exec/Combustor/GNUmakefile Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs commit 810e7bc00c2d50a0bbc9fe8958f4ff70d9e6d663 Merge: 766b12430 06499fa81 Author: jbb Date: Fri Sep 15 12:47:48 2017 -0700 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit 766b12430700e7112dc618679719b155fe301156 Author: jbb Date: Fri Sep 15 12:45:33 2017 -0700 added combustor inputs Tutorials/EB/CNS/Exec/Combustor/inputs_combustor commit ee46d14734f227b5813c3e3c97a09b9912371a7b Author: jbb Date: Fri Sep 15 12:44:52 2017 -0700 added other swirling combustor Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90_jbb Tutorials/EB/CNS/Exec/Combustor/cns_prob.F90_jbb commit 06499fa816b19df882eec249fc5597cdd5897f19 Merge: 52175793e 457d51713 Author: vince Date: Fri Sep 15 11:57:34 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 52175793ea5ee17009185fbed11e032722658558 Author: vince Date: Fri Sep 15 11:57:19 2017 -0700 return from ReadData if filetype is PROFDATA. Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/amrdata/AMReX_AmrData.cpp commit 457d517137f3115ca4d924a72f1f30441830221c Merge: 80c802c7f 30cbcb646 Author: dtgraves Date: Fri Sep 15 11:31:08 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 80c802c7ffddcaf148581e138cd99c817cf334a1 Author: dtgraves Date: Fri Sep 15 11:30:43 2017 -0700 found some more macro usages that needed to be removed for intel Src/EBAMRTools/AMReX_EBFortND.F90 commit 14677fe7361c55218acc585322c62a44f8b1f003 Author: Weiqun Zhang Date: Fri Sep 15 11:18:16 2017 -0700 WIP: Re-Redistribution Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 30cbcb646221279d6676c848a99c94da9764bff8 Merge: bcdad3a71 094da2513 Author: Andrew Myers Date: Fri Sep 15 11:16:36 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bcdad3a71467f15f68c61d8481ac1b852355dd8a Author: Andrew Myers Date: Fri Sep 15 11:10:58 2017 -0700 miscellaneous bug fixes for the new neighbor filling stuff. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 094da2513c51e2f837245f417424202be8e602bb Merge: c81ddf8e0 b36435f9d Author: dtgraves Date: Fri Sep 15 11:05:37 2017 -0700 getting fortran fix for intel compilers over commit b36435f9d138df1f713991452e48662620027fac Author: dtgraves Date: Fri Sep 15 11:02:38 2017 -0700 took out CONSTANTS.H macro usage because it was breaking on intel compilers Src/EBAMRTools/AMReX_EBFortND.F90 commit c81ddf8e0b70b9b63bd560dc3a28cce62275b59f Merge: dc6fe6be1 9bf676407 Author: WeiqunZhang Date: Fri Sep 15 09:11:44 2017 -0700 Merge pull request #129 from bcfriesen/fcompare_openmp Postprocessing: add OpenMP to fcompare tool commit 9bf676407ae31b7aba51043724fb9e6b1953c34a Author: Brian Friesen Date: Thu Sep 14 20:53:41 2017 -0700 Postprocessing: add COLLAPSE(2) to OpenMP PARALLEL DO in fcompare This will likely result in better load balance across threads where there are lots of threads. E.g., on Xeon Phi on Cori, 2 threads per core means 136 threads total, which is comparable to the trip count of the outermost loop. Tools/Postprocessing/F_Src/fcompare.f90 commit 03c603ec13c970c94a5a4038786f732a3e83923d Author: Brian Friesen Date: Thu Sep 14 17:54:32 2017 -0700 Postprocessing: add OpenMP to fcompare tool Tools/Postprocessing/F_Src/fcompare.f90 commit dc6fe6be1c4f1cb50650026c97177b7df75852c3 Merge: a14f96da2 be8dfc87a Author: Andrew Myers Date: Thu Sep 14 18:20:02 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a14f96da2aa63a450a6fef5a7288df7e81af4f4b Author: Andrew Myers Date: Thu Sep 14 17:13:46 2017 -0700 Fix bug in fillNeighbors when KDTree is used. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 6e7ae15062fb9a0ca9d97b4246cec56a153e67f0 Author: dtgraves Date: Thu Sep 14 16:55:10 2017 -0700 turned profiling on and added a benchmark inputs file Tutorials/EB/CNS/Exec/Combustor/GNUmakefile Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs commit 917c000cd94b6da565f8ee42a8766446dc2ee264 Author: Weiqun Zhang Date: Thu Sep 14 14:45:05 2017 -0700 EBFluxRegister 2D Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 commit be8dfc87a1e49b99d179ace7e54dc42234a3cd04 Merge: c84ec9f48 b41647d4d Author: dtgraves Date: Thu Sep 14 14:41:27 2017 -0700 merging so people can see EB section of the User's guide commit b41647d4dbd75ef13fd8d70b675fe86b815c96a0 Author: dtgraves Date: Thu Sep 14 14:40:04 2017 -0700 added EBFArrayBox fortran example section to user's guide Docs/AMReXUsersGuide/EB/EB.tex commit 7ccb52dcd29d284e144eabecaa60198cbf5985cc Author: Weiqun Zhang Date: Thu Sep 14 14:20:05 2017 -0700 EB Reflux works in 3D Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 0e9f79093852a4093fdf0a44d23e98faa5bdc8a3 Author: dtgraves Date: Thu Sep 14 14:16:06 2017 -0700 added EBFArrayBox section to user's guide Docs/AMReXUsersGuide/EB/EB.tex commit c84ec9f48f171c4f7502820c9cfeea80172e53ba Merge: 05807f4d3 85a5ea98b Author: Weiqun Zhang Date: Wed Sep 13 17:22:56 2017 -0700 Merge branch 'development' into weiqun/eb Conflicts: Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit 85a5ea98bc7febb09927253425d99f0385d06969 Author: Weiqun Zhang Date: Wed Sep 13 17:03:12 2017 -0700 EB regression tests inputs Tools/RegressionTesting/AMReX-tests.ini Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/inputs.regt commit 81381380355dd1553eeb3ae63f9d085c995456ac Author: Weiqun Zhang Date: Wed Sep 13 16:34:06 2017 -0700 EB/CNS: for regression test, zero out Cost_Type Tutorials/EB/CNS/Source/CNS_io.cpp commit ef39b7fbe33c67e9138e67bee6a125f96a3821b2 Author: Weiqun Zhang Date: Wed Sep 13 16:12:12 2017 -0700 BaseIFFABI: whenever copying from memory, avoid copying nan Src/GeometryShop/AMReX_BaseIFFABI.H commit 7a0303245be8e4659efbdf2f67fd57dd37be1e0c Author: Weiqun Zhang Date: Wed Sep 13 15:42:08 2017 -0700 EBData: use qnan instead of snan because gcc 4.8.4 crahes on calling std::isnan with snan Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp commit 86504d0682651a5ffa70942f7654d82ece5a65a4 Author: Weiqun Zhang Date: Wed Sep 13 15:19:55 2017 -0700 always initialize EBData to snan. we can then use std::isnan to detect whether a face has good data Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Tests/GeometryShop/ramp/main.cpp commit 65d5babaa21d870912d5de7bdf63609bd6d15324 Merge: 0f36e3dbb 8f4af5eb1 Author: vince Date: Wed Sep 13 14:56:06 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0f36e3dbb1e525624bcbc28dffc074417289cc1a Author: vince Date: Wed Sep 13 14:56:02 2017 -0700 added dirname to inputs, updated readme. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/README Tests/IOBenchmark/inputs.dirname Tests/IOBenchmark/inputs.small commit 8f4af5eb11302f850f786f66101d5d826b140b26 Merge: 5e86daf00 06802b31d Author: dtgraves Date: Wed Sep 13 14:52:37 2017 -0700 Merge branch 'development' into dtg_branch Conflicts: Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit 06802b31d63e5d1e69aace154f17b4d73317e824 Author: Weiqun Zhang Date: Wed Sep 13 14:44:20 2017 -0700 mod ramp test for debugging Tests/GeometryShop/ramp/GNUmakefile Tests/GeometryShop/ramp/main.cpp commit 5e86daf004fd83fe0d8b21984ff15bea1ed0cdde Author: dtgraves Date: Wed Sep 13 14:40:04 2017 -0700 took out debugging statements and fixed Weiqun's test so that it has some chance of passing Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/EBAMRTools/regression/runalltests.serial.sh Tests/GeometryShop/regression/ebio.cpp commit fa46476619667a919742e6f33f8ce3b382c83a1f Author: Weiqun Zhang Date: Wed Sep 13 14:26:23 2017 -0700 BaseIFFAB copy in FabArray copy is not thread safe Src/GeometryShop/AMReX_BaseIFFAB.H commit 60fde578759f0f6ce7e6b671dd5260b2bbd87195 Author: Weiqun Zhang Date: Wed Sep 13 14:24:25 2017 -0700 comment out some debug codes Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit c294ad02da3ebd50fe107e5ed2658c44422c18a2 Author: Weiqun Zhang Date: Wed Sep 13 13:58:38 2017 -0700 add an assertion Src/GeometryShop/AMReX_BaseIFFAB.H commit a6faad7fa81c9c18ad08e15c13e8c27314c56368 Author: Weiqun Zhang Date: Wed Sep 13 13:55:24 2017 -0700 The FabArray constructor that takes array of pointers must define factory data member too Src/Base/AMReX_FabArray.H commit a001a2f78ac2ae9dd9429c402403ee644dc530d5 Merge: a11c2f83c 1dfa291b5 Author: dtgraves Date: Wed Sep 13 13:09:42 2017 -0700 Merge pull request #127 from AMReX-Codes/dtg_branch Ann wanted this merged over mostly because of EB user's guide commit 1dfa291b560cb0d241b2af547f9741d865dd3108 Author: dtgraves Date: Wed Sep 13 13:07:12 2017 -0700 fixed more regression tests that were broken by recent interface changes Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/divergenceOpTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/gradientOpTest.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp Tests/EBAMRTools/regression/runalltests.mpi.sh Tests/EBAMRTools/regression/simpleMeshRefine.cpp commit f9990e8c1e8d11a9aa97ec848ea1c986aad8ebb5 Author: dtgraves Date: Wed Sep 13 12:44:24 2017 -0700 fixed regression tests that were broken by recent interface changes Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/ebgraphDistributed/GNUmakefile Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/flatPlate/GNUmakefile Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/ramp/main.cpp Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/runalltests.mpi.sh Tests/GeometryShop/runalltests.serial.sh Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp commit 3a27131e93c070bbf9eb2e2d4731b222c5aad81f Merge: 67042afc3 61564822f Author: dtgraves Date: Wed Sep 13 09:33:44 2017 -0700 Merge branch 'development' into dtg_branch commit 61564822f7e89c378eb6f4aaaf5485d3f6355c7b Author: dtgraves Date: Wed Sep 13 09:33:35 2017 -0700 make default debug=true Tests/GeometryShop/ramp/GNUmakefile commit a11c2f83c74ec02bd223eddee94dacafa6cba6a8 Author: Weiqun Zhang Date: Wed Sep 13 09:01:17 2017 -0700 fix compilation Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Tests/GeometryShop/ramp/GNUmakefile commit a92048dbb86dc6b0e789967453cd2c3f13345e39 Author: Weiqun Zhang Date: Wed Sep 13 08:53:29 2017 -0700 fix make Tests/GeometryShop/ramp/GNUmakefile commit 67042afc3ec5b2c583645bc5474f7e94bb8da5cd Merge: 384ff38d4 32fe4adbb Author: dtgraves Date: Wed Sep 13 08:48:46 2017 -0700 Merge branch 'development' into dtg_branch commit 32fe4adbb2ed25295ab5c10ca8264188a2a013af Author: Weiqun Zhang Date: Wed Sep 13 08:44:35 2017 -0700 modify test for debugging Tests/GeometryShop/ramp/inputs Tests/GeometryShop/ramp/main.cpp commit 05807f4d3749ffb46635ad0ef3bd54eda07feb54 Author: Weiqun Zhang Date: Tue Sep 12 20:32:02 2017 -0700 typo Src/GeometryShop/AMReX_EBData.cpp commit 384ff38d4df699e9fc35bb6fe8ab803c7ab1062d Author: dtgraves Date: Tue Sep 12 16:23:28 2017 -0700 more user's guide stuff. Docs/AMReXUsersGuide/EB/EB.tex commit 288e591acc1f67984d3d64557dc64ae0ce754428 Author: Weiqun Zhang Date: Tue Sep 12 15:27:37 2017 -0700 more const& Src/GeometryShop/AMReX_EBData.cpp commit f8b76565080a0f23aff2b3ff6258c17f8cf15537 Author: dtgraves Date: Tue Sep 12 15:13:45 2017 -0700 starting to flesh out EB user's guide Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/EB/graph.pdf Docs/AMReXUsersGuide/EB/multidivide.pdf Docs/AMReXUsersGuide/EB/volume.pdf Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/Particle/Particle.tex commit 23e9adb138e2d67e3aee0e79f899ff3809454969 Author: Weiqun Zhang Date: Tue Sep 12 14:48:23 2017 -0700 constexpr instead of macros Src/GeometryShop/AMReX_EBDataVarMacros.H commit a06e99f07a079c4fa09f7b87c4b58dd349dea68f Author: Weiqun Zhang Date: Tue Sep 12 13:49:03 2017 -0700 prefer make_shared; tidy Src/GeometryShop/AMReX_EBData.H commit 9185120b51d2dd040a9a268f9d86d6e5e89824b9 Author: Weiqun Zhang Date: Tue Sep 12 13:15:59 2017 -0700 built-in array to std::array; pass shared_ptr by reference Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp commit d7ca2bc19e2e95cb396e41703209a77bebfd1e21 Merge: 3256cd29b cc292eb70 Author: Klaus Weide Date: Tue Sep 12 14:49:36 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 32d0fb8b5b08f62894310d983d8708a88da054fc Author: Weiqun Zhang Date: Tue Sep 12 11:56:42 2017 -0700 small changes Src/GeometryShop/AMReX_EBGraph.cpp commit 87d0f813e1fa4e9054617ca7dc72f5ecf34d0251 Merge: 3fa322b97 cc292eb70 Author: Weiqun Zhang Date: Mon Sep 11 16:24:50 2017 -0700 Merge branch 'development' into weiqun/eb Conflicts: Src/GeometryShop/AMReX_EBGraph.cpp commit cc292eb708aa2f36da1e97b39fdfbf595e481e47 Author: Weiqun Zhang Date: Mon Sep 11 16:23:38 2017 -0700 remove unused and wrong functions with Dan's approval Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit 3fa322b9724985a9b0ef2a97688f3b00e167b3eb Author: Weiqun Zhang Date: Mon Sep 11 16:10:34 2017 -0700 tidy Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit 7a46a0fb24918b98e0f91dad7713b7e51e16dc87 Merge: e7ae77cf0 3bfd7f931 Author: Weiqun Zhang Date: Mon Sep 11 13:15:19 2017 -0700 Merge branch 'development' into weiqun/eb commit 3bfd7f93186329a7b9a5e329846093d21c2e40f7 Author: Weiqun Zhang Date: Mon Sep 11 13:15:02 2017 -0700 move LayoutData class from GeometryShop to Base Src/Base/AMReX_LayoutData.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/GeometryShop/Make.package commit f7bffd26fa7670a8464d2919c973afd9ed00f6ac Author: Weiqun Zhang Date: Mon Sep 11 12:24:47 2017 -0700 add assertion to LayoutData Src/GeometryShop/AMReX_LayoutData.H commit e7ae77cf04255e7ccc19933f1197f4452e30cd82 Merge: bfe33e931 4273e5007 Author: Weiqun Zhang Date: Mon Sep 11 12:40:43 2017 -0700 Merge branch 'development' into weiqun/eb commit 4273e50079d9593e4608f92eaca4ab5869de032d Author: Weiqun Zhang Date: Mon Sep 11 12:40:11 2017 -0700 LayoutData: operator[] now takes global index Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_LayoutData.H commit bfe33e93142161bbfb5df55b1d4a4be9ffc1fafc Author: Weiqun Zhang Date: Mon Sep 11 12:24:47 2017 -0700 add assertion to LayoutData Src/GeometryShop/AMReX_LayoutData.H commit 6f06c1fef9ec50fbb9885865467a069a1924779f Author: Weiqun Zhang Date: Mon Sep 11 12:06:50 2017 -0700 EB/CNS: test domain boundary in CNS_eb_fixup_geom Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 commit 4dc5ff41c79124bc5d54f2c662b48316a2ec211f Author: Weiqun Zhang Date: Mon Sep 11 11:18:17 2017 -0700 tidy Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp commit 402abe3aa3bd7a499351dcb00031af36e17f5a34 Merge: b91ff99ad 78b741cfa Author: Weiqun Zhang Date: Mon Sep 11 09:49:50 2017 -0700 Merge branch 'development' into weiqun/eb commit b91ff99ad2a7bf272836efdd00f75ad95c734677 Author: Weiqun Zhang Date: Mon Sep 11 09:28:37 2017 -0700 use instead of our own code Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 78b741cfa4b5d1f7e9aca56a36428cbdb998571b Merge: 9ff691f8a fe8de1796 Author: dtgraves Date: Mon Sep 11 09:25:39 2017 -0700 Merge pull request #125 from AMReX-Codes/dtg_branch merging some bug fixes back over to development commit fe8de17961ebe04242c44486c9f5af910ceef615 Author: dtgraves Date: Mon Sep 11 09:24:18 2017 -0700 in GeometryShop::fixRegularNextToCovered, corner cells outside the domain were recognized as such, causing some faces to be incorrectly labelled as non-boundary Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp commit 0bc910e519c8969652abc05b9261d5c2d52efd43 Author: Weiqun Zhang Date: Mon Sep 11 09:11:35 2017 -0700 raw pointer -> unique_ptr Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 2aeef0ef626f06102ac698a21b96d3ed60147159 Author: dtgraves Date: Mon Sep 11 09:11:59 2017 -0700 bug fix identified by Weiqun Src/GeometryShop/AMReX_GeometryShop.cpp commit 3f4b3f961929c31afad07fce1d073f0648fbe1e4 Author: Weiqun Zhang Date: Sun Sep 10 12:58:59 2017 -0700 minor Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_Moments.H commit 8bdc08ee631fc3b2080cb2403bcd22cfde1c5bf4 Author: Weiqun Zhang Date: Sat Sep 9 22:27:19 2017 -0700 tidy Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp commit 7bb8bb92488ea860dc45ec1815753b7ca1188583 Author: Weiqun Zhang Date: Sat Sep 9 21:39:53 2017 -0700 tidy Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.cpp commit 4f2a93595a01be646431984de5e94de57eb0a3da Author: Weiqun Zhang Date: Sat Sep 9 21:31:10 2017 -0700 built-in array -> std::array Src/GeometryShop/AMReX_IrregNode.H commit 9ff691f8ac695acf0b693951f44717d64a782ff5 Merge: fdacbd6c5 380c31595 Author: Andrew Myers Date: Sat Sep 9 17:50:54 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fdacbd6c56dfdb89113611b4caa141580c79c216 Author: Andrew Myers Date: Sat Sep 9 17:50:38 2017 -0700 Fix logic that enforces a minimum split size in the KD Tree load balancer. Src/Particle/AMReX_LoadBalanceKD.cpp commit 4d7bf209a7fb177fce50a9fbeef80e8962fffe89 Author: Weiqun Zhang Date: Sat Sep 9 15:48:20 2017 -0700 tidy Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit 49f80f65be68e8dcd6a4b1918bb003769d43b395 Author: Weiqun Zhang Date: Sat Sep 9 15:24:48 2017 -0700 builtin array to std::array Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit e8d8068df7db44ca2e0b574f48517cc898ab1732 Author: Weiqun Zhang Date: Sat Sep 9 14:59:43 2017 -0700 tidy Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp commit 380c31595502172d9d2066396ebee0f732034f0c Author: Weiqun Zhang Date: Sat Sep 9 14:44:32 2017 -0700 add back ivsFine Src/EBAMRTools/AMReX_EBCoarseAverage.cpp commit 820f3d26e7fff790a725f83d3200ee549f79502b Merge: f9ca99bcf 0a2601b6a Author: Weiqun Zhang Date: Sat Sep 9 14:21:26 2017 -0700 Merge branch 'development' into weiqun/eb commit 0a2601b6af1a36a3d255b1c1cd5b4a1cd1ab27e5 Merge: bda85a342 3597566b5 Author: Weiqun Zhang Date: Sat Sep 9 13:09:50 2017 -0700 Merge branch 'weiqun/cu' into development commit bda85a342934ccd39b15d2d0bc47c4827d7fdba1 Author: Weiqun Zhang Date: Sat Sep 9 13:06:37 2017 -0700 remove virtual from IrregFAB and IVFAB Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_LoHiSide.cpp commit f9ca99bcf41158913572f3e6d7216bc98349d327 Merge: 5cf42c37e 8ae698a4c Author: Weiqun Zhang Date: Sat Sep 9 13:01:23 2017 -0700 merge commit 8ae698a4c1a411969e31e5a76cd73ce7a9ada6f2 Author: Weiqun Zhang Date: Sat Sep 9 12:56:45 2017 -0700 vector -> Array Src/GeometryShop/AMReX_EBISLevel.cpp commit bbf38391af0d3443ef39f77e3eeb7d50d9bab68d Merge: 71037d4de 4a9d39d3b Author: dtgraves Date: Sat Sep 9 12:06:34 2017 -0700 Merge pull request #124 from AMReX-Codes/dtg_branch Getting some important bug fixes into development commit 4a9d39d3b4d122defeaa17ecd906d704ce481955 Merge: fa0cbfbf1 71037d4de Author: dtgraves Date: Sat Sep 9 12:06:13 2017 -0700 Merge branch 'development' into dtg_branch commit fa0cbfbf19d333ce9521e3c8a38cd1487c9cff2b Author: dtgraves Date: Sat Sep 9 12:00:24 2017 -0700 took out debugging statements Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit 93250eabfcd28bed2b7e5a86a14101a4258f8cc3 Author: dtgraves Date: Sat Sep 9 11:47:03 2017 -0700 after much wailing and gnashing of teeth (and quite a bit of software refactoring), I have fixed the nan bug that Weiqun identified. There are still a bunch of debugging statements in the code. I will remove them before merging with development Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit 71037d4de9ee784136ab8cf87f7c0d269b81a542 Author: Weiqun Zhang Date: Sat Sep 9 08:16:33 2017 -0700 vector -> Array Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp commit 0ee0828ccfc8985b0975e4aa171900967417f07e Author: Weiqun Zhang Date: Sat Sep 9 08:03:18 2017 -0700 vector -> Array to get bound checking in debug mode Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LayoutData.H Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 3597566b56f5b4cdf6f7fdaa00ea8bde4ae80132 Author: Weiqun Zhang Date: Fri Sep 8 21:47:05 2017 -0700 add virtual override Src/GeometryShop/AMReX_GeometryShop.H commit a3b305611d1e5d2b46010e2178696623a7f2289f Author: Weiqun Zhang Date: Fri Sep 8 21:38:49 2017 -0700 removed virtual from BaseIVFAB and IrregFAB Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_LoHiSide.cpp commit 96dad9a1f5422c983e831fa6649f43a0b2f329c9 Merge: 4e978226a e828afba9 Author: WeiqunZhang Date: Fri Sep 8 17:28:19 2017 -0700 Merge pull request #123 from AMReX-Codes/threaded_redistribute Threaded redistribute commit 4e978226a91ff0b47de3125b3fe5957175fca7a5 Author: Weiqun Zhang Date: Fri Sep 8 17:24:41 2017 -0700 override and minor cleanup Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_IntVectSet.cpp commit 9444122207e707041c4ee4ea0936529cd6f4f974 Author: Weiqun Zhang Date: Fri Sep 8 17:17:19 2017 -0700 minor clean up Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp commit 5cf42c37e056493c718a28b9ef4c22f157a618ab Author: Weiqun Zhang Date: Fri Sep 8 16:20:36 2017 -0700 EB/CNS: new parameter cns.refine_cutcells=1 Src/Amr/AMReX_Amr.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 1733839ceba5ea05119132cc4a345e7442f528cc Merge: 1b256042a ab6f6eec6 Author: Andrew Myers Date: Fri Sep 8 16:13:20 2017 -0700 Merge branch 'development' into threaded_neighbor_list commit 3a876f474464e21f885abd6ced802d1ae610a09d Author: Weiqun Zhang Date: Fri Sep 8 14:27:02 2017 -0700 move some scattered EB files into a new directory Src/EB Src/AmrCore/Make.package Src/Base/Make.package Src/EB/AMReX_EBAmrUtil.H Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBAmrUtil_F.H Src/EB/AMReX_EBAmrUtil_nd.F90 Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBCellFlag_F.H Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBFaceFlag.H Src/EB/AMReX_EBFaceFlag.cpp Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_1d.F90 Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Src/EB/AMReX_EBInterp_F.H Src/EB/AMReX_EBInterpolater.H Src/EB/AMReX_EBInterpolater.cpp Src/EB/AMReX_EBLevel.H Src/EB/AMReX_EBLevel.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Src/EB/AMReX_ebcellflag_mod.F90 Src/EB/AMReX_ebinterp_1d.F90 Src/EB/AMReX_ebinterp_2d.F90 Src/EB/AMReX_ebinterp_3d.F90 Src/EB/Make.package Tutorials/EB/CNS/Exec/Make.CNS commit e828afba93b6d517348edcf832e761771dc760c3 Author: Andrew Myers Date: Fri Sep 8 14:13:09 2017 -0700 Pass in the explicit tile size to the dummy mfiter Src/Particle/AMReX_ParticleContainerI.H commit ab6f6eec605771b7ef747943a195b9a254b69872 Merge: 5481f113c f9b1a78c3 Author: WeiqunZhang Date: Fri Sep 8 13:48:15 2017 -0700 Merge pull request #122 from bcfriesen/fix_vtune_linking GNUMake: update the env var pointing to the VTune directory at NERSC commit 5481f113ced48df34650384630ef3cb0944e85c7 Merge: 66a19c3ec 96d92f72c Author: WeiqunZhang Date: Fri Sep 8 13:45:02 2017 -0700 Merge pull request #121 from bcfriesen/fix_cvode_linking GNUMake: remove links to FCVODE, the old Fortran wrapper to CVODE commit c70905079eef087d2c58657256a1a4277314d076 Author: Andrew Myers Date: Fri Sep 8 13:31:58 2017 -0700 set default tiling back to false. Src/Particle/AMReX_ParticleContainerI.H commit 9674db7c5092546c1c555b6054e76e84eab824b5 Author: Andrew Myers Date: Fri Sep 8 12:58:27 2017 -0700 fix dumb mistake Src/Particle/AMReX_ParticleContainerI.H commit 66a19c3ecc3ee66ef289082d89fc95db125dac14 Author: Ann Almgren Date: Fri Sep 8 12:45:58 2017 -0700 Slight typo corrections Docs/Migration/Migration.md commit d146a132f0aee6594573d506a63b9d1655cc5fe8 Author: Andrew Myers Date: Fri Sep 8 12:45:45 2017 -0700 also handle the soa data in the threaded redistrbute. Src/Particle/AMReX_ParticleContainerI.H commit f9b1a78c3b96f32a7973193273ee96b0aaea17b6 Author: Brian Friesen Date: Fri Sep 8 12:16:47 2017 -0700 GNUMake: update the env var pointing to the VTune directory at NERSC The default version at NERSC is now VTune 2017, so we need to update this environment variable or else compiling will fail. Tools/GNUMake/tools/Make.vtune commit 96d92f72c533637fac3a8362fcd6ab34cfd2fad9 Author: Brian Friesen Date: Fri Sep 8 12:10:53 2017 -0700 GNUMake: remove links to FCVODE, the old Fortran wrapper to CVODE FCVODE comes with CVODE and provides a Fortran interface to the CVODE library, but is not thread-safe. Recently the SUNDIALS developers provided us with a Fortran 2003 interface to CVODE which uses iso_c_binding to most of the functions in the library. So remove the links to the old FCVODE library since we don't need it anymore. Tools/GNUMake/packages/Make.cvode commit 1efcea0c0f7d9eccd5f3547d2a3b4a783833a49a Author: Andrew Myers Date: Fri Sep 8 11:29:19 2017 -0700 removed this by mistake. Src/Particle/AMReX_ParticleContainerI.H commit 83db808e2ef5ff1456ffce0c432949eaefff8776 Author: Andrew Myers Date: Fri Sep 8 11:20:35 2017 -0700 fix bug affecting hydrid MPI / OpenMP redistribute. Src/Particle/AMReX_ParticleContainerI.H commit 2aeb42bae67a2a6636454d7be6b461fd6539f95d Author: Andrew Myers Date: Fri Sep 8 10:43:29 2017 -0700 also reset has_hashmap here. Src/Base/AMReX_BoxArray.cpp commit 3562ad544c2d3622fb4c2620eb61560207abc47e Author: Andrew Myers Date: Fri Sep 8 10:38:27 2017 -0700 reset has_hashmap when the map is cleared. Src/Base/AMReX_BoxArray.cpp commit b39013fadf61f06f880d77a1fd74cbb008b4c218 Merge: 6a2bbc6a9 cfb1c765f Author: Andrew Myers Date: Fri Sep 8 10:24:25 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6a2bbc6a910585ff643ce3509d323dd56544aea5 Author: Andrew Myers Date: Fri Sep 8 10:24:14 2017 -0700 enforce a min box size in the KDTree load balancer. Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp commit bd8781d7cbd9b5ee7ff6b93cfb6b02a349b7d729 Author: Weiqun Zhang Date: Fri Sep 8 09:33:19 2017 -0700 2D EBFluxRegister Src/AmrCore/AMReX_EBFluxRegister_2d.F90 commit 00a51112a23a7682a8e897fb0547858b9a53811d Author: Weiqun Zhang Date: Fri Sep 8 09:21:59 2017 -0700 minor Src/AmrCore/AMReX_EBFluxRegister_3d.F90 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 8f09e58bc35b0c10927d2ef1f2b64df5faded98e Merge: f5cd89f4c cfb1c765f Author: dtgraves Date: Fri Sep 8 08:22:39 2017 -0700 merging with development to get weiqun's test commit 3256cd29b1fa6b77179b16ce7dac4e0f285e8403 Merge: d04f9491d cfb1c765f Author: Klaus Weide Date: Fri Sep 8 00:13:18 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d1b136bbc2a9b3a76b329f76889563c9cde2117b Author: Weiqun Zhang Date: Thu Sep 7 17:31:36 2017 -0700 EB: fix init_snan Src/GeometryShop/AMReX_EBData.cpp commit cfb1c765fdb5b4da0b8e422f7472f7e4f799da1d Author: Weiqun Zhang Date: Thu Sep 7 17:31:36 2017 -0700 EB: fix init_snan Src/GeometryShop/AMReX_EBData.cpp commit 8a532558cfdf61942b5277076b86f2b19be0c800 Author: Weiqun Zhang Date: Thu Sep 7 17:09:38 2017 -0700 initialize EB data to snan to help debug Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp commit 26eac8250c42f46e9123ac5f25cd0844c6d77fc4 Author: Weiqun Zhang Date: Thu Sep 7 17:10:58 2017 -0700 EB/CNS: pass mpi rank to fortran to help debugging Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/fortran/CNS_f.F90 commit 00b2fe91270e5458a0ce43b849c54b4bf2b093f0 Author: Weiqun Zhang Date: Thu Sep 7 17:09:38 2017 -0700 initialize EB data to snan to help debug Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp commit 16fb58c4c738eb79a36585e3c97db8dbc76947ba Author: Andrew Myers Date: Thu Sep 7 16:54:43 2017 -0700 need to create any missing map entries in serial here before the parallel reduction. Src/Particle/AMReX_ParticleContainerI.H commit b4fbcdc83637bc304a2908469743d2afe35250f8 Merge: 697ed7c85 cba746153 Author: Weiqun Zhang Date: Thu Sep 7 16:13:16 2017 -0700 Merge branch 'development' into weiqun/eb commit 03913d3939c0f7be117c18d0417445a5a93481ca Author: Andrew Myers Date: Thu Sep 7 15:33:14 2017 -0700 Don't want to perform this check inside a critical region, since in particle code we call this a lot from threaded regions. Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit f5cd89f4c66a1588604e077fecf0ea6788703cb9 Merge: fdfe0bfa2 cba746153 Author: dtgraves Date: Thu Sep 7 15:17:24 2017 -0700 Merge branch 'development' into dtg_branch commit fdfe0bfa2ce5e50051e2d5369e1d870658826813 Author: dtgraves Date: Thu Sep 7 15:02:52 2017 -0700 more bugs found. need to pivot toward writing documents now. Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 697ed7c85a12d603472448dd33ef581b71d16823 Author: Weiqun Zhang Date: Thu Sep 7 14:57:50 2017 -0700 WIP: don't tag covered cells Src/AmrCore/AMReX_EBAmrUtil_nd.F90 commit 25f9f6a6fe24a69578302dbabafe6bf45651ba54 Author: Weiqun Zhang Date: Thu Sep 7 14:27:37 2017 -0700 WIP: EBFluxRegister: bug fix Src/AmrCore/AMReX_EBFluxRegister.cpp Src/AmrCore/AMReX_EBFluxRegister_3d.F90 commit 9543fbb09f9db9e4972860069afee860180bbe26 Author: Weiqun Zhang Date: Thu Sep 7 13:22:24 2017 -0700 WIP: EBFluxRegister::Reflux Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit 10960f4d68c7c265c67ea94f78b5c676b71f9765 Author: Weiqun Zhang Date: Thu Sep 7 12:41:06 2017 -0700 WIP: EBFluxRegister::FineAdd Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Src/AmrCore/AMReX_EBFluxRegister_3d.F90 Src/AmrCore/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 32e1d7f4fdf8e9f7f596efe28a8982f02039ccc4 Author: dtgraves Date: Thu Sep 7 12:05:47 2017 -0700 conductivity op seems to work now. God I hate fortran. Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Tests/EBAMRElliptic/exec/cond.inputs commit ed1313d174c6a4878c182daed79a68e8d1b8cde6 Author: Andrew Myers Date: Thu Sep 7 10:46:51 2017 -0700 accidently screwed up caching by moving this - fixing. Src/Particle/AMReX_ParticleContainerI.H commit 3c247fdb0c80aefdd25668bc8fa496bfca0cb752 Author: Andrew Myers Date: Thu Sep 7 10:07:20 2017 -0700 give the AoS insert and delete methods and use them. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit cba746153c6709602da02cfb4179cfa36f223a9f Merge: da7eb4e48 69eaea40d Author: WeiqunZhang Date: Thu Sep 7 08:47:17 2017 -0700 Merge pull request #120 from kweide/development Expose MFIter's index() method to Fortran code as grid_index() commit 69eaea40d056f8193e2e9a1ad3d0e4e954e69416 Author: Klaus Weide Date: Wed Sep 6 22:08:10 2017 -0500 Expose MFIter's index() method to Fortran code as grid_index() The Fortran multifab already has a dataPtr() method that takes an index, so there should also be a way to get such an index from an iterator over a multifab. analogous to the AMReX_octree iterator's grid_index(), whence the name Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 6cdb82016121e80a9e59c75294c2151573927dc3 Author: Weiqun Zhang Date: Wed Sep 6 17:38:03 2017 -0700 WIP: EBFluxRegister Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit fbd891715c3f28992e4028167e86adce66007637 Author: Andrew Myers Date: Wed Sep 6 16:58:34 2017 -0700 in the first pass, thread over tiles instead of threading over the particles on a tile. Src/Particle/AMReX_ParticleContainerI.H commit 25f695f651c9d34b0046e1170f94b495f312ebd9 Author: Weiqun Zhang Date: Wed Sep 6 16:18:19 2017 -0700 WIP: EBFluxRegister Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Src/AmrCore/AMReX_EBFluxRegister_1d.F90 Src/AmrCore/AMReX_EBFluxRegister_2d.F90 Src/AmrCore/AMReX_EBFluxRegister_3d.F90 Src/AmrCore/AMReX_EBFluxRegister_F.H Src/AmrCore/Make.package Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 6a51f1a19bf96953f7866d18df69a7b90fd3d771 Author: Andrew Myers Date: Wed Sep 6 15:53:03 2017 -0700 OpenMP support in Redistribute compiles and gives the right answers. Src/Particle/AMReX_ParticleContainerI.H commit da7eb4e480f804438b93dff773087442368bdad5 Merge: 09006ab32 c80c209dc Author: WeiqunZhang Date: Wed Sep 6 14:30:42 2017 -0700 Merge pull request #119 from bcfriesen/add_arch_suffix GNUMake: add arch suffix to exe name when building on a Cray commit c80c209dccd4ec7027d909df28fdd1158cb81f70 Author: Brian Friesen Date: Wed Sep 6 14:21:07 2017 -0700 GNUMake: add arch suffix to exe name when building on a Cray Cross-compiling on Cray systems is common, so adding the target architecture to the exe suffix clarifies which instruction set the binary was compiled with. Tools/GNUMake/Make.defs commit 09006ab325fff2e66d9219a3eedf89fb21e884a9 Merge: 49caf2c07 121d363fb Author: WeiqunZhang Date: Wed Sep 6 13:16:17 2017 -0700 Merge pull request #118 from bcfriesen/print_build_target_on_cray Print build target on Cray commit 121d363fb9c98067680c8fdca908681f1dc37714 Author: Brian Friesen Date: Wed Sep 6 12:56:38 2017 -0700 GNUMake: print the build target at link time if running on a Cray AMReX does not have separate compiler flags for different architectures on Cray systems, e.g., separate compile flags for AVX2 vs. AVX-512 instructions. The user is responsible for choosing the correct build target, via the "craype-" modules. To make clear which target the user is compiling for, print the target at link time. Tools/GNUMake/Make.rules commit 4e8bead59e45a6f498167c72cca6bbbc2e48e77b Author: Andrew Myers Date: Wed Sep 6 12:32:47 2017 -0700 do reduction over threads for the non-local buffer. Src/Particle/AMReX_ParticleContainerI.H commit 6b59b0ce70cc1053b0cdfd642ff47c6a29f988a2 Author: Andrew Myers Date: Wed Sep 6 11:23:52 2017 -0700 only add entries to the remote tmp map on demand Src/Particle/AMReX_ParticleContainerI.H commit f1834d6bebdef8419f2a7d7506af3ac7d6a6c143 Author: Weiqun Zhang Date: Wed Sep 6 11:16:34 2017 -0700 EB/CNS: add tagging on cutcells Src/AmrCore/AMReX_EBAmrUtil.H Src/AmrCore/AMReX_EBAmrUtil.cpp Src/AmrCore/AMReX_EBAmrUtil_F.H Src/AmrCore/AMReX_EBAmrUtil_nd.F90 Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Src/AmrCore/Make.package Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_error.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package commit 9476d7228af7aa391be20a00274f2ed560da001f Author: Andrew Myers Date: Wed Sep 6 10:49:39 2017 -0700 threading the non-local tmp container. Src/Particle/AMReX_ParticleContainerI.H commit 4c3ca285b51cd08ae9bacd5ace306efaa046bf61 Author: Andrew Myers Date: Wed Sep 6 09:52:52 2017 -0700 about the start threading the redistribute method. Src/Particle/AMReX_ParticleContainerI.H commit 96281ce5240b7d339daa02f3644a457bfa223958 Author: dtgraves Date: Tue Sep 5 15:54:16 2017 -0700 found some bugs and added some debugging tools Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_Stencils.cpp Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 49caf2c07bd5dcc8f87500a10cae6bba4eb7b720 Author: Weiqun Zhang Date: Tue Sep 5 15:09:57 2017 -0700 make GraphNode thread safe Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/GeometryShop/AMReX_GraphNode.cpp commit d427a655a317dece25b463c3114fa8da88357e0a Merge: 8fc2572b6 6feff0818 Author: WeiqunZhang Date: Tue Sep 5 12:03:10 2017 -0700 Merge pull request #117 from nncarlson/dfloat-fix Eliminate use of non-standard Fortran dfloat intrinsic commit 8fc2572b600509c31c03e257daa09793782d36c1 Author: Weiqun Zhang Date: Tue Sep 5 10:26:30 2017 -0700 remove BL_USE_FORT_STAR_PRECISION Src/Base/AMReX_REAL.H Src/Boundary/AMReX_LO_UTIL.F commit d0bfe568d169ccbd5f042730fb824ec5e04b17c1 Author: Weiqun Zhang Date: Tue Sep 5 10:12:44 2017 -0700 add linear solvers to libamrex GNUmakefile.in Src/Base/Make.package Tools/libamrex/configure.py commit 4af0473f23c97f4e6e089d060563415df4467549 Merge: 0caf60f6f e2527a8a6 Author: dtgraves Date: Tue Sep 5 09:18:25 2017 -0700 Merge pull request #116 from AMReX-Codes/weiqun/sort BaseIVFAB and BaseIFFAB commit 6feff0818cc39ed53caf831e0ddc1a28ea18abcd Author: Neil Carlson Date: Tue Sep 5 10:11:38 2017 -0600 Eliminate use of non-standard Fortran dfloat intrinsic (fixes #115) Src/AmrCore/AMReX_INTERP_3D.F commit 0caf60f6f87a9e5b132dbf3369725ecc9f7056ed Merge: 05741bbfc 89f965dec Author: WeiqunZhang Date: Tue Sep 5 08:54:14 2017 -0700 Merge pull request #114 from nncarlson/imultifab-additions Additions to the Fortran imultifab interface commit 05741bbfc6e71ff940c110751acb2909e802b747 Merge: 152687b14 a82d58178 Author: dtgraves Date: Tue Sep 5 08:50:39 2017 -0700 Merge pull request #111 from AMReX-Codes/weiqun/cfivs replace simple loop over grids with BoxArray's fast complement function commit 89f965dec521b6d8da85582eeeb42e3d9a3857cf Author: Neil Carlson Date: Mon Sep 4 21:53:12 2017 -0600 Additions to the Fortran imultifab interface This extends the Fortran imultifab interface to include the setval method, and adds the optional nodal argument to amrex_imultifab_build, as defined for amrex_multifab_build. Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit e2527a8a6c4914749063c3e9503b6b453568c747 Merge: 696b95b62 b2e9e9293 Author: Weiqun Zhang Date: Sun Sep 3 12:11:55 2017 -0700 merge commit 696b95b62f578b53cf17cd464c383a1ee28a0165 Author: Weiqun Zhang Date: Sun Sep 3 12:08:01 2017 -0700 optimize IFFAB Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H commit f2718bd0461b2368118284337bca7d03763c9b22 Author: Weiqun Zhang Date: Sun Sep 3 11:04:50 2017 -0700 refactor IVFAB to make getIndex faster Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H commit b2e9e9293a5aa2c485505b76b1cd53162149aab4 Author: Weiqun Zhang Date: Sun Sep 3 11:04:50 2017 -0700 refactor IVFAB to make getIndex faster Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H commit 152687b14154ce0775fbf56d28a44cdff2eba9c7 Author: Weiqun Zhang Date: Sat Sep 2 12:48:17 2017 -0700 inline operator== for VolIndex and FaceIndex and switch the order of comparison by comparing int first Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp commit e502a626bff4ed29d391a8c2618b8e0f93250955 Author: Weiqun Zhang Date: Sat Sep 2 12:48:17 2017 -0700 inline operator== for VolIndex and FaceIndex and switch the order of comparison by comparing int first Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp commit 58e0bad3c96c66b82ac72fcf0c3d54e4490ec134 Merge: ae1276aaf a82d58178 Author: Weiqun Zhang Date: Fri Sep 1 22:01:27 2017 -0700 Merge branch 'weiqun/cfivs' into weiqun/eb commit ae1276aaf68e26a8cb3ba7ac2b652d37a8cf7604 Merge: a580f6fa1 96e32bda6 Author: dtgraves Date: Fri Sep 1 19:40:57 2017 -0700 Merge pull request #110 from AMReX-Codes/weiqun/iffabcopy optimization of IFFAB copy commit a82d581786424c929a353d6ddb7a3e971614a075 Author: Weiqun Zhang Date: Fri Sep 1 17:58:19 2017 -0700 replace simple loop over grids with BoxArray's fast complement function Src/GeometryShop/AMReX_EBLevelGrid.cpp commit 96e32bda6d42f8f3e87c6c7aac7827d54444667d Author: Weiqun Zhang Date: Fri Sep 1 16:40:13 2017 -0700 optimization of IFFAB copy Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp commit bb82781bc39adfaf8be425cc4bcdc24cf8d78cb5 Author: dtgraves Date: Fri Sep 1 16:23:52 2017 -0700 some simplification and debugging of EB solvers Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp commit a580f6fa148ca44cbf26077fabb75fc89bb7fc7c Author: Weiqun Zhang Date: Fri Sep 1 15:14:57 2017 -0700 add some profilers Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp commit 694800f558c84f131027050a898ff7e335816f98 Merge: 447adfb57 3fc3b5713 Author: dtgraves Date: Fri Sep 1 13:31:11 2017 -0700 Merge pull request #109 from AMReX-Codes/dtg_branch putting some tweaks to IntVectSet into development commit 3fc3b5713a46aaeeca75fe1462df6bea525290aa Author: dtgraves Date: Fri Sep 1 13:29:14 2017 -0700 with Weiqun's advice, I was able to restore the move constructors to IntVectSet. Src/GeometryShop/AMReX_IntVectSet.H commit 447adfb57217e3e0e1b88530bfb28c34160dcc44 Author: Weiqun Zhang Date: Fri Sep 1 13:25:04 2017 -0700 have to remove noexcept because gcc 4 does support Src/GeometryShop/AMReX_IntVectSet.H commit 38409c0999ea3c91976a62da93e4ee3ed1eae2ce Author: dtgraves Date: Fri Sep 1 12:59:56 2017 -0700 my compiler was not eating some of weiqun's more sophistocated c++11-isms so I made IntVectSet old school again. Src/GeometryShop/AMReX_IntVectSet.H commit e440e0aeea3fd17948504aa717abe7af98409076 Author: dtgraves Date: Fri Sep 1 12:52:18 2017 -0700 fixed compilation bug in IntVectSet Src/GeometryShop/AMReX_IntVectSet.H commit ca11d79c749b609024665aeaf39b9b6e9b62b785 Merge: b7977940e 4701db386 Author: dtgraves Date: Fri Sep 1 12:49:17 2017 -0700 Merge branch 'development' into dtg_branch commit 4701db3860a5769ed3c5dda1fb8689cc30dc0686 Merge: 8b7c6e452 fdd41ce8a Author: dtgraves Date: Fri Sep 1 12:47:33 2017 -0700 Merge pull request #108 from AMReX-Codes/weiqun/intvectset Internal container of IntVectSet commit b7977940edb000c57550b45c8f270d666d18031a Author: dtgraves Date: Fri Sep 1 11:30:48 2017 -0700 eb plotfile routines now work. Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit fdd41ce8af89ad9e324b924e389a074c22cdc58d Merge: 5d24abaac 8b7c6e452 Author: Weiqun Zhang Date: Fri Sep 1 11:25:11 2017 -0700 Merge branch 'development' into weiqun/intvectset commit 8b7c6e452aa95cef7af840a3553e60a2804eff3e Author: Weiqun Zhang Date: Fri Sep 1 11:24:20 2017 -0700 more BL_PROFILE Src/GeometryShop/AMReX_EBLevelGrid.cpp commit 5d24abaace034783d766fda41d7e8315cf546148 Merge: c672e69c9 fa26cdcf4 Author: Weiqun Zhang Date: Fri Sep 1 11:02:29 2017 -0700 Merge branch 'development' into weiqun/intvectset commit fa26cdcf4913ff9fa500af0ac12e4ac7a578a113 Author: Weiqun Zhang Date: Fri Sep 1 10:59:43 2017 -0700 add/rmove some BL_PROFILEs Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_DistributionMapping.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tutorials/EB/CNS/Source/CNS.cpp commit c672e69c931adf2e9a2352805477d5c7253bac96 Author: Weiqun Zhang Date: Fri Sep 1 10:56:59 2017 -0700 IntVectSet: reimplement it with unordered_set rather than set Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp commit 1e4f61b72815b1d003b683228711fa2f57aff19c Author: Weiqun Zhang Date: Thu Aug 31 21:30:02 2017 -0700 EB/CNS: flooring Tutorials/EB/CNS/Source/fortran/CNS_f.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit cffba664b9c6763bb68f35cfea4959fd71b4ae1d Author: Weiqun Zhang Date: Thu Aug 31 16:08:51 2017 -0700 Disable MPI checking if NO_MPI_CHECKING=TRUE. Tools/GNUMake/Make.local.template Tools/GNUMake/sites/Make.unknown commit 8af7220616a2a49a90d7661ef7671750e321cabb Author: dtgraves Date: Thu Aug 31 15:43:50 2017 -0700 added utilities to output visit and amrvis-compliant plot files from EB data. I also added a debugging utility that allows data to be visualized from inside a debugger.. Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBDebugOut.cpp Tests/GeometryShop/ramp/GNUmakefile Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit 61cc4f0cc0333775fb3b9b32879340572b9a552f Author: Weiqun Zhang Date: Thu Aug 31 14:59:18 2017 -0700 less verbose Src/Amr/AMReX_Amr.cpp commit 34676fbbd26d38f6d733d34b72d3d00c9696245f Author: Weiqun Zhang Date: Thu Aug 31 14:56:55 2017 -0700 EB/CNS: override post_restart to fix up geometry Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 9e965c6f90531e3f7a05a46ce8a9fdebb48e34c9 Author: Weiqun Zhang Date: Thu Aug 31 13:58:08 2017 -0700 EB/CNS: add testing inputs Tutorials/EB/CNS/Exec/Combustor/inputs.testing commit 92e7f0c4cda2da188a6dd342f036d15b4f769ff3 Author: Weiqun Zhang Date: Thu Aug 31 13:49:52 2017 -0700 fix restart for EB Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp commit 30e5c131435b9303e87d6dfd7d4e51d47a2f09b1 Author: dtgraves Date: Thu Aug 31 11:05:00 2017 -0700 bug fix to conductivityopfactory Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp commit 59b86dd7edaffcf9a231631ecd1b930b27954ef1 Author: Weiqun Zhang Date: Thu Aug 31 09:22:40 2017 -0700 commented out FaceFlag stuff Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp commit a4e89e1d72a14e677342f22d90d8a088bfc5e86c Author: Weiqun Zhang Date: Thu Aug 31 09:17:55 2017 -0700 EB/CNS: pass amr.max_level into EBIndexSpace::define so that we don't have to build extra coarse levels Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 1d3ddd1a0ceaafbf4ea5b30404c16e55f6bb0379 Merge: 2670989ab 501ee3674 Author: Weiqun Zhang Date: Thu Aug 31 09:13:33 2017 -0700 Merge branch 'development' into weiqun/eb commit 2670989abceffd31e491cf06b488186f204aff7b Author: Weiqun Zhang Date: Thu Aug 31 09:12:55 2017 -0700 EB/CNS: if interior plus one ghost are all regular, no need to call eb functions Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 commit 9418e7ac132081cdc518fd0ff1f392ce985a0209 Author: Weiqun Zhang Date: Wed Aug 30 16:02:31 2017 -0700 EB/CNS: vectorization of riemann solver Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/analriem3d.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_hyp_wall.F90 commit 501ee3674c572168ee2f36fac5a954b7c0b56f2e Merge: d23315ae7 e5154a3e4 Author: Tan Nguyen Date: Wed Aug 30 18:12:00 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d23315ae704cb2e5723a4a9c8a154c51c34bfe02 Author: Tan Nguyen Date: Wed Aug 30 18:11:50 2017 -0700 add task association feature to support dynamic task parallelism Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_AbstractTask.cpp Src/AmrTask/graph/AMReX_DataTypes.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/rts_impls/MPI_Generic/mylock.h Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/rts_impls/MPI_Generic/rts_graphimpl.H Src/AmrTask/rts_impls/MPI_Generic/rts_taskimpl.H Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C commit e5154a3e4f7c15b0a9766bea17b5ff25050924bd Merge: 50a63610b 0fac5be3c Author: dtgraves Date: Wed Aug 30 15:56:00 2017 -0700 Merge pull request #106 from AMReX-Codes/dtg_branch merging over improved serialization of EBGraph and a bug fix to BaseIFFAB. commit 0fac5be3c45db7ed9a4617ed7cc850a9f08b1d26 Author: dtgraves Date: Wed Aug 30 15:54:23 2017 -0700 I reworked EBGraph serialization so that it will preserve the sparse nature of the object if it can. I also fixed a subtle bug in BaseIFFAB that may have been causing our valgrind troubles. Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp Tests/GeometryShop/regression/ebio.cpp commit d04f9491debd8db6f7cff554353b1594441fa973 Merge: 29989ea3b 50a63610b Author: Klaus Weide Date: Wed Aug 30 14:51:36 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fb1a21727aeeda3f2b30af8f84dcb21d4e3f498c Author: Weiqun Zhang Date: Wed Aug 30 10:41:15 2017 -0700 dynamic OpenMP scheduling in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit 17d6d71fe3caa9b1a27937facac0a66d383c7cee Author: dtgraves Date: Wed Aug 30 08:57:53 2017 -0700 bug found by weiqun Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 50a63610b60fb089be9285282b06e561440b4b9a Author: Weiqun Zhang Date: Wed Aug 30 08:49:22 2017 -0700 not thread safe Src/Base/AMReX_EBLevel.cpp commit 6f973598eb9fce331d404aed4149e576b5facd3f Author: kngott Date: Wed Aug 30 03:09:46 2017 -0700 Add functions to allow access and updating of cached DistributionMappings in StateData, AmrLevel and AmrMesh objects. Used to fix functionality with MoveAllFabs. Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H commit 4fa3c012f97d602049148bbc68fec656431890ed Author: Weiqun Zhang Date: Tue Aug 29 21:04:34 2017 -0700 turn off openmp for some eb codes because they are not thread safe yet Src/Base/AMReX_EBMultiFabUtil.cpp commit 12b4e5eaf84156fabea5ca5a6892fd6d3cdb21e3 Author: Weiqun Zhang Date: Tue Aug 29 15:15:57 2017 -0700 add headers to makefile Src/GeometryShop/Make.package commit 8f46475790f3685d56ba0e35c45536e5d3e1cc3f Merge: 70989affa 89f17aa43 Author: Weiqun Zhang Date: Tue Aug 29 14:22:29 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 70989affad94c74c21022f7622df49c75565efb7 Author: Weiqun Zhang Date: Tue Aug 29 14:22:20 2017 -0700 EB/CNS: tile size Tutorials/EB/CNS/Source/CNS_advance.cpp commit 89f17aa43cb7b7a1d1bf44009de36708e56690a0 Merge: 8164710a0 3e33ec4cd Author: vince Date: Tue Aug 29 13:25:17 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8164710a0f9b072b3a2254211e987453e2179777 Author: vince Date: Tue Aug 29 13:25:08 2017 -0700 option to graph top pct in write summary, extra information in call trac, replace spaces in function names. Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 3e33ec4cd713ffb4df084488c48f4428c89e709c Author: Weiqun Zhang Date: Tue Aug 29 13:01:58 2017 -0700 EB/CNS: don't have to go through all the eb stuff if interior plus one ghost cell are all regular Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 commit 29989ea3b6865ca7031def4e364ce081620b2ad2 Merge: 3a35a3d6c 69e7b416e Author: Klaus Weide Date: Tue Aug 29 14:54:42 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 69e7b416e377d6a63815d15df7b46dd2d885857e Author: Weiqun Zhang Date: Tue Aug 29 12:20:04 2017 -0700 use fortran for cell type counting Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBCellFlag_F.H Src/Base/AMReX_ebcellflag_mod.F90 Src/Base/Make.package commit cb6c06805d2a4ca8b4bc5b75e38a6497fe2795d9 Merge: 574196ddd fe0a0c67f Author: Weiqun Zhang Date: Tue Aug 29 11:14:15 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 574196dddd5fa593920666d015de1c165d0a6d19 Author: Weiqun Zhang Date: Tue Aug 29 11:13:53 2017 -0700 EB/CNS: disable initial load balance Tutorials/EB/CNS/Source/CNS.cpp commit fe0a0c67f24d863cd5075a2bb304330a3eda142b Merge: 373997795 917c3b458 Author: Andrew Myers Date: Tue Aug 29 10:10:23 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 37399779517e3862beb4ce6432599f18d30c0818 Author: Andrew Myers Date: Tue Aug 29 10:10:06 2017 -0700 make sure the Geometry offset is consistent with the RealBox. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 612add1f966ae81347e40e254b328869c9d8d963 Author: Weiqun Zhang Date: Tue Aug 29 10:04:29 2017 -0700 EB/CNS: dynamic load balance Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 Tutorials/EB/CNS/Source/main.cpp commit 3a35a3d6c1cd04084ba18bb4658177b6f8bb2d57 Merge: fec330191 917c3b458 Author: Klaus Weide Date: Tue Aug 29 12:01:28 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7dded4bf9ed3f5eb666a2a90e851d9c8867cc569 Author: Weiqun Zhang Date: Tue Aug 29 08:41:15 2017 -0700 EB utility function for setting single valued cells Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_EBMultiFabUtil_F.H Src/Base/AMReX_EBMultiFabUtil_nd.F90 commit 917c3b458811da2c8a38a412aded94bbd9b2f88f Author: Tan Nguyen Date: Mon Aug 28 17:53:40 2017 -0700 support local load balancing Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/MPI_Generic/README Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C commit 7d3f2ef3ffa5a4bac336f4e8b47f83f2c23f5e96 Author: Weiqun Zhang Date: Mon Aug 28 16:45:51 2017 -0700 EB/CNS: load balance Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/main.cpp commit d02c9ad6e48c64882efd1494c52fff9a76cfb5f2 Author: Weiqun Zhang Date: Mon Aug 28 16:45:14 2017 -0700 new EB_set_covered function Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp commit e12a3cbcbc7c15c07bceb679cd9745d160784c69 Author: Weiqun Zhang Date: Mon Aug 28 16:44:46 2017 -0700 add a new function to Amr for load balance Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp commit 3ea409f0d62733cd140a3d9af120da3dcf67903e Author: Weiqun Zhang Date: Mon Aug 28 15:47:51 2017 -0700 EB/CNS: fix a bug Tutorials/EB/CNS/Source/CNS_advance.cpp commit 5cb7214b367679cc17ffad92d2cb4b8a4a5148e8 Author: Weiqun Zhang Date: Mon Aug 28 15:04:36 2017 -0700 EB/CNS: set inflow velocity correctly Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90 Tutorials/EB/CNS/Exec/Combustor/cns_prob.F90 Tutorials/EB/CNS/Exec/Combustor/inputs commit a961c0b7d2f3b53b6672a4f29dc186aea5f29519 Author: Weiqun Zhang Date: Mon Aug 28 13:34:07 2017 -0700 EB/CNS: Combustor test Tutorials/EB/CNS/Exec/Combustor/GNUmakefile Tutorials/EB/CNS/Exec/Combustor/Make.package Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90 Tutorials/EB/CNS/Exec/Combustor/cns_prob.F90 Tutorials/EB/CNS/Exec/Combustor/inputs commit 368ed03c06bedbab61c8ac74bd981bf29315fda7 Author: Weiqun Zhang Date: Mon Aug 28 12:20:16 2017 -0700 fix up cells that have volume fraction and apertures be exactly one but with a covered neighbor cell touching the corner Src/Base/AMReX_ebcellflag_mod.F90 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 commit 5ddc4bbfb6b0cecc503e40924d18d4ac382eacd9 Author: Weiqun Zhang Date: Mon Aug 28 10:25:54 2017 -0700 EB/CNS: more debug info Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_hyp_wall.F90 commit 3c324806776edb894e92d0cb54dca5dd589a36ff Author: Weiqun Zhang Date: Mon Aug 28 09:57:33 2017 -0700 EB/CNS: save volume fraction in plotfile Tutorials/EB/CNS/Source/CNS_io.cpp commit 8c50b33a88319a0a2eb47970b82bd85beb3bf3f9 Author: Weiqun Zhang Date: Sun Aug 27 21:13:44 2017 -0700 EBFluxFAB is alos thread safe Src/GeometryShop/AMReX_EBFluxFAB.H commit b206c56c4ec99cf174b582d2d76cf4274b5ba5e1 Author: Weiqun Zhang Date: Sun Aug 27 21:12:14 2017 -0700 update FillBoundary for thread safety too Src/Base/AMReX_FabArray.H commit b166a1cbe961773d8116e9e774f297cb90a4302c Author: Weiqun Zhang Date: Sun Aug 27 21:04:58 2017 -0700 some GeometryShop classes are thread safe Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H commit 7f5afb59032c1f5fd973a5a4291f6bb3c9077a40 Author: Weiqun Zhang Date: Sun Aug 27 20:50:18 2017 -0700 fix AmrLevel and StateData Restart Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit bd90c4a4e2fba14804a013b130f8a83491d2fc99 Author: Weiqun Zhang Date: Sun Aug 27 16:43:18 2017 -0700 add BaseFab::isCopyOMPSafe() function so that ParallelCopy can turn off omp for unsafe FABs; add this to all EB Fabs. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBGraph.H commit 341272dadea88178b6168a0a88c8911ecaa207a0 Author: Weiqun Zhang Date: Sun Aug 27 15:02:31 2017 -0700 EB/CNS: fix a bug Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit c3219de40804d8fb5b6e2d6fcb5cc38060d2f5ba Merge: f5ffec25b d0c919e89 Author: dtgraves Date: Sun Aug 27 14:00:49 2017 -0700 Merge pull request #103 from AMReX-Codes/dtg_branch merging some small bug fixes into devlopment for weiqun commit d0c919e89d1572d4fef448d38e1bd27a07f5ac3c Author: dtgraves Date: Sun Aug 27 13:58:46 2017 -0700 using the MFIter(FabArray) constructor was breaking in EBISLevel because it seems to magically invoke OMP stuff. I switched it to MFIter(BoxArray, DM) and now it seems to work Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/ramp/GNUmakefile commit 5df6451bc81045516dd8e158e2dd56caf7efead5 Merge: 864329306 f5ffec25b Author: dtgraves Date: Sun Aug 27 13:39:38 2017 -0700 Merge branch 'development' into dtg_branch commit f5ffec25b5cd787edf4d84c44f18e8179b627a9a Merge: 2fb3140e4 71b81bb8a Author: Weiqun Zhang Date: Sun Aug 27 13:34:53 2017 -0700 Merge branch 'development' into weiqun/eb commit 8643293065b4d4c885acecbf5bf745ecc02e28ef Author: dtgraves Date: Sun Aug 27 13:34:22 2017 -0700 fixed some logic in GeometryShop Src/GeometryShop/AMReX_GeometryShop.cpp commit 2fb3140e4c9da35adb91c52c5cfea1b6712aea6a Author: Weiqun Zhang Date: Sun Aug 27 13:08:52 2017 -0700 add -lubsan for llvm when FSANITIZER is TRUE Tools/GNUMake/comps/llvm.mak commit 2823e3691e41951651fdc91fc8b60de3a9ad736c Author: Weiqun Zhang Date: Sun Aug 27 13:04:17 2017 -0700 remove an unnecessary move Src/Base/AMReX_BoxList.cpp commit 114c88a7468ad45e8a0b690b53ab465529ac133d Author: Weiqun Zhang Date: Sun Aug 27 12:36:06 2017 -0700 clear some warnings Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_ebinterp_3d.F90 Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_iMultiFab.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_IrregFABFactory.H Tutorials/EB/CNS/Source/hydro/analriem3d.F90 commit 82762138a7f1c8230489b974bf49ed115f35d205 Author: Weiqun Zhang Date: Sun Aug 27 12:18:02 2017 -0700 EB/CNS: add some override Tutorials/EB/CNS/Source/CNS.H commit 929b13741b874a82393d7b3f076edebe91e58511 Author: Weiqun Zhang Date: Sun Aug 27 11:49:17 2017 -0700 remove unused variable Src/Base/AMReX_EBMultiFabUtil.cpp commit 71b81bb8a3b9b4461132149959878c876b2597a3 Author: Michael Zingale Date: Sun Aug 27 14:43:35 2017 -0400 remove unused argument that Cray complains about Src/LinearSolvers/F_MG/mg.f90 commit d78ec64d669f70586db3f5e171fea64944ace9db Author: Weiqun Zhang Date: Sun Aug 27 11:27:45 2017 -0700 EB/CNS: LAZY := TRUE Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Source/CNS.cpp commit ddc6ac16a16c1fec3dd47d29a56569da5b80393a Author: Weiqun Zhang Date: Sun Aug 27 11:17:09 2017 -0700 EB/CNS: omp Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit 7638584b3c031af8a2dff291b578cad0ea3cc75b Author: Weiqun Zhang Date: Sun Aug 27 11:01:58 2017 -0700 EB/CNS: add profiler Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Tutorials/EB/CNS/Exec/Pulse/GNUmakefile Tutorials/EB/CNS/Exec/ShockRef/GNUmakefile Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/main.cpp commit 302fa7007c8f0bca7c20c348c1e0c4d7cbfea2eb Merge: 0b7562d0b 1a0d27705 Author: Andrew Myers Date: Sat Aug 26 20:07:43 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0b7562d0b2feee6100b459326afd03eaa76ca687 Author: Andrew Myers Date: Sat Aug 26 20:07:23 2017 -0700 don't let the kdtree load balancer make empty boxes Src/Particle/AMReX_KDTree_3d.F90 Src/Particle/AMReX_LoadBalanceKD.cpp commit d3c8d6c8322c5785bc443a7c8870bc071925bb40 Author: Weiqun Zhang Date: Sat Aug 26 15:20:10 2017 -0700 EB/CNS: minor Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit 5bbb4c5562c131b521fc39a4db5a640454f3319c Author: Weiqun Zhang Date: Sat Aug 26 14:45:07 2017 -0700 EB/CNS: fix bug Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit 985babb32991032f9bea9ded53d1a2438a269172 Author: Weiqun Zhang Date: Sat Aug 26 11:19:03 2017 -0700 EB/CNS: cleanup Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 Tutorials/EB/CNS/Source/fortran/CNS_derive.F90 Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit 003eb98fbb297e7d439177959319997aed9ff5d1 Author: Weiqun Zhang Date: Sat Aug 26 07:25:56 2017 -0700 EB/CNS: clean up Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/diffusion/diff_coef_mod.F90 Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 Tutorials/EB/CNS/Source/fortran/CNS_physics.F90 commit ff80e01a1591af10e97244ada1f6eec8c7f0750d Author: Weiqun Zhang Date: Sat Aug 26 07:08:37 2017 -0700 CNS/EB: file reorganization Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/fortran/CNS_derive.F90 Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 Tutorials/EB/CNS/Source/fortran/CNS_physics.F90 Tutorials/EB/CNS/Source/fortran/Make.package Tutorials/EB/CNS/Source/fortran/bc_fill_nd.F90 commit 109a07154bc704e9b4aa3d752561d3cfef89de8d Author: Weiqun Zhang Date: Sat Aug 26 07:02:27 2017 -0700 EB/CNS: fix a bug in parameter initialization for constant viscosity Tutorials/EB/CNS/Source/CNS_physics.F90 commit f3c9760d3f6973bb866fae80ed1bc978e532fcc4 Merge: b3ed17f7e 1a0d27705 Author: Weiqun Zhang Date: Sat Aug 26 07:01:11 2017 -0700 Merge branch 'development' into weiqun/eb commit 7bb8ed6b012fd16ca77f9cefcec38dfec5f7f543 Author: dtgraves Date: Sat Aug 26 06:31:13 2017 -0700 commented out debugging statement Src/GeometryShop/AMReX_EBISLevel.cpp commit 1a0d2770517e02ac7817155aa7dae0e3fb7b18fb Merge: 3c43ff6ae 4f2786224 Author: dtgraves Date: Sat Aug 26 06:14:36 2017 -0700 Merge pull request #102 from AMReX-Codes/dtg_branch fixed another bug Weiqun identified. EBGraph linearization needs a l… commit 4f27862240847c95f1bcf66f90245449e7c15d16 Author: dtgraves Date: Sat Aug 26 06:08:05 2017 -0700 fixed another bug Weiqun identified. EBGraph linearization needs a little work but I will commit this first because this version of linearization works. Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit b3ed17f7e586a42fb775e51788c9aeb3874ebcf9 Author: Weiqun Zhang Date: Fri Aug 25 18:43:54 2017 -0700 EB/CNS: fix index bugs Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit 7ccda851e493cf9219209c3d935de290a68d3557 Author: Weiqun Zhang Date: Fri Aug 25 17:09:41 2017 -0700 EB/CNS: add a parameter for using total energy for weighting Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_f.F90 commit 7732f125894911449f9c26bb0bd8ac4692400e5a Author: Weiqun Zhang Date: Fri Aug 25 17:03:51 2017 -0700 EB/CNS: use noslipwall for shock reflection test Tutorials/EB/CNS/Exec/ShockRef/inputs commit 3c43ff6ae2893f8bbde9d51446479d534f5bbaf8 Merge: 2eeaef73e fbec03000 Author: Andrew Myers Date: Fri Aug 25 16:31:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2eeaef73ea2aebf89b89a8436b955e3dbf6a5c96 Author: Andrew Myers Date: Fri Aug 25 16:31:04 2017 -0700 we want to compile these functions even without _OPENMP. Src/Particle/AMReX_OMPDepositionHelper_nd.F90 Src/Particle/CMakeLists.txt Src/Particle/Make.package commit fbec0300081ac628c0009f2fd426c0f3b42430c8 Author: Weiqun Zhang Date: Fri Aug 25 16:02:55 2017 -0700 modify GeomtryShop test Tests/GeometryShop/ramp/main.cpp commit 172c25bff6baabae20eb85c70a0f924aaf22d78d Merge: d090d7b7d 571231849 Author: Weiqun Zhang Date: Fri Aug 25 15:48:25 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit 9db5e45e092d9d3b618c6a68efefbf95b4b7a959 Merge: cfe29f843 d6cc2763f Author: WeiqunZhang Date: Fri Aug 25 15:40:37 2017 -0700 Merge pull request #100 from emotheau/convtools New Convergence tool to compute the composite error. Was made with Bo… commit d6cc2763f51e4599bddd643e8c685a49b880fdf0 Author: Emmanuel Motheau Date: Fri Aug 25 15:29:11 2017 -0700 New Convergence tool to compute the composite error. Was made with BoxLib, we have to convert it to amrex Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/GNUmakefile commit 5712318497fa841e83e4889be751f4da9669f035 Merge: f42e5cd9c cfe29f843 Author: Weiqun Zhang Date: Fri Aug 25 15:23:52 2017 -0700 Merge branch 'development' into eb_development Conflicts: Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit d090d7b7d64afbe94d9a7d72b9ee3c6c96d4ef10 Author: Weiqun Zhang Date: Fri Aug 25 15:03:31 2017 -0700 EB/CNS: minor Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit cfe29f843c23f6c12643cd54f76dea9d4c9bd8e2 Merge: fbdd83e68 1ce16162e Author: dtgraves Date: Fri Aug 25 14:54:05 2017 -0700 Merge pull request #99 from AMReX-Codes/dtg_branch moving bug fixes to development commit 1ce16162e38515e2b7e5b0c061374b0858258d0a Author: dtgraves Date: Fri Aug 25 14:52:33 2017 -0700 fixed parallel bug identified by Weiqun Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/ramp/main.cpp commit 7d364ac678f581b26bd7258d98dde305ac72356c Author: Weiqun Zhang Date: Fri Aug 25 14:30:31 2017 -0700 EB/CNS: add contiguous Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit b29260f49ac08168e185ba756c6354a310b44e68 Author: Weiqun Zhang Date: Fri Aug 25 13:56:32 2017 -0700 EB/CNS: print mementa and energy too Tutorials/EB/CNS/Source/CNS.cpp commit 7238c7533e1d24227005ff7ae40963c6f707f97f Author: Weiqun Zhang Date: Fri Aug 25 13:36:28 2017 -0700 EB/CNS: parameter to turn off diffusion Tutorials/EB/CNS/Source/CNS_physics.F90 commit fbdd83e683285d8a6669b1313513905862a4cfb4 Merge: 1eb820739 b3c35096f Author: WeiqunZhang Date: Fri Aug 25 13:26:46 2017 -0700 Merge pull request #97 from kweide/development give the octree iterator a clear() method commit 4a5cf90288237015979d996f2d301ae6ae5002ee Author: Weiqun Zhang Date: Fri Aug 25 13:11:15 2017 -0700 EB/CNS: add const viscosity Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/diffusion/diff_coef_mod.F90 commit a47243cb88cd5178941edee9016d44de9ea3673c Author: Weiqun Zhang Date: Fri Aug 25 12:14:48 2017 -0700 EB/CNS: need one more ghost cell Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit 1eb82073950ca122642fd96f12935577c284020b Merge: 014103e8e ff899c593 Author: Tan Nguyen Date: Fri Aug 25 11:46:17 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 014103e8eb84e26103b8f6729ccc713c9db2f43f Author: Tan Nguyen Date: Fri Aug 25 11:45:43 2017 -0700 MPI runtime implementation Src/AmrTask/rts_impls/Utils/dl_malloc.c Src/AmrTask/rts_impls/Utils/dl_malloc.h Src/AmrTask/rts_impls/Utils/sysInfo.C Src/AmrTask/rts_impls/Utils/sysInfo.H commit 4eb75f0224a362cc4e733d431241b60883a4803a Author: Tan Nguyen Date: Fri Aug 25 11:45:06 2017 -0700 MPI runtime implementation Src/AmrTask/rts_impls/MPI_Generic/Makefile Src/AmrTask/rts_impls/MPI_Generic/README Src/AmrTask/rts_impls/MPI_Generic/mylock.h Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/rts_impls/MPI_Generic/rts_graphimpl.H Src/AmrTask/rts_impls/MPI_Generic/rts_taskimpl.H commit ff899c5938fc3b685c3937c727cbbe63c2694bbd Merge: 478d0c8b3 c089232c4 Author: Andrew Myers Date: Fri Aug 25 11:33:01 2017 -0700 Merge pull request #98 from MaxThevenet/compile_on_theta Add possibility to compile on Theta ALCF commit c089232c400908260db5a243f53da8e39c576887 Author: Maxence Thevenet Date: Fri Aug 25 11:19:25 2017 -0700 Add possibility to compile on Theta ALCF Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.alcf commit b3c35096ffbf35fda8bda4dcc23f4f0b77227acb Author: Klaus Weide Date: Fri Aug 25 13:18:42 2017 -0500 give the mfiter (Fortran) iterator a fabbox() method (tested only compilation and linking so far) Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit a9d92656f533591c5ab65259a77c17f639bb0609 Author: Weiqun Zhang Date: Fri Aug 25 11:11:49 2017 -0700 EB/CNS: first pass of diffusion wall flux Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit c9f236cb44037840abbbfbdb6f5f3a75d7af9939 Merge: 3ad2a9bc9 478d0c8b3 Author: Klaus Weide Date: Fri Aug 25 13:02:25 2017 -0500 Merge branch 'development' into kw-development commit 3ad2a9bc953c92c54ddd5429f7506afc2abe94cd Author: Klaus Weide Date: Fri Aug 25 09:05:10 2017 -0500 give the octree iterator a clear() method Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 478d0c8b3547f24ba7c0d1b160c7eed1ee6ea284 Author: Tan Nguyen Date: Fri Aug 25 04:24:05 2017 -0700 add a multithreaded runtime implementation Src/AmrTask/Makefile Src/AmrTask/arch.common Src/AmrTask/arch/arch.mpi.generic Src/AmrTask/arch/arch.serial Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_AbstractTask.cpp Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/Serial/Makefile Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/todolist Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C Src/AmrTask/tutorials/UnitTests/Makefile commit e93949680c042525cd59816f64342883f99487f9 Author: Weiqun Zhang Date: Thu Aug 24 14:29:58 2017 -0700 EB/CNS: fake 2D Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/CNS_f.F90 commit 1ef1a7170b95b4aec4edb3b4e2717a03fc08c848 Author: Weiqun Zhang Date: Thu Aug 24 14:21:47 2017 -0700 EB/CNS: use current density for redistribution Tutorials/EB/CNS/Source/CNS_divop.F90 commit 9acb920316c89b6c6b27b9489018f54a5232ab00 Author: Weiqun Zhang Date: Thu Aug 24 13:47:55 2017 -0700 EB/CNS: add a parameter to PLM Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit 869961a7a620e784297881c833508cd5af56090e Author: Weiqun Zhang Date: Thu Aug 24 13:26:26 2017 -0700 EB/CNS: pass bndry centrold into Fortran Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit b99c61c80d15c3496946d4d7998803987b34f133 Author: dtgraves Date: Thu Aug 24 13:16:40 2017 -0700 fixed the bug that was breaking MPI in this branch Src/Base/AMReX_FabArrayBase.cpp commit f42e5cd9cd7b88b991b455bef51a260e1f40ebbd Author: dtgraves Date: Thu Aug 24 12:54:21 2017 -0700 removed constant declaration from argument Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 2c206d1a1899769f72bc4a382ad402cebe2144d8 Author: dtgraves Date: Thu Aug 24 12:49:40 2017 -0700 simplified geometry generation stuff somewhat Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit 46dfbbc71845001f2b895d535cb3b0fc34edd8a9 Author: Andrew Myers Date: Thu Aug 24 10:57:45 2017 -0700 remove unused variable. Src/Base/AMReX_FabArray.H commit bb026eebbc20e91ca54e9dc54d6ae137bb490409 Author: Andrew Myers Date: Thu Aug 24 10:12:59 2017 -0700 take care of unused variable warning in parallel copy Src/Base/AMReX_FabArray.H commit 23e756d99d29deb6a1ca57d928d00a6ddf038063 Author: dtgraves Date: Thu Aug 24 09:41:11 2017 -0700 took out const declaration in FabArrayBase to fix USE_MPI=TRUE compile Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 82561bac434c611195f8be303e6016d35f38ab84 Author: dtgraves Date: Thu Aug 24 08:45:58 2017 -0700 merging with branch eb_development Tests/EBAMRTools/regression/GNUmakefile commit b8e14d9effe9652aa8b1cd7b94950c05e054adb7 Author: Weiqun Zhang Date: Wed Aug 23 18:00:37 2017 -0700 EB/CNS: minor memory leak Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit baecd41317593ffdc6e75605fb66859301a846cb Author: Weiqun Zhang Date: Wed Aug 23 17:33:41 2017 -0700 EB/CNS: prepare for diffusion wall flux Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit 315f305f738fddc85e00048f4391946d993756ac Author: Weiqun Zhang Date: Wed Aug 23 17:01:38 2017 -0700 EB/CNS: start diffusion wall flux module Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/diffusion/Make.package Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 Tutorials/EB/CNS/Source/hydro/Make.package commit c604114190b2f7100555e988d3291efc7427fb63 Author: Weiqun Zhang Date: Wed Aug 23 16:40:49 2017 -0700 EB/CNS: fix EB diffusion flux Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 commit 09a2cdf685ac6214fa83ed33bb4f77b107954bda Author: Andrew Myers Date: Wed Aug 23 16:12:38 2017 -0700 need to check for the __powerpc__ macro as well Src/Base/AMReX_FPC.cpp commit aa60aaf80f29d024987ce084f9c87a5fdef61f7d Author: Andrew Myers Date: Wed Aug 23 13:00:58 2017 -0700 a few more signed/unsigned Src/Base/AMReX_TinyProfiler.cpp commit 8c3d4fb9368db403fa08e3992700808c39ec23e7 Author: Andrew Myers Date: Wed Aug 23 12:58:26 2017 -0700 fix unused variable warning. Src/Particle/AMReX_ParticleContainerI.H commit ffce1ba11af2a89df7a258156c35bba789fe137b Author: Andrew Myers Date: Wed Aug 23 12:53:38 2017 -0700 switch from C-style arrays to std::arrays to avoid zero-length array warning. Src/Particle/AMReX_Particles.H commit 6bbb7edc6ecfcc39136883d3e85a70ccd9726595 Author: Andrew Myers Date: Wed Aug 23 10:21:42 2017 -0700 fix signed/unsigned comparison. Src/Base/AMReX_Array.H commit fbddf3e352f36e3ad985bc1e30dd67f4fc6fd497 Merge: bd561295f 616b5de7d Author: kngott Date: Tue Aug 22 22:40:38 2017 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit bd561295f1f2d50fe1c09d1a5b90e9f9dd5f0715 Author: kngott Date: Tue Aug 22 22:40:34 2017 -0700 MoveAllFabs fix and updated test OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp Src/Base/AMReX_FabArray.H commit 616b5de7d2376e1b98a24e347b6e3ffc4560e419 Author: Weiqun Zhang Date: Tue Aug 22 22:02:46 2017 -0700 refactor the new amrex_boxarray_build for FLASH Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 commit 46a38a05dc37a04989a915ab8e954d027ce60d8e Merge: c063a1355 92c19a1e7 Author: WeiqunZhang Date: Tue Aug 22 21:37:50 2017 -0700 Merge pull request #93 from kweide/development Add specific build routines for constructing boxarrays and distromaps from user-provided lists in Fortran commit cf038b5098abe20a92c4f2de66e757715d8bb036 Author: Weiqun Zhang Date: Tue Aug 22 18:08:28 2017 -0700 EB/CNS: EB diffusion flux Src/Base/AMReX_ebcellflag_mod.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 commit a59ce2eaf23a3af46db550569069d337405706ec Author: Weiqun Zhang Date: Tue Aug 22 16:49:13 2017 -0700 EB/CNS: split hydro and diffsion fluxes Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit c063a1355a9473a961b469957b12c2ca04c58ca5 Merge: 69bc0a7ed 5ecff6d27 Author: WeiqunZhang Date: Tue Aug 22 16:18:55 2017 -0700 Merge pull request #95 from AMReX-Codes/perf-docs update Documentation: added IPM section to Profiling.tex commit 5ecff6d27d0d9ac35a0a05ba7b3e3098dbf3edb8 Merge: b9e7e42d2 00e9dd08d Author: Cy Chan Date: Tue Aug 22 16:15:22 2017 -0700 Merge branch 'development' into perf-docs commit b9e7e42d28d5b8ad67a66129e761c4df9a35d718 Author: Cy Chan Date: Tue Aug 22 16:07:27 2017 -0700 update Documentation added IPM section to Profiling.tex Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Profiling/Profiling.tex Docs/AMReXUsersGuide/Profiling/figs/commtopo.png Docs/AMReXUsersGuide/Profiling/figs/mpi.png Docs/AMReXUsersGuide/Profiling/figs/msgsizes.png Docs/AMReXUsersGuide/Profiling/figs/papi.png Docs/AMReXUsersGuide/Profiling/figs/summary.png Docs/AMReXUsersGuide/Profiling/figs/timings.png commit 3e40ca33e6319cf79c4369f2ee1bd0ea2184c9a8 Author: Weiqun Zhang Date: Tue Aug 22 15:18:08 2017 -0700 EB/CNS: regular diffusion terms Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 commit fec330191747a3c4c86a301b19ab0bd6c20f21a4 Merge: ed330ba6a 69bc0a7ed Author: Klaus Weide Date: Tue Aug 22 15:09:32 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 69bc0a7ed576f247b7bdf4be9ffaee508b089bea Author: vince Date: Tue Aug 22 11:37:48 2017 -0700 add move all fabs test. OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp commit 2688726e0f3e6bdd2bee638445b16438449366b8 Author: Weiqun Zhang Date: Tue Aug 22 11:26:44 2017 -0700 EB/CNS: use future mass for weighting Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit dc18f279ffb7222c2575524cd59a585ad0ad3ce0 Author: Weiqun Zhang Date: Tue Aug 22 10:58:16 2017 -0700 EB/CNS: reorganization Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/diffusion/Make.package Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/diff_coef_mod.F90 Tutorials/EB/CNS/Source/hydro/Make.package commit 180f7cf217df91cf4bb938a7e82c0522d169ec77 Author: Weiqun Zhang Date: Mon Aug 21 14:45:30 2017 -0700 EB/CNS: use air as initial condition Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/Pulse/inputs commit 82cadae4bdc01de79b2219fd6d44eee7cc563cfd Author: Weiqun Zhang Date: Mon Aug 21 14:23:18 2017 -0700 EB/CNS: add a module computing viscosity and thermal conductivity Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/cns_diff_mod.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_diff_mod.F90 Tutorials/EB/CNS/Source/hydro/diff_coef_mod.F90 commit 7074ca4192429d0ae465c22b53862dfcd152b71f Merge: a0491c979 bbe4d0d0d Author: Weiqun Zhang Date: Mon Aug 21 13:53:36 2017 -0700 Merge branch 'weiqun/eb' into eb_development commit 00e9dd08de14d59a6444c30eb128b243d651beb4 Merge: f56a800da cbb7c8b8e Author: Andrew Myers Date: Mon Aug 21 13:47:44 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f56a800da65b8d14b181b9b6ceddfc8457bf7fb7 Author: Andrew Myers Date: Mon Aug 21 13:47:26 2017 -0700 remove some debugging junk I checked in by mistake. Src/Particle/AMReX_ParticleInit.H commit bbe4d0d0d55d514398b661aee9693295a625a68d Author: Weiqun Zhang Date: Mon Aug 21 13:43:11 2017 -0700 EB/CNS: fix a bug Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 89ecb4e0c358c944af0207c02d801c7b5d7287cd Author: Weiqun Zhang Date: Mon Aug 21 10:34:09 2017 -0700 EB/CNS: make sure flux outside the domain is not used Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit ed330ba6ad24b7cd49059667df8510b5fec4c1d9 Merge: 8910997e9 cbb7c8b8e Author: Klaus Weide Date: Mon Aug 21 08:07:02 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cbb7c8b8ea23d0757d8ffe3dbd89988108d7769f Author: Weiqun Zhang Date: Sat Aug 19 13:05:59 2017 -0700 add assertion making sure BoxArray::set is not called on non-trivial objects Src/Base/AMReX_BoxArray.cpp commit a139b16a12d52272e5ad2ae8611f79d0f264c06e Merge: 81038c6ba 16b829705 Author: WeiqunZhang Date: Fri Aug 18 16:04:19 2017 -0700 Merge pull request #91 from AMReX-Codes/compiler_warnings Compiler warnings commit 16b82970563ccd793de0a6ec96f5c6655b56627e Author: Andrew Myers Date: Fri Aug 18 16:00:42 2017 -0700 give this a more descriptive name Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_Utility.H commit a0491c979bf3785842b8c543d0834e189c6dc880 Author: Weiqun Zhang Date: Fri Aug 18 15:05:20 2017 -0700 a GeometryShop test Tests/GeometryShop/ramp/GNUmakefile Tests/GeometryShop/ramp/Make.package Tests/GeometryShop/ramp/inputs Tests/GeometryShop/ramp/main.cpp commit 19c826e9470276d0eb57c74f0c0173225f84027e Author: Andrew Myers Date: Fri Aug 18 15:43:40 2017 -0700 remove some vlas Src/Amr/AMReX_Amr.cpp commit 007cca18dfdf51b86f21e0b4b70a234a56471fe7 Author: Andrew Myers Date: Fri Aug 18 15:28:15 2017 -0700 some more cleanup Src/Base/AMReX.cpp Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BC_TYPES.H Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_Particles_F.H commit 309b21221b338eb4109d6303da5b420ab81059f5 Author: Andrew Myers Date: Fri Aug 18 15:13:00 2017 -0700 initialize this variable Src/Base/AMReX_BaseFab.cpp commit 79f64a84709cd01e54f39b877d9bb822c11738a9 Author: Andrew Myers Date: Fri Aug 18 15:08:25 2017 -0700 switch this back to no by default. Tools/GNUMake/comps/gnu.mak commit 6bc9dd95583c42491ec8968ab1c7915af834a981 Author: Andrew Myers Date: Fri Aug 18 15:06:40 2017 -0700 fix bug in llvm.mak Tools/GNUMake/comps/llvm.mak commit 824d9432795c81ba7d3c141e84508d6b53ad0218 Author: Andrew Myers Date: Fri Aug 18 14:52:56 2017 -0700 turn on -Wsign-compare in Debug mode. Tools/GNUMake/comps/gnu.mak commit 9dcc8eb0afe0813af6278de5b5e906311e96aa4c Author: Andrew Myers Date: Fri Aug 18 14:46:54 2017 -0700 yet another signed/unsigned Src/Amr/AMReX_StateDescriptor.cpp commit baa4aa552c3df7101f8bd0e656f1fd72bbe5f917 Author: Andrew Myers Date: Fri Aug 18 14:38:26 2017 -0700 a few more signed / unsigned Src/Amr/AMReX_AmrLevel.cpp commit 92c19a1e76a8518045c2aa221f9db27a2ae71349 Author: Klaus Weide Date: Fri Aug 18 16:00:41 2017 -0500 Add specific build routines for constructing boxarrays and distromaps from explicit Fortran data Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_mod.F90 commit dab6cc101a49c0275a6850213086a22a9b57f5f4 Author: Andrew Myers Date: Fri Aug 18 13:53:00 2017 -0700 another signed/unsigned Src/Base/AMReX_DistributionMapping.cpp commit 2672a734580dc1dd99aebd69eb4f64217af24e7b Author: Andrew Myers Date: Fri Aug 18 13:51:21 2017 -0700 ignore this unused variable. Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_Utility.H commit e750e60ac076b7c1c58d534fc2c3a995f2ad59f6 Author: Andrew Myers Date: Fri Aug 18 13:37:22 2017 -0700 fix some signed / unsigned comparisons. Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_parmparse_fi.cpp commit bfbf52d2a1f914a407bce1b48fb646ce5898afd8 Merge: b8a701a3d 1ab5dd248 Author: Weiqun Zhang Date: Fri Aug 18 13:18:33 2017 -0700 Merge branch 'dtg_branch' into weiqun/eb commit b8a701a3d524fdedd495eb82232bda6b88c9af8c Merge: 3c5c42e57 81038c6ba Author: Weiqun Zhang Date: Fri Aug 18 13:18:19 2017 -0700 Merge branch 'development' into weiqun/eb commit 3c5c42e5716704da8c161826872a60aa47e5cef5 Author: Weiqun Zhang Date: Fri Aug 18 12:49:14 2017 -0700 we may not even have a probin file Src/Amr/AMReX_Amr.cpp commit 9a2aaf961397d5bcd9fc72dd4bb12e28b053ecb8 Author: Weiqun Zhang Date: Fri Aug 18 12:36:59 2017 -0700 EB/CNS: mod inputs Tutorials/EB/CNS/Exec/ShockRef/cns_prob.F90 Tutorials/EB/CNS/Exec/ShockRef/inputs commit 17029dee6e74c1840417b015188fecf23e31e892 Author: Michele Rosso Date: Fri Aug 18 11:58:29 2017 -0700 CMake: update config file Tools/CMake/AMReXConfig.cmake.in commit a2689c3b90ba7236decb612793f27b39c67bcf5a Author: Weiqun Zhang Date: Fri Aug 18 10:51:20 2017 -0700 EB/CNS: using mass weighting instead of volume weighting Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit f6b2f90dea5c6a47bcdde7a489a58072a61aced7 Author: Weiqun Zhang Date: Fri Aug 18 10:49:17 2017 -0700 EB/CNS: some parmparse parameters for the shock reflection test Tutorials/EB/CNS/Exec/ShockRef/cns_prob.F90 commit 81038c6ba1b554662c11d4e4c6b18ff56867b23a Author: Andrew Myers Date: Fri Aug 18 10:07:18 2017 -0700 Fix offset bug when initializing particle integer data. Src/Particle/AMReX_ParticleInit.H commit 7b426c29bec02ebbae8f193cfc7303b3bc34890d Author: Andrew Myers Date: Fri Aug 18 10:04:29 2017 -0700 Fix copy/paste issue in comment. Src/Particle/AMReX_ParticleInit.H commit bd2045e20bf9c6e6924c65488ba5b6b41603cf72 Author: Andrew Myers Date: Fri Aug 18 10:02:25 2017 -0700 Real -> amrex::Real Src/Particle/AMReX_LoadBalanceKD.H commit bb497048504639db8bc9b93b6215e78be5fbc045 Author: Weiqun Zhang Date: Fri Aug 18 09:23:45 2017 -0700 EB/CNS: fix a bug in 2-shock riemann solver; add HLL; floor density and pressure Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/analriem3d.F90 commit 8910997e93b0615893409f8535f36af862d79fa7 Merge: bf061aef5 8457d4770 Author: Klaus Weide Date: Fri Aug 18 07:36:41 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0c5f20049fa650711fe78403a1a017f6be2fef4f Author: Max Katz Date: Fri Aug 18 01:35:09 2017 -0700 Add a missing device ifdef Src/Base/AMReX_BaseFab.H commit 16dd1d1f5d646cf8db32f1743530163e15cce02b Author: Max Katz Date: Fri Aug 18 01:54:12 2017 -0400 Fix the summitdev library typo Tools/GNUMake/comps/pgi.mak commit 822c257b896a4e74c939e1854251d0903822518d Author: Michele Rosso Date: Thu Aug 17 17:29:05 2017 -0700 Doc: fix typo Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit 5b445a60018eebdc087512a61005b0c08518c0fa Author: Michele Rosso Date: Thu Aug 17 17:27:36 2017 -0700 CMake: update exports Tools/CMake/AMReXConfig.cmake.in commit 1455939bd55d710ca16e8b13a665fc3a8d32f018 Author: Michele Rosso Date: Thu Aug 17 17:17:28 2017 -0700 CMake: update doc Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Defines.cmake commit 93280c1536824becc995230a101c159306623a0f Author: Michele Rosso Date: Thu Aug 17 16:57:20 2017 -0700 CMake: update * Add support for ProfParser * Re-factor souce files lists * Change some config args. Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/Extern/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_F/CMakeLists.txt Tutorials/Amr/Advection_octree_F/CMakeLists.txt commit 1ab5dd24815edfb49ecb5216025ad3a04d9975e0 Author: dtgraves Date: Thu Aug 17 16:29:05 2017 -0700 yet another attempt to silence valgrind Src/GeometryShop/AMReX_EBISBox.cpp commit 8457d4770517bee7461e4a8d1fce01693aae60b7 Merge: 756c8e7ea 81ff56778 Author: Andrew Myers Date: Thu Aug 17 16:26:57 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ceea83872e9f2d4e9a76a9d0f14dceb71350c51d Author: Weiqun Zhang Date: Thu Aug 17 15:56:12 2017 -0700 EB/CNS: minor Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 commit 90c0c0afcbee04c53b2c297a68a67ea776eb92ac Author: Weiqun Zhang Date: Thu Aug 17 15:21:30 2017 -0700 EB/CNS: make sure dx == dy == dz Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS.cpp commit 81ff56778011e69c19d811b7f392eea51cedfaf1 Merge: a10911ad6 25c1a3f22 Author: vince Date: Thu Aug 17 15:19:07 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a10911ad6499613a1a3afd23291ed34da49eeb37 Author: vince Date: Thu Aug 17 15:18:29 2017 -0700 uniqify coarsened boxarray. Src/Extern/amrdata/AMReX_DataServices.cpp commit 927e862b85d2262879bcb150a99889024f42d343 Author: vince Date: Thu Aug 17 15:13:31 2017 -0700 make uniqify public. Src/Base/AMReX_BoxArray.H commit 272f46a29abe6579761ce74c4e1027fec77a7dab Author: Weiqun Zhang Date: Thu Aug 17 14:25:01 2017 -0700 EB/CNS: add Shock Reflection problem Src/Amr/AMReX_Amr.cpp Tutorials/EB/CNS/Exec/Pulse/GNUmakefile Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/ShockRef/GNUmakefile Tutorials/EB/CNS/Exec/ShockRef/Make.package Tutorials/EB/CNS/Exec/ShockRef/cns_prob.F90 Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 commit 756c8e7ea0c8b290f00b8a33ceebf8d7b15980e4 Author: Andrew Myers Date: Thu Aug 17 12:41:06 2017 -0700 1D and 2D versions of the KDTree fortran helper routines. Src/Particle/AMReX_KDTree_1d.F90 Src/Particle/AMReX_KDTree_2d.F90 Src/Particle/AMReX_KDTree_3d.F90 commit 415d779733a94d9e0053b4a0853013547cf08c71 Author: Andrew Myers Date: Thu Aug 17 12:34:03 2017 -0700 move the load balancing stuff to Src/Particle Src/Particle/AMReX_KDTree_3d.F90 Src/Particle/AMReX_KDTree_F.H Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/CMakeLists.txt Src/Particle/Make.package Tutorials/Particles/LoadBalance/Make.package Tutorials/Particles/LoadBalance/kdtree_F.H Tutorials/Particles/LoadBalance/main.cpp Tutorials/Particles/LoadBalance/visualize_output.ipynb Tutorials/Particles/LoadBalance/visualize_output.ipynb.REMOVED.git-id commit 25c1a3f222cb9f0a6fbdbf696c6a5b49de0c85bc Author: atmyers Date: Thu Aug 17 11:19:10 2017 -0700 This needs to be a 'C' header so it will be installed when building amrex as a library. Src/Particle/Make.package commit 30c9d83f2fc160dc7bc1059e1df5f9c33b02b114 Author: Andrew Myers Date: Thu Aug 17 10:46:22 2017 -0700 some more reorganization. Tutorials/Particles/LoadBalance/main.cpp commit 78cfae09c131f51f33a3da79eb536a661a4d0d4e Author: Weiqun Zhang Date: Thu Aug 17 10:42:38 2017 -0700 EB/CNS: forgot to call mpi reduce Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 commit a8a1cba2eff6985b701c316fb4027c8521fa2cb3 Author: Andrew Myers Date: Thu Aug 17 10:23:16 2017 -0700 some reorganization. Tutorials/Particles/LoadBalance/main.cpp commit a8c4aeefcece2a728549d7c9c89f095b8af6a69e Author: Weiqun Zhang Date: Wed Aug 16 18:04:27 2017 -0700 EB/CNS: minor Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit c1dd21ca4009755b3a32c72d7fb201341cf3bbef Merge: 0d4ce81e9 bf061aef5 Author: Klaus Weide Date: Wed Aug 16 19:52:40 2017 -0500 Merge branch 'development' into kw-development commit bf061aef54d5e726895b0e78649f87d6179277b7 Merge: 8b55b4bed 52cf20bc7 Author: Klaus Weide Date: Wed Aug 16 19:45:18 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cc571d7014f71dc4cf136c5120eec43513739f52 Author: Weiqun Zhang Date: Wed Aug 16 17:23:07 2017 -0700 EB/CNS: print out the total mass Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 32d72bc3871e049108d84a2ff854a890385dd746 Author: Weiqun Zhang Date: Wed Aug 16 16:57:26 2017 -0700 EB/CNS: bug fix Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 52cf20bc7262bde110c492c18253f2503243f851 Author: Andrew Myers Date: Wed Aug 16 16:51:24 2017 -0700 minor tweaks. Tutorials/Particles/LoadBalance/create_binary_particle_file.py Tutorials/Particles/LoadBalance/inputs Tutorials/Particles/LoadBalance/main.cpp Tutorials/Particles/LoadBalance/visualize_output.ipynb.REMOVED.git-id commit 2a8be21157da02d4f171156c56340ff7e88e4be9 Author: Andrew Myers Date: Wed Aug 16 16:51:04 2017 -0700 checked this file in by mistake. Tutorials/Particles/LoadBalance/binary_particle_file.dat.REMOVED.git-id commit 075bd73e771ebbdb586b916a3d9bc4f319d0a03c Merge: 65b4b71de 3051886b8 Author: Andrew Myers Date: Wed Aug 16 16:29:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 65b4b71de9fbb034b7f4c05cee625f6204c46c91 Author: Andrew Myers Date: Wed Aug 16 16:29:13 2017 -0700 some works towards using a kdtree for load balancing particles Tutorials/Particles/LoadBalance/GNUmakefile Tutorials/Particles/LoadBalance/Make.package Tutorials/Particles/LoadBalance/binary_particle_file.dat.REMOVED.git-id Tutorials/Particles/LoadBalance/create_binary_particle_file.py Tutorials/Particles/LoadBalance/inputs Tutorials/Particles/LoadBalance/kdtree_3d.f90 Tutorials/Particles/LoadBalance/kdtree_F.H Tutorials/Particles/LoadBalance/main.cpp Tutorials/Particles/LoadBalance/visualize_output.ipynb.REMOVED.git-id commit f0a7342c21522c1ceab75ff30088f2ca0f0d7335 Author: Weiqun Zhang Date: Wed Aug 16 15:22:22 2017 -0700 EB/CNS: clean up Tutorials/EB/CNS/Source/hydro/comp.F90 Tutorials/EB/CNS/Source/hydro/comp_2d.F90 Tutorials/EB/CNS/Source/hydro/comp_3d.F90 Tutorials/EB/CNS/Source/hydro/wall.F commit 19b4f798272bf7b03bd9e39a7fe887efe69ae663 Author: Weiqun Zhang Date: Wed Aug 16 15:20:20 2017 -0700 EB/CNS: add wall flux and the first simple test seems to work now Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/analriem3d.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_hyp_wall.F90 commit 0d4ce81e9c699b0ebc242ad0202aa2a0f8b43d64 Merge: 85ebfd03b 3051886b8 Author: Klaus Weide Date: Wed Aug 16 17:19:10 2017 -0500 Merge branch 'development' into kw-development commit 469546bf05a400a69fbe24a11e8da3bc39a56bf9 Merge: 2b291b988 3051886b8 Author: Michele Rosso Date: Wed Aug 16 14:46:04 2017 -0700 Merge branch 'development' into mr-cmake commit 2b291b98848486db8f8a306670cb135da0d48b53 Author: Michele Rosso Date: Wed Aug 16 14:45:08 2017 -0700 CMake: modify implementation of user options Tools/CMake/AMReX_Options.cmake commit a608f2676b92a4a73f2011a79443969cbe24d690 Author: Weiqun Zhang Date: Wed Aug 16 11:17:33 2017 -0700 EB/CNS: add parmparse to probin Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/Pulse/inputs commit 76b208b9635728c54ff2b338da6f8a0ba25f6f86 Author: Weiqun Zhang Date: Wed Aug 16 10:54:53 2017 -0700 fix a number of index problems Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit b572dc4528ea447ef265b86c313f1b496e64e98c Author: Weiqun Zhang Date: Tue Aug 15 18:07:33 2017 -0700 EB/CNS: fix bug Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 114b302cfa913d89454d1464de373cac522d4e1d Author: Weiqun Zhang Date: Tue Aug 15 17:52:06 2017 -0700 EB/CNS: compute eb diffop Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 3051886b8b2e9e635cbb2a955c3d9ffbd1cf3eca Merge: f760b0a09 f55c3669d Author: kngott Date: Tue Aug 15 17:51:50 2017 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit f760b0a09b63bf74e58f19c5449ea324ce233271 Author: kngott Date: Tue Aug 15 17:51:07 2017 -0700 Update to make system for profiling and new profparser setup. Uses separate PROFILE and USE_PROFPARSER variables in GNUmakefiles and eliminates depreciated NOLINEVALUES directive. OldTutorials/DataServicesTest0/GNUmakefile Src/Extern/ProfParser/Make.package Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/amrdata/AMReX_XYPlotDataList.H Src/Extern/amrdata/AMReX_XYPlotDataList.cpp Src/Extern/amrdata/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 06b391b23ef9ffdcde9358d0041bcf90491c6ea4 Author: Michele Rosso Date: Tue Aug 15 17:43:14 2017 -0700 CMake: modify way of adding include dirs Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/Extern/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReX_Utils.cmake commit f55c3669da938aa3ed8b12ad2d401cd63663903e Author: Andrew Myers Date: Tue Aug 15 17:31:45 2017 -0700 This approach to testing whether the grids cover the domain is much more memory efficient and should be equivalent if the grids are non-overlapping. Src/Particle/AMReX_ParticleContainerI.H commit 0e6f2031335c049a293890b37a2c371c857258df Author: Weiqun Zhang Date: Tue Aug 15 16:41:22 2017 -0700 build area fraction and face centroid Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 11775c1e07595e97f1464484d3790a0bc152134e Author: Michele Rosso Date: Tue Aug 15 16:28:42 2017 -0700 CMake: remove unused functions. Tools/CMake/AMReX_Utils.cmake commit 402e62b153ec2fbe328a28f5fc02cbec47c200b5 Author: Michele Rosso Date: Tue Aug 15 16:20:46 2017 -0700 CMake: move config of macro definitions to separate file Src/Extern/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake commit 026aca295230b4a9042e2d3c4355daa960756205 Author: Weiqun Zhang Date: Tue Aug 15 15:19:21 2017 -0700 EB/CNS: first pass of eb flux module Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit d6a7d2073f34c14577ff7066b00dbccb0d91b6a0 Merge: 645d4fc05 ac1109be5 Author: Andrew Myers Date: Tue Aug 15 15:07:33 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 645d4fc0563a1e01a141268ca6c87bbbbd30d5d2 Author: Andrew Myers Date: Tue Aug 15 15:07:16 2017 -0700 Restore some variable names that were changed by some over-aggresive find/replacing. Src/Particle/AMReX_ParticleInit.H commit f46229d9d088fb19b8406ad830a9358aa686e9c1 Author: Weiqun Zhang Date: Tue Aug 15 12:30:31 2017 -0700 EB/CNS: get comp_3d compile Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/comp_3d.F90 commit 04021d3b0cdfe2b5886d2be5431d57180d2ed56e Author: Weiqun Zhang Date: Tue Aug 15 10:44:07 2017 -0700 EB/CNS: add john's code Tutorials/EB/CNS/Source/hydro/comp_3d.F90 commit e43325580a0e05f35e047727f47de865613fc0e1 Author: Weiqun Zhang Date: Tue Aug 15 10:42:21 2017 -0700 EB/CNS: fix physical boundary without EB Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit c515ddaab69d0095b0dd1484a1f6eeacedd9ce48 Author: Weiqun Zhang Date: Mon Aug 14 17:49:05 2017 -0700 EB/CNS: fix some bugs Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit c4078a1926b64be81cf1bd680c3c8e559b71b8dd Author: Weiqun Zhang Date: Mon Aug 14 16:51:41 2017 -0700 EB/CNS: merge John's eb hyperbolic code Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit 275fef46b8f6e9433b9a4b3eb3453e81d612cf61 Author: Weiqun Zhang Date: Mon Aug 14 15:43:35 2017 -0700 EB/CNS: second order hydro with regular geometry works Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 commit ac1109be58434e24b154d22dad90198a26cc96d1 Author: kngott Date: Mon Aug 14 15:26:24 2017 -0700 Added BLProfParser parser files to the realclean command. Used specific names to ensure there are not accidental deletions. Tools/GNUMake/Make.rules commit 28aac30a4c2220178b6869924625242172d6c230 Author: kngott Date: Mon Aug 14 15:21:43 2017 -0700 A simple 3D TRACE profiling fix. Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp commit 9383f7ce56acf4ca8e370ab8076087eaab0312ae Author: Weiqun Zhang Date: Mon Aug 14 15:09:50 2017 -0700 EB/CNS: first order hydro with regular geometry works Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/analriem3d.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 commit 3df1ab1dfc3aa0a3469edad4dbedb2ad57f64f2e Author: kngott Date: Mon Aug 14 14:30:31 2017 -0700 Addition of profile specific requirements to standard amrex make. Should only require PROFILE=TRUE. Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 8d813b2d44ead910551b1aea46eb61d35a76099c Author: Weiqun Zhang Date: Mon Aug 14 11:04:58 2017 -0700 EB/CNS: rename to F90 Tutorials/EB/CNS/Source/hydro/analriem3d.F90 Tutorials/EB/CNS/Source/hydro/comp.F90 Tutorials/EB/CNS/Source/hydro/comp_2d.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 Tutorials/EB/CNS/Source/hydro/wall.F commit 2b92f4c3041c358758c09b7f30e45dcab670f7fb Author: Weiqun Zhang Date: Mon Aug 14 11:01:29 2017 -0700 EB/CNS: more code from John Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/analriem3d.f Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.f90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.f90 commit 9d996d3ce69ad544d806990f5464dfc00d803889 Author: Weiqun Zhang Date: Mon Aug 14 10:43:13 2017 -0700 EB/CNS: john's hydro code Tutorials/EB/CNS/Source/hydro/comp.f Tutorials/EB/CNS/Source/hydro/comp_2d.f Tutorials/EB/CNS/Source/hydro/wall.f commit 56a92eee92cd2f55edc47569db4a73cf385de7f8 Author: Weiqun Zhang Date: Mon Aug 14 10:39:37 2017 -0700 EB/CNS: set up RK2 and plotfile Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_io.cpp commit 070f9423e7e88efc2356c0f9c36f2e74bde04008 Merge: 6ffe1527b e9ef96335 Author: Michele Rosso Date: Mon Aug 14 10:36:33 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 6f57b41dd899a0ef9b3be716e57493dea1a22368 Merge: 14dbe9043 e9ef96335 Author: Max Katz Date: Mon Aug 14 01:44:02 2017 -0700 Merge branch 'development' into gpu Conflicts: Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_parmparse_mod.F90 Tools/GNUMake/Make.rules Tools/GNUMake/comps/pgi.mak commit 0a8ff6e0e71800584f89be5f9755c9d982f7f21a Author: Weiqun Zhang Date: Sun Aug 13 08:00:29 2017 -0700 EB/CNS: initialzie EB Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/main.cpp commit e9ef96335aefdf9b655621ed5c3119618e732e5f Author: Ann Almgren Date: Sat Aug 12 16:25:13 2017 -0700 Remove unused variables Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Extern/amrdata/AMReX_AmrData.cpp commit c5de995c20a0ca228560a0720dc6eb62e9643a44 Merge: 207e7af3b c763f9b41 Author: Tan Nguyen Date: Sat Aug 12 15:49:23 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 207e7af3b1c6508fa398cff1103135a4d19ef465 Author: Tan Nguyen Date: Sat Aug 12 15:49:19 2017 -0700 add Dynamic Task Parallelism support Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_DataTypes.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/rts_impls/Serial/rts_taskimpl.H Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C Src/AmrTask/tutorials/UnitTests/Makefile commit c763f9b41bab389c51ebc4f229d6985168309536 Author: kngott Date: Sat Aug 12 14:57:14 2017 -0700 Preprocessing to protect profiler services from 3D simulations. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit a2e739d73fc0412554bfdb33f5c5326caada3dd4 Author: Weiqun Zhang Date: Sat Aug 12 12:23:33 2017 -0700 EB/CNS: estimate dt Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_nd.F90 commit be4fb4f4dcab40666a3288eaa54d12be7b5b564e Author: Weiqun Zhang Date: Sat Aug 12 12:03:51 2017 -0700 EB/CNS: compute temperature Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/Make.package commit ee81d4aacac81205f04f3175618c4ccab5e6fe0c Author: Weiqun Zhang Date: Sat Aug 12 11:37:02 2017 -0700 EB/CNS: set up a simple test problem Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 commit 1462329252451079cdabd7cdfbc4d2b14b466f72 Author: Weiqun Zhang Date: Fri Aug 11 21:48:24 2017 -0700 CNS/EB: derive Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_derive.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package commit e1078134d0f8bcdc1349edbe1452ad75bf85e6d6 Author: Weiqun Zhang Date: Fri Aug 11 21:16:31 2017 -0700 EB/CNS: add physics module Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package commit 3e3a8d07f2a887552649cc3a9e42d096e3ed8916 Author: Weiqun Zhang Date: Fri Aug 11 17:59:36 2017 -0700 set up statedata Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/bc_fill_nd.F90 commit 559a74cdc089b2addfde0010d1866d79f4c48038 Author: Weiqun Zhang Date: Fri Aug 11 17:43:31 2017 -0700 EB/CNS: pass parameters to fortran Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParallelDescriptor.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package commit 3458e19420beb21ac731da1ebfd75bbfd1262003 Author: Weiqun Zhang Date: Fri Aug 11 15:16:27 2017 -0700 skeleton for EB/CNS Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Exec/Pulse/GNUmakefile Tutorials/EB/CNS/Exec/Pulse/Make.package Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNSBld.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_error.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/main.cpp commit d3567ffa10aab9c99dafcb3d09dd1555276d28de Author: Weiqun Zhang Date: Fri Aug 11 12:17:36 2017 -0700 remove old ones Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 commit 4e2b49552eaf6f4b32039a9341649b08a7623adf Author: Weiqun Zhang Date: Fri Aug 11 12:11:55 2017 -0700 move some eb fortran subrtoutines into new files Src/Base/AMReX_EBMultiFabUtil_2d.F90 Src/Base/AMReX_EBMultiFabUtil_3d.F90 Src/Base/Make.package commit 40328e250ad5e73c6541fd59f79e690ac6aeba62 Author: Weiqun Zhang Date: Fri Aug 11 09:55:46 2017 -0700 Face neighbors: this is known to be flawed, but check in before we have a better alternative Src/Base/AMReX_EBLevel.cpp commit c6a33f3030f4247b8debfba51a54039749f8b34b Merge: 69704c2aa 6e1aba2dd Author: Tan Nguyen Date: Thu Aug 10 22:30:13 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 69704c2aa529a2db97dc8b22ab7b13bf83235a70 Author: Tan Nguyen Date: Thu Aug 10 22:30:06 2017 -0700 add more routines to the runtime interface Src/AmrTask/arch.common Src/AmrTask/arch/arch.serial Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_AbstractTask.cpp Src/AmrTask/graph/AMReX_DataTypes.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/graph/Makefile Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/Serial/Makefile Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/rts_impls/Serial/rts_graphimpl.H Src/AmrTask/rts_impls/Serial/rts_taskimpl.H Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/Makefile commit d2dc94047f610952b8b73537cfff2beb1d9a6cea Author: Weiqun Zhang Date: Thu Aug 10 17:06:25 2017 -0700 wip: face neighbors Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp commit dc696a1b947fd7082fdb7750a87b0800d509798a Author: Weiqun Zhang Date: Wed Aug 9 15:54:21 2017 -0700 wip: add EBFaceFlagFab Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_EBFaceFlag.H Src/Base/AMReX_EBFaceFlag.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/Make.package commit 6e1aba2dd29e8bc7da1665a0235917f89fc024b7 Author: kngott Date: Wed Aug 9 15:24:38 2017 -0700 Adding a count of MPI function calls to the timeline profiling option. Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 34bd65c03cf68ca08fb19879cf6975ba9f4bf390 Merge: 1402b2400 10dcd0152 Author: WeiqunZhang Date: Wed Aug 9 09:49:43 2017 -0700 Merge pull request #89 from nncarlson/fix-char-kind Fix character kind declarations commit 10dcd0152e9dcb51d4d291c5e86e786a34cfd7ac Author: Neil Carlson Date: Wed Aug 9 09:12:32 2017 -0600 Fix character kind declarations Src/Base/AMReX_error_mod.F90 Src/F_BaseLib/bl_random_f.f90 Src/F_BaseLib/multifab_c.f90 Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/Base/AMReX_init_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_plotfile_mod.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/tagging_mod.F90 Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/Source/tagging_mod.F90 commit 1402b24002742190c5ab9e3c8731ec276a24fe21 Author: Tan Nguyen Date: Wed Aug 9 00:01:46 2017 -0700 update jacobi test code Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C commit e1fbb8112ba1e8df60ae656c576e847b721943bf Merge: f9f14534a 486e2149c Author: vince Date: Tue Aug 8 18:02:54 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f9f14534a8ed452be51d1cc94a95365877215f1c Author: vince Date: Tue Aug 8 18:02:48 2017 -0700 some fixes for profiling data. Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 85153e63e60a4718f04d07964932c487cdf3228b Author: Weiqun Zhang Date: Tue Aug 8 13:20:53 2017 -0700 renaming some functions Src/AmrCore/AMReX_ebinterp_1d.F90 Src/AmrCore/AMReX_ebinterp_2d.F90 Src/AmrCore/AMReX_ebinterp_3d.F90 Src/Base/AMReX_EBMultiFabUtil_nd.F90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_ebcellflag_mod.F90 commit a915391aaad606e9c61a9916b20aa7be89e73432 Author: Weiqun Zhang Date: Tue Aug 8 13:05:02 2017 -0700 EBFlagFab --> EBCellFlagFab Src/AmrCore/AMReX_EBInterpolater.cpp Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp commit 83597ca590a0870e212af79f4011f6d8e9ceffe3 Merge: 1588dcb13 96e30a474 Author: Weiqun Zhang Date: Tue Aug 8 12:37:29 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit 96e30a474d3f302d5fe02c29e29d3d79ad76dce7 Merge: 01d63265e 26b81847e Author: Weiqun Zhang Date: Tue Aug 8 12:37:10 2017 -0700 Merge branch 'dtg_branch' into eb_development commit 26b81847ed5540c514e20a02d62a35126e4e5d4c Author: dtgraves Date: Tue Aug 8 12:25:43 2017 -0700 bug fix in FlatPlate Src/GeometryShop/AMReX_FlatPlateGeom.cpp commit 1588dcb13184278f2d7eeb65ee64463ac615b526 Author: Weiqun Zhang Date: Tue Aug 8 10:03:10 2017 -0700 some pure --> elemental Src/Base/AMReX_ebcellflag_mod.F90 commit fbcf4c1ad81191bc0b4de6f2d886b5c3f8be2b2e Author: Weiqun Zhang Date: Tue Aug 8 10:00:59 2017 -0700 fillpatch now works for single-valued cells when eb is close to coarse/fine boundary Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_EBInterp_f.H Src/AmrCore/AMReX_EBInterpolater.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_ebinterp_1d.F90 Src/AmrCore/AMReX_ebinterp_2d.F90 Src/AmrCore/AMReX_ebinterp_3d.F90 Src/AmrCore/Make.package Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_ebcellflag_mod.F90 commit 486e2149cfc07525f94f4b3c54efb3b7c36b3e37 Merge: 369513b85 073c1582c Author: dtgraves Date: Mon Aug 7 19:00:05 2017 -0700 Merge pull request #88 from AMReX-Codes/dtg_branch merging to development to get bug fix over commit 073c1582c66bbc1c21ca2a6242dea81d7c0700d7 Author: dtgraves Date: Mon Aug 7 18:57:15 2017 -0700 tweak to Polygeom to try to satisfy valgrind Src/GeometryShop/AMReX_PolyGeom.cpp commit f4baf1afca3e21f0385aa5e6bbff442ad2340c25 Author: dtgraves Date: Mon Aug 7 18:55:35 2017 -0700 bug fix to divergence op Src/EBAMRTools/AMReX_DivergenceOp.cpp commit 369513b856ab27b0058b84bbbfe1f14058384beb Author: Tan Nguyen Date: Mon Aug 7 15:22:21 2017 -0700 task graph prototype Src/AmrTask/Makefile Src/AmrTask/arch.common Src/AmrTask/arch/arch.serial Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_AbstractTask.cpp Src/AmrTask/graph/AMReX_Affinity.H Src/AmrTask/graph/AMReX_Affinity.cpp Src/AmrTask/graph/AMReX_AsyncMFIter.H Src/AmrTask/graph/AMReX_AsyncMFIter.cpp Src/AmrTask/graph/AMReX_DataTypes.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/graph/AMReX_TaskGraph.cpp Src/AmrTask/graph/AMReX_WorkerThread.H Src/AmrTask/graph/AMReX_WorkerThread.cpp Src/AmrTask/graph/Makefile Src/AmrTask/graph/RTS.H Src/AmrTask/make_defaults/Cori Src/AmrTask/make_defaults/Edison Src/AmrTask/make_defaults/Summit-dev Src/AmrTask/rts_impls/README Src/AmrTask/rts_impls/Serial/Makefile Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/tutorials/AMReXApps/3DJacobi/3DJacobi.C Src/AmrTask/tutorials/AMReXApps/3DJacobi/Makefile Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C Src/AmrTask/tutorials/UnitTests/Makefile commit 2b6c406fa41f4c63199188a67523b61fdfcbf82d Author: Weiqun Zhang Date: Mon Aug 7 14:27:59 2017 -0700 add EBInterpolater stub Src/Amr/AMReX_AmrLevel.H Src/AmrCore/AMReX_EBInterpolater.H Src/AmrCore/AMReX_EBInterpolater.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/Make.package commit 4866203db7fb7945a692a5883c1aafdcdb0855a3 Author: Weiqun Zhang Date: Mon Aug 7 13:41:09 2017 -0700 fix graph walking Src/Base/AMReX_EBLevel.cpp commit d722e7a42bf8c0a9d0f9a309c3b530e7d41b30b5 Author: Weiqun Zhang Date: Mon Aug 7 13:14:29 2017 -0700 fix dangling pointer/reference due to return-by-value in some EB data structure Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.H Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp commit 66058db9273f8bd32ea9ef3e2c502864e06782d9 Author: Weiqun Zhang Date: Mon Aug 7 12:35:23 2017 -0700 add more access functions Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_MultiFab.H commit 812eeb1c45ae08756418f95f96eaaea39e048270 Merge: 03b34a8ff 01d63265e Author: Weiqun Zhang Date: Mon Aug 7 11:05:48 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit 01d63265e35d9522917af211c9d18e012565995a Merge: d9bdacd3a 723231eee Author: Weiqun Zhang Date: Mon Aug 7 11:04:49 2017 -0700 Merge branch 'development' into eb_development commit 723231eee37cc6ce2f02038aa585ccf918a610cf Merge: 7138cc9bd 005062c42 Author: WeiqunZhang Date: Mon Aug 7 11:03:09 2017 -0700 Merge pull request #87 from nncarlson/add-nag [WIP] Add GNUmakefile support for the NAG Fortran compiler commit 7138cc9bdfae58409df6da2323a69aebc71ae73a Author: Weiqun Zhang Date: Mon Aug 7 10:47:36 2017 -0700 move Tests/LinearSovlver/F_MG to boxlib test list Tools/CompileTesting/compiletesting.py commit 8630683cf98bba37dbb8afc8081589d88ae537dd Author: Weiqun Zhang Date: Mon Aug 7 10:38:33 2017 -0700 update compiletesting.py Tools/CompileTesting/compiletesting.py commit 1404633e0a1d8ed21ec19421545ed4d0aeaec75c Merge: f1faeae18 39be65269 Author: WeiqunZhang Date: Mon Aug 7 10:13:21 2017 -0700 Merge pull request #76 from akreienbuehl/clrdDiffuSolve clrdDiffuSolve commit f1faeae18dc73066a4454f68c7e7841cd26bf821 Author: Weiqun Zhang Date: Mon Aug 7 10:12:47 2017 -0700 fix compilation of a test OldTutorials/MultiFabTests_C/GNUmakefile commit 9c56eccad3f0ee39f3fcf78c085176c6ff1c3f41 Author: Weiqun Zhang Date: Mon Aug 7 09:58:10 2017 -0700 update compiletesting.py Tools/CompileTesting/compiletesting.py commit 03b34a8ffa6e9389a9c68401dfcef195dee658b4 Author: Weiqun Zhang Date: Mon Aug 7 09:43:35 2017 -0700 save pointers to ebflag fab in EbFArrayBox Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp commit 005062c424c76c83b9b0dfb23c5b64c4f063cc6f Author: Neil Carlson Date: Sun Aug 6 08:45:04 2017 -0600 Add GNUmakefile support for the NAG Fortran compiler Tools/GNUMake/Make.defs Tools/GNUMake/comps/nag.mak Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit 39be65269f41b8624b81696dbe0a2180ba4a3d8d Merge: 369b3b700 5f825d5a2 Author: Andreas Kreienbuehl Date: Sun Aug 6 12:36:36 2017 -0700 Merge branch 'clrdDiffuSolve' of https://github.com/akreienbuehl/amrex into clrdDiffuSolve commit 369b3b7009bc20044d76a9bfd0460633d07fde2f Author: Andreas Kreienbuehl Date: Sun Aug 6 12:35:54 2017 -0700 Introduced variable `m_clr_map` along the lines of `m_nCommColors` Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 7559314b97c211fbce55fb6182168bd36266b1f0 Merge: e1fdeabdb e02cf3da5 Author: Andreas Kreienbuehl Date: Sun Aug 6 09:36:40 2017 -0700 Merge branch 'development' into clrdDiffuSolve commit 14dbe9043c64d8560a43e6e31e2dc1c59ed86ac7 Author: Max Katz Date: Sat Aug 5 19:23:59 2017 -0400 Add a new wrapper around Device functions Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MFIter.cpp Src/Base/Make.package Tools/GNUMake/Make.defs commit 29517f3735940adaf24dfe301700e195a1a1a65c Merge: 6b474fbeb 3a726a1f3 Author: Max Katz Date: Sat Aug 5 18:00:19 2017 -0400 Merge branch 'development' into gpu Conflicts: Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Tools/GNUMake/Make.defs commit 6b474fbebd80ab99ad2a98f9a9ba390baed6c032 Author: Max Katz Date: Sat Aug 5 17:48:49 2017 -0400 Replace CUDA macro with AMREX_USE_CUDA Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tools/GNUMake/Make.defs Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit 417f0208030fb766ba2fef8f7ab70321a5f58e5a Author: dtgraves Date: Fri Aug 4 19:11:38 2017 -0700 my tweak to the make system that should never be pushed Tools/GNUMake/comps/gnu.mak commit e02cf3da53ae3e431039fa3f8fe47142588b4f8b Merge: c34d2728c 5c4ecd7b8 Author: Ann Almgren Date: Fri Aug 4 18:55:14 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9e4904eff515ca502be79657939e739e70878e99 Author: Marc Day Date: Fri Aug 4 18:31:28 2017 -0700 Add back changes to EB fortran in divflux...lost in merge conflict resolution Src/EBAMRTools/AMReX_EBFortND.F90 commit 2f5614277663173f2f5bb13f618745fd45664ee8 Merge: fd5da5154 d9bdacd3a Author: Marc Day Date: Fri Aug 4 18:22:18 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit d9bdacd3ad30b64ffbe11def098832e11ddf3db6 Author: Marc Day Date: Fri Aug 4 18:21:24 2017 -0700 Undo adding of declaration...sorting out multiple merges Src/EBAMRTools/AMReX_EBFortND.F90 commit 988d1ad5082562eb2eb864cd2d9ce5126a1e83bb Merge: 77d5ebff4 c66804f1e Author: Marc Day Date: Fri Aug 4 18:14:43 2017 -0700 Conflict resolution with dtg_branch commit fd5da515488e20c39418aac529c446390ff3038b Merge: fbe93e238 77d5ebff4 Author: Marc Day Date: Fri Aug 4 18:03:50 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit 77d5ebff4d7c7513d71237cdd01da5de62d13876 Author: Marc Day Date: Fri Aug 4 18:02:30 2017 -0700 Add declaration for flag Src/EBAMRTools/AMReX_EBFortND.F90 commit fbe93e238551d86febf042bee2f26592acd3aaa6 Merge: 52905cb16 5b1f8ff3c Author: Weiqun Zhang Date: Fri Aug 4 17:45:03 2017 -0700 Merge branch 'eb_development' into weiqun/eb Conflicts: Src/EBAMRTools/AMReX_EBFortND.F90 commit 5b1f8ff3cdf02bb01bf07c69f369eaef26c6b0d5 Author: Marc Day Date: Fri Aug 4 17:08:21 2017 -0700 resolve conflicts Src/EBAMRTools/AMReX_EBFortND.F90 commit 52905cb16550033248052b511f880139f5c6c1bc Author: Weiqun Zhang Date: Fri Aug 4 17:12:43 2017 -0700 fix 3d avgdown Src/Base/AMReX_EBMultiFabUtil.cpp commit 0f9ffcbcccafe51259d8d6c5a08fa79ff845a787 Author: Weiqun Zhang Date: Fri Aug 4 17:01:15 2017 -0700 missed an enddo Src/Base/AMReX_MultiFabUtil_3d.f90 commit d07dbc1316182e681cfc6fe5e8385307f7487db0 Author: Weiqun Zhang Date: Fri Aug 4 16:59:59 2017 -0700 finish eb average down Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_EBMultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 commit f323967efd42deaf0b4f7013c13458b203b92dff Author: vince Date: Fri Aug 4 16:16:16 2017 -0700 fix comment. Src/Base/AMReX_Utility.H commit 2ba3bae0a43f0ff1fe0ca91a19b9241df6441df2 Author: vince Date: Fri Aug 4 16:00:10 2017 -0700 removed old files. Src/Extern/ProfParser/backup/AMReX_AVGDOWN_2D.F Src/Extern/ProfParser/backup/AMReX_AVGDOWN_3D.F Src/Extern/ProfParser/backup/AMReX_AVGDOWN_F.H Src/Extern/ProfParser/backup/AMReX_BLProfStats.H Src/Extern/ProfParser/backup/AMReX_BLProfStats.cpp Src/Extern/ProfParser/backup/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.H Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/backup/AMReX_CommProfStats.H Src/Extern/ProfParser/backup/AMReX_CommProfStats.cpp Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.H Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.cpp Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.H Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.cpp Src/Extern/ProfParser/backup/BLProfParser.l Src/Extern/ProfParser/backup/BLProfParser.y Src/Extern/ProfParser/backup/Make.package commit d52df0586905bcba57561afa40e988b98b8450bd Merge: 83bdb1a82 5c4ecd7b8 Author: vince Date: Fri Aug 4 15:52:45 2017 -0700 Merge branch 'development' into profvisDS commit 83bdb1a824148c1f7238a1f60ef906e2a00e5e8e Merge: b47795248 21a614905 Author: vince Date: Fri Aug 4 15:44:19 2017 -0700 sync with original code. commit c66804f1ea08a8dda58ecddba7500c22dd5b0451 Author: dtgraves Date: Fri Aug 4 15:08:57 2017 -0700 added sphere option to redistribution test Tests/GeometryShop/regression/levelRedistTest.cpp Tests/GeometryShop/regression/levelredist.inputs commit 6ffe1527b7ea55cc635f45207de2cabb009cc11d Author: Michele Rosso Date: Fri Aug 4 14:51:07 2017 -0700 CMake: update docs. Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Options.cmake commit ef42e7ebd54d1f387799f462f61ba3bee25fecc7 Author: Weiqun Zhang Date: Fri Aug 4 14:13:03 2017 -0700 finish EB_set_volume_fraction Src/Base/AMReX_BaseFab.H Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_FabFactory.H commit c40fc3892cd592fe4e692aba99b25a1d700afcc7 Author: Weiqun Zhang Date: Fri Aug 4 13:44:05 2017 -0700 fix regular average_down Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_MultiFabUtil.cpp commit 88345e1c39f2b1740c1f969a971311225acf3e55 Author: Weiqun Zhang Date: Fri Aug 4 13:26:23 2017 -0700 EBFArrayBox can now get type info from EBLevel Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.cpp commit f811aa41b33e29522b56ca46425c19ca1b8cd584 Author: Weiqun Zhang Date: Fri Aug 4 13:09:59 2017 -0700 EBLevel: add FabType Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabFactory.H commit 279dcc440e9b3414ee7cd9c2d018c4c6520f1d33 Merge: a893470d3 bc4aa94a5 Author: Weiqun Zhang Date: Fri Aug 4 12:32:24 2017 -0700 Merge branch 'eb_development' into weiqun/eb Conflicts: Src/EBAMRTools/AMReX_DivergenceOp.cpp commit bc4aa94a58000139ce05b883d3c2cce62a8b14f6 Author: Marc Day Date: Fri Aug 4 12:17:28 2017 -0700 Fix a couple bugs resulting from me not correctly specifying Dans jobs...my bad. Conflicts: Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_DivergenceOp.cpp commit ccc79dcad23af8534bc3d773a8ab98de3490f6ae Author: Michele Rosso Date: Fri Aug 4 12:16:49 2017 -0700 CMake: fix defines for comm-profiling Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit a893470d3d2a7cb8751410bcf854b69f6f4b83c2 Author: Weiqun Zhang Date: Fri Aug 4 11:27:19 2017 -0700 add armrex::EB_set_volume_fraction stub Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp commit 93931db6ad0d8a2f77cd421bbe193094b10b8dd4 Merge: faee24afa 5c4ecd7b8 Author: Michele Rosso Date: Fri Aug 4 11:13:08 2017 -0700 Merge branch 'development' into mr-cmake commit c3d739fede0a1cca2bdb5bf705f82e17c0dbafb4 Author: Weiqun Zhang Date: Fri Aug 4 10:56:18 2017 -0700 fix BoxIterator for empty box Src/Base/AMReX_BoxIterator.cpp commit 5c4ecd7b8912c7761fd9333b32dc5df20076a0c5 Author: Weiqun Zhang Date: Fri Aug 4 10:17:58 2017 -0700 Fortran: boxarray%maxsize now has three versions: single integer size, three integers and an integer array of size 3 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 commit 3a2cb2fa8fba3db6a236370effbc676a0aeebab8 Author: Weiqun Zhang Date: Thu Aug 3 22:17:54 2017 -0700 fix include hell Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H commit c34d2728cf901c0fe9df82c4e4df2cc501c3f4e6 Merge: e24e66af4 12adbcf1e Author: Ann Almgren Date: Thu Aug 3 18:31:48 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 12adbcf1ecd4b2a31ce1044f814b0da90bba84bf Author: Michael Zingale Date: Thu Aug 3 20:47:06 2017 -0400 more git error control sometimes if the repo is dirty or a branch doesn't exist the checkout of the branch can silently fail Tools/RegressionTesting/repo.py commit faee24afa700f812733f125571c95a2b80d779f3 Author: Michele Rosso Date: Thu Aug 3 17:34:11 2017 -0700 CMake: add support for trace and comm profiling Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 0ac96265a2eff183475f169482982201782279b9 Author: Weiqun Zhang Date: Thu Aug 3 17:06:37 2017 -0700 use fortran to set covered cells to min vals Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_EBMultiFabUtil_F.H Src/Base/AMReX_EBMultiFabUtil_nd.F90 Src/Base/Make.package commit da58c40dcfbb1536152963e595ffdeff2c3509db Author: Michele Rosso Date: Thu Aug 3 16:46:22 2017 -0700 CMake: fix typo Src/CMakeLists.txt commit bd9c4ecd0c7700c91774ec587f5b002555bf8f0a Author: Michele Rosso Date: Thu Aug 3 16:08:17 2017 -0700 CMake: enable user to turn on/off AMReX components Src/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit b83cecb577656160df7b1190ef4d24f4682ce523 Author: Weiqun Zhang Date: Thu Aug 3 15:55:16 2017 -0700 need this for pgi compiler Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 commit 228c8ff1fbd0b6ddcd95168813a2db6544cb538e Author: Weiqun Zhang Date: Thu Aug 3 15:47:33 2017 -0700 save a copy of EBLevel in EBFabFactory, which is in turn stored in MultiFab Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_EBFabFactory.H Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_MultiFab.H Src/Base/Make.package Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_LayoutData.H commit 5045e89137fcd3291912abf648391b977dd51db3 Author: dtgraves Date: Thu Aug 3 15:08:34 2017 -0700 got the conductivity solver to run to completion. still wrong. back to writing documents. Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/GeometryShop/AMReX_EBArith.cpp Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 653ad5666d348ebf5e945a4221445291f824f3a1 Author: Michele Rosso Date: Thu Aug 3 14:47:39 2017 -0700 CMake: fix minor bugs Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 98a6d1151e0dcca201b18405243e91d02d4e31f6 Author: Weiqun Zhang Date: Thu Aug 3 14:21:26 2017 -0700 fix c_real in mempool module Src/Base/AMReX_fort_mod.F90 Src/Base/AMReX_mempool_f.f90 Src/F_BaseLib/GPackage.mak Src/F_BaseLib/amrex_fort_mod.f90 commit c036bd1f3f984cc0966359644aab6dbacf42fac0 Author: Ondřej Čertík Date: Thu Aug 3 13:43:40 2017 -0600 Compare real kinds directly In order to determine if the real kinds are equal, one can just compare them directly, they are just integers. This is simpler, and also allows these lines to be compiled with NAG. For some reason NAG does not seem to have `c_sizeof()` as part of the `iso_c_binding` module and so it fails on these lines. This commit fixes it. Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 716456a53d4be2954fefe613c64b969d57c68259 Merge: 952dd930c 4466b9a4a Author: WeiqunZhang Date: Thu Aug 3 13:22:34 2017 -0700 Merge pull request #80 from certik/size_of_fix Compare real kinds directly commit 4466b9a4a7e04b7b5c3b3cd8bd37e1cbcea26544 Author: Ondřej Čertík Date: Thu Aug 3 13:43:40 2017 -0600 Compare real kinds directly In order to determine if the real kinds are equal, one can just compare them directly, they are just integers. This is simpler, and also allows these lines to be compiled with NAG. For some reason NAG does not seem to have `c_sizeof()` as part of the `iso_c_binding` module and so it fails on these lines. This commit fixes it. Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit ea9351af4533b3fcc4870d754bd0c7293f7b2a3d Author: Weiqun Zhang Date: Thu Aug 3 11:42:23 2017 -0700 have to intersect with the domain because there is no eb information outside the domain Src/Base/AMReX_EBLevel.cpp commit 0ef222e4ed3cb720448cc019bf1029c05d52a6fe Author: Weiqun Zhang Date: Thu Aug 3 11:28:37 2017 -0700 add Fortran module for ebcellflag Src/Base/AMReX_ebcellflag_mod.F90 Src/Base/Make.package commit dd6d7f97e194dda7e0901b7d8a3f30cd309e541a Author: Weiqun Zhang Date: Thu Aug 3 10:43:56 2017 -0700 set and get number of VoFs Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBLevel.cpp commit 1d78eff7f38ce501229d34affa859d8847a65266 Author: Weiqun Zhang Date: Thu Aug 3 09:46:04 2017 -0700 reserve 3 bits for number of multi-valued cells and clean up CellFlag Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBCellFlag.cpp commit 5f825d5a2f7cc58db946777b8356fa16151f76e8 Merge: e1fdeabdb ad1ca154c Author: Andreas Kreienbuehl Date: Thu Aug 3 08:35:23 2017 -0700 Merge branch 'development' into clrdDiffuSolve commit acf5e862ad929976d8c8d72bf5206974a82830c7 Merge: 33e9bc102 ad1ca154c Author: dtgraves Date: Wed Aug 2 20:35:46 2017 -0700 Merge pull request #78 from AMReX-Codes/development trying to get bug fixes for DivergenceOp into weiqun/eb branch commit ad1ca154cbbbcd56152576824cd52c696155183d Merge: 5c3517e85 eef52795c Author: dtgraves Date: Wed Aug 2 20:31:42 2017 -0700 Merge pull request #77 from AMReX-Codes/dtg_branch getting some bug fixes over to development branch commit 33e9bc1022ac4016cfa6f33a3d10b4ef928c08bb Author: Weiqun Zhang Date: Wed Aug 2 17:36:23 2017 -0700 finish setting up EBCellFlag in C++ Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBLevel.cpp Src/Base/Make.package commit f1c290e71036a613701388b9799b8926aee10c55 Author: Weiqun Zhang Date: Wed Aug 2 14:25:47 2017 -0700 wip because pge is cutting power Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBLevel.cpp commit 5c3517e85d50f9d720fd1f9057b46b92295a5a32 Merge: 4795dfe9a 21a614905 Author: Michael Zingale Date: Wed Aug 2 17:06:36 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit 4795dfe9aed30f39a859d9cae2e9463c5540b98d Author: Michael Zingale Date: Wed Aug 2 17:06:18 2017 -0400 fix compilation + add a DO_ALL macro Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fdump.f90 commit 86acfafa7b37c4568705d10a77d8533c0683649b Author: Weiqun Zhang Date: Wed Aug 2 10:20:18 2017 -0700 start EBLevel and EBCellFlag Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/Make.package commit e24e66af425813e8a05cad5c5c777c8d5f252ed0 Merge: 63d07dec9 21a614905 Author: Ann Almgren Date: Wed Aug 2 09:47:51 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e1fdeabdb399ec502b650212910408bf4ded398d Merge: 71036bd13 21a614905 Author: Andreas Kreienbuehl Date: Wed Aug 2 09:36:07 2017 -0700 Merge branch 'development' into clrdDiffuSolve commit 7e1263217243f6e4e3d9eb08a47cc6ad02f05166 Merge: 0263ace78 21a614905 Author: Weiqun Zhang Date: Wed Aug 2 09:24:53 2017 -0700 Merge branch 'development' into eb_development commit 21a614905db98fbbd8a99728074ea82cb4429f3e Author: Ann Almgren Date: Tue Aug 1 17:48:30 2017 -0700 Need an option for mvapich (cooley.alcf.anl.go) as well in Make.unknown Tools/GNUMake/sites/Make.unknown commit 952dd930c4491283c9182fdcd8b4953d15939c9c Author: Ann Almgren Date: Tue Aug 1 17:48:30 2017 -0700 Need an option for mvapich (cooley.alcf.anl.go) as well in Make.unknown Tools/GNUMake/sites/Make.unknown commit 63d07dec9687cd1a57ee6f1a65da1715b8246d36 Merge: 27c708160 648e13f76 Author: Ann Almgren Date: Tue Aug 1 17:48:55 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 27c708160869b0808e9588bd41bd760aa6a6815f Author: Ann Almgren Date: Tue Aug 1 17:48:30 2017 -0700 Need an option for mvapich (cooley.alcf.anl.go) as well in Make.unknown Tools/GNUMake/sites/Make.unknown commit 648e13f76615a5fd67ce3b75b9070758b3034c72 Merge: 7d2f62471 76eb8fd5e Author: Michele Rosso Date: Tue Aug 1 17:12:35 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7d2f62471e50f62e7244c2b9a6c79bff873ebac3 Author: Michele Rosso Date: Tue Aug 1 17:12:24 2017 -0700 CMake: update exported info Tools/CMake/AMReXConfig.cmake.in commit 76eb8fd5e67473fe22b244dc5c1dcaf8ff5933fc Author: Ann Almgren Date: Tue Aug 1 16:54:56 2017 -0700 Fix AMReX_HOME -- one more directory down Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile commit 1de881a22807de459c938c95427a3d37b6bdfac1 Author: Ann Almgren Date: Tue Aug 1 16:54:25 2017 -0700 Fix AMREX_HOME -- one more directory down Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile commit 0263ace78357009ad756a8eb2950d3fd1c4f7fc1 Author: Weiqun Zhang Date: Tue Aug 1 16:53:24 2017 -0700 update fillpatch for eb Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 7d75c9432fa32ef88b3a6f7cf3b2f92b892b7268 Author: Michele Rosso Date: Tue Aug 1 16:38:47 2017 -0700 CMake: make assertions opt-in Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit eef52795c68d40315518895ae72dc8b36be1ff4d Author: dtgraves Date: Tue Aug 1 16:20:56 2017 -0700 EBAMRElliptic's big redesign of Chombo's elliptic stuff now compiles Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBSimpleSolver.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Src/EBAMRElliptic/Make.package Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 58849bf57ce13feba3e6dcb28bd721d5a2b8211a Author: Michael Zingale Date: Tue Aug 1 18:51:09 2017 -0400 make this work with python3 Tools/Py_util/plotsinglevar.py commit 1b256042ae582edd05f98b72f1b9da9b63859cf0 Author: Andrew Myers Date: Tue Aug 1 14:41:53 2017 -0700 threading the buildNeighborList method. Src/Particle/AMReX_NeighborParticlesI.H commit 71036bd1382515a79dcd107618b7c17e9b660f6d Merge: 89a439891 60b2d443e Author: Andreas Kreienbuehl Date: Tue Aug 1 13:27:54 2017 -0700 Merge branch 'clrdDiffuSolve' of https://github.com/akreienbuehl/amrex into clrdDiffuSolve commit 89a439891e985ad579182cc505cc26d3f0071302 Merge: 49e39e991 1ed2afc00 Author: Andreas Kreienbuehl Date: Tue Aug 1 13:27:15 2017 -0700 Merge branch 'development' into clrdDiffuSolve commit 8caa162eb46d9e395fd4c09c5e5c0afc1cf7fd54 Merge: df2c09264 f49e2e502 Author: Weiqun Zhang Date: Tue Aug 1 13:12:00 2017 -0700 Merge branch 'weiqun/eb' into eb_development commit f49e2e502f71e1becf18f64f680c00e79c460936 Author: Weiqun Zhang Date: Tue Aug 1 13:00:06 2017 -0700 use factory member variable Src/Base/AMReX_FabArray.H commit 9272161d43f8c592a95619377783893a5ff7c7f1 Author: Weiqun Zhang Date: Tue Aug 1 12:17:32 2017 -0700 fix FabType for nodal EBFArrayBox Src/Base/AMReX_EBFArrayBox.cpp commit efc473880db1a307918748fb28e7def92e65f1e6 Author: Weiqun Zhang Date: Tue Aug 1 12:14:09 2017 -0700 add a strict mode in which one must pass factory to FabArray constructor Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Extrapolater.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_MultiMask.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Tools/GNUMake/Make.defs commit df2c0926454f9a5fa17949ec78cf2798c2627308 Merge: f9b1f0486 d9500ba4f Author: Marc Day Date: Tue Aug 1 11:27:21 2017 -0700 Merge branch 'vof-work' into eb_development commit d9500ba4f52eb6753db36b341a58b407d0385fd0 Author: Marc Day Date: Tue Aug 1 11:25:43 2017 -0700 Pass the stencil box to further clean fort code Tests/GeometryShop/vofStructures/nbrsTest.cpp Tests/GeometryShop/vofStructures/nbrsTest_nd.f90 commit b5d9f84326d3108d8e6073bdff5fbb2addaf841e Author: Marc Day Date: Tue Aug 1 11:16:03 2017 -0700 Use better macros, clean resulting code Tests/GeometryShop/vofStructures/nbrsTest.cpp Tests/GeometryShop/vofStructures/nbrsTest_nd.f90 commit f9b1f0486d113864dac882189a43e3b6490a7df4 Merge: 9fc162ad5 1ed2afc00 Author: Weiqun Zhang Date: Tue Aug 1 10:00:28 2017 -0700 Merge branch 'development' into weiqun/eb commit 1ed2afc00c3c4acc6f0d1febfc4f594ccf5c1b9a Merge: 103bcf0cd ea47076aa Author: Weiqun Zhang Date: Tue Aug 1 09:52:12 2017 -0700 Merge branch 'development' Conflicts: Tools/CMake/AMReX_Config.cmake commit 91806eb7fbb61ed57b4c17747d61fec539fd1702 Author: Marc Day Date: Mon Jul 31 19:42:40 2017 -0700 Add a test code to make a simple redistribution stencil and apply it. Needs more generalization, but it shows one method of passing such data to fortran. Tests/GeometryShop/vofStructures/AMReX_EBRedist.H Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/nbrsTest.cpp Tests/GeometryShop/vofStructures/nbrsTest_mod.F90 Tests/GeometryShop/vofStructures/nbrsTest_nd.f90 commit 9fc162ad54b947c315e6f542378c39c38e176288 Author: Weiqun Zhang Date: Mon Jul 31 17:57:22 2017 -0700 AmrLevel: new MultiFabs should be built with factory member Src/Amr/AMReX_AmrLevel.cpp commit f0bd8daf3e21fe6a0ce40b65a18d3502d45b601e Author: Weiqun Zhang Date: Mon Jul 31 17:46:28 2017 -0700 store a copy of eb factory in AmrLevel Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit e466d7533a7da76e2266dd2d23772ad8b356c93c Author: Weiqun Zhang Date: Mon Jul 31 17:00:55 2017 -0700 because we don't have geometry information outside domain Src/Base/AMReX_EBFArrayBox.cpp commit 6a5bd5d2811cf3071c15d5c079c9dba5ec74efb9 Merge: 8318082b0 d28bc5f3e Author: Marc Day Date: Mon Jul 31 16:46:38 2017 -0700 Merge branch 'dtg_branch' into vof-work commit 319621700fc85a356347f2e0a28b0624544f0aef Author: Weiqun Zhang Date: Mon Jul 31 16:37:18 2017 -0700 get EBISLayout from eb factory Src/Base/AMReX_FabFactory.H commit bba2ad1b0f1d518dbbe129b8cd506c209ffb98af Author: Weiqun Zhang Date: Mon Jul 31 16:36:45 2017 -0700 add a eb utility function to set all covered to the min val for the temporary purpose of visualization Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/Make.package commit 676463eec089909eb46eded7697114fb932a993e Author: dtgraves Date: Mon Jul 31 16:29:18 2017 -0700 made EBGraph::fillIntMask more closely resemble what Marc wants. Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit 777979fe8bfbbb2f65261799e6866852b1ed7ef2 Author: dtgraves Date: Mon Jul 31 12:10:40 2017 -0700 made DivergenceOp able to support fluxes that have area multiplied in to support PeleC Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H commit ea47076aa986c37fb148c78762f208018b88d99e Merge: d4d1481f1 3465e0e9f Author: Michele Rosso Date: Mon Jul 31 12:08:00 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d4d1481f1acec809a451dac1fd3585d4043ddb3c Author: Michele Rosso Date: Mon Jul 31 12:07:14 2017 -0700 CMake:manually force C++11 compliance for Intel compiler Tools/CMake/AMReX_CMakeVariables.cmake commit 3465e0e9f42c4be515506e4bda0076e5dec26991 Author: Andrew Myers Date: Mon Jul 31 10:36:00 2017 -0700 make this test work in 2D and 3D. Tests/Particles/AssignMultiLevelDensity/main.cpp commit 520abd3b50640ccabf3db6c2501f26312032692f Author: Andrew Myers Date: Mon Jul 31 10:35:41 2017 -0700 consolidate OMP Deposition helpers. Src/Particle/AMReX_OMPDepositionHelper_1d.F90 Src/Particle/AMReX_OMPDepositionHelper_2d.F90 Src/Particle/AMReX_OMPDepositionHelper_nd.F90 Src/Particle/AMReX_ParticleContainerI.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit c08cb8371590ae070acbd14ab954dd898db25f5f Author: Andrew Myers Date: Mon Jul 31 10:11:37 2017 -0700 use PCInterp in the multilevel density deposition. Src/Particle/AMReX_ParticleContainerI.H commit c98c4024856f1a75c2784366fd1d3e7f676335eb Author: dtgraves Date: Mon Jul 31 09:54:46 2017 -0700 bug fix in DivergenceOp Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp commit 8318082b06d78e57a9b95d795cfe08704616e7f6 Author: Marc Day Date: Mon Jul 31 09:23:42 2017 -0700 Add back code to set fluid cells to unity so that amrvis2d smooth works correctly. Just for demo purposes, keep code more explicitly handling the different types of cells. Tests/GeometryShop/vofStructures/umapTest.cpp commit 8c3bea70653e8823a2c63fb13df0433fa9d4dc7a Merge: 227a7e486 b94043a26 Author: Weiqun Zhang Date: Sat Jul 29 11:49:05 2017 -0700 merge branch 'development' into weiqun/eb commit 227a7e4861c938169b483b52a1238fa8c7801d52 Author: Weiqun Zhang Date: Sat Jul 29 11:48:17 2017 -0700 update comments Src/Base/AMReX_FArrayBox.H commit b94043a2657d3b9bb8c830675ef57de57910ede3 Author: Weiqun Zhang Date: Sat Jul 29 11:45:31 2017 -0700 make FabArray friend of DistributionMapping for sidecar's moveallfabs Src/Base/AMReX_DistributionMapping.H commit 76e19d60ee9c8a82ae3370193971645a63d3c567 Author: Weiqun Zhang Date: Fri Jul 28 23:51:15 2017 -0700 fix typo Src/Amr/AMReX_AmrLevel.cpp commit 06ff71da6e0e9459e80a7e2374b3b23f941a260b Author: Weiqun Zhang Date: Fri Jul 28 23:49:31 2017 -0700 add factory and eb to AmrLevel and StateData Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit bc6b548f11e1bddb579a30f80df305a122d91bb4 Author: Weiqun Zhang Date: Fri Jul 28 22:59:59 2017 -0700 change default factory of MultiFab Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FabFactory.H commit 4e070a04ef2aaf04db35887cd97d0cdc5f394520 Author: Weiqun Zhang Date: Fri Jul 28 22:36:53 2017 -0700 add clone function to FabFactory Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseIFFactory.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_IrregFABFactory.H commit 636506e5b35e5c730c2c10e5d9347828f6b87445 Author: Weiqun Zhang Date: Fri Jul 28 17:41:53 2017 -0700 add FabType Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FArrayBox.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBISBox.H commit d096056423fbbda248ecbcd80069431e720301f1 Author: Michele Rosso Date: Fri Jul 28 17:27:07 2017 -0700 CMake: update source file list Src/F_Interfaces/CMakeLists.txt commit 7a17b4c6d3436c828b694881e2ef45353793c6f7 Merge: 64110cd18 d42d02031 Author: Michele Rosso Date: Fri Jul 28 17:21:41 2017 -0700 Merge branch 'mr-cmake' into development commit d42d0203127dff40b17a0c2906f7b75548ca3cae Author: Michele Rosso Date: Fri Jul 28 17:21:08 2017 -0700 CMake: update documentation Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit 3029ece748429fc2c2cfa9e84ed62c7e388558c6 Author: Michele Rosso Date: Fri Jul 28 17:07:53 2017 -0700 CMake: add AMReX version info Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 02f89ec0404e28e5b8efcd7847771b5bc658b2ca Author: Weiqun Zhang Date: Fri Jul 28 16:52:28 2017 -0700 add optional factory to MultiFab constructor Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 082e929545b1f2c5dc9e4fc89c885885b8e2da2e Author: Michele Rosso Date: Fri Jul 28 16:37:17 2017 -0700 CMake: build Amr tutorials CMakeLists.txt Tools/CMake/AMReX_Utils.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_F/CMakeLists.txt Tutorials/Amr/Advection_octree_F/CMakeLists.txt Tutorials/CMakeLists.txt commit d72644067493a2e4f87df16053f24e5b9ff519e7 Author: Weiqun Zhang Date: Fri Jul 28 16:35:28 2017 -0700 FArrayBoxFactory Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_MultiFab.H Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBISLayout.H commit 80bb2b858477a4deaa48d64f29110021298f508c Author: Michele Rosso Date: Fri Jul 28 16:34:06 2017 -0700 CMake: remove FindCCSE Tools/CMake/FindCCSE.cmake commit 5ae49e9ae7b745f41175945e4e59c64094e7826b Author: Michele Rosso Date: Fri Jul 28 16:32:34 2017 -0700 CMake: build fortran interfaces by default Tools/CMake/AMReX_Config.cmake commit 2596d629ff3982e5df45854b2a755b351bfdf74e Author: dtgraves Date: Fri Jul 28 15:55:57 2017 -0700 bit more progress toward eb elliptic solvers Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp commit 5536b2bb23ac248a73a731bc55e61dd1e8b71763 Author: Weiqun Zhang Date: Fri Jul 28 15:27:33 2017 -0700 add EBFArrayBox Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabFactory.H Src/Base/Make.package commit a70f9b611b03db5d0e727b693ecc9b8d2fe2f6ad Merge: 282c0ab5e 64110cd18 Author: Weiqun Zhang Date: Fri Jul 28 14:42:10 2017 -0700 Merge branch 'development' into weiqun/eb commit 64110cd18dfb67aea1087c15c4f7ec7e095c23b0 Author: Weiqun Zhang Date: Fri Jul 28 14:38:56 2017 -0700 use std::function instead of function pointer for flexibility Src/Base/AMReX.H Src/Base/AMReX.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp commit c15224322e54f974fa9c3f99b054183b2bd879ab Author: Weiqun Zhang Date: Fri Jul 28 14:23:09 2017 -0700 have to link with pgfortran if pgi is used and the main is in Fortran Src/F_Interfaces/Base/Make.package Tools/GNUMake/Make.rules Tools/GNUMake/comps/pgi.mak commit e08eb8197b2d28a86cdc406e0d57f22e7ccec4a8 Merge: 1b1eb7d2d e031e40ca Author: dtgraves Date: Fri Jul 28 11:28:02 2017 -0700 Merge pull request #73 from AMReX-Codes/dtg_branch syncing with dtg_branch so Ray can get the combustor geometry tools. commit e031e40cade125644da5430d338992cd2d4beeac Author: dtgraves Date: Fri Jul 28 11:26:08 2017 -0700 to give Ray the combustion geometry, I added Terry's transformation functions for implicit functions (Lathe (surfaces of revolution), Complement, Union, Intersection, Transforms (scale, translate, rotate) Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/Make.package commit 1b1eb7d2da8d78a6a8893c01eaf440045dd7d7ab Author: Weiqun Zhang Date: Fri Jul 28 11:06:13 2017 -0700 have to do this for pgi Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 1d1b0824465d6e002cbb846a03bfc5b3eac0fb5a Author: Michele Rosso Date: Fri Jul 28 10:43:41 2017 -0700 CMake: add missing files Src/Base/CMakeLists.txt commit 60b2d443ec8caaabc626f181f9a5275ce7ee769e Merge: 7cbf4c1f0 49e39e991 Author: Andreas Kreienbuehl Date: Fri Jul 28 07:07:53 2017 -0700 Merge branch 'clrdDiffuSolve' of https://github.com/akreienbuehl/amrex into clrdDiffuSolve commit 7cbf4c1f06879927b9b879b4b2b70567704c5082 Merge: 1697df7cb 682f56e58 Author: Andreas Kreienbuehl Date: Fri Jul 28 07:07:34 2017 -0700 Merge remote-tracking branch 'upstream/development' into clrdDiffuSolve commit 49e39e99144bb58e75db058a76d6deac2beecd42 Merge: 1697df7cb 682f56e58 Author: Andreas Kreienbuehl Date: Fri Jul 28 07:02:49 2017 -0700 Merge remote-tracking branch 'upstream/development' into clrdDiffuSolve commit 282c0ab5ed48049d23136a4d9cfc761e33004f52 Author: Weiqun Zhang Date: Thu Jul 27 17:10:35 2017 -0700 add USE_EB to make system Tools/GNUMake/Make.defs commit 07d53579414d42df37fc7516474bc103bfd77090 Author: Michele Rosso Date: Thu Jul 27 16:46:14 2017 -0700 CMake: default to Release if no build type is specified Tools/CMake/AMReX_Options.cmake commit 682f56e581b310e36f6f07d2211dfc6fe0b7daf3 Merge: d8fa2267f 5079de8f3 Author: Michael Zingale Date: Thu Jul 27 19:37:28 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit d8fa2267f31c452c5fccc0cbe12c878bfe05c133 Author: Michael Zingale Date: Thu Jul 27 19:36:39 2017 -0400 add keyword support to tests each test can now give a comma-separated lists of keywords with the `--keyword key` option, we can run only those tests with a specific keyword (e.g. gravity). Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit d28bc5f3eee4401191c8830db1bd3282eaf9f884 Author: dtgraves Date: Thu Jul 27 16:10:29 2017 -0700 fixed parallel bug identified by Marc. Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_IrregFABFactory.cpp commit df342fb53fc5926b2ec4634a50d9cb12d06c38ee Author: Michele Rosso Date: Thu Jul 27 16:04:11 2017 -0700 CMake: remove old cmake files Src/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/CCSEConfig-install.cmake.in Tools/CMake/CCSEConfigReport.cmake Tools/CMake/CCSEConfigVersion-install.cmake.in Tools/CMake/CCSELinkLine.cmake Tools/CMake/CCSEOptions.cmake Tools/CMake/CMakeParseArguments.cmake Tools/CMake/ExampleBoxLibConfig.cmake Tools/CMake/ExampleCMakeLists.txt_CCSEApp Tools/CMake/InstallManager.cmake Tools/CMake/ParseLibraryList.cmake commit 5079de8f329ea3198aee72eba0220d9762742fed Merge: ca8b11467 d699c2a2f Author: vince Date: Thu Jul 27 15:50:07 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ca8b11467b46143a0a5eb6c5809e6cce4ae78550 Author: vince Date: Thu Jul 27 15:49:52 2017 -0700 remove diagnostic. Src/Base/AMReX_DistributionMapping.cpp commit bcd7cb8fcdf62554b24b60ee31504e66fc8c0ac4 Author: Michele Rosso Date: Thu Jul 27 15:31:53 2017 -0700 CMake: modify install process CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake commit d699c2a2f05c54312b44ce884fec824ca75b9da1 Merge: 17813fc99 116e1d89a Author: dtgraves Date: Thu Jul 27 12:57:50 2017 -0700 Merge pull request #72 from AMReX-Codes/dtg_branch merging some bug fixes over commit aff1032c6032ce1f84e00434018c5b3562001a9c Author: Michele Rosso Date: Thu Jul 27 11:37:51 2017 -0700 CMake:clean-up obsolete CMakeLists.txt Src/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Tools/CMake/AMReX_Utils.cmake commit 230de365b7cca99a28f5361364b5e12947ff18e5 Author: Michele Rosso Date: Thu Jul 27 11:31:44 2017 -0700 CMake: modify structure of the build CMakeLists.txt Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/Extern/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/F_MG/sparse_solve.f90 Src/Particle/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 17813fc99aa1670561f23504c6b13cdca5e94982 Merge: 0beb09ac0 e63696fa6 Author: vince Date: Thu Jul 27 10:28:49 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 116e1d89a9dcf4b1e5684d076d9f6666d7c0e0bc Author: dtgraves Date: Thu Jul 27 10:23:57 2017 -0700 Changed MultiGrid.H to EBMultiGrid.H and AMRMultiGrid.H to AMREBMultiGrid.H per Marc's request. Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBMultiGrid.H Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit e63696fa6824d8b5e240eeaa92e0dd56d4d43c59 Author: Weiqun Zhang Date: Thu Jul 27 10:19:00 2017 -0700 fix call to mpi_finalize Tutorials/Basic/main_F/main.F90 commit d8502c443611fdc5a5d334aa3978d3d70595e3b2 Author: dtgraves Date: Thu Jul 27 10:11:49 2017 -0700 bug fixes and another argument to DivergenceOp to allow fortran bit to be bypassed Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 commit 1697df7cb05cd7fcfa9b72f8878ee89ec90abefa Author: Andreas Kreienbuehl Date: Thu Jul 27 07:13:45 2017 -0700 Simplified color-map selection Src/Base/AMReX_ParallelDescriptor.cpp commit 7b004fd92939471b16a9ccd5058167f17bcd0b6c Author: Weiqun Zhang Date: Thu Jul 27 06:29:53 2017 -0700 fix datatype Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Tutorials/Basic/main_F/main.F90 commit 0ede85f8427660ebb77e1dfdb47876a30477abae Author: Weiqun Zhang Date: Wed Jul 26 18:08:47 2017 -0700 new Tutorials/Basic/main_C Tutorials/Basic/main_C/GNUmakefile Tutorials/Basic/main_C/Make.package Tutorials/Basic/main_C/main.cpp commit b477952485e256749364b6b24f68491c19cef976 Author: kngott Date: Wed Jul 26 17:50:55 2017 -0700 First attempt to transfer ProfDataServices to amrex::DataServices. OldTutorials/DataServicesTest0/GNUmakefile Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Extern/ProfParser/AMReX_AVGDOWN_2D.F Src/Extern/ProfParser/AMReX_AVGDOWN_3D.F Src/Extern/ProfParser/AMReX_AVGDOWN_F.H Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.H Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_BLWritePlotFile.H Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/ProfParser/AMReX_XYPlotDataList.H Src/Extern/ProfParser/AMReX_XYPlotDataList.cpp Src/Extern/ProfParser/BLProfParser.l Src/Extern/ProfParser/BLProfParser.y Src/Extern/ProfParser/Make.package Src/Extern/ProfParser/backup/AMReX_AVGDOWN_2D.F Src/Extern/ProfParser/backup/AMReX_AVGDOWN_3D.F Src/Extern/ProfParser/backup/AMReX_AVGDOWN_F.H Src/Extern/ProfParser/backup/AMReX_BLProfStats.H Src/Extern/ProfParser/backup/AMReX_BLProfStats.cpp Src/Extern/ProfParser/backup/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.H Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/backup/AMReX_CommProfStats.H Src/Extern/ProfParser/backup/AMReX_CommProfStats.cpp Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.H Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.cpp Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.H Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.cpp Src/Extern/ProfParser/backup/BLProfParser.l Src/Extern/ProfParser/backup/BLProfParser.y Src/Extern/ProfParser/backup/Make.package Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 71233602c7383ee0205603eb4f76e4e82325666f Author: Weiqun Zhang Date: Wed Jul 26 17:17:10 2017 -0700 We have to pass a function adding parameters to amrex::Initialize, otherwise it might be too late. Src/Base/AMReX.H Src/Base/AMReX.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 Tutorials/Basic/main_F/main.F90 commit 0beb09ac036d4fc7a35db5d3dc7b357554c1ec6a Author: vince Date: Wed Jul 26 17:08:42 2017 -0700 merge fix. Docs/Notes.io_implementation Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Boundary/AMReX_FabSet.H Src/Particle/AMReX_Particles.H Tests/IOBenchmark/IOTestDriver.cpp commit abc9f69daca4fe4f4acf22952b58c06beb3d555c Merge: 6deffc253 8849f70ba Author: Andrew Myers Date: Wed Jul 26 16:31:44 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6deffc2532a0026847f46b932c47a6087a83466e Author: Andrew Myers Date: Wed Jul 26 16:31:34 2017 -0700 Adding a thread-safe random normal distribution to amrex. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 8849f70baf8c47cf734d20ccc076ce9183e2a526 Merge: 66a38bbb4 062ed4553 Author: vince Date: Wed Jul 26 15:49:19 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 66a38bbb43bc8e491ead43a7011047262cb93991 Merge: 4ee7b2554 f295dcdd6 Author: vince Date: Wed Jul 26 15:49:03 2017 -0700 merge fix. commit 062ed4553989fea6eddefc3739eb9eab3a86ef98 Merge: 727c64337 f295dcdd6 Author: Weiqun Zhang Date: Wed Jul 26 15:34:50 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4ee7b2554f55b2ed83b08d527629e012e8eafc5a Author: vince Date: Wed Jul 26 15:22:54 2017 -0700 some profiler optimizations. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit ee7eb3477b5caab85552a18dae72142fbdf79a4a Author: vince Date: Wed Jul 26 15:13:54 2017 -0700 minor tutorial changes. Tests/IOBenchmark/GNUmakefile commit 4f51e6a051d896eb81fc3855bc058e1fe67aadd1 Author: vince Date: Wed Jul 26 15:11:42 2017 -0700 minor tutorial changes. OldTutorials/DataServicesTest0/GNUmakefile OldTutorials/MultiFabTests_C/GNUmakefile OldTutorials/MultiFabTests_C/Make.package OldTutorials/Sidecar_EX1/NSidecarsTest.cpp commit f295dcdd670d68743731cb3e870c488fd6ba0fc7 Author: vince Date: Wed Jul 26 15:01:18 2017 -0700 dont send or clean up unused messages. Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Tests/IOBenchmark/GNUmakefile Tests/IOBenchmark/IOTest.cpp commit 727c643377ee6467de4d4f6059923235c643257f Author: Weiqun Zhang Date: Wed Jul 26 14:58:50 2017 -0700 Fortran: fix non MPI Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 7a99e7e20d7d44279738b47a1ad55cf7ad464938 Author: Weiqun Zhang Date: Wed Jul 26 14:52:30 2017 -0700 Fortran: allow users pass their own communicator and skip building parmparse database from command line arguments Src/Base/AMReX.cpp Src/Base/AMReX_ParmParse.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Tutorials/Basic/main_F/main.F90 commit d6fda8aa96d670065b3ea33d8ad6909118973e02 Author: Andreas Kreienbuehl Date: Wed Jul 26 13:12:05 2017 -0700 Introduced input parameter for choice of color-map Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit f301c71445bf0f986b527ecedfbca6b97da630d8 Author: Weiqun Zhang Date: Wed Jul 26 10:49:54 2017 -0700 Fortran parmparse: add optional return flag to query functions Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 commit a706f382ee50d57b73d8e9582e540ab18d83044c Author: Weiqun Zhang Date: Wed Jul 26 10:29:51 2017 -0700 update User's Guide Docs/AMReXUsersGuide/Fortran/Fortran.tex commit 7e38d370eb0c1d8cf67341f91f11ec1a28aa388a Author: Weiqun Zhang Date: Wed Jul 26 10:17:54 2017 -0700 remove old Fotran miniapp MiniApps/AMR_Adv_Diff_F90/GNUmakefile MiniApps/AMR_Adv_Diff_F90/GPackage.mak MiniApps/AMR_Adv_Diff_F90/advance.f90 MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 MiniApps/AMR_Adv_Diff_F90/inputs_2d MiniApps/AMR_Adv_Diff_F90/inputs_3d MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/prob.f90 MiniApps/AMR_Adv_Diff_F90/update_phi.f90 MiniApps/AMR_Adv_Diff_F90/write_plotfile.f90 commit 2a9d06f096a5a34ec77f39cfa6f960031b897d50 Author: Weiqun Zhang Date: Wed Jul 26 10:16:14 2017 -0700 Fortran: removed C++ main GNUmakefile.in Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/Amr/Advection_F/Source/fmain.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/Source/fmain.F90 Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile Tutorials/Basic/HeatEquation_EX1_F/fmain.f90 Tutorials/Basic/HelloWorld_F/fmain.f90 Tutorials/Basic/main_F/GNUmakefile commit be3e897f205cfb5b5f149303e8c79e7254f65074 Author: Weiqun Zhang Date: Wed Jul 26 07:07:53 2017 -0700 Fortran ParamParse: disable some functions for gfortran 4 because of (I believe) compiler bug Src/Base/AMReX_parmparse_mod.F90 Tutorials/Basic/main_F/main.F90 commit ad57f50837a7518d296bc64cf46e3d68131f8f95 Author: Weiqun Zhang Date: Tue Jul 25 21:38:41 2017 -0700 Fortran parmparse: trim before adding string Src/Base/AMReX_parmparse_mod.F90 commit de5584e1b5ac4300ff2c8184fd46725d1c0a7731 Author: Weiqun Zhang Date: Tue Jul 25 21:30:30 2017 -0700 Fortran ParmParse: implement add and refactor string Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 Src/Base/AMReX_string_mod.F90 Src/F_Interfaces/Base/AMReX_init_fi.cpp Tutorials/Basic/main_F/main.F90 commit 197c1eee98e06b9e2f1cc08b20d1fc10ba7fdea3 Author: Michele Rosso Date: Tue Jul 25 13:13:24 2017 -0700 Modify way of add include paths CMakeLists.txt Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Src/Particle/CMakeLists.txt commit 96d672397ae877601975f4a180989f2af1eab649 Author: Michele Rosso Date: Tue Jul 25 11:44:11 2017 -0700 Add utility to find subdirectories Tools/CMake/AMReX_Utils.cmake commit abff22ecb303c68c9fef81e679775381e4a1c65a Author: Weiqun Zhang Date: Tue Jul 25 06:46:28 2017 -0700 forgot to check in new files Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 commit 5255bbad8cc31beb4f2b5efd6391ed734e986035 Author: Weiqun Zhang Date: Tue Jul 25 06:45:43 2017 -0700 fix relative path Tutorials/Amr/Advection_F/Exec/Make.Adv Tutorials/Amr/Advection_octree_F/Exec/Make.Adv commit 0b1bc2f5fc5c5765acf5d101657f6af4c1f6af70 Author: Weiqun Zhang Date: Mon Jul 24 17:31:27 2017 -0700 Fortran: allow main in Fortran GNUmakefile.in Src/Base/AMReX_ParallelDescriptor.cpp Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/Make.package Tutorials/Basic/main_F/GNUmakefile Tutorials/Basic/main_F/Make.package Tutorials/Basic/main_F/main.F90 commit 9f0b9d5f6280fc03d780d6358eac1fdf194d2368 Author: Marc Day Date: Mon Jul 24 14:43:10 2017 -0700 wip Tests/GeometryShop/vofStructures/umapTest.H Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/umapTest_mod.f90 Tests/GeometryShop/vofStructures/umapTest_nd.f90 commit 894e15d5a8f1d4a67fe17cc389127b9fb59e76b9 Author: Weiqun Zhang Date: Mon Jul 24 14:17:11 2017 -0700 Fortran: add sum_boundary and average_sync Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit f191bb8ac6bfaaddd05a45a32ad54dc4f07554cc Author: Weiqun Zhang Date: Mon Jul 24 12:57:06 2017 -0700 OwnerMask is now iMultiFab Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 9f78b74a256d57020b300e9c1ca6e11440495788 Author: Michael Zingale Date: Mon Jul 24 15:06:47 2017 -0400 util_module -> box_util_module Tools/Postprocessing/F_Src/fnan.f90 commit cdddbf656f6056a0adcc0b36fedc4421251a6510 Author: Weiqun Zhang Date: Mon Jul 24 11:59:19 2017 -0700 add some specialized ifab functions Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 commit 724c202b0ee52205fb31346091fa7116e2dfadd5 Author: Andrew Myers Date: Fri Jul 21 17:28:36 2017 -0700 reverting Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 8c5d9228859cb030e0f76232412ab32248af2c56 Author: Andrew Myers Date: Fri Jul 21 16:00:19 2017 -0700 revert the periodic shift optimization for now Src/Particle/AMReX_NeighborParticlesI.H commit 979eee688c3ade49525b3347d0e1c63a8deea066 Merge: db71b1c74 3a726a1f3 Author: Andrew Myers Date: Fri Jul 21 15:22:49 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit db71b1c74e52111d5957f50a3de3e270568706d8 Author: Andrew Myers Date: Fri Jul 21 15:22:41 2017 -0700 some minor optimization /refactoring of the neighbor particle code. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit bf663f5ffebadfa895a89b1822e163688060386b Author: Max Katz Date: Fri Jul 21 11:23:02 2017 -0400 Link against the IBM OpenMP library Tools/GNUMake/comps/ibm.mak commit 3a726a1f3b49b971fb5e41888739a1996f33baf3 Author: Andy Nonaka Date: Thu Jul 20 17:39:01 2017 -0700 added a makeSFC distribution mapping interface (similar to the knapsack and roundrobin cases) Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit c52d2b3788feaa067c22f512c090a4ef73fb54ca Author: Weiqun Zhang Date: Thu Jul 20 15:34:54 2017 -0700 F_Interfaces: owner mask and override_sync Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 18834c9f86f28a5989df733f9c712ba15c3f03ec Merge: 030f1c504 aa6f31235 Author: Andrew Myers Date: Thu Jul 20 14:54:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 030f1c5049a4e933154551f319ce73037f31411d Author: Andrew Myers Date: Thu Jul 20 14:54:37 2017 -0700 Update these Tutorials to account for the recent changes to NeighborParticleContainer. Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/neighbor_list_2d.f90 Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit aa6f31235278767b927713389b219c30416627ab Author: Weiqun Zhang Date: Thu Jul 20 14:46:00 2017 -0700 fix comment Src/Base/AMReX_MultiFab.H commit bb5e29def605c9f4b2654c6a77feaad855940ad8 Merge: d2b4e447d c7eb385b4 Author: dtgraves Date: Thu Jul 20 14:16:30 2017 -0700 Merge pull request #61 from AMReX-Codes/dtg_branch fixed some bugs and wrote gradient operator that Marc wanted. commit c7eb385b4779e1cc0d9f3a66433a08f4fbb770d2 Author: dtgraves Date: Thu Jul 20 14:15:02 2017 -0700 a few random bug fixes along with a brand new EB gradient operator that passes its test. Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_AggStencilI.H Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/aggpwlfp.inputs Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/divop.inputs Tests/EBAMRTools/regression/ebcoarave.inputs Tests/EBAMRTools/regression/gradientOpTest.cpp Tests/EBAMRTools/regression/gradop.inputs Tests/EBAMRTools/regression/nwoebquadcfi.inputs commit d2b4e447dd4ef4c6aadcf3f0fd09a1ca15f48577 Author: Weiqun Zhang Date: Thu Jul 20 14:08:20 2017 -0700 add OwnerMask and OverrideSync functions that let owners override nonowners Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 8a60deec2dafbd83e1a0cd2055c781abc82560d0 Merge: 747210d86 9aae7fdb2 Author: Andrew Myers Date: Thu Jul 20 14:05:50 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 747210d86b3d3d597cdb2227772e9b605bbb200e Author: Andrew Myers Date: Thu Jul 20 14:05:40 2017 -0700 remove openmp pragmas from neighbor list code for now. Src/Particle/AMReX_NeighborParticlesI.H commit 9aae7fdb23ec9e4c5aedb7dec496d87bf7942597 Author: Weiqun Zhang Date: Thu Jul 20 10:01:47 2017 -0700 add a function performing nodal data sync via averaging Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 61e3fb1bd76022885f34c9ac302cbd544cd7c805 Author: Andrew Myers Date: Thu Jul 20 10:37:49 2017 -0700 left out a #ifdef for MPI. Src/Particle/AMReX_NeighborParticlesI.H commit 5c670eea608e1c69bec43431eda3e181735f49f0 Merge: 6365f16e6 8f367b16e Author: Andrew Myers Date: Thu Jul 20 10:25:54 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6365f16e61d634444ae7375dde6e2827a3835a28 Author: Andrew Myers Date: Thu Jul 20 10:25:42 2017 -0700 do not recompute the number of snds / rcvs unless it changes. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 8f367b16e472f871a45ce840bc19df5d6205165c Author: Weiqun Zhang Date: Thu Jul 20 09:34:47 2017 -0700 fix typo Docs/AMReXUsersGuide/Basics/Basics.tex commit e2b8a7c9f3b8200de4b991a2210e09f1de37d189 Merge: df1242597 7da68d2f5 Author: Weiqun Zhang Date: Thu Jul 20 09:35:08 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5a9d0179355781420c735635cffc705a3707ce71 Author: Marc Day Date: Wed Jul 19 17:53:42 2017 -0700 WIP for umap tests Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/umapTest.H Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/umapTest_mod.f90 Tests/GeometryShop/vofStructures/umapTest_nd.f90 commit 7da68d2f53b90b754dc3c5e29504c2b5e84edc3f Author: Andrew Myers Date: Wed Jul 19 13:57:05 2017 -0700 don't hard-code this cutoff. Src/Particle/AMReX_Particle_mod_3d.F90 commit e0d53c5c79393eeec3d527ada99b0c7b79d930e1 Merge: 6a289a2b9 9e88860b9 Author: Andrew Myers Date: Wed Jul 19 13:21:39 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6a289a2b9af95cb71b45f9a1538976d9959a1fb5 Author: Andrew Myers Date: Wed Jul 19 13:21:22 2017 -0700 add method to update the neighbor buffers without refilling them. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 9e88860b9ca33790ea7b4399477427b8011fc6c3 Merge: 9b702218a 826506003 Author: WeiqunZhang Date: Wed Jul 19 12:30:09 2017 -0700 Merge pull request #59 from zingale/development rewrite some of the area and volume terms commit 82650600310c60fc97a044ae95bf1f39d07fa616 Author: Michael Zingale Date: Wed Jul 19 14:45:25 2017 -0400 rewrite some of the area and volume terms this reduces roundoff for large values of r also use Pi and other constants from the constants header this closes #29 Src/Base/AMReX_COORDSYS_1D.F Src/Base/AMReX_COORDSYS_2D.F commit df1242597e2bf521c749d6444b32bd9953cb409d Author: Weiqun Zhang Date: Wed Jul 19 10:22:38 2017 -0700 quiet compiler Src/Amr/AMReX_StateData.H commit 69dc79e990078b69d6876bfeb20b6fbeea3b6d0d Merge: 7309fe78a 9b702218a Author: Weiqun Zhang Date: Wed Jul 19 10:01:17 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9b702218aa5cc660c5ba3c4d6c1f4c5d737e7841 Author: Weiqun Zhang Date: Wed Jul 19 10:00:50 2017 -0700 replace UINT32_MAX with std::mt19937::max() Src/F_BaseLib/bl_random_c.cpp commit 7309fe78a27113abbd36a385c1d589e23a614a76 Merge: b94723333 1a785555e Author: Weiqun Zhang Date: Wed Jul 19 09:41:14 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1a785555ee96f74b2a36b6f084c537aa38f90cb9 Author: Andrew Myers Date: Tue Jul 18 17:41:19 2017 -0700 Fortran version of buildNeighborList Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H commit 90a144e617d268e31b2ebfd5aaa2d42fb71fa465 Author: dtgraves Date: Tue Jul 18 15:10:44 2017 -0700 bug fix in divergenceop Src/EBAMRTools/AMReX_DivergenceOp.cpp commit 1ca92b8f4f226f2b910cd1d8f021a6dd22654683 Author: Michele Rosso Date: Tue Jul 18 13:42:51 2017 -0700 Update documentation Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit 5b16bdd57508b0ff778846b2fb92c8b3b84ae474 Author: Michele Rosso Date: Tue Jul 18 13:33:49 2017 -0700 Provide default install dir other than /usr/local Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake commit ffffd78dde1ce8ac86df88ce8fb5a5fd7410eab4 Author: Michele Rosso Date: Tue Jul 18 12:44:39 2017 -0700 Add CMake options to turn on/off FPE compiler flags Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 65997e8a0acfcfcbc2fe98374adadc56cc9e1fbf Merge: 757a5606b ed2d324be Author: dtgraves Date: Tue Jul 18 11:15:52 2017 -0700 Merge pull request #58 from AMReX-Codes/dtg_branch some bug fixes and a new divergence operator commit ed2d324be0a61571c83f6c23e35461ace7806643 Author: dtgraves Date: Tue Jul 18 11:14:39 2017 -0700 DivergenceOp now passes its test. Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Tests/EBAMRTools/regression/divergenceOpTest.cpp commit 05aeba879056087ddb90dd6cf9cb27c1d34e3867 Author: dtgraves Date: Mon Jul 17 16:54:47 2017 -0700 Per Marc's request, I added a standalone hybrid divergence operator. It compiles but testing is not complete Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/divergenceOpTest.cpp Tests/EBAMRTools/regression/divop.inputs commit 757a5606b3838eb46a125b1019702e994f781d5c Merge: fb7491037 9a48811f2 Author: Andrew Myers Date: Mon Jul 17 14:48:19 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fb7491037db632cf492f7dd311087d01917eece3 Author: Andrew Myers Date: Mon Jul 17 14:48:09 2017 -0700 optimizing / simplifying the neighbor list code. Src/Particle/AMReX_NeighborParticlesI.H commit 9a48811f2e0cd81f0ea3a7e3ee57343a35bcd7c4 Author: Weiqun Zhang Date: Mon Jul 17 12:47:26 2017 -0700 assert that we are not using tag that's too large Src/Base/AMReX_NFiles.cpp commit f922ac3337cde11212673e726fddf921cb7b8920 Author: Weiqun Zhang Date: Mon Jul 17 12:42:06 2017 -0700 Abort if MPI_Comm_get_attr failes to get MPI_TAG_UB. Add ParallelDescriptor::MaxTag() Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit acb7b7ad36244b708741624fd5569c7564886a2c Author: Andrew Myers Date: Mon Jul 17 10:33:16 2017 -0700 check getcwd error code. Src/F_BaseLib/backtrace_c.cpp commit 4d8fb6de09bb630cf5a714680dbb70f9573f00f8 Author: Andrew Myers Date: Mon Jul 17 10:20:08 2017 -0700 check return code of std::system in amrex::UtilCreateDirectoryDestructive Src/Base/AMReX_Utility.cpp commit 99cec8974d387ef7a5e07a8cd817e7343cf2e165 Merge: 6c6497e23 6eb1678eb Author: Andrew Myers Date: Mon Jul 17 09:59:06 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6c6497e2355d5c0028e117cd20a78956c3e7c670 Author: Andrew Myers Date: Mon Jul 17 09:58:55 2017 -0700 add option to sort nl after constructing it (useful for exactly comparing against the N^2 calculation. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 6eb1678eb93c82b883b6b2cbbd3b25b4c5ecb577 Author: Weiqun Zhang Date: Sat Jul 15 16:42:43 2017 -0700 more reduce funcitons Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 525d961ac4a74e7fb697a05cf8e9776a69c9bd9b Author: Weiqun Zhang Date: Sat Jul 15 16:17:15 2017 -0700 add more reduce functions that do multiple reductions without user packing and unpack into arrays Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit e55d878024c5e7a0dd7d62eb7399b9657a2a5c34 Author: Weiqun Zhang Date: Sat Jul 15 15:50:54 2017 -0700 reorganize reduce functions Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit cf34b31589dca8772b973c87484fe7afd175ff2d Author: Max Katz Date: Sat Jul 15 04:13:58 2017 -0400 Fix the offset in copytomem/copyfrommem again Src/Base/AMReX_BaseFab_nd.F90 commit 9a522156ac25d0141c2016db3e43816c7301e0d4 Author: Max Katz Date: Sat Jul 15 03:51:01 2017 -0400 Add device syncs after copyToMem/copyFromMem Src/Base/AMReX_FabArray.H commit 083347f1b96fc97b4940cf8552cfc8ada8fcb16f Author: Max Katz Date: Sat Jul 15 02:02:31 2017 -0400 Only do reductions when CUDA is enabled Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit e9ccf955d511f97018807b502ac9720fc4f3dcb8 Author: Max Katz Date: Sat Jul 15 01:45:50 2017 -0400 Fix the offset in copytomem/copyfrommem Src/Base/AMReX_BaseFab_nd.F90 commit 4ab1a8865ccb8f84558c7a4bdc92f1f930cb8acc Author: Max Katz Date: Sat Jul 15 00:11:16 2017 -0400 Do not perform Device operations for non-CUDA code Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_MFIter.H commit 481ce13b15b56ad858a7f363f756a3b5a0d849cd Merge: 278078c16 bf70914ee Author: Andrew Myers Date: Fri Jul 14 17:21:18 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 278078c16c9c0b514f4c158dd2141cbce15ff7c8 Author: Andrew Myers Date: Fri Jul 14 17:19:55 2017 -0700 also creating neighbor lists for ghost particles. Src/Particle/AMReX_NeighborParticlesI.H commit 435377ef4e1fda98c4f2b7aaff2e1ae83d848b83 Author: dtgraves Date: Fri Jul 14 16:45:27 2017 -0700 more progress on EBAMRElliptic. Parking this for now so I can write Pele operators. Src/EBAMRElliptic/AMReX_AMRMultiGrid.H Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/AMReX_MultiGrid.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_NoOpSolver.H Src/EBAMRElliptic/AMReX_VCAggStencil.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp commit bf70914ee57cd835ca6213a85e26ae98e619b353 Author: Weiqun Zhang Date: Fri Jul 14 16:09:28 2017 -0700 hypre: provide initial guess and add BoomerAMG to inputs Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Tutorials/HYPRE/ABecLaplacian/inputs commit 955b3806ff8a3ca5790de08693776b17c213266d Author: Weiqun Zhang Date: Fri Jul 14 15:56:14 2017 -0700 Hypre tutorial: print out error Tutorials/HYPRE/ABecLaplacian/ABL.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp Tutorials/HYPRE/ABecLaplacian/ABL_F.F90 Tutorials/HYPRE/ABecLaplacian/ABL_F.H commit d7ddf9ba42b5d082b53b294f04dc239d77d6198c Author: Weiqun Zhang Date: Fri Jul 14 14:28:53 2017 -0700 first pass of Hypre Boomer AMG Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp commit 3348b9c21b4822a93ccbc9cfbdf2e2ac775e10e1 Author: Weiqun Zhang Date: Fri Jul 14 10:31:37 2017 -0700 remove the inclusion of Hypre's Make.package from Make.hypre Tools/GNUMake/packages/Make.hypre Tutorials/HYPRE/ABecLaplacian/GNUmakefile commit 141307673586a9616d8297b1415ccd2cfa890541 Author: Andrew Myers Date: Fri Jul 14 15:12:29 2017 -0700 Offset the neighbor particle number by Np Src/Particle/AMReX_NeighborParticlesI.H commit b94723333e7d5436453cbf7860b41c70024d8c9f Author: Weiqun Zhang Date: Fri Jul 14 10:23:47 2017 -0700 Abort if message sizes in parallel copy and fillboundary do not match Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 1b0b3262d13fb544ebcc516cd0ff7ee7b9a1f234 Author: Weiqun Zhang Date: Thu Jul 13 21:05:02 2017 -0700 flush AMReX::Print by default Src/Base/AMReX_Print.H commit b0e893766c9ae802602a15e1eef9a767667563d7 Merge: ad88aa397 77c323b3f Author: vince Date: Fri Jul 14 12:21:49 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 61bb9c0a634679e45ca42bd1db4b7099d191dc3c Author: dtgraves Date: Fri Jul 14 12:19:39 2017 -0700 you know you have been staring at stuff too long when it pisses you off that Dirichlet and Neumann have different numbers of letters Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit ad88aa3974d369e4f4d02eae652b383e05ac2a72 Author: vince Date: Fri Jul 14 12:19:07 2017 -0700 call CleanUpMessages for nfilesiter. Src/Base/AMReX_NFiles.cpp commit 77c323b3f152cf863e34ccb95d72d357191cf2f5 Merge: 203267a6f ed780271e Author: Andrew Myers Date: Fri Jul 14 10:54:41 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 203267a6fd3685bea912d76917a14c8ccd6ed2c1 Author: Andrew Myers Date: Fri Jul 14 10:54:30 2017 -0700 update the short range force tutorials to reflect recent changes in NeighborParticleContainer. Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/main.cpp commit ed780271e9f530a11c71125f06dfe816e0c06dde Author: Ann Almgren Date: Thu Jul 13 21:42:56 2017 -0700 Add the ability to pass weights into the knapsack and round robin strategies -- the algorithms then use the weights instead of numpts. Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 6e88e97fdd66f8387ad67c1041959289cb770da6 Author: Andrew Myers Date: Thu Jul 13 19:04:12 2017 -0700 fixing fill neighbors for the case of ng>1 Src/Particle/AMReX_NeighborParticlesI.H commit 7d64ddbafb2daabb46c8a50e9371e5d2bdc7a5e8 Author: Andrew Myers Date: Thu Jul 13 18:59:27 2017 -0700 fixing another bug... Src/Particle/AMReX_NeighborParticlesI.H commit 425d87b75fa79484b3a2c3d2b17e91dd2933ed3f Author: Andrew Myers Date: Thu Jul 13 18:56:59 2017 -0700 got a sign wrong here. Src/Particle/AMReX_NeighborParticlesI.H commit e34b429e1d0165268c4fa81ff3dadba6519ddba4 Author: Andrew Myers Date: Thu Jul 13 18:53:08 2017 -0700 make these protected instead of private. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit aa3e8c835c817e227a9a31143796dc954df3a0cc Merge: 14efed3d1 d1299272c Author: Andrew Myers Date: Thu Jul 13 18:21:32 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 14efed3d1ccff85cb2c886f8ba1dea67ab2653d2 Author: Andrew Myers Date: Thu Jul 13 18:21:19 2017 -0700 use the input dmap and geom rather than getting it from the pc. Src/Particle/AMReX_NeighborParticlesI.H commit d1299272c15acf4dbd18b562fb78a5baa7daa690 Author: Weiqun Zhang Date: Thu Jul 13 18:12:31 2017 -0700 BoxArray intersection for a corner case in which the box array has a single nodal box with a single node in one of the directions Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.cpp commit a3bd15fdec1e4ea147f553d1abd455e8602c067f Author: Andrew Myers Date: Thu Jul 13 17:45:43 2017 -0700 make the applyPeriodic and packGhost functions take the lev Src/Particle/AMReX_NeighborParticlesI.H commit a2e5fa893d1712b67f816161d85a3c7b5cef2f28 Author: Andrew Myers Date: Thu Jul 13 17:42:37 2017 -0700 fix another typo. Src/Particle/AMReX_NeighborParticlesI.H commit c8ec9b8fd8e0e798c8776b88c80c0316f6dd2b2e Author: Andrew Myers Date: Thu Jul 13 17:40:59 2017 -0700 fix typo Src/Particle/AMReX_NeighborParticles.H commit 5d394139359e36e5c5bd73083db76c507078dd16 Author: Andrew Myers Date: Thu Jul 13 17:38:09 2017 -0700 Add some asserts for safety. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit afb6b010a8041492f7e3308da87c7e99227a1da5 Author: Andrew Myers Date: Thu Jul 13 17:02:32 2017 -0700 add a ParGDB constructor to the neighbor particle container. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit abb2495db5188530c830db4386d68fdcc684dbd0 Author: dtgraves Date: Thu Jul 13 16:17:10 2017 -0700 EBAMRElliptic continues to slouch toward Bethlehem Src/EBAMRElliptic/AMReX_AMRMultiGrid.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/Make.package Tests/EBAMRElliptic/exec/GNUmakefile Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 2989b715fc67fdee00730f02a774537900c4f4c7 Author: Weiqun Zhang Date: Thu Jul 13 11:08:21 2017 -0700 remove plt_compare_diff_grids Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit f3739b0f4d2f0b85c6a6b17be0fe8ed4c5b6c324 Author: Weiqun Zhang Date: Tue Jul 11 18:28:24 2017 -0700 WIP: hypre BoomerAMG Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/HYPRE/Make.package Tutorials/HYPRE/ABecLaplacian/ABL.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp commit 88c0f585ca11c6c892030689cbfc7d2e0290eb25 Merge: c65d02c68 6d3bc9b4e Author: Max Katz Date: Thu Jul 13 12:05:47 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 6d3bc9b4e71c22cd1495f922fc9f8bda2e22a523 Author: Michael Zingale Date: Wed Jul 12 19:24:30 2017 -0400 fix the case where no B params are specified Tools/F_scripts/write_probin.py commit 8dadd2905f96ed28f6fe03f77984bc8daac0a4d9 Author: Donald Willcox Date: Wed Jul 12 16:54:29 2017 -0400 In write_probin, use --managed flag to turn on CUDA managed probin vars (off by default). Tools/F_scripts/write_probin.py commit a7c486085e81fd5cf456c9590b29ed7f3552a57f Author: Donald Willcox Date: Wed Jul 12 16:33:42 2017 -0400 Modified write_probin to use argparse instead of getopt. Tools/F_scripts/write_probin.py commit 5f13821bd47581a8961f84315db4d9a7be51e86d Author: vince Date: Wed Jul 12 12:46:56 2017 -0700 fix for AddProcsToComp. Src/Amr/AMReX_Amr.cpp commit 0037cfce44defd4c009efd0f957dfe545fb0d5bb Author: Donald Willcox Date: Wed Jul 12 03:14:02 2017 -0400 Modified write_probin to use managed memory. Tools/F_scripts/write_probin.py commit 15e586b02fe8b6c4bce92914286f47e97ae2a8c8 Merge: d44b8df6e d8fb51dd2 Author: WeiqunZhang Date: Tue Jul 11 17:18:39 2017 -0700 Merge pull request #56 from zingale/development add a print_state (and print_state_n) method commit d8fb51dd2c5e5c2b324963dfc2c45d19bf40c8d6 Author: Michael Zingale Date: Tue Jul 11 20:17:05 2017 -0400 wrong one -- single component gets more precision Src/Base/AMReX_MultiFabUtil.cpp commit 2000c345b39c35a8c3cf48fda899c3ca76905986 Author: Michael Zingale Date: Tue Jul 11 20:15:00 2017 -0400 max precision Src/Base/AMReX_MultiFabUtil.cpp commit f879e99c784895b067fb1d573e687f46bc5037cc Author: Michael Zingale Date: Tue Jul 11 20:02:59 2017 -0400 much nicer C++ implementation of print_state (thanks to Weiqun for pointers) Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H commit 09a8dc7a486e64b1e32ca052f4f8b7a66e97d591 Merge: e06c008c7 d44b8df6e Author: Michael Zingale Date: Tue Jul 11 19:28:20 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit d44b8df6e8027afb084fc9a9b2b02df6f82286fb Author: Andrew Myers Date: Tue Jul 11 16:18:35 2017 -0700 adding a new test for tracer particles Tools/RegressionTesting/AMReX-tests.ini commit 1b7eeb231998e04d3545d0056877b0f053ab2414 Author: Andrew Myers Date: Tue Jul 11 16:17:23 2017 -0700 adding myself to the list of people who get emailed if the AMReX tests fail. Tools/RegressionTesting/AMReX-tests.ini commit c840d0d44781ee0ff72d1b75e2e89e7f634cac22 Author: Andrew Myers Date: Tue Jul 11 16:16:03 2017 -0700 set up one of the advection tutorials to use tracer particles. Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers commit e06c008c7c02dd73986a9cdb75d03f365a0ff53c Merge: e2c59d4f2 8f6badf40 Author: Michael Zingale Date: Tue Jul 11 19:00:18 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 8f6badf4064f2a0e52896d25f2db808462b947a8 Merge: 27cba3e54 6a8a0e561 Author: Andy Nonaka Date: Tue Jul 11 15:02:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 27cba3e54062b5c024e126f5f3ab61c088803b8b Author: Andy Nonaka Date: Tue Jul 11 15:01:47 2017 -0700 some extra documentation for the Base code Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/figs/flowchart.odg Docs/AMReXUsersGuide/Basics/figs/flowchart.pdf Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit e2c59d4f28726364d614101512067be9c75d0c7b Author: Michael Zingale Date: Tue Jul 11 17:33:34 2017 -0400 add a print_state (and print_state_n) method Useful for dumping out the state for a single zone, for debugging Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H commit 6a8a0e561d6fc976486a13beb377b0e9e3a6ae84 Author: Andrew Myers Date: Tue Jul 11 14:06:13 2017 -0700 1D and 2D versions of the deposit_particle_dx routines, while I'm at it. Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 commit 1f90147991d77bb289ff72b51f6a04c0f7f0e1d0 Author: Andrew Myers Date: Tue Jul 11 13:17:15 2017 -0700 Fix a couple of bugs in the routine I just added. Src/Particle/AMReX_Particle_mod_3d.F90 commit 1f7d650e0a2f41bb016f864b31127e922fa4724d Merge: 9bb4e5bc9 049b71662 Author: Andrew Myers Date: Tue Jul 11 12:47:10 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 049b7166273fe64bce52a23df609ab5b115d69d5 Merge: 49750ac87 f4cf063d2 Author: Weiqun Zhang Date: Tue Jul 11 12:37:26 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 49750ac879216cb7abe4fe885030df9c753d48bf Author: Weiqun Zhang Date: Tue Jul 11 12:37:15 2017 -0700 fix memory profiling for BoxArray Src/Base/AMReX_BoxArray.cpp commit 9bb4e5bc9593d7754cb750f6210e9fc93e229c2d Author: Andrew Myers Date: Tue Jul 11 11:04:10 2017 -0700 Fix copy/paste error. Src/Particle/AMReX_Particle_mod_3d.F90 commit e23c5c3b658ebf596f7282af2615023bbbc75d3e Author: Andrew Myers Date: Tue Jul 11 10:53:02 2017 -0700 Fortran routine for deposition when dx != particle_dx Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H commit f4cf063d242d5dfa067771f6bd37ac4da38ed372 Merge: ee888fd91 3984c7aa0 Author: Andrew Myers Date: Tue Jul 11 09:28:52 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ee888fd91413634296b89905f688552d8be86347 Author: Andrew Myers Date: Tue Jul 11 09:28:39 2017 -0700 can't assume one ghost cell here because of sub-cycling Src/Particle/AMReX_ParticleContainerI.H commit 3984c7aa0e1024654464c5fd20aea5118a8a7f47 Author: atmyers Date: Tue Jul 11 00:17:16 2017 -0700 DistributionMapping() -> DistributionMap() - the Mapping() version actually constructs an empty dm instead of returning the one used by this mf. Src/Base/AMReX_MultiFab.cpp commit 480376b3cfddaea98367540e1070740cb33742be Author: Ann Almgren Date: Mon Jul 10 18:30:59 2017 -0700 Remove unused pmap Src/Particle/AMReX_ParticleContainerI.H commit ca48266eb160a5fe6be9f021c236af744443c151 Merge: bad9d47de f6aa3ca0f Author: Andrew Myers Date: Mon Jul 10 17:53:05 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bad9d47dec8e188cb760e232d94f18a493eed418 Author: Andrew Myers Date: Mon Jul 10 17:52:29 2017 -0700 add some stuff to the docs about neighbor lists. Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Particle/neighbor_list.pdf Docs/AMReXUsersGuide/Particle/neighbor_list.tex commit f6aa3ca0f1884307f4d640f92d41bf706beaf0b9 Author: Weiqun Zhang Date: Mon Jul 10 17:05:02 2017 -0700 hypre: no need to make a new distributionmapping Src/Extern/HYPRE/AMReX_HypreABecLap.cpp commit 3bde0ea24193aa78f250fd40d1cdf392c2e92027 Merge: ed5bc4729 ffac06fd3 Author: atmyers Date: Mon Jul 10 16:48:01 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ed5bc4729314da931e1d089dcbf1bde63e421ad5 Author: atmyers Date: Mon Jul 10 16:47:19 2017 -0700 Turn on OpenMP by default in the NeighborList Tutorial. Tutorials/Particles/NeighborList/GNUmakefile commit b37e65b498c67080d83668191077028496a7225e Author: atmyers Date: Mon Jul 10 16:46:56 2017 -0700 turn on tiling and domain decomposition by default in the NeighborList Tutorial inputs file. Tutorials/Particles/NeighborList/inputs commit 4d0575b33a1145ef9d3b3b61529d6a8cb57c05d8 Author: atmyers Date: Mon Jul 10 16:37:38 2017 -0700 Much of the functionality of these tutorials is now implemented in AMReX. Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/inputs Tutorials/Particles/ShortRangeParticles/GNUmakefile Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/inputs Tutorials/Particles/ShortRangeParticles/main.cpp commit 1ff0614519e38166979941821931ae86eeb59129 Author: atmyers Date: Mon Jul 10 16:36:47 2017 -0700 move the neighbor list stuff to Src/Particle Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit ffac06fd3dba3295388a5bf86285c069a14d26a8 Author: Weiqun Zhang Date: Mon Jul 10 16:34:58 2017 -0700 add inputs Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Tutorials/HYPRE/ABecLaplacian/ABL.cpp Tutorials/HYPRE/ABecLaplacian/inputs commit a3d5f26018ab4ccbb7c07d59548cb778791aaa57 Author: atmyers Date: Mon Jul 10 16:22:24 2017 -0700 slight change to the check_pair method. Tutorials/Particles/NeighborList/NeighborListParticleContainer.H commit b3679c6f6c8e9bdcb133b212450a67a227e0cf9e Author: Weiqun Zhang Date: Mon Jul 10 16:14:56 2017 -0700 hypreabeclap: add communicator Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp commit 0556a141d21fd018b4ef20b762480fa641ce2bf2 Author: dtgraves Date: Mon Jul 10 16:10:51 2017 -0700 progress made in EBAMRElliptic. I am close to where I can start actually trying to run stuff. Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBSimpleSolver.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp commit 4ac962cabc6e096c5d70ff0688a8a48eb66ce372 Author: Weiqun Zhang Date: Mon Jul 10 16:02:08 2017 -0700 add hypre tutorial Tutorials/HYPRE/ABecLaplacian/ABL.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp Tutorials/HYPRE/ABecLaplacian/ABL_F.F90 Tutorials/HYPRE/ABecLaplacian/ABL_F.H Tutorials/HYPRE/ABecLaplacian/GNUmakefile Tutorials/HYPRE/ABecLaplacian/Make.package Tutorials/HYPRE/ABecLaplacian/main.cpp commit ea19c1d7c72360f9dcd539a1607ec0b8a034e9ea Author: Weiqun Zhang Date: Mon Jul 10 16:01:00 2017 -0700 more hypre Src/Boundary/AMReX_LO_BCTYPES.H Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp commit a263823cb346e09745a7d8382957203c927e55f0 Author: atmyers Date: Mon Jul 10 15:49:32 2017 -0700 make the distance function a 'check_pair' function. Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 289a15595c723df2073e174605fd2642efb35133 Author: atmyers Date: Mon Jul 10 15:38:56 2017 -0700 Moving the neighbor particle stuff into Src/Particle so it can be re-used elsewhere. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 4357692d5fc31d69f1bfa0be2f37050596326916 Author: atmyers Date: Mon Jul 10 15:37:05 2017 -0700 making these static constexpr seems to improve performance slightly. Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 286323caabf7ab2ccf448065f0cfbf790f2c6f66 Author: Weiqun Zhang Date: Mon Jul 10 11:16:13 2017 -0700 add some support for Hypre Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABec_3D.F Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/HYPRE/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.hypre commit e84a38298527fd06238de244dc0eae06f1211fe7 Author: Weiqun Zhang Date: Mon Jul 10 10:19:20 2017 -0700 converting size to int instead of int to unsigned. this is what the compiler implicitly does for us. Src/Base/AMReX_FabArray.H commit 1452440a99222f4e22d0679a7684d008dbf985b2 Author: Weiqun Zhang Date: Mon Jul 10 10:13:35 2017 -0700 move Make.local to the last Tools/GNUMake/Make.defs commit 43bf4f11919910769f750ec7734a0e82e2f20eed Author: atmyers Date: Mon Jul 10 10:08:28 2017 -0700 fix unsigned to signed integer comparison. Src/Base/AMReX_FabArray.H commit 5136b5385de7693e18244ba9b6a93a2c30d7ea10 Merge: bcae199f7 3d4394b1f Author: asalmgren Date: Sun Jul 9 16:32:48 2017 -0700 Merge pull request #55 from bcfriesen/add_craypat_docs_part1 Docs: add section describing simple profiling with CrayPat commit 3d4394b1fa6f7aa1181fdd75f39e7f671efd64af Author: Brian Friesen Date: Sun Jul 9 16:24:36 2017 -0700 Docs: add section describing simple profiling with CrayPat Info about advanced profiling techniques with CrayPat will come separately. Docs/AMReXUsersGuide/Profiling/Profiling.tex commit bcae199f717e93a82c17a82bc7c79703eabe7239 Merge: 6b1bec72c 0441a7a7b Author: asalmgren Date: Sun Jul 9 14:53:55 2017 -0700 Merge pull request #51 from atmyers/development Have the test suite also send an email if it has to abort for… commit 6b1bec72ce2eec5775129aa3619375e60b30d918 Merge: 260590e08 8518e5a3d Author: asalmgren Date: Sun Jul 9 14:53:31 2017 -0700 Merge pull request #54 from bcfriesen/add_craypat Add CrayPAT support commit 8518e5a3d5bbabbb7fed80fd27b97616fc1acea2 Author: Brian Friesen Date: Fri Jul 7 09:24:48 2017 -0700 Tools: add support for tracing user-defined regions with CrayPAT Tools/GNUMake/Make.defs Tools/GNUMake/tools/Make.craypat commit 4dc8e8782ffe3d501d4afe972af3f0ac632c384a Author: dtgraves Date: Sat Jul 8 18:26:46 2017 -0700 needed some functions to get FabArray to compile Src/GeometryShop/AMReX_EBFluxFAB.H commit c65d02c6838926ccef1c8aa9dff90ce2ba4f21c1 Author: Max Katz Date: Sat Jul 8 21:24:03 2017 -0400 Prefer L1 cache to shared memory when available Src/Base/AMReX_CUDA.F90 commit 22d28d234dadea2aeda70bbff2bebc05e15b9fe9 Author: Max Katz Date: Sat Jul 8 20:20:25 2017 -0400 Fix the kernel bounds in AmrLevel::Derive Src/Amr/AMReX_AmrLevel.cpp commit 4fea0da1fa71eb547921cff325e6f82e3a74b426 Author: Max Katz Date: Sat Jul 8 20:11:30 2017 -0400 Turn off CUDA 8 support on Titan Src/Base/AMReX_CUDA.F90 Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.olcf commit 67988f08ffd0b388566899f67edbb2f6f0abe82a Author: Max Katz Date: Sat Jul 8 20:10:48 2017 -0400 Return value to suppress compiler warning Src/Base/AMReX_MFIter.H commit 00417f9ada4061be9abcd07ed5654f972e9c2017 Author: Max Katz Date: Sat Jul 8 17:10:11 2017 -0400 Use correct deleter on operator new[] data Src/Base/AMReX_Device.H commit 19bf27838695cd7ca32f8c1c67b5fc4641250512 Author: Max Katz Date: Sat Jul 8 16:14:43 2017 -0400 Use smaller hunk sizes for small data Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.cpp Src/Base/AMReX_RealBox.cpp commit 2868ddcc03d1eadcf038e5fde96e87f173ce12a5 Author: Max Katz Date: Sat Jul 8 15:59:46 2017 -0400 Use the correct RealBox lo expression in derive Src/Amr/AMReX_AmrLevel.cpp commit f5e9c542c870a677f7eb5a0a7dbbb021e912c139 Author: Max Katz Date: Sat Jul 8 15:59:29 2017 -0400 Fix the nullification of RealBox data Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit fe3b0b548670c512ffd63fda494d2aa1c2fdd927 Author: Max Katz Date: Sat Jul 8 01:37:46 2017 -0400 Clean up various parts of BaseFab Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit c7f5a1755cbe4838f52da1e5f2401dff07e2f1e9 Author: Max Katz Date: Sat Jul 8 01:31:05 2017 -0400 Port copyToMem and copyFromMem to GPU Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 83a89e162698c89c8275a52696d45cb962717eba Author: Max Katz Date: Sat Jul 8 01:15:55 2017 -0400 Make copyToMem and copyFromMem void and thread-safe Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit c09c8fd61ceac96217afbac25028dd5041c33e34 Author: Max Katz Date: Sat Jul 8 01:15:15 2017 -0400 Add missing return statement Src/Base/AMReX_Device.H commit 23f70eee5a967bdd249257b0dc6c9fc36b732777 Author: Max Katz Date: Sat Jul 8 00:38:52 2017 -0400 Port BaseFab::norm, sum, dot product to GPU Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit eea091f190e705b20e11d04aa25fb075320eaf93 Author: Max Katz Date: Sat Jul 8 00:38:34 2017 -0400 Add a function to create a device pointer Src/Base/AMReX_Device.H commit 260590e08bf78f42564b404c988f1d4709e50bf2 Author: atmyers Date: Fri Jul 7 19:07:03 2017 -0700 move building the neighbor list into the compute forces routine. Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 220d3b3facbb416cefadd31d3e7226ab8f05be61 Merge: d432a3f6c 5b239ce3a Author: atmyers Date: Fri Jul 7 16:14:10 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d432a3f6c645e73845fb6d3401651e758b0e1b1b Author: atmyers Date: Fri Jul 7 16:13:56 2017 -0700 A tutorial that shows how to do neighbor lists for particles the see short-range forces. Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/Make.package Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/compare.py Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/neighbor_list_2d.f90 Tutorials/Particles/NeighborList/neighbor_list_3d.f90 Tutorials/Particles/NeighborList/neighbor_list_F.H commit 5b239ce3a1f34fe5bd3f44aa0eb4c3739f4db18e Merge: 5a8fbc29a ee4c5bbf2 Author: dtgraves Date: Fri Jul 7 15:16:58 2017 -0700 Merge pull request #53 from AMReX-Codes/dtg_branch Bug fix pull request. commit ee4c5bbf26a0b10862bbe7a2198630266fb7b335 Author: dtgraves Date: Fri Jul 7 13:45:53 2017 -0700 got face averaging to work. found subtle bug in EBFaceFAB in the process Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp Tests/EBAMRTools/regression/ebcoarave.inputs commit 9c12241f566123eb96b5df591d569716475dbe20 Author: Max Katz Date: Fri Jul 7 08:10:42 2017 -0400 Make cudaSetDevice be the first thing we do Src/Base/AMReX_CUDA.F90 commit dc1231993fdff49e5e373152140364311adbcae4 Author: Max Katz Date: Fri Jul 7 07:09:39 2017 -0400 Clean up the output about which GPU we're using Src/Base/AMReX_CUDA.F90 commit e2f9fd0cd5d0fd7a94554d350bc2c2118a975ca7 Author: Max Katz Date: Fri Jul 7 01:28:08 2017 -0700 Fix Intel Fortran compiler preprocessing of AMReX_REAL.H Src/Base/AMReX_REAL.H commit f1bc3ca1596dd109aee1d3267f388f2d1110d8c4 Author: Max Katz Date: Fri Jul 7 03:15:16 2017 -0400 Add some math functions to amrex_fort_module Src/Base/AMReX_fort_mod.F90 commit f60b74cc9879490cb173730d2a1825a9782188f9 Author: dtgraves Date: Thu Jul 6 16:21:51 2017 -0700 added the ability to averaging face centered data with EB. Does not pass its test yet. Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp commit 5a8fbc29a49e15b057e2ae37577e95e7c231a357 Author: Weiqun Zhang Date: Thu Jul 6 15:43:23 2017 -0700 fix one-sided MPI Src/Base/AMReX_FabArray.H commit 103bcf0cde8c29e89cab42d506941fe978fdc0ef Author: Michele Rosso Date: Thu Jul 6 10:12:52 2017 -0700 Fix typo in Cmake files. Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 9d32f94b125e75f67234e8351dcffca6ebabc060 Author: Michele Rosso Date: Thu Jul 6 10:12:52 2017 -0700 Fix typo in Cmake files. Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 1155ebf72b7edb32860fe901eb4862cc5dce6521 Author: Max Katz Date: Thu Jul 6 07:36:34 2017 -0400 Use an Arena to store device reducer data Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit fe71a5173edd6a42c3b819f4d8277d45fd3a3fc3 Author: Max Katz Date: Thu Jul 6 06:36:07 2017 -0400 Add a MFIter reduction operation for Reals Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 630421c06292ed6e8fede222657c5c41d86fa9ae Author: Max Katz Date: Thu Jul 6 04:06:28 2017 -0400 Add a MFIter function to register a RealBox Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_MFIter.H commit bc253977bf347ad274789fecaa982c22d3012d85 Author: dtgraves Date: Wed Jul 5 15:47:58 2017 -0700 Just to keep these messages different, I am looking for synonyms for 'slog'. Trudge? Schlep? Src/EBAMRElliptic/AMReX_AMRMultiGrid.H Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/Make.package Tests/EBAMRElliptic/exec/GNUmakefile Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit f71b74c71c6922baa87ebd40e4428948d6d58c78 Author: Max Katz Date: Wed Jul 5 01:13:17 2017 -0400 Make the CUDA device ID public Src/Base/AMReX_CUDA.F90 commit 5f231e7221f43a5c27c713704b3a0f20db80de16 Author: Max Katz Date: Tue Jul 4 19:10:00 2017 -0400 Get F90 build with CUDA working again Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/GPackage.mak commit e655d4a9ff90e9190c7d4739679a1b0f970c5bf9 Author: Max Katz Date: Tue Jul 4 18:36:15 2017 -0400 Do not compile dim3 without using nvcc Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 5112d1eb055a105a4c6a4c339ef4ac19da62acb4 Author: Max Katz Date: Tue Jul 4 03:18:32 2017 -0400 Fix the synchronize strategy in ParallelCopy Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_FabArray.H commit 94d5605b5a6ff22a0533fdf49e68961251240c09 Author: Max Katz Date: Tue Jul 4 01:53:24 2017 -0400 Make StateData::FillBoundary asynchronous Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit c31ccc764e598b094925b4c6245665a357aa44d0 Author: dtgraves Date: Mon Jul 3 15:45:03 2017 -0700 Continued the EBAMRElliptic slog. There is a lot here. Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp commit f8df87ff2af5d73e0689e355f3868bbc905ec031 Author: Max Katz Date: Mon Jul 3 18:34:01 2017 -0400 Disable FabArrayBase tiling when using CUDA Src/Base/AMReX_FabArrayBase.cpp commit 5486da25d003f5c44fc3bcc261d44e33df7a03fe Author: Max Katz Date: Mon Jul 3 17:43:54 2017 -0400 Use MFIter pointer registration in AmrLevel::Derive Src/Amr/AMReX_AmrLevel.cpp commit ed99ef01a179cfe66be66bf4dddb963a68b0edbb Author: Max Katz Date: Mon Jul 3 17:18:25 2017 -0400 Add MFIter::get_fortran_pointer to assist with scalar values for device routines There are cases in the code where we pass scalar values like the current time to a Fortran kernel, and we pass it by reference. An example is AmrLevel::Derive. For backward compatibility we do not want to change the interface -- that would break a lot of codes. But we also want to pass a device pointer for the CUDA version, and to allow asynchrony across MFIter indices. The solution is to store a shared_ptr with a pinned host (or device, but I've gone with pinned host for now to avoid a cudaMemcpy call) copy of the data, so that the lifetime of the data is the lifetime of the MFIter. For the CPU version of the code, the function effectively does nothing. Src/Base/AMReX_MFIter.H commit 010b8ff1f0b3305e7e022d59ef8b3695f172efec Author: Max Katz Date: Mon Jul 3 16:38:55 2017 -0400 Clean up temporary pointer creation Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_Device.H commit 282f5cec222d6fa889f02f81dd6ed19131a07ca5 Author: Ann Almgren Date: Sun Jul 2 17:07:19 2017 -0700 Fix the construction of the cost function in makeKnapSack Src/Base/AMReX_DistributionMapping.cpp commit d66f8057dd2d3c4c986e73f1ef3a0159424068b4 Author: Max Katz Date: Mon Jul 3 05:28:07 2017 -0400 Add hook to start profiler Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit 9e7792564cf370817b9e6c293082d2451b08ad8f Author: Max Katz Date: Mon Jul 3 05:09:01 2017 -0400 Avoid use of parallel module in CUDA initialization Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 28cddce212be7ca9098019963e14fb787eb493df Author: Max Katz Date: Mon Jul 3 04:46:06 2017 -0400 Avoid calls to cudaFree/cudaFreeHost at end of program Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 5d6d86864a73efbe82d678e51df52dd86af5597f Author: Max Katz Date: Mon Jul 3 04:03:48 2017 -0400 Do not throw error for CUDA runtime unloading Src/Base/AMReX_CUDA.F90 commit 4dd5f01065936020a26c8bec33ecc2206a96a140 Author: Max Katz Date: Mon Jul 3 03:37:35 2017 -0400 Delay initialization of the RealBox device memory Geometry contains a static RealBox object, and it was creating problems that a CUDA API call (to allocate memory) was being called before we got to the initialize_cuda step. By delaying allocation of the device memory until the first time we actually access the data, we still get the desired behavior from RealBox while not breaking the intended behavior that no CUDA API calls are done until we've mapped the MPI ranks to GPUs. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 4cfab94b8efd870c769554a4f8f3de142df586b7 Author: Max Katz Date: Mon Jul 3 01:59:38 2017 -0400 Enable round-robin assignment of MPI ranks to GPUs Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 9d9191ba0d3043f83b1913d1b8b305663e084c1e Author: Max Katz Date: Mon Jul 3 01:59:14 2017 -0400 Use nvcc as the MPI host compiler Tools/GNUMake/sites/Make.olcf commit bdcc57c67a3ff16e45e6a42396dfc0412f844f6d Author: Max Katz Date: Mon Jul 3 01:58:43 2017 -0400 Define a host compiler variable Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/pgi.mak commit 41e091eb86ce558cceaf983a79fcb52b38e6ea64 Author: Max Katz Date: Sun Jul 2 21:14:14 2017 -0400 Add NVML build support Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.olcf commit 402845a474d71b0dc71d96fd8411bd27411b4475 Author: Ann Almgren Date: Sun Jul 2 17:07:19 2017 -0700 Fix the construction of the cost function in makeKnapSack Src/Base/AMReX_DistributionMapping.cpp commit e2ddb568d4a141464dd1845c13c1d982b82794d9 Author: Max Katz Date: Sun Jul 2 17:59:28 2017 -0400 Port more BaseFab routines to the GPU Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit a5733db482c59bdd2eeeded48f529a30042f9a63 Author: Max Katz Date: Sun Jul 2 16:36:17 2017 -0400 Add function to get threads and blocks in C++ Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 23da7b926a347f9f31d7370ed45ecb6c3dbcafca Author: Max Katz Date: Sun Jul 2 16:35:56 2017 -0400 Remove the CUDA compiler Tools/GNUMake/Make.defs Tools/GNUMake/comps/cuda.mak commit 70e4805d195fadc7f756e3642e5ce71115de498d Author: Max Katz Date: Sun Jul 2 16:33:33 2017 -0400 Use nvcc/g++ as C/C++ compiler when using CUDA with IBM Tools/GNUMake/comps/ibm.mak commit 7017151f3dcd824f455ce97390a34fd8a40fca4d Author: Max Katz Date: Sun Jul 2 13:56:15 2017 -0400 Use nvcc/g++ as C/C++ compiler when using CUDA with PGI Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/pgi.mak commit 4ffdac87df294a2152dd72654a366f5abd75ff39 Author: Max Katz Date: Sun Jul 2 13:50:04 2017 -0400 Use the new dx call in advance Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit d5942652745d3f154c9ab755ea6b702c026a5fbe Author: Weiqun Zhang Date: Sun Jul 2 08:47:47 2017 -0700 avoid self-move Src/Particle/AMReX_ParticleContainerI.H commit 489b30dd72f44ab5ef140bbde6f0121e2cd69c88 Author: Max Katz Date: Sun Jul 2 05:12:32 2017 -0400 Use pinned data for RealBox and CoordSys Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 3f37361285e09a0385d697abf6e6ff5d8e1e87fc Author: Max Katz Date: Sun Jul 2 05:11:48 2017 -0400 Make get_host_pointer a no-op for non-CUDA builds Src/Base/AMReX_Device.cpp commit 6935925bff74344e7b6d16b616b9515eca613047 Author: Max Katz Date: Sun Jul 2 03:50:49 2017 -0400 Insert a device synchronize after MultiFab creation Src/Base/AMReX_FabArray.H commit b2264768035b9bd2029e390481ec6cd2fca49426 Author: Max Katz Date: Sat Jul 1 07:45:02 2017 -0400 Get FillDomainBoundary working on the GPU Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit 2e4eec0d6221c02c88d6d6cc222a38020e1778c0 Author: Max Katz Date: Sat Jul 1 07:29:07 2017 -0400 Fix error in the BaseFab arenas Src/Base/AMReX_BaseFab.cpp commit 9192d5f7301d3e0a2abc66b0d7225b1291c0a314 Author: Max Katz Date: Sat Jul 1 07:20:23 2017 -0400 Make some some arguments const Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 7eb20c26eb92c52fa07de7bae74a203a8799991a Author: Max Katz Date: Sat Jul 1 05:20:04 2017 -0400 Port the 1D and 2D filcc to GPU-friendly versions Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 commit 5faa9223b2c34fc02f6f3992d01d400eab842cff Author: Max Katz Date: Sat Jul 1 04:09:40 2017 -0400 Complete GPU-friendly port of 3D filcc Src/Base/AMReX_FILCC_3D.F90 commit bdae016df0e7ed1de63eedec5b2f04758caa6847 Merge: 5d5adbb6f ae5bba0f5 Author: Max Katz Date: Sat Jul 1 00:52:08 2017 -0400 Merge branch 'gpu' into gpu_lessmanaged commit ae5bba0f5cd6d1596d3d6ee09cfedd69aaef9940 Author: Max Katz Date: Sat Jul 1 00:51:27 2017 -0400 Use a new thread block layout Src/Base/AMReX_CUDA.F90 commit 38073b46d734547aa52f9d5e33577d7cbd288583 Author: dtgraves Date: Fri Jun 30 15:44:13 2017 -0700 the slog continues Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/AMReX_VCAggStencil.H Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/simpleMeshRefine.cpp commit 0441a7a7b4459c6fd758c225232e54ae0ba301a0 Author: Andrew Myers Date: Fri Jun 30 15:35:49 2017 -0700 Have the test suite also send an email if it has to abort for whatever reason (if emails are turned on...) Tools/RegressionTesting/params.py Tools/RegressionTesting/test_util.py commit ecedcbc9ed0b4b5ef1776d144e9dde03a34ec59d Author: Weiqun Zhang Date: Fri Jun 30 15:03:01 2017 -0700 option to turn off checkInput() Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit ea023eb640ede33b00c912f689f1d9ccb6f112a1 Merge: 79153d30b c86200557 Author: Weiqun Zhang Date: Fri Jun 30 12:23:07 2017 -0700 Merge branch 'master' into development Conflicts: Tools/CMake/PreprocessAMReXFortran90.cmake commit 79153d30bda597c06628c431839e819ea8801bd4 Author: Ann Almgren Date: Fri Jun 30 09:44:23 2017 -0700 Fix the sizing and offset of mf_to_be_filled in AssignDensityFort. Src/Particle/AMReX_ParticleContainerI.H commit 3d88f58fd35891655f08f7ab8f3570c4eec9d91d Author: Andrew Myers Date: Thu Jun 29 23:00:29 2017 -0700 fix momentum deposition for Nyx. Src/Particle/AMReX_Particle_mod_3d.F90 commit d754f3d7aa7de087861a65fd939cc2a7b0f63dee Author: Andrew Myers Date: Thu Jun 29 22:58:49 2017 -0700 don't need my own plot file routine for this test. Tests/Particles/AssignDensity/main.cpp commit 5d5adbb6fb0c01755f066a51cbfcea64f9a0f1ce Merge: 09ee3bc4f db80a1a43 Author: Max Katz Date: Fri Jun 30 01:47:28 2017 -0400 Merge branch 'gpu' into gpu_lessmanaged commit 09ee3bc4fcacae9c89c1f4c82b8aa6de8c1bda57 Author: Max Katz Date: Fri Jun 30 01:43:56 2017 -0400 Remove managed memory in Box class Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit db80a1a43045c26882fd96f150f8f5d01488ed49 Author: Max Katz Date: Fri Jun 30 01:14:22 2017 -0400 Fix the obsolete macros Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit 0aca9e5e419aaf707520dcb943d51c8c047e3b4a Author: Max Katz Date: Fri Jun 30 01:09:54 2017 -0400 Add some forgotten files to the heat equation case Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/physbc.cpp commit 43856da0ad863b52f560b57e93bd61155a98e54d Author: Max Katz Date: Fri Jun 30 01:00:52 2017 -0400 Set the null stream as the default stream Src/Base/AMReX_CUDA.F90 commit 72397fcc1ff73e7a5626989d7d57f4d70acb1c30 Merge: 9b8bd5e90 afd51fb2c Author: Max Katz Date: Fri Jun 30 00:58:12 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit f496f22e98a8ca3d92913360abd3ec844042fb7f Merge: d5c6d1b63 232da02dd Author: vince Date: Thu Jun 29 17:27:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d5c6d1b630dfe9ee3f5cd107287bb26b9e0ef426 Author: vince Date: Thu Jun 29 17:27:12 2017 -0700 fixes for 1d slicing. Src/Extern/amrdata/AMReX_DataServices.cpp commit 232da02dd7ee903b5d809743a40344347b5046d2 Merge: 615cd94e2 5ab90a41f Author: Andrew Myers Date: Thu Jun 29 17:26:14 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 615cd94e2ebafcd0d84c909d8a2405ad069c322d Author: Andrew Myers Date: Thu Jun 29 17:25:57 2017 -0700 Make eps an optional argument instead of a static member of RealBox. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 5ab90a41f8495085975d04d2a8ebb817d1b73799 Author: Ann Almgren Date: Thu Jun 29 16:39:02 2017 -0700 Add some checking of input parameters -- the tests here are a subset of the tests that Amr.cpp does. Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit c6a065498ae7c9106acabfad2cab110db4273b5d Author: Ann Almgren Date: Thu Jun 29 16:38:49 2017 -0700 Fix the error messages Src/Amr/AMReX_Amr.cpp commit a3c4bb7d7e22ec2302a3a0f3543e2623aada515e Merge: 456c37688 ebc701840 Author: Ann Almgren Date: Thu Jun 29 12:52:42 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 456c3768867272bfa7b7c70597c86ffdc19db17f Author: Ann Almgren Date: Thu Jun 29 12:50:05 2017 -0700 Update how grids are created (section 5.3.5) Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit ebc701840d2a94537bf7df92dc2e9c4ce5405be9 Merge: 01d058330 8696d1b3e Author: Michele Rosso Date: Thu Jun 29 12:37:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 01d05833066cf1209fcb2ef5858bc6b9ff26f478 Author: Michele Rosso Date: Thu Jun 29 12:37:24 2017 -0700 Some Cmake clean-up CMakeLists.txt Tools/CMake/TransformVersion.cmake commit afd51fb2c243fcdce2fa29cd1c5f584f677fd970 Merge: dc35e9b28 8696d1b3e Author: Michael Zingale Date: Thu Jun 29 04:44:04 2017 -0400 Merge branch 'development' into gpu commit 8696d1b3e53af8bc935e71c8053036c3fdce5035 Author: Weiqun Zhang Date: Wed Jun 28 17:31:57 2017 -0700 fix amrex_particle_real for typecheck Tools/GNUMake/Make.rules commit 247574b6590b96287306f75645a3d40968ad5b17 Merge: cfc4d5f7b 0ca8d80d9 Author: vince Date: Wed Jun 28 17:11:57 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit cfc4d5f7b47fdcb4bea6ed1a6321e68484aae070 Author: vince Date: Wed Jun 28 17:11:42 2017 -0700 added to the profiling and visualization documentation. Docs/AMReXUsersGuide/Profiling/Profiling.tex Docs/AMReXUsersGuide/Visualization/Visualization.tex commit 0ca8d80d9ac422c9e9036a964bcae1c1b83507c7 Merge: 4a7597617 1115ee894 Author: Ann Almgren Date: Wed Jun 28 16:55:17 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4a75976175a060c7503f0d9f98240c2aae829381 Author: Ann Almgren Date: Wed Jun 28 16:54:44 2017 -0700 Update the Grid Creation subsection. Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit e578f94691799e6b8370acf5449eecfdfafe35db Author: Ann Almgren Date: Wed Jun 28 16:54:33 2017 -0700 fix typo in comment Src/AmrCore/AMReX_AmrMesh.cpp commit 1115ee8945fe22c05fd28d12a9fdbb5a50d8e433 Merge: 8b8b39e77 a7ab67e2c Author: Michele Rosso Date: Wed Jun 28 16:29:22 2017 -0700 Merge branch 'mr-cmake' into development commit a7ab67e2cd4115faf8cc56f21677572f8c1ab069 Author: Michele Rosso Date: Wed Jun 28 16:28:37 2017 -0700 Update documentation on cmake Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit 550972afaac237dc26f1e0d5f5b5a3c3f45930b8 Author: Michele Rosso Date: Wed Jun 28 15:52:00 2017 -0700 Add new pre-preprocessor flags to cmake implementation Tools/CMake/AMReX_Config.cmake commit e5dec5966738a17e52f231e052ba0250b31a04f3 Merge: 3c88bb047 9e591871e Author: Michele Rosso Date: Wed Jun 28 15:34:44 2017 -0700 Merge branch 'development' into mr-cmake commit 8b8b39e7796232d7b2aac1e7f9776400ad0ec89a Author: Weiqun Zhang Date: Wed Jun 28 15:28:59 2017 -0700 User's Guide: wip Docs/AMReXUsersGuide/Debugging/Debugging.tex commit 7c472ae911762f4341a9c681d56fe7beaaa83e26 Author: Weiqun Zhang Date: Wed Jun 28 15:22:46 2017 -0700 update deprecated gfortran option Tools/GNUMake/comps/gnu.mak commit 3c88bb047c6633f041434e33ef4f769e2a2713eb Author: Michele Rosso Date: Wed Jun 28 14:57:44 2017 -0700 Some clean-up Tools/CMake/InstallManager.cmake commit 786958cf7d9d4ec5e1ffbdf9c46161b21606d418 Author: Michele Rosso Date: Wed Jun 28 13:29:04 2017 -0700 Fix typo CMakeLists.txt commit e51728ed19fd87a820b565dfd1b13c517d9ca4f7 Author: Michele Rosso Date: Wed Jun 28 13:03:22 2017 -0700 More changes to cmake system CMakeLists.txt Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/InstallManager.cmake commit 9e591871ecc4555469433e4ec9955d1fb14abdd8 Author: Andrew Myers Date: Wed Jun 28 10:02:29 2017 -0700 switch order of these loops. Src/Particle/AMReX_OMPDepositionHelper_1d.F90 Src/Particle/AMReX_OMPDepositionHelper_2d.F90 Src/Particle/AMReX_OMPDepositionHelper_3d.F90 commit 98a3e56f6025c90710f2289923afbb7f83ccac3f Author: Ann Almgren Date: Wed Jun 28 09:27:20 2017 -0700 Resolve amrex namespace problems. Src/Extern/hpgmg/BL_HPGMG.H Src/Extern/hpgmg/BL_HPGMG.cpp commit 3b310d13e3fe3e97e63e2886bc9ecd02eae6109a Author: Ann Almgren Date: Tue Jun 27 18:10:42 2017 -0700 Make sure to resize the local fab to be tile_size*ncomp (to allow for ncomp > 1) Src/Particle/AMReX_ParticleContainerI.H commit b11da912796adf3e2311ca5316278ee7315b7fc3 Merge: 814538ec5 0bb538de1 Author: Andrew Myers Date: Tue Jun 27 17:44:37 2017 -0700 merging commit 814538ec531d5395effa499e37dc0ce52ebbe77b Author: Andrew Myers Date: Tue Jun 27 17:43:35 2017 -0700 Forgot to turn off ncomp check here. Src/Particle/AMReX_ParticleContainerI.H commit 0bb538de18e73c41b53bc4e1a8be1a06624232ca Author: Ann Almgren Date: Tue Jun 27 17:43:11 2017 -0700 1) Fix incorrect print statement 2) Remove assertion on (ncomp == 1) in AssignDensityFort since we now correctly take ncomp > 1 cases. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit a85084617cd5c73aec11009dcce39a08f4dd5785 Author: Ann Almgren Date: Tue Jun 27 16:57:27 2017 -0700 Fix initialization of nthreads -- move it into InitRandom Src/Base/AMReX_Utility.cpp commit 4f09beb593fd62c373f72205f68520598add716e Author: Andrew Myers Date: Tue Jun 27 16:41:15 2017 -0700 generalize fortran deposition routines to use ncomps. Src/Particle/AMReX_OMPDepositionHelper_1d.F90 Src/Particle/AMReX_OMPDepositionHelper_2d.F90 Src/Particle/AMReX_OMPDepositionHelper_3d.F90 Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H commit 4c789f63fe7f63edb196f0aab1e12515b711e39a Merge: fa21635cd 99603c558 Author: Ann Almgren Date: Tue Jun 27 16:00:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit fa21635cd38d307e252b3abc6467a4703ff0535c Author: Ann Almgren Date: Tue Jun 27 16:00:01 2017 -0700 Added run-time parameters and an explanation of how grids are created Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit 99603c558ff47362f9f7e5481ca037a3eff2fc81 Author: Andy Nonaka Date: Tue Jun 27 15:25:13 2017 -0700 updates to doc Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex commit df8a80c977f191902d0f8a311f9f2bb8cd4973e0 Author: Weiqun Zhang Date: Tue Jun 27 10:14:16 2017 -0700 User's Guide: octree Docs/AMReXUsersGuide/Fortran/Fortran.tex commit 4ba990a7a5d91af69138365c61b9b2dcd08d804b Author: Michele Rosso Date: Tue Jun 27 08:58:35 2017 -0700 Add source file for tiny profiling Src/Base/CMakeLists.txt commit 7c9415eae07538212b996b123e28188dcb444cec Author: Weiqun Zhang Date: Tue Jun 27 06:33:29 2017 -0700 remove old license Src/Base/OpenSource.txt commit 55fd11d0ca138d92a1b94b03989de024db21d487 Author: Weiqun Zhang Date: Tue Jun 27 06:28:08 2017 -0700 fix tutorials Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 commit 9b8bd5e90b0911db404cafe9f9c5627f16224917 Author: Max Katz Date: Mon Jun 26 23:51:58 2017 -0400 Start the profiler at the end of Amr initialization Src/Amr/AMReX_Amr.cpp commit d0af2865040b0d15d8d3704958deeba913b9d279 Author: Max Katz Date: Mon Jun 26 23:46:11 2017 -0400 Add C++ hooks to start and stop the profiler Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit cadf29a89d13eb2d39b0a5ae1b0834d0b4e6e894 Author: Weiqun Zhang Date: Mon Jun 26 18:05:24 2017 -0700 User's Guide: AMR in Fortran interface Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/Fortran/Fortran.tex Docs/AMReXUsersGuide/GNUmakefile commit 8c867b1d67d65a02006e359a2115f4f4a34878cb Author: Michele Rosso Date: Mon Jun 26 17:40:13 2017 -0700 Add option for tiny profiling Tools/CMake/AMReX_Config.cmake commit 5763df03a787f543bd8e11d14ebcacc7397a4f29 Author: Weiqun Zhang Date: Mon Jun 26 16:46:53 2017 -0700 F_Interfaces: fix component index bug Docs/AMReXUsersGuide/Fortran/Fortran.tex Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit ebc2e4f15a974b3e824b04cba8eed85f9f2c4e3a Author: Weiqun Zhang Date: Mon Jun 26 14:18:58 2017 -0700 User's Guide: Fortran interface basics Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Fortran/Fortran.tex Tutorials/Basic/HeatEquation_EX1_F/advance.f90 commit 8b55b4bedb74fc8d9d93974d5617b3c17d53a4ad Merge: 61c9d955f f55be70bf Author: Klaus Weide Date: Mon Jun 26 15:14:10 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f55be70bfdd5f33ef7fecf0c6d5e6c9fa0cc3af1 Author: Weiqun Zhang Date: Mon Jun 26 12:40:26 2017 -0700 F_interfaces: fix bug in setval and parallelcopy; note that the component index starts with 1 in Fortran Src/Base/AMReX_fort_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 61c9d955fa08d5f0387c2fcee037868f8609db90 Merge: dd6e4360b e2abf3f8e Author: Klaus Weide Date: Mon Jun 26 11:26:44 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit dc35e9b2837ff419e4d68e290e84d2f1e8563653 Author: Michael Zingale Date: Mon Jun 26 05:05:51 2017 -0400 fix linking with IBM XL and CUDA Tools/GNUMake/comps/ibm.mak Tools/GNUMake/sites/Make.olcf commit 68952a5265ce175479f181507044bdaed16ed38d Author: Max Katz Date: Mon Jun 26 03:06:51 2017 -0400 Skip finalization routine if using XL Src/Base/AMReX_parmparse_mod.F90 commit 2e5f43273d5165ae8206826753a06ed4a608e8f5 Author: Max Katz Date: Mon Jun 26 02:52:34 2017 -0400 Remove CUF kernels; these should be replaced with real CUDA later Src/Base/AMReX_BaseFab_nd.F90 commit 463a3a4f72775ca00eaf64aa013267e9283411ec Author: Max Katz Date: Mon Jun 26 02:48:24 2017 -0400 Replace logical with integer to satisfy bind(c) property Src/Base/AMReX_CUDA.F90 commit 3973c3bff8f7e3c4358e1bc27d045da1bc2141cb Author: Max Katz Date: Mon Jun 26 02:41:19 2017 -0400 Create interface to cudaProfilerStart/cudaProfilerStop Src/Base/AMReX_CUDA.F90 commit 1fcb19e22cdfb6614c82f0807cbf224cab68edd2 Author: Max Katz Date: Mon Jun 26 02:30:09 2017 -0400 Use thread-safe XL compiler when using CUDA Tools/GNUMake/comps/ibm.mak commit ce35354fa6c5f8ff529f067866bb9656c912cb3b Author: Max Katz Date: Mon Jun 26 01:40:24 2017 -0400 Redefine the CUDA attributes(global/device) macros Tools/GNUMake/Make.defs commit 17ffe789826d0f3685755d7fa8dce2efe61a4e33 Author: Max Katz Date: Mon Jun 26 01:09:13 2017 -0400 Create device copies of data in AmrLevel::derive Src/Amr/AMReX_AmrLevel.cpp commit 2cd7e86550eab1c1f532ace078b8995f80104ea3 Author: Max Katz Date: Mon Jun 26 00:27:39 2017 -0400 Create device copies of data in FillBoundary Src/Amr/AMReX_StateData.cpp commit dfdeb01f14489a453e5012d8ece676c8d422ec1c Author: Max Katz Date: Sun Jun 25 17:21:39 2017 -0400 Add Device hook for stream synchronize Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit e2abf3f8e2cbb14a2aaaf44e15a77b1133b66a5a Author: atmyers Date: Sun Jun 25 11:33:03 2017 -0700 don't need to define partMF in this test anymore. Tests/Particles/AssignMultiLevelDensity/main.cpp commit 2496146ee560c0e196c5919d8d1d55ed7b82a554 Author: atmyers Date: Sun Jun 25 11:30:46 2017 -0700 make behavior of AssignDensityFort consistent with AssignDensity in that the mfs don't need to be defined before being passed in. Src/Particle/AMReX_ParticleContainerI.H commit b109461da16346cb6f1a07cc51e2c9de5837220e Author: Max Katz Date: Sun Jun 25 06:01:40 2017 -0400 Have registerBox return the box Src/Base/AMReX_MFIter.H commit 896b2c7de8ccdac6b8a83971089a4448ec159f1c Author: Max Katz Date: Sun Jun 25 05:11:02 2017 -0400 Add Device hooks for malloc, free, memcpy Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit c4f048ffdcb29d1e16b1985c3999184ec76352a4 Author: Weiqun Zhang Date: Sat Jun 24 22:09:06 2017 -0700 F_Interfaces: add amrex_multifab%parallel_copy Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 1dd25ae16d681a6f136fa8406672a1aaedde58e5 Author: Max Katz Date: Sat Jun 24 21:19:08 2017 -0400 Use long x-blocks for coalesced memory access Src/Base/AMReX_CUDA.F90 commit 732be31ad965d38d16251926676328e2187786be Author: Ann Almgren Date: Sat Jun 24 16:57:16 2017 -0700 Remove all references to STATIONDATA, SLABSTAT or MAKESLICE in AMReX_Amr* or Make.package or CMakelists.txt Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/CMakeLists.txt Src/Amr/Make.package commit aeb8df3acd9e76d7f3f7cf2b19293c6408cda379 Author: Ann Almgren Date: Sat Jun 24 16:53:27 2017 -0700 None of the applications use MAKESLIDE_3D any more (and it can always be recovered from git history and/or the old BoxLib repo) Src/Amr/AMReX_MAKESLICE_3D.F Src/Amr/AMReX_MAKESLICE_F.H commit 9fdd37e2a9b03e2cf1ed23c55a454baaff6067ec Author: Ann Almgren Date: Sat Jun 24 16:52:17 2017 -0700 None of the applications use SlabStat any more (and it can always be recovered from git history and/or the old BoxLib repo) Src/Amr/AMReX_SLABSTAT_1D.F Src/Amr/AMReX_SLABSTAT_2D.F Src/Amr/AMReX_SLABSTAT_3D.F Src/Amr/AMReX_SLABSTAT_F.H Src/Amr/AMReX_SlabStat.H Src/Amr/AMReX_SlabStat.cpp commit 814b8242225c7dccc0d81d5ac9a49e1d362e59db Author: Ann Almgren Date: Sat Jun 24 16:49:49 2017 -0700 None of the applications use StationData any more (and it can always be recovered from git history and/or the old BoxLib repo) Src/Amr/AMReX_StationData.H Src/Amr/AMReX_StationData.cpp commit fe4de436ba9ef6463043fbd5408c70c3e2e4e9c7 Author: Ann Almgren Date: Sat Jun 24 16:47:52 2017 -0700 Update the Profiling section and spell-check the entire document. Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/Fortran/Fortran.tex Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Profiling/Profiling.tex Docs/AMReXUsersGuide/Visualization/Visualization.tex commit 67a5ce31f1c2d46d2bb0933b08ff2480f7595ba7 Author: Ann Almgren Date: Sat Jun 24 16:31:45 2017 -0700 Add material from Readme.profiling -- but this still needs Vince to make a pass. Docs/AMReXUsersGuide/Profiling/Profiling.tex commit cc2a94927e841b873af7f8c4f90f6f558a11f40f Author: Max Katz Date: Sat Jun 24 18:07:12 2017 -0400 Sync up HeatEquation with development The filcc call had to be modified temporarily until we get the BCs working on the GPU. Src/Base/AMReX_BCUtil.cpp Tutorials/GPU/HeatEquation_EX1_C/Make.package Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit 9043be6156adcdd9ab75f91103aa6d21f5fbba72 Author: Max Katz Date: Sat Jun 24 17:35:33 2017 -0400 Create a device pointer for a FAB's nvar Src/Base/AMReX_Arena.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 85ebfd03b27b0c9f2810d28f3959aa42a9fd3860 Merge: dd6e4360b 798a23f1b Author: Klaus Weide Date: Sat Jun 24 16:15:19 2017 -0500 Merge branch 'development' into kw-development commit 637f96c9ccb212c931dd1fa146fbab9894da2334 Author: Max Katz Date: Sat Jun 24 17:04:05 2017 -0400 Set blocks and threads before entering Fortran Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit da0a5391b4ac1f9ec330112e5147d5bbf334b2f3 Author: Max Katz Date: Sat Jun 24 16:24:51 2017 -0400 Create a current CUDA stream variable Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_CUDA.F90 commit 798a23f1b9944fe07387e406ba90de046ce94c5d Merge: 142b1d40a 0c4a25ff5 Author: Andrew Myers Date: Sat Jun 24 12:56:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 142b1d40ab51cc79cfad9c489768671da0809f8b Author: Andrew Myers Date: Sat Jun 24 12:56:24 2017 -0700 A version of the electrostatic pic tutorial that works in 2D. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/GNUmakefile Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_2d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit 002721675fa5b3612dea66bec74b543cf007df52 Author: Max Katz Date: Sat Jun 24 12:57:51 2017 -0400 Clarify intent of dm Src/F_BaseLib/knapsack.f90 commit 6cfd3a24d614cae9e76c323be158a97ead0346e9 Merge: 074362db1 3b9a83664 Author: Max Katz Date: Sat Jun 24 09:55:55 2017 -0700 Merge pull request #47 from dwillcox/gpu Workaround for AMReX Issue 46 commit 074362db10bb23b2c4cfcb1624d3b860d4109408 Author: Max Katz Date: Sat Jun 24 03:08:09 2017 -0400 Lower the optimization level when using CUDA Tools/GNUMake/comps/pgi.mak commit e58e2d4f8917472d1d0a32b46a4bf5dc6d004084 Author: Max Katz Date: Sat Jun 24 01:43:39 2017 -0400 Do not set default stream, to avoid compiler bug Src/Base/AMReX_CUDA.F90 commit 3b9a83664ec612ddd61c8242d734af61aeb62e73 Merge: 6b967d0f4 f48070b78 Author: dwillcox Date: Sat Jun 24 00:54:07 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 6b967d0f42e3d6071a5fa6a65b9cf09e368006a2 Author: dwillcox Date: Sat Jun 24 00:53:25 2017 -0400 Pass dm to function make_box_key as workaround for suspected PGI 17.4 bug. Src/F_BaseLib/knapsack.f90 commit f48070b78c9c09716a8ea65ef30ae51d7f05ba62 Author: Max Katz Date: Fri Jun 23 23:15:15 2017 -0400 Initialize with NULL value for non-CUDA Src/Base/AMReX_Device.cpp commit 7bfff2613f28bf43beb239889d90d078e6c69dcc Author: Max Katz Date: Fri Jun 23 23:14:09 2017 -0400 Remove unnecessary CUDA ifdef Src/Base/AMReX_Device.cpp commit 297f2d35e96e033f892269cd167e2ff13362a972 Merge: 007719d19 0c4a25ff5 Author: Max Katz Date: Fri Jun 23 23:10:48 2017 -0400 Merge branch 'development' into gpu commit 0c4a25ff5c794939c7ab1befd2b132daa561f59a Author: Andy Nonaka Date: Fri Jun 23 18:48:22 2017 -0700 updates to Amr source doc Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex commit 17bc75c1aa2d06dd6085fac333bbacb8e5a40e2f Author: Michele Rosso Date: Fri Jun 23 18:04:14 2017 -0700 Downgrade cmake minimum required version to 3.3 CMakeLists.txt commit 87de2655f18183bfd58a4e2479ec7375c88c2795 Author: Andy Nonaka Date: Fri Jun 23 15:07:05 2017 -0700 note on running particles in Advection_AmrLevel Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex commit 84bfb385d8f481b4746be819c8eb7e3297c7b260 Author: Andy Nonaka Date: Fri Jun 23 15:02:04 2017 -0700 particle stuff in Advection_AmrLevel Src/Amr/AMReX_AmrLevel.H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs commit ca8b2d30c19b3c37404aa03eebe1b4b77047728a Author: dtgraves Date: Fri Jun 23 13:52:35 2017 -0700 fixed a broken test. now all the EBAMRTools tests also run in parallel Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/runalltests.mpi.sh commit 9efec27a4fd07891d866a044a9f7d7c86ecb8594 Author: Michele Rosso Date: Fri Jun 23 13:16:36 2017 -0700 Fix bugs in new cmake implementation Src/AmrCore/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/FindCCSE.cmake commit dd6e4360b037f9e6284af8d2ae8b985121ad6f39 Merge: c62cab7fb 4de9874ca Author: Klaus Weide Date: Fri Jun 23 14:31:06 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4de9874ca28b16592cf394ac1cab19ff4f57d612 Author: Andy Nonaka Date: Fri Jun 23 11:55:40 2017 -0700 various small cleanups to tutorial code Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/probin Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 commit 59006ca0794d8340e1c775d13b22785d481c300d Author: Michele Rosso Date: Fri Jun 23 11:19:36 2017 -0700 Comment out 'Find Perl' code Tools/CMake/FindCCSE.cmake commit 029be9937c2ab6e255f5703485ea8e8b5b41afdb Merge: cdbb70905 f1ea38539 Author: dtgraves Date: Fri Jun 23 10:26:12 2017 -0700 Merge pull request #45 from AMReX-Codes/dtg_branch Push parallel fixes to development. commit c62cab7fbedb35679fce45294c362f38dd1aa889 Merge: 3c83c7d20 cdbb70905 Author: Klaus Weide Date: Fri Jun 23 11:56:14 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f1ea385394dad42075be12d0ae5d650bfbef6f0c Author: dtgraves Date: Fri Jun 23 09:32:22 2017 -0700 All EB tests now work in parallel, including I/O. Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMDI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/regression/ebio.2.inputs Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/runalltests.mpi.sh commit cdbb70905b5d34d34b6e343b5582f34e9b23d9a1 Author: Weiqun Zhang Date: Fri Jun 23 06:47:24 2017 -0700 remove ifdef USE_PARTICLES around function declarations Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles_F.H commit 5670d4e368b9e4e0836736a370aed9aa96b3d9db Author: Andy Nonaka Date: Thu Jun 22 18:19:56 2017 -0700 Remove old BoxLib docs. You can find the tex in the BoxLib repo if you need it (or in the git history here) Docs/BoxLibUsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex Docs/BoxLibUsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/subcycling_algorithm.eps Docs/BoxLibUsersGuide/GNUmakefile Docs/BoxLibUsersGuide/GettingStarted/GettingStarted.tex Docs/BoxLibUsersGuide/GettingStarted/VisIt_2D.eps Docs/BoxLibUsersGuide/GettingStarted/VisIt_3D.eps Docs/BoxLibUsersGuide/GettingStarted/edison.run Docs/BoxLibUsersGuide/GettingStarted/edison_omp.run Docs/BoxLibUsersGuide/Introduction/AMR.eps Docs/BoxLibUsersGuide/Introduction/Introduction.tex Docs/BoxLibUsersGuide/Introduction/boxlib_directory_bw2.eps Docs/BoxLibUsersGuide/Introduction/castro_scaling.eps Docs/BoxLibUsersGuide/Introduction/data_loc.odg Docs/BoxLibUsersGuide/Introduction/data_loc2.eps Docs/BoxLibUsersGuide/Introduction/index_grid.odg Docs/BoxLibUsersGuide/Introduction/index_grid2.eps Docs/BoxLibUsersGuide/Introduction/lmc_scaling.eps Docs/BoxLibUsersGuide/Introduction/maestro_scaling.eps Docs/BoxLibUsersGuide/Introduction/varden1.eps.REMOVED.git-id Docs/BoxLibUsersGuide/Introduction/varden2.eps.REMOVED.git-id Docs/BoxLibUsersGuide/Introduction/varden3.eps.REMOVED.git-id Docs/BoxLibUsersGuide/Introduction/varden4.eps.REMOVED.git-id Docs/BoxLibUsersGuide/LinearSolvers/LinearSolvers.tex Docs/BoxLibUsersGuide/Preface/Preface.tex Docs/BoxLibUsersGuide/README Docs/BoxLibUsersGuide/Regression/test_suite.tex Docs/BoxLibUsersGuide/Regression/testsuite.eps Docs/BoxLibUsersGuide/UsersGuide.tex commit a106491ec30ca57e6ab3ff9ff9a5dcb125dcc395 Author: Andy Nonaka Date: Thu Jun 22 18:04:39 2017 -0700 more doc work Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex commit 6ddf6afba1f88f620673f0be6dc792841c9e2d57 Author: Andy Nonaka Date: Thu Jun 22 17:43:12 2017 -0700 docs update Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.odg Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.pdf Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv commit 5399420b861636340fd0eaaccf221c3d3d970a6a Author: Marc Day Date: Thu Jun 22 16:40:23 2017 -0700 Start eb fortran work by copying the test code for inf norm. Also, build face aperatures and eb geom info in a form suitable for passing to fortran. Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/umapTest_nd.f90 commit 1896b077308726d3898a759002133040bfe95bb4 Author: Andy Nonaka Date: Thu Jun 22 16:32:52 2017 -0700 make AmrLevel::thePlotFileType() and AmrLevel::okToContinue virtual (and not pure virtual) removed overriding functions from tutorial Src/Amr/AMReX_AmrLevel.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 43eac5cc24fb0e9678487d8c555ecb6650a93377 Author: Michele Rosso Date: Thu Jun 22 16:26:14 2017 -0700 Disable c++11 gnu extensions CMakeLists.txt commit 5b56f85f01b792df59ef3ed5f8ecaf8bccf44c1c Author: Michele Rosso Date: Thu Jun 22 16:14:13 2017 -0700 Fix some bugs with new cmake CMakeLists.txt Src/Base/CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 110516c2dc0c02ba956763a2e355498752488811 Author: Andy Nonaka Date: Thu Jun 22 16:13:04 2017 -0700 AmrLevel::writePlotFile is no longer pure virtual (it is simply virtual with a default implementation) change the Advection_AmrLevel tutorial to call the default implementation. Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit de4352bb221c9a969660538d46cc23912a69eb72 Author: Marc Day Date: Thu Jun 22 15:51:10 2017 -0700 Create eb data structrues in order to facilitate building lapl op, for example. Tests/GeometryShop/vofStructures/umapTest.cpp commit 2e49665f47a079af81baf3efde63a77e520d30a6 Author: Marc Day Date: Thu Jun 22 15:50:21 2017 -0700 Comment out unused variables in BaseUmap.H Src/Base/AMReX_BaseUmap.H commit 5ada997ad4a2b3fd1cf14ebbb63190e8e1fb0a76 Author: Michele Rosso Date: Thu Jun 22 14:59:15 2017 -0700 Move some utility functions in AMReX_Utils.cmake Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/PreprocessAMReXFortran.cmake commit 374f524a971252e8113bc5c73c79f4c332891a1f Merge: 7c8dd3cb6 1e2d71c6e Author: Marc Day Date: Thu Jun 22 13:29:54 2017 -0700 Merge branch 'rgrout/sparse_fab' into vof-work commit 7c8dd3cb6c8a7c5256742e214d59746f4ee26400 Author: Marc Day Date: Thu Jun 22 13:28:45 2017 -0700 WIP: nothing interesting Tests/GeometryShop/vofStructures/umapTest.cpp commit 06c25fca883cdb203df5d5602600bf915be5e07c Author: Andrew Myers Date: Thu Jun 22 13:03:08 2017 -0700 do domain decomposition by default. Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit 0aeda4d83c1564f9c79f4f4456b4863573569aa3 Author: Michele Rosso Date: Thu Jun 22 12:44:32 2017 -0700 Re-organize CMake structure CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake commit 1e2d71c6e071b00ec45632790eb328c6142d440f Merge: ec39f28d4 98103684f Author: Grout Date: Thu Jun 22 11:18:18 2017 -0600 Merge branch 'rgrout/sparse_fab' of github.com:AMReX-Codes/amrex into rgrout/sparse_fab commit ec39f28d44bfb15ce3df6a8ac7ea0e1c2d7e8eb1 Author: Grout Date: Thu Jun 22 11:17:55 2017 -0600 Stripped allocation check that did not make sense with new object Src/Base/AMReX_BaseUmap.H commit 484da6a088ed93a8d63e78a5b1ecd19a2715b602 Author: Andrew Myers Date: Thu Jun 22 10:01:24 2017 -0700 removing some more unused variables. Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/main.cpp commit 2a3f318178f7dadded12a65b56288f500f6041ee Merge: 805bfeb92 b06249277 Author: Andrew Myers Date: Thu Jun 22 09:53:30 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 805bfeb92ffde7696321b4121c27732130e0efa1 Author: Andrew Myers Date: Thu Jun 22 09:52:54 2017 -0700 remove some more no-longer-needed temporaries. Tutorials/Particles/ElectrostaticPIC/main.cpp commit 55d3f8999a3fe72d7c5c8d2d7457aac53f9f31c8 Author: Andrew Myers Date: Thu Jun 22 09:51:57 2017 -0700 remove tmp_phi, which is not actually used anymore. Tutorials/Particles/ElectrostaticPIC/main.cpp commit c327b0fc3112c2fa5f95240d4eeec646e8cf2870 Author: Andrew Myers Date: Thu Jun 22 09:50:51 2017 -0700 Change the setup of this test to match Vay et. al. 2012. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit b0a90efdede70856c7c618b7698e7433f26da89f Merge: bee2c1079 98103684f Author: Marc Day Date: Thu Jun 22 09:49:03 2017 -0700 Merge branch 'rgrout/sparse_fab' into vof-work commit b062492771eac7e2365aff1b058cd36e6670ca4c Author: Weiqun Zhang Date: Thu Jun 22 09:40:20 2017 -0700 The plot file type needs to be "HypreCLaw-V1.1", not "AMReX". Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 5516e530fad13cd15d94db5e79d8ea6342e91227 Author: Weiqun Zhang Date: Thu Jun 22 09:35:50 2017 -0700 fix path to amrex home Tutorials/Amr/Advection_F/Exec/Make.Adv Tutorials/Amr/Advection_octree_F/Exec/Make.Adv commit 007719d19fd41682e1d43439c4443813fdf97ae5 Author: Max Katz Date: Thu Jun 22 06:02:16 2017 -0400 Fix a logic error in when to update the device copies Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_RealBox.H commit 342f9da65a40e98b049798a2c14919d98eaddfdb Author: Max Katz Date: Thu Jun 22 03:50:51 2017 -0400 Insert device synchronizes in DEBUG mode Src/Base/AMReX_MFIter.cpp commit 0c88bc1b8727af7836fa8dd8087b18014f786461 Author: Max Katz Date: Thu Jun 22 02:37:03 2017 -0400 Refactor a little to hide CUDA in Device class Src/Base/AMReX.cpp Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp commit 8e078bb9a77bac32883cc60224d16774c3ffdbfd Author: Max Katz Date: Thu Jun 22 02:00:35 2017 -0400 Do error checking in MFIter Src/Base/AMReX_MFIter.cpp commit 23fca5156778f588a3b2ec065b844d53c3486fc1 Author: Max Katz Date: Thu Jun 22 02:00:21 2017 -0400 Add a test for any runtime/kernel launch errors Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 56deb77ce559f261a707c4aa6a72c0e96b28cc41 Author: Max Katz Date: Thu Jun 22 01:40:01 2017 -0400 Use loVectF/hiVectF in BL_TO_FORTRAN macros Src/Base/AMReX_ArrayLim.H commit bee2c1079fcb540279dfa8543c3ecca879416ef5 Author: Marc Day Date: Wed Jun 21 17:57:09 2017 -0700 WIP: Remove debugging info Tests/GeometryShop/vofStructures/umapTest.cpp commit 98103684f8817a3ec9634601122928f91db8823f Author: Marc Day Date: Wed Jun 21 17:54:06 2017 -0700 Fix case on include file Tests/C_BaseLib/tUMap.cpp commit caa4c4f980e0dfb700e0f2488ea5aefafbf52930 Author: Marc Day Date: Wed Jun 21 17:34:43 2017 -0700 WIP: rework umap test to build CutCells and CutFaces with cell index of parent coarse object to allow that multi-level eb operations can be done in Fortran. Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/umapTest.cpp commit 8df2cea69466efe6ddbb6ee0132fb77649e6c167 Author: Weiqun Zhang Date: Wed Jun 21 16:50:11 2017 -0700 User's Guide: start Fortran chapter Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Fortran/Fortran.tex Docs/AMReXUsersGuide/GNUmakefile Tutorials/Basic/HelloWorld_F/GNUmakefile Tutorials/Basic/HelloWorld_F/fmain.f90 commit dd66e7cd9ddaf002a9be0523917cabe7203ca7d8 Author: Andy Nonaka Date: Wed Jun 21 14:01:41 2017 -0700 tutorial cleanup Tutorials/Amr/Advection_AmrLevel/Source/main.cpp commit de13f1e51b92f89ae79fa19faa87054294fe9678 Author: Grout Date: Wed Jun 21 14:32:15 2017 -0600 Add skeleton of how to access Umap from fortran; temporarily turn off failure for non-existant data; test to compute norm using fortran interface Src/Base/AMReX_BaseUmap.H Src/Base/AMReX_BaseUmap_f.H Src/Base/AMReX_BaseUmap_nd.f90 Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tUMap.cpp commit e792ce1a20faa7cfcc2e487fe3e370ee839a623a Merge: 48daaedb5 06bfb7e6c Author: WeiqunZhang Date: Wed Jun 21 12:46:50 2017 -0700 Merge pull request #43 from kweide/development some simple corrections to UsersGuide commit 3c83c7d20c9efaeba8f59bf67ab0af78d5f54473 Merge: 06bfb7e6c 48daaedb5 Author: Klaus Weide Date: Wed Jun 21 14:36:02 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 48daaedb58ad014def2e96e09b359507498e6dfd Author: Andy Nonaka Date: Wed Jun 21 11:22:24 2017 -0700 cout -> amrex::Print() Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/main.cpp commit 9ce323f59f537d29848eb5473c119b9dd06e36c5 Merge: 8929a2223 b0c1a59d1 Author: Andy Nonaka Date: Wed Jun 21 11:05:30 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8929a2223e8b98dd82a84d0c5a10a5c16e5499c0 Author: Andy Nonaka Date: Wed Jun 21 11:05:07 2017 -0700 State_Type -> Phi_Type (to avoid confusion) more documentation Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 9ed7257d8c9454c534f5bfa75c82a5c7b06899f4 Author: Andy Nonaka Date: Wed Jun 21 11:03:38 2017 -0700 State_Type -> Phi_Type (avoid confusion) Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex commit b0c1a59d13b723a645fd77ea0dc87e951ca536be Author: Weiqun Zhang Date: Wed Jun 21 10:12:36 2017 -0700 move some new Fortran tutorials from OldTutorials to Tutorials Tutorials/Amr/Advection_F/Exec/Make.Adv Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_F/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/Amr/Advection_F/Exec/SingleVortex/inputs Tutorials/Amr/Advection_F/Exec/SingleVortex/inputs.physbc Tutorials/Amr/Advection_F/Exec/SingleVortex/inputs.rt Tutorials/Amr/Advection_F/README Tutorials/Amr/Advection_F/Source/Make.package Tutorials/Amr/Advection_F/Source/Src_2d/Make.package Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_F/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_F/Source/amr_data_mod.F90 Tutorials/Amr/Advection_F/Source/averagedown_mod.F90 Tutorials/Amr/Advection_F/Source/bc_mod.F90 Tutorials/Amr/Advection_F/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/fillpatch_mod.F90 Tutorials/Amr/Advection_F/Source/fmain.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 Tutorials/Amr/Advection_F/Source/tagging_mod.F90 Tutorials/Amr/Advection_octree_F/Exec/Make.Adv Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/inputs Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/inputs.rt Tutorials/Amr/Advection_octree_F/README Tutorials/Amr/Advection_octree_F/Source/Make.package Tutorials/Amr/Advection_octree_F/Source/Src_2d/Make.package Tutorials/Amr/Advection_octree_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_octree_F/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_octree_F/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_octree_F/Source/amr_data_mod.F90 Tutorials/Amr/Advection_octree_F/Source/averagedown_mod.F90 Tutorials/Amr/Advection_octree_F/Source/bc_mod.F90 Tutorials/Amr/Advection_octree_F/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_octree_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_octree_F/Source/fillpatch_mod.F90 Tutorials/Amr/Advection_octree_F/Source/fmain.F90 Tutorials/Amr/Advection_octree_F/Source/initdata.F90 Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/Source/plotfile_mod.F90 Tutorials/Amr/Advection_octree_F/Source/tagging_mod.F90 commit cf87a98cdf10be8003ef59e2d1cadbeedfa6bfeb Author: Andy Nonaka Date: Wed Jun 21 09:59:08 2017 -0700 added back in check to make sure a fine level already hasn't been regridded from a coarser level regrid Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 9037d3e6396e3a03dba5640c4d2f4056547ce542 Author: Michele Rosso Date: Wed Jun 21 09:46:46 2017 -0700 Start re-writing of AMReX Cmake CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit ed2e194ba59f8340c01e47926649910ff857f535 Author: Andy Nonaka Date: Wed Jun 21 09:29:50 2017 -0700 cleanup tutorial Tutorials/Amr/Advection_AmrLevel/Source/Adv.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_advance.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_dt.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_io.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_setup.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/LevelBldAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/Make.package commit 9d68e3c300ca2f9959e03e3aeadb615c09321aa9 Author: Andy Nonaka Date: Wed Jun 21 08:56:36 2017 -0700 move AMR_Adv_C example into Tutorials/Amr/Advection_AmrLevel and get it compiling/running again OldTutorials/AMR_Adv_C/README Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/probin Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Make.package Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/probin Tutorials/Amr/Advection_AmrLevel/README Tutorials/Amr/Advection_AmrLevel/Source/Adv.H Tutorials/Amr/Advection_AmrLevel/Source/Adv.cpp Tutorials/Amr/Advection_AmrLevel/Source/AdvBld.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_F.H Tutorials/Amr/Advection_AmrLevel/Source/Adv_advance.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_dt.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_io.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_setup.cpp Tutorials/Amr/Advection_AmrLevel/Source/Make.package Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Make.package Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Make.package Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Make.package Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 Tutorials/Amr/Advection_AmrLevel/Source/main.cpp commit ee45cbd6b9e48fbb59c9c6223cb25fb57ab36244 Author: Andy Nonaka Date: Wed Jun 21 08:26:09 2017 -0700 cleanup of tutorial and associated documentation Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore/Source/Make.package Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit 717c03163a4d4960758f606ec8bbf4fe868998c0 Author: Max Katz Date: Wed Jun 21 05:01:56 2017 -0400 Use default stream to simplify logic Src/Base/AMReX_CUDA.F90 commit 8d7abb2b29d649b537178c70efe23c6ef656939f Author: Max Katz Date: Wed Jun 21 04:58:38 2017 -0400 Create a gpu_error function Src/Base/AMReX_CUDA.F90 commit ea621137507c077270534618ae81206ad0386203 Author: Max Katz Date: Wed Jun 21 04:43:10 2017 -0400 Add a hook to set the GPU stack limit Src/Base/AMReX_CUDA.F90 commit ad95089007d20c28c6c83be4f9c01f1e57eb690f Author: Max Katz Date: Wed Jun 21 04:15:47 2017 -0400 Avoid undefined non-CUDA behavior Src/Base/AMReX_Device.cpp commit f33ff3cba9714d02990f794f76f183d1c6b64205 Author: Max Katz Date: Wed Jun 21 04:12:57 2017 -0400 Add BaseFab hook to return pinned Box memory Src/Base/AMReX_BaseFab.H commit b4fdaf1d2197f2047529d47a85e3b5a6aea67044 Author: Max Katz Date: Wed Jun 21 03:31:37 2017 -0400 Add a pinned memory version of Box data Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 1994e0cb31329e14604e1a2566cd061cfd0cb431 Author: Max Katz Date: Wed Jun 21 03:14:38 2017 -0400 Use BL_TO_FORT macro in HeatEq again Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit d9b1f4209f570d8d7a6180c29138b1361bc23afb Author: Max Katz Date: Wed Jun 21 02:53:39 2017 -0400 Add C++ hook to get host pointer for pinned memory Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit a4307741bcc36a25c0040711fe7586a0b110845e Author: Max Katz Date: Wed Jun 21 02:36:43 2017 -0400 Reset to the default stream on MFIter destruction Src/Base/AMReX_MFIter.cpp commit 8a9ff32d271d5a229973c1d5bb174c53fcd374db Author: Max Katz Date: Wed Jun 21 02:36:16 2017 -0400 Add cuda_streams(0) as the default stream Src/Base/AMReX_CUDA.F90 commit f8c0dc7d023304d221013e6bb34ca1739af9d1ff Author: Max Katz Date: Wed Jun 21 02:17:10 2017 -0400 Add function to return current stream index Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit e61b3a031ffe03c0444584b5f12c8d991c6d12ee Author: Max Katz Date: Wed Jun 21 01:49:42 2017 -0400 Register a box for asynchronous execution Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit 06bfb7e6c53db039a05432955466f4e74c52364a Author: Klaus Weide Date: Wed Jun 21 00:29:59 2017 -0500 triv Docs/AMReXUsersGuide/Basics/Basics.tex commit fac5319c6725fe2a517afff87999329623c7168f Author: Max Katz Date: Wed Jun 21 01:04:35 2017 -0400 Update the RealBox device pointer in more cases Src/Base/AMReX_RealBox.H commit 114aba6485afa5519f24b7ed9c9f2bb3dd87d040 Merge: 59481acf2 18965fd7d Author: Klaus Weide Date: Tue Jun 20 23:52:48 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 59481acf207906d34dbc12a39c6217c18978611a Author: Klaus Weide Date: Tue Jun 20 23:52:30 2017 -0500 trivial edits Docs/AMReXUsersGuide/Basics/Basics.tex commit 18965fd7d0c564d32f3dfd2be56b19d2f0d605fb Merge: a17ab5210 1218dcc45 Author: Weiqun Zhang Date: Tue Jun 20 21:27:14 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a17ab52101a4a854116af9a8f50e0b4e6817fa81 Author: Weiqun Zhang Date: Tue Jun 20 21:26:35 2017 -0700 make bl_random_f seeding thread safe Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 commit 1218dcc4542e4e06fdf72c9a6725ac658f96c399 Merge: 6d9d4114b c1323257d Author: Andy Nonaka Date: Tue Jun 20 21:00:01 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 6d9d4114bce6591b1e4a202b71ceac33a94f7f82 Author: Andy Nonaka Date: Tue Jun 20 18:04:14 2017 -0700 more documentation Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit 0a2f40ef15592d4d0b20c432fa8002ca2a5bff68 Author: Andy Nonaka Date: Tue Jun 20 17:37:20 2017 -0700 comments Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp commit a4cb9427d420aa67b8daf104e4e3bdab14590ac5 Merge: 99219b039 c1323257d Author: Marc Day Date: Tue Jun 20 17:32:03 2017 -0700 Merge branch 'development' into vof-work commit c1323257d2448bb7180f6fc7e69d61de1de34e4d Author: Marc Day Date: Tue Jun 20 17:31:37 2017 -0700 Indexing bug in VolIndex output function Src/GeometryShop/AMReX_VolIndex.cpp commit d7af48a635c2ccdad6cfe2ee706865e66ff894d6 Merge: 4a558260d d6a60f0a1 Author: atmyers Date: Tue Jun 20 17:18:40 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4a558260df130c2f4dd3fd46dc164b95d7bb4d84 Author: atmyers Date: Tue Jun 20 17:18:29 2017 -0700 use enum instead of integer for specifying cartesian coordinates in the tutorials. Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/main.cpp Tests/Particles/ParticleIterator/GNUmakefile Tests/Particles/ParticleIterator/main.cpp Tests/Particles/main.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/CVODE/EX1/main.cpp Tutorials/CVODE/EX2/main.cpp Tutorials/Particles/ElectrostaticPIC/main.cpp Tutorials/Particles/ShortRangeParticles/main.cpp commit d6a60f0a1ee86f63cbb689daa33bb400b11cc1fe Merge: d8cf76812 71a5bce22 Author: Weiqun Zhang Date: Tue Jun 20 16:21:02 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d8cf7681225f409a235ac0e644b440c3e271ef31 Author: Weiqun Zhang Date: Tue Jun 20 16:20:56 2017 -0700 make max_grid_size and blocking_factor IntVect Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp commit 71a5bce22e246c5053339f3a2e37487a3295fcb3 Merge: a7d733ff7 de95d45d7 Author: WeiqunZhang Date: Tue Jun 20 16:14:23 2017 -0700 Merge pull request #42 from AMReX-Codes/dtg_branch bunch of small parallel fixes commit de95d45d7fddb94c757ae7c7558a34992dfa3a63 Author: dtgraves Date: Tue Jun 20 16:08:12 2017 -0700 put in the repo the working input file Tests/GeometryShop/regression/ebio.inputs commit a7d733ff78b9e4e9d155175632b98000002564d2 Merge: 023a758e2 bb8a8c46f Author: Andy Nonaka Date: Tue Jun 20 14:14:33 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 023a758e2eef70f3d8a379297c56ffc1b718e51e Author: Andy Nonaka Date: Tue Jun 20 14:14:19 2017 -0700 minor updates to doc Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp commit bb8a8c46fcf79f9c710ddda27b657fc67d1c1af7 Merge: fd7e44d71 7a16363b1 Author: Weiqun Zhang Date: Tue Jun 20 13:27:25 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fd7e44d71c7ddedbacbdadadc62bdbc23cdd61aa Author: Weiqun Zhang Date: Tue Jun 20 13:27:13 2017 -0700 add assertion to FabArray::operator[] making sure DistributionMapping is the same Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H commit 7a16363b1b727bb71d607230a43a654003f05633 Author: Andy Nonaka Date: Tue Jun 20 13:25:08 2017 -0700 more AmrCore doc and some code cleanup Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit e576c0f996f5a6e42582d30da635d97506ce1fd0 Author: dtgraves Date: Tue Jun 20 12:00:43 2017 -0700 parallel I/O of FabArray objects is now correct Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/fabio.cpp commit a9d90c7e5f172649f98280bda37b9afc60f2b2e5 Author: Michele Rosso Date: Mon Jun 12 17:20:04 2017 -0700 Modify main CMakeLists.txt CMakeLists.txt Tools/CMake/AMReX_Utils.cmake commit 7d293ce0f32f47382acfd9157498585ac36a0a4d Author: Michele Rosso Date: Mon Jun 12 14:13:04 2017 -0700 Add missing file from source list Src/Base/CMakeLists.txt commit 2bfad9e4eb28bb1ee6f208c1e5700571f324a669 Author: Michele Rosso Date: Fri Jun 9 15:30:21 2017 -0700 Modify previous fix to circular dependency problem Tools/CMake/FindCCSE.cmake commit d241ec9475ef9bd47b4b239350bb4a2acaeb7550 Author: Michele Rosso Date: Fri Jun 9 10:06:39 2017 -0700 Force VERBOSE ON by default CMakeLists.txt commit 36ae8d1ff64e98472313a657cfbb747b06c403f7 Author: Michele Rosso Date: Thu Jun 8 15:59:33 2017 -0700 Modify preprocessing for F77 files Tools/CMake/PreprocessAMReXFortran.cmake commit cada0fc97e3aa43b49bb9cc365102f6c9a8d61f6 Author: Michele Rosso Date: Thu Jun 8 10:46:20 2017 -0700 Get rid of PreprocessAMReXFortran90 CMakeLists.txt Src/Base/CMakeLists.txt Src/CMakeLists.txt Tools/CMake/PreprocessAMReXFortran90.cmake commit fbfe92005748ed7c5b6ed6830676a8a3e60f8c77 Author: Max Katz Date: Tue Jun 20 00:05:03 2017 -0400 Further restrict the device synchronizes Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.cpp commit d435c1af44f05b8dc5951c78ea0b042e94184db5 Author: Max Katz Date: Mon Jun 19 23:53:21 2017 -0400 Suppress warning about driver shutting down Src/Base/AMReX_CUDA.F90 commit a61330bb7317d697b8375d83ad6595561ef10004 Author: Max Katz Date: Mon Jun 19 23:28:53 2017 -0400 Use a less restrictive device sync policy Src/Base/AMReX_Device.H Src/Base/AMReX_FabArray.H commit efb282fb5557fb1aa08ba0362f34a8f16c95da1f Author: Max Katz Date: Mon Jun 19 23:14:32 2017 -0400 Add a GPU synchronize on MFIter destruction Src/Base/AMReX_MFIter.cpp commit 54a23fd33c69cca3ffc60a2b9be49b4ea7e101a1 Author: Max Katz Date: Mon Jun 19 23:13:17 2017 -0400 Add a stream synchronize hook Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 04c83f566c0cb3c96c1abe75ff17f718c0ff9b9a Author: Max Katz Date: Mon Jun 19 22:42:31 2017 -0400 Handle device stream index automatically in MFIter Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp commit 99219b03962f1da2695c24de1f459b2a985b41fe Merge: 538f0f068 6387464b5 Author: Marc Day Date: Mon Jun 19 19:14:33 2017 -0700 Merge branch 'development' into vof-work commit 0c97825edae2c0749031f8014f63024032816670 Author: Max Katz Date: Mon Jun 19 22:14:22 2017 -0400 Revert "Remove an unnecessary device synchronize" This reverts commit 0b597e8cd4f99fd400285ae1af4edf5a67a59b2d. Src/Base/AMReX_Device.H commit 6387464b59148e1d803a41b3f78e5e3ed4507d54 Merge: eff3a77d4 52adb7ac9 Author: Marc Day Date: Mon Jun 19 19:14:06 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit eff3a77d4db73a444db5e266a8a252ec1102db8e Author: Marc Day Date: Mon Jun 19 19:13:53 2017 -0700 Rename dummy arguments in EBLevelGrid.H for refine function Src/GeometryShop/AMReX_EBLevelGrid.H commit 63c962bf7df1da407948054150a97045fec9cbfd Merge: 83f484574 c62802ca6 Author: Max Katz Date: Mon Jun 19 21:25:51 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit c62802ca68e92418acbfc688b0bd8fbc62e3d2ab Author: Michael Zingale Date: Mon Jun 19 21:22:59 2017 -0400 prevent ppc and little_endian from clashing on IBM power 8 Src/Base/AMReX_FPC.cpp commit 64eab00e6a3559e1679a20ba44441133d8f54303 Author: Michael Zingale Date: Mon Jun 19 21:17:03 2017 -0400 wrap the comments in #if 0 ... #endif so we can compile with xlf Src/Base/AMReX_REAL.H commit 538f0f068e76dbf536b602692f5660ae1261af9d Author: Marc Day Date: Mon Jun 19 16:30:37 2017 -0700 Fix a problem associated with reference-counted semantics Tests/GeometryShop/vofStructures/umapTest.cpp commit 39c627a4129b22adeef3fdfa756cd06b209bc8ce Author: dtgraves Date: Mon Jun 19 15:52:11 2017 -0700 fixed nasty little parallel bug that was only happening when the EB ends near a box boundary. I/O is still broken in parallel but the other stuff seems to work. Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_GraphNode.cpp Tests/GeometryShop/regression/fabio.cpp commit 52adb7ac9138927f1ecf9f2a4e4a2113308163a1 Author: Andrew Myers Date: Mon Jun 19 12:48:12 2017 -0700 Use PCInterp instead of CellConservativeLinear in multi-level assign density. Src/Particle/AMReX_ParticleContainerI.H commit a239e83e1dc54c50c523e631f14b94b571ac599a Merge: 61cbc7c5f 33040bdb1 Author: Marc Day Date: Mon Jun 19 12:39:35 2017 -0700 Merge branch 'development' into vof-work commit c30b4d0f69e4e450b53f20a15e6f5319db342107 Author: atmyers Date: Mon Jun 19 12:26:21 2017 -0700 Add more detail about single precision particles in the docs. Docs/AMReXUsersGuide/Particle/Particle.tex commit 61cbc7c5fbd0822767b2813fc5aab28a67ada5b5 Author: Marc Day Date: Mon Jun 19 12:15:08 2017 -0700 Remove ebXXXID Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/umapTest.cpp commit dae257ae487b7874c9f18f0ffc8571cfe9e36421 Author: Marc Day Date: Mon Jun 19 12:11:19 2017 -0700 WIP: Remove vofStructure sample code, choosing Umap structures over the original Node (IntVect-based) concept. Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 233ccdd4ed05a12bb9926ca6b271ff176fd7cdd6 Author: Andrew Myers Date: Mon Jun 19 11:14:06 2017 -0700 move amrex_particle_real to AMReX_fort_mod.F90 Src/Base/AMReX_fort_mod.F90 Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 commit 07f2a413762133147fa68370263fb7aeb438430b Author: Andrew Myers Date: Mon Jun 19 10:57:38 2017 -0700 Allow for single precision particles to be handled by Fortran routines. Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H Tools/GNUMake/Make.defs Tutorials/Particles/ShortRangeParticles/main.cpp Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 commit 83f484574473e088d5c5647c7253be530342f679 Author: Max Katz Date: Mon Jun 19 05:09:13 2017 -0400 Handle stream indices more cleanly and consistently Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit c1a30df5016d268ee1aaa007309942089c75b12c Author: Max Katz Date: Mon Jun 19 04:43:42 2017 -0400 Prevent OpenMP when using CUDA Tools/GNUMake/Make.defs commit abe66b8813415eb76c28cec0d4cf19af6bb60e66 Author: Max Katz Date: Mon Jun 19 03:10:09 2017 -0400 Make the device index thread safe Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 8252c4fb601c048b8648c11f4b21ab65d55e4cde Author: Max Katz Date: Mon Jun 19 02:38:19 2017 -0400 Return to old MFIter style since boxes are now saved Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit e114240c9e49bce2d2ed97102415e437ed7907ea Author: Max Katz Date: Mon Jun 19 02:37:38 2017 -0400 Register boxes created by MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit ccfe89826096262453585a534376d3edf06d9dda Author: Max Katz Date: Mon Jun 19 01:58:50 2017 -0400 Remove index from Fab interfaces Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 380dc18253c3bc397528e115f9eaffe52c39b297 Author: Max Katz Date: Mon Jun 19 01:50:07 2017 -0400 Make the MultiFab operations asynchrony-safe Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit 0b597e8cd4f99fd400285ae1af4edf5a67a59b2d Author: Max Katz Date: Mon Jun 19 01:33:22 2017 -0400 Remove an unnecessary device synchronize Src/Base/AMReX_Device.H commit 16345f8e9736645b22209cc126a1e3c99370e79e Author: Max Katz Date: Mon Jun 19 01:07:55 2017 -0400 Add a stream index variable Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 2c5f181b475ea06b9dceb8793ce381248ad1947c Author: Max Katz Date: Sun Jun 18 23:12:03 2017 -0400 Add PGI compiler major and minor version definitions Tools/GNUMake/comps/pgi.mak commit 7b0ce1069ac441fef42d52335caee8d24e509e18 Author: Michael Zingale Date: Sun Jun 18 20:55:29 2017 -0400 ifdef out some CUDA stuff Src/Base/AMReX_Device.cpp commit fdb26d77ea2d99900b82c024236a8b77e1495226 Author: Max Katz Date: Sun Jun 18 20:24:08 2017 -0400 Automatically pick up CUDA path on Titan and Summitdev Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.olcf commit dfd783874eabcb55911cebb8977292580cc6b0f4 Author: Max Katz Date: Sun Jun 18 16:43:06 2017 -0400 Get the CUDA device ID from Fortran Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 740b51d609046f5d7caff0bc47093ce3fdb1c37f Author: Max Katz Date: Sun Jun 18 16:30:49 2017 -0400 Drive CUDA initialization from C++ Src/Base/AMReX.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit f010bb54e54d4019774ee1b83cdf7c1094fce789 Author: Max Katz Date: Sun Jun 18 15:29:37 2017 -0400 Query GPU properties, use in avoiding unsupported calls Src/Base/AMReX_CUDA.F90 commit 93f82c0c82c73839edbd99ffbcd45d5708590855 Author: Max Katz Date: Sun Jun 18 15:29:14 2017 -0400 Initialize CUDA before class initializations Src/Base/AMReX.cpp commit 18d30437c70e96c6cd73afd265aa810ad337adac Author: Max Katz Date: Sun Jun 18 01:17:12 2017 -0400 Create managed copy of RealBox data Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 191110e8fdb96a826cc7a75d8c0835c14a24165b Author: Max Katz Date: Sun Jun 18 00:48:40 2017 -0400 Add function to return number of MFIter indices Src/Base/AMReX_MFIter.H commit 39e40e7c63ff5cecd828198daec6b82243005df7 Author: Max Katz Date: Sat Jun 17 23:14:26 2017 -0400 Fix the argument passing to cudaMemAdvise Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Device.H commit 7aa44d177838e7cf17048404c4e720868b8d6776 Author: Max Katz Date: Sat Jun 17 22:00:19 2017 -0400 Insert CUDA finalization Src/Base/AMReX.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit efe94d3fcd600e2e58fcee8b14c42f5f22fe5c26 Author: Max Katz Date: Sat Jun 17 21:13:23 2017 -0400 Disable broken error checking for cudamemadvise Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CUDA.F90 commit 7665f2ea0da333c160e337c858c21ce5c2022edd Author: Max Katz Date: Sat Jun 17 20:32:45 2017 -0400 Add capability to use hostalloc'ed data Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp commit 83aab7793d4fbdcf54e94aebc3307a81368bcb4a Author: Max Katz Date: Sat Jun 17 20:31:10 2017 -0400 Clean up CUDA functions, add error checking Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit c6af601ee59ea74e13a9625b5ccda35442c21e7f Author: Max Katz Date: Sat Jun 17 20:30:11 2017 -0400 Increase length of error string Src/Base/AMReX_BLBoxLib_F.f commit 69faf1ba2e9007c7c2fc812fbeccae64a1439bd8 Author: dtgraves Date: Sat Jun 17 16:14:08 2017 -0700 took out unnecessary fillboundary calls Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp commit 79ca2e3d891012a7f217f6359527c1c8198cb1f1 Merge: 124f2fc46 8467ae21d Author: Max Katz Date: Sat Jun 17 06:31:37 2017 -0700 Merge pull request #40 from atmyers/gpu An approach to managed memory for particle data commit 124f2fc46030a389e055c0cb18b3b1da553b7cb7 Author: Max Katz Date: Sat Jun 17 09:04:34 2017 -0400 Always use CArena in Box Src/Base/AMReX_Box.cpp commit ecaa7cc951c212e6c268b4ddeb45f2068453f379 Author: Max Katz Date: Sat Jun 17 05:13:53 2017 -0400 Rely on data that is now managed Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 07c65a5804c96d5775a5bf9f910ff7158faff33a Author: Max Katz Date: Sat Jun 17 04:17:07 2017 -0400 Add an option to use cudaMalloc, not cudaMallocManaged Src/Base/AMReX_Arena.H Src/Base/AMReX_CArena.cpp commit d4a8dadf0b98bdc23baf377c2d73eea87bccff58 Author: Max Katz Date: Sat Jun 17 04:13:21 2017 -0400 Use the default stream if passed an invalid index Src/Base/AMReX_CUDA.F90 commit 193ee594da3ed6d75851580972a99b5de7869c25 Author: Marc Day Date: Fri Jun 16 19:29:25 2017 -0700 Add faces to graph in Umap form. Src/Base/AMReX_BaseUmap.H Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/umapTest.cpp commit 8467ae21dec1bbf0b38f700b3c5cef8901516dd8 Author: Andrew Myers Date: Fri Jun 16 17:28:36 2017 -0700 removing file checked in by mistake. Tests/Particles/ManagedCUDADeposition/make.out commit 79fcb387ec77e88ba86d9feb3c358d18f29a5734 Author: Andrew Myers Date: Fri Jun 16 17:17:37 2017 -0700 check in test problem for Managed Cuda particle deposition. Tests/Particles/ManagedCUDADeposition/GNUmakefile Tests/Particles/ManagedCUDADeposition/Make.package Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/inputs Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/make.out Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp commit b0f351e28d988bd1aae88c77b8256c6bdaf1a398 Author: Andrew Myers Date: Fri Jun 16 17:16:59 2017 -0700 remove old version of custom allocator from problem directory Tests/Particles/CUDADeposition/CUDAManagedAllocator.H commit 95492c92dd2563c4c7415a4968195f06f0dc7d00 Author: Andrew Myers Date: Fri Jun 16 17:16:18 2017 -0700 Add a custom allocator that uses Cuda managed memory and use it in the ParticleContainer when Cuda is enabled. Src/Particle/AMReX_CudaManagedAllocator.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/Make.package commit b17d1aea59291cbe0f6f5e280b1a3a25530f5fe9 Author: Andrew Myers Date: Fri Jun 16 17:14:01 2017 -0700 modify AMReX_Array to optionally take a custom allocator (off by default) Src/Base/AMReX_Array.H commit 5304b747bb2cdfb3b95068215d002303d079da5f Author: Andy Nonaka Date: Fri Jun 16 16:48:12 2017 -0700 more AmrCore documentation Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/flowchart.odg Docs/AMReXUsersGuide/AmrCore/figs/flowchart.pdf commit 87785dad84c1d8b7a3a51f56e4b42df46cf8e822 Author: Andrew Myers Date: Fri Jun 16 15:17:19 2017 -0700 Enabling OpenMP in the ShortRangeParticleContainer and adding timers. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit 0a4b577c2ac11dc934a0eea49f391075b8a41201 Author: Weiqun Zhang Date: Fri Jun 16 14:47:39 2017 -0700 User's Guide: proofread Docs/AMReXUsersGuide/Basics/Basics.tex commit 2ac8c8ba4a691d708be014dcae5f4c4d80f75c23 Merge: 137c4c92b b57c5c272 Author: vince Date: Fri Jun 16 12:46:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 137c4c92b76bd619761f91a1757d765eadefdec3 Author: vince Date: Fri Jun 16 12:46:23 2017 -0700 fix uniform_int_distribution call to be consistent with header comments. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit b57c5c27295156d6cef222a88d04cb0afcfc67f8 Author: atmyers Date: Fri Jun 16 11:25:22 2017 -0700 Clean up use of Fortran intent / const in the Particle tutorials. Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ShortRangeParticles/short_range_F.H commit 2d33d99daade673866b0621da164e616905c3d8f Author: Marc Day Date: Fri Jun 16 11:10:25 2017 -0700 For BaseUmap::const_iterator, add access to IntVect, L and n. Src/Base/AMReX_BaseUmap.H Tests/GeometryShop/vofStructures/umapTest.cpp commit 70c5d484ee39bb24da1553791c295f8549803552 Author: atmyers Date: Fri Jun 16 11:03:54 2017 -0700 Proofreading pass of particle documentation. Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Visualization/Visualization.tex commit 99efc96b4ed419e4fb4552f0bce408c2e07151fb Author: Marc Day Date: Fri Jun 16 10:59:01 2017 -0700 Add an iterator to BaseUMap to allow iterating over all explicitly defined data....needs some work though Src/Base/AMReX_BaseUmap.H Tests/GeometryShop/vofStructures/umapTest.cpp commit 5c018b61ace9578c09aa342e834777137d9d46ad Author: Marc Day Date: Fri Jun 16 09:58:35 2017 -0700 Merge vof-work and sparse-fab stuff...wip Src/Base/AMReX_BaseUmap.H Src/Base/Make.package Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/vofStructures.cpp commit 2a380324ae19138da3edab66f52b09cac504853f Merge: 305e93470 806ded972 Author: Michele Rosso Date: Fri Jun 16 10:00:09 2017 -0600 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 305e934705f4d0f7cbb5d905e3da1bc55426a204 Author: Michele Rosso Date: Fri Jun 16 10:00:02 2017 -0600 CMake: disable tiny_profiler for the time being Src/Base/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 806ded9721db45b8145d662a1fb13d2db7aef801 Author: Andrew Myers Date: Thu Jun 15 19:43:20 2017 -0700 use an explicit amrex:: namespace in the BL_PROFILE macro definitions. Src/Base/AMReX_BLProfiler.H commit 2f20baa62e801244198df3f2e2ec614bedb31f6a Merge: 22f6db05c 74110f274 Author: Andrew Myers Date: Thu Jun 15 17:25:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 22f6db05c9c4c88426e5094895679e7edd26d4e3 Author: Andrew Myers Date: Thu Jun 15 17:23:04 2017 -0700 Same for the interpolation operation. Src/Particle/AMReX_ParticleContainerI.H commit 5b850929f9ea30e97175edc6854bfb4d3dd8c027 Author: Andrew Myers Date: Thu Jun 15 17:10:02 2017 -0700 Make the deposition operation OpenMP-capable. Src/Particle/AMReX_ParticleContainerI.H commit 74110f274a38441c64ba62ef6bea383178fda490 Author: Weiqun Zhang Date: Thu Jun 15 17:01:39 2017 -0700 minor changes Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit 2d81ce3930a6c1ece9cd45299c5393153c926c92 Author: Andrew Myers Date: Thu Jun 15 16:49:48 2017 -0700 Functions to assist with particle deposition with OpenMP. Src/Particle/AMReX_OMPDepositionHelper_1d.F90 Src/Particle/AMReX_OMPDepositionHelper_2d.F90 Src/Particle/AMReX_OMPDepositionHelper_3d.F90 Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 0a6f897c38c561a5d920f1361cf13b589e2a496e Merge: 5cbacf4da 51d12f21f Author: Marc Day Date: Thu Jun 15 16:48:40 2017 -0700 Merge branch 'rgrout/sparse_fab' into vof-merge commit 33040bdb1c788c2fa5f2e7af048da45836720cec Author: Andy Nonaka Date: Thu Jun 15 16:44:49 2017 -0700 cleaned up tutorial code, added lots of comments Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrMesh.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvError.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvIO.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvInit.cpp Tutorials/Amr/Advection_AmrCore/Source/Make.package Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit 7e2076993edeebec59ee73b35c83daedc01aa7fd Author: dtgraves Date: Thu Jun 15 15:13:14 2017 -0700 another parallel bug found. More stuff works but not everything. Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_IrregFABFactory.cpp Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/runalltests.mpi.sh Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs commit 410211f4a17a6de45b67279eeeddc55aa4aafb64 Author: Weiqun Zhang Date: Thu Jun 15 14:59:42 2017 -0700 User's Guide: Boundary Docs/AMReXUsersGuide/Basics/Basics.tex commit 63be359c8b0b7f1638f50113146485e325de6364 Merge: 314708a25 bfb61626e Author: Andy Nonaka Date: Thu Jun 15 14:35:50 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 314708a2593bd6e72c57a2d7635df1a30b4f46bc Author: Andy Nonaka Date: Thu Jun 15 14:35:34 2017 -0700 small documentation adds Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp commit 19586607365c18bad8c4c98c5092e611b9d6b84f Author: Andy Nonaka Date: Thu Jun 15 14:28:24 2017 -0700 tex version of subcycling fig Docs/AMReXUsersGuide/AmrCore/figs/subcycling.tex commit bfb61626e33ca23553e9b81a71b59987a9b3329d Author: Andrew Myers Date: Thu Jun 15 14:27:06 2017 -0700 adding in the *.tex files for the new figures. Docs/AMReXUsersGuide/Particle/neighbor_particles.tex Docs/AMReXUsersGuide/Particle/particle_arrays.tex commit 12f128bfa8ed32c4d2bf186915f14fdb97af1a0e Merge: f73536e3e 6d5e3acb2 Author: Andrew Myers Date: Thu Jun 15 14:25:41 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6d5e3acb2b9021bad282d6bb30f30615166847c2 Merge: c5e9b0400 db5e371b3 Author: atmyers Date: Thu Jun 15 14:20:50 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c5e9b0400222e47cc52f4e9e00295bb3d6359e6b Author: atmyers Date: Thu Jun 15 14:20:35 2017 -0700 adding a couple of figures to the particle section of the user's guide. Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Particle/neighbor_particles.pdf Docs/AMReXUsersGuide/Particle/particle_arrays.pdf commit db5e371b3f7b5b0f5a6292e565d9b5c28fafcf18 Author: Weiqun Zhang Date: Thu Jun 15 13:44:31 2017 -0700 update heat equation tutorial using the new amrex::FillDomainBoundary function Tutorials/Basic/HeatEquation_EX1_C/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc.H Tutorials/Basic/HeatEquation_EX1_C/physbc.cpp commit 9bcf46202a949265b7388e3952173c784c46c4a8 Author: Weiqun Zhang Date: Thu Jun 15 13:39:56 2017 -0700 add some helper functions for filling physical domain boundary conditions Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_BLassert.H Src/Base/AMReX_bc_types_mod.F90 Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/Base/Make.package Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/inputs_2d Tutorials/Basic/HeatEquation_EX1_C/inputs_3d Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit cc7908541e2269aab60fe36ba5b50156f42e2718 Merge: 6168d6a11 2a2b423dd Author: Michele Rosso Date: Thu Jun 15 14:00:40 2017 -0600 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 51d12f21fdbe629d7f258b099f771d4c7aca697f Merge: c5b480ac5 2a2b423dd Author: Grout Date: Thu Jun 15 13:59:20 2017 -0600 Merge branch 'development' of github.com:AMReX-Codes/amrex into rgrout/sparse_fab commit 6168d6a113789d3df4aa2beb5c72c36a1261e144 Author: Michele Rosso Date: Thu Jun 15 13:57:11 2017 -0600 Make TinyProfiler the deault profiling tool Src/Base/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 5cbacf4dacadce08148826fd5be11127fb3c2ab9 Author: Marc Day Date: Thu Jun 15 12:52:11 2017 -0700 WIP: Fixup test code for mv cells Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 937cb52dcaa310a2954f17ce31071b2f2c360836 Author: Michele Rosso Date: Thu Jun 15 13:43:13 2017 -0600 Update cmake with new source files Src/Base/CMakeLists.txt commit c5b480ac54c49ca521c3871e46a912f102be3a83 Author: Grout Date: Thu Jun 15 13:40:15 2017 -0600 Start of sparse fab Src/Base/AMReX_BaseUmap.H Tests/C_BaseLib/tUMap.cpp commit d6c962a1da2638d732033043aac188918bf785c6 Merge: cf8c05478 2a2b423dd Author: atmyers Date: Thu Jun 15 12:21:05 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fedfd6ce0aadda8c597bb9abd182de2fab98a34c Merge: 7df5436cc 2a2b423dd Author: Marc Day Date: Thu Jun 15 11:52:17 2017 -0700 Merge branch 'development' into vof-work commit 7df5436cc2de7316270d611da6398ec56c2fd211 Merge: 2e6000b81 afdf2c7ba Author: Marc Day Date: Thu Jun 15 11:52:12 2017 -0700 resolve merge conflicts commit 2a2b423ddfbb1518ea43a8ee826c9d6cafa03183 Author: Marc Day Date: Thu Jun 15 11:49:31 2017 -0700 Add arguments to pltfile functions that enable passing versionName to writer so we can make CartGrid_V2.0 files Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit 2e6000b8137ac1e7eaa019660637844745d7d396 Author: Marc Day Date: Thu Jun 15 11:47:35 2017 -0700 WIP: Write plotfile with vfrac info Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures.cpp commit d67ca9e5e8d2158ec6bc3ef47c934ec2e532393c Author: dtgraves Date: Thu Jun 15 10:51:01 2017 -0700 more bug fixes. EB I/O still broken for nproc > 1 Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/AMReX_IrregFABFactory.cpp Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/runalltests.mpi.sh commit 83e9ebf4dd03737490d9badb6c6923cefc8876ce Author: Weiqun Zhang Date: Thu Jun 15 09:21:21 2017 -0700 move OldTutorials/HelloWorld_CF Tutorials/HelloWorld_F Tutorials/Basic/HelloWorld_F/GNUmakefile Tutorials/Basic/HelloWorld_F/Make.package Tutorials/Basic/HelloWorld_F/fmain.f90 commit 057034b1dc91462dc7818ce02b56f411b641e3e7 Author: Weiqun Zhang Date: Thu Jun 15 09:17:01 2017 -0700 User's Guide: add some discussion on const& and return by value Docs/AMReXUsersGuide/Basics/Basics.tex commit 493aa1b85cbb9dc31584e56a0dc32850490a45dc Author: Weiqun Zhang Date: Thu Jun 15 09:16:17 2017 -0700 move OldTutorials/HeatEquation_EX1_CF to Tutorials/HeatEquation_EX1_F Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile Tutorials/Basic/HeatEquation_EX1_F/Make.package Tutorials/Basic/HeatEquation_EX1_F/advance.f90 Tutorials/Basic/HeatEquation_EX1_F/fmain.f90 Tutorials/Basic/HeatEquation_EX1_F/init_phi.f90 Tutorials/Basic/HeatEquation_EX1_F/inputs commit 9c2d95c7ae496648cecbe4322bab8763ff5538d6 Author: Max Katz Date: Thu Jun 15 10:23:45 2017 -0400 Always reset device memory when applying a Box transformation The original idea was to only reset the shared pointer containing the memory for routines that returned a new box by value rather than modifying the existing box by reference. Thus we could keep the CUDA managed memory without reallocating it if one did Box bx = mfi.validbox(), but create a new allocation if one did Box bx = surroundingNodes(mfi.validbox()). However, this is defeated by the use case where one first creates the box copy, and then applies the transformation operation in a second step. So the only safe approach is to always reset the allocation if the box is transformed. Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 2322895e441ef854eacb776a2589a926f514e738 Author: Max Katz Date: Thu Jun 15 10:20:53 2017 -0400 Do nothing with BL_TO_FORTRAN_3D when CUDA is enabled Since we are using managed memory to hold a copy of the box bounds, we want to directly access the pointer containing that memory, rather than save a temporary copy. The CUDA version automatically enables the same functionality as the macro because the lo and hi vectors contain zeroes in unused spatial dimensions. Src/Base/AMReX_ArrayLim.H commit b38b0b9d79b003086b5d8f5eb949d21d6c60c51b Author: Marc Day Date: Wed Jun 14 19:14:28 2017 -0700 WIP: prepare for multi-level work by making a couple of EBLevelGrid objects to start with. Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit e05e3124854227fc33b769ca81fd8ec645eeda57 Author: Weiqun Zhang Date: Wed Jun 14 17:56:06 2017 -0700 User's Guide: bl_allocate, Abort and ASSERT Docs/AMReXUsersGuide/Basics/Basics.tex commit f99d7b460b060b0411c1257513b549c5f8021ec5 Author: Weiqun Zhang Date: Wed Jun 14 17:44:09 2017 -0700 add AMREX_ASSERT and AMREX_ALWAYS_ASSERT Src/Base/AMReX_BLassert.H commit abd1c7563e44d9e69d25bd7e64cc2af9a95efedb Author: Weiqun Zhang Date: Wed Jun 14 16:31:43 2017 -0700 remove debug line Src/Base/AMReX_FabArray.H commit d8d832aeea6a073832142507a42705d4dda15f5b Merge: 56a7a3971 b51c18133 Author: Weiqun Zhang Date: Wed Jun 14 16:30:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 56a7a397137dfc9a4274a798aeb2dbf783aba883 Author: Weiqun Zhang Date: Wed Jun 14 16:30:41 2017 -0700 User's Guide: IO Docs/AMReXUsersGuide/Basics/Basics.tex commit d2c02bd11319232f8d90ab0fdea414b71898a955 Author: dtgraves Date: Wed Jun 14 15:56:17 2017 -0700 fixed IrregFABFactory parallel bug Src/GeometryShop/AMReX_EBCellFactory.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp commit f73536e3ee2de0e08f7ee7a90cc1368d3398dd42 Author: Andrew Myers Date: Wed Jun 14 15:33:23 2017 -0700 remove some debugging junk from the ElectrostaticPIC example. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 commit b51c181338b0cbd8f384f4081c01e4ccb6e3beaf Merge: cba1331ca 345fe63d8 Author: WeiqunZhang Date: Wed Jun 14 14:52:40 2017 -0700 Merge pull request #38 from AMReX-Codes/dtg_branch Peter M. wants some of the tools in dtg_branch and this should not break anything commit 345fe63d8b3b33713ad3ae5a1893decbdfcd4aa6 Author: dtgraves Date: Wed Jun 14 14:47:29 2017 -0700 took out debugging statements Src/Base/AMReX_FabArray.H commit 45349adf1a2939429eef10323f143ac53a24adc7 Author: dtgraves Date: Wed Jun 14 14:10:38 2017 -0700 found subtle parallel bug. More of the EB regression tests now pass in parallel. Src/Base/AMReX_FabArray.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Tests/GeometryShop/regression/dataArith.cpp commit cba1331caae2b4ca07cd111f14a99c6ab013abd0 Merge: 05e8e4bd8 ae613fb5b Author: Andy Nonaka Date: Wed Jun 14 14:01:50 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 05e8e4bd8cb6bd5298611602f77ed2df595e8791 Author: Andy Nonaka Date: Wed Jun 14 14:01:29 2017 -0700 code comments, pseudocode of algorithm for AmrCore DesignDoc Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdvError.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp commit c2f322d6c3d6888a81afebfa383280ac259f892a Author: Andy Nonaka Date: Wed Jun 14 12:56:35 2017 -0700 cleaning up the code, no functional changes Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvIO.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvInit.cpp commit cf8c05478b6279811856c826b29eec01679166b9 Author: atmyers Date: Wed Jun 14 12:35:16 2017 -0700 Adding more information about neighbor particles. Docs/AMReXUsersGuide/Particle/Particle.tex commit e291805d77a9f81d372108543f5d0bb462bab628 Merge: 086253931 ae613fb5b Author: atmyers Date: Wed Jun 14 12:12:26 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 08625393187ca09c3c9be32f1cd5dd853c002c0f Author: atmyers Date: Wed Jun 14 12:12:17 2017 -0700 Adding some stuff about the ShortRangeTutorial. Docs/AMReXUsersGuide/Particle/Particle.tex commit ae613fb5b27f21285d626bfaad1ed35c87915c94 Author: Michael Zingale Date: Wed Jun 14 15:09:53 2017 -0400 fix build Docs/AMReXUsersGuide/Particle/Particle.tex commit 8fa1d462bf6fa2d5412e8e3ef258f4042f0c22a1 Author: atmyers Date: Wed Jun 14 12:05:44 2017 -0700 Particle IO section in docs. Docs/AMReXUsersGuide/Particle/Particle.tex commit 8168b8012f297bc37a85057bd21964d0a277d560 Author: Weiqun Zhang Date: Wed Jun 14 11:46:38 2017 -0700 User's Guide: boundary Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Debugging/Debugging.tex commit bb4959ff683cc23bf9d98559fda7aceb9500e45e Merge: df898fe92 3e7229ccd Author: Weiqun Zhang Date: Wed Jun 14 09:27:32 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit df898fe92463213d6715f1a7b1e199ab1b974c05 Author: Weiqun Zhang Date: Wed Jun 14 09:26:20 2017 -0700 merge Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/Adv1.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv1.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv2.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv2.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv3.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv3.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv4.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv4.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv5.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv5.pdf Docs/AMReXUsersGuide/AmrCore/figs/subcycling.eps Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf commit 123f6d12b9ee0c0a0dcc9002a5cc79360a68d5fc Author: Andy Nonaka Date: Wed Jun 14 08:26:35 2017 -0700 fix cropping issue in figure Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf commit 856d80b314e865f5561d1573d1dc07f4cf64d78e Merge: 716567b20 3e7229ccd Author: Max Katz Date: Wed Jun 14 01:19:35 2017 -0400 Merge branch 'development' into gpu commit 716567b204b23bc30dc5b60fb9b06aafff9f9d5f Merge: 9eeba24d3 060259bc2 Author: Max Katz Date: Tue Jun 13 21:34:40 2017 -0400 Merge branch 'gpu' into gpu_var2 commit 9eeba24d3a9bb841d14c493c570d24b742087272 Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Define a CUDA attributes macro Tools/GNUMake/Make.defs Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit e46062bc7a3edd670a38426b92f6224b13cd8acf Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Clean up the update_phi interface Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit 63bcdff5eda1697e8c966eb282240614396b11a4 Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Allocate the flux box bounds in C++ driver Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit ddc68adf205ec820ff4570f9e9de94d0ff42241f Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Refactor to make directional splitting explicit Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit 07b1fc7eaf107364a5d0d79b890a08a032b4b0ea Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Set readonly for CoordSys dx Src/Base/AMReX_CoordSys.cpp commit efbab18b9aac37f5c3c34c1544d951b99ca1baf0 Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Set preferred on BaseFab arena Src/Base/AMReX_BaseFab.cpp commit 28f773007fc8ead0096fb6b28d0b8722050d9a12 Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Set read only to the Box arena Src/Base/AMReX_Box.cpp commit 0f74ed4a157519125c6490f243ee6afbe41bdeda Author: Weiqun Zhang Date: Tue Jun 13 17:25:32 2017 -0700 let's use BL_TO_FORTRAN_BOX Src/AmrCore/AMReX_FillPatchUtil.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit 3e7229ccd87669caf1e7b944206215079f3bcc88 Merge: e8e1bb408 c6cc2a0fb Author: Andy Nonaka Date: Tue Jun 13 17:18:04 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e8e1bb408284b786eef25ae88976494a3a1a444a Author: Andy Nonaka Date: Tue Jun 13 17:17:48 2017 -0700 convert eps to pdf. some small updates to doc Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/Adv1.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv1.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv2.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv2.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv3.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv3.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv4.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv4.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv5.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv5.pdf Docs/AMReXUsersGuide/AmrCore/figs/subcycling.eps Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf commit 060259bc2586a79164c064df1929f3b9cafcc21f Author: atmyers Date: Tue Jun 13 17:13:44 2017 -0700 An allocator that wraps cudaMallocManaged for use with std::vector Tests/Particles/CUDADeposition/CUDAManagedAllocator.H Tests/Particles/CUDADeposition/Make.package commit c6cc2a0fb099cf2448b70b168d8ec9692082e9fc Author: Weiqun Zhang Date: Tue Jun 13 17:12:57 2017 -0700 User's Guide: calling Fortran Docs/AMReXUsersGuide/Basics/Basics.tex commit ccc82c1fb8b358e4b075821d3a2466df9c6f4887 Merge: 2ea416869 a04f0f661 Author: Andy Nonaka Date: Tue Jun 13 16:25:41 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 2ea4168691ab01554a601be15628e3b60bd40bb2 Author: Andy Nonaka Date: Tue Jun 13 16:25:10 2017 -0700 added a short explanation of the AMR algorithm for explicit advection before going into code details Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/Adv1.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv2.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv3.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv4.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv5.eps Docs/AMReXUsersGuide/AmrCore/figs/subcycling.eps commit a04f0f6617ff0af4bd86c4fe8887cce940195146 Merge: cfb354bb9 4e1fb3714 Author: Andrew Myers Date: Tue Jun 13 16:11:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cfb354bb990e095400156de7f409aaa547610a4e Author: Andrew Myers Date: Tue Jun 13 16:11:31 2017 -0700 Use a mask to shift the interpolation to the coarse level for particles near boundary. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit 215b0bbfadfe4bf0a49ff6d92eeace5edaffcef6 Author: Andy Nonaka Date: Tue Jun 13 15:39:11 2017 -0700 get rid of references to boxlib Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 commit d3c0c3cf81bab3ceda1cb9fe04337dd272b3b782 Author: Andy Nonaka Date: Tue Jun 13 15:05:02 2017 -0700 update problem description Tutorials/Amr/Advection_AmrCore/README commit 185a59447b51c6cb65fb85b2737a9f168c4dc8e7 Author: Andy Nonaka Date: Tue Jun 13 14:46:20 2017 -0700 boxlib ref -> amrex Tutorials/Amr/Advection_AmrCore/README commit 4e1fb371472843d7bba8800b2b4b56408b148e2e Merge: 0e02cedcd eb8364aaa Author: Weiqun Zhang Date: Tue Jun 13 14:27:34 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0e02cedcddf53a01f4a036e55d3ec18c78e07d23 Author: Weiqun Zhang Date: Tue Jun 13 14:27:26 2017 -0700 move AmrCore advection tutorial out of OldTutorials Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/README Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvBC.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdvError.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvIO.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvInit.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdv_F.H Tutorials/Amr/Advection_AmrCore/Source/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit eb8364aaa96f01402cd6ebfe8d353fc1fc76f100 Merge: abe54c2b0 77ded8cc1 Author: Andy Nonaka Date: Tue Jun 13 14:26:24 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit abe54c2b07ea20560b4c6697dabc85ee1331c78a Author: Andy Nonaka Date: Tue Jun 13 14:26:09 2017 -0700 start of doc for amrcore Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit 77ded8cc1735c65d0bacf4cc94f6851f7a433848 Author: Weiqun Zhang Date: Tue Jun 13 14:14:15 2017 -0700 User's Guide: MFIter and tiling Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/cc_growbox.pdf Docs/AMReXUsersGuide/Basics/cc_tilebox.pdf Docs/AMReXUsersGuide/Basics/cc_validbox.pdf Docs/AMReXUsersGuide/Basics/ec_growbox.pdf Docs/AMReXUsersGuide/Basics/ec_tilebox.pdf Docs/AMReXUsersGuide/Basics/ec_validbox.pdf commit eb777114255ef0262c3aa2dc3b073759a262764a Merge: 6264479ab 8eb1b680c Author: atmyers Date: Tue Jun 13 13:18:33 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6264479ab4d9ed629f0cc8081ed6400aaf3515ca Author: atmyers Date: Tue Jun 13 13:18:22 2017 -0700 more work on the Particle docs. Docs/AMReXUsersGuide/Particle/Particle.tex commit afdf2c7ba882c5561b1c11a1e50738f41ae5fb86 Author: dtgraves Date: Tue Jun 13 13:00:55 2017 -0700 After much wailing and gnashing of teeth, I found the bug that was causing Marc's test to fail in initialization (it now fails in his code). Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Tests/GeometryShop/vofStructures/vofStructures.cpp commit c8c40c0638374010da400f594f1349be92b0ecb4 Author: Marc Day Date: Tue Jun 13 12:09:05 2017 -0700 WIP: Rename Node.H Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 8eb1b680c4dc812e6715d2bc1f91f829e51c8723 Author: vince Date: Tue Jun 13 11:32:06 2017 -0700 fix sleep seconds. Src/Base/AMReX_Utility.cpp commit 5d32e0fbaeb4d2794e325b709fb9e96356728cdd Merge: 19a5376ea 7ab8def26 Author: vince Date: Tue Jun 13 11:30:55 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 193a1edbabf03370ff29f59cb85a2b28935b261f Author: Max Katz Date: Tue Jun 13 13:47:54 2017 -0400 Add Arena flags for cudaMemAdvise Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 7ab8def26e9dd4ae3a58c1f863d4a446ec5d5f46 Merge: f18d1ffa4 454589a61 Author: WeiqunZhang Date: Tue Jun 13 10:38:38 2017 -0700 Merge pull request #36 from bcfriesen/misc_cvode Misc CVODE commit f18d1ffa47d859f7dc37c74ef864b25134a8bd5b Merge: 7162a5067 b8b1ea1fd Author: WeiqunZhang Date: Tue Jun 13 10:38:29 2017 -0700 Merge pull request #37 from bcfriesen/update_cray_flags Update Cray flags commit b8b1ea1fd5f5eb0d9d29794e731ba99602331461 Author: Brian Friesen Date: Thu Jun 8 15:09:54 2017 -0700 GNUMake: if DEBUG=TRUE, add Cray compiler flag that inits Fortran reals/complexes to NaN Tools/GNUMake/comps/cray.mak commit 0fb6c61723fbf606a96c14487871241aae466614 Author: Brian Friesen Date: Wed Jun 7 16:02:56 2017 -0700 Tools/GNUMake: add optimization report output to Cray compiler Tools/GNUMake/comps/cray.mak commit 454589a61f0ce8ef92a4b7faa22f2f8585c1ca3f Author: Brian Friesen Date: Tue Jun 13 10:12:14 2017 -0700 VODE: add misc functions for querying integration statistics Src/Extern/CVODE/Make.package Src/Extern/CVODE/integrator_stats.f90 commit be3cca32619bc38ef3a4f3fb190d68208cc5e20e Author: Max Katz Date: Tue Jun 13 12:57:28 2017 -0400 Use an arena for Box data Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit ca17549ea4cc3b6877e979d7700d1bf8b316272e Author: Max Katz Date: Tue Jun 13 12:17:22 2017 -0400 Avoid a Box conversion call if unnecessary Src/Base/AMReX_BoxArray.cpp commit c8481ebd4e42876ce29da4eaf8c5ad13b9690148 Merge: 673887ce0 82ea6cbb3 Author: dtgraves Date: Tue Jun 13 08:38:48 2017 -0700 merging with dtg_branch before fixing some bugs commit 9916fc0e9099f143d81ddfbf513d26ad6efa282a Author: Max Katz Date: Tue Jun 13 10:17:20 2017 -0400 Move GPU heat equation example to new directory Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Make.package Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit fd020af2fa8010603a3cf75780423a13c1c26599 Author: Max Katz Date: Tue Jun 13 10:01:13 2017 -0400 Pass idir and dt by value Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 673887ce0332504404230d3591e9ba570cdd8d7e Author: Marc Day Date: Mon Jun 12 21:14:25 2017 -0700 WIP: enforce that faces between regular and cut cells are regular, and seen that way from within the cut cell Tests/GeometryShop/vofStructures/Node.H Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 5cfbce3238c6c2b220c412b6dc147dabc67e4c06 Author: Max Katz Date: Mon Jun 12 23:14:13 2017 -0400 Rely on managed memory in heat equation Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit 002c516328c7d827834ffc743ba98d0b5b583db3 Merge: 791c64814 1b9b259bb Author: Max Katz Date: Mon Jun 12 23:05:30 2017 -0400 Merge branch 'gpu' into gpu_var2 commit 791c64814c8abdbec69bdcfa0b1f1b2ccd17ebb8 Author: Max Katz Date: Mon Jun 12 22:48:52 2017 -0400 Use a managed memory approach for the Box lo and hi bounds A shared pointer is created that stores the managed memory versions of lo and hi (which mirror what smallend and bigend store). The shared pointer is reset when a transforming function like surroundingNodes is called. Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 11099ff5ccc76e7ca33f9b546516c9b1179412ae Author: Marc Day Date: Mon Jun 12 19:44:19 2017 -0700 WIP: remove unused member data from local struct Tests/GeometryShop/vofStructures/vofStructures.cpp commit ce273baaa85fe14f36c4398a9ca86658827af909 Author: Marc Day Date: Mon Jun 12 19:39:31 2017 -0700 WIP: move fort graph construction into function call Tests/GeometryShop/vofStructures/vofStructures.cpp commit 1b9b259bb40cf67882446c5694c24acac9d2d3dd Merge: 5d1b92efb 86aeb3fca Author: Max Katz Date: Mon Jun 12 19:30:20 2017 -0700 Merge pull request #35 from xinshengqin/gpu2 Add 3d cuda version of the heat equation tutorial commit 7162a50671f7434dbba86ca2ae7f0174881742f8 Merge: 1e2e15468 f20bbf8d9 Author: Andrew Myers Date: Mon Jun 12 17:51:10 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1e2e154687e2d3e97bb64ed4a121e35981bb17e3 Author: Andrew Myers Date: Mon Jun 12 17:33:12 2017 -0700 generalize build mask to take a number of buffer cells instead of assuming 1. Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/main.cpp commit cc6c68c678b4be0d531a860ec5de9c1736cb04a9 Author: Andrew Myers Date: Mon Jun 12 17:32:02 2017 -0700 Need to special case num_levels = 1 here. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp commit f20bbf8d97e65448d2582054a670a8b3f86789c2 Merge: 73890f1d2 3aea35807 Author: Andy Nonaka Date: Mon Jun 12 17:20:53 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 73890f1d2a2c4671e7fb1a475bc923c0d067119b Author: Andy Nonaka Date: Mon Jun 12 17:20:24 2017 -0700 added basic documentation for how to open 3d plotfiles and amrex particle data with paraview Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex Docs/AMReXUsersGuide/Visualization/ParaView.eps Docs/AMReXUsersGuide/Visualization/ParaView_particles.eps.REMOVED.git-id Docs/AMReXUsersGuide/Visualization/Visualization.tex Docs/AMReXUsersGuide/amrexsymbols.tex commit 3aea35807b425a11fc087578754672068be6be15 Author: Weiqun Zhang Date: Mon Jun 12 16:56:22 2017 -0700 User's Guide: MFiter without tiling Docs/AMReXUsersGuide/Basics/Basics.tex commit 593ffe74c96d613d3316c2e6c224368aaf8f118f Merge: ba9ec36d8 acb7f17af Author: atmyers Date: Mon Jun 12 16:44:34 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ba9ec36d82a8c79d885532d8887b165f866e2c2a Author: atmyers Date: Mon Jun 12 16:44:27 2017 -0700 fix comment. Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 commit 0846cb596d07ac5afb1111c21a22937373fbb36a Author: atmyers Date: Mon Jun 12 16:43:34 2017 -0700 some more work on the Particle docs. Docs/AMReXUsersGuide/Particle/Particle.tex commit acb7f17afc0ef4316679e35e80775f9eac0cac50 Merge: af709e39c 001e00f82 Author: Andy Nonaka Date: Mon Jun 12 16:22:59 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit af709e39ce27b7bae5984d59bf4dfa2cefb6dff7 Author: Andy Nonaka Date: Mon Jun 12 16:22:20 2017 -0700 for python script to convert amrex particle data to .vtp format, throw out extra four lines in header (after # of particles) Tools/Py_util/amrex_particles_to_vtp/amrex_particles_to_vtp.py commit 770aeebd51369c3dcea9c7ee3c47c59994608085 Author: dtgraves Date: Mon Jun 12 16:22:08 2017 -0700 bugs found in EBGraph, FaceIterator Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_FaceIterator.cpp commit 001e00f82749cc29f17c75059a54c54691ff96d3 Author: Weiqun Zhang Date: Mon Jun 12 15:32:41 2017 -0700 User's Guide: parallel copy Docs/AMReXUsersGuide/Basics/Basics.tex commit 82ea6cbb3bd662bda2d099ea104479c173d07c39 Author: dtgraves Date: Mon Jun 12 15:24:33 2017 -0700 added some parallel debugging tools Src/Base/AMReX_FabArray.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMD.cpp Src/Base/AMReX_SPMDI.H Src/Base/AMReX_parstream.H Src/Base/AMReX_parstream.cpp Src/Base/Make.package Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/Make.package Tests/GeometryShop/ebgraphDistributed/GNUmakefile Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile Tests/GeometryShop/flatPlate/GNUmakefile Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/dataarith.inputs Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs Tests/GeometryShop/runalltests.mpi.sh Tests/GeometryShop/runalltests.serial.sh Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphereEBISBox/GNUmakefile commit 4dda54d4134b2768cb455e8c748e3b77399db046 Author: Marc Day Date: Mon Jun 12 15:20:12 2017 -0700 WIP: Try to add flat plate geom, but there are issues... Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp commit e1b4d94939dda4eb13b66c727b3be281ad0ea6d9 Author: Andrew Myers Date: Mon Jun 12 12:44:57 2017 -0700 removing some commented-out code. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit b20b85fdf3b29093b1a48fc6bf8214a1c84a4b2a Author: Marc Day Date: Mon Jun 12 12:38:05 2017 -0700 WIP: fix bug in eb f90 struct, add some checking of faces in fortran. Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 6c61218cec4d70d79cc558b269bb4a5bf5166a51 Author: Weiqun Zhang Date: Mon Jun 12 11:19:46 2017 -0700 User's Guide: FillBoundary Docs/AMReXUsersGuide/Basics/Basics.tex commit ac42272ee3c3b2de5eee46874f5bab61b85dcd76 Author: Marc Day Date: Mon Jun 12 11:18:01 2017 -0700 WIP: Pass face-based structs to fortran, add note in README Tests/GeometryShop/vofStructures/README.txt Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 7b7201919433b09aebb613a3f6e68a9c3e43a34c Author: Weiqun Zhang Date: Mon Jun 12 11:17:00 2017 -0700 add ParallelCopy to FabArray to make the parallel part clearer Src/Base/AMReX_FabArray.H commit d0cb009134cd783f325a49850c21888bcd8fa920 Author: Marc Day Date: Mon Jun 12 10:52:33 2017 -0700 WIP: Move eb struct def into mod file Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit e8370e9026fe349fbbd6c36189d3c33ccdf0710a Author: Andrew Myers Date: Mon Jun 12 10:36:14 2017 -0700 check in working version of ES single particle test. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit 86aeb3fca44b6ba76f897466e904547227a91285 Author: Xinsheng (Shawn) Qin Date: Sun Jun 11 14:33:19 2017 -0700 change blo(2) and bhi(2) in advance_2d to blo(3) and bhi(3) to avoid warning Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit 5aa6b5cc6bcb1abb490b30811cc1e52f9e11f10e Merge: 704cf79e8 5d1b92efb Author: Xinsheng (Shawn) Qin Date: Sun Jun 11 14:01:23 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit 5d1b92efb22881519f1420f469f4c391f5d7d576 Author: Max Katz Date: Sun Jun 11 16:02:48 2017 -0400 Fix loop bounds in update_phi_doit Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit 4ebaf67182602449724b3fd9682d3d0a486f6c39 Author: Max Katz Date: Sun Jun 11 14:56:57 2017 -0400 Do not copy dx now that it is managed memory Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit 201cfc8f26dde726f065913b1c4c5435c3b3499f Author: Max Katz Date: Sun Jun 11 14:56:24 2017 -0400 Create managed dx object in Geometry, returned by CellSize() Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp commit 704cf79e8fee0873cfe9eace07c513151eab8e2a Author: Xinsheng (Shawn) Qin Date: Sat Jun 10 23:22:43 2017 -0700 finish CUDA 3D version. Result tested. Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 7325b12f3c19e0cbfd27e4d077eaffa857d02442 Merge: 923385c63 328915650 Author: Xinsheng (Shawn) Qin Date: Sat Jun 10 23:17:21 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit 9a7cd7db9d142ba725104ceb8be944dee2d22072 Merge: 38bcfcc22 a3dd3cd79 Author: Marc Day Date: Sat Jun 10 19:34:38 2017 -0700 Merge branch 'dtg_branch' into vof-work commit 38bcfcc2299e6e14b9b1ef14450c3919b8ec5636 Author: Marc Day Date: Sat Jun 10 19:33:54 2017 -0700 WIP: Add 3d fort for vofstructures test Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 3289156503e1b93ab13af811ab1373befe0d51d1 Author: Max Katz Date: Sat Jun 10 19:58:20 2017 -0400 Move C interfaces into a module Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit bd180365a8e14f5a8bf6d47ab42d316dff1805a2 Author: Max Katz Date: Sat Jun 10 19:56:14 2017 -0400 Launch kernels directly, avoiding CUDA wrappers Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit 923385c63f0e74909df81d5e30681a7a43e3906b Author: Xinsheng (Shawn) Qin Date: Sat Jun 10 16:38:11 2017 -0700 CUDA 3D version results checked Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit b21c68f10d81e81ac79576630934c164ef48c9c5 Author: Xinsheng (Shawn) Qin Date: Sat Jun 10 15:51:36 2017 -0700 Fix some issues for CPU part. CPU results checked Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit ff7edb5bd49c68aaa9a8adad6deeb35845b4c6a9 Author: Max Katz Date: Sat Jun 10 14:19:23 2017 -0400 Fix some issues in the GPU heat equation Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H commit 6f2ecd77ae082ee758070c9af178404df9ab4e51 Merge: 53368ab5c 191c36a9f Author: Max Katz Date: Sat Jun 10 12:17:46 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 0417d17cfc77e50dc75db752749d7ee446c23166 Author: Marc Day Date: Sat Jun 10 00:44:12 2017 -0700 Add a comment while I remember what I did. Tests/GeometryShop/vofStructures/vofStructures.cpp commit c7d297ee53c739351811dc6fe63f8c9ecf6848b4 Author: Marc Day Date: Sat Jun 10 00:41:41 2017 -0700 Add ebFaceID to CNode struct Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/Node.H Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit a3dd3cd79472eae17c658c2decf8bd87e6d4ddeb Author: dtgraves Date: Fri Jun 9 19:57:49 2017 -0700 fixed IntVectSet to accomodate the fact that std::set is weird Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IntVectSet.cpp commit 191c36a9f781abcbac3450eb4674a914cb0b6ffb Merge: 1619dddd7 9ee92ad86 Author: Michael Zingale Date: Fri Jun 9 13:01:06 2017 -0400 Merge branch 'development' into gpu commit 9ee92ad8620fc6f865e5a5241f93cb01974002be Author: atmyers Date: Fri Jun 9 12:51:05 2017 -0400 CMakeLists.txt was missing this header file. Src/AmrCore/CMakeLists.txt commit 19a5376ea6563fa56ee0690a7f3b9a14950b487f Merge: c345c6ef5 36408c018 Author: vince Date: Fri Jun 9 09:37:36 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 36408c018fb29c38b50740db0f3e8fa50609c2df Author: Weiqun Zhang Date: Fri Jun 9 09:10:28 2017 -0700 make: strip leading and trailing whitespace from many make variables Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines commit 1619dddd7bb44e41d61434c5b81ec661f977d4d0 Merge: be4064f95 5864b47d7 Author: Andrew Myers Date: Fri Jun 9 11:40:21 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit be4064f95e4939eeac36bf0f8682106228b23b6d Author: Andrew Myers Date: Fri Jun 9 11:40:15 2017 -0400 some renaming. Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/main.cpp commit 53368ab5c3b676dee0b9fe72acb358aceb5e7efb Author: Max Katz Date: Fri Jun 9 11:24:29 2017 -0400 Strip out unnecessary CUDA wrappers Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_fort_mod.F90 commit 6c3eb230ef774877f17284b54ac4dbbe344bf24f Author: Andrew Myers Date: Fri Jun 9 11:02:18 2017 -0400 reorganizing the CUDA-enabled particle container. Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp commit 5864b47d7e39267c75388002114a085529848b23 Author: Max Katz Date: Fri Jun 9 08:45:29 2017 -0400 Don't do threads_and_blocks without BL_SPACEDIM Src/Base/AMReX_CUDA.F90 commit c1dd9f3cce7880cf0d57cd5e408f5f6405fe5d17 Author: Max Katz Date: Thu Jun 8 22:23:37 2017 -0400 Remove incorrect underscore Src/Base/GPackage.mak commit eccd5db4ad5e5b9d8e4c2e310d3c67a25217a683 Merge: a9db60c60 122e8534f Author: Andrew Myers Date: Thu Jun 8 21:20:07 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit a9db60c60d3bc77965f69930f8434a569be0df1c Author: Andrew Myers Date: Thu Jun 8 21:19:59 2017 -0400 implementing multiple streams for the Cuda PIC example/ Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp commit 1f85eaff2da7a4bfd48f8a32d5f7e442c29a224d Author: Marc Day Date: Thu Jun 8 18:11:44 2017 -0700 WIP: More testing of vof stuff in fortran Tests/GeometryShop/vofStructures/Node.H Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit 00a9369ff37faddfc2c6dfe21e5fadce0fcb4fc6 Author: Marc Day Date: Thu Jun 8 17:06:48 2017 -0700 WIP: Move defines for mask type into .H file Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/Node.H Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit d237f080f14d9e9e4f384515c82811bfffa7830c Author: Marc Day Date: Thu Jun 8 15:54:27 2017 -0700 WIP: fix fortran and grow cell issue Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit 122e8534f96e462e67d4d6eebb00674dcdbc0142 Merge: 27e9bfff2 638e331c0 Author: Max Katz Date: Thu Jun 8 18:40:34 2017 -0400 Merge pull request #33 from xinshengqin/gpu2 change Tools/GNUMake/Make.rules to be shell-independent commit 638e331c0ef5fc0b4e36fd74a3f9fac37f72e778 Merge: 3757679ed 27e9bfff2 Author: Xinsheng (Shawn) Qin Date: Thu Jun 8 15:16:28 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit 3757679ed1e61b6eca2f9f0f4331f0b1f8804733 Author: Xinsheng (Shawn) Qin Date: Thu Jun 8 15:15:59 2017 -0700 update Make.rules to use shell-independent if condition Tools/GNUMake/Make.rules commit 27e9bfff26f28643545a61f749edba445e0ea3c9 Author: Max Katz Date: Thu Jun 8 17:50:42 2017 -0400 Add in CUDA C++ to F90 build Src/Base/GPackage.mak commit eddf13ae61d4a7f57aed80d1261401c5a80212e7 Author: Max Katz Date: Thu Jun 8 17:03:37 2017 -0400 Add an alternate FOEXTRAP version of filcc Src/Base/AMReX_FILCC_3D.F90 commit 428a1520e4a33063fa6bb028ede17732894d937f Author: Marc Day Date: Thu Jun 8 13:19:58 2017 -0700 WIP: Try adding a grow cell...failure Tests/GeometryShop/vofStructures/vofStructures.cpp commit 9870052357ce78a80f03bc791093327c2a3c25db Merge: 84b2b5abf bb03918ba Author: Max Katz Date: Thu Jun 8 16:12:59 2017 -0400 Merge pull request #32 from alancalder/gpu Gpu What should complete the cudaizing of the advance_3d.F90 routine for the Heat Equation Test. commit f005aa2f94781767b255d51443bde291c6e0b7a1 Merge: cf56b7b80 13e0db1ad Author: WeiqunZhang Date: Thu Jun 8 13:03:38 2017 -0700 Merge pull request #31 from bcfriesen/CVODE_tutorial_fixes Tutorials: fix pointer mistake in CVODE/EX1 and CVODE/EX2 commit 84b2b5abfd4e5a21b1ac7391e72c6c71901ddf36 Author: Andrew Myers Date: Thu Jun 8 16:01:41 2017 -0400 use cuda streams when running with multiple boxes. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 commit bb03918ba345eb6d7d394feee381dae8b17dfe39 Author: Alan Calder Date: Thu Jun 8 15:57:10 2017 -0400 Another pass at the advance_3d.F90 routine from the Heat Equation Test. Should be complete this time. Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 13e0db1ad02d35034f82cf029e9e0969a4a28a39 Author: Brian Friesen Date: Thu Jun 8 12:38:54 2017 -0700 Tutorials: fix pointer mistake in CVODE/EX1 and CVODE/EX2 I mistakenly thought that the CVODE function N_VMake_Serial() allocates a new C array and deep copies the data from the corresponding Fortran. But in fact it simply creates a C pointer that points to the Fortran data. Tutorials/CVODE/EX1/integrate_ode.f90 Tutorials/CVODE/EX2/integrate_ode_no_jac.f90 Tutorials/CVODE/EX2/integrate_ode_with_jac.f90 commit 272e8df7624f6a9e287cc5b325aafe02ed0f25e3 Author: Marc Day Date: Thu Jun 8 12:38:12 2017 -0700 WIP: Rework eb structures a bit, add fortran to test Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/README.txt Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructuresA.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit cf56b7b8055d97c4a9e3b95abc318978c3950d54 Merge: 307c5a7de a127bec01 Author: WeiqunZhang Date: Thu Jun 8 12:36:31 2017 -0700 Merge pull request #30 from AMReX-Codes/dtg_branch initial indications are that two-stage communication seems to be working commit a127bec01d3a8e23137fb8ea022ad8249ad75c75 Merge: b698187b1 307c5a7de Author: dtgraves Date: Thu Jun 8 12:22:49 2017 -0700 merging with development branch commit b698187b1f598a2423634b7b43ffc2676db62d91 Author: dtgraves Date: Thu Jun 8 12:21:35 2017 -0700 took out some unused variables Src/GeometryShop/AMReX_EBGraph.cpp commit 987e5980cb0e291ca1ce4f19fd317add3261ff5a Author: dtgraves Date: Thu Jun 8 11:08:17 2017 -0700 made EBData holders (since they are templated) preallocatable = false without a ton of thought. We can revisit this for template specializations where we know it to be true. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBGraph.H commit 04e10db39eeed060527e2eecd2fdafdb440eefd1 Author: dtgraves Date: Thu Jun 8 10:56:43 2017 -0700 fixed merge bug Src/EBAMRTools/AMReX_EBFortND_F.H commit 1a50c06e827322e67d51bc3a958c3725e3a88303 Merge: d16c596bd 67ef79763 Author: dtgraves Date: Thu Jun 8 10:53:16 2017 -0700 merging with weiqun/2passes commit c6bb9dc74c98380c52b4bdd9cb51048e4e04035f Author: Andrew Myers Date: Thu Jun 8 13:46:32 2017 -0400 Adding another timer. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/main.cpp commit ea1de653b6ef1d928457cf903f27a6c19f59c4b0 Author: Andrew Myers Date: Thu Jun 8 13:43:20 2017 -0400 Also doing the Poisson solve. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp commit d16c596bd0634a364d7b9a0c6b8a9334eee1e8a8 Author: dtgraves Date: Thu Jun 8 10:40:24 2017 -0700 EBIndexSpace read/write now works and is tested. Src/Base/AMReX_Utility.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Tests/GeometryShop/README Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs Tests/GeometryShop/regression/fabio.cpp commit d129fd85eb2687d2b6b147a7bfe61ac334350fd4 Merge: 78798d524 d1ec6c184 Author: Andrew Myers Date: Thu Jun 8 12:03:21 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit d1ec6c184d870a9c43f463d40ad5e5358ad16afe Merge: bef191267 307c5a7de Author: Max Katz Date: Thu Jun 8 11:58:43 2017 -0400 Merge branch 'development' into gpu commit 307c5a7de6d86625fc7629c05732a379675ebf8e Author: Max Katz Date: Thu Jun 8 11:55:34 2017 -0400 Specify CUDA 8.0 for OpenACC Tools/F_mk/comps/Linux_pgi.mak commit 78798d524914dc962387fec237695d0dfa4dfa4d Author: Andrew Myers Date: Thu Jun 8 11:49:21 2017 -0400 fix capitalization issue. Tests/Particles/CUDADeposition/Make.package commit 185424ade5fb0c23a163adbf0f75cf18d6a04bbd Author: Andrew Myers Date: Thu Jun 8 11:47:14 2017 -0400 This compiles and runs correctly both with and without CUDA. Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/main.cpp commit 427c6db66b4fdc479f8a46ebb13ffe36069ffaf2 Author: Andrew Myers Date: Thu Jun 8 11:27:27 2017 -0400 making this thing compile both with and without CUDA. Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 commit e6177d9952e1382f2ea1bf1e3168f027b3f6dc8a Author: Andrew Myers Date: Thu Jun 8 11:13:45 2017 -0400 bringing over some stuff needed for the MG solves. Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp commit bef191267e50cee9a977a27a11a82f7145de3177 Merge: 3929652df c892d0c55 Author: Andrew Myers Date: Thu Jun 8 10:59:56 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 3929652dfe09285ffc4af8d60b7bceeb011c4c06 Author: Andrew Myers Date: Thu Jun 8 10:57:17 2017 -0400 fixed double-counting issue. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/main.cpp commit c892d0c556de86460647a3658d17aa72ed39978f Merge: 1dcf8cd5f 441090acf Author: Michael Zingale Date: Thu Jun 8 10:51:30 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu commit 1dcf8cd5f867670ca5efe77fb2e88a5175fdd0dc Author: Michael Zingale Date: Thu Jun 8 10:51:14 2017 -0400 remove the rest of the arraylim stuff for clarity Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 commit 441090acfcbab43c2f319467896927d9981d88aa Author: Max Katz Date: Thu Jun 8 10:32:28 2017 -0400 More cleanup of filcc interfaces Src/Base/AMReX_FILCC_3D.F90 commit 8f1b7ee41c98faa32da199be2b8eb814bb676d82 Merge: cb7367be5 6ab429139 Author: Michael Zingale Date: Thu Jun 8 10:25:20 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu commit cb7367be5eb8e8367aad95bcc2b30a50d94ebe42 Author: Michael Zingale Date: Thu Jun 8 10:25:07 2017 -0400 remove dim macros for clarity Src/Base/AMReX_FILCC_3D.F90 commit 6ab429139d61dcccc9353d651b91a2b3b34df17c Author: Max Katz Date: Thu Jun 8 10:18:54 2017 -0400 Add some FabArray/MultiFab profiling Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit 6e91722ed7c716490604d5da07fbcce4c1db6d63 Merge: 926e548db 5edf1a08d Author: Michael Zingale Date: Thu Jun 8 09:58:30 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu commit 926e548dbee255798e2f522d8810aa42e4a1d95b Author: Michael Zingale Date: Thu Jun 8 09:58:11 2017 -0400 make these free-form Src/Base/AMReX_FILCC_1D.F Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F Src/Base/AMReX_FILCC_3D.F90 Src/Base/Make.package commit 5edf1a08d2e1014d24157debd700232596f96a2d Author: Max Katz Date: Thu Jun 8 08:31:19 2017 -0400 Fix CPU versions of saxpy and plus Src/Base/AMReX_BaseFab_nd.F90 commit b6cc9419114ee7e83d73c414ce8459305b9f9c1d Author: Marc Day Date: Wed Jun 7 20:17:30 2017 -0700 WIP: Remove covered faces from data set Tests/GeometryShop/vofStructures/vofStructuresA.cpp commit 49bdddae98f157dfdd9c3a951909712db5bc8d3c Author: Marc Day Date: Wed Jun 7 20:08:27 2017 -0700 WIP: Rename FLUID to REGULAR Tests/GeometryShop/vofStructures/vofStructuresA.cpp commit 315d2476d2f2e9862eea97f190af9661dd2836d7 Author: Marc Day Date: Wed Jun 7 20:00:46 2017 -0700 WIP: An alternative set of structures to chase the graph in Fortran. Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructuresA.cpp commit 45e74d329fc82a303cb3ffca92edd5a5eaaac10b Author: Andrew Myers Date: Wed Jun 7 21:55:59 2017 -0400 fix to domain decomposed version. Tests/Particles/CUDADeposition/deposit_3d.f90 commit fb84a237d95bf4cc6c3447c3355769f81b9c58f7 Merge: 9184fefc5 559bd89c7 Author: Andrew Myers Date: Wed Jun 7 20:25:51 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 9184fefc506e2a990bf68eeaa7628434a8daba22 Merge: 0d8e35929 df2f0a566 Author: Andrew Myers Date: Wed Jun 7 20:25:25 2017 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into gpu commit 0d8e3592967a15d8e71e7095066143a7738e9f22 Author: Andrew Myers Date: Wed Jun 7 20:25:08 2017 -0400 converting more pic kernels to cuda. Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/main.cpp commit b19e739c665637831f6f8a52574cdf9bc61c84e8 Author: dtgraves Date: Wed Jun 7 16:24:10 2017 -0700 fixed an I/O bug. Added istream for RealVect. On to trying out two-phase communication Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs Tests/GeometryShop/regression/fabio.inputs commit 559bd89c72e73e8b47633ea9a20318b941d60f63 Author: Michael Zingale Date: Wed Jun 7 19:14:27 2017 -0400 enable CUDA for IBM Tools/GNUMake/comps/ibm.mak commit 5a6285ddd0ffc6940833f295152cc2554af6418a Merge: 643512d6a df2f0a566 Author: Michael Zingale Date: Wed Jun 7 19:08:54 2017 -0400 Merge branch 'development' into gpu commit 67ef79763a05360d6540a5ae8039e7a9df526cf1 Author: Weiqun Zhang Date: Wed Jun 7 15:23:46 2017 -0700 fix deadlock in 2-pass communication Src/Base/AMReX_FabArray.H commit c8620055727f4c3e192c0bc9f7164eb532de801a Merge: 24fe19abc 028d4088e Author: WeiqunZhang Date: Wed Jun 7 15:06:45 2017 -0700 Merge pull request #28 from AMReX-Codes/weiqun/tmp Add Intel to the list of compilers we test on to set the --traditiona… commit 028d4088eb23246a865659530d80e4a19de9fdd5 Author: Ann Almgren Date: Wed Jun 7 14:59:49 2017 -0700 Add Intel to the list of compilers we test on to set the --traditional flag Tools/CMake/PreprocessAMReXFortran90.cmake commit df2f0a5669ab8c46da5b775a077078c32d5a3fdd Merge: 65cc49582 65e038dd0 Author: Ann Almgren Date: Wed Jun 7 15:00:07 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 65cc495822ba35048ccdb1710ad5a64e6fd9fe01 Author: Ann Almgren Date: Wed Jun 7 14:59:49 2017 -0700 Add Intel to the list of compilers we test on to set the --traditional flag Tools/CMake/PreprocessAMReXFortran90.cmake commit 643512d6af6929f5c49f099595ed099896bdf9f3 Author: Max Katz Date: Wed Jun 7 17:45:39 2017 -0400 Write proper kernels for copy, saxpy, setval, and plus Src/Base/AMReX_BaseFab_nd.F90 commit 65fce5f9a15eedef4aae2cab4bfce7815e1cbdb0 Author: Andrew Myers Date: Wed Jun 7 17:18:10 2017 -0400 some more work on the domain decomp stuff. Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/inputs commit f190c26464098901b9be509c3bffc6b4384ab15a Merge: f658e4830 85e4515c4 Author: Xinsheng (Shawn) Qin Date: Wed Jun 7 13:49:17 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit 6631f2851e8731b5020268f9c9271274825cd15d Author: dtgraves Date: Wed Jun 7 13:37:19 2017 -0700 I/O for FabArray (for T = EBGraph, EBData and BaseEBCellFAB) seems to work fine. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_EBData.H Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs commit 85e4515c4a1afaeeac360f0e397bf54dae389d6e Merge: 3ed3ca103 d0d8cfed9 Author: Michael Zingale Date: Wed Jun 7 16:37:03 2017 -0400 Merge pull request #27 from alancalder/gpu Alan's pass at cudaizing the 3-d advance routine for the heat commit d0d8cfed904450a93ad11596b83428340175bcf5 Author: Alan Calder Date: Wed Jun 7 16:34:13 2017 -0400 Fixed two bugs in advance_3d.F0 of the heat equation test identified by Mike and Max. Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit df6d1e500bf9ab9ed8a1aa15607eb415efefadb6 Author: Weiqun Zhang Date: Wed Jun 7 13:30:12 2017 -0700 have to sum up number of bytes for each communication tile because of metadata Src/Base/AMReX_FabArray.H commit 8074f4b1466c8401356d8612dff13778af65cce4 Author: Alan Calder Date: Wed Jun 7 15:59:24 2017 -0400 Alan's pass at cudaizing the 3-d advance routine for the heat equation test. Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 86c3ff799405cf95a3c183ea8d7490bbc0246406 Author: Weiqun Zhang Date: Wed Jun 7 12:42:21 2017 -0700 Perform 2-pass communication if the receiver cannot preallocate the receive buffer. FAB in FabArray needs to have a preAllocatable() function indicate this. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit 33049a64e2bb97d1ed2bf6bee05de78d3887f16f Author: dtgraves Date: Wed Jun 7 11:45:14 2017 -0700 serialization for everything in sight (EBGraph, EBData, BaseIFFAB, BaseIVFAB) seems to work in the test. Src/GeometryShop/AMReX_BaseIFFABI.H Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/serialization.cpp commit 3ed3ca103cbfa67b8130dd2f86ad42f94a4a9621 Merge: 6e20c0573 99328c051 Author: Michael Zingale Date: Wed Jun 7 14:25:38 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/AMReX into gpu commit 6e20c0573e7952d026ba6bb71464779f5b90c5ef Author: Michael Zingale Date: Wed Jun 7 14:25:28 2017 -0400 add an INCLUDE_LOCATIONS for CUDA Tools/GNUMake/Make.defs commit 99328c051f29763f945f5f231a3aa7f2e36ef903 Author: Max Katz Date: Wed Jun 7 14:20:52 2017 -0400 Use CArena for CUDA Src/Base/AMReX_CArena.cpp Tools/GNUMake/Make.defs commit 65c5f3702fca285a7169249dddae869b4aa5dfca Merge: 8eb8e05ec dbd9220ca Author: Max Katz Date: Wed Jun 7 14:19:32 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit f658e4830378337fc2da2b07c349b9b0a303702d Merge: 44bbbe2e3 dbd9220ca Author: Xinsheng (Shawn) Qin Date: Wed Jun 7 11:08:31 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit dbd9220caf910553060d56a9fa7d2252314a8a8a Author: Michael Zingale Date: Wed Jun 7 13:09:54 2017 -0400 fix compilation on summit with PGI Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_pgi.mak commit 4a1e50f6e36c32d37313d3deea42e247c33b979c Author: Andrew Myers Date: Wed Jun 7 13:07:30 2017 -0400 some work towards working with domain decomposition. Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs commit 94b10e3055a366b415a223ec1ceb4a6b54d3aa1e Merge: e331e9370 65e038dd0 Author: Michael Zingale Date: Wed Jun 7 13:00:57 2017 -0400 Merge branch 'development' into gpu commit e331e9370692e6b30581b050af0133ca56c1ab50 Merge: b09b1f141 2cdb022fc Author: Michael Zingale Date: Wed Jun 7 12:21:08 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/AMReX into gpu commit 65e038dd08ea8f4d7bef609200652dac9d0e0483 Author: Michael Zingale Date: Wed Jun 7 11:54:09 2017 -0400 some initial support for summit -- note, cpp doesn't work with -traditional there so we override Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit 8eb8e05eccf6a9581bab6e54cca5cdf628f7b71e Author: Max Katz Date: Wed Jun 7 10:57:23 2017 -0400 Use synchronize after phi update Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit c17a4fe640b0d113a2816729058e48cd75d0ea11 Author: Max Katz Date: Wed Jun 7 10:23:47 2017 -0400 Get the thread block count working in 2D Src/Base/AMReX_CUDA.F90 commit 8fdff43e9ebf8aaa62f429271f67bdbe9904845f Author: Max Katz Date: Wed Jun 7 10:23:24 2017 -0400 Get update_phi on the device Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H commit 2cdb022fca2aa157e78af13a007fdbc4ea218b4e Merge: d65c0329e 9c6f2f0d6 Author: Andrew Myers Date: Wed Jun 7 09:37:56 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit d65c0329ecae14c9eb73d08cd47e3b930656f6c0 Author: Andrew Myers Date: Wed Jun 7 09:37:47 2017 -0400 Fixing a couple more bugs. Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 commit e5608ca5bd57681de9316af08dfcb4ca6b60583c Author: Max Katz Date: Wed Jun 7 09:35:19 2017 -0400 Use separate streams in HeatEquation Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H commit b09b1f1418210e8786687a74267e6c1064cc672d Merge: 9c6f2f0d6 48f0d4368 Author: Michael Zingale Date: Wed Jun 7 09:19:39 2017 -0400 Merge branch 'development' into gpu commit 9c6f2f0d69a74911905184ac25d701cde1c6f41a Author: Max Katz Date: Wed Jun 7 09:06:27 2017 -0400 Fix errors in advance_2d Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit c9ca66fbf46d558e1b1fd26b432a8157332e1f08 Author: Andrew Myers Date: Tue Jun 6 23:43:35 2017 -0400 a few bug fixes. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 commit 5376b7f7cfc39b91b93253462cf4b35f4f9f261d Author: Andrew Myers Date: Tue Jun 6 22:10:10 2017 -0400 Code that deposits a bunch of particles, with no domain decomposition for now. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/main.cpp commit e7729ec065b93e10ef3b2a75acb32ddb967033b5 Merge: 2368092d7 77537d9f4 Author: Andrew Myers Date: Tue Jun 6 20:51:53 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 2368092d72de04412308777c2b4fd2edea1edd08 Author: Andrew Myers Date: Tue Jun 6 20:51:03 2017 -0400 remove file added my mistake Tests/Particles/CUDADeposition/.bashrc commit ea29e96ca5c5585f403cbf6d422537fcfa70d902 Author: Marc Day Date: Tue Jun 6 17:48:56 2017 -0700 Make vof struct pod Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/Make.package Tests/GeometryShop/vofStructures/vofStructures.cpp commit d408872b1677c82e65235f12bd8da15db9b2bedf Author: Andrew Myers Date: Tue Jun 6 20:42:05 2017 -0400 successfully passing a chunk of particles to the GPU and processing them. Tests/Particles/CUDADeposition/.bashrc Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/main.cpp commit 8885c06cc0299d984e585141ffb438699f51e100 Author: dtgraves Date: Tue Jun 6 16:38:46 2017 -0700 The Good News: EBGraph serializaton is correct to the degree that I can test it. Bad news: Parallel EB still broken until I can get two-pass communication. Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Tests/GeometryShop/regression/serialization.cpp commit 77537d9f4ee316a0b2d6a62e6a4b36fef89d3a98 Author: Max Katz Date: Tue Jun 6 16:42:36 2017 -0400 Disable tiling if CUDA is enabled Src/Base/AMReX_FabArrayBase.cpp Tools/GNUMake/Make.defs commit 48f0d4368f5cdf451489ddb55284abae460f0046 Author: Weiqun Zhang Date: Tue Jun 6 11:26:26 2017 -0700 add amrex:growLo and amrex::growHi for Box Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit ba7d236b2cebc53add9332a668c792c4dd77b111 Merge: e42ca15ee 17f2ad918 Author: Michael Zingale Date: Tue Jun 6 12:04:35 2017 -0400 Merge branch 'development' into gpu commit e42ca15ee85d1c10717b29eb80868754c27a0883 Author: Max Katz Date: Tue Jun 6 10:30:25 2017 -0400 Put compute_flux on the GPU Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 commit 84c4da8553bfdb57752a6857b6233b881a7fcbc8 Author: Andrew Myers Date: Tue Jun 6 10:01:09 2017 -0400 Makings of a CUDA Deposition example program. Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp commit 17f2ad91822408a4d0d69bfa7b80fef5b1062b6a Author: Michael Zingale Date: Tue Jun 6 09:20:16 2017 -0400 fix spacing for global additions Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py commit cd654f099b35820600094d92bb9e4ae32668ff4b Author: Michael Zingale Date: Mon Jun 5 23:14:00 2017 -0400 a .F90 version of the programs syntax Tools/F_mk/GMakerules.mak commit fe37819de9a5126c4e1f0a11da476ad43d979898 Merge: a568d043b 15e199d7d Author: Michael Zingale Date: Mon Jun 5 21:27:37 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 15e199d7dfbe58a3991b04149baefc47fdc2aed1 Author: Weiqun Zhang Date: Mon Jun 5 17:15:36 2017 -0700 User's Guide: more on MultiFab Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/indextypes.pdf Docs/BoxLibUsersGuide/GettingStarted/GettingStarted.tex commit bc6895445eeb8efbc43f35226e6ba3d3c0794f4b Author: dtgraves Date: Mon Jun 5 16:21:48 2017 -0700 fixed some bugs in serialization. There are more to find. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/AMReX_SPMD.H Tests/GeometryShop/README Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs commit 3ed86c9555edd3aede5ddc921c5b5ca5891a18f4 Author: Weiqun Zhang Date: Mon Jun 5 15:28:20 2017 -0700 fix memory profiler Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MultiFab.cpp commit 44bbbe2e3b651e69514fd927fdc13006feefedd1 Merge: 9503eb510 0ce7d3362 Author: Weiqun Zhang Date: Mon Jun 5 13:42:37 2017 -0700 Merge branch 'development' into gpu2 commit 0ce7d3362c53eacc97752abbc2ff6c73445da2e6 Merge: 6bdddd8ab 246815956 Author: Weiqun Zhang Date: Mon Jun 5 12:11:20 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6bdddd8ab3ac79edab990c7924137f68a3bf3666 Author: Weiqun Zhang Date: Mon Jun 5 12:11:16 2017 -0700 User's Guide: FabArray Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/amrgrids.pdf commit a568d043b64a25a9e308edeffe1f60d49a39f100 Merge: 8df048010 246815956 Author: Michael Zingale Date: Mon Jun 5 14:47:20 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 2468159568b44df9dd783ce8651bcaae3d8ee3b3 Merge: ecf9eb9c1 8f21ae602 Author: atmyers Date: Mon Jun 5 13:40:25 2017 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ecf9eb9c1101d7ed051aa4221782a1d9370908b7 Author: atmyers Date: Mon Jun 5 13:40:10 2017 -0400 fix silly mistake in convert script. Tools/Py_util/amrex_particles_to_vtp/amrex_binary_particles_to_vtp.py commit 9503eb51009f4c3bf8617c31e1cbf6fcf5c36153 Author: Max Katz Date: Mon Jun 5 12:24:28 2017 -0400 Use CUDA 8.0 Tools/F_mk/comps/Linux_pgi.mak commit a1e6d854482dd48cbf1b377e8c43bd792c64e790 Author: Weiqun Zhang Date: Mon Jun 5 08:50:05 2017 -0700 typechecker: print debug information Tools/typechecker/typechecker.py commit 8f21ae602fc8319e664d6d372695d476e5400a20 Merge: a0b33efee f590f4998 Author: WeiqunZhang Date: Mon Jun 5 08:43:54 2017 -0700 Merge pull request #25 from bcfriesen/update_cvode_docs Update CVODE docs commit 7eac156f8c651302e2c5c508ea6d0c4379dadd8a Author: Max Katz Date: Mon Jun 5 10:31:28 2017 -0400 Use streams for MultiFab operations Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit ee219b502e03ffe8c945054054869b635cec1b57 Author: Max Katz Date: Mon Jun 5 10:24:23 2017 -0400 Remove Castro-specific variable Src/Base/AMReX_CUDA.F90 commit 8df048010af68745eb48460a5f2294b770a486b2 Merge: 7e10670b0 a0b33efee Author: Michael Zingale Date: Mon Jun 5 10:20:04 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit a0b33efee506851d150f0ffd5d7d600520712580 Merge: fb616cb79 3577dd316 Author: Brian Friesen Date: Sun Jun 4 22:37:46 2017 -0700 Merge branch 'cvode_fixes' into development commit 3577dd316640dc56c5ae22b7c2476a7259bce5ba Author: Brian Friesen Date: Sun Jun 4 22:36:37 2017 -0700 CVODE, Tools/GNUmake: add -DUSE_CVODE preprocessor flag when USE_CVODE=TRUE Tools/GNUMake/packages/Make.cvode commit fb616cb79caab95396ac193f66a68f7082f66bbf Author: atmyers Date: Mon Jun 5 01:20:47 2017 -0400 Adding a script to write from the particle binary format to vtp. Tools/Py_util/amrex_particles_to_vtp/README Tools/Py_util/amrex_particles_to_vtp/amrex_binary_particles_to_vtp.py Tools/Py_util/amrex_particles_to_vtp/amrex_particles_to_vtp.py commit f590f4998a79492c204213b48d798fa1c95d4f1c Author: Brian Friesen Date: Sun Jun 4 20:55:04 2017 -0700 Docs: remove Readme.cvode The material in this Readme has been moved to the User Guide. Docs/Readme.cvode commit 070ae7e469bfb62a32b9d3fff8111190db5dee57 Author: Brian Friesen Date: Sun Jun 4 20:54:13 2017 -0700 Docs: add chapter to user guide regarding CVODE with the new Fortran 2003 interface Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/CVODE/CVODE.tex Docs/AMReXUsersGuide/amrexsymbols.tex commit 17e6d94a95f285e5f5c3185149f74e46979ae8c4 Merge: e28aa1879 730487b3d Author: atmyers Date: Sun Jun 4 23:29:32 2017 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 730487b3dd1fb4d6d189cbe3f55c0e6e6864ab04 Merge: b230cc0ab c77b1b750 Author: Brian Friesen Date: Sun Jun 4 19:44:53 2017 -0700 Merge branch 'use_f03_cvode' into development These commits add support for the new Fortran 2003 interface to CVODE. They also migrate the two CVODE tutorials ("EX1" and "EX2") to this new interface. commit c77b1b75019185e9c3264e778986eedc52652ad4 Author: Brian Friesen Date: Sun Jun 4 19:41:41 2017 -0700 Tutorials/CVODE/EX2: switch to new Fortran 2003 interface to CVODE Tutorials/CVODE/EX2/Make.package Tutorials/CVODE/EX2/fcvdjac.f90 Tutorials/CVODE/EX2/fcvfun.f90 Tutorials/CVODE/EX2/integrate_ode_no_jac.f90 Tutorials/CVODE/EX2/integrate_ode_with_jac.f90 Tutorials/CVODE/EX2/ode_mod.f90 commit f77e395a96ef6769dea4a1a3bf922ff4affd7a16 Author: Brian Friesen Date: Sun Jun 4 17:05:07 2017 -0700 Tutorials/CVODE/EX1: switch to new Fortran 2003 interface to CVODE Tutorials/CVODE/EX1/Make.package Tutorials/CVODE/EX1/fcvfun.f90 Tutorials/CVODE/EX1/integrate_ode.f90 Tutorials/CVODE/EX1/ode_mod.f90 commit 65c3119c0c2755596f34785cd6420cf6708f4c20 Author: Brian Friesen Date: Sun Jun 4 17:02:39 2017 -0700 CVODE: add Fortran 2003 interface to CVODE This interface uses iso_c_binding and enables one to call CVODE C functions directly from Fortran without using FCVODE. It also includes a few helper functions which ease programming by, e.g., converting C array pointers to Fortran array pointers. AMReX will compile these modules if the USE_CVODE variable is set to TRUE. This interface was contributed by the SUNDIALS team. Src/Extern/CVODE/Make.package Src/Extern/CVODE/cvode_interface.f90 Src/Extern/CVODE/fnvector_serial.f90 Src/Extern/CVODE/sundials_fdlsmat.f90 Tools/GNUMake/packages/Make.cvode commit e28aa187924cf8c29673f0a7b3528fa8271a465c Author: atmyers Date: Sun Jun 4 17:16:06 2017 -0700 Some work on the Particle section of the Users Guide. Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Particle/Particle.tex commit ea79cf704375825d5197e668b95ede591a68aecc Author: Max Katz Date: Sun Jun 4 13:27:30 2017 -0400 Put the device synchronizes in a sane place Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_MultiFab.cpp commit 62a39044ff61b8d23e1a30a4607599eb1c9d3028 Author: Max Katz Date: Sun Jun 4 11:37:47 2017 -0400 Add CUDA to executable name Tools/GNUMake/Make.defs commit fe61a5a826d338834a02cfc2409c386e5665d61a Author: Max Katz Date: Sun Jun 4 11:25:28 2017 -0400 Collapse the fab copy loop Src/Base/AMReX_BaseFab_nd.F90 commit 671c5831ceb58544babbafbdeb437e194e9f47d0 Author: Max Katz Date: Sun Jun 4 04:28:34 2017 -0400 Port more FAB functions Src/Base/AMReX_BaseFab_nd.F90 commit ce402444bc6ed5c8cf6370c693fc93bfab1b70f8 Author: Max Katz Date: Sun Jun 4 03:31:43 2017 -0400 Build in NVTX into TinyProfiler Src/Base/AMReX_Device.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 39492303e8bc24e3766c545f7ca0901926275de8 Author: Max Katz Date: Sun Jun 4 03:05:23 2017 -0400 Add support for NVTX Src/Base/AMReX_Device.H Tools/GNUMake/Make.defs commit 43ab36a0d67744cd4b6227f35d3461dec98f3a58 Author: Max Katz Date: Sun Jun 4 02:13:50 2017 -0400 Undo unintentionally committed comments Src/Base/AMReX_BaseFab.H commit c58e04fe220fad798e5b69b029b0aa6d646fd6db Author: Max Katz Date: Sun Jun 4 02:11:58 2017 -0400 Start putting FAB functionality on device Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/Make.package commit ac3c41bd910b57a1045208158b4354bdcac71014 Author: Max Katz Date: Sun Jun 4 02:11:35 2017 -0400 Set preferred location to device Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit b230cc0abef0e0eb8442026b36b2a23eec724617 Author: Weiqun Zhang Date: Sat Jun 3 16:30:54 2017 -0700 it makes more sense to have SetPosition function in ParIter instead of ParIterBase Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 19ea6e2d3612422245b2cdd86e28c19ba477e37c Author: Weiqun Zhang Date: Sat Jun 3 14:30:02 2017 -0700 fix ParConstIter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit dc30c17c7c26fb6e6622a7aa06558015b76c7b73 Author: Weiqun Zhang Date: Sat Jun 3 13:18:50 2017 -0700 fix ParContIter's enable_if Src/Particle/AMReX_Particles.H commit 3f9578118a55fd6c9a079c817ea9b7bd9fb80ee7 Author: Weiqun Zhang Date: Sat Jun 3 13:05:19 2017 -0700 add ParConstiter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 95c921791277d4fab42ba6b64dbd8d47ca0d9781 Author: Weiqun Zhang Date: Fri Jun 2 19:04:16 2017 -0700 option to turn off limiter Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H commit d416595f5d02fc358ced7ad1ed523923a2a5e46f Author: Weiqun Zhang Date: Fri Jun 2 18:40:10 2017 -0700 fix a bug in the new interp function for warpx Src/AmrCore/AMReX_FillPatchUtil_2d.F90 commit d073a9e070f7ebe15088c3c8b66938963affcda2 Author: Marc Day Date: Fri Jun 2 18:36:33 2017 -0700 Start some new data structure dev/test code Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/Make.package Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp commit 63f48e85f0db4de5c998e22f512038b39b89d5ff Author: Weiqun Zhang Date: Fri Jun 2 14:07:35 2017 -0700 added some 2D functions for interpolation of EM fields Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H Src/Base/AMReX_fort_mod.F90 commit 6b75946e5c68aa180561cd28885f9514cc281bfe Author: dtgraves Date: Thu Jun 1 16:25:49 2017 -0700 Burrowing further into serialization routines. The tea at this unbirthday party is terrible. Many more tests coming so I can work my way out of this stuff. Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IrregFAB.cpp commit 230bfb540c3a37be223877d305e974ee25cd34f7 Author: dtgraves Date: Thu Jun 1 16:22:55 2017 -0700 added a test for more fabarray objects Tests/GeometryShop/regression/fabio.cpp commit 7e10670b092b02463697d361d98b4784065b2b36 Merge: 1f2bc2ced 24fe19abc Author: Michael Zingale Date: Thu Jun 1 11:44:53 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 08856a8ab6adaf9886e5efc06b11a350a2f63a3b Author: Max Katz Date: Thu Jun 1 02:01:39 2017 -0400 Also add -DCUDA to FPPFLAGS Tools/F_mk/GMakedefs.mak commit 1f165a03bb1ce40d2ad44c7dad5fbe71b087a288 Author: Max Katz Date: Thu Jun 1 01:49:07 2017 -0400 Add -DCUDA Tools/F_mk/GMakedefs.mak commit 24fe19abc762de0abd3ba75663427c77298f9373 Author: Weiqun Zhang Date: Wed May 31 17:21:17 2017 -0700 User's Guide: BoxArray and DistributionMapping Docs/AMReXUsersGuide/Basics/Basics.tex Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_FabArrayBase.cpp commit 490d783ee7a78bd9d5325044ea00d27616460e39 Author: dtgraves Date: Wed May 31 16:02:40 2017 -0700 This is an awfully deep rabbit hole. And what kind of rabbit carries a pocket watch? Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/fabio.inputs commit ba901a1dccd3b6524162d8de4ef55b5ebb42992f Author: dtgraves Date: Wed May 31 16:01:47 2017 -0700 added a utility to create a directory but moving the old one, it destroys it. Will only work on Unix Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit d2f64e3b22fa849bb4c0029898099153bff5f148 Author: Weiqun Zhang Date: Wed May 31 14:24:57 2017 -0700 User's Guide: BaseFab Docs/AMReXUsersGuide/Basics/Basics.tex commit 0145044c8d92a357a08a494521664ef95310146d Author: hsitaram Date: Wed May 31 14:49:41 2017 -0600 python script added to convert ascii amrex particle files to vtp (#23) * python script added to convert ascii amrex particle files to vtp * deleted extra particle plotfiles Tools/Py_util/amrex_particles_to_vtp/README Tools/Py_util/amrex_particles_to_vtp/amrex_particles_to_vtp.py Tools/Py_util/amrex_particles_to_vtp/samplefiles/particles00000 Tools/Py_util/amrex_particles_to_vtp/samplefiles/particles00001 Tools/Py_util/amrex_particles_to_vtp/samplefiles/particles00002 Tools/Py_util/amrex_particles_to_vtp/write_pview_file.py commit 7f7923402cc342f14699c3239ff0a24ac5f2cba3 Author: Ann Almgren Date: Wed May 31 12:24:23 2017 -0700 Add the functionality to pass the variable names into WritePlotFile as well as into CheckPoint. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit efc81f58ce953968f65023b93d8fd604da2790e8 Author: Weiqun Zhang Date: Wed May 31 11:18:07 2017 -0700 User's Guide: Geometry Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit b4475a6a8c2104a830b19b8d7f6b33153f538242 Author: Max Katz Date: Wed May 31 01:22:48 2017 -0400 Add CUDA to PGI in F_mk Tools/F_mk/comps/Linux_pgi.mak commit 6152aa9d4bf37ce61acfe804e4570833d410e9f0 Author: dtgraves Date: Tue May 30 16:40:53 2017 -0700 more progress on EB I/O. Serialization ain't fun. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp commit 11dda5523bf08f7aae758a1b4b142038ed0154d3 Author: dtgraves Date: Tue May 30 16:39:55 2017 -0700 added a couple of funtions to Box and IntVect to make my life a bit easier Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H commit 1f2bc2ced639bb4dcca0f25b9a67d9537e7a8062 Merge: 202534854 ff0e93a93 Author: Michael Zingale Date: Tue May 30 15:48:33 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 063f196ec84955f6a40eb34b8860320637c48b32 Author: dtgraves Date: Mon May 29 16:39:33 2017 -0700 More progress on I/O for EB. Marc will be glad to hear that I added a couple of classes. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Tests/GeometryShop/regression/fabio.cpp commit ff0e93a9368c8ae19f37f9d7465fd50c13712a2e Author: Weiqun Zhang Date: Mon May 29 12:11:12 2017 -0700 removeOverlap: option not to simplify Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 202534854aea6bf31b09cea5c3fb339789e3e041 Merge: 16b28de67 e6fee826e Author: Michael Zingale Date: Mon May 29 12:07:16 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit e6fee826eaf7644928700bb5ab525025a8309bc7 Author: Weiqun Zhang Date: Mon May 29 07:19:28 2017 -0700 move printGridSummary function from Amr to AmrCore Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp commit 70497ac406edab15bd2deefe4516c8c4f95deabb Author: dtgraves Date: Sun May 28 18:36:54 2017 -0700 more progress toward (less general) I/O for more general objects Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/FabArrayIO.H Src/GeometryShop/Make.package Tests/GeometryShop/regression/fabio.cpp commit 46e379a9cb7aff74a95610b37352947be6a1d0bb Merge: a479739a2 9f40822e1 Author: Max Katz Date: Sun May 28 12:04:06 2017 -0400 Merge branch 'development' into gpu commit 16b28de67b87f9973e7fb21e8718a72dfd1b5ba0 Merge: bd22d1b55 9f40822e1 Author: Michael Zingale Date: Sun May 28 09:45:12 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 9f40822e1c3322f8237bc07c74e2df9f9ff71ac0 Author: Weiqun Zhang Date: Sat May 27 19:39:36 2017 -0700 fix a bug in removeOverlap Src/Base/AMReX_BoxArray.cpp commit d180064514ada8f8cfa4a467f23f76784daa5fb0 Author: Max Katz Date: Sat May 27 18:02:36 2017 -0400 Provide null implementation for post_restart Src/Amr/AMReX_AmrLevel.H commit a502e1d0b2592ea5a75ba27914ead7211bc47e24 Author: Max Katz Date: Sat May 27 17:45:36 2017 -0400 Make post_restart not be pure virtual Src/Amr/AMReX_AmrLevel.H commit 759e172a0cfff0fc5fdee5eed8289caf264eaeed Author: dtgraves Date: Fri May 26 16:32:09 2017 -0700 started getting some EB elliptic stuff moved over Src/EBAMRElliptic/AMReX_AMRMultiGrid.H Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H Src/EBAMRElliptic/AMReX_BiCGStabSolver.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/AMReX_LinearSolver.H Src/EBAMRElliptic/AMReX_MultiGrid.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/Make.package commit b92b5126f9b923768c14283c8c763252928401e9 Author: dtgraves Date: Fri May 26 16:31:35 2017 -0700 started the bare bones of more general I/O with lots of help from Vince Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/FabArrayIO.H Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/fabio.inputs commit 7ad06248c190844a18eb41c5a9370151546067cc Merge: ad1989bfe 03d0f1bb2 Author: Andrew Myers Date: Fri May 26 15:40:02 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ad1989bfe5c82c3b8c3c610247a5a9ecf1691daa Author: Andrew Myers Date: Fri May 26 15:39:52 2017 -0700 1D and 2D version of the particle deposition / interpolation operations. Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 commit 03d0f1bb26eae775190752c913114a816cc9bb14 Author: Weiqun Zhang Date: Fri May 26 14:20:17 2017 -0700 make FillBoundary work for overlapping BoxArray Src/Base/AMReX_FabArrayBase.cpp commit 5f17416b0e7532758fed0dc4988cac995529f43b Author: Ann Almgren Date: Fri May 26 13:53:52 2017 -0700 Don't initialize integers with 0.d0 Tools/Postprocessing/F_Src/fextract.f90 commit 21b4f759dc1e1e2d223cb2212dfb0a059a6b63ab Author: Michele Rosso Date: Fri May 26 13:37:17 2017 -0700 Fix bug in fextract Tools/Postprocessing/F_Src/fextract.f90 commit bd22d1b557d5dba04ce5bdb8cfd2fbcd0704a31a Merge: c16c9de8d 9ef41cec8 Author: Michael Zingale Date: Fri May 26 16:04:27 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 9ef41cec81ed775533f49cff32aa93496cd75049 Merge: 6e5b8ca22 738b8363a Author: Andrew Myers Date: Fri May 26 10:57:32 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6e5b8ca22980b1e110dca1caa6670fcdac6e3340 Author: Andrew Myers Date: Fri May 26 10:57:19 2017 -0700 rename ghosts to neighbors to have a different name from Nyx-style ghost particles. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/main.cpp Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 Tutorials/Particles/ShortRangeParticles/short_range_F.H commit 738b8363a99208ded45a2aa38e8be506ca0a50db Merge: 4bc3681a6 07cb175c0 Author: WeiqunZhang Date: Fri May 26 10:55:34 2017 -0700 Merge pull request #21 from bcfriesen/cvode_tutorial_updates CVODE tutorial updates commit 07cb175c03e4bdf20e2fd4a6244ce1a130fad9b8 Author: Brian Friesen Date: Fri May 26 10:50:38 2017 -0700 Docs: added Readme.cvode with instructions for building CVODE/FCVODE Docs/Readme.cvode commit 3a35767592bc574b4302baeeaccca0696275c7fc Author: Brian Friesen Date: Fri May 26 10:48:49 2017 -0700 Tutorials/CVODE/EX1: replace custom writePlotFile() with amrex::WriteSingleLevelPlotfile() Tutorials/CVODE/EX1/Make.package Tutorials/CVODE/EX1/main.cpp Tutorials/CVODE/EX1/writePlotFile.H Tutorials/CVODE/EX1/writePlotFile.cpp commit f09b877d53b9ce56210de04689b1b02c57aa9042 Author: Brian Friesen Date: Fri May 26 10:43:02 2017 -0700 Tutorials/CVODE: added "EX2" tutorial This tutorial solves a set of 3 coupled ODEs in each cell. It is taken from the "fcvRoberts_dns.f" file in the CVODE examples. Tutorials/CVODE/EX2/GNUmakefile Tutorials/CVODE/EX2/Make.package Tutorials/CVODE/EX2/fcvdjac.f90 Tutorials/CVODE/EX2/fcvfun.f90 Tutorials/CVODE/EX2/inputs Tutorials/CVODE/EX2/integrate_ode_no_jac.f90 Tutorials/CVODE/EX2/integrate_ode_with_jac.f90 Tutorials/CVODE/EX2/main.cpp Tutorials/CVODE/EX2/myfunc_F.H commit 4bc3681a6a0f4118adfa0f9194c1d2888bd9d82f Merge: 07be1d1f9 25ed2baa3 Author: Andrew Myers Date: Fri May 26 10:23:13 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 07be1d1f93303b9f31e128340d102720048ee614 Author: Andrew Myers Date: Fri May 26 10:23:00 2017 -0700 Handle periodic boundaries in the short range particle tutorial. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit 25ed2baa3993ea336c4067e8d6a5f1d0c6680a6a Merge: d228a420e 7ac299c22 Author: WeiqunZhang Date: Fri May 26 09:29:40 2017 -0700 Merge pull request #20 from akreienbuehl/clrdDiffuSolve Fixed `Make.unknown` commit 7ac299c22a1803052cf9593e0b0056f7b7728a44 Author: Andreas Kreienbuehl Date: Fri May 26 09:23:19 2017 -0700 Made fix more readable Tools/GNUMake/sites/Make.unknown commit d301fbfd2e01e7dd742fb14abf345f80ce665a99 Author: Andreas Kreienbuehl Date: Fri May 26 08:49:25 2017 -0700 Fixed Makefile Tools/GNUMake/sites/Make.unknown commit d228a420eee8d15b891a6ae54c2181ef87ee72ba Merge: 06de48459 7f29fa5c0 Author: WeiqunZhang Date: Fri May 26 08:45:17 2017 -0700 Merge pull request #19 from AMReX-Codes/ibm_make add the ability to specify a prefix to preprocessor variables commit 7f29fa5c09e61f539afdbda220e174b9b2d7f6cb Author: Michael Zingale Date: Thu May 25 21:43:46 2017 -0400 use the flush() intrinsic of Fortran 2003 instead of call flush() to get link issues resolved. Also add more to the library lines Src/Base/AMReX_BLBoxLib_F.f Src/F_BaseLib/layout.f90 Src/F_BaseLib/parallel.f90 Tools/GNUMake/comps/ibm.mak commit 06de48459b3396b23205bf19a4d90907058aa7da Author: Weiqun Zhang Date: Thu May 25 16:54:58 2017 -0700 fix ParallelDescriptor for non MPI Src/Base/AMReX_ParallelDescriptor.cpp commit b894bdf8d4cc6d710f8af9bc2f0eb7d20bade96f Author: Michael Zingale Date: Thu May 25 18:56:39 2017 -0400 defer the initialization of prefixes to the CPP_FLAGS to allow for user-code defines to be caught Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit e508642075339ae42eb4539aaeb20e3537b20f99 Merge: 62437d0a3 2f66653ed Author: WeiqunZhang Date: Thu May 25 15:55:24 2017 -0700 Merge pull request #18 from akreienbuehl/clrdDiffuSolve clrdDiffuSolve commit 2f66653ede5b3cd13a15faa8daa5fd73fdd98453 Author: Andreas Kreienbuehl Date: Thu May 25 15:38:10 2017 -0700 Fixed issue with `std::vector::resize' and the MPICH installation prefix can now contain `mpich' in upper case as well Src/Base/AMReX_ParallelDescriptor.cpp Tools/GNUMake/sites/Make.unknown commit c16c9de8d7449da9eb1073681af9ba197bc2aff8 Merge: 395f02dbd 62437d0a3 Author: Michael Zingale Date: Thu May 25 18:33:30 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 62437d0a3c871e520f7ae6e9fd707c73b33d022b Author: Weiqun Zhang Date: Thu May 25 13:10:30 2017 -0700 User's Guide: Box Docs/AMReXUsersGuide/Basics/Basics.tex commit 264831791a43d3a10aa779132cafe7f8fe16bd7c Author: Brian Friesen Date: Thu May 25 12:30:38 2017 -0700 Tutorials: move CVODE_EX1 to CVODE/EX1 Tutorials/CVODE/EX1/GNUmakefile Tutorials/CVODE/EX1/Make.package Tutorials/CVODE/EX1/fcvfun.f90 Tutorials/CVODE/EX1/inputs Tutorials/CVODE/EX1/integrate_ode.f90 Tutorials/CVODE/EX1/main.cpp Tutorials/CVODE/EX1/myfunc_F.H Tutorials/CVODE/EX1/writePlotFile.H Tutorials/CVODE/EX1/writePlotFile.cpp commit b4d9e9f6668eed15e7b993aa2c8d8411a55a7480 Author: Michael Zingale Date: Thu May 25 15:06:02 2017 -0400 this gets IBM to the link stage (if you hack the endianness stuff) Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/ibm.mak commit 8034bb919842ee63e23c79ea96fb432ff998f96b Author: Michael Zingale Date: Thu May 25 14:00:06 2017 -0400 use -gnu99 standard for C Tools/GNUMake/comps/ibm.mak commit 809b8db645361240f39aa1681a30ca009143ba9a Merge: 6a0322d93 8d9718f7b Author: WeiqunZhang Date: Thu May 25 10:44:25 2017 -0700 Merge pull request #17 from akreienbuehl/clrdDiffuSolve clrdDiffuSolve commit 99fb87f256c14d603fbec5201e1da0210718b7fd Author: Brian Friesen Date: Thu May 25 10:42:22 2017 -0700 Tutorials/CVODE_EX1: add comment clarifying what the tutorial does Tutorials/CVODE_EX1/main.cpp commit 8d9718f7b53adfadf4e767923bdc9a1d6acea8f6 Author: Andreas Kreienbuehl Date: Thu May 25 10:07:31 2017 -0700 Improved initialization and color-free case Src/Base/AMReX_ParallelDescriptor.cpp commit e05eaef73fe5f9c073fa4a8a29e922645179c664 Author: Andreas Kreienbuehl Date: Wed May 24 21:05:51 2017 -0700 Added new var. `m_first_procs_clr' to header as well Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 4547a69a747ae7b76d3d83d53b9302490d9e553f Author: Andreas Kreienbuehl Date: Wed May 24 16:37:47 2017 -0700 Testing `nProcs%nClrs != 0' Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 395f02dbd7169252eacacc8f400763a9fa0653ca Merge: a5cd8de99 6a0322d93 Author: Michael Zingale Date: Wed May 24 19:17:14 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 6a0322d9344f29cd3a1216a4d584b2809b19a089 Author: Weiqun Zhang Date: Wed May 24 15:18:15 2017 -0700 fix bug in amrex_interp_div_free_bfield Src/AmrCore/AMReX_FillPatchUtil_3d.F90 commit 2e03841bae0c92a63d9ef0baf164776ecab25c00 Author: Weiqun Zhang Date: Wed May 24 10:51:35 2017 -0700 add optional arguments Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit de59b215f9ebf4bbc4c61100a06718e23357d83f Author: dtgraves Date: Wed May 24 10:01:35 2017 -0700 added clarifying comment and made sure added EBGraph::fillIntMask does not reach outside domain Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit c62f46202c0d77eb146c1e7c58e09d435c63c54f Merge: ce18382a4 fe5582c79 Author: WeiqunZhang Date: Wed May 24 09:58:27 2017 -0700 Merge pull request #16 from bcfriesen/yt_at_nersc Docs: add documentation for using yt commit 0e7ff86d1f6054b444512626dec2c73b0efead9d Author: dtgraves Date: Wed May 24 09:52:38 2017 -0700 added EBGraph::fillIntMask Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit fe5582c7927f7649345c0cbff3c90e697b3a24a9 Author: Brian Friesen Date: Wed May 24 09:47:40 2017 -0700 Docs: added section about visualization with yt This includes instructions for running yt on both a local workstation and at NERSC. The NERSC part is somewhat of a moving target because the dust is still settling on the implementation of Jupyter and IPython; the docs should be updated if those things change in the future. Docs/AMReXUsersGuide/Visualization/Visualization.tex Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_slice.png Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_vol_rend.png commit ce18382a45d84b7e37560bfdf7367b55923ae3d6 Merge: d910e9c85 ccc63c73c Author: WeiqunZhang Date: Wed May 24 09:39:14 2017 -0700 Merge pull request #14 from zingale/development define __LITTLE_ENDIAN__ commit d910e9c85e33315d7e8333455f005d7b9b7ed73e Merge: de84aaf95 bf6d103cc Author: WeiqunZhang Date: Wed May 24 09:38:55 2017 -0700 Merge pull request #12 from bcfriesen/add_cvode Add CVODE commit de84aaf95cff34016da943c9c425093e234ff8f0 Author: Weiqun Zhang Date: Wed May 24 09:22:13 2017 -0700 fix a bug in the new amrex_interp_efield Src/AmrCore/AMReX_FillPatchUtil_3d.F90 commit 34aae37d664151bb83e38cc252e959ca4d080a5a Author: Weiqun Zhang Date: Wed May 24 08:41:53 2017 -0700 User's Guide: more place holders Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Docs/AMReXUsersGuide/Debugging/Debugging.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Profiling/Profiling.tex commit b125f8eeae8e38cea5752f4fc598fa5fd1c1b324 Author: Andreas Kreienbuehl Date: Wed May 24 07:01:51 2017 -0700 Toward `nProcs%nClrs != 0' Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 677e7d9878ac3640ea1299362b4baa33c64aa05c Author: Weiqun Zhang Date: Tue May 23 16:56:55 2017 -0700 more options to CFinfo Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit cd7b1855ccefff5b6e460929129010a3ad8dcaa3 Author: Weiqun Zhang Date: Tue May 23 12:17:49 2017 -0700 Print: use the precision of the ostream argument Src/Base/AMReX_Print.H commit 80543a93a6fc8154f3edb27eb91b0064b2fd766c Author: Weiqun Zhang Date: Tue May 23 11:26:49 2017 -0700 User's Guide: IntVect and IndexTyp Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit 77992f833efbc266c33efa8f986c8dc0fcdd8122 Author: Andy Nonaka Date: Tue May 23 11:23:55 2017 -0700 revert the precision modifiers until we figure out how to set the global precision to be persistent Src/Base/AMReX_Print.H commit 1604428da3d96492a9f06befee1799eed48df3bd Author: Andy Nonaka Date: Tue May 23 10:49:09 2017 -0700 create amrex::Print().Precision functionality that replicates std::cout.precision() Src/Base/AMReX_Print.H commit 2f250010c28654e343f15b5c1e65f31cf2fc1e02 Author: Andrew Myers Date: Mon May 22 17:47:57 2017 -0700 Simply call std::map's clear here. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit df8a995b14624bc52cf28cab1129522c0e6227cf Author: Weiqun Zhang Date: Mon May 22 13:45:25 2017 -0700 make IntVect::operator[] (int) const return a const& instead of value to avoid potentially passing addresss of temporary return value Src/Base/AMReX_IntVect.H commit 0499153d82bf10c1af01df8c1405b95c233d92a2 Author: Weiqun Zhang Date: Mon May 22 13:26:31 2017 -0700 User's Guide: ParmParse Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Src/Base/AMReX_REAL.H commit 6eb59423c6f4661028b11be9a2ed8ced6cc0be12 Author: Ann Almgren Date: Mon May 22 12:49:45 2017 -0700 Fix clearGhosts routine. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit a5cd8de996f3722629301211021a8e23fdc08ad7 Merge: 7fa5cad68 f8b2b68e0 Author: Michael Zingale Date: Mon May 22 13:58:36 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit f8b2b68e0802704005a3a00a3a8bb603a22d9a51 Author: Weiqun Zhang Date: Mon May 22 10:56:36 2017 -0700 turn off ghost cells in amrex::WriteMultiLevelPlotfile Src/Base/AMReX_PlotFileUtil.cpp commit 98e29b5c109ccfd9e1bcfe69f5af882e40f01bc6 Author: Weiqun Zhang Date: Mon May 22 09:56:07 2017 -0700 add AMREX_SPACEDIM Src/Base/AMReX_SPACE.H Tools/GNUMake/Make.defs commit 7cadc850414ef9339fe4e77533346510f8b1882c Author: Weiqun Zhang Date: Mon May 22 09:46:18 2017 -0700 Remove some old scripts. If you miss them, revert my commit. Tools/C_scripts/boxlib-build.sh Tools/C_scripts/compressor Tools/C_scripts/gen_release_tarball commit 5f3cd9f7dfe26fb749d5c53ff160993bafff060f Merge: 59f0f0e15 eb4b2dd37 Author: Andrew Myers Date: Sat May 20 20:16:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 59f0f0e15ed9130aade587c05cf37dd838f5c3b2 Author: Andrew Myers Date: Sat May 20 20:16:09 2017 -0700 remove unused variable. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp commit 332b6d8906922710fc79599f6e4803768601483c Author: Andrew Myers Date: Sat May 20 20:15:48 2017 -0700 properly fillpatch the ghost cells for phi. Tutorials/Particles/ElectrostaticPIC/main.cpp commit ccc63c73ced53f78f15502f4291f6f4e7d587f75 Merge: b8c02ea1d 7fa5cad68 Author: Michael Zingale Date: Sat May 20 20:13:08 2017 -0400 Merge branch 'development' of ssh://github.com/zingale/amrex into development commit b8c02ea1d2b3306e962dca9c83507c9a4e6e992d Merge: a419688d3 eb4b2dd37 Author: Michael Zingale Date: Sat May 20 20:11:29 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit eb4b2dd378eb6a431f590bf6c205436cb42c2375 Author: Weiqun Zhang Date: Sat May 20 16:24:32 2017 -0700 implement 3d amrex_interp_efield Src/AmrCore/AMReX_FillPatchUtil_3d.F90 commit 16dc08cef9b46fdf40bef37c25b8cb4f30d625ea Author: Michael Zingale Date: Sat May 20 18:40:58 2017 -0400 a hack for summit to find libatomic. This assumes that you've pointed PGI/17.4 to the gcc/5.4.0 install using the makelocalrc in PGI Tools/GNUMake/comps/pgi.mak commit a419688d3d55cd304e15000a3de9bcb5b6031b1e Merge: b21655933 7bf7d47d6 Author: Michael Zingale Date: Sat May 20 18:21:37 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 7fa5cad686f9f0a0d7b239d19c882ea0e8b06110 Merge: 7bf7d47d6 db01f53c9 Author: Michael Zingale Date: Sat May 20 18:19:43 2017 -0400 Merge branch 'development' of ssh://github.com/zingale/amrex into development commit 7bf7d47d6d3eaeb6dbd9325e7905676a7c4ab5f6 Author: Max Katz Date: Sat May 20 17:44:51 2017 -0400 Move internal subroutine out to avoid a PGI 17.4 bug Src/F_BaseLib/multifab_c.f90 commit d87fa117441bd9a8082182442bbd904b6a240e38 Author: Max Katz Date: Sat May 20 17:44:29 2017 -0400 Restrict a use statement to avoid a PGI 17.4 bug Src/F_BaseLib/knapsack.f90 commit c2f3c228e48a64a7e3c34819efc5dcc09781cdff Author: Weiqun Zhang Date: Sat May 20 11:23:26 2017 -0700 add amrex_intep_efield stub Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_1d.F90 Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H commit b216559334ddea6c3b44f7b6e4051d71ca1d0241 Merge: db01f53c9 6943903f8 Author: Michael Zingale Date: Sat May 20 13:34:11 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 6943903f8c028781fce5e8e52ec99cb662112db8 Author: Michael Zingale Date: Fri May 19 22:11:42 2017 -0400 fix compilation error Src/AmrCore/AMReX_FillPatchUtil_1d.F90 commit a09bd7425e72384d8a3fa00103605889f85bcf81 Author: Andrew Myers Date: Fri May 19 17:12:19 2017 -0700 do the proper coarse/fine interpolation before computing the electric field. Tutorials/Particles/ElectrostaticPIC/main.cpp commit 5db5ea6c2af57e9c43733249ffa97aeebc624f8f Merge: f3c141381 8936f9486 Author: Andrew Myers Date: Fri May 19 16:58:39 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f3c141381e5a2978fc03c74bda3d98e48640a761 Author: Andrew Myers Date: Fri May 19 16:58:24 2017 -0700 change the default inputs parameters Tutorials/Particles/ElectrostaticPIC/inputs commit c9aedf5cc3c4623137f4f3d62698ee9b07702256 Author: Andrew Myers Date: Fri May 19 16:58:00 2017 -0700 Some tweaks to the nodal poisson solve. Tutorials/Particles/ElectrostaticPIC/main.cpp commit 27f1ce66f373457c13ffe9c5a583baa24fe9d3aa Author: Andrew Myers Date: Fri May 19 16:57:46 2017 -0700 Only initialize the particles on one process. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp commit 8936f948633b0762ad7c968a58868ea4f6304b28 Author: Weiqun Zhang Date: Fri May 19 10:58:14 2017 -0700 fix a bug in SumBoundary Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/Base/AMReX_MultiFab.cpp commit 9e1d9a8b9c382bf9addc72c8c2810039a90bd4ba Merge: a2eb0eecd a02b449f0 Author: Andrew Myers Date: Fri May 19 10:14:26 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a2eb0eecdea426ee9a9b39a4f01d638b3a6bec84 Author: Andrew Myers Date: Fri May 19 10:14:13 2017 -0700 Adding some commentary. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H commit a02b449f051eac7112e35db18d5985d96750207a Merge: d1411bdee 51638c85f Author: Weiqun Zhang Date: Fri May 19 09:41:20 2017 -0700 Merge branch 'weiqun/bfield' into development commit a479739a2409db8641cd0cc6b0c96fb4d9e55a19 Author: Max Katz Date: Fri May 19 03:55:20 2017 -0400 Place device updates in non-default streams Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 79abe67a8badcb758cf3ade371f201cfef8c5501 Author: Max Katz Date: Fri May 19 03:23:59 2017 -0400 Enable CUDA in the PGI compiler Tools/GNUMake/comps/pgi.mak commit 05c721d93682b7ca4187b747fbb5f0850321a18f Author: Max Katz Date: Fri May 19 03:03:20 2017 -0400 Move CUDA calls to Fortran Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit d1411bdee788850d93847ed1ff0221f2fdc011dd Merge: 781dc86a2 ba2b9481a Author: Andrew Myers Date: Thu May 18 17:10:59 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 781dc86a2c1d9a1791be443e9bf8f70258d0f4a1 Author: Andrew Myers Date: Thu May 18 17:10:37 2017 -0700 Some work on the ES PIC Tutorial Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit ba2b9481a65a5f58a61c34694fb98dc87a66c848 Author: Weiqun Zhang Date: Thu May 18 16:03:16 2017 -0700 make it typechecker friendly Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/Make.package commit cbeed0e7ee2a3f775c2afe7b5d2826fd2a40f3fe Author: dtgraves Date: Thu May 18 15:21:15 2017 -0700 fixed some 3d bugs and I think finally have EBFineInterp working Src/EBAMRTools/AMReX_EBFortND.F90 Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebfineinterp.inputs commit 49f5b9e68a7fe611186f28e3d0721bfabc6b5ac4 Author: dtgraves Date: Thu May 18 15:19:24 2017 -0700 took out unwanted function Src/Base/AMReX_BaseFab.H commit a543984935bacb868e3211ff4b1dbe125854a5a9 Author: Andrew Myers Date: Thu May 18 11:27:10 2017 -0700 Adding a nodal average down function. Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H commit dec2d8bdb32d9ba5959aecbbb05a8329134c5f40 Merge: 01ad059fc 0569a5362 Author: Michele Rosso Date: Thu May 18 11:23:10 2017 -0700 Merge branch 'mr-cmake' into development commit 01ad059fc7591ad56d41e7b0466a97e212ef743f Author: Max Katz Date: Thu May 18 12:47:30 2017 -0400 Revert "Create a unique MFIter index" This reverts commit f20630351987a9597814cf76d73ec3a541581361. Src/Base/AMReX_MFIter.H commit bf6d103ccdce06fe0aa96755ed25b5af6c7a0495 Merge: 4bdb389bb 64fd0eba3 Author: Brian Friesen Date: Thu May 18 09:42:20 2017 -0700 Merge branch 'CVODE_EX1_cleanup' into add_cvode This cleans up a few misc problems with the CVODE_EX1 tutorial, and adds OpenMP tiling support (although currently FCVODE, the Fortran interface to CVODE, is not thread-safe). commit 64fd0eba3f43580047fdda914bd758f4461ca91c Author: Brian Friesen Date: Thu May 18 09:40:13 2017 -0700 Tutorials/CVODE_EX1: remove incorrect comment Tutorials/CVODE_EX1/main.cpp commit 783d8c44028d6e0423edf5d2291d946abc53867c Author: Brian Friesen Date: Thu May 18 09:39:52 2017 -0700 Tutorials/CVODE_EX1: remove unused variable "dx[]" Tutorials/CVODE_EX1/main.cpp commit bde51e22842063ecae84c8e35b8c15706db1c0a9 Author: Brian Friesen Date: Thu May 18 09:39:21 2017 -0700 Tutorials/CVODE_EX1: remove doubly declared variable "is_periodic[]" Tutorials/CVODE_EX1/main.cpp commit fa7dba0d099737e760d9d7c1961f770da02dac81 Author: Brian Friesen Date: Thu May 18 09:38:33 2017 -0700 Tutorials/CVODE_EX1: add OpenMP tiling option Tutorials/CVODE_EX1/inputs Tutorials/CVODE_EX1/main.cpp commit 8061d9abab6d35d6196234ae079b02c47be23c89 Merge: c9a1d862e f20630351 Author: dtgraves Date: Thu May 18 09:30:53 2017 -0700 Merge branch 'development' into dtg_branch commit c9a1d862e4b24152b3610889bafa860cc0cad543 Merge: 552f0c972 e3fae2b26 Author: dtgraves Date: Thu May 18 09:30:40 2017 -0700 Merge branch 'dtg_branch' of https://github.com/AMReX-Codes/amrex into dtg_branch commit 552f0c9727c1aee04f4c9919974c6ace0dc9d4f9 Author: dtgraves Date: Thu May 18 09:28:44 2017 -0700 some progress toward higher order EBFineInterp Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Tests/EBAMRTools/regression/ebFineInterpTest.cpp commit f20630351987a9597814cf76d73ec3a541581361 Author: Max Katz Date: Sun May 14 20:38:34 2017 -0400 Create a unique MFIter index Src/Base/AMReX_MFIter.H commit db01f53c9bd518a4bffc18c5279457e873349d52 Author: Michael Zingale Date: Thu May 18 09:20:18 2017 -0400 fix little endian locations Src/Base/AMReX_FPC.cpp commit dc7d2a360173b5b79ccbc7f68e10dca1ea487250 Merge: c7eb6a938 e3fae2b26 Author: WeiqunZhang Date: Wed May 17 20:29:04 2017 -0700 Merge pull request #13 from AMReX-Codes/dtg_branch EB bug fixes for Marc commit e3fae2b267c6bdb08211d277b38bbd57191b1c8c Merge: 1c99f720e c7eb6a938 Author: dtgraves Date: Wed May 17 19:04:19 2017 -0700 Merge branch 'development' into dtg_branch commit 4bdb389bb52409a823a761f28797d85f861d42e9 Author: Brian Friesen Date: Wed May 17 18:57:55 2017 -0700 CVODE: move Make.cvode into Tools/GNUMake/packages Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.cvode commit 4b1062fbd194ddc2341974951336f47b3e81d499 Author: Michael Zingale Date: Wed May 17 21:53:02 2017 -0400 define __LITTLE_ENDIAN__ Src/Base/AMReX_FPC.cpp commit c7eb6a938493b4d64eea218e4ee453752586c45c Author: Michael Zingale Date: Wed May 17 21:47:18 2017 -0400 revert the CPP_PREFIX stuff required for IBM, since it breaks GNU. THis means that IBM will not work until we find a better way to define preprocessor variables Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 74ff011c618aaa4ee3a1c907c4cf00077991733f Author: Michael Zingale Date: Wed May 17 21:17:56 2017 -0400 some library fixes for GNU/summit Tools/GNUMake/sites/Make.olcf commit c4e424616067f72da47b90ac1c196976eda89b2d Merge: 1d4ea3059 de38250fc Author: Michael Zingale Date: Wed May 17 20:39:46 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 1d4ea3059b2c9d9c480bf8265b9c8816d7c311d8 Author: Michael Zingale Date: Wed May 17 20:39:35 2017 -0400 fix the dependency checking Tools/GNUMake/Make.rules commit de38250fcddeb7e58c8a15d8c63e9eef36cb3cba Merge: cd475d2dd 7797ee7a1 Author: Andrew Myers Date: Wed May 17 17:30:41 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cd475d2dd484f1fd9f34b04e3e4933fd34942786 Author: Andrew Myers Date: Wed May 17 17:26:08 2017 -0700 Adding a tutorial for electrostatic pic calculations. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/GNUmakefile Tutorials/Particles/ElectrostaticPIC/Make.package Tutorials/Particles/ElectrostaticPIC/PhysConst.H Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit 0825460d6ec61b5ca18edf146d97eb7f75e96bbd Author: Andrew Myers Date: Wed May 17 17:25:41 2017 -0700 Move the short range particles tutorial to the new tutorials directory. Tutorials/Particles/ShortRangeParticles/GNUmakefile Tutorials/Particles/ShortRangeParticles/Make.package Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/inputs Tutorials/Particles/ShortRangeParticles/main.cpp Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 Tutorials/Particles/ShortRangeParticles/short_range_F.H commit 7797ee7a1553f9eddb36566bd784dc345f072a7b Author: Michael Zingale Date: Wed May 17 20:22:28 2017 -0400 more progress with IBM -- only the F90 needs the -WF,-D... stuff. Also, the .F has uses cpp directly, so no need for the prefix there Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/ibm.mak commit 9844b9b2daddfee5ed6f6fcfdf6a57346b08384d Author: Andrew Myers Date: Wed May 17 17:15:13 2017 -0700 use scientific notation in particle compare. Tools/Postprocessing/C_Src/particle_compare.cpp commit 51317c3384c40310a6ddedb25ab9cbb0ee439efe Author: Michael Zingale Date: Wed May 17 20:01:46 2017 -0400 add a CPP_PREFIX option that should do nothing for all compilers except IBM XL, which wants the preprocessor directives in the form -WF,-DFOO=BAR Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/ibm.mak commit aaffb1ae6c83d67700a66d52a43a175400c84e8f Author: Michael Zingale Date: Wed May 17 19:33:51 2017 -0400 initial support for the IBM xl-series compilers Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/comps/ibm.mak commit ce104b25ba111f22de8f37e3b5eff531c1b88c7d Author: Michael Zingale Date: Wed May 17 19:16:48 2017 -0400 add summit -- hopefully this doesn't break titan :) Tools/GNUMake/sites/Make.olcf commit 51638c85fd1be5d3fabbd95407a44e2b3254d041 Merge: 6c1d9d2dc 9aacd4cf2 Author: Weiqun Zhang Date: Wed May 17 16:08:58 2017 -0700 Merge branch 'development' into weiqun/bfield commit 1c99f720e44214fa35528cc43e3ec3791d1d05ee Author: dtgraves Date: Wed May 17 15:32:46 2017 -0700 fixed a bug in graph coarsening that Marc found. Src/EBAMRTools/AMReX_EBFortND.F90 Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/sphereEBISBox/GNUmakefile commit 6c1d9d2dca9d946be331514c1b65cf00fb20931c Author: Weiqun Zhang Date: Wed May 17 15:03:35 2017 -0700 remove debug line Src/AmrCore/AMReX_FillPatchUtil.cpp commit 2fa20dd26cc3127a9c21f887439da907bb6f6692 Author: Weiqun Zhang Date: Wed May 17 14:58:35 2017 -0700 first pass of 3d amrex_interp_div_free_bfield Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_1d.F90 Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H commit 759d8bddfc795b0398f86361b7fdec46d5fd4689 Author: Brian Friesen Date: Wed May 17 12:47:24 2017 -0700 CVODE: add link hooks, Readme, and tutorial for using CVODE Tools/GNUMake/Make.cvode Tools/GNUMake/Make.defs Tutorials/CVODE_EX1/GNUmakefile Tutorials/CVODE_EX1/Make.package Tutorials/CVODE_EX1/fcvfun.f90 Tutorials/CVODE_EX1/inputs Tutorials/CVODE_EX1/integrate_ode.f90 Tutorials/CVODE_EX1/main.cpp Tutorials/CVODE_EX1/myfunc_F.H Tutorials/CVODE_EX1/writePlotFile.H Tutorials/CVODE_EX1/writePlotFile.cpp commit b8b4b36f71c806e0406f18f0ecfeeb25887a1972 Author: dtgraves Date: Wed May 17 11:54:15 2017 -0700 found a subtle bug in EBFineInterp. Convergence rates are now correct. Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebfineinterp.inputs commit 9aacd4cf2950929314d17dc627d9bcc68228b4ac Author: Weiqun Zhang Date: Wed May 17 11:01:20 2017 -0700 remove BL_ALWAYS_FIX_DENORMALS Src/Extern/amrdata/AMReX_AmrData.cpp Tools/CMake/CCSEOptions.cmake commit 5a14fb8201e04cf57947497b4fbdcfcf1946b701 Author: Max Katz Date: Wed May 17 13:39:23 2017 -0400 Add AMReX_CUDA.F90 Src/Base/AMReX_CUDA.F90 commit 2c6db3bfb798919bba04093ea6cbc572e24fad03 Merge: 1cdeeb2cc c56164653 Author: Max Katz Date: Wed May 17 13:39:07 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 4e010f9a3003dd8731ebd96a6849ece3de3e29a0 Author: Weiqun Zhang Date: Wed May 17 10:30:47 2017 -0700 removed a number of old if names: BL_AIX, BL_CRAY, BL_CRAYX1, BL_HOPPER, BL_SIM_HOPPER, BL_SIM_HOPPER_MAKE_TCFAB, and BL_T3E. Src/AmrCore/AMReX_FLUXREG_3D.F Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Utility.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F Src/Extern/amrdata/AMReX_AmrData.cpp commit c561646534c3e11f3c15b34d6a64333ad6bb9512 Author: Michael Zingale Date: Wed May 17 13:13:38 2017 -0400 wrap a CUDA call Src/Base/AMReX_Device.H commit c307314b0ece87f54bc40d7f6574491f3e608a2a Merge: e88a2d3b1 018ae35dc Author: Michael Zingale Date: Wed May 17 13:02:13 2017 -0400 Merge branch 'development' into gpu commit 018ae35dc7d9f1642dd016ad755aa00484688b67 Author: Weiqun Zhang Date: Wed May 17 09:51:24 2017 -0700 some BL_ --> AMREX_ Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex OldTutorials/AMR_Adv_C/Source/Adv.cpp OldTutorials/AMR_Adv_C/Source/Adv_F.H OldTutorials/AMR_Adv_C/Source/Adv_advance.cpp OldTutorials/AMR_Adv_C/Source/Adv_dt.cpp OldTutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp OldTutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H OldTutorials/HeatEquation_EX2_C/main.cpp OldTutorials/MeshRefinement/main.cpp OldTutorials/MultiColor_C/main.cpp OldTutorials/MultiGrid_C/main.cpp OldTutorials/ShortRangeParticles/main.cpp OldTutorials/Tiling_C/main.cpp OldTutorials/TwoGrid_PIC_C/split_boxes.cpp OldTutorials/libamrex_C/main.cpp Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPACE.H Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_MeshRefine.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_VolIndex.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/AMReX_TracerParticles.cpp Tests/C_BaseLib/tVisMF.cpp Tests/EBAMRTools/regression/regFluxRegTest.cpp Tests/GeometryShop/sphere/sphereTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/Particles/main.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit bfa937d85e50e29dac0aea63f03f28639244d998 Author: Weiqun Zhang Date: Wed May 17 09:36:02 2017 -0700 D_EXPR --> BL_D_EXPR Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPACE.H commit 9bf3b325f6693d57fd10e0d0393b55408d1f5fa8 Author: Weiqun Zhang Date: Wed May 17 09:32:06 2017 -0700 D_TERM --> BL_D_TERM OldTutorials/TwoGrid_PIC_C/split_boxes.cpp Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_Periodicity.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPACE.H Src/Boundary/AMReX_InterpBndryData.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFastFR.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_VolIndex.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_TracerParticles.cpp Tests/EBAMRTools/regression/regFluxRegTest.cpp Tests/GeometryShop/sphere/sphereTest.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/Particles/main.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 081a7164f1152b8db71b149f1610250ed5e9ac20 Author: Weiqun Zhang Date: Wed May 17 09:28:18 2017 -0700 D_PICK --> BL_D_PICK Src/Base/AMReX_SPACE.H Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 4ee9528ecf04a518236d0224a057715d04d899c5 Author: Weiqun Zhang Date: Wed May 17 09:24:05 2017 -0700 D_DECL --> BL_D_DECL Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex OldTutorials/AMR_Adv_C/Source/Adv.cpp OldTutorials/AMR_Adv_C/Source/Adv_F.H OldTutorials/AMR_Adv_C/Source/Adv_advance.cpp OldTutorials/AMR_Adv_C/Source/Adv_dt.cpp OldTutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp OldTutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H OldTutorials/HeatEquation_EX2_C/main.cpp OldTutorials/MeshRefinement/main.cpp OldTutorials/MultiColor_C/main.cpp OldTutorials/MultiGrid_C/main.cpp OldTutorials/ShortRangeParticles/main.cpp OldTutorials/Tiling_C/main.cpp OldTutorials/libamrex_C/main.cpp Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPACE.H Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/EBAMRTools/AMReX_MeshRefine.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_Moments.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/AMReX_TracerParticles.cpp Tests/C_BaseLib/tVisMF.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit 1a3c9272a3013933e0e5a45a61475443fc32ae02 Author: Weiqun Zhang Date: Wed May 17 09:36:49 2017 -0700 User's Guide add more place holders Docs/AMReXUsersGuide/Basics/Basics.tex commit e88a2d3b1f857a6038d6497628b2bea4d08d4c8a Merge: a7ea94d02 ac3289be7 Author: Michael Zingale Date: Wed May 17 08:35:26 2017 -0400 Merge branch 'development' into gpu commit ac3289be787409ebd72143b6f79daf29298c30b0 Author: Max Katz Date: Wed May 17 01:31:21 2017 -0400 Initialize post_step_regrid to 0 in constructor Src/Amr/AMReX_AmrLevel.cpp commit 0569a536266a407789a3e2f27e8f457ddc8c65aa Author: Michele Rosso Date: Tue May 16 17:16:56 2017 -0700 Add section on CMake in AMReX documentation Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit 9177b6edab394dafba91e74664735c0d9f00dc52 Author: Weiqun Zhang Date: Tue May 16 16:53:09 2017 -0700 wip Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_1d.F90 Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit c345c6ef51714259a01d3af83e4a92d1c237fec5 Author: vince Date: Tue May 16 16:43:37 2017 -0700 fix warnings for serial. delete perstreams after read. Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 2b17ae7aef99995315243e7f0464e6466ba83b97 Author: vince Date: Tue May 16 16:23:21 2017 -0700 profdata filetype. Src/Extern/amrdata/AMReX_AmrvisConstants.H commit efae9dfe83a71e3b74b295edf928e00cd320e05c Author: Weiqun Zhang Date: Tue May 16 13:25:14 2017 -0700 add coarse fine boundary cache Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit a2f875b657037e0af509d41fe3b2396d280a1f50 Merge: 9401c0682 a90293dac Author: Andrew Myers Date: Tue May 16 12:55:29 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9401c06825fb1be2936ebf8f7864241392390308 Author: Andrew Myers Date: Tue May 16 12:55:10 2017 -0700 update the test suite to use the compiled particle compare utility. Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit a90293dacfd54865837bb280272d4729388ec480 Author: Andrew Myers Date: Tue May 16 12:54:47 2017 -0700 a few more tweaks to the particle compare utility. Tools/Postprocessing/C_Src/particle_compare.cpp commit 3e72a5c3a6c68c524373bdfcf82dc2ad92b45a08 Author: Weiqun Zhang Date: Tue May 16 11:29:13 2017 -0700 User's Guide Basics Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_ccse-mpi.H commit b08c817ed6c0b6ff7859e8b9e854d06b6c0cbb89 Merge: dcfdd989a 79ad54a08 Author: Ann Almgren Date: Tue May 16 11:13:08 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit dcfdd989a2d6384406b8294a343c52be511bf868 Author: Ann Almgren Date: Tue May 16 11:12:42 2017 -0700 We need to update the dummy_mf after the grids have changed even if we haven't added levels. Src/Particle/AMReX_ParticleContainerI.H commit 7ef957e98fb39b6c51688b7d61d05c827ba50369 Author: dtgraves Date: Tue May 16 09:13:15 2017 -0700 Fixed bug in graph coarsening. EBFineInterp still needs some work. Src/Base/AMReX_BaseFab.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebfineinterp.inputs commit 79ad54a08bda5229ee6dbad134380fe71491b186 Author: Weiqun Zhang Date: Mon May 15 16:52:58 2017 -0700 User's Guide: a little on basics Docs/AMReXUsersGuide/Basics/Basics.tex commit 1a1e956f8968ab57a9458346feff8309a671238f Author: Weiqun Zhang Date: Mon May 15 14:48:57 2017 -0700 User's Guide: make Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HelloWorld_C/GNUmakefile commit 5335b1c86430de49f66e6f28c4818941df726e76 Author: Weiqun Zhang Date: Mon May 15 10:56:19 2017 -0700 Force DIM to be set. Minor edits in User's Guide Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Tools/GNUMake/Make.defs Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HelloWorld_C/GNUmakefile commit c17683ee7b33454e70f012074456c1ff7e8d52d6 Author: Weiqun Zhang Date: Mon May 15 10:24:47 2017 -0700 fix path to OldTutorials OldTutorials/AMR_Adv_C/Exec/Make.Adv OldTutorials/AMR_Adv_CF/Exec/Make.Adv OldTutorials/AMR_Adv_CF_octree/Exec/Make.Adv OldTutorials/AMR_Adv_C_v2/Exec/Make.Adv OldTutorials/Sidecar_EX1/GNUmakefile commit 1cdeeb2cc48336e4e240c395f35dc681a87464ac Author: Max Katz Date: Sun May 14 20:38:34 2017 -0400 Create a unique MFIter index Src/Base/AMReX_MFIter.H commit a7ea94d020024d786083246db60b4540dff9405b Author: Max Katz Date: Sun May 14 20:14:22 2017 -0400 Create a CUDA fortran module Src/Base/AMReX.cpp Src/Base/AMReX_Device.H Src/Base/Make.package commit 37d7f5c60b1611f45b99574e79031cbd83238342 Author: Max Katz Date: Sun May 14 19:06:28 2017 -0400 Move CUDA device ID into device class Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H commit 8c2f793cc825c7ae0defb0690b250f2a955b9f80 Author: Max Katz Date: Sun May 14 18:51:32 2017 -0400 Make a variable private Src/Base/AMReX_Device.H commit 26bac069d3dad525fd94d1e9ae5fdaf505454d4a Author: Max Katz Date: Sun May 14 18:23:31 2017 -0400 Synchronize device at end of kernel region Src/Base/AMReX_Device.H commit bd35cfc0c974497e0647cf5f55840fb345467653 Author: Max Katz Date: Sun May 14 17:14:16 2017 -0400 Add return type to null registerFab Src/Base/AMReX_MFIter.H commit da61eacbfcf2582d4272aabd747a3355bf273551 Author: Max Katz Date: Sun May 14 16:34:30 2017 -0400 Use the result of registerFab Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H commit 8c92d7f9ccd8936c1c5a14a0737d5067adaf1dab Author: Max Katz Date: Sun May 14 16:16:39 2017 -0400 If in device launch region, return device pointer Src/Base/AMReX_BaseFab.H commit 1d8bb8523721403287aac011a64506ae2bf1b2cc Author: Max Katz Date: Sun May 14 15:57:09 2017 -0400 Only do device transfer if a FAB is not registered Src/Base/AMReX_MFIter.H commit 03030752b5bbe47bcd76e07158778279824f9f47 Author: Max Katz Date: Sun May 14 14:18:42 2017 -0400 Move device code to a separate header Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/Make.package commit 627403e152c78d75907eae1b2bd86667d2f0c80b Author: Max Katz Date: Sun May 14 04:43:39 2017 -0400 Fix registerFab Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 738571ee220651fede97910a3d46c2d8ed1e02fa Author: Max Katz Date: Sun May 14 03:02:33 2017 -0400 Add a device copy of data to BaseFab, with hooks up to StateData Using the MFInfo struct, a MultiFab can optionally allocate a device copy of its data. A hook has been added to StateData so that this can be done there as well. Right now the device implementation is for NVIDIA GPUs with CUDA, but in principle other devices that require offloading could be used. Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H commit 4c184ecab2d124cb41da2a87ff72cff4a744a6a5 Author: Max Katz Date: Sat May 13 23:22:43 2017 -0400 Merge CUDArena into BArena Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CUDArena.H Src/Base/AMReX_CUDArena.cpp Src/Base/Make.package commit fea98bbe3ede2a531685104553f176f4626d7f8e Author: Max Katz Date: Sat May 13 23:07:50 2017 -0400 USE_CUDA_UM switches between managed and normal allocations Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CUDArena.cpp Tools/GNUMake/Make.defs commit 8a16a0c7d771002c588fa9c0acd75b292570ce8f Merge: 19488406c 364d92d8c Author: Max Katz Date: Sat May 13 20:49:59 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 19488406c71eb946adb5e0862d93741eea4f8e4c Author: Max Katz Date: Sat May 13 20:49:42 2017 -0400 Create toDevice and toHost in BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.cpp commit 89df80b669dc5ff2bb051abf4e5d8a0be49c5d2b Author: Max Katz Date: Sat May 13 20:14:48 2017 -0400 Store FAB pointers instead of FAB member pointers Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 364d92d8c464a6209ab949f8f8317886e7706f06 Merge: 42150f4fa 53662d558 Author: Michael Zingale Date: Sat May 13 16:34:23 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu commit 42150f4fa3f14e83849a2a30cfbf2f645cf89988 Author: Michael Zingale Date: Sat May 13 16:34:06 2017 -0400 add cudafor to the ignores Tools/F_scripts/dep.py commit 9f0f2728982f0e9153621297a5dfa1dac050ec4b Author: Weiqun Zhang Date: Fri May 12 21:06:46 2017 -0700 Revert "add optional argument to FillPatchUtil indicating ghost cells data are valid" This reverts commit e0d444086f00b5662edfec0816eb7cf7d9713586. Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit a5b58b8ce4db1dd23b80576aa68de4b56e12cca8 Author: Weiqun Zhang Date: Fri May 12 21:05:59 2017 -0700 clean up comments Src/AmrCore/AMReX_Interpolater.H commit 3f5fdefb42678f7a6fc8950395f27dfbf67080ba Merge: 9ae09d8dc fd67910c6 Author: Weiqun Zhang Date: Fri May 12 21:05:22 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9ae09d8dcff381892348a81c3541083bb4f7b1b4 Author: Weiqun Zhang Date: Fri May 12 21:04:55 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Visualization/Amrvis_2d.eps Docs/AMReXUsersGuide/Visualization/Amrvis_3d.eps Docs/AMReXUsersGuide/Visualization/VisIt_2D.eps Docs/AMReXUsersGuide/Visualization/VisIt_3D.eps Docs/AMReXUsersGuide/Visualization/Visualization.tex Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/particle_compare.cpp commit fd67910c6be38c6d38ce27ed975c0dfff8d7d617 Author: Andrew Myers Date: Fri May 12 17:50:04 2017 -0700 Better error handling in the particle compare program. Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/particle_compare.cpp commit 1ad6626258ebe4356bafdeaa1c848db2200db80b Author: dtgraves Date: Fri May 12 17:02:13 2017 -0700 made some progress on more general interpolation but I have exposed a bug in EBIS coarsening. Not fixed yet. Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp commit 3dd9da7df5c17ab71bb8351678064fc05a5998a3 Author: Andy Nonaka Date: Fri May 12 15:53:35 2017 -0700 more visualization stuff Docs/AMReXUsersGuide/Visualization/Visualization.tex commit 8d6f0e0c68b1b9460b143e3769342d58abf67119 Author: Andy Nonaka Date: Fri May 12 15:20:38 2017 -0700 added instructions for amrvis and visit Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Visualization/Amrvis_2d.eps Docs/AMReXUsersGuide/Visualization/Amrvis_3d.eps Docs/AMReXUsersGuide/Visualization/VisIt_2D.eps Docs/AMReXUsersGuide/Visualization/VisIt_3D.eps Docs/AMReXUsersGuide/Visualization/Visualization.tex commit e0d444086f00b5662edfec0816eb7cf7d9713586 Author: Weiqun Zhang Date: Fri May 12 14:50:10 2017 -0700 add optional argument to FillPatchUtil indicating ghost cells data are valid Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit a4e1ff36489023ee305d65db326a5f38729a506d Author: Weiqun Zhang Date: Fri May 12 14:00:58 2017 -0700 make default BCRec contain bogus bc instead of uninitialized values Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit 48953300ca9d93d6beb1516be7f42151ac8d97fd Author: Andy Nonaka Date: Fri May 12 13:53:29 2017 -0700 start of a Vis section Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Visualization/Visualization.tex commit 07b584d79bd8e70108f13bbdffa1eea67faa0497 Merge: e9f6a15f3 011e16a98 Author: WeiqunZhang Date: Fri May 12 12:12:42 2017 -0700 Merge pull request #9 from kweide/development support for Flash as a site, machine "asterix" commit e9f6a15f3ceaac775535026490b50cc7e84c5a90 Author: Weiqun Zhang Date: Fri May 12 11:12:21 2017 -0700 a bit more on make Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit 653a0ec1797a7563706ed065d924ba33146d1dd4 Author: Weiqun Zhang Date: Fri May 12 11:06:05 2017 -0700 add BL_TO_FORTRAN_ANYD, update tutorial Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H commit 16b59fc8d5c84a588d2489807550c4ea1efc6676 Author: Weiqun Zhang Date: Fri May 12 09:59:17 2017 -0700 update AMREX_HOME Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HelloWorld_C/GNUmakefile commit 2be711e828629314f9e26be3986e6857db373900 Author: Weiqun Zhang Date: Fri May 12 09:53:17 2017 -0700 move HelloWorld_C and HeatEquation_EX1_C Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/inputs_2d Tutorials/Basic/HeatEquation_EX1_C/inputs_3d Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H Tutorials/Basic/HelloWorld_C/GNUmakefile Tutorials/Basic/HelloWorld_C/Make.package Tutorials/Basic/HelloWorld_C/main.cpp commit d284bd5e8422c0aa5b8fe263b9fe167daff9e0c4 Author: Weiqun Zhang Date: Fri May 12 09:50:58 2017 -0700 rename Tutorials to OldTutorials OldTutorials/.gitignore OldTutorials/AMR_Adv_C/Exec/Make.Adv OldTutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile OldTutorials/AMR_Adv_C/Exec/SingleVortex/Make.package OldTutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90 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OldTutorials/WaveEquation_F/advance.f90 OldTutorials/WaveEquation_F/init_data.f90 OldTutorials/WaveEquation_F/inputs_2d OldTutorials/WaveEquation_F/inputs_3d OldTutorials/WaveEquation_F/main.f90 OldTutorials/WaveEquation_F/write_plotfile.f90 OldTutorials/libamrex_C/GNUmakefile OldTutorials/libamrex_C/MyAmr.H OldTutorials/libamrex_C/MyAmr.cpp OldTutorials/libamrex_C/main.cpp OldTutorials/libamrex_C/myf.f90 commit 011e16a98ecbac24afda1ebb20d167602e324db9 Author: Klaus Weide Date: Fri May 12 09:55:52 2017 -0500 support for Flash as a site, machine "asterix" Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.flash commit cab1dad14299b21f7af675db5d95ccce9c1c4585 Author: Max Katz Date: Fri May 12 02:22:09 2017 -0400 Remove unnecessary device synchronize Src/Base/AMReX_CUDArena.cpp commit 53662d55847df16a76ae018d549abe1788911f05 Author: Max Katz Date: Fri May 12 01:50:48 2017 -0400 Add capability to do UM prefetches to/from device By setting the new parameter do_device_transfers in MFIter, one can enable the ability to prefetch any FArrayBox accessed by that MFIter to the device. Then, when the MFIter index is incremented or the object is destroyed, all of the prefetches are reversed, bringing the data back to the host. For now, we default to moving everything to GPU 0. In the future, we should generalize this so that we can operate on multiple devices. Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 944f5332ea758a75e48cb13c52fce5986f311b56 Merge: 34a166e30 a28725065 Author: Michael Zingale Date: Thu May 11 20:52:27 2017 -0400 Merge branch 'development' into gpu commit 8b002e112fe14a289a5c6d705729764e5413bd7f Author: Ann Almgren Date: Thu May 11 17:29:20 2017 -0700 Remove print statement that shouldn't have been committed. Src/Particle/AMReX_ParticleContainerI.H commit c861ab1a564e07de6dc593dc6d207916d926e751 Author: Weiqun Zhang Date: Thu May 11 16:13:08 2017 -0700 add average_down_edges to MultiFabUtil Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/Base/Make.package commit ce901f4e7cc2678db41973338d5e449ed126ad06 Merge: 27cf2911e 5aff33b2c Author: Andrew Myers Date: Thu May 11 16:00:13 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 27cf2911e6f766690a008c4fbdba3c7b4e2a9eaf Author: Andrew Myers Date: Thu May 11 15:59:47 2017 -0700 A tool for comparing particle data in plt files for Regression testing. Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/Make.package Tools/Postprocessing/C_Src/particle_compare.cpp commit c6e0d7bb20ef17b6659dee10c2c6ac9cc33777d7 Author: dtgraves Date: Thu May 11 15:50:05 2017 -0700 prolongation operator passes its first test Src/EBAMRTools/AMReX_EBFineInterp.cpp Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebfineinterp.inputs commit ab41987195562bac7c35ba06825b00e26c68d140 Author: dtgraves Date: Thu May 11 15:09:54 2017 -0700 EBCoarseAverage now does the right thing with the new fortran Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFortND.F90 commit 1ad604fa6ffb61b6dba4d8649b66b6628aa917ac Author: dtgraves Date: Thu May 11 15:08:48 2017 -0700 fixed the new macros to actually work Src/Base/AMReX_ArrayLim.H commit f28805d15afe9b550522fe2c1b8bc5df22570b12 Author: dtgraves Date: Thu May 11 14:36:19 2017 -0700 I added a macro to ArrayLim and a function to BaseFab to make calling Fortran slightly less painful. Also I added some fortran source to EBAMRTools since the relevant MultiFab utilities did communication. Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BaseFab.H Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/Make.package commit 5aff33b2c69f87d6b946f3c5af3f019c9cd2a44b Merge: b722ba3f2 d585ff2ff Author: Ann Almgren Date: Thu May 11 14:17:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b722ba3f230ee55dd933d9b3c3a17f3bef02a07c Author: Ann Almgren Date: Thu May 11 14:16:46 2017 -0700 Must resize the dummy_mf when we resize m_particles in AddParticlesAtLevel Src/Particle/AMReX_ParticleContainerI.H commit d585ff2ffbe2227fc358c273f4a0b804e14999c9 Author: Weiqun Zhang Date: Thu May 11 13:36:53 2017 -0700 add back BoxList BoxList intersection because Amrvis uses it Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 8676d5e489adc0c980ec148bdc5c0b00c430a9b4 Author: Weiqun Zhang Date: Thu May 11 13:21:18 2017 -0700 clean up Tutorials/HeatEquation_EX1_C Tutorials/HeatEquation_EX1_C/Make.package Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp commit 234569709c5e4053350e3a7e9fac4f02c54a7890 Author: Weiqun Zhang Date: Thu May 11 10:41:44 2017 -0700 User's Guide: add new file for Building AMReX Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit 71a0b748c0552bd9edb754c1bce1f75a9e408372 Author: Weiqun Zhang Date: Thu May 11 10:32:45 2017 -0700 User's Guide: Getting Started Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Tutorials/HeatEquation_EX1_C/main.cpp commit 1d01c139156e63191fa8dab92a810b4b53bc4b35 Author: Weiqun Zhang Date: Thu May 11 09:33:57 2017 -0700 update typechecker for gcc 7 Tools/typechecker/typechecker.py commit 57fb40e0fff376ba4e80090745b7623dd0ad443d Author: dtgraves Date: Wed May 10 16:26:34 2017 -0700 took out stray file Src/EBAMRTools/AMReX_EBPWLFineInterp.H commit f9637aa16df6c86c61342ce868721782bb6bb950 Author: dtgraves Date: Wed May 10 16:25:28 2017 -0700 I am most of the way there to having (regridding, multigrid) interpolation/prolongation operator for EB. Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBPWLFineInterp.H Src/EBAMRTools/AMReX_EBPWLFineInterp.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp commit a2872506558f631395fb25c876cb1f8cb0ed4748 Author: Weiqun Zhang Date: Wed May 10 10:13:16 2017 -0700 If ref_ratio, n_error_buf, max_grid_size, or blocking_factor from inputs has fewer counts than the number of levels, fill the rest with the last value. The old behavior was to abort except in the single value case. Src/AmrCore/AMReX_AmrMesh.cpp commit 5ad7574c62f4bbd99b751876324a95c0e973cf07 Merge: 9718535d0 aff70ea7e Author: WeiqunZhang Date: Wed May 10 12:14:33 2017 -0700 Merge pull request #8 from AMReX-Codes/dtg_branch stuff from dtg_branch requested by jrood commit aff70ea7e30f00776c7f604fde50dae992c86e9e Author: dtgraves Date: Wed May 10 11:52:10 2017 -0700 ported over some functions as requested by jrood Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Src/GeometryShop/Make.package Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit 34a166e3004d8d86f5b84b1a29b20bfb4fd17aa2 Merge: ed2ec40ab 9718535d0 Author: Michael Zingale Date: Wed May 10 14:45:10 2017 -0400 Merge branch 'development' into gpu commit 4c3a8eef0fd9268bfdebeb7d5af09f7eb3509ae8 Author: Andrew Myers Date: Wed May 10 11:20:22 2017 -0700 Write out particle box array information to the plt / chk files. Src/Particle/AMReX_ParticleContainerI.H commit 9718535d0d14f016622d25255e2e1c8b4edd1f3c Author: Weiqun Zhang Date: Wed May 10 09:29:32 2017 -0700 clean up BoxArray::GetBndryCells Src/Base/AMReX_BoxArray.cpp commit b7f1563975a9ce48a0778c111df814627f3b112f Author: Weiqun Zhang Date: Wed May 10 08:38:00 2017 -0700 consistent names Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_FabArrayBase.cpp commit 97bcd979e7d16ed99611eef6babb1d9087fd84ce Author: Weiqun Zhang Date: Wed May 10 08:28:26 2017 -0700 Revert "Remove unused variable." This reverts commit c16a1afb7b68c7aa67c4ab1703dd4f759ca539c2. Src/Base/AMReX_IntVect.H commit b51fb45f1c31130a3b52d1977e59aae1dd2b5133 Author: dtgraves Date: Wed May 10 08:25:24 2017 -0700 High order CFInterp now works with as many ghost cells as you like (as long as the nesting radius supports it) Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp commit ed2ec40ab55c8d2c06afdbad775b294b780c9df6 Author: Max Katz Date: Wed May 10 03:45:45 2017 -0400 Use pgfortran as the linker Tools/GNUMake/Make.rules Tools/GNUMake/comps/cuda.mak commit ee75a8480462dedd633ac1812bb2f6cecb515c00 Author: Max Katz Date: Wed May 10 03:15:41 2017 -0400 Add in the cuda.mak file Tools/GNUMake/comps/cuda.mak commit 1d85d31a9258a59f6d13453c1778bbb0207d74a8 Merge: c16a1afb7 1f8544ed4 Author: Ann Almgren Date: Tue May 9 20:36:22 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit c16a1afb7b68c7aa67c4ab1703dd4f759ca539c2 Author: Ann Almgren Date: Tue May 9 20:35:32 2017 -0700 Remove unused variable. Src/Base/AMReX_IntVect.H commit 97190a4b880843197d85f85f8a361df6ca6a9f88 Merge: de0fd9a14 1f8544ed4 Author: Max Katz Date: Tue May 9 21:13:18 2017 -0400 Merge branch 'development' into gpu commit 1f8544ed4b374d478448cfddb301341e1c72f1c7 Merge: bac340853 4dd384daf Author: Weiqun Zhang Date: Tue May 9 16:58:48 2017 -0700 Merge branch 'development' into boxlist commit 4dd384daf973a17d2ec73aac63a940f8c232f85c Merge: 543cd0c99 f66117daf Author: Ann Almgren Date: Tue May 9 16:50:35 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 543cd0c99bb6ff66491592b5e9332ee86641d354 Author: Ann Almgren Date: Tue May 9 16:50:03 2017 -0700 Remove unused variables. Src/Particle/AMReX_ParticleInit.H commit f66117dafc38a4a13a50ba6edfb53ff82109b497 Merge: 1f192b085 f845e4b49 Author: Andrew Myers Date: Tue May 9 16:32:36 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1f192b0857ec437bad778bb55cb5613fcf2812ff Author: Andrew Myers Date: Tue May 9 16:32:28 2017 -0700 make num ghosts a property of the container. Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/ShortRangeParticles/main.cpp commit 932509be51292e8bb562672ecdce301c2267c379 Author: dtgraves Date: Tue May 9 16:29:54 2017 -0700 nwoEBQuadCFInterp has had many bug fixes Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp Src/GeometryShop/AMReX_EBArith.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp commit bac34085347d8a44ed93bb6f211a022d68d3dea1 Author: Weiqun Zhang Date: Tue May 9 16:17:48 2017 -0700 fix recursive call Src/Base/AMReX_BoxArray.cpp commit b747c59ae5ca4743a24353a72862ca19e66d5d24 Merge: e61dc0cba f845e4b49 Author: Weiqun Zhang Date: Tue May 9 16:04:24 2017 -0700 Merge branch 'development' into boxlist commit f845e4b49db2c053e296a3d70dfe3b1a46bdb569 Author: Ann Almgren Date: Tue May 9 15:54:41 2017 -0700 Get rid of warning with DIM=1 about unused variable. Src/Base/AMReX_BaseFab.H commit e61dc0cba5bfa650ede68b9b8b4537cb0e450006 Merge: deaa1d13e b57929279 Author: Weiqun Zhang Date: Tue May 9 14:38:37 2017 -0700 Merge branch 'development' into boxlist Conflicts: Tools/F_scripts/f90cat.py commit deaa1d13e109a0ec1b2418cb89586bd71552aeec Author: Weiqun Zhang Date: Tue May 9 14:08:31 2017 -0700 minor optimizations Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit b57929279d56b4baa5cefd7bd5318c8e453aff31 Author: Andrew Myers Date: Tue May 9 14:32:40 2017 -0700 Update advection tutorial to reflect changes in particle initialization routines. Tutorials/AMR_Adv_C/Source/Adv.cpp commit 842984e46754b3d9168fb42323ac7332c18aad76 Author: dtgraves Date: Tue May 9 14:00:52 2017 -0700 bug fix for NWOEBQuadCFInterp Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp commit d1b713c1902ea4c9377d16cd392da961edb43f36 Author: Weiqun Zhang Date: Tue May 9 13:33:38 2017 -0700 minor optimization BoxDomain: need to remove empty boxes Src/Base/AMReX_BoxDomain.cpp commit b891c6245ffffede1e3109bd89fd0643fda1fe68 Merge: fb6bab72e 207d23213 Author: Andrew Myers Date: Tue May 9 13:38:24 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fb6bab72e650ae6735b5f882439e5a34cce57817 Author: Andrew Myers Date: Tue May 9 13:38:10 2017 -0700 fix copy / paste error in previous commit. Src/Particle/AMReX_ParticleInit.H commit 207d23213d040d9376f528b283b5d4aafee730fa Merge: 56eca3f73 389d7c754 Author: WeiqunZhang Date: Tue May 9 13:22:58 2017 -0700 Merge pull request #7 from AMReX-Codes/dtg_branch bug fixes from Dtg branch commit 389d7c754727f9c43f635bf308527034f8ed930b Author: dtgraves Date: Tue May 9 13:11:33 2017 -0700 more aggstencil pointer tricks for better performance. Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp commit 56eca3f735984e8dba722a63c63a671d8270e297 Merge: 9604f3bb0 eddd07e43 Author: Andrew Myers Date: Tue May 9 12:43:59 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9604f3bb0eb5ed16992c6020a10631ff209c2cfd Author: Andrew Myers Date: Tue May 9 12:43:45 2017 -0700 Make the particle initialization routines agnostic as to the names of the components or how they are laid out in memory. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/inputs Tests/Particles/AssignMultiLevelDensity/main.cpp commit d9cc550c4a8dcddc02b3041829031717c364b9b3 Author: Weiqun Zhang Date: Tue May 9 12:40:15 2017 -0700 change plot_int Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs commit f2d564081e387bf67586f38377cce07e62d653c4 Author: dtgraves Date: Tue May 9 12:39:47 2017 -0700 fixed another regression failure that Marc found Src/GeometryShop/AMReX_IrregFABFactory.H commit eddd07e4379f5298d2cf6be6922e3cf4968905dd Author: Michael Zingale Date: Tue May 9 15:28:36 2017 -0400 take a list of F90 files, determine their interdependencies and perform a topological sort. Then output a single .F90 file with all input files concatenated together Tools/F_scripts/f90cat.py commit 5cf2ee163995182ce9d8af27d9f32af32454aba7 Author: Weiqun Zhang Date: Tue May 9 12:02:34 2017 -0700 remove unused function Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 4d94543ec16dc653cd54d477ebae816e7d32c81e Author: Weiqun Zhang Date: Tue May 9 11:55:53 2017 -0700 minor Src/Base/AMReX_BoxList.cpp commit 991062b2614e5d06c99e6938c052908b35ced897 Author: dtgraves Date: Tue May 9 11:42:24 2017 -0700 bit of trickery to get more performance when making AggStencils Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp commit 6932733cd87719ce45b29796f2563ef4e9082b21 Author: Weiqun Zhang Date: Tue May 9 11:01:02 2017 -0700 change BoxList complement algorithm Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit 813ff9da210500a3c163ce2679c4b8e5452ae0d7 Author: Weiqun Zhang Date: Tue May 9 10:26:24 2017 -0700 wip: finished first pass Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit eff6ee383285037f20a0702786d5bd6cde2be273 Author: dtgraves Date: Tue May 9 09:11:00 2017 -0700 Marc noticed one of the regression tests was failing. This fixes that failure. Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_RedistStencil.cpp commit b1c9ef6256ce0959aa9067114785a0823a150b8a Author: Michael Zingale Date: Mon May 8 22:58:37 2017 -0400 concatenate a bunch of fortran files, first sorting them by dependency Tools/F_scripts/f90cat.py commit 202e3b83407c3cad6d4105ec6342fc98f868b299 Author: Weiqun Zhang Date: Mon May 8 18:10:28 2017 -0700 wip: remove some unused functions Src/Amr/AMReX_AuxBoundaryData.cpp Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 3066ddfce7229c307059b5048cb054e78dd977b3 Author: dtgraves Date: Mon May 8 16:44:55 2017 -0700 Another day, another class. I added high order coarse-fine interpolation (with EB). The test does not show the proper convergence rate yet. Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp Src/EBAMRTools/Make.package Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp Tests/EBAMRTools/regression/nwoebquadcfi.inputs commit b514fc87d14d6ca2182f30702a0cb3a451a64ef2 Author: Weiqun Zhang Date: Mon May 8 12:07:03 2017 -0700 wip: use Array instead of std::list as the internal data structure for BoxList Src/Amr/AMReX_Amr.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit ab6f8b893debf71201f4d04e2a573b68ee6bd0e3 Author: Michele Rosso Date: Mon May 8 15:19:39 2017 -0700 Add amrex_fabio_c.f90 and amrex_timer_c.f90 to cmake build. Src/F_BaseLib/CMakeLists.txt commit 0ecd7a8a81e85207a3d3c8a02b06aa0a496e1447 Author: Weiqun Zhang Date: Sun May 7 16:55:27 2017 -0700 unit test for typechecker Tests/TypeCheck/GNUmakefile Tests/TypeCheck/Make.package Tests/TypeCheck/f.f90 Tests/TypeCheck/f_F.H commit df66be77180c054938608e4ab87832261a2a0f70 Author: Weiqun Zhang Date: Sun May 7 13:24:25 2017 -0700 typecheck: add readme Docs/Readme.typecheck commit 085d8cf6d302b6d62affcfa97f27b713dae32018 Author: Weiqun Zhang Date: Sun May 7 13:03:49 2017 -0700 type check: takes only the first part of the name Tools/typechecker/typechecker.py commit cb441f62c31fdb1560f545e6c93f2d145a1cdc57 Merge: 00525735c cd9ef8b41 Author: WeiqunZhang Date: Sun May 7 12:10:32 2017 -0700 Merge pull request #1 from AMReX-Codes/maxpkatz/post_timestep_regrid Add a hook so that an AmrLevel can force a post-timestep regrid commit 00525735cc286f233bfbeac3072b6d67837262aa Author: Weiqun Zhang Date: Sun May 7 07:44:11 2017 -0700 fix print Tools/typechecker/typechecker.py commit 12061bd793e69a9fc3714fc5324921675af170ac Author: Weiqun Zhang Date: Sun May 7 07:12:22 2017 -0700 typechecker: get rid of global variables and print more info Tools/typechecker/typechecker.py commit fe4c415730941d339ab586978a630328d9492815 Author: Weiqun Zhang Date: Sat May 6 21:30:57 2017 -0700 typo Tests/C_BaseLib/TPROFILER_F.H commit 5589ab1923bf562b5db34851d5de8a192f75ebe0 Author: Weiqun Zhang Date: Sat May 6 19:09:14 2017 -0700 fix conflict due to merge Tutorials/ShortRangeParticles/short_range_F.H commit 3d945cffd24fd798bddec557427afb5e63f70170 Merge: b5d3aff3d b470c44ef Author: Weiqun Zhang Date: Sat May 6 19:06:52 2017 -0700 merge commit b470c44ef823525bd0aa33847e005723a50f93d0 Author: Weiqun Zhang Date: Sat May 6 16:51:02 2017 -0700 type Tools/typechecker/typechecker.py commit 14a615d52de94aeaba0257b5c9942fe104aa31ea Author: Weiqun Zhang Date: Sat May 6 15:37:59 2017 -0700 typecheck: optimization Tools/typechecker/typechecker.py commit edae53ab6616a7743badb71e9249b25e30bb6c13 Author: Weiqun Zhang Date: Sat May 6 11:58:58 2017 -0700 typecheck: remove whitespace lines because they mess up the block detection Tools/typechecker/typechecker.py commit 0f24dd850544b1ae958984c3fe3a81bed0a68bc9 Author: Weiqun Zhang Date: Sat May 6 11:21:17 2017 -0700 found missing argument thanks to typcheck Src/AmrCore/AMReX_INTERP_1D.F commit ed1deb22341a91ff19378f29fca922df2b2de135 Author: Weiqun Zhang Date: Sat May 6 11:20:48 2017 -0700 better error message Tools/typechecker/typechecker.py commit c62a5ec9b9c758575e28032d2072352398ba7474 Author: Weiqun Zhang Date: Sat May 6 10:53:04 2017 -0700 match void* with any fortran reference Tools/typechecker/typechecker.py commit 52bb8f9ad5a1a03deb2b6fc81320f2b9970f2479 Author: Weiqun Zhang Date: Sat May 6 08:49:45 2017 -0700 fix sed Tools/GNUMake/Make.rules commit 5f4fff603b39d50f4f6858233c27a9713873cb63 Author: Weiqun Zhang Date: Sat May 6 08:42:59 2017 -0700 minor tweak Src/Base/AMReX_BLFort.H Tools/GNUMake/Make.rules commit 4ac86fbce5d45a24a76cabdd1764c639809d28f8 Author: Weiqun Zhang Date: Sat May 6 08:31:35 2017 -0700 started #ifdef __cplusplus in EB tests, but quickly gave up Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H commit 658c6331875b94eb3d2a16f776893310e2251c0a Author: Weiqun Zhang Date: Sat May 6 08:22:47 2017 -0700 don't need to build executable to use typecheck, but we do still need to compile fortran codes Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit bc05f0cd7e8e6c08be91dcd56d5b415dfa91cc08 Author: Weiqun Zhang Date: Sat May 6 07:50:17 2017 -0700 #ifdef __cplusplus Tests/LinearSolvers/C_TensorMG/main_F.H commit d04f3425e794020eaddb738c1dbd1ed6b6b01cb6 Author: Weiqun Zhang Date: Sat May 6 07:43:27 2017 -0700 remove non-existing header Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F commit 104f697a6e16af9d495a0f3ddd111d62a0712263 Author: Weiqun Zhang Date: Sat May 6 07:30:09 2017 -0700 fix type(c_ptr), value and character(c_char) Tools/typechecker/typechecker.py commit 8a5e951c3ec8d81b74894c041a1056272c2447e2 Author: Weiqun Zhang Date: Sat May 6 07:19:38 2017 -0700 fix node.args is NoneType Tools/typechecker/typechecker.py commit d5e62c9b39db68e9672830028740e80022d0a339 Author: Weiqun Zhang Date: Sat May 6 07:09:37 2017 -0700 type errors in C_CellMG4 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F commit 51859250c795fca48fba78eeb0649277de436ac1 Author: Weiqun Zhang Date: Sat May 6 07:07:44 2017 -0700 fix type errors in C_CellMG4 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F commit dff5a7f0bde69dcefa7bda3ef30700e014657608 Author: Weiqun Zhang Date: Sat May 6 07:00:35 2017 -0700 add variable name Tools/typechecker/typechecker.py commit 21ac7441bb9fd6eef2609ccf91ff09ebb732abfb Author: Weiqun Zhang Date: Sat May 6 06:54:43 2017 -0700 add support for array such as int lo[] Tools/typechecker/typechecker.py commit f94403a8be883d414cee313d4df64a32fbcbd67f Author: Weiqun Zhang Date: Sat May 6 06:36:27 2017 -0700 remove 2d FORT_SETVOLPT that didn't have correct function signature (thanks to typechecker) Src/Base/AMReX_COORDSYS_2D.F Tools/typechecker/typechecker.py commit 4de68796548af45ef55c4c1c6ebb5eab1f89fa9f Author: Weiqun Zhang Date: Fri May 5 23:48:45 2017 -0700 typecheck .f and .F files too Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/typechecker/typechecker.py commit bdb525e5c0f37f50d2466105f1cc5cfae9a1f0f3 Author: Weiqun Zhang Date: Fri May 5 23:00:27 2017 -0700 tweak output of typecheck Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/typechecker/typechecker.py commit b08561cffc189e5109e8cfab31b4d1d2103ff382 Author: Weiqun Zhang Date: Fri May 5 21:56:34 2017 -0700 fix amrex::Real, amrex_real and & Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 1e3b1f1b66a12adf6aef860965599767d9f9d25c Author: Weiqun Zhang Date: Fri May 5 18:00:21 2017 -0700 refactor typechecker to handle both module and non-moudle procedures. add missing headers Src/AmrCore/AMReX_INTERP_F.H Tools/typechecker/typechecker.py Tutorials/AMR_Adv_C/Source/Adv_F.H commit b5d3aff3d6afe034dfd27dc0afd40aa7cc1ab8ca Author: Andrew Myers Date: Fri May 5 17:57:36 2017 -0700 Make WriteAsciiFile include the template parameters in the output. Src/Particle/AMReX_ParticleContainerI.H commit 8249a9851ba2ca0dc8644fbea81c5f35adaf275e Merge: 9a92f979f 6169428f2 Author: Andrew Myers Date: Fri May 5 16:49:25 2017 -0700 Merging. commit 07371725c3f7044176378af4063fbacb391c2dc3 Author: Weiqun Zhang Date: Fri May 5 16:01:24 2017 -0700 add missing header Src/Particle/AMReX_Particles_F.H Tools/GNUMake/Make.rules commit 22cbc4bd7feb0c81e7f6034f44d256eda65f7d33 Author: dtgraves Date: Fri May 5 15:35:56 2017 -0700 added EBCoarseAverage (with an improved interface from Chombo) which calls a nifty function from MultiFab_Util for the regular grid bits. It passes its convergence test. Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/Make.package Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/ebCoarseAveTest.cpp Tests/EBAMRTools/regression/ebcoarave.inputs commit 021bedb5e41bf577c282b3e952ed9b8b474379ca Author: Weiqun Zhang Date: Fri May 5 15:10:45 2017 -0700 first pass of typechecker.py Src/Base/AMReX_SPACE.H Tools/GNUMake/Make.rules Tools/typechecker/typechecker.py commit e906e5528ef5f521a305d3f430dfc9be0bfa4f8a Author: Weiqun Zhang Date: Fri May 5 11:33:30 2017 -0700 rule for making CPP'd headers Tools/GNUMake/Make.rules commit 2c9f2bedfc12bacb79732d226e9ed43c777f8135 Author: Weiqun Zhang Date: Fri May 5 11:32:37 2017 -0700 rm pycparser Tools/typechecker/pycparser/LICENSE Tools/typechecker/pycparser/__init__.py Tools/typechecker/pycparser/_ast_gen.py Tools/typechecker/pycparser/_build_tables.py Tools/typechecker/pycparser/_c_ast.cfg Tools/typechecker/pycparser/ast_transforms.py Tools/typechecker/pycparser/c_ast.py Tools/typechecker/pycparser/c_generator.py Tools/typechecker/pycparser/c_lexer.py Tools/typechecker/pycparser/c_parser.py Tools/typechecker/pycparser/ply/LICENSE Tools/typechecker/pycparser/ply/__init__.py Tools/typechecker/pycparser/ply/cpp.py Tools/typechecker/pycparser/ply/ctokens.py Tools/typechecker/pycparser/ply/lex.py Tools/typechecker/pycparser/ply/yacc.py Tools/typechecker/pycparser/ply/ygen.py Tools/typechecker/pycparser/plyparser.py commit fded07ba762f990e6226fda41dec6ba00d56a222 Author: Weiqun Zhang Date: Fri May 5 10:45:52 2017 -0700 add a script for amrex::Real --> amrex_real Tools/Migration/amrex_real.sh commit a29078400d357eb8e17ab840ad6373a7c801f17e Author: Weiqun Zhang Date: Fri May 5 10:44:59 2017 -0700 amrex::Real --> amrex_real in *_F.H and *_f.H files so that c parser can parse them MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/RHS_F.H MiniApps/PGAS_SMC/SMC_F.H Src/Amr/AMReX_MAKESLICE_F.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_SLABSTAT_F.H Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_INTERP_F.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_MultiFabUtil_F.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/F_BaseLib/MultiFab_C_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/Particle/AMReX_Particles_F.H Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Statistics/AVGDOWN_F.H Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/myfunc_F.H Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/RHS_F.H Tutorials/ShortRangeParticles/short_range_F.H commit 2b12a1210f7185d2356f0ec76260a6a684135d23 Author: Weiqun Zhang Date: Fri May 5 10:35:35 2017 -0700 more #ifdef __cplusplus MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/RHS_F.H MiniApps/PGAS_SMC/SMC_F.H Src/Base/AMReX_BLFort.H Tests/C_BaseLib/AMRPROFTEST_F.H Tests/C_BaseLib/TPROFILER_F.H Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/myfunc_F.H Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H Tutorials/MultiGrid_C/RHS_F.H Tutorials/ShortRangeParticles/short_range_F.H commit 0771c3da02bdf5de888da1402de6eaa23e6fbc9f Author: Weiqun Zhang Date: Fri May 5 10:18:44 2017 -0700 wrap extern C around ifdef __cplusplu. this will allow the headers to be included in C codes and be parsed by a C parser Src/Amr/AMReX_MAKESLICE_F.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_SLABSTAT_F.H Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_INTERP_F.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_MultiFabUtil_F.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/F_BaseLib/MultiFab_C_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/Particle/AMReX_Particles_F.H commit 4a691512cf6847ceb27032fbf95e24046ffe9da4 Author: Weiqun Zhang Date: Fri May 5 10:05:16 2017 -0700 restart typeChecker.py Tools/GNUMake/Make.defs Tools/typechecker/typeChecker.py Tools/typechecker/typechecker.py commit 6169428f26c4e6d7242febcf8e2dd5eddbe8f3c1 Author: Michael Zingale Date: Fri May 5 11:32:26 2017 -0400 comment out an OpenMP version assert because of a PGI bug Src/Base/AMReX.cpp commit 0d5276927788d2a034a8c9341c1a5f60c0e1ab5d Author: Michael Zingale Date: Fri May 5 08:43:40 2017 -0400 fix compilation with PROF=t Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_prof.f90 commit de0fd9a1484bcc132846f3f7b41af97af0e45144 Merge: 9a7183c46 f4ce1736d Author: Max Katz Date: Fri May 5 02:47:08 2017 -0400 Merge branch 'development' into gpu commit 9a92f979fe58ad0d08b42b86f497667698984a6f Merge: feabb1cab 1cb66d597 Author: Andrew Myers Date: Thu May 4 17:34:40 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit feabb1cab28ee1e33de7d62670ac24bb85723064 Author: Andrew Myers Date: Thu May 4 17:34:28 2017 -0700 have the fillGhosts routine take a number of ghost zones as an argument. Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/ShortRangeParticles/main.cpp commit 15bba93903392cb72839ab1a680b16626302557f Author: Andrew Myers Date: Thu May 4 17:31:50 2017 -0700 update the ShortRangeParticle example to show the use of the particle derived type in fortran Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/ShortRangeParticles/short_range_2d.f90 Tutorials/ShortRangeParticles/short_range_3d.f90 Tutorials/ShortRangeParticles/short_range_F.H commit f4ce1736ded06f292b25730ba42d2c89d4902cb3 Author: Michael Zingale Date: Thu May 4 18:09:33 2017 -0400 fix AMReX testing Tools/RegressionTesting/suite.py commit e2317d93c3eb2e5459d3d875f53ecc5722cfa68c Author: Weiqun Zhang Date: Thu May 4 12:43:01 2017 -0700 add pycparse license Tools/typechecker/pycparser/LICENSE commit 6b18c2424807bf0265e997217bb099ac93c130da Author: dtgraves Date: Thu May 4 11:56:41 2017 -0700 fixed EBFastFR. amrex::FluxRegister could really use a memory scrub. Src/AmrCore/AMReX_FluxRegister.cpp Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/GeometryShop/AMReX_EBFaceFAB.cpp Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/fluxreg.inputs Tests/EBAMRTools/regression/regFluxRegTest.cpp commit d312eb072b4ad4905d9c937a800c597caa057a9b Author: Weiqun Zhang Date: Thu May 4 11:18:28 2017 -0700 fix merge Src/Base/Make.package commit b1151453172b074c6b47f6fb903658950c1be132 Merge: 02c921186 7f70711fe Author: Weiqun Zhang Date: Thu May 4 11:10:58 2017 -0700 Merge branch 'development' into fortran_check Conflicts: Src/Base/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 7f70711fe2de193dccee6bc75e8830ed97713a61 Author: Weiqun Zhang Date: Thu May 4 11:06:09 2017 -0700 minor changes in User's Guide Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex commit 045f0549b93d7a69ab6ca2c36fab8b7a5b208eb3 Author: Weiqun Zhang Date: Thu May 4 10:22:52 2017 -0700 more in .gitignore Docs/AMReXUsersGuide/.gitignore commit 44ef0132187bb1a8a6f79df0fbf3cce45f986dfa Author: Michael Zingale Date: Thu May 4 09:16:06 2017 -0400 need iso_c_binding to compile Src/F_BaseLib/fabio.f90 commit 9a7183c4636b615a90e9a03b7a2f241a48f81f31 Author: Max Katz Date: Thu May 4 04:34:20 2017 -0400 Add a CUDA compiler option (using nvcc+pgfortran) Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 67e766e859e61fc85b893a190dd4164e022a9cb6 Merge: 0d6b44580 573089aa0 Author: Max Katz Date: Thu May 4 03:16:15 2017 -0400 Merge branch 'development' into gpu commit 573089aa0daae5ae5ba72a15306d0b2be54e5f8f Author: Max Katz Date: Thu May 4 02:16:56 2017 -0400 Use ISO C bindings for timer_c and fabio_c Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/amrex_fabio_c.f90 Src/F_BaseLib/amrex_timer_c.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/parallel_stubs.f90 Src/F_BaseLib/timer_c.c commit b33f3376770e62de0f4bd8cacea8ccdbefcb0e7b Author: dtgraves Date: Wed May 3 16:20:08 2017 -0700 added a couple of clarifying (to me) comments to FluxRegister.H. EBFastFR still does not work but I am on the case. Src/AmrCore/AMReX_FLUXREG_2D.F Src/AmrCore/AMReX_FluxRegister.H Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/fluxreg.inputs Tests/EBAMRTools/regression/regFluxRegTest.cpp commit 36a6e20fcc651388d8118ea49a34b0ed239c981f Author: dtgraves Date: Wed May 3 14:10:08 2017 -0700 added all-regular flux register test that also fails. Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/regFluxRegTest.cpp commit 55944054d3bdb114b4737d48917ebb089f429245 Author: dtgraves Date: Wed May 3 11:43:59 2017 -0700 adding README files that list the tests and what they do Tests/EBAMRTools/README Tests/GeometryShop/README commit 0d6b44580c116b53b7955c2e326a8d8fd5724f50 Merge: af364f2ac 636404b57 Author: Max Katz Date: Wed May 3 01:37:09 2017 -0400 Merge branch 'development' into gpu commit aa6d70d42a0137cc2a03b0ff4aa3d33d96a9ad55 Author: dtgraves Date: Tue May 2 16:48:52 2017 -0700 we now have an EB flux register and a test (that fails for now) Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/fluxreg.inputs commit 636404b575a44437f3686708143e44d5286250f5 Merge: c6bf22211 873e825ea Author: Michael Zingale Date: Tue May 2 15:23:32 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit c6bf22211f6745a42d3c35c08b327f279884791e Author: Michael Zingale Date: Tue May 2 15:23:21 2017 -0400 boxlib -> amrex Tools/F_scripts/makebuildinfo.py commit 873e825ea58d5617246ea8c83e1f69d4a18d2379 Merge: f3dc5f406 9595c4bf7 Author: Michael Zingale Date: Tue May 2 15:05:07 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit f3dc5f406789e43f922c142796ca7f563dcf1884 Author: Michael Zingale Date: Tue May 2 15:04:36 2017 -0400 fix the summary table info to be at the start of a line close some files that were left openned Tools/RegressionTesting/regtest.py commit 9595c4bf7d76873cf9caa0b0d6efdfdc762f2d3f Author: Weiqun Zhang Date: Tue May 2 12:01:03 2017 -0700 assertion Src/Base/AMReX_FabArrayBase.cpp commit 00e0608bb2a5605c978a5f2e5db634597306a650 Merge: 36687bb24 bc274fcf0 Author: WeiqunZhang Date: Tue May 2 10:21:02 2017 -0700 Merge pull request #3 from AMReX-Codes/dtg_branch Dtg branch commit bc274fcf073872aef15733be3c54331bab711a13 Author: dtgraves Date: Tue May 2 10:12:31 2017 -0700 removing unwanted files Tests/GeometryShop/regression/Backtrace.rg_0_rl_0 Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000 Tests/GeometryShop/regression/bl_prof/bl_call_stats_H Tests/GeometryShop/regression/bl_prof/bl_call_stats_H_00000 Tests/GeometryShop/regression/bl_prof/bl_comm_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_H commit 36687bb24104eb09ef26911cd0c938f8d936bb17 Merge: 2972ca732 3aaaa52c7 Author: Michael Zingale Date: Tue May 2 13:00:17 2017 -0400 Merge pull request #4 from WeiqunZhang/weiqun/regtest fix suite.py commit 2972ca732feb013ea86eb22009cbe3f1e548a96f Author: Weiqun Zhang Date: Tue May 2 09:18:29 2017 -0700 AMR_Adv_CF: should use contains not intersects Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit 7bfbb1d2fcd89fee3d6c0093ed48a98225f68232 Author: Weiqun Zhang Date: Tue May 2 09:17:59 2017 -0700 amrex_box_module: add contains function Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 3aaaa52c77643b1db0164ad931235282d952560d Author: Weiqun Zhang Date: Tue May 2 08:59:22 2017 -0700 fix suite.py Tools/RegressionTesting/suite.py commit cf0c02bfec6579c1737ae00dcd21ca632b438e34 Author: Weiqun Zhang Date: Tue May 2 06:01:14 2017 -0700 forgot a new file Src/Base/AMReX_filcc_mod.F90 commit af364f2acf9b4a859bbfce77c52814135e088ede Merge: 0b693bcf8 68fe11d4e Author: Max Katz Date: Tue May 2 01:46:32 2017 -0400 Merge branch 'development' into gpu commit 68fe11d4e025fd52c920660b3ba57f5bfdbc405d Author: Weiqun Zhang Date: Mon May 1 17:26:26 2017 -0700 add inputs.physbc Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs.physbc commit 0acc0707761c59ddad986f1f8d709a250129880e Author: Weiqun Zhang Date: Mon May 1 17:24:12 2017 -0700 amrex_box_module: implement intersects Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 9267d3755bd54589d726c328bb94ab969bbded91 Author: Weiqun Zhang Date: Mon May 1 16:18:52 2017 -0700 add amrex_filcc_module and add non-periodic boundaries to AMR_Adv_CF example Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Tutorials/AMR_Adv_CF/Source/bc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit f5cf7a28ca0a37e9cb80068cdb9a5fb861454582 Author: Weiqun Zhang Date: Mon May 1 13:40:14 2017 -0700 Physbc module: add geometry Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_FPhysBC.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_physbc_fi.cpp Src/F_Interfaces/Base/AMReX_physbc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/fillpatch_mod.F90 commit 8783a3f0c33c7bbe0dd6582382e95378c85fb5be Author: Dan Graves Date: Mon May 1 16:27:57 2017 -0700 added EBNormalizeByVolumeFraction (catchy name, no?) so we can do the whole conservative and non-conservative divergence thing. Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/Make.package Tests/GeometryShop/regression/Backtrace.rg_0_rl_0 Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_H Tests/GeometryShop/regression/ebnormalizeTest.cpp Tests/GeometryShop/regression/ebnormtest.inputs commit 1cb66d597d98e125798976915a6068f892bea5cf Author: Andy Nonaka Date: Mon May 1 11:08:58 2017 -0700 update scripts used to compile VARDEN Tools/F_scripts/makebuildinfo.py commit b30d64e48efecd6cef486e7ba2234d709eb09c05 Author: Michael Zingale Date: Mon May 1 12:29:20 2017 -0400 allow "source" to also contribute to the compile_string Tools/RegressionTesting/params.py Tools/RegressionTesting/suite.py commit 4356189d5fb905ad7c73e0f3081f8c9d75dc66c7 Author: Weiqun Zhang Date: Mon May 1 09:25:07 2017 -0700 give omp critical a name Src/Particle/AMReX_ParticleI.H commit cd9ef8b41219dd3427e11de2c0f6adbe87d00583 Author: Max Katz Date: Mon May 1 02:31:08 2017 -0400 Add a hook so that an AmrLevel can force a post-timestep regrid The motivation for this change is that sometimes, during the course of a coarse timestep, the timestep will found to be unstable due to a lack of resolution. In this case the coarse level may want to signal that more resolution is required immediately (as opposed to waiting for a future regrid), because even a single unstable step may cause significant harm to the integrity of the simulation. An example is a spurious numerical detonation caused by insufficient resolution in a thermonuclear burning region. If this numerically-seeded detonation is detected at the end of a timestep, more levels can be added immediately so that the fine levels can improve the situation and quench the detonation (since they will overwrite the coarse data at the end of the timestep). Each AmrLevel now has a member variable post_step_regrid. To trigger a regrid at the end of a step, but before any fine timesteps would be taken, they only need to set this variable to one. At the beginning of every timestep, it will be reset to 0. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H commit 539158c220a48cfb9de13d30baff100461616634 Author: Weiqun Zhang Date: Fri Apr 28 20:48:01 2017 -0700 add EB to doxygen and move doxygen stuff to its own directory Docs/Doxygen/doxygen.conf Docs/Doxygen/main.dox commit 86f202ffeea0c4b347dff8cb9eb9d50b632a253f Author: Dan Graves Date: Fri Apr 28 16:43:53 2017 -0700 started work on hybrid flux register. this one should be interesting Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp commit c3dac35b1fa68e756e3fdb3813f7fb3cf94eb6d9 Merge: 09c86ec44 b008f5c06 Author: Weiqun Zhang Date: Fri Apr 28 16:04:08 2017 -0700 Merge branch 'master' into development commit b008f5c064f116bcb3a7560b54c329b64ebc90fc Author: Weiqun Zhang Date: Fri Apr 28 15:48:08 2017 -0700 add a main page Docs/doxygen.conf Docs/doxygenmain.dox commit 09c86ec44517860d3965a8b55e8e5f658c69b233 Author: Weiqun Zhang Date: Fri Apr 28 14:47:07 2017 -0700 update migration guide Docs/Migration/Migration.md commit 1a28c13a677ff1561bf699eaa5defae74e9b1a47 Author: Weiqun Zhang Date: Fri Apr 28 14:47:07 2017 -0700 update migration guide Docs/Migration/Migration.md commit c908fd516a9fde900c2fb614ab244cd9e4c01e57 Author: Weiqun Zhang Date: Fri Apr 28 14:28:48 2017 -0700 simplify helloworld Tutorials/HelloWorld_C/Make.package Tutorials/HelloWorld_C/main.cpp Tutorials/HelloWorld_C/work.f90 commit 04f3465c905072314858d7ac94c02266b752311a Author: Weiqun Zhang Date: Fri Apr 28 14:25:00 2017 -0700 start AMReX User's Guide Docs/AMReXUsersGuide/.gitignore Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex Docs/AMReXUsersGuide/Preface/Preface.tex Docs/AMReXUsersGuide/README.md Docs/AMReXUsersGuide/amrexsymbols.tex commit a5b189c844054c069cc3b29dc9777ac9f50ab250 Author: Weiqun Zhang Date: Fri Apr 28 13:53:20 2017 -0700 rename UsersGuide to BoxLibUsersGuide Docs/BoxLibUsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex Docs/BoxLibUsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/subcycling_algorithm.eps Docs/BoxLibUsersGuide/GNUmakefile Docs/BoxLibUsersGuide/GettingStarted/GettingStarted.tex Docs/BoxLibUsersGuide/GettingStarted/VisIt_2D.eps Docs/BoxLibUsersGuide/GettingStarted/VisIt_3D.eps Docs/BoxLibUsersGuide/GettingStarted/edison.run Docs/BoxLibUsersGuide/GettingStarted/edison_omp.run Docs/BoxLibUsersGuide/Introduction/AMR.eps Docs/BoxLibUsersGuide/Introduction/Introduction.tex Docs/BoxLibUsersGuide/Introduction/boxlib_directory_bw2.eps Docs/BoxLibUsersGuide/Introduction/castro_scaling.eps Docs/BoxLibUsersGuide/Introduction/data_loc.odg Docs/BoxLibUsersGuide/Introduction/data_loc2.eps Docs/BoxLibUsersGuide/Introduction/index_grid.odg Docs/BoxLibUsersGuide/Introduction/index_grid2.eps Docs/BoxLibUsersGuide/Introduction/lmc_scaling.eps Docs/BoxLibUsersGuide/Introduction/maestro_scaling.eps Docs/BoxLibUsersGuide/Introduction/varden1.eps.REMOVED.git-id Docs/BoxLibUsersGuide/Introduction/varden2.eps.REMOVED.git-id Docs/BoxLibUsersGuide/Introduction/varden3.eps.REMOVED.git-id Docs/BoxLibUsersGuide/Introduction/varden4.eps.REMOVED.git-id Docs/BoxLibUsersGuide/LinearSolvers/LinearSolvers.tex Docs/BoxLibUsersGuide/Preface/Preface.tex Docs/BoxLibUsersGuide/README Docs/BoxLibUsersGuide/Regression/test_suite.tex Docs/BoxLibUsersGuide/Regression/testsuite.eps Docs/BoxLibUsersGuide/UsersGuide.tex commit 5f994adf6482bf1acb2b841e1f73a765a86d7388 Merge: b35d80636 943e9fe38 Author: Weiqun Zhang Date: Fri Apr 28 19:30:30 2017 +0000 Merged in development (pull request #28) Development commit 943e9fe38699a66be19400093076f4566b39fe02 Merge: 473f640a2 7c04defb4 Author: Weiqun Zhang Date: Fri Apr 28 12:28:30 2017 -0700 Merge branch 'master' into development commit 7c04defb4930150f3ebca0289cdf83f1ffb45774 Author: Weiqun Zhang Date: Fri Apr 28 12:27:36 2017 -0700 update copyright notice and license agreement README.txt license.txt commit 473f640a26388d613b8e483e30de3aaa8c938ab9 Merge: 7ad754e31 3384eabe3 Author: Andrew Myers Date: Thu Apr 27 16:35:18 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 3384eabe3b94ebd6b5ebe890acdadae3824db23e Author: Weiqun Zhang Date: Thu Apr 27 16:21:35 2017 -0700 print origin and value in addition to the fully expanded value when `make print-%` is invoked Tools/GNUMake/Make.rules commit 7b0f4cb519fd35fe67b9a7836ca9ae7a3623810b Merge: 02442b8af 172dd063a Author: Dan Graves Date: Thu Apr 27 14:56:58 2017 -0700 getting Weiqun's fixes to aliasing stuff commit 02442b8af72d49e1aca0bbd5187f39c0a3387dc3 Author: Dan Graves Date: Thu Apr 27 14:55:43 2017 -0700 found the bug that was making PWLFP get the wrong convergence rates. Looks good now. On to trying to figure out how to integrate with MultiFab fillpatch Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit 7ad754e31ecd2ca4e0cbec158eee7db2aa06903d Author: Andrew Myers Date: Thu Apr 27 14:55:31 2017 -0700 Make the C interface to the nodal multigrid solver a bit more general. Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit a109e0c40c78d595c3a6ff6754fb49008e531e48 Author: Dan Graves Date: Thu Apr 27 13:55:43 2017 -0700 another change of a MFIter declaration Src/GeometryShop/AMReX_EBLevelGrid.cpp commit 975cba9f821ea7745b0d41439b0015f56a716d23 Author: Dan Graves Date: Thu Apr 27 13:54:27 2017 -0700 added fancier static initialization to IntVect::Zero and IntVect::Unit from Chombo Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit 172dd063ac42507db962e045ff765fd11fdcb70b Author: Weiqun Zhang Date: Thu Apr 27 13:25:49 2017 -0700 support amrex::Print() << std::endl Src/Base/AMReX_Print.H commit d7ba37fed65f0dd9ce072dc0c31154b2cd83a90d Author: Weiqun Zhang Date: Thu Apr 27 12:26:21 2017 -0700 add new FArrayBox constructor that takes a Real* Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit 21a933c2bc9f07a6597894b668b404fce40c2dc4 Author: Dan Graves Date: Thu Apr 27 12:00:27 2017 -0700 some bug fixes improve convergence rate but not quite enough Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp commit 41426fc1fd4aa0a69d23c0b662901b9fdba6ee82 Author: Dan Graves Date: Thu Apr 27 11:54:52 2017 -0700 apparently using a LayoutData for defining a MFIter makes bad things happen Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp commit 503511916f8fd7a0332036c4e096a003cea25dbf Author: Dan Graves Date: Thu Apr 27 11:53:55 2017 -0700 added bounds checking to BaseIVFAB Src/GeometryShop/AMReX_BaseIVFABI.H commit 2c54addf5b6d358ece633b14aa9b08e27af96bcb Merge: 449239cea a3ceaefa2 Author: Weiqun Zhang Date: Thu Apr 27 11:16:29 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit a3ceaefa2965558c48d5f0054ada2019dae501d3 Merge: 6f44a4e6e 0fc48b3a2 Author: Dan Graves Date: Thu Apr 27 18:16:09 2017 +0000 Merged in dtg_branch (pull request #27) Dtg branch--merge to get Ray the dataholders he wants commit 449239ceace31ca40e220ff2ad2df60527715d16 Author: Weiqun Zhang Date: Thu Apr 27 10:20:10 2017 -0700 add new MultiFab/FabArray constructors that take non-owning pointers; clean up FabArray StatusType Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/Make.package commit 6f44a4e6e5af0a5e00abca56078a4e5609eafa15 Author: Andy Nonaka Date: Wed Apr 26 17:17:13 2017 -0700 added random number engine copy Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 commit 0fc48b3a2482755c9adb35e0657840fdc2ae94e5 Author: Dan Graves Date: Wed Apr 26 15:58:31 2017 -0700 I added EBFluxFAB, IrregFAB and their associated factories. They pass their a simple test. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBFluxFAB.cpp Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBFluxFactory.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregFAB.cpp Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Src/GeometryShop/Make.package Tests/EBAMRTools/regression/aggpwlfp.inputs Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/GeometryShop/regression/Backtrace.rg_0_rl_0 Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_H Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/dataarith.inputs commit bde177139c6fd18902ac3fdde3e8ff2524a47d01 Author: Weiqun Zhang Date: Wed Apr 26 08:49:46 2017 -0700 fix shebang configure commit 744be16ecda3fd5fe1888c4a82fa411f36891757 Author: Dan Graves Date: Tue Apr 25 16:26:45 2017 -0700 Good news: PWL fill patch test works. Bad news: convergence rate is wrong. Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Tests/EBAMRTools/regression/aggpwlfp.inputs Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/sphere.inputs commit c2e5702721fabf52ca318cc6ce027443a1cdb51e Author: Dan Graves Date: Tue Apr 25 12:44:32 2017 -0700 EBAMRTools again compiles. I added a bunch of EBLevelDataOps functionality Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/GeometryShop/AMReX_EBCellFAB.cpp Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit 0faf79700e22af9b62bccf0d1646c6325cf2dc30 Author: Dan Graves Date: Tue Apr 25 12:25:59 2017 -0700 added IntVect::Zero and IntVect::Unit because TheZeroVector() was pissing me off Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit 8eccdb3eb503a18e63bcc387a1cb8f7e226bd4fd Author: Andrew Myers Date: Tue Apr 25 09:49:49 2017 -0700 fix the advection tutorial. Src/Particle/AMReX_ParticleInit.H commit e2f885c26d4382c3291778a221221eb5c4fae40b Author: Dan Graves Date: Mon Apr 24 16:11:25 2017 -0700 I ported over a bunch of tools I use to write tests Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit 0c7642b61bed921181ef467909fc7ac6c5b21ac3 Author: Andrew Myers Date: Mon Apr 24 15:54:05 2017 -0700 Use the new syntax to get the Real data from the struct-of-arrays. Src/Particle/AMReX_ParticleContainerI.H commit 07b87c6db3a0eff345bb8d8d2e4b59a9fe38b100 Author: Andrew Myers Date: Mon Apr 24 15:47:35 2017 -0700 give the AmrParticleContainer 4 components as well. Src/AmrCore/AMReX_AmrParticles.H commit 18175f9c96081f9a91ec7d61b43e9f8e0c4dadb3 Author: Andrew Myers Date: Mon Apr 24 10:50:45 2017 -0700 add some additional accessor methods to StructOfArrays. Src/Particle/AMReX_Particles.H commit e371eaf7aba70e290f468a5e99ecdd8c27aca7c2 Merge: 1a036584c 6f8475b22 Author: Andrew Myers Date: Mon Apr 24 09:43:08 2017 -0700 Merge branch 'integer_soa_data' into development commit 1a036584ce55d8bb855f9771cb1b012372ba5d7e Author: Weiqun Zhang Date: Mon Apr 24 08:51:58 2017 -0700 move some rules out of Tools/GNUMake to avoid potential conflicts GNUmakefile.in Tools/GNUMake/Make.rules commit 7cc436205df8c48b7ec9a959ede113b8f72f4736 Author: Weiqun Zhang Date: Sun Apr 23 12:42:37 2017 -0700 configure: enforce libamrex and application are consistent on the use of OpenMP Tools/GNUMake/Make.rules Tools/libamrex/mkconfig.py commit b4c585bb6a00415049364771f829a9ce115e140c Author: Weiqun Zhang Date: Sun Apr 23 12:19:43 2017 -0700 configure: by default enforce the same compiler is used to build application Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit 28e94d3065e7fc30a54b4792bf600c43f2586781 Author: Weiqun Zhang Date: Sun Apr 23 12:17:29 2017 -0700 minor tweak Tutorials/libamrex_C/GNUmakefile commit 9cdd34b19b3ba30e3a0efd73e4d356289574b41d Author: Weiqun Zhang Date: Sat Apr 22 22:14:00 2017 -0700 minor tweak of make GNUmakefile.in Tools/GNUMake/Make.rules commit ef5c301fc233c8a1a13a0273aadc3d6de8b20a24 Author: Weiqun Zhang Date: Sat Apr 22 21:56:13 2017 -0700 add a note for linking to C++11 and Fortran libraries INSTALL commit f218fd3839b6b78ce95d9e5605e81cb5285039d1 Merge: 8dcb53320 8ba64d97d Author: Weiqun Zhang Date: Sat Apr 22 21:41:14 2017 -0700 Merge branch 'libamrex' into development commit 8ba64d97d986e00982962ccc94c42e35f4f92006 Author: Weiqun Zhang Date: Sat Apr 22 21:40:31 2017 -0700 add INSTALL INSTALL Tools/libamrex/configure.py commit 63a2ee02d172961457f6fb3d63de4a381a731c12 Author: Weiqun Zhang Date: Sat Apr 22 21:19:38 2017 -0700 add configure GNUmakefile.in Tools/libamrex/configure.py configure commit 879d84dfd49c201f60ebcd622c406854b3fcdf1b Author: Weiqun Zhang Date: Sat Apr 22 15:46:16 2017 -0700 create a directory for libarmex scripts Tools/GNUMake/Make.defs Tools/libamrex/mkconfig.py commit 998544cc3dfd38780e44bce932f371d5b0210b69 Author: Weiqun Zhang Date: Sat Apr 22 09:07:31 2017 -0700 An example using libamrex Tutorials/libamrex_C/GNUmakefile Tutorials/libamrex_C/MyAmr.H Tutorials/libamrex_C/MyAmr.cpp Tutorials/libamrex_C/main.cpp Tutorials/libamrex_C/myf.f90 commit c18e42c4fd4db87790c6fc22fd6f8661ce23704e Author: Weiqun Zhang Date: Sat Apr 22 08:24:46 2017 -0700 install headers and modules GNUmakefile Src/Base/Make.package Tools/C_scripts/mkconfig.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 0488479179d38b3fcc5e55143f757476429a1d46 Author: Weiqun Zhang Date: Fri Apr 21 18:04:45 2017 -0700 add a top level GNUmakefile for building libamrex GNUmakefile Src/Amr/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 6f8475b22bc116c9fdccd2e6125e69939d50209c Merge: de664ee35 8dcb53320 Author: Andrew Myers Date: Fri Apr 21 17:33:29 2017 -0700 Merging development into integer_soa_data commit 8dcb53320d203447aebd43a29f988efe97018973 Merge: 77c5698f5 5e5e7f281 Author: Andrew Myers Date: Fri Apr 21 17:19:44 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 77c5698f56fbcf904117dfb774de223108803ace Author: Andrew Myers Date: Fri Apr 21 17:19:29 2017 -0700 Make Reset() return the particle location data. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit be6abd36092827eabb8532c17db6fd12fd13df16 Author: Dan Graves Date: Fri Apr 21 16:02:08 2017 -0700 starting to wade into EBLevelDataOps. I managed to cut out everything I think is redundant and just keep what I think is useful. Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBLevelRedist.cpp commit de664ee357d199a78d5fddeba41c08d33521b00c Author: Andrew Myers Date: Fri Apr 21 15:03:43 2017 -0700 fix dumb mistake. Src/Particle/AMReX_ParticleContainerI.H commit 8982946e952064ad299d9f946c5f41132decd7ac Merge: 39d1baa03 bf54e3009 Author: Andrew Myers Date: Fri Apr 21 12:57:34 2017 -0700 Merge branch 'integer_soa_data' of bitbucket.org:berkeleylab/amrex into integer_soa_data commit 39d1baa03960d5f17641dd088d54d941fd23518f Author: Andrew Myers Date: Fri Apr 21 12:57:13 2017 -0700 rename these variables. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit c1f8f1589bee174ec4035b7bdea7c22e710b225d Author: Andrew Myers Date: Fri Apr 21 12:52:40 2017 -0700 reset this to TRUE Tests/Particles/GNUmakefile commit bf54e30096df54a61af08e5bc7e8be3f81be1f28 Merge: d4e9f23ba 5e5e7f281 Author: Andrew Myers Date: Fri Apr 21 12:38:01 2017 -0700 Merge branch 'development' into integer_soa_data commit d4e9f23bae5d9bdd9c9f697f8349637c6c73ac6a Author: Andrew Myers Date: Fri Apr 21 12:15:18 2017 -0700 change the struct-of-array interface to make it harder to make mistakes. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tests/Particles/main.cpp commit cb59093ddab9e4d7b46e9fc091f14655a4650ccb Author: Andrew Myers Date: Fri Apr 21 10:51:33 2017 -0700 Fix bug in assert statements. Src/Particle/AMReX_ParticleContainerI.H commit 5e5e7f281e433b2b131dc3d867e5546926e0dc51 Merge: 96659ee00 da9993487 Author: Dan Graves Date: Fri Apr 21 17:17:08 2017 +0000 Merged in dtg_branch (pull request #25) Dtg branch Approved-by: Weiqun Zhang commit da9993487fb78a8d80d5d43839ce1a9130c57f6a Merge: 38e7177d9 96659ee00 Author: Dan Graves Date: Fri Apr 21 09:50:42 2017 -0700 getting the latest from the development branch commit 96659ee004dbf1ab3b8d0ac1407e8333f14251e6 Author: Weiqun Zhang Date: Fri Apr 21 08:58:30 2017 -0700 add default move constructor to MFIter Src/Base/AMReX_MFIter.H commit 3c7459576c24a4dc8664315479bec277f25ad2b6 Author: Andrew Myers Date: Thu Apr 20 17:23:14 2017 -0700 Update test of the particle struct-of-arrays to also test the integer components. Src/Particle/AMReX_ParticleContainerI.H Tests/Particles/GNUmakefile Tests/Particles/main.cpp commit 724c2db554e40928fdbdf09a1885d9af5052ef67 Author: Andrew Myers Date: Thu Apr 20 17:04:48 2017 -0700 Add support for integer particle stored in the struct-of-arrays style. Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit 7b816739be5060e457881780992d4d2bf0876bf7 Author: Weiqun Zhang Date: Thu Apr 20 16:19:58 2017 -0700 add new MFIter constructors that take BoxArray and DistributionMapping Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 38e7177d92b47e24a745d826b3f49f9d0de6c905 Author: Dan Graves Date: Thu Apr 20 15:44:33 2017 -0700 after some bug fixes, we now have working, single-level redistribution. Src/EBAMRTools/AMReX_MeshRefine.cpp Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_EBLevelRedist.cpp Tests/GeometryShop/regression/Backtrace.rg_0_rl_0 Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/Make.package Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000 Tests/GeometryShop/regression/bl_prof/bl_call_stats_H Tests/GeometryShop/regression/bl_prof/bl_call_stats_H_00000 Tests/GeometryShop/regression/bl_prof/bl_comm_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_H Tests/GeometryShop/regression/levelRedistTest.cpp Tests/GeometryShop/regression/levelredist.inputs commit 095491ed7e2167bf6324104ab623affa9031019b Author: Andrew Myers Date: Thu Apr 20 13:17:17 2017 -0700 rename the particle template parameters to be more expressive. Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit 6ab7f3b266b0deff9b9f2e55db4a00daf63fc351 Author: Dan Graves Date: Thu Apr 20 11:31:44 2017 -0700 Porting over EBLevelRedist was trickier than I thought. It compiles now. On to testing Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_LayoutData.H Src/GeometryShop/Make.package commit d71c1849225f7d52a856f6ca9e7c82e26e045ed1 Author: Andrew Myers Date: Wed Apr 19 20:25:19 2017 -0700 If you restore the random state using more threads than you saved it with, give the RNG a sensible seed on the new threads. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 6d4dbaffe72928aad5d4c441c21e10d41fd5fc8d Merge: c0499c799 31adc1e87 Author: Andrew Myers Date: Wed Apr 19 18:05:23 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit c0499c7994e138f179cd28cfb6cfa54f3faed047 Author: Andrew Myers Date: Wed Apr 19 18:04:50 2017 -0700 A hopefully more portable way of saving the random state. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 638067eacc04fef16412ac3c359873b6545f8945 Author: Andrew Myers Date: Wed Apr 19 17:23:50 2017 -0700 use critical here instead of atomic capture on older versions of gcc Src/Particle/AMReX_ParticleI.H commit 0e18753129b44564f035acc20ba17a61b167bd98 Author: Andrew Myers Date: Wed Apr 19 17:16:18 2017 -0700 replace the the current implementation of the thread-safe RNG with an array-of-generators, since clang doesn't support thread_local. Src/Base/AMReX_Utility.cpp commit 31adc1e875d83d7848994514ce2dbaa70beb2348 Merge: 7e3a47f99 4c863ebc4 Author: Michael Zingale Date: Wed Apr 19 23:07:37 2017 +0000 Merged in mzingale/amrex/development (pull request #24) add more compilation info to the build info routines commit 00309aae0f2b65ec2812ed4df17a8c8d8f8e5a0d Author: Dan Graves Date: Wed Apr 19 15:58:39 2017 -0700 RedistStencil now compiles. Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/Make.package commit d4ea80795a0809a3199014e1c41956d87939488d Author: Dan Graves Date: Wed Apr 19 15:32:36 2017 -0700 ported over the most important bits of EBArith. I only kept the bits that did not involve communication. The full level stuff I will leave to EBLevelDataOps (previously they had a lot of redundant functionality) Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp commit 4c863ebc4feef0412d750fa289c9335ab4bc20dc Author: Michael Zingale Date: Wed Apr 19 17:50:20 2017 -0400 clean things up considerably Tools/C_scripts/makebuildinfo_C.py commit 7e3a47f99eaf352b2ad867dbc5669fa4cfc0109a Merge: 39b43d9b6 3e0eb9566 Author: Andrew Myers Date: Wed Apr 19 14:46:51 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 39b43d9b6d65981a5cc4c245104f22fbecde3438 Author: Andrew Myers Date: Wed Apr 19 14:46:38 2017 -0700 Break up the short-range particle container into multiple files. Tutorials/ShortRangeParticles/Make.package Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/ShortRangeParticles/main.cpp commit 70c7845abd8fb0231a09e3b6f9aed4513b59cdc3 Author: Michael Zingale Date: Wed Apr 19 17:29:44 2017 -0400 more compiler options Tools/C_scripts/AMReX_buildInfo.H Tools/C_scripts/makebuildinfo_C.py commit 3e0eb95660f706624ed510e87a2ca341f74585a2 Author: Andy Nonaka Date: Wed Apr 19 13:48:10 2017 -0700 revert last commit - this affects things in codes I wasn't aware of which assumed specifically dimensioned strings Src/F_BaseLib/fabio.f90 commit b6c330db30c0f83c74eb1068951eac4838f6208f Merge: 48b399ffb dfdae0292 Author: Andy Nonaka Date: Wed Apr 19 13:32:22 2017 -0700 Merge branch 'development' of https://bitbucket.org/berkeleylab/amrex into development commit 48b399ffb0b3003d24162a05ea69bf76224d8034 Author: Andy Nonaka Date: Wed Apr 19 13:32:07 2017 -0700 FABIO_MAX_VAR_NAME = 64 Src/F_BaseLib/fabio.f90 commit dfdae0292d1a2a7518d9bc485f7f14dbf4ed8b61 Merge: bf3703667 31c8ec003 Author: Andrew Myers Date: Wed Apr 19 11:05:59 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit bf3703667b9402384f1547c317081c9080f305a6 Author: Andrew Myers Date: Wed Apr 19 11:05:45 2017 -0700 Save and restore the state of the random number generator using an Array of ulongs. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 31c8ec00380b17cad8a9d8449e03a17541f7e50c Author: Weiqun Zhang Date: Tue Apr 18 19:50:43 2017 -0700 must include BaseFab header in TypeTraits otherwise it may give wrong results if the type is incomplete Src/Base/AMReX_TypeTraits.H commit 5ec774f97e4b9592dfd345f44f35491ed47ad3cc Author: Weiqun Zhang Date: Tue Apr 18 17:40:47 2017 -0700 need to include otherwise gcc 6 won't compile Src/Particle/AMReX_Particles.H commit 2c12df1f7b68474298f1ec5f3bde0b5101b79f68 Author: Andrew Myers Date: Tue Apr 18 17:31:27 2017 -0700 update the dependencies of this particle test, now that additional packages are required. Tests/Particles/GNUmakefile commit 27ec5cfa6b54c9209834e9829adde040462c5977 Author: Andrew Myers Date: Tue Apr 18 17:30:31 2017 -0700 no need to do this now - the random number generator will get different seeds on different threads by default. Src/Particle/AMReX_ParticleContainerI.H commit 233dae85ad0401d53f0d085a50599429d035a3d1 Author: Andrew Myers Date: Tue Apr 18 16:03:38 2017 -0700 fix MoveRandom after changes to RNG stuff. Src/Particle/AMReX_ParticleContainerI.H commit 1b0805bc8086b349f3ba6a0dad2902ae8182fd72 Author: Weiqun Zhang Date: Tue Apr 18 12:40:33 2017 -0700 move the specialization of IsBaseFab into AMReX_TypeTraits Src/Base/AMReX_BaseFab.H Src/Base/AMReX_TypeTraits.H commit 2adb6aa3a5e02250c53d97d59e71e398b47afa0f Author: Andrew Myers Date: Tue Apr 18 15:39:05 2017 -0700 remove AMReX's C++ implemention of the Mersenne twister in favor of the one in C++11. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit af6bc0fc45bc5e19b051d059ae82c1c571e337f8 Author: Weiqun Zhang Date: Tue Apr 18 10:13:33 2017 -0700 update cmake Src/Base/CMakeLists.txt Src/Base/Make.package commit 62aef837f9050120a69624feba89bb80ead40f82 Author: Weiqun Zhang Date: Tue Apr 18 10:05:24 2017 -0700 enable_if a number of FabArray functions that make senses only if FAB is really a BaseFab Src/Base/AMReX_FabArray.H commit 84c1bfa1a435e8d80536490ebc686f7b696447f1 Author: Weiqun Zhang Date: Tue Apr 18 09:28:23 2017 -0700 add AMReX_TypeTraits for SFINAE Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_TypeTraits.H commit 0334bb25179871040a55d9a66b73dc71d8bbabff Author: Dan Graves Date: Mon Apr 17 16:08:53 2017 -0700 started porting over redistribution (on a single level) objects Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RedistStencil.cpp commit 62d69337a15a757e703f17bb318a4fb2f6bed6e8 Author: Dan Graves Date: Mon Apr 17 14:33:54 2017 -0700 fixed bug in MeshRefine test. Seems to work fine now. Src/GeometryShop/AMReX_EBFluxFAB.H Tests/EBAMRTools/regression/meshref.inputs Tests/EBAMRTools/regression/simpleMeshRefine.cpp commit 6eec2f6f4eb1bd9ddbdeb320244faa2069555aea Author: Weiqun Zhang Date: Mon Apr 17 13:12:50 2017 -0700 move MakeType to a new header Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MakeType.H Src/Base/CMakeLists.txt Src/Base/Make.package commit f457a4b9e2f6112d4ca36a8b052b6e5c84ac103d Merge: 744c58396 c8a30e580 Author: Andrew Myers Date: Mon Apr 17 13:01:23 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 744c583969fb44b97134faf150a97a4dcae9071b Author: Andrew Myers Date: Mon Apr 17 13:00:55 2017 -0700 Use the c++11 random number generator here. Src/Particle/AMReX_ParticleInit.H commit c8a30e580b8b6332e8fd1a7f802fca1e5c5af37d Author: Weiqun Zhang Date: Mon Apr 17 11:15:16 2017 -0700 add new make_alias constructor for MultiFab and iMultiFab Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 18a90796b9fd760c99d145005b5840ba9ecf9e16 Author: Weiqun Zhang Date: Mon Apr 17 10:54:49 2017 -0700 add a new FabArray constructor for making alias; I think it's very confusing to make a deep copy with constructor so make_deep_copy is not support for FabArray Src/Base/AMReX_FabArray.H commit 76031a2557bafbbebbb98e051b7c50d20fbb2bec Author: Dan Graves Date: Mon Apr 17 10:41:22 2017 -0700 adding debugging tools so I can figure out what is wrong with AMReX_MeshRefine Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/Make.package commit 538b248eeceb2879d3f0288e8801f2b8afadb6ef Author: Dan Graves Date: Mon Apr 17 10:40:58 2017 -0700 added face-centered stuff Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H commit 2bd57481da6aa3e22b5fae94456d7a98c704b753 Author: Weiqun Zhang Date: Mon Apr 17 09:45:35 2017 -0700 add StatusType to FabArray Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit 1a5b2494de358ce883eec1deb5c818283ef0778a Author: Marc Day Date: Sun Apr 16 22:15:48 2017 -0700 Partial fix of CMakeLists.txt files - still need to fix mpi CMakeLists.txt Tutorials/MultiGrid_C/CMakeLists.txt Tutorials/MultiGrid_C/main.cpp commit 58d6e618073703b1acf5934fc828de1184a2abb7 Author: Weiqun Zhang Date: Sun Apr 16 18:49:47 2017 -0700 new IArrayBox constructor for making alias or deep copy Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp commit 64c42dcab1873fba9765654d29313b4efc34d472 Author: Weiqun Zhang Date: Sun Apr 16 18:36:27 2017 -0700 new FArrayBox constructor for make alias or deep copy Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit bcd4adc110e9aacf311c95023ddcf8ea5f9bac68 Author: Andrew Myers Date: Sat Apr 15 20:38:26 2017 -0700 a couple of changes to the InitRandomPerBox routine. Src/Particle/AMReX_ParticleInit.H commit 9fb2d3b7ea62c9c38b4aa8e3f275a1f73546cbb0 Author: Ann Almgren Date: Sat Apr 15 19:25:25 2017 -0700 Clarify the comment and error message Src/Particle/AMReX_ParticleInit.H commit 6179cfd8ad901b4551bea46a1f76130fb1d6de5b Author: Ann Almgren Date: Sat Apr 15 18:59:20 2017 -0700 Add a new initialization routine for particles -- InitRandomPerBox -- which is used when we want the particle distribution to be random within a box but we want to be able to replicate the box exactly for a scaling study. Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit 55f8e2a44ad47eb484666615ec2f7927fdc4dfe2 Author: Weiqun Zhang Date: Sat Apr 15 07:56:57 2017 -0700 mod migration script for IAMR Fortran code Tools/Migration/step-7-bindc/bindc.sh commit 43f50eeba4cf44918ed230496ce2981dd82e9ea6 Author: Andrew Myers Date: Fri Apr 14 15:50:08 2017 -0700 ParmParse inputs. Tutorials/ShortRangeParticles/main.cpp commit 7c0746edafec5c9b4599b0b8fcb092afbb6b4a46 Author: Andrew Myers Date: Fri Apr 14 14:30:05 2017 -0700 updating this thing to work in 3D as well. Tutorials/ShortRangeParticles/main.cpp commit 1c61d94bb09c3477c00284f62adbbc70fd5e0206 Merge: 6f43405d9 0cc044603 Author: Andrew Myers Date: Fri Apr 14 13:09:46 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 6f43405d994dd2cdabb35d79feef8a93aea4b62e Author: Andrew Myers Date: Fri Apr 14 13:09:22 2017 -0700 add 3d versions of fortran routines. Tutorials/ShortRangeParticles/main.cpp Tutorials/ShortRangeParticles/short_range_2d.f90 Tutorials/ShortRangeParticles/short_range_3d.f90 commit f18ce7d465a6f2aeb7cfe930f4421724de3fa0cb Author: Andrew Myers Date: Fri Apr 14 12:59:06 2017 -0700 renaming / reorganization. Tutorials/ShortRangeParticles/Make.package Tutorials/ShortRangeParticles/main.cpp Tutorials/ShortRangeParticles/short_range_2d.f90 Tutorials/ShortRangeParticles/short_range_F.H commit 68b4efda763b7ddd6e2130875798b41ddcdfc386 Author: Andrew Myers Date: Fri Apr 14 12:55:18 2017 -0700 removing some now un-needed code. Tutorials/ShortRangeParticles/main.cpp commit 163212e803b88c60c3ad5dd4038955b78378d681 Author: Andrew Myers Date: Fri Apr 14 12:48:24 2017 -0700 move the particle time integration to a fortran subroutine. Tutorials/ShortRangeParticles/compute_force_2d.f90 Tutorials/ShortRangeParticles/compute_force_F.H Tutorials/ShortRangeParticles/main.cpp commit 0cc044603a793f8ff02cdfb967f42879d720f7a0 Author: Weiqun Zhang Date: Fri Apr 14 09:48:00 2017 -0700 new BaseFab constructor that makes either an alias or a deep copy Src/Base/AMReX_BaseFab.H commit 2ee64d81b071a0da3e95b92e5952d5f4d6200985 Author: Dan Graves Date: Fri Apr 14 11:04:34 2017 -0700 EBIS coarsening issues resolved for now. BoxArray's ostream operator does seem to have weird integer overflow issues, however. Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/EBAMRTools/regression/meshref.inputs commit cd73337237b28678716fb0f248887377d39bcb31 Author: Dan Graves Date: Fri Apr 14 10:43:48 2017 -0700 made another destructor virtual to get the compiler to shut up. Src/Base/AMReX_BaseFab.H commit 67c6ad040b023e254582ba5fa0b18af81afea7a8 Author: Andrew Myers Date: Fri Apr 14 09:52:21 2017 -0700 more comments. Tutorials/ShortRangeParticles/main.cpp commit 613cf90701f8dfb729adc915062be91e2662c9ca Merge: ed24ddb64 4b0117769 Author: Andrew Myers Date: Thu Apr 13 23:08:37 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit ed24ddb643cfd8525aa76ff04d712ae8abb32c70 Author: Andrew Myers Date: Thu Apr 13 23:08:05 2017 -0700 MPI communication for ghost particles working now. Tutorials/ShortRangeParticles/main.cpp commit 2605bc9eb56d5a8ca4ae87297c3f041690f474f5 Author: Dan Graves Date: Thu Apr 13 15:39:47 2017 -0700 did I forgot to add these? Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp commit 56f540eed9b9e70db54659835a3bf8a6019ba7a6 Author: Dan Graves Date: Thu Apr 13 15:39:06 2017 -0700 made one base constructor virtual to shut the compiler up. I also coded up a standalone meshrefine and a test from Weiqun's example. EBIndexSpace coarsening is currently having some problems. Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/Base/AMReX_IArrayBox.H Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IntVectSet.cpp Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/Make.package Tests/EBAMRTools/regression/meshref.inputs Tests/EBAMRTools/regression/simpleMeshRefine.cpp commit bc9c4ae72a77ffbc418852a7f38182c5f12128c9 Author: Andrew Myers Date: Thu Apr 13 14:27:20 2017 -0700 first stab at getting the MPI comm stuff working. Tutorials/ShortRangeParticles/main.cpp commit 4b0117769568494638f4432e5cecd748b5a99359 Author: Weiqun Zhang Date: Thu Apr 13 14:00:43 2017 -0700 add average_node_to_cellcenter Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H commit b052343fb4500f3c2b002477dc0a5f6806c68497 Merge: fb73f698e fd037d52e Author: Andrew Myers Date: Thu Apr 13 11:22:08 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit fb73f698e7dcb646c1bc35f254ef86eb3fa2c7cc Author: Andrew Myers Date: Thu Apr 13 11:21:53 2017 -0700 more functionality for the particle neighbors tutorial. this works in serial now. Tutorials/ShortRangeParticles/Make.package Tutorials/ShortRangeParticles/compute_force_2d.f90 Tutorials/ShortRangeParticles/compute_force_F.H Tutorials/ShortRangeParticles/main.cpp commit 6ee0ffd10fba4667d8e759989fc5ccf40b047688 Merge: 1e47645d1 fd037d52e Author: Dan Graves Date: Thu Apr 13 10:23:23 2017 -0700 merging with dev branch commit fd037d52e2df6283bba9218fcecc94c5a92990f1 Author: Weiqun Zhang Date: Thu Apr 13 10:20:11 2017 -0700 fix assertion Src/AmrCore/AMReX_AmrMesh.H commit 5afba3ccb0e23951c48fddb378e352ac3121ea2a Author: Andrew Myers Date: Wed Apr 12 23:20:13 2017 -0700 more work on the ghost particle stuff. Tutorials/ShortRangeParticles/main.cpp commit 0a66e5b5073d85438ddda0390e40e899fd20ab7e Merge: 2ceedce1c 513e1a837 Author: Andrew Myers Date: Wed Apr 12 17:01:16 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 2ceedce1c370053885fdb5bf814e7d3c2960ed91 Author: Andrew Myers Date: Wed Apr 12 17:00:50 2017 -0700 Some work towards neighbor computation for particles that see short-range forces. Src/Particle/AMReX_ParticleContainerI.H Tutorials/ShortRangeParticles/GNUmakefile Tutorials/ShortRangeParticles/Make.package Tutorials/ShortRangeParticles/main.cpp commit 513e1a837f176c74c4bb0021af71ae24ba263571 Author: Weiqun Zhang Date: Wed Apr 12 16:07:42 2017 -0700 Box: remove the lengthy overflow check because I don't think it could happen on exascale machines unless they run Windows Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 1e47645d1c357ece906bcc91dd576c7ab1a5de8e Merge: b448f33eb 6d2f47edc Author: Dan Graves Date: Wed Apr 12 15:56:15 2017 -0700 merging to get new fancier mesh generator commit 6d2f47edc2218b7b9545f76ae67fd72c0ef963bc Author: Weiqun Zhang Date: Wed Apr 12 15:41:02 2017 -0700 clean up the MeshRefinement example Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Tutorials/MeshRefinement/main.cpp commit b448f33eb5ab751cba79fc53f9775c56aa4d7e74 Author: Dan Graves Date: Wed Apr 12 15:29:34 2017 -0700 EBAMRTools first tool now compiles. Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/Make.package Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit 76e5ae3414da72a610447f1263c4fb217cdd161a Author: Weiqun Zhang Date: Wed Apr 12 14:40:10 2017 -0700 Geometry: allow default coordinates and let passed in paramters take precedence over parmparse parameters Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 4de535348ee3139d1a9841058a182b36bcd88f9a Author: Weiqun Zhang Date: Wed Apr 12 14:20:31 2017 -0700 AmrMesh: add some set functions Src/AmrCore/AMReX_AmrMesh.H commit cbe7c7950c14d75a3fab5b0b8f06d0ade06ab7cc Author: Weiqun Zhang Date: Wed Apr 12 13:41:17 2017 -0700 add assertion Src/Base/AMReX_MFIter.cpp commit a5af63aae16e382ba1f7210b27ec4e4926ac4695 Author: Weiqun Zhang Date: Wed Apr 12 13:12:37 2017 -0700 minor optimization Src/Base/AMReX_ParmParse.cpp commit b902b1bc342b8f45b0d3fcf0cbae949b4fb4fdda Author: Weiqun Zhang Date: Wed Apr 12 13:09:49 2017 -0700 move BoxIterator from GeometryShop to Base Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxIterator.cpp Src/Base/AMReX_RealVect.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/GeometryShop/Make.package commit a3eec0f400417b3fd3a7ed188bee12037dafb164 Author: Weiqun Zhang Date: Wed Apr 12 12:58:53 2017 -0700 move RealVect from GeometryShop to Base Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/GeometryShop/Make.package commit 2aae191b1487976ca7f685f2dca30a8c0d074018 Author: Dan Graves Date: Wed Apr 12 11:18:06 2017 -0700 more fixes to get all the geometryshop tests working again (now with hybrid EBCellFAB) Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseIndex.H Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp commit 722beb41ce4eb4ecb2b7c3dbeedde9ef01c031f1 Merge: 752935ecf c72c4f118 Author: Dan Graves Date: Wed Apr 12 11:02:13 2017 -0700 merging with deveopment branch because I have to add a function to BaseFab commit 752935ecf1583e2464b3de7e5693e0d8a456d4c4 Author: Dan Graves Date: Wed Apr 12 11:00:35 2017 -0700 tweaking test to fit changing API (EBCellFAB is no longer just a wrapper) Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit 2575c5a8abd5c25847f88dd498b88201f74c216b Author: Dan Graves Date: Wed Apr 12 10:30:46 2017 -0700 changed argument names to make the API less of a lie Src/GeometryShop/AMReX_EBGraph.H commit fe27475171a2b667d6856bf0b9ae6a726a25c355 Author: Dan Graves Date: Wed Apr 12 10:29:56 2017 -0700 fixed this test to reflect API changes Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp commit c72c4f1183a1907284478e6d9baa97b793da36a0 Author: Weiqun Zhang Date: Tue Apr 11 16:55:02 2017 -0700 add clang-analyze and clang-tidy to make Tools/GNUMake/Make.rules commit 665a2df80a37e334a6862e48932a75d86dec7f0b Author: Dan Graves Date: Tue Apr 11 16:07:40 2017 -0700 had to put in real EBCellFAB and associated stuff Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBCellFactory.cpp commit d29e5ac5c9311e8fcf9581ed96f6b99a8c0f4882 Author: Weiqun Zhang Date: Tue Apr 11 13:00:38 2017 -0700 add llvm Tools/GNUMake/Make.defs Tools/GNUMake/comps/llvm.mak commit dbc1e489a8f7d8c16558077679f6e421575cb4dd Author: Weiqun Zhang Date: Tue Apr 11 12:31:57 2017 -0700 add some braces Src/Base/AMReX_ArrayLim.H commit cfc2de9155acc34bba642b61dc8ff1beca42168f Author: Weiqun Zhang Date: Tue Apr 11 10:04:31 2017 -0700 add override Tutorials/AMR_Adv_C/Source/Adv.H commit 4e515d6df5513ea33495f12f89c41022fb9bdb0c Author: Weiqun Zhang Date: Tue Apr 11 10:02:14 2017 -0700 reimplement a few macros so that Clang 4.0.0 is happy. Src/Base/AMReX_ArrayLim.H commit b08c564a2fdb90536496027904f5968067a8f0f4 Author: Weiqun Zhang Date: Fri Apr 7 12:59:10 2017 -0700 add a new AmrMesh constructor Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 0b693bcf8be16167ec03832d702c7cf7f14ce047 Merge: 4841df8bb f676319ba Author: Max Katz Date: Mon Apr 10 00:53:27 2017 -0400 Merge branch 'development' into gpu commit f676319bafb78a166f43442500421144e6e7111c Merge: 029b3ec0b 594d3150c Author: Jon Rood Date: Fri Apr 7 21:05:48 2017 +0000 Merged in jrood-nrel/amrex/nrel_intel_make_fix (pull request #23) Fixing GCC in the make files for NREL machines. Approved-by: Jon Rood commit 029b3ec0b2452bf6687d40fccd805844c64f3661 Author: Weiqun Zhang Date: Fri Apr 7 12:53:38 2017 -0700 need to call some initialization functions in one of the AmrMesh constructor Src/AmrCore/AMReX_AmrMesh.cpp commit 594d3150c1e22a9e78c92829c9483467df7b1fba Author: Jon Rood Date: Fri Apr 7 10:39:30 2017 -0600 Fixing GCC in the make files for NREL machines. Tools/GNUMake/sites/Make.nrel commit 384b18d58234402d9a3f4e2fe455de7078c0f17d Author: Jon Rood Date: Fri Apr 7 10:10:57 2017 -0600 Fixing GCC in the make files for NREL machines. Tools/GNUMake/sites/Make.nrel commit c52fa7fce6bfc0d7fc0962200ec4b27f0b39f6fd Merge: 1a79b04a4 aeef35681 Author: Dan Graves Date: Thu Apr 6 15:54:28 2017 -0700 Merge branch 'development' into dtg_branch commit 1a79b04a4d13d79d2190e9eeb3a1612c88c2eea4 Author: Dan Graves Date: Thu Apr 6 15:53:31 2017 -0700 commit premerge with development branch Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBLevelGrid.H Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/Make.package Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/sphere.inputs Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit aeef3568137d8256743679b93b37c05ea079b650 Merge: 5aaa28e34 c9064cb24 Author: Jon Rood Date: Thu Apr 6 20:09:05 2017 +0000 Merged in jrood-nrel/amrex/nrel_intel_make_fix (pull request #21) Adding Intel compiler compatiblity into make system for NREL machines. Approved-by: Ray Grout commit c9064cb24d38e9788c7bab4534fe40d081ac1397 Author: Jon Rood Date: Thu Apr 6 13:59:38 2017 -0600 Adding Intel compiler compatiblity into make system for NREL machines. Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nrel commit 5aaa28e344e14cacd84d9d7539b994c908eb365c Author: Weiqun Zhang Date: Wed Apr 5 17:12:15 2017 -0700 MeshRefinement test: write a mf with value set to amr level Tutorials/MeshRefinement/main.cpp commit c8430fd0d0304f4083718d651be97ce10ed83004 Author: Weiqun Zhang Date: Wed Apr 5 17:02:51 2017 -0700 Add an example showing how to generate Amr meshes for testing Tutorials/MeshRefinement/GNUmakefile Tutorials/MeshRefinement/Make.package Tutorials/MeshRefinement/MyAmr.H Tutorials/MeshRefinement/MyAmr.cpp Tutorials/MeshRefinement/main.cpp commit b1b2507bd2de658b82f669e92d885fd968f98f84 Author: Weiqun Zhang Date: Wed Apr 5 15:59:12 2017 -0700 add AmrMesh::SetFinestLevel Src/AmrCore/AMReX_AmrMesh.H commit d3d7bc2da2f9598293a1b4b613e8eb89f97b860a Author: Weiqun Zhang Date: Wed Apr 5 15:16:03 2017 -0700 add const Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrMesh.H commit 586443e2dbd62c7d5e4e2caf3a4a505bf4724a8b Author: Weiqun Zhang Date: Wed Apr 5 13:56:36 2017 -0700 add comments Src/AmrCore/AMReX_AmrMesh.H commit 971bba7ef271275f76ff6e896661fa0a706a5fd2 Author: Weiqun Zhang Date: Wed Apr 5 13:42:48 2017 -0700 make AmrMesh concrete Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 49380d0c431c2483cb5e5e9b6cbbcc0d74768e0a Author: Weiqun Zhang Date: Wed Apr 5 10:54:16 2017 -0700 Split AmrCore into two. The new AmrMesh class will allow for more flexible grids generation for testing. Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit c288ddd301e475925d094cab1cce8561479e98ec Author: Weiqun Zhang Date: Tue Apr 4 12:45:21 2017 -0700 add kiryu to CCSE_MACHINES make Tools/GNUMake/Make.machines commit 8d4b41b531fc4d15ad0a7a170b25d4ce6041692a Merge: ff0b2a1d4 4ded3ea78 Author: Michele Rosso Date: Tue Apr 4 03:38:29 2017 +0000 Merged in mrosso84/amrex/cmake_build_tools (pull request #20) Cmake build tools commit 4ded3ea788a92cc9ae975eebcb5b70ba114b5116 Author: Michele Rosso Date: Mon Apr 3 16:32:03 2017 -0700 Use plt_compare_diff_grids instead of fcompare for cmake-enabled projects Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit 66666277aec9826f8333a1fb2cf7872a02ba4dfb Author: Michele Rosso Date: Mon Apr 3 16:15:38 2017 -0700 Add plt_compare_diff_grids to cmake build Tools/Postprocessing/F_Src/CMakeLists.txt commit 8d374be2fba21c601cbeb019c17d76b4032c87e0 Author: Dan Graves Date: Mon Apr 3 15:45:57 2017 -0700 As Zhukov said to Eisenhower, If we come to a minefield, our infantry attacks exactly as if it were not there. Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp commit b35d80636cf9e1794b6132e1b72b5ab0b0d3110d Merge: 072aa45b9 ff0b2a1d4 Author: Weiqun Zhang Date: Mon Apr 3 17:18:51 2017 +0000 Merged in development (pull request #19) AMReX 17.04 commit ff0b2a1d46461a8490b93822829d3463b5148a9c Merge: 072aa45b9 06fa2462e Author: Weiqun Zhang Date: Mon Apr 3 10:12:29 2017 -0700 Merge branch 'development' commit 06fa2462e01ab556479803c1948c9a48f03f11a7 Author: Weiqun Zhang Date: Mon Apr 3 09:55:45 2017 -0700 Reimplement BoxArray::RefID, DistributionMapping::RefID and FabArrayBase::BDKey using std::less for pointer comparison. This fixes the undefined behavior in the old implementation. In C++11, std::less is guaranteed to work for pointers (even if operator < does not). Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 26eb7c719ed5a00e8db495c836256e74d73eeb6e Author: Weiqun Zhang Date: Sat Apr 1 19:05:00 2017 -0700 have to include MultiFab.H because it's used as template paramter for Array Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 143a1ea2b773cb10432452ad6f13b9515c1ceb4c Author: Ann Almgren Date: Sat Apr 1 17:13:30 2017 -0700 Revert the latest revert. Src/Base/AMReX_MultiFabUtil.H commit 6e1080826712ca65b351bfa70b78d1f2f964a25f Author: Weiqun Zhang Date: Sat Apr 1 15:31:52 2017 -0700 add include back to MulitFabUtil.H Src/Base/AMReX_MultiFabUtil.H commit 9ca6775d6dc020ecd9d287dd0d49694d308d9b0d Author: Weiqun Zhang Date: Sat Apr 1 10:57:58 2017 -0700 add MultiFab::OverlapMask function that counts how many duplicates are at each point; add new versions of norm1 and norm2 that do not double count for nodal data Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 8e6e05514a7b4559b8307797b3046e078ed795ab Author: Weiqun Zhang Date: Sat Apr 1 10:34:36 2017 -0700 add FabArrayBase::ixType() and other minor changes Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 3c89d504e1adf590ae92ff0af18cd1a30b908bf4 Author: Weiqun Zhang Date: Fri Mar 31 16:12:22 2017 -0700 fix a new bug in BoxArray::minimalBox Src/Base/AMReX_BoxArray.cpp commit f90406b9b385d6d90fcd0dcf8d5676358cf57b14 Author: Weiqun Zhang Date: Fri Mar 31 15:54:56 2017 -0700 use uint64_t instead of long long in initializing snan Src/Base/AMReX_MemPool.cpp commit a4cf7b4c269d3d660f48c6fb03fc9cd4a983a483 Author: Weiqun Zhang Date: Fri Mar 31 15:31:07 2017 -0700 fix some particle initialization functions for 1d and 2d Src/Particle/AMReX_ParticleInit.H commit 0c495ecb81d75ef63f7fcf8ae450076980769886 Merge: 9de54a3ba 547254880 Author: Weiqun Zhang Date: Fri Mar 31 14:55:03 2017 -0700 Merge branch 'development' into weiqun/cba commit 547254880b97351df85b68b64db15de2d41f6de6 Author: Weiqun Zhang Date: Fri Mar 31 14:53:09 2017 -0700 add a missing header Src/Base/AMReX_FabArrayBase.cpp commit 9de54a3bad4782a6258ba3d8d8c57df46733d13e Author: Weiqun Zhang Date: Fri Mar 31 14:08:12 2017 -0700 fix a new bug Src/Base/AMReX_BoxArray.cpp commit f91919a255a00ef3befcf3ee87158812aff0ef07 Author: Weiqun Zhang Date: Fri Mar 31 13:24:29 2017 -0700 minor Src/Amr/AMReX_Amr.cpp commit 7ad20e59a120fa5cafe4edac1d94c737898e056a Author: Dan Graves Date: Fri Mar 31 13:17:56 2017 -0700 EBLevelGrid and LayoutData now compile. On to porting the tools that use them Src/Base/AMReX_BoxArray.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_LayoutData.H Src/GeometryShop/Make.package commit dddc3c16cc0a3fab0fed85f38248ca0294dd95e0 Author: Weiqun Zhang Date: Fri Mar 31 13:09:53 2017 -0700 update FluxRegister for crse_ratio Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Boundary/AMReX_BndryRegister.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.H Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.H Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H commit 8f4238a6ef07850f808b4670bf043a2641c04b1b Author: Ann Almgren Date: Fri Mar 31 11:49:33 2017 -0700 Oops -- that was the wrong file for plt_compare_diff_grids.f90 -- this one should work. Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit ebae6e5f6d768297c3745c32eb08c62992099d7d Author: Ann Almgren Date: Fri Mar 31 11:41:59 2017 -0700 Build plt_compare_diff_grids.f90 instead of fcompare.f90 Tools/Postprocessing/F_Src/CMakeLists.txt commit 085dbfdc2fe35da7dadafc11a9844ac0683ac082 Author: Ann Almgren Date: Fri Mar 31 11:31:33 2017 -0700 Add a new file that can be used to compare plotfiles that have the same problem domain at each level but that have different grids covering that domain. This is particularly useful for comparing different domain decompositions of the same problem Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit 5696e024b1a9c11b4b736438bb80adb313a5ba01 Merge: dccf46b08 97a1e8c42 Author: Weiqun Zhang Date: Fri Mar 31 11:26:46 2017 -0700 Merge branch 'development' into weiqun/cba commit dccf46b0819920f91e62fa00a50a362f3d74c2fa Author: Weiqun Zhang Date: Fri Mar 31 11:25:49 2017 -0700 update tiling for crse_ratio Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 3157d643ce085e8dd754e604430490e1d498d35b Author: Weiqun Zhang Date: Fri Mar 31 10:29:09 2017 -0700 update FillBoundary for crse_ratio Src/Base/AMReX_BoxArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 0439c72ca2d2dfe18ad7f461be6cb212922a8cc4 Author: Weiqun Zhang Date: Fri Mar 31 09:58:42 2017 -0700 more changes due to the addition of crse ratio to BoxArray Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 97a1e8c420becbbce0dea7e3db93696c25ead689 Author: Weiqun Zhang Date: Fri Mar 31 08:35:03 2017 -0700 add a missing header Tutorials/MultiGrid_C/writePlotFile.cpp commit 5996b8338b7cd8f888547f3485da8ce883268632 Author: Weiqun Zhang Date: Fri Mar 31 08:31:09 2017 -0700 fix a typo Src/F_Interfaces/Base/AMReX_multifab_fi.cpp commit 405181421ce594ad631adbbf755afc6ff5dbf63d Author: Weiqun Zhang Date: Fri Mar 31 08:29:26 2017 -0700 remove a print Src/Base/AMReX_DistributionMapping.cpp commit 1d17982f6e64c513e866938caede70e6836dbefc Merge: a9695369f de7b6d105 Author: Dan Graves Date: Fri Mar 31 15:25:46 2017 +0000 Merged in dtg_branch (pull request #16) eb sort of works so it should be merged commit a9695369f482d1a5f58707e1caa652b73860b6ad Merge: 147c45d32 c755cebc6 Author: Michele Rosso Date: Thu Mar 30 23:49:44 2017 +0000 Merged in mrosso84/amrex/cmake-mpi-build (pull request #18) Add fextract and fcompare as part of the install commit 5357ad27176130e0c051785a4183110df0b66766 Author: Weiqun Zhang Date: Thu Mar 30 16:47:30 2017 -0700 changes due the addition of crse ratio to BoxArray Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit c755cebc62a5a2b00d8c4388481aabd955a8bd16 Author: Michele Rosso Date: Thu Mar 30 16:04:29 2017 -0700 Add fextract and fcompare as part of the install CMakeLists.txt Tools/Postprocessing/F_Src/CMakeLists.txt commit d12033413ea953355e53d48df7d7d923d780d2fe Author: Weiqun Zhang Date: Thu Mar 30 14:12:08 2017 -0700 BoxArray: moved some functions from .H to .cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit a47160506a6b45f843ae213ee618e9740d5de2b6 Author: Weiqun Zhang Date: Thu Mar 30 13:48:32 2017 -0700 Coarsen the boxes in BoxArray::uniqify Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit f527c4d0952b469a1151103b8cbdf3c0dc8fda68 Author: Weiqun Zhang Date: Thu Mar 30 13:00:47 2017 -0700 rm BoxArray::shiftHalf Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 2d106b4a8282ab55a2d101f5c9c6f71f7fb5c058 Author: Weiqun Zhang Date: Thu Mar 30 11:27:18 2017 -0700 add a special case to IntVect::coarsen Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit fb5494cdc5bf89a5342014c207fd07f0833545f3 Author: Weiqun Zhang Date: Thu Mar 30 10:55:22 2017 -0700 add crse ratio to BoxArray class Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit de7b6d105c433eefa44743c313fd5a0f8bfe5133 Merge: b6356f234 147c45d32 Author: Dan Graves Date: Thu Mar 30 10:53:59 2017 -0700 Merge branch 'development' into dtg_branch commit b6356f234f829fa1355fcccaed183191d4262e64 Author: Dan Graves Date: Thu Mar 30 10:53:48 2017 -0700 committing some temporary stuff so I can merge with development branch Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelGrid.cpp commit b67c5654078c5d690193f0ab7fede006d6f68353 Author: Dan Graves Date: Thu Mar 30 10:52:30 2017 -0700 committing some temporary stuff so I can merge with development branch Tests/GeometryShop/sphereEBISBox/sphere.inputs commit 77607a636f7dd139ab785fb2e98c681c645b463e Author: Dan Graves Date: Thu Mar 30 10:51:52 2017 -0700 committing some temporary stuff so I can merge with development branch Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H commit 8ebc00999c1832d8a74d5747fc220859a8387724 Author: Dan Graves Date: Thu Mar 30 10:49:23 2017 -0700 starting adding multi-level EB objects into EBAMRTools layer Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBPWLFineInterp.H Src/EBAMRTools/AMReX_EBPWLFineInterp.cpp Src/EBAMRTools/Make.package commit 147c45d32513989dd892eef21b4236ee17db2d6c Author: Weiqun Zhang Date: Wed Mar 29 13:12:05 2017 -0700 add FabArray::setDomainBndry Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H commit 3d46ebe92e3595813bcabb429b6c58bb8d1ee1af Author: Weiqun Zhang Date: Wed Mar 29 12:24:19 2017 -0700 To avoid confusion, remove nodal flag from FabArray constructor. Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_FabArray.H Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/Particle/AMReX_TracerParticles.cpp Tutorials/MultiColor_C/main.cpp commit ae888a2cd71c667c678f8c1bbe8efd17210a1048 Merge: fb86f9728 680a53c4f Author: Michele Rosso Date: Thu Mar 30 13:27:31 2017 +0000 Merged in mrosso84/amrex/regtest_fix (pull request #17) Fix regtest bug for builds using cmake Approved-by: Michael Zingale commit fb86f9728bb61668f69350d89df1f54079fb596e Author: Weiqun Zhang Date: Wed Mar 29 21:05:12 2017 -0700 make clean: rm dSYM directory Tools/GNUMake/Make.rules commit 680a53c4fc35c3545a36fc03cf176124624d5d82 Author: Michele Rosso Date: Wed Mar 29 17:37:25 2017 -0700 Fix regtest bug for builds using cmake Tools/RegressionTesting/suite.py commit c9cad1e7f11e917abc3ddfb92ea8e36c7d430630 Author: Dan Graves Date: Wed Mar 29 14:27:28 2017 -0700 one more bug fix Src/GeometryShop/AMReX_EBISLevel.cpp commit 09fae1d08e259be05dc8238a43c1aa2ead3d7300 Merge: 7d33c4aef 943815a99 Author: Michele Rosso Date: Wed Mar 29 18:22:36 2017 +0000 Merged in mrosso84/amrex/cmake-mpi-build (pull request #15) Cmake mpi build commit e012bede7b6077a2a72a3f67115520688a082aeb Author: Dan Graves Date: Wed Mar 29 10:09:59 2017 -0700 needed to recompute normals and boundary areas after copies (otherwise they can be wrong at box boundaries) Src/GeometryShop/AMReX_EBData.cpp commit aa8b40bf0307c509e92c679410ea4d1b415d7761 Author: Dan Graves Date: Tue Mar 28 15:46:30 2017 -0700 after many bug fixes, I got an actual test that uses EBISLayout and EBIndexSpace and everythign to run correctly. Src/Base/AMReX_Box.H Src/Base/AMReX_DistributionMapping.cpp Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/sphereEBISBox/sphere.inputs commit 1e50e1acd9c6413d0289e600a4c46fdbe884f2f4 Author: Dan Graves Date: Tue Mar 28 11:41:12 2017 -0700 this unholy union is proceeding according to our fiendish plan Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/sphereEBISBox/Make.package Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit e9696c092363bf393eff03fc5cc8c477a4888237 Author: Dan Graves Date: Mon Mar 27 15:56:08 2017 -0700 I added a first test for the new classes Tests/GeometryShop/sphereEBISBox/GNUmakefile Tests/GeometryShop/sphereEBISBox/Make.package Tests/GeometryShop/sphereEBISBox/sphere.inputs Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit d2df4f995b817656843b5377b47f815d570f15e9 Author: Dan Graves Date: Mon Mar 27 13:04:47 2017 -0700 everything compiles, off to testing the core stuff Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit 7d33c4aefdeea6621400b8e9944b772a68c21bcf Author: Weiqun Zhang Date: Sat Mar 25 11:06:58 2017 -0700 put temp build directory d/ o/ f/ into tmp_build_dir/ .gitignore Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 54fcf02225f6e8b863d64de616701ebfc262377c Author: Dan Graves Date: Fri Mar 24 15:56:48 2017 -0700 lots of progress but still many compilation errors. Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_SPMD.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/GeometryShop/Make.package commit 5456060baaffceb240f5f9f8c654a52bb728225a Author: Weiqun Zhang Date: Fri Mar 24 13:06:45 2017 -0700 add num_multifabs back, but wrap them inside BL_MEM_PROFILING Src/Base/AMReX_MultiFab.cpp commit 4d28672aa1e94ead342966ad8db9a383681ba812 Merge: bea2d9158 108750a3b Author: Weiqun Zhang Date: Fri Mar 24 13:00:47 2017 -0700 Merge branch 'dtg_branch' into development commit 108750a3b537b58d4555ab74dc3eefd17a09eb20 Author: Dan Graves Date: Fri Mar 24 11:43:02 2017 -0700 But wait, there's more! Now EBISLevel has many fewer communication stages in coarsening! Now how much would you pay? Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp commit bea2d915809c28ed6c467b21891a426d2d54424b Merge: 7dea03d8d a7fb2815a Author: Weiqun Zhang Date: Fri Mar 24 11:00:07 2017 -0700 Merge branch 'development' into weiqun/split_fabarray commit 7dea03d8db7b0d31d773493b9dead96fe8d923cb Author: Weiqun Zhang Date: Fri Mar 24 10:58:12 2017 -0700 update AmrData Src/Extern/amrdata/AMReX_AmrData.cpp commit ce5905ee0110e1d566bbc1bb491962348d227a50 Author: Weiqun Zhang Date: Fri Mar 24 10:01:09 2017 -0700 update cmake Src/Base/CMakeLists.txt commit a1cd520f7836a264972d744e5e192fc9d1be7d93 Author: Dan Graves Date: Thu Mar 23 18:51:15 2017 -0700 redesign of EBISLevel::coarsenVoFs. Now with fewer temporaries and communications. Not available in stores. Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp commit a7fb2815a4c15addfa143287a33e4803cd7c7164 Author: Weiqun Zhang Date: Thu Mar 23 17:12:36 2017 -0700 make mpi-2 happy by const_cast Src/Base/AMReX_ParallelDescriptor.H commit b4a390e44763778197a9db4e5439163aee2b490b Author: Weiqun Zhang Date: Thu Mar 23 16:29:34 2017 -0700 more on splitting FabArray Src/Amr/AMReX_StateData.H Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFCopyDescriptor.H Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/Make.package commit 8191d1a4ecda06808c8749ae1b3594170705e4f7 Author: Weiqun Zhang Date: Thu Mar 23 13:05:19 2017 -0700 change how gfortran library is linked Tools/GNUMake/comps/gnu.mak commit 0bf2623b554b7f241841aed0f80cdb91fd1fb522 Author: Weiqun Zhang Date: Thu Mar 23 11:05:30 2017 -0700 split off MFIter Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/Make.package commit 05302eec84131d986eb6b30939173c8a7406eba1 Author: Weiqun Zhang Date: Thu Mar 23 10:55:42 2017 -0700 split off FabArrayBase Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/Make.package commit af2844275dc6495906f72a694f7fb94dbfbb329f Merge: b327acfe1 ab1eb9f66 Author: atmyers Date: Thu Mar 23 10:53:01 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit b327acfe1a8fe7ca174cb9e719e32a08f8278fcb Author: atmyers Date: Thu Mar 23 10:52:44 2017 -0700 move the num local tiles function to ParticleContainer. Src/Particle/AMReX_Particles.H commit ab1eb9f66d0f7a3f57a0cafefd7222f438c4f3cf Author: Weiqun Zhang Date: Thu Mar 23 09:08:16 2017 -0700 make: strip the whitespace around DIM to make the make system more robust Tools/GNUMake/Make.defs commit e7e59a718f894f0f8b495f65bba4c0464ac65d65 Author: atmyers Date: Wed Mar 22 16:55:43 2017 -0700 Add a function ParIter to return the total number of tiles. Src/Particle/AMReX_Particles.H commit a849417c2ac92c785063bf3ff6b3c09e03bae2fe Author: Dan Graves Date: Wed Mar 22 15:03:57 2017 -0700 still pretty deep in the weeds over here Src/Base/AMReX_Box.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_SPMD.cpp commit 943815a9944cdd1a172e5a13f098929eb6116ccc Author: Michele Rosso Date: Wed Mar 22 13:50:55 2017 -0700 Fix cmake mpi-enabled build. Tools/CMake/FindCCSE.cmake commit 82ea10329c5c0b76ea9fdc3fd75c631334f6ed60 Author: Dan Graves Date: Tue Mar 21 16:16:11 2017 -0700 slogged my way through EBIndexSpace and EBISLayout--some minor redesign (and some major cleanup) from the Chombo versions Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp commit 77e414d7c946619afd62a7a404285f9eb0bac150 Author: Michele Rosso Date: Tue Mar 21 14:44:34 2017 -0700 Remove all references to PETSc and X11. Tools/CMake/FindCCSE.cmake commit 6f026b24ed9b2e404c66ffaef95cc4ba13a3a7a2 Author: Michele Rosso Date: Tue Mar 21 13:31:51 2017 -0700 Replace "BOXLIB" with "AMREX" in CMake variables name. Src/Base/CMakeLists.txt Src/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 35561e1f01302d0c7f6daeb377d23bdd49127d8e Merge: 5aafb61b3 0d4cb177c Author: Weiqun Zhang Date: Tue Mar 21 13:16:08 2017 -0700 Merge branch 'fortran_interface' into development commit 0d4cb177c7bcbc4b00f2093cc642fa91bb39c2e7 Author: Weiqun Zhang Date: Tue Mar 21 13:15:30 2017 -0700 fixe memory leaks Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90 commit 7d6cea2729397a2a0212a4252ea2979ee8ff99af Author: Weiqun Zhang Date: Tue Mar 21 12:47:45 2017 -0700 fix reflux due grids coveed by fine do not have fluxes computed Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 commit 5674cdf80104470a2178a2bc1cbc120492a6c7a6 Author: Weiqun Zhang Date: Tue Mar 21 11:17:35 2017 -0700 tidy Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 commit 7cd3779ccfbb396182f4330fb513cad0f5ffea0f Author: Weiqun Zhang Date: Tue Mar 21 11:03:55 2017 -0700 add octree iterator Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90 commit 4feee626cd17ea6116eee4a411aec11d063ab4b0 Author: Weiqun Zhang Date: Tue Mar 21 08:35:43 2017 -0700 build octree leaf nodes Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 commit 5aafb61b3e042a8072898b0095c2e470b5faf61a Author: Weiqun Zhang Date: Tue Mar 21 08:28:52 2017 -0700 add a new MFIter::tilebox takes nodal IntVect flag Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit d441bd0f3e94755b1ee2a400e55a64d4b7d3c9e1 Author: Weiqun Zhang Date: Mon Mar 20 12:48:12 2017 -0700 add F_Interfaces/Octree Src/AmrCore/AMReX_AmrCore.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Src/F_Interfaces/Octree/Make.package Tutorials/AMR_Adv_CF_octree/Exec/Make.Adv Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_CF_octree/Source/fmain.F90 commit 17e7cb92c3a54f362a2b1bba00b587c73ed336cb Author: Dan Graves Date: Mon Mar 20 11:00:07 2017 -0700 EBData, EBISBox, and PolyGeom all compile now. On to writing more tests. Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_PolyGeom.cpp commit 02f16e6995a845ee2ab31473fbbb92032cb254c9 Author: Weiqun Zhang Date: Mon Mar 20 08:46:43 2017 -0700 AMR_Adv_CF_octree: no subcycling Tutorials/AMR_Adv_CF/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF_octree/Exec/Make.Adv Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF_octree/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/plotfile_mod.F90 commit e2199418d91142d5db5a85bc9abaf9ff54c9f84e Merge: b58e95927 d15eac8e9 Author: Michael Zingale Date: Fri Mar 17 20:34:23 2017 -0400 Merge branch 'development' of ssh://bitbucket.org/berkeleylab/AMReX into development commit b58e95927fcbf68fd4e7bfc8f0f45f9b454adfa7 Author: Michael Zingale Date: Fri Mar 17 20:34:14 2017 -0400 don't need FCOMP for C++ codes Tools/RegressionTesting/suite.py commit d15eac8e930b75162ce020556a077c8561a9fe2b Merge: d59d6343a 7daaee09e Author: Michele Rosso Date: Fri Mar 17 23:59:58 2017 +0000 Merged in mrosso84/amrex/cmake-regtest (pull request #14) Enable AMReX regression testing tools to build using CMake. commit 40a6543b734f08b5b2c2eee8f45ee0c893139cb6 Author: Dan Graves Date: Fri Mar 17 16:02:49 2017 -0700 finished EBData/EBISBox/PolyGeom transition --- still working on getting it all to compile Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/Make.package commit 7daaee09e606e6eb602b21a3ae0e3f56c90f6678 Author: Michele Rosso Date: Wed Mar 15 13:52:59 2017 -0700 Enable AMReX regression testing tools to build using CMake. Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit d3357a446e6750a31ad77c439d89d54306f3fa2c Author: Weiqun Zhang Date: Fri Mar 17 12:35:40 2017 -0700 start Tutorials/AMR_Adv_CF_octree Tutorials/AMR_Adv_CF_octree/Exec/Make.Adv Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_CF_octree/README Tutorials/AMR_Adv_CF_octree/Source/Make.package Tutorials/AMR_Adv_CF_octree/Source/Src_2d/Make.package Tutorials/AMR_Adv_CF_octree/Source/Src_2d/advect_2d_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/Src_2d/compute_flux_2d.f90 Tutorials/AMR_Adv_CF_octree/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_CF_octree/Source/amr_data_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/bc_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/fmain.F90 Tutorials/AMR_Adv_CF_octree/Source/initdata.F90 Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/plotfile_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/tagging_mod.F90 commit 3b3d4f198aea3c520cf21aa221f90e09bd871562 Author: Weiqun Zhang Date: Fri Mar 17 12:12:59 2017 -0700 allow blocking factor greater than max_grid_size Src/AmrCore/AMReX_AmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp commit d59d6343ab570b41793b04964ace57e8584cff80 Merge: 4b66112b5 a6c7e4fa3 Author: Weiqun Zhang Date: Thu Mar 16 14:56:48 2017 -0700 Merge branch 'fortran_interface' into development commit a6c7e4fa3bd8e088c638b973742bac4ae7700261 Author: Weiqun Zhang Date: Thu Mar 16 14:55:57 2017 -0700 add some assertions to fortran amrcore Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp commit f18af0a1d010e8a280463cf14353ce56be89da6b Author: Weiqun Zhang Date: Thu Mar 16 14:55:31 2017 -0700 assert blocking factor is not too small relative to ref_ratio Src/AmrCore/AMReX_AmrCore.cpp commit d02032d38043fe41b2888eafcaa60c470be03c94 Author: Weiqun Zhang Date: Thu Mar 16 13:59:14 2017 -0700 add string version of amrex::Abort, Warning and Error Src/Base/AMReX.H Src/Base/AMReX.cpp commit 4b66112b5319f8883fc3cdcab965fd2e40bc28d2 Author: Andrew Myers Date: Thu Mar 16 09:45:06 2017 -0700 fixing the Nyx restart test. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H commit fea84d328e8a0c5a7aab10d7439f6540b36b6f16 Merge: 05f820e07 ff24069df Author: Weiqun Zhang Date: Thu Mar 16 08:27:34 2017 -0700 Merge branch 'fortran_interface' into development commit a2cb8a1c842c3b304561255c2c1ae3d9a383c5ad Author: Dan Graves Date: Wed Mar 15 16:06:25 2017 -0700 progress made on EBData (and I took it out of the make.package in case people want to compile this branch) Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/Make.package commit ff24069df64855d28b8198244c23b83abecdc909 Author: Weiqun Zhang Date: Wed Mar 15 15:03:45 2017 -0700 cleanup Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 commit 13a2a0ee37bc49b9fbecd7d5be5121e01ecbd928 Author: Weiqun Zhang Date: Wed Mar 15 14:52:43 2017 -0700 make some variables in fortran geometry static Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 8a60b84b823f1cd9a4a28a3cf88608138496d92c Author: Weiqun Zhang Date: Wed Mar 15 13:59:20 2017 -0700 simplify the regrid logic Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit fe43208d22ce1e6884793340649d955a8658c888 Author: Weiqun Zhang Date: Wed Mar 15 12:22:26 2017 -0700 comments Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 05f820e07016ba944d62e703053fa9799ec9d6a4 Author: atmyers Date: Wed Mar 15 12:15:08 2017 -0700 increment particle version string. Src/Particle/AMReX_ParticleI.H commit 8243f3d5f167092f52eda88deb2ae34fd6567d36 Author: Dan Graves Date: Tue Mar 14 16:13:41 2017 -0700 starting the long slog of redesigning ebdata Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/Make.package commit 52e9f2f833fdded272445c205a25fc8f50630732 Author: Weiqun Zhang Date: Tue Mar 14 16:02:27 2017 -0700 add Fortran fillcoarsepatch and tweak the test problem to test teh new functionality Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF/Source/tagging_mod.F90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 2ee27b21bf9ca39682fe741e435db63057a8cee2 Author: Weiqun Zhang Date: Tue Mar 14 14:14:06 2017 -0700 add a new regression test inputs Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs.rt commit afca0741e5248b6a085d18df75cec0131f326769 Author: Weiqun Zhang Date: Tue Mar 14 14:12:32 2017 -0700 fix a bug in fortran fillpatch Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 commit 6356ffa50e8a0c8a0dedb7b998567891cf7bbbe4 Merge: 608e11bbd 1e22bdbef Author: Weiqun Zhang Date: Tue Mar 14 13:23:46 2017 -0700 Merge branch 'fortran_interface' into development commit 1e22bdbef58fa51a80e1acdfe29b3e647fea8628 Merge: c3e72f638 232da81b6 Author: Weiqun Zhang Date: Tue Mar 14 13:23:08 2017 -0700 Merge branch 'development' into fortran_interface commit 608e11bbdc713d3098c37caaab44f0b877f06b1d Merge: 4eff9e1c3 864458fd5 Author: Michele Rosso Date: Tue Mar 14 20:16:28 2017 +0000 Merged in mrosso84/amrex/cmake-installation-fix (pull request #13) Fix issue with Tools not being copied to installation dir. commit 864458fd58b5925af99baabe248e4afa1425c475 Author: Michele Rosso Date: Tue Mar 14 13:09:20 2017 -0700 Fix issue with Tools not being copied to installation dir. Src/CMakeLists.txt commit f0439c248c9b693d9eceba49fe58753cf8982374 Author: Dan Graves Date: Tue Mar 14 13:08:10 2017 -0700 sparse data tests pass now Src/GeometryShop/AMReX_BaseIVFABI.H commit 4eff9e1c3801598070cd7920005a262399ccd93a Author: Michael Zingale Date: Tue Mar 14 15:27:42 2017 -0400 PGI explicitly needs libatomic to link Tools/GNUMake/comps/pgi.mak commit 1da21811a0b62e6ab20163552c68dbaf45d5ee88 Merge: 232da81b6 48b076b36 Author: Michael Zingale Date: Tue Mar 14 16:04:28 2017 +0000 Merged in mzingale/amrex/development (pull request #8) some reporting fixes commit 7b814fa67a4c2d786247a8e9555996df455a007d Author: Dan Graves Date: Mon Mar 13 14:29:13 2017 -0700 got sparse, distributed data test to run to complettion but still failing one of the tests Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFab.cpp Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFactory.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFactory.H Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp commit 232da81b625c4f33c2aa5178b4ca5304787f8595 Merge: 1c307e220 5bff9218a Author: Michele Rosso Date: Mon Mar 13 16:44:58 2017 +0000 Merged in mrosso84/amrex/cmake-regtest (pull request #12) Fix CMake dependencies issue. commit 5bff9218aea70da20f8a92b93fcd4a82140dda59 Author: Michele Rosso Date: Fri Mar 10 16:44:35 2017 -0800 Fix CMake dependencies issue. Src/Amr/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/Particle/CMakeLists.txt commit 1c307e220e2601c12000003ba50660b565484eb1 Merge: c7f847d2c e8631de77 Author: Ray Grout Date: Sat Mar 11 21:40:35 2017 +0000 Merged in regtest_for_gitlabci (pull request #11) Adjust regtest script to allow empty branch and return number of failures as exit code commit e8631de77cb50abab7c059b8edf69ed8e78cef20 Merge: ea53e9028 c7f847d2c Author: Ray Grout Date: Sat Mar 11 12:01:30 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into regtest_for_gitlabci commit ea53e90283c5ebee1f59af1ed232681c5852bf36 Author: Ray Grout Date: Sat Mar 11 12:01:07 2017 -0700 Adjust regtest script to allow empty branch and return number of failures as exit code Tools/RegressionTesting/regtest.py commit c7f847d2ce7caff1039da009dbd395af6196fc07 Author: atmyers Date: Sat Mar 11 09:33:24 2017 -0800 explicitly mark these methods as override. Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_MultiFab.H commit a1829c85603f81781cef3f384717a40ac6c706c4 Author: atmyers Date: Sat Mar 11 08:20:27 2017 -0800 fix GetArrayData function. Src/Particle/AMReX_ParticleContainerI.H commit 4841df8bbbe92b1c79b91082213d459e17fb7f08 Author: Max Katz Date: Sat Mar 11 01:19:57 2017 -0500 Add a CUDArena memory management system using CUDA UM CUDA Unified Memory (available for NVIDIA GPUs of the Kepler generation or newer) allows a single pointer to point to a region of memory that can live either on the CPU or the GPU, and switches back and forth on demand. This is done by declaring a managed memory allocation using cudaMallocManaged, a drop-in replacement for malloc. The CUDArena as currently written is a drop-in replacement for BArena. Credit for the name and original idea belong to Brian Friesen. Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CUDArena.H Src/Base/AMReX_CUDArena.cpp Src/Base/Make.package commit 3919163643b2ffad987f368667dc09618cccf0bb Author: Max Katz Date: Sat Mar 11 01:12:37 2017 -0500 Allow C/C++ builds with nvcc using USE_CUDA This replaces the CC/CXX executable with nvcc, and sets the nvcc host compiler to what was previously set there (based on COMP). Tools/GNUMake/Make.defs commit 3c8e997c2e281d85d511552a1b2a92434f6ff003 Merge: 48329b0a4 ba8669a64 Author: atmyers Date: Fri Mar 10 21:43:48 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 48329b0a41b880c119589def505112378a90f024 Author: atmyers Date: Fri Mar 10 21:43:37 2017 -0800 Adding methods for getting the SoA data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ba8669a648fcccb440dde7f4238db061a4bbc034 Merge: b57d05636 a3df796ec Author: Andrew Myers Date: Fri Mar 10 15:43:24 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit b57d05636864994dfb31fc4e384fd5fc3f6987a5 Author: Andrew Myers Date: Fri Mar 10 15:43:09 2017 -0800 Adding fortran CIC interpolation function. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/inputs Tests/Particles/AssignMultiLevelDensity/main.cpp commit a3df796ec9a60f95683884c58cf3d19c555f75a9 Author: Weiqun Zhang Date: Fri Mar 10 15:08:59 2017 -0800 have to initialize the data otherwise it may crash due to fpe Src/Boundary/AMReX_FabSet.cpp commit c3e72f6382e029145eadbcff366532542043abb9 Author: Weiqun Zhang Date: Thu Mar 9 16:20:12 2017 -0800 AMR_Adv_v2: finished reflux Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit f2aec04eac26df872c2e9f17c182fe3f6dda55a9 Author: Weiqun Zhang Date: Thu Mar 9 14:17:48 2017 -0800 fix a bug I introduced when FillBoundary was modified a few days ago Src/Base/AMReX_FabArray.cpp commit 46b83dbbb5476e649d298793d82f152b8a3c0bc3 Author: Weiqun Zhang Date: Thu Mar 9 14:00:20 2017 -0800 AMR_Adv_CF: start to add flux register Tutorials/AMR_Adv_CF/Source/amr_data_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 1e0dd1a5167a6ce1e1a261a4f8a78cfb7947af77 Author: Weiqun Zhang Date: Thu Mar 9 11:10:38 2017 -0800 add fluxregister module Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 Src/F_Interfaces/AmrCore/Make.package commit 36e8da52db69b15cbac8d44c98a40a959f03c979 Author: Weiqun Zhang Date: Thu Mar 9 10:25:17 2017 -0800 AMR_Adv_CF runs Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 4087e3a4347f714a7817f6e471fcb25a178f7788 Author: Weiqun Zhang Date: Thu Mar 9 10:20:33 2017 -0800 fix fortran index Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 commit 7f09a48e862bbc92145beffa33838684bd6116f2 Author: Weiqun Zhang Date: Thu Mar 9 10:11:43 2017 -0800 refactor fillpatch module Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/amr_data_mod.F90 Tutorials/AMR_Adv_CF/Source/bc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 362204271ac20a1c1ffd9c88be5914ecf3581360 Author: Weiqun Zhang Date: Wed Mar 8 18:10:45 2017 -0800 wip: need to fix circular dependency of fortran modules Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit 545425f68c48ffed52780e32c502d2a9c3951bba Merge: 781c66099 4815f4f02 Author: Dan Graves Date: Wed Mar 8 15:33:31 2017 -0800 Merge branch 'development' into dtg_branch commit 4526bf0663e7b0835aa7e51ceaedb1ec1785517b Author: Weiqun Zhang Date: Wed Mar 8 14:44:39 2017 -0800 wip Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 781c66099728f9aa78c96b7c5c9e8656a8cbbacc Author: Dan Graves Date: Wed Mar 8 14:39:13 2017 -0800 sparse data holders pass single grid test Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/Make.package Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile Tests/GeometryShop/sparseDataSingleGrid/Make.package Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp Tests/GeometryShop/sparseDataSingleGrid/sphere.inputs commit fd52f4cc6885923557e2ac44ec141f084d57fe0d Author: Weiqun Zhang Date: Wed Mar 8 11:53:32 2017 -0800 add more virtual functions Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 4815f4f0276590035cfc0dd9c8991b91b63b4db9 Author: Weiqun Zhang Date: Wed Mar 8 10:38:21 2017 -0800 do a const_cast in make_aliase Src/Base/AMReX_BaseFab.H commit 692b8e6ab3ff29d7e82d1d6add587eee58e17dbc Merge: 5592fb7b5 12f6c1c94 Author: Weiqun Zhang Date: Wed Mar 8 09:59:49 2017 -0800 Merge branch 'development' into fortran_interface commit 12f6c1c9405352efb6581695a967a4f3baed57d7 Author: Andrew Myers Date: Tue Mar 7 16:39:50 2017 -0800 More fixes to the build system from Michele Rosso. Tools/CMake/FindCCSE.cmake commit 984e95ebbab2f14583eee1ce22a4cd9254686de2 Author: Dan Graves Date: Tue Mar 7 16:21:23 2017 -0800 added (as yet still untested) sparse data holders Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H commit 5349fe31bbe23df53931fc66647efcf166d1d6c0 Author: Andrew Myers Date: Tue Mar 7 14:41:50 2017 -0800 Fix CMake build stuff for AMReX. CMakeLists.txt Src/Amr/CMakeLists.txt Src/Base/CMakeLists.txt Src/CMakeLists.txt commit 8b3816ac97ce25e17cf875a191906bcbc036db1a Author: Dan Graves Date: Tue Mar 7 11:18:52 2017 -0800 after figuring out that FabArray and LevelData have somewhat different copy semantics, I was able to get FabArray to behave as advertised Src/GeometryShop/AMReX_EBGraph.cpp Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp commit 0aa8c2a687bb9430c1cdace845da00738dd0a657 Merge: aa20228c6 3a7758da2 Author: Ann Almgren Date: Tue Mar 7 11:07:45 2017 -0800 Merge branch 'development' of https://bitbucket.org/berkeleylab/amrex into development commit aa20228c6eb35d698218a8ff0827a5191c488ec8 Author: Ann Almgren Date: Tue Mar 7 11:07:17 2017 -0800 Change instances of BoxLib/boxlib/BOXLIB to AMReX/amrex/AMREX. This occurs only in cmake stuff and README* CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_Version.cmake Tools/CMake/PreprocessAMReXFortran.cmake Tools/CMake/PreprocessAMReXFortran90.cmake Tutorials/README_C Tutorials/README_F commit 3a7758da2bd287c4960910b7755fad402c31c501 Merge: 0e3403ff2 5931b3c74 Author: Andrew Myers Date: Mon Mar 6 17:17:18 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 0e3403ff229ff60e55b09413953aa5745c6f7e5d Author: Andrew Myers Date: Mon Mar 6 17:15:34 2017 -0800 Avoid redefined macro warning in AMReX_INTERP_1D.F Src/AmrCore/AMReX_INTERP_1D.F commit e23aa58aab899a5c4247de589de5bf1540a91a45 Author: Dan Graves Date: Mon Mar 6 16:16:25 2017 -0800 working on distributed graph Src/Base/AMReX_BaseFab.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_SPMD.cpp Src/GeometryShop/AMReX_SPMDI.H Tests/GeometryShop/ebgraphDistributed/GNUmakefile Tests/GeometryShop/ebgraphDistributed/Make.package Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphDistributed/sphere.inputs commit 5931b3c74b4db252076b8eb6604b6e15c6b0bc47 Author: Andrew Myers Date: Fri Mar 3 21:47:07 2017 -0800 Capture the return code of the analysis scripts in the test suite. Tools/RegressionTesting/regtest.py commit 8a2aa1edae821a9fbc85c682fca148d6d21f5861 Author: Andrew Myers Date: Mon Mar 6 13:54:22 2017 -0800 porting some changes to the CMake stuff from BoxLib to AMReX. CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 072aa45b9e3460192de61636babf93e8af4dc525 Merge: a3ae08c4c 99f41bf1e Author: Weiqun Zhang Date: Mon Mar 6 17:01:58 2017 +0000 Merged in development (pull request #9) Development commit 99f41bf1e214145d9cd4ac25f25184bda62f63a0 Merge: 73fb9d8cd 6f326d751 Author: Andrew Myers Date: Sun Mar 5 10:39:36 2017 -0800 Merge branch 'development' into particle_refactor commit 73fb9d8cd6f8273a54c75b60c7d40df774032ff6 Author: Weiqun Zhang Date: Sun Mar 5 07:35:05 2017 -0800 explicitly mark amrex_deposit_cic public Src/Particle/AMReX_Particle_mod_3d.F90 commit 33aaf75f2f4641218874fb0cb28c14ddadbc5b68 Author: Weiqun Zhang Date: Sun Mar 5 07:31:36 2017 -0800 merge SingleLevelWhere into Where Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt commit 6f326d7511c671fa90544db73e4f7f57891ef486 Author: Andrew Myers Date: Fri Mar 3 17:12:28 2017 -0800 Add my computer name to the list of CCSE machines. Tools/GNUMake/Make.machines commit e503389d12dd0f5df19968211f3b36165110eabf Merge: 4b3488970 c65ce4960 Author: Andrew Myers Date: Fri Mar 3 17:09:06 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit 4b34889700a311d7f678435fe8ccf678f31fd04b Author: Andrew Myers Date: Fri Mar 3 17:08:11 2017 -0800 Move the new deposition stuff to the fortran particle module. Src/Particle/AMReX_Deposition_F.F90 Src/Particle/AMReX_Deposition_F.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/Make.package commit c65ce4960f4c50a29c9ace6faf7b13c057115212 Author: Weiqun Zhang Date: Fri Mar 3 16:28:16 2017 -0800 fix an assertion and a static constexpr Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit b8038571f74710d88825db1e1b4f70cd6555d142 Author: Dan Graves Date: Fri Mar 3 14:52:51 2017 -0800 added linearization routines to EBGraph. On to seeing if I can get this to work with FabArray Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit 218a84d363f9b9382833515f35331a056c54ce0d Author: Andrew Myers Date: Fri Mar 3 12:38:25 2017 -0800 fixing restart. Src/Particle/AMReX_ParticleContainerI.H commit 7b7429d899d14467753a38484869ed53cc34c3ad Author: Andrew Myers Date: Fri Mar 3 11:10:51 2017 -0800 Making redistribute work when lev_min = lev_max (needed by virtual particles). Src/Particle/AMReX_ParticleContainerI.H commit 96bcdb916871cef729014fbb0421ad8a3498a194 Merge: 3970a4d5f 1c55eaa6a Author: Weiqun Zhang Date: Fri Mar 3 10:54:51 2017 -0800 Merge branch 'dtg_branch' into development Conflicts: Src/Base/AMReX_FabArray.H commit 3970a4d5f12251dd77b7940bab55507b9b7b9581 Author: Weiqun Zhang Date: Fri Mar 3 10:36:20 2017 -0800 fix conflict Src/Base/AMReX_FabArray.H commit b1777f7b192c10030fcfbe6a93c7c5c4f651926b Author: Weiqun Zhang Date: Fri Mar 3 09:53:13 2017 -0800 fix FillBoundary's cross option Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 389e2c6d63df3b3ac87a625bdfb32adbf25914fb Author: Weiqun Zhang Date: Fri Mar 3 08:33:23 2017 -0800 fix a new bug Src/Base/AMReX_FabArray.H commit b5122351ce4ba56e89490b30d2f945f5c6556ffe Author: Weiqun Zhang Date: Thu Mar 2 20:49:06 2017 -0800 fix some issues copyInter Src/Base/AMReX_FabArray.H commit c79184bcf0cc2615d849e406fd38b02bef36fa6f Author: Weiqun Zhang Date: Thu Mar 2 17:17:59 2017 -0800 modified FabArray's communication for EB Conflicts: Src/Base/AMReX_FabArray.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit e25c91a4edb5ba9e50500403f4b05438613fcffc Author: Weiqun Zhang Date: Mon Feb 27 17:12:23 2017 -0800 forgot a new file in last commit Src/Base/AMReX_FabFactory.H commit 5ff3db714c7ca145923c71299547623db86b3dc1 Author: Weiqun Zhang Date: Mon Feb 27 17:09:51 2017 -0800 add Fab factory; note that dynamic sidecar and FabArrayCopyDescriptor do not work with non-default factory Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 1c55eaa6a8b67a25aee64c73694c3750c0838c1b Merge: 224379f49 5186175f8 Author: Weiqun Zhang Date: Fri Mar 3 09:57:57 2017 -0800 Merge branch 'weiqun/mpibuffer' into dtg_branch commit 5186175f8d2387f05cc8133f970233dbd3789a6d Author: Weiqun Zhang Date: Fri Mar 3 09:53:13 2017 -0800 fix FillBoundary's cross option Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 68c2790d11a82fe5779aeed91b37bcf78e7d5c7a Author: Weiqun Zhang Date: Fri Mar 3 08:33:23 2017 -0800 fix a new bug Src/Base/AMReX_FabArray.H commit fd1f437b3ff76047bb43e993d1623ecaa1683e1c Author: Weiqun Zhang Date: Thu Mar 2 20:49:06 2017 -0800 fix some issues copyInter Src/Base/AMReX_FabArray.H commit 2c5625bb49544f47bcf95590a72374ed055d95da Author: Weiqun Zhang Date: Thu Mar 2 17:17:59 2017 -0800 modified FabArray's communication for EB Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 224379f498f8cd20c7dac55e7683c9b510c405ec Author: Dan Graves Date: Thu Mar 2 15:52:55 2017 -0800 ebgraph test now also tests coarsening Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp commit 7a78a2eba4bb0dfc888289aede7330f7ea8fdc0a Author: Dan Graves Date: Thu Mar 2 13:32:03 2017 -0800 EBGraph passes its first test Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp commit 026ece8f12e2bdf7f67e290b73a3d45b52a69e74 Author: Dan Graves Date: Wed Mar 1 16:12:20 2017 -0800 added a test for the graph Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile Tests/GeometryShop/ebgraphSingleGrid/Make.package Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/ebgraphSingleGrid/sphere.inputs commit e0407d1786fea70efec777768c431243b635918d Author: Andrew Myers Date: Wed Mar 1 14:49:49 2017 -0800 fix container resizing in redistribute Src/Particle/AMReX_ParticleContainerI.H commit fc4bb2877bfce1bf0b3d0d65ee6232cac99c86b3 Author: Andrew Myers Date: Wed Mar 1 13:42:51 2017 -0800 There is no need for a Where() call here. Src/Particle/AMReX_ParticleContainerI.H commit 33f920536fbf378f98549abf9eb41edf623fa606 Author: Andrew Myers Date: Wed Mar 1 13:04:55 2017 -0800 Have AddParticlesAtLevel clear the input container, as before. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit b080f2698a2ddf6619c6e2b47f86ed040ac86633 Author: Andrew Myers Date: Wed Mar 1 12:17:52 2017 -0800 Check whether we need to resize m_particles in AddParticlesAtLevel() Src/Particle/AMReX_ParticleContainerI.H commit 12c054148c0b6765ddcdd7be3e76834fcaeba22a Author: Andrew Myers Date: Wed Mar 1 11:13:10 2017 -0800 Rename here also. Src/Particle/AMReX_ParticleContainerI.H commit c879056e4be253cf0d1e12acd7759b1a44022760 Merge: 38f8bbfef ade2cf8f4 Author: Andrew Myers Date: Wed Mar 1 11:11:59 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit 38f8bbfef69a8b968ee85c9d6e0de36e62501505 Author: Andrew Myers Date: Wed Mar 1 11:11:47 2017 -0800 forgot to include this file. Src/Particle/AMReX_ParticleContainerI.H commit 7201b375c2858eaad42809415ec10aabef7478ed Author: Andrew Myers Date: Wed Mar 1 11:11:17 2017 -0800 Give the AddParticlesAtLevel function an nGrow argument. Src/Particle/AMReX_Particles.H commit ade2cf8f48bd5a694ff5e534ba60ddb32998172e Merge: e524336ff 97ea54b96 Author: Andrew Myers Date: Wed Mar 1 11:10:01 2017 -0800 merging commit e524336ff43e29032d2e32ab9581fe028206b18a Author: Andrew Myers Date: Wed Mar 1 11:08:23 2017 -0800 rename SingleLevelWhere and give it a default of 0 grow cells. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 4fc053676157354337948420a36609361b0b9345 Author: Dan Graves Date: Wed Mar 1 10:15:08 2017 -0800 I managed to wedge EBGraph into AMReX. Only missing the parallel communication stuff now. I can now start testing it. Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_SPMD.H Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/GeometryShop/Make.package commit 97ea54b9606fc0f63e5042634711147b6adedb05 Merge: 615a12dd3 379fe78a1 Author: Weiqun Zhang Date: Wed Mar 1 09:23:02 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor Conflicts: Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 615a12dd382293da78d9ad2a66b4f85857b23afe Author: Weiqun Zhang Date: Wed Mar 1 09:18:25 2017 -0800 add functions to get/set particle positions Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 379fe78a120ed0d8fec949daabc0204b7270909f Author: Andrew Myers Date: Tue Feb 28 18:05:34 2017 -0800 remove unused variable. Src/Particle/AMReX_ParticleInit.H commit 229880b0c5de2196a38365e96e32272052fe7c90 Author: Andrew Myers Date: Tue Feb 28 18:05:08 2017 -0800 Fix an assertion. Src/Particle/AMReX_ParticleContainerI.H commit 0df8cb3caaf9585f0fce67d849a5c2da2326a60a Merge: d37ae41bd 7e9c88cce Author: Andrew Myers Date: Tue Feb 28 17:46:28 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit d37ae41bd83eab5131f9b546ae2e6e311e838a72 Author: Andrew Myers Date: Tue Feb 28 17:27:42 2017 -0800 update advection tutorial to use the new form of Redistribute() Tutorials/AMR_Adv_C/Source/Adv.cpp commit 37f71f072aa4dd3980fd21902a08e2811cbac64f Author: Andrew Myers Date: Tue Feb 28 17:25:34 2017 -0800 Making the new particle data structures work with Nyx. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit ae376527defd9291de4078e64fe7d62b1b6991fd Author: Andrew Myers Date: Tue Feb 28 17:23:54 2017 -0800 Fix a bug in an assert. Src/Base/AMReX_MultiFabUtil.cpp commit cdc636747a9deb855ccb2685b558b1b0634bb550 Author: Weiqun Zhang Date: Tue Feb 28 15:13:53 2017 -0800 renaming Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit ad3791edda0b3b78354a519bbe336d66527874cf Author: Dan Graves Date: Tue Feb 28 14:51:36 2017 -0800 added more of the components of EBGraph---I had forgotten how complicated this stuff is Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_SPMD.H Src/GeometryShop/AMReX_SPMD.cpp Src/GeometryShop/AMReX_SPMDI.H Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Src/GeometryShop/Make.package commit 7e9c88ccebf5a5fa0ccdddb3ee61160582116d7e Author: Weiqun Zhang Date: Tue Feb 28 13:59:42 2017 -0800 fix an assertion Src/Base/AMReX_MultiFabUtil.cpp commit 4cfeecd9de6139a719ea39cd2de38e313db39c07 Author: Weiqun Zhang Date: Tue Feb 28 13:57:16 2017 -0800 add some push_back and access functions Src/Particle/AMReX_Particles.H commit 48b076b3623ef34f48621f036a52c4aa412d9ad7 Author: Michael Zingale Date: Tue Feb 28 10:27:39 2017 -0500 handle the reporting for when no benchmark is found. Also don't get confused by variable names that start with diff Tools/RegressionTesting/test_report.py commit c37619c79941fad2ce79a429bc32e30c8148f8ce Author: Weiqun Zhang Date: Mon Feb 27 17:12:23 2017 -0800 forgot a new file in last commit Src/Base/AMReX_FabFactory.H commit 47b59d49318059f4de9c7db55477bc07ff411110 Author: Weiqun Zhang Date: Mon Feb 27 17:09:51 2017 -0800 add Fab factory; note that dynamic sidecar and FabArrayCopyDescriptor do not work with non-default factory Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 33fa4eb4e5cddb10509288f7de132bf2b709a119 Author: Andrew Myers Date: Mon Feb 27 14:12:40 2017 -0800 minor. Src/Particle/AMReX_ParticleContainerI.H commit 7fc361ff7f95988ffa98ffaed27f173c76f21261 Author: Andrew Myers Date: Mon Feb 27 13:52:42 2017 -0800 Use fancy new helper functions to access the particle data pointer, instead of doing it manually. Src/Particle/AMReX_ParticleContainerI.H commit 62d10e42a15e9e5fe0b0454f63500b631111eb97 Merge: 57c0052b8 458f4adc9 Author: Andrew Myers Date: Mon Feb 27 12:22:40 2017 -0800 merging. commit 57c0052b83ff4e6040796c58491a91a286d59f22 Author: Andrew Myers Date: Mon Feb 27 12:21:00 2017 -0800 Also call average_down at the end of AssignDensityFort Src/Particle/AMReX_ParticleContainerI.H commit eac127acd756f8af8917c44ab3b31b7fc8ec2d06 Author: Andrew Myers Date: Mon Feb 27 12:20:06 2017 -0800 An extra sanity check for the sum_fine_to_coarse function. Src/Base/AMReX_MultiFabUtil.cpp commit 118201af7495b64f7fd7b793455a0329d8dea5b8 Author: Dan Graves Date: Mon Feb 27 11:38:33 2017 -0800 keeping up with the development branch--some fortran stuff had changed names. Also, fortran declarations need to be in amrex namespace. Also, moved some files from test directory to Src/GeometryShop. Stuff compiles again Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_BaseIndex.H Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_Stencils.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Src/GeometryShop/Make.package Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H Tests/GeometryShop/stencilTestbed/src/Make.package Tests/GeometryShop/stencilTestbed/src/lapl_nd.F90 Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H commit b0926c9fd72506b56f3e158cb55f16dd239a244b Author: Dan Graves Date: Mon Feb 27 10:37:03 2017 -0800 paring this down to the minimum number of files because I am about to add a bunch more Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp commit 458f4adc972eae7e9752f84b779097d91e37e9de Author: Weiqun Zhang Date: Mon Feb 27 09:11:00 2017 -0800 add a new IntVect::operator== for comparing IntVect with int, and fix an out of bound problem Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil.cpp commit c2bc83c3a7e78a63d21ba18c4794a941909764f5 Author: Andrew Myers Date: Fri Feb 24 16:22:56 2017 -0800 quick bug fix to TotalNumberOfParticles in parallel. Src/Particle/AMReX_ParticleContainerI.H commit 982ae05ccb7b364415e6f39a9e281a24ef61965a Author: Dan Graves Date: Fri Feb 24 15:55:02 2017 -0800 bug fix for flat plate Src/GeometryShop/AMReX_FlatPlateGeom.cpp commit 44edd4d479e89cdc58c4ec63cb843d49a1f5db58 Author: Dan Graves Date: Fri Feb 24 15:10:54 2017 -0800 got flat plate geometry working as far as I have tested it Src/GeometryShop/AMReX_FlatPlateGeom.cpp Tests/GeometryShop/flatPlate/GNUmakefile Tests/GeometryShop/flatPlate/Make.package Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/flatPlate/flatplate.inputs commit ad4d34fc4b47abaa8f105b33d407b11917762bbe Author: Andrew Myers Date: Fri Feb 24 13:46:24 2017 -0800 Also write out the extra integer components. Src/Particle/AMReX_ParticleContainerI.H commit 328e173848980ec4560ce930cf2e39518ea93a9e Author: Andrew Myers Date: Fri Feb 24 13:32:25 2017 -0800 Also write out whether this is a checkpoint format particle file or not. Src/Particle/AMReX_ParticleContainerI.H commit 65d9cef9ffdb021442e8f8adebc4ba3a1f25b654 Author: Andrew Myers Date: Fri Feb 24 13:08:52 2017 -0800 Add ability to specify particle component names for IO. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tests/Particles/AssignMultiLevelDensity/main.cpp commit 8fa744dcac7e40efec7aa3e9ad7883571d3125fe Merge: a3c9800cb 92ec13d40 Author: Andrew Myers Date: Fri Feb 24 10:57:35 2017 -0800 merging. commit a3c9800cb748b07a438d4938b0e07381b96ebe8a Author: Andrew Myers Date: Fri Feb 24 10:35:23 2017 -0800 rewrite the multi-level charge deposition code. Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Particle/AMReX_Deposition_F.F90 Src/Particle/AMReX_Deposition_F.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/AssignDensity/GNUmakefile Tests/Particles/AssignDensity/Make.package Tests/Particles/AssignDensity/inputs Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/GNUmakefile Tests/Particles/AssignMultiLevelDensity/Make.package Tests/Particles/AssignMultiLevelDensity/inputs Tests/Particles/AssignMultiLevelDensity/main.cpp Tutorials/PIC_C/GNUmakefile commit 02c921186749e46e0b7a3029ed9f66dadf96318d Author: Tan Nguyen Date: Thu Feb 23 23:10:02 2017 -0800 just used this version to test castro, and no bug was found Tools/typechecker/typeChecker.py commit e452ab58bc357bac1416dc944a9f3e340119b703 Merge: 101b039b2 e5e4dbde0 Author: atmyers Date: Thu Feb 23 17:35:15 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development merging # the commit. commit 101b039b25fd294e8512a96458bb0e19da9e5e9c Author: atmyers Date: Thu Feb 23 17:34:48 2017 -0800 Fixing a bug in the PIC_C tutorial pointed out by Matthias Frey. Tutorials/PIC_C/two_level.cpp commit faf106e858d575368ccd31579eb87b31546ea9e7 Author: Andrew Myers Date: Thu Feb 23 17:30:25 2017 -0800 Fixing a bug in the PIC_C tutorial pointed out by Matthias Frey. Tutorials/PIC_C/two_level.cpp commit 4d852e613c7bba4be86f4a1bc94b146d54945eda Author: Dan Graves Date: Thu Feb 23 16:11:04 2017 -0800 made some progress on flat plate goem. trickier than I thought (story of my life) Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/Make.package commit f388df0202457298fd9eed78b38314da83b8bda4 Merge: 9b502a104 e5e4dbde0 Author: Dan Graves Date: Thu Feb 23 09:08:06 2017 -0800 Merge branch 'development' into dtg_branch commit b7683d4fadf3d16ddb33ec5ed9493e1a9b1339c9 Author: Tan Nguyen Date: Wed Feb 22 18:42:01 2017 -0800 type checker can handler C++ input Tools/typechecker/typeChecker.py commit 92ec13d407f7df24b262d6b64a4008ca15fa47ce Author: Weiqun Zhang Date: Tue Feb 21 16:59:38 2017 -0800 Particle: merge two maps into one Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit da9c145bfa7f5ef19e35bd63cbe10d624baf414e Author: Weiqun Zhang Date: Tue Feb 21 09:45:31 2017 -0800 no need to reset dummy mulitfab if the boxarray and distribution map do not change Src/Particle/AMReX_ParticleContainerI.H commit d9973cd9ee6325e343b36b00c870d56b03f20089 Author: Weiqun Zhang Date: Tue Feb 21 09:32:54 2017 -0800 remove the where_already_called flag from Redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tutorials/AMR_Adv_C/Source/Adv.cpp commit d6d965258321f1a991749983730d5765b2d5f315 Author: Weiqun Zhang Date: Mon Feb 20 10:49:49 2017 -0800 update AmrParticleContainer Src/AmrCore/AMReX_AmrParticles.H commit fb666db52d432cea93cbaa1f75ce8e837a685179 Author: Weiqun Zhang Date: Mon Feb 20 10:26:29 2017 -0800 ParticleContainer::GetParticles --> GetAoSMap; add GetSoAMap Src/Particle/AMReX_Particles.H commit 0bfa46b9e1946bfe8de6649d9e152670e9bd84b2 Author: Weiqun Zhang Date: Mon Feb 20 10:17:26 2017 -0800 define dummy multifab in resizeData Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d546c2d1a1b0c811ba1856dd60c4dcc37be28145 Author: Weiqun Zhang Date: Mon Feb 20 07:52:16 2017 -0800 add ParticleContainer::MakeMFiter that returns a normal MFIter Src/Particle/AMReX_Particles.H commit 77140c59fada962d481985c5389744e33c4dd88b Author: Weiqun Zhang Date: Mon Feb 20 07:43:57 2017 -0800 fix typo Src/Particle/AMReX_Particles.H commit 0ca667ea8ae2a2c792b4edc4a12d0d9a84b2e060 Author: Weiqun Zhang Date: Mon Feb 20 07:26:59 2017 -0800 add a few functions to ParticleContainer for convenience Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 1dda880bf1e7cfe9aff4500b907aba39981fedea Author: Weiqun Zhang Date: Sun Feb 19 15:43:59 2017 -0800 ParIter: skip tiles that do not exist in maps Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 9acaeebf989777b009f805cc964af844b74332af Author: Weiqun Zhang Date: Sun Feb 19 15:17:02 2017 -0800 Make sure [] will insert a new item to the map even when SoA has no data, otherwise erase may fail Src/Particle/AMReX_ParticleContainerI.H commit 6afd20a2a064e5d3279ee0b58fe5fa2b4203d9c9 Author: Weiqun Zhang Date: Sun Feb 19 15:15:09 2017 -0800 add const to MFIte::isValid() Src/Base/AMReX_FabArray.H commit 82ff020a1500ec7d75644d0d50fa76a156f17393 Author: Weiqun Zhang Date: Sun Feb 19 12:07:56 2017 -0800 Particle Iterator: rename Src/Particle/AMReX_Particles.H commit d73a0df391a5f4bee4a51ba68fb481c63bd5b3a3 Author: Weiqun Zhang Date: Sun Feb 19 10:16:47 2017 -0800 add class ArrayOfStructs Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 66c37f3887e7311f221512790335f3d9121c77dd Author: Weiqun Zhang Date: Sat Feb 18 16:34:37 2017 -0800 rm the iterator get functions for a single component to avoid being called repeatedly; one can always get the whole data and access each component. some other minor changes Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d6fad844e1256a1a755a157e46c9211efc6d7866 Author: Weiqun Zhang Date: Sat Feb 18 12:40:35 2017 -0800 add ParIter Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.H commit 2214a79bbdce5d253a044ce23d4e38c5f6fa091e Author: Weiqun Zhang Date: Sat Feb 18 11:32:48 2017 -0800 add static assertion the size of particle is a multiple of the size of real Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d0f3c6bf49b19d075817d7dbc25f66f6febbb16f Author: Weiqun Zhang Date: Sat Feb 18 11:30:37 2017 -0800 typo Src/Particle/CMakeLists.txt commit fd935b99e53e5e2838d06c7e92dbb89e45442391 Merge: 9ed4a3b6c a3b443ac8 Author: Andrew Myers Date: Fri Feb 17 16:48:40 2017 -0800 merging. commit 9ed4a3b6c6b2f4db9fc76f2361dd4dd3e34a1da2 Author: Andrew Myers Date: Fri Feb 17 16:45:05 2017 -0800 Faster particle deposition routines. Src/Particle/AMReX_Deposition_F.F90 Src/Particle/AMReX_Deposition_F.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit a3b443ac8bc123d5e62e2d82ee879649916e4818 Merge: 18c195334 e5e4dbde0 Author: Weiqun Zhang Date: Fri Feb 17 15:43:45 2017 -0800 Merge branch 'development' into particle_refactor commit e5e4dbde01b51e65b11af19a31674656175295c4 Author: Weiqun Zhang Date: Fri Feb 17 15:42:55 2017 -0800 de-virtualize some BoxArray functions Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 6636822e84d02e0ca851015e4e328be8cdbd5c41 Author: Weiqun Zhang Date: Fri Feb 17 14:49:48 2017 -0800 add amrex::Print::SetPrecision Src/Base/AMReX_Print.H commit 18c195334ea85dd706191a6ee399cb229da5581b Author: Weiqun Zhang Date: Fri Feb 17 14:51:24 2017 -0800 tweak locateParticle to handle particles right on domain boundary Src/Particle/AMReX_ParticleContainerI.H commit 4bd158a8f8eb3f90fa57c451bd0180923bd8cb8d Author: Weiqun Zhang Date: Fri Feb 17 14:49:48 2017 -0800 add amrex::Print::SetPrecision Src/Base/AMReX_Print.H commit 4b7e5e394d5e97ddc4c263ae2779d65d2baf7aaa Author: Weiqun Zhang Date: Fri Feb 17 13:33:42 2017 -0800 refactor OK() Src/Particle/AMReX_ParticleContainerI.H commit 9a4319c62759d4d279d51aa87c5a24c3200a048e Author: Weiqun Zhang Date: Fri Feb 17 13:28:22 2017 -0800 refactor OK and locateParticle Src/Particle/AMReX_ParticleContainerI.H commit ca40440e80d9f807990519d1cb98fc772fb7e504 Author: Weiqun Zhang Date: Fri Feb 17 12:15:18 2017 -0800 fix SingleLevelGrownWhere Src/Particle/AMReX_ParticleContainerI.H commit 34c03b8d227d5d0d0d7c6006563508d1446b57e4 Author: Weiqun Zhang Date: Fri Feb 17 10:50:30 2017 -0800 refactor Where and OK Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit c8070cbb19f8a0ea256718bcd58e864fd929c10b Author: Weiqun Zhang Date: Fri Feb 17 09:53:21 2017 -0800 rm single level where Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit ccf00b6a7d2e58da00b4423fd32b2a9097ea81f7 Author: Weiqun Zhang Date: Fri Feb 17 08:54:56 2017 -0800 minor optimization Src/Particle/AMReX_ParticleContainerI.H commit adae91af12176b615c1877546d8ac4d3d1dfa16d Merge: 56ef14662 d76ec1c90 Author: Andrew Myers Date: Thu Feb 16 13:14:22 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit 56ef1466236bbde99b62e1e286eb7b1c0cd82815 Author: Andrew Myers Date: Thu Feb 16 13:13:59 2017 -0800 Implementing particle restart for the advection test. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv_io.cpp commit d76ec1c9025994427002e8c4cd543af62f1677cf Merge: 222dcc247 dbfc42d8b Author: Weiqun Zhang Date: Thu Feb 16 10:50:47 2017 -0800 Merge branch 'development' into particle_refactor commit 222dcc247a63b7075a1021c80cc24dae0420c8cf Author: Weiqun Zhang Date: Thu Feb 16 10:19:14 2017 -0800 make the particle tiling consistent with MFIter tiling Src/Base/AMReX_FabArray.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 20dbfcdead7ae61ca7995ea68e95b96bcc883202 Author: Weiqun Zhang Date: Thu Feb 16 09:29:37 2017 -0800 optimization of Where Src/Particle/AMReX_ParticleContainerI.H commit b424e405a37ff7ac2f19c37c3abd1e65a3eb7e6b Author: Andrew Myers Date: Thu Feb 16 09:34:58 2017 -0800 also read the extra int information from checkpoint files. Src/Particle/AMReX_ParticleContainerI.H commit 5107af27e6d17435a80395bcbbbcb4bcd1b8e363 Author: Andrew Myers Date: Wed Feb 15 20:14:38 2017 -0800 cleaning up the particle restart routines. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 9b502a104130fb00f4ade65c5f4fa5539d10a9ca Author: Marc Day Date: Wed Feb 15 19:20:55 2017 -0800 Fix up MSD version of stencil test again. Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp commit 3988e9aef5b7b8b4e0ecf0a6e1b6ef0e8ef09544 Merge: aa72f1ef6 46635b718 Author: Andrew Myers Date: Wed Feb 15 17:46:53 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging commit aa72f1ef67cf501c926011bc5e15300c333fa14e Author: Andrew Myers Date: Wed Feb 15 17:46:25 2017 -0800 Remove duplicate versions of ReadParticles by using a template function. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 46635b718ef33d095c702b2b1abb6b93acc3a2aa Author: Weiqun Zhang Date: Wed Feb 15 17:01:08 2017 -0800 need to test for nullptr Src/Particle/AMReX_ParticleContainerI.H commit 4f26057b5b8a4a2bfafd1130572c8b253680f55f Author: Weiqun Zhang Date: Wed Feb 15 16:55:57 2017 -0800 add dummy multifabs to particle container Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit ca0f86fcd81087dbd256021c346346979922e4f2 Author: Weiqun Zhang Date: Wed Feb 15 15:47:37 2017 -0800 add tilebox and gridbox to particle location data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 8bedf58e7aaddd832c0da2c9744108683b7dcadd Author: Weiqun Zhang Date: Wed Feb 15 15:24:46 2017 -0800 Where: optimization Src/Particle/AMReX_ParticleContainerI.H commit 8e8e24de9f9405c7919823cd71b0f8fda9aa8cfa Author: Andrew Myers Date: Wed Feb 15 16:16:00 2017 -0800 This reference can't be const, as this function updates the particles. Src/Particle/AMReX_ParticleContainerI.H commit dae67a4f7af6c6e2f6b16a2021a7db01975ab7ce Author: Andrew Myers Date: Wed Feb 15 15:12:48 2017 -0800 Add the SoA data to the restart routines Src/Particle/AMReX_ParticleContainerI.H commit 9e6f661802425365bb28001abf80d014e1ebedcf Author: Marc Day Date: Wed Feb 15 13:00:44 2017 -0800 Fix the mess I made in the stencilTest folder...still messy, but correct. Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_F.H Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H commit 9c95d917caaa6b817f9354bd4c022600a58f99c4 Author: Weiqun Zhang Date: Wed Feb 15 11:06:41 2017 -0800 add a static Initialize function to ParticleContainer Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit daa0585923477eca9f31d60b3f268eb902a5ef44 Author: Weiqun Zhang Date: Wed Feb 15 10:53:44 2017 -0800 minor Src/Particle/AMReX_ParticleContainerI.H commit 6ac5d1e5d9af665b5ad2cec92a6c072c4f9e27e1 Author: Weiqun Zhang Date: Wed Feb 15 10:46:03 2017 -0800 fix assertion Src/Particle/AMReX_ParticleContainerI.H commit 987266663f6ab7c49e8775ef8f84db4061325a0f Author: Weiqun Zhang Date: Wed Feb 15 10:43:13 2017 -0800 update tutorial because of the interface of Redistribute Tutorials/AMR_Adv_C/Source/Adv.cpp commit c7aee617f6bc8becbe4ab0841f10987d764fe012 Author: Weiqun Zhang Date: Wed Feb 15 10:31:18 2017 -0800 refactor Redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 85a49bd07870478abfdee9c79ad57a851be9c54d Author: Marc Day Date: Tue Feb 14 18:43:09 2017 -0800 Add logic to shift bc interp stencil to avoid extrapolations and more smoothly continue with sign changes of the normal components. Not sure if this has a direct analogue in 3d yet. Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 commit a7fa5dfc782a4d76665e1a9865a1fd2eb4bd051e Author: Weiqun Zhang Date: Tue Feb 14 17:29:43 2017 -0800 fix last commit Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 8fb4e9854356e1effb731f4f525576bdd92f2364 Author: Weiqun Zhang Date: Tue Feb 14 17:02:10 2017 -0800 clean up and add a test for trivally copyable Src/Particle/AMReX_ParticleContainerI.H commit 4da2c4583a7a60a1024d10b768bd543d8e5ef5a7 Author: Weiqun Zhang Date: Tue Feb 14 16:56:19 2017 -0800 Assertion on pointers obtained with c type cast won't work. Src/Particle/AMReX_ParticleContainerI.H commit 5364daddf19a98a2870b782e1a0cb57a535832a1 Author: Weiqun Zhang Date: Tue Feb 14 16:48:40 2017 -0800 minor Src/Particle/AMReX_ParticleContainerI.H commit 23de4ae531a3081bcf15f41cdaea69f1a5a43fcf Author: Weiqun Zhang Date: Tue Feb 14 15:58:13 2017 -0800 add where_already_called option to Redistribution Src/Particle/AMReX_ParticleContainerI.H commit a85d42dc28ea56c276be37efa46806ee5e1124bd Author: Marc Day Date: Tue Feb 14 15:21:02 2017 -0800 Nearly trivial hack to stencil Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/dirichletTest_F.H commit e68558361c35c040c5e6b77df27d3ddcf5daa61e Author: Weiqun Zhang Date: Tue Feb 14 15:06:13 2017 -0800 remove SoA data too Src/Particle/AMReX_ParticleContainerI.H commit af18c48c5fdfa4f745cf4f9f111fc13e3945f9c3 Author: Weiqun Zhang Date: Tue Feb 14 14:56:49 2017 -0800 remove some duplicated code Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit bdefc0095cb3d82c080f1e580d4b6b258dc244d9 Author: Weiqun Zhang Date: Tue Feb 14 14:28:27 2017 -0800 some cout --> Print() Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit e480193c7166aa0ab221026b0f9f2374361a84ab Author: Weiqun Zhang Date: Tue Feb 14 13:27:13 2017 -0800 add some optional argument for skipping mpi reduction Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d8a7866b32ac2ee7276ba2c554d162976313d536 Author: Weiqun Zhang Date: Tue Feb 14 13:05:35 2017 -0800 add some optional argument for skipping mpi reduction Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 323e5c2cdde23b2c03e058cb64c15e4593d29fbf Author: Weiqun Zhang Date: Tue Feb 14 12:46:39 2017 -0800 add SoA to ByteSpread Src/Particle/AMReX_ParticleContainerI.H commit 93d8f872e26fb113609ff388b1a2298c515a6a03 Author: Weiqun Zhang Date: Tue Feb 14 12:41:08 2017 -0800 fix a bug: when tiling is on, we may visit a grid multiple times Src/Particle/AMReX_ParticleContainerI.H commit a15c1923915b13c361fca3f0388d4690afe59cc3 Author: Weiqun Zhang Date: Tue Feb 14 12:25:45 2017 -0800 forgot #ifdef; use unique_ptr Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp commit 2167cbcc40464241e2b8189baa73d4fa60f58cc9 Author: Weiqun Zhang Date: Tue Feb 14 12:19:13 2017 -0800 unroll a loop Src/Particle/AMReX_ParticleContainerI.H commit bd0838a647be08f8d3cc59d54fb9ecf36e7845b8 Author: Marc Day Date: Tue Feb 14 09:49:19 2017 -0800 Minor mod to stencil test. Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 commit 554b81623e2211f71e855aea271d2932b7936de6 Author: Marc Day Date: Tue Feb 14 09:46:24 2017 -0800 Working on EB stencil stuff, pushing WIP Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/dirichletTest_F.H Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H commit c0989b8bb41a2dd2770ecd541d30ee42fd257f47 Merge: 065a74b3a 9fb55cee1 Author: Andrew Myers Date: Mon Feb 13 16:29:48 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit 065a74b3a39d54366be26cc088d3c34c15264d12 Author: Andrew Myers Date: Mon Feb 13 16:29:25 2017 -0800 remove redundant Where() call Src/Particle/AMReX_ParticleContainerI.H commit 9fb55cee131aa0bcd661cdca94e1f89fffb904e3 Author: Weiqun Zhang Date: Mon Feb 13 15:46:07 2017 -0800 take a shortcut in Where Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 35fbfc60f22b93f866c53036b8970f584f79ac7f Author: Andrew Myers Date: Mon Feb 13 14:33:28 2017 -0800 Initialize the communicate_comp member properly Src/Particle/AMReX_Particles.H commit 5428aad5aab4c87215b6634ad6bc8a9ae838dbdf Merge: cc966b2f6 c73751ecb Author: Andrew Myers Date: Mon Feb 13 14:12:36 2017 -0800 Merging. commit cc966b2f6460f05b72afd40e731b5bbff20d0dbc Author: Andrew Myers Date: Mon Feb 13 13:57:53 2017 -0800 Some renaming for clarity. Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit c73751ecbae61818dcbaae2065b0599a4a944c9f Author: Weiqun Zhang Date: Mon Feb 13 13:41:14 2017 -0800 rm using std::make_pair from headers Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 90ee02bb1cd74ef7803ddf69418cdccaf889faff Author: Weiqun Zhang Date: Mon Feb 13 13:02:58 2017 -0800 use std::vector instead of built-in array because zero size built-in array is not allowed Src/Particle/AMReX_Particles.H commit 1a8f35be36f051a06ead10705baedce8e4fc9582 Author: Weiqun Zhang Date: Mon Feb 13 12:45:33 2017 -0800 minor changes for consistence Src/Particle/AMReX_Particles.H commit 48d4c8a8b4356ba2514f332ced5390a146def74d Author: Weiqun Zhang Date: Mon Feb 13 12:43:21 2017 -0800 use amrex::Array instead of std::vector in some places Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 826fa8674e927a782f6da787180f9d27dd736e9d Author: Weiqun Zhang Date: Mon Feb 13 12:25:17 2017 -0800 fix omp race conditions Tutorials/AMR_Adv_C/Source/Adv_advance.cpp commit e4f34c03519a29bc80b0f4d0b8e04aa36b4eaf4e Author: Weiqun Zhang Date: Mon Feb 13 12:24:41 2017 -0800 delete particle container Tutorials/AMR_Adv_C/Source/Adv_setup.cpp commit 55dbe14ca6828eb755e77952e95662e604039ccc Author: Weiqun Zhang Date: Mon Feb 13 11:17:04 2017 -0800 rename to avoid confusion Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 90982cf05f2445d00174e664cbd0c37083d5e316 Author: Weiqun Zhang Date: Mon Feb 13 10:38:49 2017 -0800 CoordSys: bcast inv_dx and set default inv_dx to infinity Src/Base/AMReX_CoordSys.cpp commit 5592fb7b51f152fdb6689b5e2e640a03b0037c68 Author: Weiqun Zhang Date: Thu Feb 9 21:52:42 2017 -0800 AMR_Adv_CF: multiple levels without regridding works Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit b994d7f62a33e8363bde00ed3237d93a682a3c2f Author: Weiqun Zhang Date: Thu Feb 9 17:09:15 2017 -0800 add amrex_bc_types_module and fillpatch from two levels Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Src/F_Interfaces/Base/AMReX_bc_types_mod.F90 Src/F_Interfaces/Base/Make.package commit 1f37d6f4dd7cf1f5830b780acb039bb55cc20838 Merge: c6a2860bc dbfc42d8b Author: Tan Nguyen Date: Thu Feb 9 16:28:32 2017 -0800 resolve a confict when merging dev to check_fortran commit 2cbde3dcecda5c1f31e48bd75ecc80b0511a7592 Author: Weiqun Zhang Date: Thu Feb 9 15:35:28 2017 -0800 AMR_Adv_CF: add clear level function Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/Make.package Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 4283ccfcb574fd0c1d29a40d121e08ebb19cc7ec Author: Weiqun Zhang Date: Thu Feb 9 15:33:35 2017 -0800 add amrex_interpolater_module Src/F_Interfaces/AmrCore/AMReX_interpolater_mod.F90 commit 49cd87ac6c80b1cd9d7c2a3a40436477e4906f1b Author: Andrew Myers Date: Thu Feb 9 13:34:56 2017 -0800 Also write out the SoA data to the plt files. Src/Particle/AMReX_ParticleContainerI.H commit 4598948b0eb952c812d6fdd214b921c3b194b609 Author: Andrew Myers Date: Thu Feb 9 11:38:14 2017 -0800 Updating the AMR_Adv_C tutorial to optionally use tracer particles. Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp commit 0c3cca12782bfc40fd2cdfa4e1817c551025eaef Author: Andrew Myers Date: Thu Feb 9 11:37:07 2017 -0800 Updating the tiled particles to use a pair-indexed map. Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tests/Particles/main.cpp commit 716858a07ba3a2dae43445186491339840a2cf40 Author: Weiqun Zhang Date: Thu Feb 9 10:53:55 2017 -0800 AMR_Adv_CF: works for single level now Src/F_Interfaces/Base/AMReX_box_mod.F90 Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_CF/Source/Src_2d/Make.package Tutorials/AMR_Adv_CF/Source/Src_2d/advect_2d_mod.F90 Tutorials/AMR_Adv_CF/Source/Src_2d/compute_flux_2d.f90 Tutorials/AMR_Adv_CF/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit cbc0274d5af97069169b6a4356ba09f325697c88 Author: Weiqun Zhang Date: Thu Feb 9 10:14:08 2017 -0800 fix box type for amrex_mfiter Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 8cc0940db330473c9c8d0502851d3c0de54dbcef Author: Weiqun Zhang Date: Thu Feb 9 09:52:48 2017 -0800 AMR_Adv_CF: get face velocity Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit 3ff7485bbe6f58970bd24994bd8539064ff5a2e2 Author: Weiqun Zhang Date: Thu Feb 9 09:40:16 2017 -0800 simplify amrex_print Src/F_Interfaces/Base/AMReX_box_fi.cpp Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_mod.F90 commit 07082172b850b6ddcccd4ff9c095f5898343a315 Author: Weiqun Zhang Date: Thu Feb 9 09:30:33 2017 -0800 add nodal flag to amrex_box Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 76841906e4cb469b10b4eca9c136895ce342122a Author: Weiqun Zhang Date: Thu Feb 9 08:56:56 2017 -0800 clean up by using fab%resize Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Tutorials/AMR_Adv_CF/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 commit f88cce56f934439f56f87ff1d4628205077da5c0 Author: Weiqun Zhang Date: Wed Feb 8 21:05:32 2017 -0800 more amrex fab procedures Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 9b71209227cfe56c331c5562c93288e565cfcc6f Author: Weiqun Zhang Date: Wed Feb 8 17:04:34 2017 -0800 start amrex_fab_module Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit 929805eb07b5a5b88b12f0c5b21f0ab8a2be13ed Author: Weiqun Zhang Date: Wed Feb 8 16:50:52 2017 -0800 add amrex prefix to mempool functions Src/Base/AMReX.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_mempool_f.f90 Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/fab.f90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit 12afca58d02454e1c69c38ed21d76abceca84592 Author: Weiqun Zhang Date: Wed Feb 8 15:38:29 2017 -0800 add generic assignment for tagboxarray Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 19bfe7a683c09f311524b78f6ebe8fabfab9021b Author: Weiqun Zhang Date: Wed Feb 8 15:32:27 2017 -0800 define some amrex function interfaces a user code must provide Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/Base/AMReX_physbc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit e5a556bc08c124853289dddf43c62fe148bc8dcf Author: Weiqun Zhang Date: Wed Feb 8 14:44:06 2017 -0800 add amrex_fillpatch_single Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Src/F_Interfaces/AmrCore/Make.package Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit 7c6e78ed3ca0fed374ca6be5ab9d86f258bf15f9 Author: Weiqun Zhang Date: Wed Feb 8 14:12:35 2017 -0800 add physbc Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_physbc_fi.cpp Src/F_Interfaces/Base/AMReX_physbc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 544a50fc5a15cbd58519fca17302670d52d86319 Author: Weiqun Zhang Date: Wed Feb 8 12:49:25 2017 -0800 rename for consistence Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/Make.package Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 28199fda86e6573058f3c1b22a1929d6c167b153 Author: Weiqun Zhang Date: Wed Feb 8 12:40:04 2017 -0800 add AMReX_FPhysBC Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_FPhysBC.cpp Src/F_Interfaces/Base/AMReX_physbc_fi.cpp Src/F_Interfaces/Base/AMReX_physbc_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit c6a2860bcce8893bac42f38082bdb627596e9927 Author: Tan Nguyen Date: Wed Feb 8 11:56:25 2017 -0800 update type checker Tools/typechecker/typeChecker.py commit 33a304c7c95e45b9136d51aba9f66fede5e8ec61 Author: Tan Nguyen Date: Wed Feb 8 11:52:01 2017 -0800 fix a few fortran headers Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_INTERP_F.H Src/Base/AMReX_COORDSYS_F.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H commit 2d68a817ec613db42c6d03d026e09e14fb37e6ed Author: Weiqun Zhang Date: Wed Feb 8 10:21:31 2017 -0800 call regrid Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF/Source/plotfile_mod.F90 commit af33b94564691d6d76f64eb0e660bd6b9d89ee57 Author: Weiqun Zhang Date: Wed Feb 8 08:54:28 2017 -0800 change how amrex_mpi_real is initialzied Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 68fbcc9ca7188ddfaf6e797c2e99129e1411f953 Author: Weiqun Zhang Date: Tue Feb 7 20:40:55 2017 -0800 mpi_amrex_real --> amrex_mpi_real Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 63792fc9142d4a830dc540b54c23a9eb34e0fdcb Author: Weiqun Zhang Date: Tue Feb 7 17:09:39 2017 -0800 add recursive timestep function Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit 172fd516a7b219ae3360768587b910837841a7f8 Author: Weiqun Zhang Date: Tue Feb 7 17:01:18 2017 -0800 add some parallel reduce functions Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 679cb91d75f20a218976e6d059a6ff00022a6eef Author: Weiqun Zhang Date: Tue Feb 7 16:17:38 2017 -0800 implement compute dt Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_CF/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit ce432452203d70b5faeae4cc890021ff97eabcf7 Author: Weiqun Zhang Date: Tue Feb 7 14:33:23 2017 -0800 move geometry array into amrex_famrcore module Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF/Source/plotfile_mod.F90 commit b8d8223b3e2c2c8e4e9f7aac363a1821b4eef2b7 Author: Weiqun Zhang Date: Tue Feb 7 14:26:59 2017 -0800 add evolve module Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/fmain.F90 commit 5e5cf7c3a90e4a2708e63443daec1b5161d5841b Author: Weiqun Zhang Date: Tue Feb 7 14:23:36 2017 -0800 add missing use module Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 8c90bec9b98ba578fd741a378638c5497d4559f8 Author: Weiqun Zhang Date: Tue Feb 7 14:22:48 2017 -0800 add implicit none to interface blocks Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 84b9272b4dc5386580206d6e7e585052a5c7ec17 Author: Weiqun Zhang Date: Tue Feb 7 14:17:08 2017 -0800 add multifabutil module Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_multifabutil_fi.cpp Src/F_Interfaces/Base/AMReX_multifabutil_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/initdata.F90 commit e01ca0d84e03347e379a7bf7c5c8e8dbfd85cdfe Author: Weiqun Zhang Date: Tue Feb 7 13:48:58 2017 -0800 write plotfile Src/Base/AMReX_string_mod.F90 Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_fi.cpp Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp Src/F_Interfaces/Base/AMReX_plotfile_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/error_estimate_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF/Source/plotfile_mod.F90 Tutorials/AMR_Adv_CF/Source/tagging_mod.F90 commit b3d799ce2ae5583d265354b66da2a80e5834c356 Author: Weiqun Zhang Date: Tue Feb 7 11:10:10 2017 -0800 finish error estimate module for the example Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Tutorials/AMR_Adv_CF/Source/error_estimate_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 022eb2ad39a3f287ab6f41d8937b1e01bead04eb Author: Weiqun Zhang Date: Tue Feb 7 10:42:03 2017 -0800 add getarr and queryarr for int and real Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 commit dbfc42d8b7069edb55de9aeffeefabcf2ef4cc21 Author: Weiqun Zhang Date: Tue Feb 7 09:08:13 2017 -0800 fix extra argument Src/Base/AMReX_BaseFab_nd.f90 commit 840d36e3fe4228e058fb184207499e42c7d8dbc9 Author: Weiqun Zhang Date: Tue Feb 7 09:04:43 2017 -0800 rename amrex_module to amrex_base_module Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_fi_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/HeatEquation_EX1_CF/advance.f90 Tutorials/HeatEquation_EX1_CF/fmain.f90 Tutorials/HeatEquation_EX1_CF/init_phi.f90 Tutorials/HelloWorld_CF/fmain.f90 commit 315d278f5bc39f5ca6c92f286ba3c6132a04caba Author: Weiqun Zhang Date: Tue Feb 7 08:56:48 2017 -0800 add amrex_tagbox_module Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/AmrCore/Make.package Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 6dd01b47da73cbbe9039a6d02e92f0b8f35b598e Author: tannguyen Date: Tue Feb 7 03:39:25 2017 -0800 first version of the static type checker Tools/typechecker/pycparser/__init__.py Tools/typechecker/pycparser/_ast_gen.py Tools/typechecker/pycparser/_build_tables.py Tools/typechecker/pycparser/_c_ast.cfg Tools/typechecker/pycparser/ast_transforms.py Tools/typechecker/pycparser/c_ast.py Tools/typechecker/pycparser/c_generator.py Tools/typechecker/pycparser/c_lexer.py Tools/typechecker/pycparser/c_parser.py Tools/typechecker/pycparser/ply/LICENSE Tools/typechecker/pycparser/ply/__init__.py Tools/typechecker/pycparser/ply/cpp.py Tools/typechecker/pycparser/ply/ctokens.py Tools/typechecker/pycparser/ply/lex.py Tools/typechecker/pycparser/ply/yacc.py Tools/typechecker/pycparser/ply/ygen.py Tools/typechecker/pycparser/plyparser.py Tools/typechecker/typeChecker.py commit 13e92b846e675b98fea7db8f7dd11ba0fe9fdf63 Author: Andrew Myers Date: Mon Feb 6 17:38:36 2017 -0800 Don't go through this if tiling is turned off. Src/Particle/AMReX_ParticleContainerI.H commit f54486a8011b1ad350d9c6c182c9e08621ef5ce8 Author: Weiqun Zhang Date: Mon Feb 6 16:42:07 2017 -0800 add imultifab and errorest Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/error_estimate_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 20eccfa7467dbe7487af5bed4e328b0fabde7e87 Merge: 65577edd0 886c677d8 Author: Andrew Myers Date: Mon Feb 6 15:11:22 2017 -0800 Merge branch 'development' of https://bitbucket.org/berkeleylab/amrex into particle_refactor merging with development. commit 886c677d86a58922306470367336aa4947e67e22 Author: Weiqun Zhang Date: Mon Feb 6 15:01:02 2017 -0800 start to support virtual functions in F_Interface Src/AmrCore/AMReX_AmrCore.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H commit 65577edd0fdc2698e41fdd4966ef805869e842c5 Author: Andrew Myers Date: Mon Feb 6 14:52:04 2017 -0800 Fixing a couple of tiling-related bugs. Src/Particle/AMReX_ParticleContainerI.H commit fadd68755cf1e45e63d3ae51c1a2eda841973b9e Author: Weiqun Zhang Date: Mon Feb 6 13:31:12 2017 -0800 fix typo Src/Amr/AMReX_Amr.H commit 3295fedfcaf4eacd4cc666a97097644ab14b1878 Author: Weiqun Zhang Date: Mon Feb 6 13:20:20 2017 -0800 add a few virtual functions to AmrCore Src/Amr/AMReX_Amr.H Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit c63ed87b150d211c27d8a1434f55121466d1264c Author: Andrew Myers Date: Mon Feb 6 12:41:56 2017 -0800 Adding tiling information to the particle location functions. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 73b40f726b31470f89af25d3997f0cc0f3f0dc54 Author: Andrew Myers Date: Mon Feb 6 11:27:39 2017 -0800 Moving many of the Particle static methods to the ParticleContainer class instead. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit b443940df7e274a42e20f570ed7fb2c7e211db58 Author: Andrew Myers Date: Mon Feb 6 10:12:20 2017 -0800 Restructure unpacking the particle data so we don't have to call Where twice. Src/Particle/AMReX_ParticleContainerI.H Tests/Particles/test.py commit f727599fc92060a1b5a197da3a9f3a74afcd9941 Author: Andrew Myers Date: Sun Feb 5 19:15:10 2017 -0800 Communicate the particle data in one MPI burst instead of two. Src/Particle/AMReX_ParticleContainerI.H commit b6c5c08d0426dc6ba652dd469c2ba47e0a92ff2b Author: Weiqun Zhang Date: Fri Feb 3 21:25:31 2017 -0800 update amrex_multifab_build Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 985b0b6ee960d05b64426120519f2d1bad4f4797 Author: Weiqun Zhang Date: Fri Feb 3 17:14:50 2017 -0800 build fine levels Tutorials/AMR_Adv_CF/Source/initdata.F90 commit c79e1d47d2ba80cf6b160659eebed6ea5e2b1c50 Author: Weiqun Zhang Date: Fri Feb 3 16:33:06 2017 -0800 add amrex_multifab_write Src/F_Interfaces/Base/AMReX_fi_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_vismf_fi.cpp Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_CF/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_CF/Source/initdata.F90 commit 79b3a9a91916d853485f503f6cb153e0f616d74a Author: Andrew Myers Date: Fri Feb 3 16:08:59 2017 -0800 Have the particle iterator inherit as much as possible from MFITer Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tests/Particles/ParticleIterator/main.cpp commit a589555de5c5b745640d8f94414e59da185b8dd6 Author: Andrew Myers Date: Fri Feb 3 15:57:20 2017 -0800 Allocating dummy multifabs in the particle container for helping with iteration. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit 2f6849002973ef7770cfe9fd08e1068c5b9ac243 Author: Weiqun Zhang Date: Fri Feb 3 15:13:28 2017 -0800 Add amrex_fi_module. It doesn't do anything now. But in the future we might do some fortran specific init and finalize stuff Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/initdata.F90 commit 752b58f1b8231223652f723615a3f831a42d771f Author: Andrew Myers Date: Fri Feb 3 15:06:28 2017 -0800 Adding a couple of useful tile-related methods to MFIter. Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 6d690045b3421d2a7af6cbffb91615ba6cbd7003 Author: Weiqun Zhang Date: Fri Feb 3 14:56:21 2017 -0800 make base level Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 96ef975de03260fdcc683be70bea81fe6994d9c1 Author: Weiqun Zhang Date: Fri Feb 3 13:36:13 2017 -0800 add some set functions Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 commit 43e7779db5a63e87114e0b43f4fa70f1326fa66d Author: Andrew Myers Date: Fri Feb 3 11:47:13 2017 -0800 update main particle test. Tests/Particles/main.cpp commit c62060150e651a9a0ad904f7e59542b8ac8c7da1 Merge: 7659ba1b3 da27df5e2 Author: Andrew Myers Date: Fri Feb 3 11:46:15 2017 -0800 Merge branch 'particle_refactor' of https://bitbucket.org/berkeleylab/amrex into particle_refactor merging. commit 7659ba1b3ae45edd9f0ddb0ff2297e68a24061c4 Author: Andrew Myers Date: Fri Feb 3 11:44:04 2017 -0800 Make the_next_id static member data of particle. Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_Particles.H commit da27df5e220ed93eb2ed08a0ed54114bade8934d Author: Weiqun Zhang Date: Fri Feb 3 10:48:54 2017 -0800 minor Src/Particle/AMReX_Particles.H commit efe4ca8363897a6d310449c2c40e11f2c45c3544 Author: Weiqun Zhang Date: Fri Feb 3 09:48:15 2017 -0800 fix cpu() and add const & version of some functions Src/Particle/AMReX_Particles.H commit 34e08d86fb7e172f9f99e4f3da7cc8d193e89dfb Author: Weiqun Zhang Date: Fri Feb 3 09:28:52 2017 -0800 some constexpr Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_Particles.H commit 363898f113da1c0737f6e10ba73ee40ff8bb1066 Author: Weiqun Zhang Date: Fri Feb 3 08:49:35 2017 -0800 mark some finalization procedures as impure elemental Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 72898b849c04e62fb0ce9642165605bf56dfa3fc Author: Andrew Myers Date: Thu Feb 2 17:43:27 2017 -0800 Allocate the appropriate data structures for the tiling case. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 9b35a9813180b46081561c51ff00aa06e81aa269 Author: Weiqun Zhang Date: Thu Feb 2 17:04:20 2017 -0800 need to clear the old level and update finest_level variable Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 16a6c875701c6f6c403dbe1810621d517e8d43f7 Author: Andrew Myers Date: Thu Feb 2 16:44:47 2017 -0800 Replacing the loops in the particle code with ones that use the tiling iterators. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tests/Particles/ParticleIterator/main.cpp commit 4b94cd59c6e08144958981c8afeebc5930bc2a7d Author: Weiqun Zhang Date: Thu Feb 2 16:24:26 2017 -0800 add amrex_print to box, boxarray and distromap modules Src/Base/AMReX_Print.H Src/F_Interfaces/Base/AMReX_box_fi.cpp Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/initdata.F90 commit f596029bf6f4d67163220255df5c3834347fdfdd Author: Weiqun Zhang Date: Thu Feb 2 15:13:15 2017 -0800 add some get functions Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit ea9b5a4fa05c7f62706504dc3166f52987df2fa7 Author: Andrew Myers Date: Thu Feb 2 14:01:44 2017 -0800 A tiling particle iterator that works in parallel. Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tests/Particles/ParticleIterator/main.cpp commit de96be0defaa9ddf3a85433445213de6a3635197 Author: Weiqun Zhang Date: Thu Feb 2 12:28:47 2017 -0800 amrex_famr_core: add static data Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit a8b51d679944ce26e80afa0cd267e2102b8cbc9e Author: Andrew Myers Date: Thu Feb 2 11:36:48 2017 -0800 Some renaming for clarity. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit a918a7074e9f93eac272372fa7fc9849ddf961f0 Author: Andrew Myers Date: Thu Feb 2 11:21:51 2017 -0800 Some work towards implementing tiling for the Particle Container. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 2b18516cf891f1a613e1c077611838a5bf2b5e33 Author: Weiqun Zhang Date: Thu Feb 2 10:52:44 2017 -0800 add amrex_error_module and call amrex_abort if amrex_mfiter assignment is called Src/Base/AMReX_error_fi.cpp Src/Base/AMReX_error_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/Base/AMReX_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit f8da60be689898c98d1c05f05adffceb9962f6e5 Author: Weiqun Zhang Date: Thu Feb 2 10:14:19 2017 -0800 define assignment operator for types containing c_ptr Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 9582a62229a77a39963a0dfa38871ea1a87f751b Author: Andrew Myers Date: Wed Feb 1 19:29:02 2017 -0800 Cleaning up the code a bit with some typedefs. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 5accc7978e088f891672abee59a36258e0bb971a Author: Andrew Myers Date: Wed Feb 1 19:16:42 2017 -0800 an iterator for doing tiling with particles and a test. Tests/Particles/ParticleIterator/GNUmakefile Tests/Particles/ParticleIterator/Make.package Tests/Particles/ParticleIterator/main.cpp commit 75522cc5e984389997749ab416c8756ea6518087 Author: Andrew Myers Date: Wed Feb 1 17:13:42 2017 -0800 don't need this data structure to store pointers. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit 0d3e6f28defe4a73fc44854c733b97b7ab041dac Merge: 5e6bccb22 ca7babcd0 Author: Weiqun Zhang Date: Wed Feb 1 17:07:55 2017 -0800 Merge branch 'development' into fortran_interface commit ca7babcd0e222bd1685e8639baeb57ea24897820 Author: Weiqun Zhang Date: Wed Feb 1 17:07:12 2017 -0800 fix BLBackTrace namespace issue Src/Base/AMReX_BLBackTrace.H commit 5e6bccb2249bca3cebdd49bf66e1066839155564 Author: Weiqun Zhang Date: Wed Feb 1 17:07:12 2017 -0800 fix BLBackTrace namespace issue Src/Base/AMReX_BLBackTrace.H commit 58910c843a438c19e03293aa75c309a1f0fac41f Author: Weiqun Zhang Date: Wed Feb 1 16:12:32 2017 -0800 WIP: F_Interfaces/AmrCore Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/Make.package Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/fmain.f90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile commit 2eb7d1fc2744d72112affdf4123acd8245b92bbf Author: Andrew Myers Date: Wed Feb 1 16:04:56 2017 -0800 No longer shift particles silently in add particle / initialization routines. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 7368263bb9ca8e9528b4cf82d34f6570d1e424f8 Author: Weiqun Zhang Date: Wed Feb 1 14:15:22 2017 -0800 fix HelloWorld_CF Tools/CompileTesting/compiletesting.py Tutorials/AMR_Adv_CF/README Tutorials/HeatEquation_EX1_CF/GNUmakefile Tutorials/HelloWorld_CF/GNUmakefile Tutorials/HelloWorld_CF/fmain.f90 commit 28a70d8856458a157812ffc28800a37cd5a51d15 Author: Andrew Myers Date: Tue Jan 31 12:55:28 2017 -0800 Make communicating SOA data optional. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/main.cpp commit a263a5e5f0814872e39b29d032cf0ef65d11b65b Author: Andrew Myers Date: Tue Jan 31 12:31:06 2017 -0800 Fix bug in initialization. Src/Particle/AMReX_ParticleInit.H commit d713e5d13dfa43119b3c06d07c807d9fdc052417 Author: Andrew Myers Date: Tue Jan 31 12:20:52 2017 -0800 Don't template on the particle container type. We always use std::vector. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.H commit 7b4bf85d4c95311d8fb86c69902548334926acaf Author: Andrew Myers Date: Tue Jan 31 10:25:09 2017 -0800 Making the SOA particle test use two levels. Tests/Particles/main.cpp commit fa47bebcf6b417cdea5adcd8932b76aa7d7ad485 Author: Andrew Myers Date: Mon Jan 30 17:01:22 2017 -0800 Make this zero by default. Src/Particle/AMReX_Particles.H commit 90c97943b4bb0742d7054b2fc9f856169c10c25e Author: Andrew Myers Date: Mon Jan 30 16:45:54 2017 -0800 Use zero SoA attributes by default. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/main.cpp Tests/Particles/test.py commit d8dc1b9807319faa19347eb6331d00d5708991f7 Author: Andrew Myers Date: Mon Jan 30 15:54:07 2017 -0800 Implementing MPI communication of struct-of-array style particle data and adding a test. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/GNUmakefile Tests/Particles/Make.package Tests/Particles/main.cpp Tests/Particles/test.py commit 0b7b9242a56e507050fb7321b385f550b608a943 Author: Weiqun Zhang Date: Mon Jan 30 14:54:28 2017 -0800 add --always to git describe as fallback. some codes may not have tags Tools/C_scripts/makebuildinfo_C.py commit c1c6ddd6d44e3a1c23292d8d7177320671ac2de9 Merge: 6b20b325a 6a0622405 Author: Weiqun Zhang Date: Mon Jan 30 10:33:33 2017 -0800 Merge branch 'fortran_interface' into development commit 6a0622405ef62338ee4a1258698410313a7e4ee7 Author: Weiqun Zhang Date: Mon Jan 30 10:32:44 2017 -0800 set pointer to null after being deleted Src/F_Interfaces/Base/AMReX_geometry_mod.F90 commit baf070fc95b41c08d5324185341b419b87cad9ca Author: Weiqun Zhang Date: Mon Jan 30 10:20:10 2017 -0800 fix gfortran macro Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 6b20b325a515bf4ae80a3aaf6d0cee25feb3b2d8 Merge: f7e5f72aa 9bf35516a Author: Michael Zingale Date: Mon Jan 30 15:40:03 2017 +0000 Merged in mzingale/amrex/development (pull request #7) some updates to the Fortran commandline tools commit 9bf35516aafe7cbfa5225ee1a8303ad1976bb2a1 Author: Michael Zingale Date: Sun Jan 29 12:01:36 2017 -0500 extend the `-v` option to take a string of space-separated variable to allow for outputing a specific set of variables. Previously it only allowed for a single variable. Tools/Postprocessing/F_Src/fextract.f90 commit 49becefdce77733efa5ec0477cf698961a5ac96e Author: Michael Zingale Date: Sun Jan 29 12:01:25 2017 -0500 also output the % of domain covered Tools/Postprocessing/F_Src/fboxinfo.f90 commit c5649f8d875da8be5ca16ec77606b31e299ab93e Author: Weiqun Zhang Date: Sat Jan 28 15:37:59 2017 -0800 add contiguous to Fortran pointers Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit f7e5f72aadb375d2b872d37bee925bd7240190ed Author: Weiqun Zhang Date: Sat Jan 28 12:54:55 2017 -0800 clean up Src/F_Interfaces/Base/AMReX_parallel_fi.cpp Src/F_Interfaces/Base/Make.package commit f6798d346ebcf56414caa04509a6cb04404833dd Author: Weiqun Zhang Date: Sat Jan 28 12:50:49 2017 -0800 add DistributionMapping fortran wrapper Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_mod.F90 commit e434e688e8edc19e60f634d41635683b38867b9f Author: Weiqun Zhang Date: Sat Jan 28 12:48:33 2017 -0800 forgot to check in a new file Src/Base/AMReX_omp_mod.F90 commit 27fee08a04a53c427618968b1ab24f2d4ca7694f Author: Weiqun Zhang Date: Sat Jan 28 12:45:35 2017 -0800 remove deprecated threadbox.f90 Src/Base/AMReX_threadbox.f90 Src/Base/CMakeLists.txt Src/Base/Make.package commit 8760d7171a6ff6697d8c3681b6be62d1ed16b36c Author: Weiqun Zhang Date: Sat Jan 28 12:43:13 2017 -0800 change the way of passing a c null char array because pgi didn't like it Src/Base/AMReX_parmparse_mod.F90 Src/Base/AMReX_string_mod.F90 commit e69b28293cd720fee22ee373356bc9a753a8b674 Author: Weiqun Zhang Date: Sat Jan 28 12:11:00 2017 -0800 fix macro around final and add destroy calls Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/HeatEquation_EX1_CF/advance.f90 Tutorials/HeatEquation_EX1_CF/fmain.f90 Tutorials/HeatEquation_EX1_CF/init_phi.f90 commit 0666bd6ca6139fe320ca88642ec03eb0445338fb Author: Weiqun Zhang Date: Sat Jan 28 10:41:16 2017 -0800 turn on finalize for gfortran > 4 Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 75316f583701b77a59df78931bdf773101aa8147 Author: Weiqun Zhang Date: Sat Jan 28 10:35:02 2017 -0800 make F_Interfaces compile again in AMReX Src/Base/AMReX.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_parmparse_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_omp_mod.F90 Src/F_Interfaces/Base/AMReX_parallel_fi.cpp Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/HeatEquation_EX1_CF/GNUmakefile Tutorials/HeatEquation_EX1_CF/advance.f90 Tutorials/HeatEquation_EX1_CF/fmain.f90 Tutorials/HeatEquation_EX1_CF/init_phi.f90 commit 786e602479a4db3fcfd8f3f81378e755bccd99f8 Author: Andrew Myers Date: Fri Jan 27 22:12:52 2017 -0800 Provide a more convenient API for working with the new particle class. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 65bc6900e892335ffe493f2c5c6122f5bd419a81 Author: Andrew Myers Date: Fri Jan 27 16:42:31 2017 -0800 Splitting the implementation of the particle and particle container classes into seperate files. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit eee84c6d71c940bfa2b6ea7508054c69c79ecbe4 Author: Andrew Myers Date: Fri Jan 27 16:23:17 2017 -0800 Removing the full_where option - making this always true. Src/Particle/AMReX_Particles.H commit 24db11bc566973aab03672180ac62ca5a544f2f7 Author: Andrew Myers Date: Fri Jan 27 16:06:40 2017 -0800 Remove where_already_called option, since the particles no longer store their cell / level / grid data. Src/Particle/AMReX_Particles.H commit 298929198f999b3f287689ce82fb7aa1dd329649 Author: Andrew Myers Date: Fri Jan 27 15:27:40 2017 -0800 This version gets the same test results as before the refactor, in parallel and on multiple levels. Src/Particle/AMReX_Particles.H commit 44c7376d3ebaf88953cf99d20bd940a9a41291d6 Author: Andrew Myers Date: Fri Jan 27 15:15:24 2017 -0800 make sure to call Where in MoveKick Src/Particle/AMReX_Particles.H commit 9bef64a82207cfbe17baf57fb06fb02d6ef80711 Author: Andrew Myers Date: Fri Jan 27 13:00:57 2017 -0800 Fix bug I just introduced into the MPI communication code. Src/Particle/AMReX_Particles.H commit 6f70f3034d3646abb1435d327202b510928ad1ce Author: Andrew Myers Date: Fri Jan 27 12:40:48 2017 -0800 Getting rid of the extra arrays in the particle struct. Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 1102cd484132207bf57d027a3a47459ef025311a Merge: 167bdb4c8 634792844 Author: Weiqun Zhang Date: Fri Jan 27 12:32:45 2017 -0800 Merge branch 'development' into fortran_interface Conflicts: Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_fort_mod.F90 Src/Base/AMReX_mempool_f.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 commit 634792844da4f48e88d9fc994ce60a0cddc1694b Author: Weiqun Zhang Date: Fri Jan 27 10:34:05 2017 -0800 migration doc Docs/Migration/Migration.md commit 3156c47dbc938c724215827fbec8e621a9360471 Author: Andrew Myers Date: Fri Jan 27 09:47:05 2017 -0800 Making Particle a POD type. Src/Particle/AMReX_Particles.H commit 08681206f872c94685a8c2bd3adc8fa70f630de8 Merge: 88b3b2b01 efca85699 Author: Andrew Myers Date: Thu Jan 26 20:41:31 2017 -0800 merging. commit 88b3b2b01bdc613eb22e15c4c250cd47a066ab10 Author: Andrew Myers Date: Thu Jan 26 20:33:17 2017 -0800 Removing the lev, grid, and cell attributes from the particle class - compute these on the fly instead. Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 2e78c3a574ddd681f28978db0aa78cbe5d631b5e Author: Marc Day Date: Thu Jan 26 18:02:36 2017 -0800 New version of stencil test, stenciTestMSD.cpp that takes a flag compute_geom to either compute or read EB info Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp commit 1e12306c6dd7722eeeae81251cb1eef0686f12e1 Author: Weiqun Zhang Date: Thu Jan 26 16:02:54 2017 -0800 Real --> amrex::Real MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/RHS_F.H MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC_F.H Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_MAKESLICE_F.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_SLABSTAT_F.H Src/Amr/AMReX_SlabStat.H Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_INTERP_F.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_MemPool.H Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_REAL.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_bl_fort_module.F90 Src/Base/AMReX_fort_mod.F90 Src/Base/AMReX_mempool_f.f90 Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 Src/Base/AMReX_string_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/F_BaseLib/MultiFab_C_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/Particle/AMReX_Particles_F.H Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Statistics/AVGDOWN_F.H Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 Tutorials/HeatEquation_EX2_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/RHS_F.H commit 167bdb4c8995ffee8a8df998b53a8d55d73d267c Author: Weiqun Zhang Date: Thu Jan 26 13:31:12 2017 -0800 more renaming Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_boxlib_mod.F90 Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/AMReX_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/Make.package commit a8333b58cb5c19e4a2c57d970671d2a650e03c85 Author: Andrew Myers Date: Thu Jan 26 13:14:33 2017 -0800 Fix error in template instantiation. Src/Particle/AMReX_Particles.H commit 112b26826253a63755cccc787f46ae3a1ffae855 Author: Weiqun Zhang Date: Thu Jan 26 13:12:16 2017 -0800 F_Interfaces/BaseLib --> F_Interfaces/Base for consistence Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxlib_mod.F90 Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_omp_mod.F90 Src/F_Interfaces/Base/AMReX_parallel_fi.cpp Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Src/F_Interfaces/Base/Make.package commit deac4bab0b001e3e750e6ed0f7c2f62396b2363b Author: Weiqun Zhang Date: Thu Jan 26 13:11:09 2017 -0800 add AMReX prefix Src/F_Interfaces/BaseLib/AMReX_box_mod.F90 Src/F_Interfaces/BaseLib/AMReX_boxarray_fi.cpp Src/F_Interfaces/BaseLib/AMReX_boxlib_mod.F90 Src/F_Interfaces/BaseLib/AMReX_fi_main.cpp Src/F_Interfaces/BaseLib/AMReX_geometry_fi.cpp Src/F_Interfaces/BaseLib/AMReX_geometry_mod.F90 Src/F_Interfaces/BaseLib/AMReX_multifab_fi.cpp Src/F_Interfaces/BaseLib/AMReX_omp_mod.F90 Src/F_Interfaces/BaseLib/AMReX_parallel_fi.cpp Src/F_Interfaces/BaseLib/AMReX_parallel_mod.F90 Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/multifab_mod.f90 commit 9f6e4b59cee44f80b4e860dd229f7ed5b65daac8 Author: Weiqun Zhang Date: Thu Jan 26 12:59:17 2017 -0800 no longer need bl_space_module Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/bl_space_mod.F90 commit 5ca90f7a1f51fc34bb24dd8e2692c2263661f269 Author: Weiqun Zhang Date: Thu Jan 26 12:58:13 2017 -0800 bl_fort_module --> amrex_fort_module Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_fort_mod.F90 Src/Base/AMReX_mempool_f.f90 Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 commit 975e6198bff5da6b631aafc7bb99471fbec87d08 Author: Weiqun Zhang Date: Thu Jan 26 12:46:45 2017 -0800 rm parparse from F_Interfaces because they are now in Base Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/parmparse_fi.cpp Src/F_Interfaces/BaseLib/parmparse_mod.f90 Src/F_Interfaces/BaseLib/string_mod.f90 commit 0dccefa3c6fcb5bacfa5ff44f23bef15590f2770 Author: Weiqun Zhang Date: Thu Jan 26 12:39:04 2017 -0800 add parmparse to Fortran Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 Src/Base/AMReX_string_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit 9648c4111d35c916e2057edc2e6d352d7e10a671 Author: Andrew Myers Date: Thu Jan 26 12:22:09 2017 -0800 Precompute the inverse cell spacing for particle binning. Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp Src/Particle/AMReX_Particles.H commit efca85699bba03c7c4b6c8f283cbd68ca214214e Author: Weiqun Zhang Date: Thu Jan 26 09:45:00 2017 -0800 reorder data layout Src/Particle/AMReX_Particles.H commit 1ca8d111c029e3ff34f804abcf625eb0639cc80c Author: Weiqun Zhang Date: Wed Jan 25 21:13:18 2017 -0800 fix some tests Tests/C_BaseLib/tVisMF.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp commit 88c8ec9c47ee2d2e5ed5941b654012ebccbed09b Author: Weiqun Zhang Date: Wed Jan 25 21:04:49 2017 -0800 replace the timer using gettimeofday with C++ timer Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tutorials/HelloWorld_C/main.cpp commit da215ae2a7b4f730f90396c19bfc900241446985 Author: Weiqun Zhang Date: Wed Jan 25 16:19:40 2017 -0800 use constexpr and get rid of if in IntVect::shift_hasher Src/Base/AMReX_IntVect.H Src/Base/AMReX_Utility.H commit 4a71a5110afadbff1ffa78f916dcdbfe2790da44 Author: Andrew Myers Date: Wed Jan 25 14:54:45 2017 -0800 use a typedef to save typing Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit b550d21702f69e2a070f5e62ebf1c5e5a48425d7 Author: Andrew Myers Date: Wed Jan 25 14:37:19 2017 -0800 Begin refactor of Particle classes. Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles.cpp Src/Particle/AMReX_TracerParticles.cpp Src/Particle/CMakeLists.txt Src/Particle/Make.package commit ba2580c179c6d98f007d8d0e5abde69ae0fb1730 Author: Weiqun Zhang Date: Wed Jan 25 14:10:56 2017 -0800 remove WIN32 macro MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FPC.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/F_BaseLib/fabio_c.c Src/F_BaseLib/timer_c.c Tests/C_BaseLib/tCArena.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tools/CMake/CCSEConfigReport.cmake Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/mfMinMax.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFcol.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit 553fc33e7bbcf2baab0fb8457ae5dc05dbb5a731 Author: Weiqun Zhang Date: Wed Jan 25 13:49:27 2017 -0800 remove BL_USE_SETBUF macro MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_VisMF.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Tools/CMake/CCSEOptions.cmake Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit 603edd9d2a08cff465169b1035537f8378ecd5ab Author: Weiqun Zhang Date: Wed Jan 25 12:26:57 2017 -0800 fix some util tools Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp commit 209167abb052c6fa3d0f88d86159d8bc63fd0748 Author: Andrew Myers Date: Tue Jan 24 17:00:12 2017 -0800 Porting changes to regression test suite forward from BoxLib. Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit fcd6cedbb42ed24c025f968f44b25f4de5cfa02b Merge: 6096bdf0c 82fa46778 Author: Weiqun Zhang Date: Mon Jan 23 12:12:17 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit dda199301eb7d74edbe5b90501770b87940b443a Author: Marc Day Date: Mon Jan 23 11:54:47 2017 -0800 Add access to tileindex in MFIter and use that to cache EB data in stencil test code. Src/Base/AMReX_FabArray.H Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 commit 82fa46778526b1969626f1b1d1280236a34b832c Author: tannguyen Date: Sat Jan 21 23:50:15 2017 -0800 add some more comments Src/Amr/AMReX_AuxBoundaryData.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BoxArray.H Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryRegister.H commit 4ee004f3f18f6011154b65088b02fa1682e19ddb Author: Tan Nguyen Date: Sat Jan 21 22:48:56 2017 -0800 fix doxygen comments Src/Amr/AMReX_AuxBoundaryData.H Src/Base/AMReX_BoxArray.H commit b3ed2e880be7a0b3513f99db0285b925256bcbf8 Author: Tan Nguyen Date: Sat Jan 21 22:40:52 2017 -0800 hide the description of some internal classes Src/Amr/AMReX_AuxBoundaryData.H Src/Base/AMReX_BoxArray.H commit 8e640f341d926962c8fb1877e8ce5918b393a783 Author: Marc Day Date: Fri Jan 20 18:45:03 2017 -0800 More minor cleaning of stencil testBench Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencilI.H commit 3d6428e1db97d72dea11e02e8eb0384927096c76 Author: Marc Day Date: Fri Jan 20 14:27:06 2017 -0800 Make boundary treatment the same for all the different forms of the stencil operator in the stencelTests Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp commit 344e453e1d7969e4b30762150e5fbc71304f3988 Merge: b93233a15 3eb28eced Author: Marc Day Date: Fri Jan 20 13:55:03 2017 -0800 Merge branch 'dtg_branch' of bitbucket.org:berkeleylab/amrex into dtg_branch commit b93233a154015580a28cd76ebe781195a0c651bf Author: Marc Day Date: Fri Jan 20 13:54:50 2017 -0800 Fix a bug in the irregular stencils for the stencil tests Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 commit 3eb28eced9825fc6aefc02047e6d65d8ed4a7596 Merge: 8f6a69575 002bac56f Author: Dan Graves Date: Fri Jan 20 12:35:14 2017 -0800 Merge branch 'development' into dtg_branch commit 8f6a6957581dd55e8dc2469e736fd95be6092314 Author: Dan Graves Date: Fri Jan 20 12:34:16 2017 -0800 added counts Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencilI.H commit ebf3fbfe77e5eed3041b0f41713b55f77ff10444 Author: Marc Day Date: Fri Jan 20 11:11:32 2017 -0800 Fix up fortran-only stencils in stencil testbed, add nontrivial initial data. Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H commit f93494fab7b063fba0e26a2fcdacdfa874fdaddf Author: Marc Day Date: Fri Jan 20 10:07:19 2017 -0800 Remove div by kappa in fortran-only Laplace stencil test. Minor reformatting. Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit c5100ee4cf4c4cfcbff125c14a7c94d8947902c3 Merge: 6dba31f49 ac782e1a1 Author: Marc Day Date: Thu Jan 19 20:24:54 2017 -0800 Merge branch 'dtg_branch' of bitbucket.org:berkeleylab/amrex into dtg_branch commit 6dba31f498908ab0e7bcc01f736c2021f5b01233 Author: Marc Day Date: Thu Jan 19 20:23:55 2017 -0800 Add Fortran-only version to stencilTest, add some timers... still need to confirm correctness Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit 002bac56f7864d70396ba2d7ac860e8b1abce1b3 Author: Tan Nguyen Date: Thu Jan 19 19:17:29 2017 -0800 fix hash func Src/Base/AMReX_IntVect.H commit ac782e1a170dfb0851c90aec3affe35124f17c09 Author: Dan Graves Date: Thu Jan 19 15:52:27 2017 -0800 ported the regular-kitty-corner-to-covered fix from Pele Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit d23cb07e63cda8973e65b044369d9bd1ffac6688 Author: Tan Nguyen Date: Thu Jan 19 12:32:43 2017 -0800 hash boxArray Src/Base/AMReX_BoxArray.H Src/Base/AMReX_IntVect.H commit d11e68d1b4e54b599390db0667872c897f34c606 Author: Dan Graves Date: Thu Jan 19 09:53:08 2017 -0800 bug fix for bug found by Marc Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit 6096bdf0ca3c2dabda40004bb3e2e362c30bd296 Author: Weiqun Zhang Date: Wed Jan 18 10:48:39 2017 -0800 use some C++11 headers and remove some Windows stuff Src/Base/AMReX.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/f2kgetcl.c commit 613c04945f47cbc8e13a3ef5ad735755cd7378c0 Author: Weiqun Zhang Date: Wed Jan 18 08:57:40 2017 -0800 add -P to cpp Tools/GNUMake/Make.rules commit 650988cb17e2cd01c57d729a8b3923cbb2b88bd8 Author: Weiqun Zhang Date: Tue Jan 17 13:46:19 2017 -0800 save cpp'd headers containing C binding of Fortran function Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit fcda9b6aa0481b63ff6c936e4d85b31a045011ea Author: Weiqun Zhang Date: Tue Jan 17 12:45:09 2017 -0800 typo Src/Base/Make.package commit dbc907c2c7e9806962b785b9d4213e5733be332e Author: Weiqun Zhang Date: Tue Jan 17 12:44:13 2017 -0800 start to tweak the make sytem for fortran call checking Src/Base/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 0c4e01afa1b56c855761cf5b4d1be76735ae7dcd Author: Weiqun Zhang Date: Fri Jan 13 16:03:38 2017 -0800 add a function AmrData to return Distribution Map Src/Extern/amrdata/AMReX_AmrData.H commit 877f7219bf9470d1ba84d72d328197d4d6586c8e Merge: 887ffb391 0911d7f1f Author: Weiqun Zhang Date: Fri Jan 13 15:33:36 2017 -0800 Merged in mzingale/amrex/development (pull request #6) switch from a hash to describe --tags --dirty commit 0911d7f1f1c914b71403326d0c601f2a41b76199 Author: Michael Zingale Date: Fri Jan 13 18:05:32 2017 -0500 switch from a hash to describe --tags --dirty to get a more complete picture of the state Tools/C_scripts/makebuildinfo_C.py commit 887ffb391c62b212b79e4c561f8b8b41f974afd5 Author: Tan Nguyen Date: Fri Jan 13 14:08:39 2017 -0800 fix comments in AMReX_Print.H Src/Base/AMReX_Print.H commit 062bb1508af1527ed3af1bbe01844661f93bab5e Author: Tan Nguyen Date: Fri Jan 13 13:56:44 2017 -0800 add some more comments Src/Amr/AMReX_Amr.H Src/AmrCore/AMReX_AmrCore.H Src/Base/AMReX_Print.H commit 0b718401826c88b70ed1a064d5581e5ebf4577e3 Author: Tan Nguyen Date: Fri Jan 13 00:22:25 2017 -0800 add more comments in AMReX_FabArray.H Src/Base/AMReX_FabArray.H commit 0ab27c3f31ff192d7049c34fc22dde0dfd20f48d Author: Tan Nguyen Date: Thu Jan 12 21:13:30 2017 -0800 fix a comment Src/Base/AMReX_FabArray.H commit 35e8972126fe37fb731580bb045db8320f287565 Author: Tan Nguyen Date: Thu Jan 12 19:03:53 2017 -0800 add comments to functions in AMReX_FabArray.H Src/Base/AMReX_FabArray.H commit 3a7c6244abac1b4e148dee5f70060b84321c776c Author: Michael Zingale Date: Thu Jan 12 12:44:57 2017 -0500 switch to unicode by default, since some source files have unicode characters Tools/F_scripts/dep.py commit 452702ac8efbc0d943df35fba54124b011215bae Author: Dan Graves Date: Wed Jan 11 16:51:06 2017 -0800 stencil test bed is complete and seems to work for the four cases I have programmed Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp Tests/GeometryShop/stencilTestbed/src/Make.package Tests/GeometryShop/stencilTestbed/src/lapl_nd.F90 Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H commit 073a73846fe3e4608a30b4f7118c586e49e087f9 Author: Weiqun Zhang Date: Wed Jan 11 13:28:50 2017 -0800 add amrex::AllPrint() to save some typing Src/Base/AMReX_Print.H Tutorials/HelloWorld_C/main.cpp commit 3c57b7dbbde231fbe7b9b06c660cc6128f520e94 Author: Dan Graves Date: Wed Jan 11 11:27:08 2017 -0800 trying to keep up with the development branch Src/GeometryShop/AMReX_IntVectSet.H commit 044a3c9ed654649cabfe95b267b02012d905c40a Merge: 7d4e7d466 ba0e1919a Author: Dan Graves Date: Wed Jan 11 11:22:51 2017 -0800 Merge branch 'development' into dtg_branch commit 7d4e7d4668b08f55b6bf3a2e19e348ef5448f8bd Author: Dan Graves Date: Wed Jan 11 11:19:33 2017 -0800 added some files to make.package Src/GeometryShop/Make.package commit 14bdcdd246d9b6514bd63e8fd5cd811c5cff90ff Author: Dan Graves Date: Wed Jan 11 11:16:08 2017 -0800 The AggSten everywhere example works now. On to figuring out how to get AMReX to call fortran Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/src/#AMReX_FaceIndex.H# Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencil.H Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencilI.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit ba0e1919ac8e351afd1cda3c92d5cf4ea5292cf3 Author: Weiqun Zhang Date: Tue Jan 10 16:17:06 2017 -0800 minor Src/Base/AMReX_mempool_f.f90 commit 6af03daad2281c00a1d313f7cc8e8a48f9b7a746 Author: Weiqun Zhang Date: Tue Jan 10 16:16:00 2017 -0800 don't have bl_fort_module for Fortran build Src/Base/AMReX_mempool_f.f90 commit 07a8b0809fd0e8600b42045cca12b5f46ab3ba6b Author: Weiqun Zhang Date: Tue Jan 10 16:03:25 2017 -0800 some double precision --> real(c_real) Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_mempool_f.f90 Src/F_BaseLib/fab.f90 Src/Particle/AMReX_Particles.H commit 72cb7ebd4c4971a85bdae0496d467f239c159e53 Author: Dan Graves Date: Tue Jan 10 16:00:29 2017 -0800 put initialize and bl_profile_start/stop calls into test so we can get stats Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp commit 751e6dd6d715a5b6f3d4d1955d509c29dc9d6f23 Author: Dan Graves Date: Tue Jan 10 15:16:08 2017 -0800 simplest version of the testbed now runs Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.H Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit 1186aefc81c5f0588d8f0ba46f39d51748b776c2 Author: Weiqun Zhang Date: Tue Jan 10 14:56:47 2017 -0800 std:iota can be used now. Src/Base/AMReX_FabArray.cpp commit 1df6d1eb316d8556624f95171d2eb4d145b12b4c Author: Weiqun Zhang Date: Tue Jan 10 14:46:48 2017 -0800 removed hack for Cray compiler Src/Base/AMReX_FArrayBox.cpp commit c4e43bc8244d24cccaf69074b76f5db7c3c170ec Author: Weiqun Zhang Date: Tue Jan 10 14:35:12 2017 -0800 if AMREX_GIT_VERSION is not defined, reutrn Unknown Src/Base/AMReX.cpp commit c3be767c8b8cfa7fb18a2ce6c9b3bc97d3f9b6da Author: Weiqun Zhang Date: Tue Jan 10 14:26:15 2017 -0800 add amrex::Version() Src/Base/AMReX.H Src/Base/AMReX.cpp Tools/GNUMake/Make.defs Tutorials/HelloWorld_C/main.cpp commit 547329fdfdcf9a51ce7f154c903f05e4aebe5e1c Author: Weiqun Zhang Date: Tue Jan 10 13:41:35 2017 -0800 rm BL_USE_ARLIM Src/Base/AMReX_ArrayLim.H commit 67422b71ebd8156e8149274eedff95fe1a8b7074 Author: Weiqun Zhang Date: Tue Jan 10 12:59:38 2017 -0800 make_build_info_cpp no longer used Tools/C_scripts/make_build_info_cpp commit 10cb06eff33a535956caa761e5d44ef0b9c926f1 Author: Weiqun Zhang Date: Tue Jan 10 12:58:04 2017 -0800 start to use Print in some places Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/AmrCore/AMReX_AmrCore.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H commit 1269f2c5d8cea9430cad493d1508f998257f5c7b Author: Dan Graves Date: Tue Jan 10 11:22:32 2017 -0800 got the testbed to compile on this branch Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.H Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.H Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_VolIndex.H commit 570a41b78cbee3cb455324f1bdfe17e95c8b4646 Author: Weiqun Zhang Date: Tue Jan 10 11:02:14 2017 -0800 Revert "Print: change the default to print on all calling processes. To print on IO Process only, do Print(Print::IOProc) << ..." This reverts commit b5a0461fac5343053d0370a9ac659c6bd39e4126. Src/Base/AMReX_Print.H Tutorials/HelloWorld_C/main.cpp commit b5a0461fac5343053d0370a9ac659c6bd39e4126 Author: Weiqun Zhang Date: Tue Jan 10 10:16:05 2017 -0800 Print: change the default to print on all calling processes. To print on IO Process only, do Print(Print::IOProc) << ... Src/Base/AMReX_Print.H Tutorials/HelloWorld_C/main.cpp commit d0466177c797ea66fb6af660d8b6a6cd4ac5e0b6 Author: Weiqun Zhang Date: Tue Jan 10 09:31:19 2017 -0800 minor Src/Particle/AMReX_Particles.H commit e2f8f317e37ebc11f198e01be01429265bf9d9a6 Author: Weiqun Zhang Date: Tue Jan 10 09:26:13 2017 -0800 Add amrex::Print. One can use this to replace if (ParallelDescriptor::IOProcessor() { std::cout << ....; } with amrex::Print() << ....; To print on all processes, one can do amrex::Print(amrex::Print::AllProcs) << ...; To print on a particular process in a communicator, one can do amrex::Print(rank_for_print, communicator) << ...; By default Print uses std::cout. By it also takes an optional std::ostream argument. Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_Print.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/HelloWorld_C/main.cpp commit 9ad04f0677844003b2d25f6f879e08469d36428c Merge: 5ff830e9e 837a31d61 Author: Dan Graves Date: Mon Jan 9 20:55:44 2017 -0800 Merge branch 'dtg_branch' of https://bitbucket.org/berkeleylab/amrex into dtg_branch commit 5ff830e9e8553416fcb7c97ee43c9c034836b8c2 Author: Dan Graves Date: Mon Jan 9 20:55:14 2017 -0800 I had the variable names incorrect Tests/GeometryShop/stencilTestbed/src/Make.package commit 9aceec28b250c8ff243c45359f9be69de60f0e5b Author: Dan Graves Date: Mon Jan 9 20:49:43 2017 -0800 forgot to add the src directory into the makefile Tests/GeometryShop/stencilTestbed/exec/GNUmakefile commit 837a31d61b70006f3f1da3f76f3bc067d1cad61f Author: Brian VS Date: Mon Jan 9 18:17:47 2017 -0800 needed right std::sqrt Src/GeometryShop/AMReX_RealVect.H commit 63a58cfc0b403e36b04094eb0c3d1b799748a6d1 Author: Dan Graves Date: Mon Jan 9 16:43:06 2017 -0800 lots of progress on the testbed. should have it compiling soon. Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/src/#AMReX_FaceIndex.H# Tests/GeometryShop/stencilTestbed/src/AMReX_BaseIndex.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.H Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.H Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_VolIndex.H Tests/GeometryShop/stencilTestbed/src/AMReX_VolIndex.cpp Tests/GeometryShop/stencilTestbed/src/Make.package commit 8bcb720656d9d8856694afa9abb3ea5581fa601f Author: Weiqun Zhang Date: Mon Jan 9 10:45:19 2017 -0800 minor MiniApps/PGAS_SMC/SMC_io.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp commit 8f472a37f61d246efffd8b983144618b96fe77fb Merge: 57b2b14e9 4b0a24c96 Author: Weiqun Zhang Date: Sun Jan 8 12:31:43 2017 -0800 Merge branch 'development' into weiqun/development commit 57b2b14e91ab50bb6d6c11d038947474e2e56891 Author: Weiqun Zhang Date: Sun Jan 8 12:31:29 2017 -0800 forward --> move in non-template function Src/Base/AMReX_MemProfiler.cpp commit 4b0a24c9602ee31899b6ac8a6cc1f9fe5b88b9e0 Merge: b5dc8f984 f9a653f31 Author: Tan Nguyen Date: Sun Jan 8 00:20:05 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit b5dc8f9848ad5c670eea133146cef7fbf6d8a8e6 Author: Tan Nguyen Date: Sun Jan 8 00:19:31 2017 -0800 modify comments in BoxArray.H Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/F_BaseLib/MemProfiler_f.cpp Tools/GNUMake/Make.rules commit 6a486815d4c452d266b42b6d5a7b5b04b8f1d78d Author: Tan Nguyen Date: Sun Jan 8 00:11:46 2017 -0800 modify comments in BoxArray.H Src/Base/AMReX_BoxArray.H commit a39d99571d439da770f485c6a1528a481e14d21e Author: Weiqun Zhang Date: Sat Jan 7 20:27:56 2017 -0800 removed some Array Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp commit b371198da5432a396e8700f35c0276d91a8f0f73 Author: Weiqun Zhang Date: Sat Jan 7 13:04:44 2017 -0800 explicitly delete some constructors and operator= Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_MacBndry.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H commit 32fbcd1cb587f14b2bb6e36646202ec5536b27e5 Author: Weiqun Zhang Date: Sat Jan 7 12:41:43 2017 -0800 make Tuple simply a template alias of std:array; add move constructors to FabSet, FluxRegister, BndryRegister, etc. Src/AmrCore/AMReX_FluxRegister.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Tuple.H Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp commit 4c4e58d8dd5f28810021834ac8df9733d1362f8c Author: Weiqun Zhang Date: Sat Jan 7 10:39:13 2017 -0800 store MultiMasks in Array Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_MultiMask.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp commit 63372f9ad042ec5b50d6b28013ccadda07db7732 Author: Weiqun Zhang Date: Sat Jan 7 08:01:30 2017 -0800 move constructor for Mask and MultiMask Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.H commit f9a653f310d9a04fdbfad5250eac25a885f2bffc Author: Weiqun Zhang Date: Fri Jan 6 21:31:42 2017 -0800 F_BaseLib: fix memory profiling by add using namespace amrex Src/F_BaseLib/MemProfiler_f.cpp commit e44c8838ba1f78aa0860ef7813f400d3cd5981b5 Author: Weiqun Zhang Date: Fri Jan 6 17:22:55 2017 -0800 minor Src/Base/AMReX_BaseFab.H commit 830fd8496afd95299858841df76764fd12db916e Author: Weiqun Zhang Date: Fri Jan 6 17:13:45 2017 -0800 add noexcept Src/Base/AMReX_FabArray.H commit d28fe6462a0d21f822f2d32a3fc7b641e97803fd Author: Weiqun Zhang Date: Fri Jan 6 17:04:10 2017 -0800 add noexcept Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H commit 6871a060bd0ac1d16f199dc463feab29f6516f37 Author: Weiqun Zhang Date: Fri Jan 6 17:02:33 2017 -0800 add move constructor to MultiFab, iMultiFab, and TagBoxArray Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H commit 4aaf772eb3aa20c41da1ea4034aec061a492b7ef Author: Weiqun Zhang Date: Fri Jan 6 16:50:45 2017 -0800 move constructor for FabArray Src/Base/AMReX_FabArray.H commit d1c1922d77ae2e394de54aa0b77966fef4862806 Author: Dan Graves Date: Fri Jan 6 16:31:07 2017 -0800 made some slow progress on the testbed Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp commit 0445fef74d2652410021dafbfd53ede54183bb1d Author: Weiqun Zhang Date: Fri Jan 6 15:47:28 2017 -0800 move constructor for FArrayBox, IArrayBox, and TagBox Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp commit 9ff8738dada39b6cd6bc71ca89ee6f692629f6a2 Author: Weiqun Zhang Date: Fri Jan 6 15:30:22 2017 -0800 BaseFab: add move constructor Src/Base/AMReX_BaseFab.H commit 5cbffc50ab946179b760002498b932ed3fb1ebf0 Author: Weiqun Zhang Date: Fri Jan 6 15:23:14 2017 -0800 add a BARef constructor taking a single Box Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 5b118cfe14b0097441bf4044dd64b4178519373d Author: Weiqun Zhang Date: Fri Jan 6 15:17:18 2017 -0800 add explicit to a BoxList ctor taking a single Box, and tidy Src/Base/AMReX_BoxList.H commit 56a3de456d4b4ec642bbf5dd975aa1fc8f0ad360 Author: Weiqun Zhang Date: Fri Jan 6 15:10:15 2017 -0800 remove Geometry's copy ctor and dtor to let compilers auto-generate copy and move constructors. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 8dc5518a2e3bbb71471af8d90f402316b6891653 Author: Weiqun Zhang Date: Fri Jan 6 15:08:56 2017 -0800 remove the do-nothing ~CoordSys so that compilers will auto-generate copy and move constructors. Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp commit a682ca10938519b23ffc9ac91da56a1c904287e7 Author: Weiqun Zhang Date: Fri Jan 6 14:59:16 2017 -0800 minor Tools/GNUMake/Make.rules commit 6ed9bf87f64ead40e112247dfef47e62fa126a28 Author: Weiqun Zhang Date: Fri Jan 6 14:54:17 2017 -0800 comments on make Tools/GNUMake/Make.rules commit 709b31f3d2445051ca06be651bd2d66b3e3a4e6f Author: Weiqun Zhang Date: Fri Jan 6 12:50:55 2017 -0800 change due to IntVect operator<= change Src/Base/AMReX_BoxArray.cpp commit f20c924c3c7c04f205033ed56969c54f0cd434db Merge: 51ddd3039 9826741d9 Author: Weiqun Zhang Date: Fri Jan 6 11:45:47 2017 -0800 Merge branch 'weiqun/development' of bitbucket.org:WeiqunZhang/amrex into weiqun/development Conflicts: Src/Base/AMReX_Box.cpp commit 51ddd3039d29045943ec122c5bbb7be0dadebced Author: Weiqun Zhang Date: Fri Jan 6 11:09:09 2017 -0800 Change the behavior of IntVect::operator< and >. They now do lexicographical comparisons that are suitable for STL. The per component comparison is now done by IntVec::allLT, allLE, allGT, and allGE. We have also removed IntVect::Compare, IntVect::lexLT, and IntVect::lexGT for simplicity. Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Particle/AMReX_Particles.H Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 9826741d9c6d056de644be4f7c0072dad30bdcf8 Author: Weiqun Zhang Date: Fri Jan 6 11:09:09 2017 -0800 Change the behavior of IntVect::operator< and >. They now do lexicographical comparisons that are suitable for STL. The per component comparison is now done by IntVec::allLT, allLE, allGT, and allGE. We have also removed IntVect::Compare, IntVect::lexLT, and IntVect::lexGT for simplicity. Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Particle/AMReX_Particles.H Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 2891e66f727f91d4ff46e73d2097239f8bc3bcc4 Author: Weiqun Zhang Date: Thu Jan 5 16:29:39 2017 -0800 migration doc Docs/Migration/Migration.md commit 177c72624a14da7c7e1ea2ee686ae77f0aedc6d7 Merge: 5bf0d0df9 7de1eb76d Author: Weiqun Zhang Date: Thu Jan 5 15:25:49 2017 -0800 Merge branch 'development' into weiqun/development Conflicts: Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AmrLevel.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_PList.H Src/Base/AMReX_Pointers.H Src/Base/AMReX_UseCount.H commit 5bf0d0df966640e9448166bb31b415fc2f3a2a7e Author: Weiqun Zhang Date: Thu Jan 5 13:48:21 2017 -0800 rm PList Src/Base/AMReX_PList.H Src/Base/CMakeLists.txt commit 5cddb6f831e34716ec7c93c2dfed33023ebb27c4 Author: Weiqun Zhang Date: Thu Jan 5 13:45:43 2017 -0800 rm UseCount Src/Base/AMReX_UseCount.H Src/Base/AMReX_UseCount.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 31f16a7928663b6cdd22c3cc9ad77a2142b2e537 Merge: 8b764a3e5 7de1eb76d Author: Dan Graves Date: Thu Jan 5 10:16:59 2017 -0800 Merge branch 'development' into dtg_branch commit 7de1eb76db7136a8c62cd1caab4ba92b6dd620d5 Author: Weiqun Zhang Date: Thu Jan 5 08:42:48 2017 -0800 CompileTesting: Change the default to running a small set of tests; add --full for running the full testing. Tools/CompileTesting/compiletesting.py commit 50f15baad9515938776392bfca58c68c7818c30f Author: Weiqun Zhang Date: Wed Jan 4 22:12:23 2017 -0800 add a compile testing script Tools/CompileTesting/compiletesting.py commit d4d471c214f6b3f02939751ae42f978df93ab742 Author: Weiqun Zhang Date: Wed Jan 4 21:49:43 2017 -0800 fix comment line Src/Amr/AMReX_AmrLevel.H commit e151382b5bf8c1552699918ec52cc875ac0a05b1 Author: Weiqun Zhang Date: Wed Jan 4 21:48:34 2017 -0800 revert AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.H commit b8851dff629a658b83c01f7416c405f2d8fb06a5 Author: Weiqun Zhang Date: Wed Jan 4 21:46:41 2017 -0800 remove a duplicated line Src/Base/AMReX_BaseFab.H commit e3a78890dbecd97f645eb3cad50db3408aa5494b Author: Weiqun Zhang Date: Wed Jan 4 21:43:52 2017 -0800 fix comment line Src/Base/AMReX_Pointers.H commit 7beb273d1dfeeecfeef34a943e4ff3c0ed872472 Author: Weiqun Zhang Date: Wed Jan 4 21:40:54 2017 -0800 Too hard to fix. I am just going to revert to back to a working vesion. The lost works are comments Src/Base/AMReX_FabArray.H commit a47703ee2357fb08c12584ab44eb7d084726233e Author: Weiqun Zhang Date: Wed Jan 4 21:32:41 2017 -0800 fix more merge problems Src/Base/AMReX_DistributionMapping.H commit 0d272890be84d1c79e5df7154a2f7ea17c2098d0 Author: Weiqun Zhang Date: Wed Jan 4 21:07:46 2017 -0800 fix more merge problems Src/Base/AMReX_DistributionMapping.H commit b863afebe6b3717cf0c78715a186410c44180153 Author: Weiqun Zhang Date: Wed Jan 4 20:41:07 2017 -0800 fix conflicts from previous merge Src/Base/AMReX_Box.H Src/Base/AMReX_FPC.H Src/Base/AMReX_MultiFab.H commit 903bf44c20a3e4af4c63686014b689707d6b140d Author: Weiqun Zhang Date: Wed Jan 4 20:28:36 2017 -0800 MultiFab.H no longer exists Src/Base/MultiFab.H commit ff07516343a40e9cc426874c4ad61ce669347af9 Author: tannguyen Date: Wed Jan 4 18:51:43 2017 -0800 add comments to the amr and amrLevel files Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AmrLevel.H commit 60bfa00f832ba5ccfeefcd6a54acb8e80b95a349 Merge: 6df5adb53 5f99dcda0 Author: tannguyen Date: Wed Jan 4 16:44:17 2017 -0800 resolved conflit commit ffc00feb095ecaa9aeaf845998bd1c01f55a185e Author: Weiqun Zhang Date: Wed Jan 4 16:32:16 2017 -0800 make Amr & AmrLevel::derive return std::unique_ptr instead of raw ptr Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit 6df5adb5311f64b07b4186d817c2e23f4b119f33 Author: tannguyen Date: Wed Jan 4 16:18:33 2017 -0800 update header files with comments Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BLPgas.H Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxList.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FPC.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabConv.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Looping.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_Orientation.H Src/Base/AMReX_PList.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParmParse.H Src/Base/AMReX_Periodicity.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_Pointers.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_Tuple.H Src/Base/AMReX_UseCount.H Src/Base/AMReX_Utility.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_ccse-mpi.H Src/Base/AMReX_iMultiFab.H Src/Base/MultiFab.H commit ea3b83fecc1d6a28ca3284a6563ef7c89d759ea0 Author: Weiqun Zhang Date: Wed Jan 4 16:10:37 2017 -0800 turn on C++14 for Intel >= 17 Src/Base/AMReX_DistributionMapping.H Tools/GNUMake/comps/intel.mak commit 28d704b660ca9157883b1171d5957c5d2ccdaa48 Author: Weiqun Zhang Date: Wed Jan 4 16:02:47 2017 -0800 For gcc >= 6, C++14 is on by default. Src/Base/AMReX_DistributionMapping.H Tools/GNUMake/comps/gnu.mak commit 5e8b69d7174e1cceb0e88c825e77f598d00a2b25 Author: Weiqun Zhang Date: Wed Jan 4 15:52:06 2017 -0800 fix a bug in last commit Src/Base/AMReX_FabArray.cpp commit 90911bbaf9a330ecd16c7dc1429330b8cbc17d25 Author: Weiqun Zhang Date: Wed Jan 4 15:25:21 2017 -0800 get rid of the sentinel in DistributionMapping Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit 363a6ecd22d9f92e85cabaf236ffc02bea5020dd Author: Weiqun Zhang Date: Wed Jan 4 13:43:02 2017 -0800 remove AMReX_Pointers.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_Pointers.H Src/Base/CMakeLists.txt Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H commit cfbc1319e97a4bba811a8f66363bd7421ff6de8c Author: Weiqun Zhang Date: Wed Jan 4 13:39:12 2017 -0800 FArrayBox: use unique_ptr instead of CpClassPtr for RealDescriptor Src/Base/AMReX_FArrayBox.cpp commit 464d307b672447fd51a4616567d07019cba9b71d Author: Weiqun Zhang Date: Wed Jan 4 13:25:09 2017 -0800 remove the use of LnPtr and LnClassPtr Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp commit cd2483e32c86804d01a211beade18794291d1988 Author: Weiqun Zhang Date: Wed Jan 4 13:07:17 2017 -0800 PhysBCFunct: use std::unique_ptr Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp commit 8b764a3e555a29eef638ce20b6080a1f01b49b60 Author: Dan Graves Date: Wed Jan 4 13:03:09 2017 -0800 AMReX_GeometryShop now does the right thing with its test once I realized IntVect::operator < is stupid Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/Make.package Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphere/sphere.inputs Tests/GeometryShop/sphere/sphereTest.cpp commit fed8befdbd42d4d772b89b802aeac155ae3183c2 Author: Weiqun Zhang Date: Wed Jan 4 12:51:26 2017 -0800 remove unsafe assertion Src/Base/AMReX_BoxArray.cpp commit c2a6e1c45d6ca901745f4955dacc16de8eb1306c Author: Weiqun Zhang Date: Wed Jan 4 12:21:43 2017 -0800 BoxArray::clear() should leave it at a valid state Src/Base/AMReX_BoxArray.cpp commit cec55bac927deeb9a02a3bccacc204192d3f8437 Author: Weiqun Zhang Date: Wed Jan 4 10:50:56 2017 -0800 BoxArray: move constructor Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 43266031df20f08cca78d80fe10ddae4352db90d Author: Weiqun Zhang Date: Wed Jan 4 10:44:52 2017 -0800 BoxArray: use std::shared_ptr Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H commit ff3c966b2f589accc7319d5c394137a175cc3dd9 Author: Weiqun Zhang Date: Tue Jan 3 16:16:59 2017 -0800 DistributionMapping: use std::shared_ptr and add move constructor Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 2af510e0dcc15eefbd785113183a4bc999d7a85b Merge: 453976871 5f99dcda0 Author: Dan Graves Date: Tue Jan 3 15:09:33 2017 -0800 Merge branch 'development' into dtg_branch commit 453976871c17b6b6c6ccdce4177107f97b124d76 Author: Dan Graves Date: Tue Jan 3 15:08:33 2017 -0800 more paranoid commits Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_SphereIF.H commit 07f2b5b24d22be8397af48294b85f661612e6a7d Author: Dan Graves Date: Tue Jan 3 15:07:35 2017 -0800 committing so that I can merge with development changes Tests/GeometryShop/sphere/sphere.inputs Tests/GeometryShop/sphere/sphereTest.cpp commit 5f99dcda0766b80efa0df10d54fa6ee720f2e6b8 Merge: e3b5cfe5d 930e0df61 Author: Weiqun Zhang Date: Tue Jan 3 14:52:17 2017 -0800 Merge branch 'weiqun/development' into development commit e3b5cfe5daa587c72b838882162b65a15c13bd65 Author: Weiqun Zhang Date: Tue Jan 3 13:30:38 2017 -0800 typo Docs/Migration/Migration.md commit 930e0df61c86638105cc9fd55cead008ed4a0710 Author: Weiqun Zhang Date: Tue Jan 3 12:59:43 2017 -0800 comments on dtor, copy-ctor, copy-op=, move-ctor, and move-op= Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealBox.H commit 571783d0233dcad395653fe2f7821548faf035d1 Author: Dan Graves Date: Tue Jan 3 11:24:40 2017 -0800 geometryshop port now compiles. on to testing. Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/sphere/sphereTest.cpp commit a7c32d886b3e79110fa6dc58d98c14583f751c8f Author: Weiqun Zhang Date: Tue Jan 3 11:01:16 2017 -0800 add assertion for OpenMP >= 3.1 Src/Base/AMReX.cpp commit c4c46002f8b1c2fb8c177b8a8eec1e1c5e9167f5 Author: Weiqun Zhang Date: Fri Dec 30 13:20:38 2016 -0800 add explicit to DistributionMapping constructors Src/Base/AMReX_DistributionMapping.H Tutorials/MultiFabTests_C/GridMoveTest.cpp commit 8a9eee1e76eb6efae5a071d4e08a123e272fa972 Merge: dc20767ad 120fa2176 Author: Weiqun Zhang Date: Fri Dec 30 12:58:11 2016 -0800 Merged in mzingale/amrex/development (pull request #5) this fixes an issue when using ⁠⁠-copy_benchmarks⁠⁠ on tests that crashed and did not output commit 120fa2176aa9595bbafeab7eae6dcdb41a25b44a Author: Michael Zingale Date: Fri Dec 30 10:25:51 2016 -0500 this fixes an issue when using ⁠⁠-copy_benchmarks⁠⁠ on tests that crashed and did not output Tools/RegressionTesting/regtest.py commit dc20767ad300a8eb51365075d48b91f342136826 Author: Weiqun Zhang Date: Thu Dec 29 21:47:01 2016 -0800 forgot to check in step 5 script Tools/Migration/step-5-amrex-namespace/amrex-namespace.sh commit 20fca5b8c39b0a69103c58e47f2f67c58c10e66b Author: Weiqun Zhang Date: Thu Dec 29 21:44:13 2016 -0800 update buildInfo Docs/Migration/Migration.md Tools/C_scripts/AMReX_buildInfo.H Tools/C_scripts/makebuildinfo_C.py Tools/Migration/step-8-deboxlib/deboxlib.sh commit a75a5b0865acddcc5044e57de74ac787d8b02545 Author: Weiqun Zhang Date: Thu Dec 29 12:49:33 2016 -0800 Migration document Docs/Migration/Migration.md commit 06209f45b1b0cf523f615a22e8113fb594308c0b Author: Weiqun Zhang Date: Thu Dec 29 12:16:21 2016 -0800 more BoxLib --> AMReX MiniApps/MultiGrid_C/GNUmakefile Src/Amr/Make.package Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLassert.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabConv.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_REAL.H Src/Base/AMReX_SPACE.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/Make.package Src/Boundary/Make.package Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/Particle/AMReX_Particles.H Src/Particle/Make.package commit c3e297304b0ea2d07bd6efc22d2823c517eadeb4 Author: Weiqun Zhang Date: Thu Dec 29 11:46:20 2016 -0800 rm BoxLib version and change ParmParse parameters starting with boxlib. to amrex. Src/Base/AMReX.cpp commit 5e89906c138bcac8252037279eefef635663047c Author: Weiqun Zhang Date: Thu Dec 29 11:36:35 2016 -0800 AMReX_BoxLib --> AMReX Docs/Readme.backtrace Docs/Readme.profiling Docs/Readme.sidecars Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLassert.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_Orientation.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Pointers.H Src/Base/AMReX_UseCount.H Src/Base/AMReX_Utility.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/BaseLib/main.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/Migration/step-8-deboxlib/deboxlib.sh Tutorials/AMR_Adv_C_v2/Source/main.cpp Tutorials/HelloWorld_C/main.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp Tutorials/Tiling_C/main.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp commit 834c983c29a368a973058dc4ad2a03b782242127 Author: Weiqun Zhang Date: Thu Dec 29 09:04:46 2016 -0800 add migration step 8 script and rm #include MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_ccse-mpi.H Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Tests/C_BaseLib/tFillFab.cpp Tests/C_BaseLib/tMF.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/MKDir/MKDir.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tools/Migration/step-8-deboxlib/deboxlib.sh Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit 547378a4f0735f72cd443418a88490c19a013e69 Author: Weiqun Zhang Date: Thu Dec 29 08:40:40 2016 -0800 remove Base/GNUmakefile and winstd.H Src/Base/AMReX_winstd.H Src/Base/CMakeLists.txt Src/Base/GNUmakefile commit 358468dc6445f8ee6c4d4602164da7b187a73b25 Author: Weiqun Zhang Date: Wed Dec 28 12:46:49 2016 -0800 migration document Docs/Migration/Migration.md commit 4f908ec54e66a1226af1e883f92807a02d5281e0 Author: Weiqun Zhang Date: Wed Dec 28 12:37:46 2016 -0800 fix typo in migration doc Docs/Migration/Migration.md commit 49ad9027bf34e9d2f998fc2dc39f29bed3d645e6 Author: Weiqun Zhang Date: Wed Dec 28 12:14:31 2016 -0800 migration script for bind(c) Tools/Migration/step-7-bindc/bindc.sh commit e945029d5c5c7e5c3f89c0ca12beebbc11a07026 Author: Weiqun Zhang Date: Wed Dec 28 12:13:29 2016 -0800 fix subroutine probinit Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 commit d2c7626e51ffbe5ca48b27ed7c43a5bb8de848af Author: Weiqun Zhang Date: Wed Dec 28 11:48:00 2016 -0800 FORT_PROBINIT --> amrex_probinit and remove unused BL_SYNC_RANTABLES Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_PROB_AMR_F.H commit 6c23c170de61bebe3a71b6befd1977400ebb8d99 Author: Weiqun Zhang Date: Wed Dec 28 10:56:47 2016 -0800 remove unused AMReX_FLUSH_F.H Src/Amr/AMReX_FLUSH_F.H Src/Amr/CMakeLists.txt commit 4b9cc72d207f5e28076eb039f18674c89def9cca Merge: 848985c5c 73e7797d5 Author: Weiqun Zhang Date: Wed Dec 28 10:45:39 2016 -0800 Merge branch 'migration/6-distributionmap' into development commit 73e7797d5664d6c938b0e0db2cbf5d1bc88b55b3 Author: Weiqun Zhang Date: Wed Dec 28 10:45:22 2016 -0800 some bugs fixed: forgot to pass MFInfo to MultiFab constructor Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 848985c5c775ad598389a01434d48a78b7b2c8b2 Merge: 189ae998a dc4639f6d Author: Weiqun Zhang Date: Wed Dec 28 08:16:54 2016 -0800 Merge branch 'migration/6-distributionmap' into development commit dc4639f6d923634554eaa3327189a35070c22da2 Author: Weiqun Zhang Date: Wed Dec 28 08:16:11 2016 -0800 Set Amr's BoxArray and DistributionMapping in AmrLevel::restart. This is safer Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp commit c680d093302f3a8598f0d5df981c39df2c5aa6f9 Author: Weiqun Zhang Date: Tue Dec 27 23:21:07 2016 -0800 make sure FluxRegister, BndryRegister and FabSet::read() functions only read data into predefined objects. Src/AmrCore/AMReX_FluxRegister.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.cpp commit 189ae998a8d91816424cd26cf4ba4b623d093efd Merge: d2abe37a6 ac5f563b4 Author: Weiqun Zhang Date: Tue Dec 27 16:39:46 2016 -0800 Merge branch 'migration/6-distributionmap' into development commit ac5f563b4f43ba0349b991a3425c2efc5f32f022 Author: Weiqun Zhang Date: Tue Dec 27 16:39:32 2016 -0800 typo Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit d2abe37a6a8a23301fdf3db9b8e5da7d49070432 Merge: a9b5bceae 39cd48bc7 Author: Weiqun Zhang Date: Tue Dec 27 13:28:30 2016 -0800 Merge branch 'migration/6-distributionmap' into development commit 39cd48bc7416984d013878f7738b7d61cfebb5c8 Author: Weiqun Zhang Date: Tue Dec 27 13:28:13 2016 -0800 minor update to migration document Docs/Migration/Migration.md commit 1121f8a863841f7771a7e9e5e666e9476acd7bb2 Author: Weiqun Zhang Date: Tue Dec 27 13:18:45 2016 -0800 update migration document Docs/Migration/Migration.md commit a58f76bfc08fbe59303b337cad64db362caf4ca0 Author: Weiqun Zhang Date: Tue Dec 27 12:02:14 2016 -0800 update C_TensorMG Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/testVI.cpp commit 4a6686d54d6ebe45ffff4474eb0d003c80c132d1 Author: Weiqun Zhang Date: Tue Dec 27 08:33:40 2016 -0800 update more tests MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/MultiGrid_C/main.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tMFcopy.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tVisMF2.cpp Tests/FillBoundaryComparison/main.cpp Tests/IOBenchmark/IOTest.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp commit 0e2373f8bd34c1eb7bef87799da244b11d9abdbf Author: Weiqun Zhang Date: Tue Dec 27 07:39:21 2016 -0800 update Particles Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/two_level.cpp commit 4ac6a313f04d3e5240bd9b28228386ff3e4034b5 Author: Weiqun Zhang Date: Mon Dec 26 16:56:02 2016 -0800 update C_CellMG4 and C_to_F_MG Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Tutorials/MultiGrid_C/main.cpp commit 2d00bd1badaad6d0d8f53370fed531ed658bee20 Author: Weiqun Zhang Date: Mon Dec 26 16:27:16 2016 -0800 update C_CellMG Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Tutorials/MultiColor_C/main.cpp commit c32a1d8d61c96b1c6ba2ef614411220fe39ded2e Author: Weiqun Zhang Date: Mon Dec 26 15:38:17 2016 -0800 update Amr Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_DistributionMapping.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.cpp Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/main.cpp commit a9b5bceae07d8ad424e8c02ac88fdbc971219769 Author: Weiqun Zhang Date: Sun Dec 25 11:47:43 2016 -0800 uncomment BaseFab::size Src/Base/AMReX_BaseFab.H commit 69d0a4b492a6e456ecc8f27570d3dcdee51d9d1b Author: Weiqun Zhang Date: Sun Dec 25 20:49:39 2016 -0800 update Boundary and AmrCore Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_MultiMask.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit 23e84e4850c2b803a8147db655c1df7f72da7a71 Author: Weiqun Zhang Date: Sun Dec 25 12:18:22 2016 -0800 modify VisMF::Read to allow predefined MF Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 47808ed97b1cd1cc0db9a734f65e9d9413767bab Author: Weiqun Zhang Date: Sun Dec 25 11:54:30 2016 -0800 make FabArray::define virtual Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_iMultiFab.H commit cef0bc0335c619b3466245770cba1a47ce57b653 Author: Weiqun Zhang Date: Sun Dec 25 11:47:56 2016 -0800 fix a number of tutorials Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Tiling_C/main.cpp Tutorials/Tiling_Heat_C/main.cpp Tutorials/WaveEquation_C/main.cpp commit def31ae0437e539db17060a4d5f298cc2bc98c89 Author: Weiqun Zhang Date: Sun Dec 25 11:47:43 2016 -0800 uncomment BaseFab::size Src/Base/AMReX_BaseFab.H commit a93ac4024c23bf60e1ee3f24319388f63ec46b29 Author: Weiqun Zhang Date: Sun Dec 25 08:33:08 2016 -0800 fix AmrData Src/Base/AMReX_FabArray.H Src/Extern/amrdata/AMReX_AmrData.cpp Tutorials/DataServicesTest0/DataServicesTest0.cpp commit d43418b463d4ea87a31c5e139c038efe8223493a Author: Weiqun Zhang Date: Sun Dec 25 07:44:59 2016 -0800 removed DistributionMapping cache Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Utility.cpp commit d82abdf0c80cc9d526f2c8813ffe5c585ea0c83c Author: Weiqun Zhang Date: Sun Dec 25 07:26:41 2016 -0800 DistributionMapping is now a required argument of FabArray and hence MultiFab constructors. Docs/Migration/Migration.md Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Tutorials/HelloWorld_C/main.cpp commit ed4415740ce8eb7e4178030617ead123bd033551 Author: Dan Graves Date: Thu Dec 22 16:46:20 2016 -0800 these are too useful to go away Src/GeometryShop/AMReX_LoHiSide.H Src/GeometryShop/AMReX_LoHiSide.cpp commit 484dce6668f330771e4c16e5566fb1ee98be5ff4 Author: Dan Graves Date: Thu Dec 22 16:45:40 2016 -0800 more progress toward geometry port Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BoxIterator.H Src/GeometryShop/AMReX_BoxIterator.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_RealVect.H Src/GeometryShop/AMReX_RealVect.cpp Src/GeometryShop/Make.package Tests/GeometryShop/sphere/GNUmakefile commit 043f632aca84b810dbdb3e7c4bcb4b980408b9ab Author: Dan Graves Date: Thu Dec 22 16:08:34 2016 -0800 some casts to make stuff compile on our crappy mpi platform Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelDescriptor.cpp commit d9b0b94fffc8ff9dd301a05bdd276ef55ff723b5 Author: Dan Graves Date: Thu Dec 22 15:29:28 2016 -0800 adding some files Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/Make.package Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphere/sphereTest.cpp commit 7e2754ef45479ea9293e2386d68bb57b63a87726 Author: Dan Graves Date: Thu Dec 22 15:26:46 2016 -0800 making more progress on geometry Src/GeometryShop/AMReX_HyperPlaneIF.H Src/GeometryShop/AMReX_HyperPlaneIF.cpp Src/GeometryShop/AMReX_HyperSphereIF.H Src/GeometryShop/AMReX_HyperSphereIF.cpp Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphere/Make.package Tests/GeometryShop/sphere/sphere.inputs Tests/GeometryShop/sphere/sphereConvTest.cpp Tests/GeometryShop/sphere/sphereTest.cpp commit c5bf39ba316677a0161726ab591f9c67ca57905b Merge: a53949df8 7f41d2d3f Author: Weiqun Zhang Date: Thu Dec 22 10:31:13 2016 -0800 Merged in mzingale/amrex/zingale/work (pull request #3) update regtest to AMReX commit a53949df8869b16d58ee2dda33a2d5588bc23856 Merge: 7664ee2fa 44fb7bc4b Author: tannguyen Date: Wed Dec 21 16:19:45 2016 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 7664ee2fa04d46d06b8603f36f77f5234fd805db Author: tannguyen Date: Wed Dec 21 16:18:48 2016 -0800 mark up a few dot H files Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BaseFab.H commit 7f41d2d3f70b85edb59a54d56752589bbd0310ef Merge: ebd67a213 750427c3f Author: Michael Zingale Date: Wed Dec 21 14:29:43 2016 -0500 Merge branch 'development' into zingale/work commit 44fb7bc4b545221fcbaf2a4e90851778cd79e9d7 Merge: 015c830b3 750427c3f Author: Michael Zingale Date: Wed Dec 21 14:28:34 2016 -0500 Merged in mzingale/amrex/development (pull request #4) add --log_file option to the test suite commit 750427c3f80576ca603a8f12551dd37b37e1cd86 Author: Michael Zingale Date: Wed Dec 21 14:22:10 2016 -0500 add a --log_file option to direct output to a log file (it still goes to stdout too) Tools/RegressionTesting/params.py Tools/RegressionTesting/test_util.py commit 29c107ab5ba3267f5762b7c41d5422093e5da7f6 Merge: 56a4f36c3 015c830b3 Author: Michael Zingale Date: Wed Dec 21 11:26:58 2016 -0500 Merge branch 'development' of ssh://bitbucket.org/berkeleylab/AMReX into development commit 015c830b3d03623dcc68f547118c092b39dfadc8 Author: tannguyen Date: Tue Dec 20 19:47:38 2016 -0800 doxygen config file Docs/doxygen.conf commit 1d0fddfa150e98bdae745d4088977b24935438e5 Author: Dan Graves Date: Tue Dec 20 15:35:28 2016 -0800 lots of progress made here but not quite done Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BoxIterator.H Src/GeometryShop/AMReX_BoxIterator.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_MultiSphereIF.H Src/GeometryShop/AMReX_MultiSphereIF.cpp Src/GeometryShop/AMReX_RealVect.H Src/GeometryShop/AMReX_RealVect.cpp Src/GeometryShop/Make.package commit bdbe733c3f6f3736961e481f13e7f2bd270362c7 Author: Dan Graves Date: Mon Dec 19 16:21:57 2016 -0800 starting the geometryshop port in this branch Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BoxIterator.H Src/GeometryShop/AMReX_BoxIterator.cpp Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_HyperPlaneIF.H Src/GeometryShop/AMReX_HyperPlaneIF.cpp Src/GeometryShop/AMReX_HyperSphereIF.H Src/GeometryShop/AMReX_HyperSphereIF.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_MultiSphereIF.H Src/GeometryShop/AMReX_MultiSphereIF.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_RealVect.H Src/GeometryShop/AMReX_RealVect.cpp Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/Make.package commit ebd67a21377d3e289f6c078251d0d7484a177a3b Author: Michael Zingale Date: Sun Dec 18 20:53:29 2016 -0500 update ini Tools/RegressionTesting/AMReX-tests.ini commit 62b3bbca68e2357578cefc6a7eb5bf4411ff0014 Author: Michael Zingale Date: Sun Dec 18 20:51:56 2016 -0500 remove old inis Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/VARDEN-tests.ini Tools/RegressionTesting/radiation-tests.ini commit e18e53ce0bee1baee0e05a93fe3df661c3f251ba Author: Michael Zingale Date: Sun Dec 18 20:51:21 2016 -0500 switch to AMReX Tools/RegressionTesting/README Tools/RegressionTesting/example-tests.ini Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit 56a4f36c3cc939e93341d56857367f41e53dad04 Merge: 2c64f7aeb 67bfbc308 Author: Michael Zingale Date: Sun Dec 18 20:14:35 2016 -0500 Merge /home/zingale/temp/AMReX into development commit 2c64f7aebf4338066da11492ccee52830f263ccf Merge: 2b2be2c87 a3ae08c4c Author: Michael Zingale Date: Sun Dec 18 20:10:48 2016 -0500 Merge ssh://bitbucket.org/berkeleylab/AMReX into development commit 67bfbc30820247bec111616b9174935334f991af Author: Weiqun Zhang Date: Sun Dec 18 07:15:32 2016 -0800 fix tests MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/MultiGrid_C/main.cpp MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_advance.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/main.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Tests/BBIOBenchmark/BBIOTest.cpp Tests/BBIOBenchmark/BBIOTestDriver.cpp Tests/C_BaseLib/AMRProfTestBL.cpp Tests/C_BaseLib/t8BIT.cpp Tests/C_BaseLib/tBA.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tDM.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tFillFab.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tMFcopy.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tRABcast.cpp Tests/C_BaseLib/tRan.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tVisMF2.cpp Tests/C_BaseLib/tread.cpp Tests/FillBoundaryComparison/main.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/MKDir/MKDir.cpp commit c64870ee4c88752e20c17af32163c7a59fed10e4 Author: Weiqun Zhang Date: Sun Dec 18 06:41:25 2016 -0800 put pgas into amrex namespace Src/Base/AMReX_BLPgas.H commit 626553905203b7504da8d540917e00a0dc293f54 Author: Weiqun Zhang Date: Sun Dec 18 06:36:26 2016 -0800 fix some name conflicts in amrdata Docs/Migration/Migration.md Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.H Tutorials/DataServicesTest0/DataServicesTest0.cpp Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/writePlotFile.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.H Tutorials/PGAS_HEAT/writePlotFile.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/InTransitAnalysis.H Tutorials/Sidecar_EX1/InTransitAnalysis.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp Tutorials/Tiling_C/main.cpp Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.H Tutorials/Tiling_Heat_C/writePlotFile.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp commit cdd6f0b6a6804e8934f580333afaf3ddca70e281 Author: Weiqun Zhang Date: Sat Dec 17 17:15:36 2016 -0800 add amrex namespace to particle Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles.cpp Src/Particle/AMReX_TracerParticles.H Src/Particle/AMReX_TracerParticles.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp commit 192a50e948a536884c38d6a8dc488949f8a06a16 Author: Weiqun Zhang Date: Sat Dec 17 17:09:30 2016 -0800 add amrex namespace to linear solvers Docs/Migration/Migration.md Src/F_BaseLib/MultiFab_C_F.H Src/F_BaseLib/MultiFab_C_F.cpp Src/F_BaseLib/backtrace_c.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H Tutorials/MultiGrid_C/main.cpp Tutorials/MultiGrid_C/writePlotFile.H Tutorials/MultiGrid_C/writePlotFile.cpp commit 74133aa3ba71c3c444ea3767b85db3e128ece309 Author: Weiqun Zhang Date: Sat Dec 17 16:59:49 2016 -0800 move a few variables in amrex namespace into amrex::system namespace; one of the variables, verbose, was likely to cause conflict when using namespace amrex is used. Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.cpp commit 63fc1748463471622aa6736d97dff93116d755da Author: Weiqun Zhang Date: Sat Dec 17 15:56:19 2016 -0800 add namespace to Amr Docs/Migration/Migration.md Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_Extrapolater.H Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_SlabStat.H Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Amr/AMReX_StationData.H Src/Amr/AMReX_StationData.cpp Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_dt.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/main.cpp commit 408b6e0c53e3a4131ce5223071d27632497c18fd Author: Weiqun Zhang Date: Sat Dec 17 15:14:38 2016 -0800 add namespace to Boundary and AmrCore Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_MultiMask.cpp Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp Tutorials/AMR_Adv_C_v2/Source/main.cpp commit f968ea1082ae323fecab8d5e77ef46800eb2efbf Author: Weiqun Zhang Date: Fri Dec 16 15:56:09 2016 -0800 add namespace to Base Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_Lazy.H Src/Base/AMReX_Lazy.cpp Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MemProfiler.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_Orientation.H Src/Base/AMReX_Orientation.cpp Src/Base/AMReX_PList.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_Pointers.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Tuple.H Src/Base/AMReX_UseCount.H Src/Base/AMReX_UseCount.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_ccse-mpi.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Tutorials/HelloWorld_C/main.cpp commit 18563c0d75bb187e08f4de1ba194843c1f658591 Author: Weiqun Zhang Date: Fri Dec 16 13:32:07 2016 -0800 namespace BoxLib --> namespace amrex Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_SPACE.H Src/Base/AMReX_Utility.H commit cec98853d5d49ce39432669b6536dda2ce3832d3 Author: Weiqun Zhang Date: Fri Dec 16 12:58:01 2016 -0800 BoxLib:: --> amrex:: Docs/Migration/Migration.md Docs/Readme.profiling MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/MultiGrid_C/main.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/main.cpp Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BLassert.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_Orientation.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/hpgmg/BL_HPGMG.cpp Src/F_BaseLib/MultiFab_C_F.cpp Src/F_Interfaces/BaseLib/main.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles.cpp Src/Particle/AMReX_TracerParticles.cpp Tests/BBIOBenchmark/BBIOTest.cpp Tests/BBIOBenchmark/BBIOTestDriver.cpp Tests/C_BaseLib/AMRProfTestBL.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp Tests/C_BaseLib/tBA.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tDM.cpp Tests/C_BaseLib/tDir.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tFillFab.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tMFcopy.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tRABcast.cpp Tests/C_BaseLib/tRan.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tVisMF2.cpp Tests/C_BaseLib/tread.cpp Tests/FillBoundaryComparison/main.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/MKDir/MKDir.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/mfMinMax.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFcol.cpp Tools/C_util/ViewMF/viewMFdiff.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/main.cpp Tutorials/DataServicesTest0/DataServicesTest0.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.cpp Tutorials/HelloWorld_C/main.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/MultiGrid_C/writePlotFile.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp Tutorials/Tiling_C/main.cpp Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.cpp commit 261d73f46dc56b9a4ca915cc560bac7ce1ef4087 Author: Weiqun Zhang Date: Fri Dec 16 10:39:36 2016 -0800 AMReX:: --> amrex:: Docs/Migration/Migration.md Src/Base/AMReX_Array.H Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp commit 08f0891a5422221b823d8a8fd7cfac66199c4e7b Author: Weiqun Zhang Date: Fri Dec 16 09:43:57 2016 -0800 fix Fortran BoxLib tests too Src/F_BaseLib/GPackage.mak Tools/Migration/step-1-amrex_home/amrex_home.sh commit 8d43b15f138cec47fd1a636365c9c7a84959e8f5 Author: Weiqun Zhang Date: Fri Dec 16 09:19:46 2016 -0800 update migration document and scripts Docs/Migration/Migration.md Tools/Migration/step-1-amrex_home/amrex_home.sh Tools/Migration/step-3-amrex-prefix/amrexprefix.sh Tools/Migration/step-4-dirname/dirname.sh commit 5b87f27b1258a3850453d690ad91533d776280ab Author: Weiqun Zhang Date: Fri Dec 16 09:00:16 2016 -0800 update make files for the directory name changes MiniApps/FillBoundary/GNUmakefile MiniApps/MultiGrid_C/GNUmakefile MiniApps/PGAS_SMC/GNUmakefile Src/Amr/Make.package Src/AmrCore/Make.package Src/Base/GNUmakefile Src/Base/Make.package Src/Boundary/Make.package Src/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/Particle/Make.package Tests/BBIOBenchmark/GNUmakefile Tests/C_BaseLib/BcastClasses/GNUmakefile Tests/C_BaseLib/GNUmakefile Tests/FillBoundaryComparison/GNUmakefile Tests/IOBenchmark/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile.dumpi Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/MKDir/GNUmakefile Tools/C_util/AmrDeriveTecplot/GNUmakefile Tools/C_util/Convergence/GNUmakefile Tools/C_util/Statistics/GNUmakefile Tools/C_util/dbgTools/GNUmakefile Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/README.md Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/DataServicesTest0/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/GettingStarted_C/GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_CF/GNUmakefile Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HelloWorld_C/GNUmakefile Tutorials/HelloWorld_CF/GNUmakefile Tutorials/MultiColor_C/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiGrid_C/GNUmakefile Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PIC_C/GNUmakefile Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Tiling_C/GNUmakefile Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/TwoGrid_PIC_C/GNUmakefile Tutorials/WaveEquation_C/GNUmakefile commit 3c0d2fcde396c6d656d3359e10f4ec0223251a51 Author: Weiqun Zhang Date: Fri Dec 16 08:53:23 2016 -0800 shorten directory names Src/Amr/AMReX_ARRAYLIM_1D.F Src/Amr/AMReX_ARRAYLIM_2D.F Src/Amr/AMReX_ARRAYLIM_3D.F Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_Extrapolater.H Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_FLUSH_F.H Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_MAKESLICE_3D.F Src/Amr/AMReX_MAKESLICE_F.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_SLABSTAT_1D.F Src/Amr/AMReX_SLABSTAT_2D.F Src/Amr/AMReX_SLABSTAT_3D.F Src/Amr/AMReX_SLABSTAT_F.H Src/Amr/AMReX_SlabStat.H Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Amr/AMReX_StationData.H Src/Amr/AMReX_StationData.cpp Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/Amr/CMakeLists.txt Src/Amr/Make.package Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FLUXREG_1D.F Src/AmrCore/AMReX_FLUXREG_2D.F Src/AmrCore/AMReX_FLUXREG_3D.F Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_1D.F Src/AmrCore/AMReX_INTERP_2D.F Src/AmrCore/AMReX_INTERP_3D.F Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLBoxLib_F.f Src/Base/AMReX_BLFort.H Src/Base/AMReX_BLParmParse_F.f Src/Base/AMReX_BLPgas.H Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BLProfiler_F.f Src/Base/AMReX_BLassert.H Src/Base/AMReX_BLutil_F.f Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CONSTANTS.H Src/Base/AMReX_COORDSYS_1D.F Src/Base/AMReX_COORDSYS_2D.F Src/Base/AMReX_COORDSYS_3D.F Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FILCC_1D.F Src/Base/AMReX_FILCC_2D.F Src/Base/AMReX_FILCC_3D.F Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_Lazy.H Src/Base/AMReX_Lazy.cpp Src/Base/AMReX_Looping.H Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MemProfiler.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_Orientation.H Src/Base/AMReX_Orientation.cpp Src/Base/AMReX_PList.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_Pointers.H Src/Base/AMReX_REAL.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_SPACE.H Src/Base/AMReX_SPACE_F.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Tuple.H Src/Base/AMReX_UseCount.H Src/Base/AMReX_UseCount.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_bc_types.fi Src/Base/AMReX_bl_flush.f Src/Base/AMReX_bl_fort_module.F90 Src/Base/AMReX_ccse-mpi.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Src/Base/AMReX_mempool_f.f90 Src/Base/AMReX_threadbox.f90 Src/Base/AMReX_winstd.H Src/Base/CMakeLists.txt Src/Base/GNUmakefile Src/Base/GPackage.mak Src/Base/Make.package Src/Base/OpenSource.txt Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_LO_UTIL.F Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/Boundary/OpenSource.txt Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles.cpp Src/Particle/AMReX_Particles_1D.F Src/Particle/AMReX_Particles_2D.F Src/Particle/AMReX_Particles_3D.F Src/Particle/AMReX_Particles_F.H Src/Particle/AMReX_TracerParticles.H Src/Particle/AMReX_TracerParticles.cpp Src/Particle/CMakeLists.txt Src/Particle/Make.package commit efd5f98217bc71fbfbe672ab2a42386006f1381e Author: Weiqun Zhang Date: Fri Dec 16 08:48:28 2016 -0800 rename C_mk to GNUMake Tools/GNUMake/Make.defs Tools/GNUMake/Make.local.template Tools/GNUMake/Make.machines Tools/GNUMake/Make.rules Tools/GNUMake/Make.upcxx Tools/GNUMake/README.md Tools/GNUMake/comps/cray.mak Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/intel.mak Tools/GNUMake/comps/pgi.mak Tools/GNUMake/packages/Make.hpgmg Tools/GNUMake/sites/Make.ccse Tools/GNUMake/sites/Make.nersc Tools/GNUMake/sites/Make.olcf Tools/GNUMake/sites/Make.unknown Tools/GNUMake/tools/Make.vtune commit 461d92f70c6428c0123e02d1520eb57ba5a8a041 Author: Weiqun Zhang Date: Fri Dec 16 08:35:21 2016 -0800 migration script: limit the scope of search and replace for performace Tools/Migration/step-3-amrex-prefix/amrexprefix.sh commit f8e7ec860056dd3df00d52a986b8b398b6aefca3 Author: Weiqun Zhang Date: Thu Dec 15 17:11:34 2016 -0800 add migration step 3 script Tools/Migration/step-3-amrex-prefix/amrexprefix.sh commit 00f52694287ece3a033a021ca2a7257513125aa4 Author: Weiqun Zhang Date: Thu Dec 15 17:06:32 2016 -0800 missed a few names Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H commit 77ebc80c39f3549f292be4f3f9e9bf5b3a7b563c Author: Weiqun Zhang Date: Thu Dec 15 16:39:37 2016 -0800 remove duplicated AMReX_ Src/C_AMRLib/AMReX_ARRAYLIM_1D.F Src/C_AMRLib/AMReX_ARRAYLIM_2D.F Src/C_AMRLib/AMReX_ARRAYLIM_3D.F Src/C_AMRLib/AMReX_Amr.H Src/C_AMRLib/AMReX_Amr.cpp Src/C_AMRLib/AMReX_AmrLevel.H Src/C_AMRLib/AMReX_AmrLevel.cpp Src/C_AMRLib/AMReX_AuxBoundaryData.H Src/C_AMRLib/AMReX_AuxBoundaryData.cpp Src/C_AMRLib/AMReX_Derive.H Src/C_AMRLib/AMReX_Derive.cpp Src/C_AMRLib/AMReX_Extrapolater.H Src/C_AMRLib/AMReX_Extrapolater.cpp Src/C_AMRLib/AMReX_FLUSH_F.H Src/C_AMRLib/AMReX_LevelBld.H Src/C_AMRLib/AMReX_MAKESLICE_3D.F Src/C_AMRLib/AMReX_MAKESLICE_F.H Src/C_AMRLib/AMReX_PROB_AMR_F.H Src/C_AMRLib/AMReX_SLABSTAT_1D.F Src/C_AMRLib/AMReX_SLABSTAT_2D.F Src/C_AMRLib/AMReX_SLABSTAT_3D.F Src/C_AMRLib/AMReX_SLABSTAT_F.H Src/C_AMRLib/AMReX_SlabStat.H Src/C_AMRLib/AMReX_SlabStat.cpp Src/C_AMRLib/AMReX_StateData.H Src/C_AMRLib/AMReX_StateData.cpp Src/C_AMRLib/AMReX_StateDescriptor.H Src/C_AMRLib/AMReX_StateDescriptor.cpp Src/C_AMRLib/AMReX_StationData.H Src/C_AMRLib/AMReX_StationData.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit 8523c2109a8f6a6970317462b8bc00a38d217edf Author: Weiqun Zhang Date: Thu Dec 15 16:34:15 2016 -0800 update Migration document Docs/Migration/Migration.md commit f5c1eafe444649460a0ed8ef394e127e284a3b22 Author: Weiqun Zhang Date: Thu Dec 15 16:29:12 2016 -0800 add AMReX_ to include Docs/Readme.backtrace MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/MultiGrid_C/COEF_3D.F MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/RHS_3D.F MiniApps/MultiGrid_C/RHS_F.H MiniApps/MultiGrid_C/main.cpp MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_F.H MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/main.cpp Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_1D.F Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_2D.F Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_3D.F Src/C_AMRLib/AMReX_AMReX_Amr.H Src/C_AMRLib/AMReX_AMReX_Amr.cpp Src/C_AMRLib/AMReX_AMReX_AmrLevel.H Src/C_AMRLib/AMReX_AMReX_AmrLevel.cpp Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.H Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.cpp Src/C_AMRLib/AMReX_AMReX_Derive.H Src/C_AMRLib/AMReX_AMReX_Derive.cpp Src/C_AMRLib/AMReX_AMReX_Extrapolater.H Src/C_AMRLib/AMReX_AMReX_Extrapolater.cpp Src/C_AMRLib/AMReX_AMReX_LevelBld.H Src/C_AMRLib/AMReX_AMReX_MAKESLICE_3D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_1D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_2D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_3D.F Src/C_AMRLib/AMReX_AMReX_SlabStat.H Src/C_AMRLib/AMReX_AMReX_SlabStat.cpp Src/C_AMRLib/AMReX_AMReX_StateData.H Src/C_AMRLib/AMReX_AMReX_StateData.cpp Src/C_AMRLib/AMReX_AMReX_StateDescriptor.H Src/C_AMRLib/AMReX_AMReX_StateDescriptor.cpp Src/C_AMRLib/AMReX_AMReX_StationData.H Src/C_AMRLib/AMReX_AMReX_StationData.cpp Src/C_AmrCoreLib/AMReX_AmrCore.H Src/C_AmrCoreLib/AMReX_AmrCore.cpp Src/C_AmrCoreLib/AMReX_AmrParGDB.H Src/C_AmrCoreLib/AMReX_AmrParticles.H Src/C_AmrCoreLib/AMReX_Cluster.H Src/C_AmrCoreLib/AMReX_Cluster.cpp Src/C_AmrCoreLib/AMReX_ErrorList.H Src/C_AmrCoreLib/AMReX_ErrorList.cpp Src/C_AmrCoreLib/AMReX_FLUXREG_1D.F Src/C_AmrCoreLib/AMReX_FLUXREG_2D.F Src/C_AmrCoreLib/AMReX_FLUXREG_3D.F Src/C_AmrCoreLib/AMReX_FLUXREG_F.H Src/C_AmrCoreLib/AMReX_FillPatchUtil.H Src/C_AmrCoreLib/AMReX_FillPatchUtil.cpp Src/C_AmrCoreLib/AMReX_FluxRegister.H Src/C_AmrCoreLib/AMReX_FluxRegister.cpp Src/C_AmrCoreLib/AMReX_INTERP_1D.F Src/C_AmrCoreLib/AMReX_INTERP_2D.F Src/C_AmrCoreLib/AMReX_INTERP_3D.F Src/C_AmrCoreLib/AMReX_INTERP_F.H Src/C_AmrCoreLib/AMReX_Interpolater.H Src/C_AmrCoreLib/AMReX_Interpolater.cpp Src/C_AmrCoreLib/AMReX_TagBox.H Src/C_AmrCoreLib/AMReX_TagBox.cpp Src/C_BaseLib/AMReX_Arena.H Src/C_BaseLib/AMReX_Arena.cpp Src/C_BaseLib/AMReX_Array.H Src/C_BaseLib/AMReX_ArrayLim.H Src/C_BaseLib/AMReX_BArena.H Src/C_BaseLib/AMReX_BArena.cpp Src/C_BaseLib/AMReX_BCRec.H Src/C_BaseLib/AMReX_BCRec.cpp Src/C_BaseLib/AMReX_BLBackTrace.cpp Src/C_BaseLib/AMReX_BLFort.H Src/C_BaseLib/AMReX_BLPgas.H Src/C_BaseLib/AMReX_BLPgas.cpp Src/C_BaseLib/AMReX_BLProfiler.H Src/C_BaseLib/AMReX_BLProfiler.cpp Src/C_BaseLib/AMReX_BLassert.H Src/C_BaseLib/AMReX_BaseFab.H Src/C_BaseLib/AMReX_BaseFab.cpp Src/C_BaseLib/AMReX_BaseFab_f.H Src/C_BaseLib/AMReX_Box.H Src/C_BaseLib/AMReX_Box.cpp Src/C_BaseLib/AMReX_BoxArray.H Src/C_BaseLib/AMReX_BoxArray.cpp Src/C_BaseLib/AMReX_BoxDomain.H Src/C_BaseLib/AMReX_BoxDomain.cpp Src/C_BaseLib/AMReX_BoxLib.H Src/C_BaseLib/AMReX_BoxLib.cpp Src/C_BaseLib/AMReX_BoxList.H Src/C_BaseLib/AMReX_BoxList.cpp Src/C_BaseLib/AMReX_CArena.H Src/C_BaseLib/AMReX_CArena.cpp Src/C_BaseLib/AMReX_CONSTANTS.H Src/C_BaseLib/AMReX_COORDSYS_1D.F Src/C_BaseLib/AMReX_COORDSYS_2D.F Src/C_BaseLib/AMReX_COORDSYS_3D.F Src/C_BaseLib/AMReX_COORDSYS_F.H Src/C_BaseLib/AMReX_CoordSys.H Src/C_BaseLib/AMReX_CoordSys.cpp Src/C_BaseLib/AMReX_DistributionMapping.H Src/C_BaseLib/AMReX_DistributionMapping.cpp Src/C_BaseLib/AMReX_FArrayBox.H Src/C_BaseLib/AMReX_FArrayBox.cpp Src/C_BaseLib/AMReX_FILCC_1D.F Src/C_BaseLib/AMReX_FILCC_2D.F Src/C_BaseLib/AMReX_FILCC_3D.F Src/C_BaseLib/AMReX_FPC.H Src/C_BaseLib/AMReX_FPC.cpp Src/C_BaseLib/AMReX_FabArray.H Src/C_BaseLib/AMReX_FabArray.cpp Src/C_BaseLib/AMReX_FabConv.H Src/C_BaseLib/AMReX_FabConv.cpp Src/C_BaseLib/AMReX_Geometry.H Src/C_BaseLib/AMReX_Geometry.cpp Src/C_BaseLib/AMReX_IArrayBox.H Src/C_BaseLib/AMReX_IArrayBox.cpp Src/C_BaseLib/AMReX_IndexType.H Src/C_BaseLib/AMReX_IndexType.cpp Src/C_BaseLib/AMReX_IntVect.H Src/C_BaseLib/AMReX_IntVect.cpp Src/C_BaseLib/AMReX_Lazy.cpp Src/C_BaseLib/AMReX_MemPool.cpp Src/C_BaseLib/AMReX_MemProfiler.cpp Src/C_BaseLib/AMReX_MultiFab.H Src/C_BaseLib/AMReX_MultiFab.cpp Src/C_BaseLib/AMReX_MultiFabUtil.H Src/C_BaseLib/AMReX_MultiFabUtil.cpp Src/C_BaseLib/AMReX_MultiFabUtil_F.H Src/C_BaseLib/AMReX_NFiles.H Src/C_BaseLib/AMReX_NFiles.cpp Src/C_BaseLib/AMReX_Orientation.H Src/C_BaseLib/AMReX_Orientation.cpp Src/C_BaseLib/AMReX_ParallelDescriptor.H Src/C_BaseLib/AMReX_ParallelDescriptor.cpp Src/C_BaseLib/AMReX_ParmParse.cpp Src/C_BaseLib/AMReX_Periodicity.H Src/C_BaseLib/AMReX_Periodicity.cpp Src/C_BaseLib/AMReX_PhysBCFunct.H Src/C_BaseLib/AMReX_PhysBCFunct.cpp Src/C_BaseLib/AMReX_PlotFileUtil.H Src/C_BaseLib/AMReX_PlotFileUtil.cpp Src/C_BaseLib/AMReX_Pointers.H Src/C_BaseLib/AMReX_RealBox.H Src/C_BaseLib/AMReX_RealBox.cpp Src/C_BaseLib/AMReX_SPACE_F.H Src/C_BaseLib/AMReX_TinyProfiler.H Src/C_BaseLib/AMReX_TinyProfiler.cpp Src/C_BaseLib/AMReX_Tuple.H Src/C_BaseLib/AMReX_UseCount.H Src/C_BaseLib/AMReX_UseCount.cpp Src/C_BaseLib/AMReX_Utility.H Src/C_BaseLib/AMReX_Utility.cpp Src/C_BaseLib/AMReX_VisMF.H Src/C_BaseLib/AMReX_VisMF.cpp Src/C_BaseLib/AMReX_ccse-mpi.H Src/C_BaseLib/AMReX_iMultiFab.H Src/C_BaseLib/AMReX_iMultiFab.cpp Src/C_BoundaryLib/AMReX_BndryData.H Src/C_BoundaryLib/AMReX_BndryData.cpp Src/C_BoundaryLib/AMReX_BndryRegister.H Src/C_BoundaryLib/AMReX_BndryRegister.cpp Src/C_BoundaryLib/AMReX_BoundCond.H Src/C_BoundaryLib/AMReX_FabSet.H Src/C_BoundaryLib/AMReX_FabSet.cpp Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_1D.F Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_F.H Src/C_BoundaryLib/AMReX_InterpBndryData.H Src/C_BoundaryLib/AMReX_InterpBndryData.cpp Src/C_BoundaryLib/AMReX_LO_UTIL.F Src/C_BoundaryLib/AMReX_MacBndry.H Src/C_BoundaryLib/AMReX_MacBndry.cpp Src/C_BoundaryLib/AMReX_Mask.H Src/C_BoundaryLib/AMReX_Mask.cpp Src/C_BoundaryLib/AMReX_MultiMask.H Src/C_BoundaryLib/AMReX_MultiMask.cpp Src/C_ParticleLib/AMReX_ParGDB.H Src/C_ParticleLib/AMReX_Particles.H Src/C_ParticleLib/AMReX_Particles.cpp Src/C_ParticleLib/AMReX_Particles_F.H Src/C_ParticleLib/AMReX_TracerParticles.H Src/C_ParticleLib/AMReX_TracerParticles.cpp Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/amrdata/AMReX_FABUTIL_1D.F Src/Extern/amrdata/AMReX_FABUTIL_2D.F Src/Extern/amrdata/AMReX_FABUTIL_3D.F Src/Extern/hpgmg/BL_HPGMG.H Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/MultiFab_C_F.H Src/F_BaseLib/backtrace_c.cpp Src/F_Interfaces/BaseLib/boxarray_fi.cpp Src/F_Interfaces/BaseLib/geometry_fi.cpp Src/F_Interfaces/BaseLib/main.cpp Src/F_Interfaces/BaseLib/multifab_fi.cpp Src/F_Interfaces/BaseLib/parallel_fi.cpp Src/F_Interfaces/BaseLib/parmparse_fi.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F Src/LinearSolvers/C_CellMG/AMReX_AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/ABec2.H Src/LinearSolvers/C_CellMG4/ABec2_F.H Src/LinearSolvers/C_CellMG4/ABec4.H Src/LinearSolvers/C_CellMG4/ABec4_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D1.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D2.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D3.F Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_3D.F Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/DV_2D.mF Src/LinearSolvers/C_TensorMG/DV_3D1.mF Src/LinearSolvers/C_TensorMG/DV_3D2.mF Src/LinearSolvers/C_TensorMG/DV_3D3.mF Src/LinearSolvers/C_TensorMG/DV_3D4.mF Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Tests/BBIOBenchmark/BBIOTest.cpp Tests/BBIOBenchmark/BBIOTestDriver.cpp Tests/C_BaseLib/AMRProfTestBL.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp Tests/C_BaseLib/t8BIT.cpp Tests/C_BaseLib/tBA.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tDM.cpp Tests/C_BaseLib/tDir.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tFillFab.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tMFcopy.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tRABcast.cpp Tests/C_BaseLib/tRan.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tVisMF2.cpp Tests/C_BaseLib/tread.cpp Tests/FillBoundaryComparison/main.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/LinearSolvers/C_CellMG/COEF_2D.F Tests/LinearSolvers/C_CellMG/COEF_3D.F Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_2D.F Tests/LinearSolvers/C_CellMG/MACOPERATOR_3D.F Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/main_2D.F Tests/LinearSolvers/C_TensorMG/main_3D.F Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/COEF_1D.F Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_3D.F Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/MKDir/MKDir.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/AVGDOWN_2D.F Tools/C_util/Statistics/AVGDOWN_3D.F Tools/C_util/Statistics/AVGDOWN_F.H Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/PltFileFluxAve.H Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.H Tools/C_util/Statistics/PltFileXAve.cpp Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/mfMinMax.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFcol.cpp Tools/C_util/ViewMF/viewMFdiff.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/main.cpp Tutorials/DataServicesTest0/DataServicesTest0.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/FILCC_2D.F Tutorials/HeatEquation_EX2_C/FILCC_3D.F Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HelloWorld_C/main.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/MultiGrid_C/COEF_2D.F90 Tutorials/MultiGrid_C/COEF_3D.F90 Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H Tutorials/MultiGrid_C/RHS_2D.F90 Tutorials/MultiGrid_C/RHS_3D.F90 Tutorials/MultiGrid_C/RHS_F.H Tutorials/MultiGrid_C/main.cpp Tutorials/MultiGrid_C/writePlotFile.H Tutorials/MultiGrid_C/writePlotFile.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.H Tutorials/PGAS_HEAT/writePlotFile.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/InTransitAnalysis.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp Tutorials/Tiling_C/main.cpp Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.H Tutorials/Tiling_Heat_C/writePlotFile.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp commit 8b06440262bffbcca2e1d540f638319bba71e304 Author: Weiqun Zhang Date: Thu Dec 15 15:34:10 2016 -0800 rm Tests/F_BaseLib Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/ball_def.14656 Tests/F_BaseLib/conn_defs Tests/F_BaseLib/def_knapsack.out Tests/F_BaseLib/fornberg_weights.f90 Tests/F_BaseLib/inputs.domain Tests/F_BaseLib/main.f90 Tests/F_BaseLib/makefile Tests/F_BaseLib/mt19937ar.f90 Tests/F_BaseLib/t_bl_prof.f90 Tests/F_BaseLib/t_bx.f90 Tests/F_BaseLib/t_bxasc.f90 Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_knapsack.f90 Tests/F_BaseLib/t_main.f90 Tests/F_BaseLib/t_particles.f90 commit beec626d6dd716ea7335c84e48dec4e7d4b48ca1 Author: Weiqun Zhang Date: Thu Dec 15 15:33:28 2016 -0800 rm Src/Python Src/Python/.gitignore Src/Python/F90/Makefile Src/Python/F90/README Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/boxarray.py Src/Python/F90/fboxlib/fab.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/fboxlib/multifab.py Src/Python/F90/fboxlib/regrid.py Src/Python/F90/setup.py Src/Python/F90/src/blobjects.f90 Src/Python/F90/src/blobjects.py Src/Python/F90/src/boxlib_numpy_c.c Src/Python/F90/src/boxlib_numpy_f.f90 Src/Python/F90/src/fboxlib.f90 Src/Python/F90/src/fboxlib_c.c Src/Python/F90/src/make_new_grids.f90 Src/Python/F90/src/regrid.f90 Src/Python/F90/src/tag_boxes.f90 Src/Python/F90/tests/regrid.py Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak Src/Python/GPackage.mak Src/Python/README Src/Python/boxlib/__init__.py Src/Python/boxlib/bl1.py Src/Python/boxlib/bl2.py Src/Python/boxlib/bl3.py Src/Python/contrib/chemSupport.H Src/Python/contrib/chemSupport.cpp Src/Python/contrib/support.H Src/Python/contrib/support.cpp Src/Python/setup.py Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id Src/Python/swig/boxlib.i Src/Python/swig/numpy.i Src/Python/tests/test-multifab.py commit 3ab050052e1eaffe0dbca75a356b4dc7de2b66dd Author: Weiqun Zhang Date: Thu Dec 15 15:32:50 2016 -0800 add AMReX prefix to file names Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_1D.F Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_2D.F Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_3D.F Src/C_AMRLib/AMReX_AMReX_Amr.H Src/C_AMRLib/AMReX_AMReX_Amr.cpp Src/C_AMRLib/AMReX_AMReX_AmrLevel.H Src/C_AMRLib/AMReX_AMReX_AmrLevel.cpp Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.H Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.cpp Src/C_AMRLib/AMReX_AMReX_Derive.H Src/C_AMRLib/AMReX_AMReX_Derive.cpp Src/C_AMRLib/AMReX_AMReX_Extrapolater.H Src/C_AMRLib/AMReX_AMReX_Extrapolater.cpp Src/C_AMRLib/AMReX_AMReX_FLUSH_F.H Src/C_AMRLib/AMReX_AMReX_LevelBld.H Src/C_AMRLib/AMReX_AMReX_MAKESLICE_3D.F Src/C_AMRLib/AMReX_AMReX_MAKESLICE_F.H Src/C_AMRLib/AMReX_AMReX_PROB_AMR_F.H Src/C_AMRLib/AMReX_AMReX_SLABSTAT_1D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_2D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_3D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_F.H Src/C_AMRLib/AMReX_AMReX_SlabStat.H Src/C_AMRLib/AMReX_AMReX_SlabStat.cpp Src/C_AMRLib/AMReX_AMReX_StateData.H Src/C_AMRLib/AMReX_AMReX_StateData.cpp Src/C_AMRLib/AMReX_AMReX_StateDescriptor.H Src/C_AMRLib/AMReX_AMReX_StateDescriptor.cpp Src/C_AMRLib/AMReX_AMReX_StationData.H Src/C_AMRLib/AMReX_AMReX_StationData.cpp Src/C_AMRLib/AMReX_extrapolater_1d.f90 Src/C_AMRLib/AMReX_extrapolater_2d.f90 Src/C_AMRLib/AMReX_extrapolater_3d.f90 Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/Make.package Src/C_AmrCoreLib/AMReX_AmrCore.H Src/C_AmrCoreLib/AMReX_AmrCore.cpp Src/C_AmrCoreLib/AMReX_AmrParGDB.H Src/C_AmrCoreLib/AMReX_AmrParticles.H Src/C_AmrCoreLib/AMReX_Cluster.H Src/C_AmrCoreLib/AMReX_Cluster.cpp Src/C_AmrCoreLib/AMReX_ErrorList.H Src/C_AmrCoreLib/AMReX_ErrorList.cpp Src/C_AmrCoreLib/AMReX_FLUXREG_1D.F Src/C_AmrCoreLib/AMReX_FLUXREG_2D.F Src/C_AmrCoreLib/AMReX_FLUXREG_3D.F Src/C_AmrCoreLib/AMReX_FLUXREG_F.H Src/C_AmrCoreLib/AMReX_FillPatchUtil.H Src/C_AmrCoreLib/AMReX_FillPatchUtil.cpp Src/C_AmrCoreLib/AMReX_FluxRegister.H Src/C_AmrCoreLib/AMReX_FluxRegister.cpp Src/C_AmrCoreLib/AMReX_INTERP_1D.F Src/C_AmrCoreLib/AMReX_INTERP_2D.F Src/C_AmrCoreLib/AMReX_INTERP_3D.F Src/C_AmrCoreLib/AMReX_INTERP_F.H Src/C_AmrCoreLib/AMReX_Interpolater.H Src/C_AmrCoreLib/AMReX_Interpolater.cpp Src/C_AmrCoreLib/AMReX_TagBox.H Src/C_AmrCoreLib/AMReX_TagBox.cpp Src/C_AmrCoreLib/CMakeLists.txt Src/C_AmrCoreLib/Make.package Src/C_BaseLib/AMReX_Arena.H Src/C_BaseLib/AMReX_Arena.cpp Src/C_BaseLib/AMReX_Array.H Src/C_BaseLib/AMReX_ArrayLim.H Src/C_BaseLib/AMReX_BArena.H Src/C_BaseLib/AMReX_BArena.cpp Src/C_BaseLib/AMReX_BCRec.H Src/C_BaseLib/AMReX_BCRec.cpp Src/C_BaseLib/AMReX_BC_TYPES.H Src/C_BaseLib/AMReX_BLBackTrace.H Src/C_BaseLib/AMReX_BLBackTrace.cpp Src/C_BaseLib/AMReX_BLBoxLib_F.f Src/C_BaseLib/AMReX_BLFort.H Src/C_BaseLib/AMReX_BLParmParse_F.f Src/C_BaseLib/AMReX_BLPgas.H Src/C_BaseLib/AMReX_BLPgas.cpp Src/C_BaseLib/AMReX_BLProfiler.H Src/C_BaseLib/AMReX_BLProfiler.cpp Src/C_BaseLib/AMReX_BLProfiler_F.f Src/C_BaseLib/AMReX_BLassert.H Src/C_BaseLib/AMReX_BLutil_F.f Src/C_BaseLib/AMReX_BaseFab.H Src/C_BaseLib/AMReX_BaseFab.cpp Src/C_BaseLib/AMReX_BaseFab_f.H Src/C_BaseLib/AMReX_BaseFab_nd.f90 Src/C_BaseLib/AMReX_Box.H Src/C_BaseLib/AMReX_Box.cpp Src/C_BaseLib/AMReX_BoxArray.H 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Src/C_BaseLib/AMReX_IArrayBox.H Src/C_BaseLib/AMReX_IArrayBox.cpp Src/C_BaseLib/AMReX_IndexType.H Src/C_BaseLib/AMReX_IndexType.cpp Src/C_BaseLib/AMReX_IntVect.H Src/C_BaseLib/AMReX_IntVect.cpp Src/C_BaseLib/AMReX_Lazy.H Src/C_BaseLib/AMReX_Lazy.cpp Src/C_BaseLib/AMReX_Looping.H Src/C_BaseLib/AMReX_MemPool.H Src/C_BaseLib/AMReX_MemPool.cpp Src/C_BaseLib/AMReX_MemProfiler.H Src/C_BaseLib/AMReX_MemProfiler.cpp Src/C_BaseLib/AMReX_MultiFab.H Src/C_BaseLib/AMReX_MultiFab.cpp Src/C_BaseLib/AMReX_MultiFabUtil.H Src/C_BaseLib/AMReX_MultiFabUtil.cpp Src/C_BaseLib/AMReX_MultiFabUtil_1d.f90 Src/C_BaseLib/AMReX_MultiFabUtil_2d.f90 Src/C_BaseLib/AMReX_MultiFabUtil_3d.f90 Src/C_BaseLib/AMReX_MultiFabUtil_F.H Src/C_BaseLib/AMReX_NFiles.H Src/C_BaseLib/AMReX_NFiles.cpp Src/C_BaseLib/AMReX_Orientation.H Src/C_BaseLib/AMReX_Orientation.cpp Src/C_BaseLib/AMReX_PList.H Src/C_BaseLib/AMReX_ParallelDescriptor.H Src/C_BaseLib/AMReX_ParallelDescriptor.cpp Src/C_BaseLib/AMReX_ParmParse.H Src/C_BaseLib/AMReX_ParmParse.cpp Src/C_BaseLib/AMReX_Periodicity.H Src/C_BaseLib/AMReX_Periodicity.cpp Src/C_BaseLib/AMReX_PhysBCFunct.H Src/C_BaseLib/AMReX_PhysBCFunct.cpp Src/C_BaseLib/AMReX_PlotFileUtil.H Src/C_BaseLib/AMReX_PlotFileUtil.cpp Src/C_BaseLib/AMReX_Pointers.H Src/C_BaseLib/AMReX_REAL.H Src/C_BaseLib/AMReX_RealBox.H Src/C_BaseLib/AMReX_RealBox.cpp Src/C_BaseLib/AMReX_SPACE.H Src/C_BaseLib/AMReX_SPACE_F.H Src/C_BaseLib/AMReX_TinyProfiler.H Src/C_BaseLib/AMReX_TinyProfiler.cpp Src/C_BaseLib/AMReX_Tuple.H Src/C_BaseLib/AMReX_UseCount.H Src/C_BaseLib/AMReX_UseCount.cpp Src/C_BaseLib/AMReX_Utility.H Src/C_BaseLib/AMReX_Utility.cpp Src/C_BaseLib/AMReX_VisMF.H Src/C_BaseLib/AMReX_VisMF.cpp Src/C_BaseLib/AMReX_bc_types.fi Src/C_BaseLib/AMReX_bl_flush.f Src/C_BaseLib/AMReX_bl_fort_module.F90 Src/C_BaseLib/AMReX_ccse-mpi.H Src/C_BaseLib/AMReX_iMultiFab.H Src/C_BaseLib/AMReX_iMultiFab.cpp Src/C_BaseLib/AMReX_mempool_f.f90 Src/C_BaseLib/AMReX_threadbox.f90 Src/C_BaseLib/AMReX_winstd.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/GNUmakefile Src/C_BaseLib/GPackage.mak Src/C_BaseLib/Make.package Src/C_BoundaryLib/AMReX_BndryData.H Src/C_BoundaryLib/AMReX_BndryData.cpp Src/C_BoundaryLib/AMReX_BndryRegister.H Src/C_BoundaryLib/AMReX_BndryRegister.cpp Src/C_BoundaryLib/AMReX_BoundCond.H Src/C_BoundaryLib/AMReX_FabSet.H Src/C_BoundaryLib/AMReX_FabSet.cpp Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_1D.F Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_F.H Src/C_BoundaryLib/AMReX_InterpBndryData.H Src/C_BoundaryLib/AMReX_InterpBndryData.cpp Src/C_BoundaryLib/AMReX_LO_BCTYPES.H Src/C_BoundaryLib/AMReX_LO_UTIL.F Src/C_BoundaryLib/AMReX_MacBndry.H Src/C_BoundaryLib/AMReX_MacBndry.cpp Src/C_BoundaryLib/AMReX_Mask.H Src/C_BoundaryLib/AMReX_Mask.cpp Src/C_BoundaryLib/AMReX_MultiMask.H Src/C_BoundaryLib/AMReX_MultiMask.cpp Src/C_BoundaryLib/CMakeLists.txt Src/C_BoundaryLib/Make.package Src/C_ParticleLib/AMReX_ParGDB.H Src/C_ParticleLib/AMReX_ParticleInit.H Src/C_ParticleLib/AMReX_Particles.H Src/C_ParticleLib/AMReX_Particles.cpp Src/C_ParticleLib/AMReX_Particles_1D.F Src/C_ParticleLib/AMReX_Particles_2D.F Src/C_ParticleLib/AMReX_Particles_3D.F Src/C_ParticleLib/AMReX_Particles_F.H Src/C_ParticleLib/AMReX_TracerParticles.H Src/C_ParticleLib/AMReX_TracerParticles.cpp Src/C_ParticleLib/CMakeLists.txt Src/C_ParticleLib/Make.package Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/amrdata/AMReX_FABUTIL_1D.F Src/Extern/amrdata/AMReX_FABUTIL_2D.F Src/Extern/amrdata/AMReX_FABUTIL_3D.F Src/Extern/amrdata/CMakeLists.txt Src/Extern/amrdata/Make.package Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F Src/LinearSolvers/C_CellMG/AMReX_AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG/AMReX_lo_bctypes.fi Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_CellMG4/Make.package Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D1.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D2.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D3.F Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_3D.F Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/CMakeLists.txt Src/LinearSolvers/C_TensorMG/Make.package Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/Make.package commit f141a37c0f3b8fa4d436292dc157b07f8bf9846c Author: Weiqun Zhang Date: Thu Dec 15 14:52:55 2016 -0800 fix Tensor MG test Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/main_2D.F Tests/LinearSolvers/C_TensorMG/main_3D.F Tests/LinearSolvers/C_TensorMG/main_F.H commit d12b6d0ea206228857613a3b4d96059b45110d34 Author: Weiqun Zhang Date: Thu Dec 15 14:52:40 2016 -0800 rm duplicated source file Tests/LinearSolvers/C_CellMG/Make.package commit 59eb9e6e65e1612f7597862348b8c4b5c07cdfa9 Author: Weiqun Zhang Date: Sun Dec 11 16:00:58 2016 -0800 rm Tests/StencilOrder Tests/StencilOrder/README Tests/StencilOrder/program.f90 commit 4031d584790874e7e77003ad23d5c9af1cc846b7 Author: Weiqun Zhang Date: Sun Dec 11 15:58:57 2016 -0800 rm LinearSolvers/F_MG_Old_Nodal_Stencil Conflicts: Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/bc_interp.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_multi.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_rhs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/compute_defect.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_1lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_2lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_1lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_2lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/init_cell_coeffs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.cross Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.dense Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.cross Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.dense Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/itsol.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/main.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/makefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_nd.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_solve.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_interface_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_cpp.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_tower_smoother.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_multi.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_rhs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_smoothers.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_apply.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_fill.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_sync_resid.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/regression Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_smoother.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/wrapper.f90 commit faafd2cdf45b1111b8cdaf709173a036f77ea5fc Author: Weiqun Zhang Date: Sun Dec 11 08:16:23 2016 -0800 rm Tutorials/MultiFab_C_F Conflicts: Tutorials/MultiFab_C_F/GNUmakefile Tutorials/MultiFab_C_F/main.cpp Tutorials/MultiFab_C_F/GNUmakefile Tutorials/MultiFab_C_F/Make.package Tutorials/MultiFab_C_F/ff.f90 Tutorials/MultiFab_C_F/main.cpp commit 7da71ecef4d2dadce59d1a76c57dc073f8043abb Author: Weiqun Zhang Date: Sat Dec 10 11:43:48 2016 -0800 rm AMR_Trilinos_C Conflicts: Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/AMR_Trilinos_C/Solver.H Tutorials/AMR_Trilinos_C/Solver.cpp Tutorials/AMR_Trilinos_C/driver.cpp Tutorials/AMR_Trilinos_C/writePlotFile.H Tutorials/AMR_Trilinos_C/writePlotFile.cpp Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/AMR_Trilinos_C/Make.package Tutorials/AMR_Trilinos_C/README Tutorials/AMR_Trilinos_C/Solver.H Tutorials/AMR_Trilinos_C/Solver.cpp Tutorials/AMR_Trilinos_C/SolverBoundary.cpp Tutorials/AMR_Trilinos_C/driver.cpp Tutorials/AMR_Trilinos_C/inputs Tutorials/AMR_Trilinos_C/writePlotFile.H Tutorials/AMR_Trilinos_C/writePlotFile.cpp commit 8df7abc6a1cf001b0150b1b33ce59f74236c8519 Author: Weiqun Zhang Date: Thu Dec 15 14:28:52 2016 -0800 rm boxlib release notes ReleaseNotes/release-notes-16.12.1 commit 1809a2d88da8be69a9ef415bf55b10495bf9e42c Author: Weiqun Zhang Date: Sat Dec 10 10:59:17 2016 -0800 rm BoxLib ReleaseNotes Conflicts: ReleaseNotes/release-notes-16.11 ReleaseNotes/release-notes-16.04 ReleaseNotes/release-notes-16.05 ReleaseNotes/release-notes-16.06 ReleaseNotes/release-notes-16.07 ReleaseNotes/release-notes-16.08 ReleaseNotes/release-notes-16.09 ReleaseNotes/release-notes-16.10 ReleaseNotes/release-notes-16.11 ReleaseNotes/release-notes-16.12 commit 8473b732c9426724f09228b071c0fe1249619253 Author: Weiqun Zhang Date: Fri Dec 9 13:18:25 2016 -0800 rm Extern/gslib Src/Extern/gslib/CMakeLists.txt Src/Extern/gslib/acorni.f Src/Extern/gslib/backtr.f Src/Extern/gslib/beyond.f Src/Extern/gslib/blue.f Src/Extern/gslib/chknam.f Src/Extern/gslib/chktitle.f Src/Extern/gslib/cova3.f Src/Extern/gslib/dlocate.f Src/Extern/gslib/dpowint.f Src/Extern/gslib/dsortem.f Src/Extern/gslib/gauinv.f Src/Extern/gslib/gcum.f Src/Extern/gslib/getindx.f Src/Extern/gslib/getz.f Src/Extern/gslib/green.f Src/Extern/gslib/hexa.f Src/Extern/gslib/ksol.f Src/Extern/gslib/ktsol.f Src/Extern/gslib/locate.f Src/Extern/gslib/nscore.f Src/Extern/gslib/numtext.f Src/Extern/gslib/ordrel.f Src/Extern/gslib/picksupr.f Src/Extern/gslib/powint.f Src/Extern/gslib/psfill.f Src/Extern/gslib/psline.f Src/Extern/gslib/pstext.f Src/Extern/gslib/rand.f Src/Extern/gslib/red.f Src/Extern/gslib/resc.f Src/Extern/gslib/scal.f Src/Extern/gslib/setrot.f Src/Extern/gslib/setsupr.f Src/Extern/gslib/sortem.f Src/Extern/gslib/sqdist.f Src/Extern/gslib/srchsupr.f Src/Extern/gslib/strlen.f commit 7fb882bb494461e29748428ee928e234666073f6 Author: Weiqun Zhang Date: Fri Dec 9 13:17:43 2016 -0800 rm Tutorials/Chemotaxis_F Conflicts: Tutorials/Chemotaxis_F/GNUmakefile Tutorials/Chemotaxis_F/GNUmakefile Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/README Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/kernels.f90 Tutorials/Chemotaxis_F/main.f90 Tutorials/Chemotaxis_F/sdcquad.f90 Tutorials/Chemotaxis_F/write_plotfile.f90 Tutorials/README_F commit 37b08bf93a067a10de98383763998e055f694d6e Author: Weiqun Zhang Date: Thu Dec 15 14:25:15 2016 -0800 add a readme for migration tools Tools/Migration/README.md commit efb191d6dfccc065f43914cd1cee2a69af500752 Author: Weiqun Zhang Date: Thu Dec 15 14:14:30 2016 -0800 update migration document for step 2 Docs/Migration/Migration.md commit 4e7a2295273b5622a27338d98ac76eef21ae0872 Author: Weiqun Zhang Date: Thu Dec 15 13:59:14 2016 -0800 start to use AMReX namespace for new functions Src/C_BaseLib/Array.H Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp commit bf56848daacf9b117c26f4e053b34198b5a90df5 Author: Weiqun Zhang Date: Thu Dec 15 09:24:14 2016 -0800 add the equivalent of PArray::clear() Src/C_BaseLib/Array.H commit a3ae08c4cb86800d8b7b3d806e9f30f70ef2ea1d Merge: 41e78fc3a a858d833e Author: John Bell Date: Wed Dec 14 15:49:18 2016 -0800 Merged in license (pull request #2) fixed copyright commit a858d833e0d98b37c707982f69c0282cb9c8ce8b Author: jbb Date: Wed Dec 14 15:48:00 2016 -0800 fixed copyright README.txt license.txt commit 74a4cccbdd97e96e659e82fba4a964c744178266 Merge: 2b2be2c87 13fe8835e Author: Weiqun Zhang Date: Wed Dec 14 12:48:56 2016 -0800 Merge branch 'weiqun/tmp' into migration/2-parray Conflicts: Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Make.package commit 2b2be2c87ed1d1bc2aa968925246dadcb1f39af9 Author: Weiqun Zhang Date: Wed Dec 14 12:24:12 2016 -0800 start migration document Docs/Migration/Migration.md Tools/Migration/step-1-amrex_home/amrex_home.sh commit c8bef76bd142d6bc24424b91be1e2bfb81bf951d Author: Weiqun Zhang Date: Wed Dec 14 10:47:59 2016 -0800 fix compilation of some tests Tests/FillBoundaryComparison/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/Tiling_Heat_C/GNUmakefile commit 99b43c22f5bbe6449b78ea1f2bb667e0bc8fd585 Author: Weiqun Zhang Date: Wed Dec 14 10:11:09 2016 -0800 some Fortran BoxLib update Tools/C_mk/README.md Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/Migration/step-1-amrex_home/amrex_home.sh commit beebbfc33d266b2c1aeb0fe51441944bf031d917 Author: Weiqun Zhang Date: Wed Dec 14 09:42:19 2016 -0800 Migration step 1: replace BOXLIB_HOME with AMREX_HOME MiniApps/AMR_Adv_Diff_F90/GNUmakefile MiniApps/FillBoundary/GNUmakefile MiniApps/MultiGrid_C/GNUmakefile MiniApps/PGAS_SMC/GNUmakefile MiniApps/SMC/GNUmakefile Src/C_AMRLib/Make.package Src/C_AmrCoreLib/Make.package Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package Src/C_BoundaryLib/Make.package Src/C_ParticleLib/Make.package Src/Extern/amrdata/Make.package Src/Extern/hpgmg/Make.package Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/unittests/GNUmakefile Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG4/Make.package Src/LinearSolvers/C_TensorMG/Make.package Src/LinearSolvers/C_to_F_MG/Make.package Src/LinearSolvers/F_MG/FParallelMG.mak Tests/BBIOBenchmark/GNUmakefile Tests/C_BaseLib/BcastClasses/GNUmakefile Tests/C_BaseLib/GNUmakefile Tests/F_BaseLib/GNUmakefile Tests/FillBoundaryComparison/GNUmakefile Tests/IOBenchmark/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile Tests/MKDir/GNUmakefile Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/C_mk/packages/Make.hpgmg Tools/C_util/AmrDeriveTecplot/GNUmakefile Tools/C_util/Convergence/GNUmakefile Tools/C_util/Statistics/GNUmakefile Tools/C_util/ViewMF/GNUmakefile Tools/C_util/dbgTools/GNUmakefile Tools/Migration/step-1-amrex_home/amrex_home.sh Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_xrb/GNUmakefile Tools/Postprocessing/F_Src/tutorial/GNUmakefile Tools/Py_util/GNUmakefile Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/Chemotaxis_F/GNUmakefile Tutorials/DataServicesTest0/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/GettingStarted_C/GNUmakefile Tutorials/GettingStarted_F/GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_CF/GNUmakefile Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HeatEquation_EX2_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GNUmakefile Tutorials/HelloWorld_C/GNUmakefile Tutorials/HelloWorld_CF/GNUmakefile Tutorials/MultiColor_C/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFab_C_F/GNUmakefile Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_F/GNUmakefile Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PIC_C/GNUmakefile Tutorials/Random_F/GNUmakefile Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Tiling_C/GNUmakefile Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/Tiling_Heat_F/GNUmakefile Tutorials/TwoGrid_PIC_C/GNUmakefile Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_F/GNUmakefile commit 41e78fc3a2b459710cd91a54ef91449ecf07e72b Merge: d4c9fd3bd 816f4e785 Author: Weiqun Zhang Date: Wed Dec 14 09:01:26 2016 -0800 Merged in development (pull request #1) fix 2d addNParticles commit 816f4e785154c46e00e7d2c9df5cdd00ee55503f Merge: d4c9fd3bd 6c3216ef5 Author: Weiqun Zhang Date: Wed Dec 14 08:56:45 2016 -0800 Merge branch 'github-development' into development commit 6c3216ef5e42c70e36a7e321370132d31d792c7d Author: Weiqun Zhang Date: Wed Dec 14 08:54:56 2016 -0800 fix 2d addNParticles Src/C_ParticleLib/Particles.H commit d4c9fd3bd93960931e606166de4fd92cd7fc02e0 Merge: f76840cde 38bf06512 Author: Weiqun Zhang Date: Tue Dec 13 14:46:28 2016 -0800 Merge branch 'github' commit f76840cde6807cd4eaddbfc837786b8eb7e87cb4 Merge: 001805229 19f33fb2f Author: Weiqun Zhang Date: Tue Dec 13 14:46:01 2016 -0800 Merge branch 'master' into development commit 38bf065123d5b5cdb179f31d0a07e9d2b939c956 Author: Weiqun Zhang Date: Tue Dec 13 14:24:13 2016 -0800 Release 16.12.1 ReleaseNotes/release-notes-16.12.1 commit 4a136ee6fcf098275088aa37a55454d618957535 Merge: 2da8d8d46 bc82627c1 Author: Weiqun Zhang Date: Tue Dec 13 13:56:06 2016 -0800 Merge branch 'master' into development commit 2da8d8d46e77dfabc4b494f0d38134a889f499f2 Author: Weiqun Zhang Date: Tue Dec 13 13:27:09 2016 -0800 fix generic plotfile writer Src/C_BaseLib/PlotFileUtil.cpp commit 3892093c7e819f1307bb6a26fc4c57bc0ae99a9c Author: vince Date: Tue Dec 13 11:40:41 2016 -0800 fix comment, format. Src/C_BaseLib/PlotFileUtil.H commit 685b71d8d2978674db4b7c678b1f6bca101c3242 Author: vince Date: Tue Dec 13 11:34:57 2016 -0800 clarify comment. Src/C_BaseLib/PlotFileUtil.H commit 2fd460ef6fbe1b7d010f608f45b38c5e65802b76 Merge: fe6b64049 e99e2a4ac Author: vince Date: Tue Dec 13 11:27:06 2016 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit fe6b640493978e190a89af629108a2f309d1fcfd Author: vince Date: Tue Dec 13 11:26:45 2016 -0800 fix comments, back. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 3c49247a88861ce4307876df7e52ab4a0e3aaa75 Author: vince Date: Tue Dec 13 11:25:04 2016 -0800 call new function to prebuild directories. Src/C_AMRLib/Amr.cpp commit e99e2a4acb1d8eea193787655675ca01a8e4c371 Author: Michael Zingale Date: Mon Dec 12 19:44:12 2016 -0500 switch from getopt to argparse to get self-help Tools/C_scripts/makebuildinfo_C.py commit bc82627c132c68f293c2bf743a39b49dd94e81ac Author: Ann Almgren Date: Mon Dec 12 16:29:21 2016 -0800 First pass at addNParticles function in ParticleContainer class. Src/C_ParticleLib/Particles.H commit bfd9da39ed4447db3514af16d55c94e7727f8dd0 Author: Michael Zingale Date: Mon Dec 12 14:36:05 2016 -0500 the generic COMP_VERSION variable is used by the build info scripts to put the compiler version into job_info Tools/C_mk/comps/cray.mak Tools/C_mk/comps/gnu.mak Tools/C_mk/comps/intel.mak Tools/C_mk/comps/pgi.mak commit ed5c4b57936b88ed1ca2cbd2a089726a1f81161d Author: Weiqun Zhang Date: Fri Dec 9 12:11:19 2016 -0800 put instruction on how to use addr2line into Backtrace files Src/C_BaseLib/BLBackTrace.cpp commit 900a96c50603982308786052fe39d6999b2e8dfe Author: vince Date: Fri Dec 9 12:04:16 2016 -0800 remove static. Src/C_BaseLib/PlotFileUtil.H commit 885f5503c9c89bac8092b417604f8ae0074f5ec1 Author: Weiqun Zhang Date: Fri Dec 9 10:13:40 2016 -0800 better way to detect Open MPI Tools/C_mk/sites/Make.unknown commit 143f53b6149c980b44d3ad0ed27c0acc8fb94068 Author: vince Date: Thu Dec 8 16:11:07 2016 -0800 support for new cartgrid format. Src/Extern/amrdata/AmrData.H Src/Extern/amrdata/AmrData.cpp commit e0ae1df7ef5ae63041f5f724fdcf1933b9450710 Author: vince Date: Thu Dec 8 16:01:24 2016 -0800 functions for generic plotfiles. Src/C_BaseLib/PlotFileUtil.H Src/C_BaseLib/PlotFileUtil.cpp commit 19f33fb2fe15ce449a4cd50ee686e4daf8b2e84b Author: vince Date: Thu Dec 8 15:13:08 2016 -0800 bitbucketpushtest. Docs/Notes.io_implementation commit 0018052297337ea42d75efc3b31c5fb170b4f736 Merge: 632640dd4 a5568940e Author: Michael Zingale Date: Sat Dec 3 16:41:25 2016 -0500 Merge pull request #16 from nbren12/development raise error in dep.py if fortran preprocessor fails commit 632640dd4da4364f719fea58e6b6ac9bb4672090 Author: Weiqun Zhang Date: Fri Dec 2 15:43:46 2016 -0800 add support for trapping ABRT. this allows for backtracing interger overflow with gcc. Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp commit c222467f1efdf78f665e7cbd7666a2f2999c3fcb Author: Weiqun Zhang Date: Fri Dec 2 13:48:26 2016 -0800 gfortran: in debug mode use 2^31 - 1 as the initial value for integers Tools/C_mk/comps/gnu.mak commit 54b703c465160bb53f3e9ffa23ac8343c8239ac7 Author: Weiqun Zhang Date: Fri Dec 2 13:07:59 2016 -0800 make missing f90.depends an error so that error messages become more helpful Tools/C_mk/Make.rules Tutorials/HelloWorld_C/Make.package commit e8f41712ef7ef4f069e6405b34bd6b3893c7e3b5 Author: Weiqun Zhang Date: Fri Dec 2 10:35:33 2016 -0800 because of pgi compiler issue, have to remove -traceback Tools/C_mk/comps/pgi.mak commit 13fe8835ee4fe00e810ff04d3985ab7c6076f28c Merge: 5e350c37a 650327da6 Author: Weiqun Zhang Date: Fri Dec 2 09:04:37 2016 -0800 Merge branch 'development' into experimental commit 650327da65624ee069445b7aed363abaaee8ec2a Author: Weiqun Zhang Date: Fri Dec 2 09:02:56 2016 -0800 Release Notes for BoxLib 16.12 ReleaseNotes/release-notes-16.12 commit 9ed9d498f5bd793ffc7571aa885e09288da4a294 Merge: 97142e632 6027b8e4c Author: Weiqun Zhang Date: Fri Dec 2 08:35:31 2016 -0800 Merge branch 'master' into development commit 97142e63240f72420bf6268b9a61fc765da1a002 Merge: 3408453ff 753a8362f Author: Michael Zingale Date: Fri Dec 2 01:12:57 2016 -0500 Merge pull request #18 from BoxLib-Codes/preprocessing continue if we encounter a module that is not provided commit 753a8362fb5fc3dd25ff26210c303f02172b94a9 Author: Michael Zingale Date: Fri Dec 2 01:11:32 2016 -0500 use a GNU make $(warning...) to report unfound module dependencies. We retain the print to stderr too, so we can easily see these by simply redirecting stdout if desired Tools/F_scripts/dep.py commit f7a062fcf27a6a9599f3f1f4e29705f214e6bce4 Author: Michael Zingale Date: Thu Dec 1 20:12:21 2016 -0500 if we file requests a module that nothing provides then continue on to the next. This was the intended behavior originally, but we missed a `continue` statement. This allows for system-provided modules to work without them in the `IGNORES` list. This fixes a bug that Brian ran into Tools/F_scripts/dep.py commit 3408453ffec9e03d86ed7ffb945315ae6f728264 Merge: 71ae16382 5b6d179b2 Author: Michael Zingale Date: Thu Dec 1 20:03:18 2016 -0500 Merge pull request #17 from BoxLib-Codes/preprocessing catch dep.py errors and have make abort with an error message commit 5b6d179b23869864421faad5c2c02cfb5aaa6ce9 Author: Michael Zingale Date: Thu Dec 1 19:22:12 2016 -0500 address Weiqun's PR comments Tools/F_scripts/dep.py commit 1bea892e800c6779cbf4ad0447e378ab58c54877 Author: Michael Zingale Date: Thu Dec 1 19:14:43 2016 -0500 catch dep.py errors and have make abort with an error message explaining how to enable debug info in the dependency checking Tools/C_mk/Make.rules Tools/F_scripts/dep.py commit 71ae16382c2bb88f71f943117e78f0204f4491b0 Author: vince Date: Thu Dec 1 14:09:42 2016 -0800 make extra stream flushes the default for now. Src/C_BaseLib/VisMF.cpp commit 56a7a8410ab981ce4d1ae57c71fbf53fb9cfedbf Merge: 6258dfedc 1a6ca1b70 Author: vince Date: Thu Dec 1 13:23:17 2016 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 1a6ca1b70184f8f9d9fe8f92f7269e1afbac5e73 Author: Weiqun Zhang Date: Thu Dec 1 12:43:35 2016 -0800 intel: link with multi-threaded fortran library Tools/C_mk/comps/intel.mak commit 171a60c99e0229a7f5ebffe408d8dbe9a26572b4 Author: Weiqun Zhang Date: Thu Dec 1 10:14:52 2016 -0800 delete more potential unsafe functions Src/C_BaseLib/BCRec.H Src/C_BaseLib/Box.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp commit b43be2394070fb1db01a79ae213ea1222e6245ed Author: Weiqun Zhang Date: Wed Nov 30 22:22:23 2016 -0800 move the distribution map check into BL_ASSERT and make sure it does not dereference null ptr Src/C_BaseLib/FabArray.H commit a5568940ec947794b6980ba57384bec8c1244dba Author: Noah D. Brenowitz Date: Wed Nov 30 22:45:55 2016 -0500 remove bash stuff Tools/F_scripts/dep.py commit 5df703a4b4646fa6e2eacf42eb520c80bf03be51 Author: Noah D. Brenowitz Date: Wed Nov 30 22:37:59 2016 -0500 raise error if fortran preprocessor fails Fixes https://github.com/BoxLib-Codes/BoxLib/issues/15 Tools/F_scripts/dep.py commit 1b3d8de9b629e976f7d447b84d18a5b647e92e5f Author: vince Date: Wed Nov 30 17:39:38 2016 -0800 added flush options to try to fix titan. Src/C_BaseLib/VisMF.cpp commit 916d16b10e6c0ff0108665632054454493ac780a Author: Weiqun Zhang Date: Wed Nov 30 16:10:02 2016 -0800 more compiler flag tweaks Tools/C_mk/comps/intel.mak Tools/C_mk/comps/pgi.mak commit 6258dfedc718597ec1535e23bdabbef8c08b893d Merge: 9acde8afc b46d3301b Author: vince Date: Wed Nov 30 14:32:13 2016 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 4bd885ea8a157f506c05f51bbe5aa98fce97ddff Author: Weiqun Zhang Date: Wed Nov 30 14:27:32 2016 -0800 gcc: trap integer overflow Tools/C_mk/comps/gnu.mak commit b46d3301bf9710b04a7e9ebf6e1863d3dc4efcf9 Author: Weiqun Zhang Date: Wed Nov 30 10:14:24 2016 -0800 fix due to recently deleted functions Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit e1158a7ebc009df62511bfa07455d5f0d4d4b428 Author: Weiqun Zhang Date: Wed Nov 30 10:13:30 2016 -0800 we can now safely inline validbox and fabbox Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit be96a07ed4556d9e65a99ba1469c579196710442 Author: Weiqun Zhang Date: Wed Nov 30 09:17:17 2016 -0800 fix make for a test Tests/C_BaseLib/GNUmakefile commit 8e6450c9ac0084866fb833c4556739d2450edd78 Author: Weiqun Zhang Date: Wed Nov 30 08:55:47 2016 -0800 fix a dangling pointer Src/C_BaseLib/FabArray.H commit f2fab6992013e10baa735128f9f4d9487bbd1cf1 Author: Weiqun Zhang Date: Wed Nov 30 08:51:00 2016 -0800 delete functions that return a pointer to internal data of rvalue objects Src/C_BaseLib/BCRec.H Src/C_BaseLib/Box.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/RealBox.H commit 9acde8afc7e6c4849ff6a2f11a2839b8990322e5 Merge: 37f8bb599 69b9bc3e3 Author: vince Date: Tue Nov 29 10:43:30 2016 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 69b9bc3e3b2dd5e5d6d617d2115ef9f6cafae4cf Author: Weiqun Zhang Date: Mon Nov 28 14:43:33 2016 -0800 remove duplicated function arguments Src/F_BaseLib/cc_restriction.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/LinearSolvers/F_MG/mg.f90 commit 20281549bc84b16e8d417d443df87113d2ec1393 Author: Weiqun Zhang Date: Mon Nov 28 14:15:10 2016 -0800 fix memory leak Src/C_BaseLib/VisMF.cpp commit cf6dfed17b7f76977596e5a5f1a9c5246a9a0cf9 Author: Ann Almgren Date: Mon Nov 28 13:01:32 2016 -0800 Don't want to get compile error because of call to 3d routine with lo,hi hardwired to lo(2),hi(2) Tutorials/GettingStarted_F/work_on_data.f90 commit 6027b8e4c985d1c79b71fcf1cf9d3d09745dd324 Author: Ann Almgren Date: Mon Nov 28 13:00:05 2016 -0800 Don't want to get warning about calling 3d routine with lo,hi hardwired to lo(2),hi(2) Tutorials/GettingStarted_F/work_on_data.f90 commit 39baea948b0506ff3f5dc29fb9b72f083450968e Merge: 978bea7de 751c9f20c Author: WeiqunZhang Date: Mon Nov 28 10:25:40 2016 -0800 Merge pull request #12 from zingale/development add USE_GPROF to enable profiling with gprof commit 751c9f20cd4e74eef64f3cfd8917279612b3e1a4 Author: Michael Zingale Date: Mon Nov 28 13:19:15 2016 -0500 add USE_GPROF to enable profiling with gprof Tools/C_mk/comps/gnu.mak commit 978bea7deb298c13de8ef0aaea7c6f47ec7f2d83 Author: Michael Zingale Date: Sun Nov 27 18:46:11 2016 -0500 remove tcsort -- this is not used by anything Tools/F_mk/GMakedefs.mak Tools/F_scripts/tcsort.pl commit a67b52a971f338c07c17f2396fdd56a5583862dd Author: Weiqun Zhang Date: Sat Nov 26 22:42:53 2016 -0500 isinf --> std::isinf Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 8dc1b3cc2a5718fa43499105797886cbca17545a Author: Weiqun Zhang Date: Sat Nov 26 17:03:53 2016 -0800 Intel: -openmp --> -qopenmp for Intel >= 16 because -openmp is deprecated. Tools/C_mk/comps/intel.mak commit 760972de2ef309ea0618a3eab79a6bff192bea3b Author: Weiqun Zhang Date: Sat Nov 26 12:32:47 2016 -0800 Intel: add more checks Tools/C_mk/comps/intel.mak commit 1f2e13327aadce6ff7f88417970390e54998c95c Author: Weiqun Zhang Date: Sat Nov 26 12:06:57 2016 -0800 PGI: add fpe trap and force implicit none on f90 files Tools/C_mk/comps/pgi.mak commit 592e18cd46ceb5f5614ceaa2e9fd724f378b50c9 Author: Weiqun Zhang Date: Sat Nov 26 12:06:04 2016 -0800 GNU: initialize fortran integers to a large bogus number in debug mode Tools/C_mk/comps/gnu.mak commit 7cf6fc0e394702544223cc0ec47c3efa3e51938c Author: Weiqun Zhang Date: Sat Nov 26 11:26:39 2016 -0800 force implicit none for f90 files with gnu Tools/C_mk/comps/gnu.mak commit 5e350c37a8736b77ef6b0cb097399fa5f33c327c Author: Weiqun Zhang Date: Sat Nov 26 10:57:22 2016 -0800 typo Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 37f8bb5990854b62f336b75873fb8bd11e3a3cbf Author: vince Date: Wed Nov 23 11:42:50 2016 -0800 fix comments. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 3354078cb7f8d24402ec90328b85734c4d5db30b Author: Weiqun Zhang Date: Tue Nov 22 15:53:05 2016 -0800 mpic++ -> mpicxx because some systems do not seem to have mpic++ Tools/C_mk/sites/Make.unknown commit 41849f68803e42439dd52e92e128113e4a26c574 Author: Weiqun Zhang Date: Tue Nov 22 15:03:47 2016 -0800 amr_level is a unique_ptr Src/C_AMRLib/Amr.cpp commit e7166ffc434ac0c8f1087ae2905b194f1b39e8fe Merge: bf0164576 30e67b677 Author: Weiqun Zhang Date: Tue Nov 22 14:53:10 2016 -0800 Merge branch 'development' into experimental Conflicts: Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/CMakeLists.txt Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp commit 30e67b67719a97478e5f54b52c87f5676dcc39c7 Author: Weiqun Zhang Date: Tue Nov 22 13:34:22 2016 -0800 add python version check and force make to exit if requirement is not met Tools/C_mk/Make.defs commit 7641739be7759a629c0a7b8ddcce852b47df2167 Author: Weiqun Zhang Date: Tue Nov 22 11:11:25 2016 -0800 fix Tutorials/AMR_Adv_C_v2 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp commit 827897be87f72ad3eab98b9e19fc8bddac5c8631 Author: Weiqun Zhang Date: Tue Nov 22 11:11:03 2016 -0800 std::min -> std::min because Array::size() returns size_t now Src/C_BaseLib/VisMF.cpp commit 8ba46f878ef64b979378c528f895f1f94408083a Author: Weiqun Zhang Date: Thu Nov 17 10:45:54 2016 -0800 more helpful message Tools/C_mk/Make.rules commit 8c617bc3743908bcfdcdc2a5cc8875beea692865 Author: Weiqun Zhang Date: Tue Nov 15 17:01:10 2016 -0800 mpif90 --> Tools/C_mk/sites/Make.unknown commit ecf80e3d5edea85c95a669a9c69dfbf8d1138860 Author: Weiqun Zhang Date: Tue Nov 15 16:14:53 2016 -0800 more intelligent way of adding link flags Tools/C_mk/sites/Make.unknown commit 23a79c85bf0c4318599b59e4de34e5dd8e577da4 Author: Weiqun Zhang Date: Sat Nov 12 12:47:43 2016 -0800 turn on C++11 in F_mk Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/gfortran.mak commit dccc134baaed527a21b0f3f35d24b3ad7ec4c575 Author: Weiqun Zhang Date: Fri Nov 11 13:23:05 2016 -0800 rm Rose Tests/RoseTests/CPP/NullTransTest/GNUmakefile Tests/RoseTests/CPP/NullTransTest/PROB_3D.F Tests/RoseTests/CPP/NullTransTest/PROB_F.H Tests/RoseTests/CPP/NullTransTest/README Tests/RoseTests/CPP/NullTransTest/RoseNullTest.cpp Tests/RoseTests/F90/Readme Tests/RoseTests/F90/test1/GNUmakefile Tests/RoseTests/F90/test1/main.f90 Tests/RoseTests/F90/test2/GNUmakefile Tests/RoseTests/F90/test2/main.f90 Tests/RoseTests/F90/test3/GNUmakefile Tests/RoseTests/F90/test3/bc.f90 Tests/RoseTests/F90/test4/GNUmakefile Tests/RoseTests/F90/test4/main.f90 Tests/RoseTests/F90/test5/GNUmakefile Tests/RoseTests/F90/test5/main.f90 Tests/RoseTests/F90/test6/GNUmakefile Tests/RoseTests/F90/test6/main.f90 Tests/RoseTests/F90/test6/omp.f90 Tests/RoseTests/F90/test7/GNUmakefile Tests/RoseTests/F90/test7/main.f90 Tests/RoseTests/F90/test7/probin.f90 Tests/RoseTests/F90/test7/runtime.f90 Tests/RoseTests/F90/test8/GNUmakefile Tests/RoseTests/F90/test8/init_data.f90 Tests/RoseTests/F90/test8/main.f90 commit 681af15bd4a30f481fc7cec4fdb1bf7075cf5241 Author: Weiqun Zhang Date: Fri Nov 11 12:59:41 2016 -0800 rm C_TowerLib with Marc's permission Src/C_TowerLib/Layout.H Src/C_TowerLib/Layout.cpp Src/C_TowerLib/MFTower.H Src/C_TowerLib/MFTower.cpp Src/C_TowerLib/MFTower_2D.F Src/C_TowerLib/MFTower_3D.F Src/C_TowerLib/MFTower_F.H Src/C_TowerLib/Make.package Tutorials/AMR_PETSc_C/Exec/Make.PETSc Tutorials/AMR_PETSc_C/Exec/UniformVelocity/.gdbinit Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Make.package Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_2lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_3lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_PETSc_C/README Tutorials/AMR_PETSc_C/Source/Darcy.H Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F Tutorials/AMR_PETSc_C/Source/DarcySNES_F.H Tutorials/AMR_PETSc_C/Source/Darcy_2D.f90 Tutorials/AMR_PETSc_C/Source/Darcy_F.H Tutorials/AMR_PETSc_C/Source/MLBoundary.H Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp Tutorials/AMR_PETSc_C/Source/Make.package Tutorials/AMR_PETSc_C/Source/extern_probin.template Tutorials/AMR_PETSc_C/Source/interpolate.f90 Tutorials/AMR_PETSc_C/Source/main.cpp Tutorials/README_C commit b71f76e806f146bcd6060a31339c01c0149e3015 Author: Weiqun Zhang Date: Fri Nov 11 12:34:56 2016 -0800 add a few functions for converting array of (unique) pointers to array of (const) pointers Src/C_BaseLib/Array.H commit 1876e60cc7d1035bd5ef752e637cea48bbcc6fcc Author: Weiqun Zhang Date: Fri Nov 11 12:29:20 2016 -0800 fix in make Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit bd7f8cac2849c6ab72b057d57e52f8e637c4af84 Merge: f67819baa 90595472a Author: Weiqun Zhang Date: Tue Nov 22 10:48:07 2016 -0800 Merge branch 'before-parray' into dev-exp-make-array Conflicts: Src/C_BaseLib/CMakeLists.txt commit f67819baab5047372b54c3d7dcd84694005bab8b Author: vince Date: Mon Nov 21 13:24:13 2016 -0800 fix for ieee_32 rd. Src/C_BaseLib/VisMF.cpp commit 6652eff1cae54ba33285ddad5a2d099b54fca5a0 Author: vince Date: Fri Nov 18 14:54:22 2016 -0800 clean up debugging diagnostics. Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp commit 902b3cab83a3118b77fd718c678e738d22c42870 Merge: e7adec596 afdef8515 Author: vince Date: Fri Nov 18 13:00:50 2016 -0800 merge fix. commit e7adec596c6c3cb344947e9cabc3ee9e420cc3d9 Author: vince Date: Fri Nov 18 12:57:26 2016 -0800 output cleanup. Src/C_BaseLib/VisMF.cpp commit 974a43b8b0cad35b7411f26ce075c1e441b6dd87 Author: vince Date: Fri Nov 18 12:56:33 2016 -0800 additions to i/o documentation. Docs/Notes.io_implementation Docs/Readme.io commit 85bccb3141ff9792c0635bd4057411e9a61206fe Merge: ff92fc959 983f9e996 Author: vince Date: Fri Nov 18 12:07:28 2016 -0800 Merge branch 'optio' of https://github.com/BoxLib-Codes/BoxLib into optio commit 983f9e9965150bc9496251f9facc80b3e20b3528 Author: vince Date: Thu Nov 17 16:19:15 2016 -0800 combine nfiles dependent iterators. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp commit bf01645769fa027cba0ebd34fad2c3c9670c7ad4 Author: Weiqun Zhang Date: Thu Nov 17 10:45:54 2016 -0800 more helpful message Tools/C_mk/Make.rules commit a1d408fdce3ac909d25026286f7219e258315293 Author: Weiqun Zhang Date: Thu Nov 17 10:34:00 2016 -0800 rm MLSDCAmr Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/MLSDCAmr.cpp Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_AMRLib/Make.package commit afdef851547ef67c7b11dd5875bc4f628243b85e Author: Weiqun Zhang Date: Wed Nov 16 16:56:53 2016 -0800 bl_avg_eg_to_cc for 2 and 1D Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit ff92fc9596b901b2b189336d95f79585d2970ca6 Author: vince Date: Wed Nov 16 15:33:02 2016 -0800 fix comment. Src/C_BaseLib/NFiles.H commit 192d871d718cf9561077a450bc48ffa6731a878b Author: Marc Day Date: Wed Nov 16 15:16:56 2016 -0800 Fixup README to use the example-tests.py example file instead of one that no longer exists. Tools/RegressionTesting/README commit 4ea2cc82a23c7dbd66c9f2b505425faf784e908f Merge: 9a5555176 b92a7b290 Author: Michael Zingale Date: Wed Nov 16 16:16:52 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 9a5555176460a69c0e4d216e6c7be346b743e0cb Author: Michael Zingale Date: Wed Nov 16 16:16:37 2016 -0500 add a heavily commented example inputs file Tools/RegressionTesting/example-tests.ini commit b92a7b290143e7ae404ca9a8549fa0fdbd14911c Merge: 467ecfe66 ccef5dc3a Author: Weiqun Zhang Date: Wed Nov 16 09:18:11 2016 -0800 Merge branch 'fnodalfillpatch' into development commit 467ecfe66b847cd22d25b46a7664356aafbb7b5c Author: Max Katz Date: Wed Nov 16 01:25:59 2016 -0500 Fix error message Src/C_AMRLib/Amr.cpp commit 52ad8c8e7ec671f16f904158bfd04dbea6f05b17 Author: Michael Zingale Date: Tue Nov 15 22:27:14 2016 -0500 fix the --no_update functionality to work when a repo is specified Tools/RegressionTesting/regtest.py commit b4ba5ef36c28a5695d0e760a36799a7de7b145af Author: Weiqun Zhang Date: Tue Nov 15 17:01:10 2016 -0800 mpif90 --> Tools/C_mk/sites/Make.unknown commit b63792092e40151d194cf1c7979af96c92195611 Author: Weiqun Zhang Date: Tue Nov 15 16:14:53 2016 -0800 more intelligent way of adding link flags Tools/C_mk/sites/Make.unknown commit 5d458fed043e7ad90f433f2256cdf129101f4448 Merge: f3b6d4bf8 0775508fa Author: Michael Zingale Date: Tue Nov 15 18:03:32 2016 -0500 Merge pull request #11 from jrood-nrel/development Adding exception handling to a particular shutil.rmtree(). commit 0775508fa9f7628f514e7c2c21e9927c31dbfe85 Author: Jon Rood Date: Tue Nov 15 15:59:44 2016 -0700 Reducing exception to only OSError. Tools/RegressionTesting/regtest.py commit b2e47b80c264fdfde6a25a62f7b0a53a98804e30 Author: Jon Rood Date: Tue Nov 15 15:12:43 2016 -0700 Adding exception handling to a particular shutil.rmtree(). Otherwise, this command can cause errors on certain filesystems and the test suite can completely fail before finishing. Tools/RegressionTesting/regtest.py commit f07997a1a78e4b4fe04540b51271d68c6ff35ac5 Author: Weiqun Zhang Date: Tue Nov 15 13:20:21 2016 -0800 fix more int and unsigned comparisons for OPAL because it uses -Werror=sign-compare. Src/C_ParticleLib/Particles.H commit f1e283732e322c87dceec6d251ab4b96bcd2ee5b Author: Weiqun Zhang Date: Tue Nov 15 12:12:45 2016 -0800 typo Src/C_ParticleLib/Particles.H commit 428e348abb2b8ff1cb980182e1d0b78187b39a08 Author: Weiqun Zhang Date: Tue Nov 15 12:12:01 2016 -0800 fix more int and unsigned comparisons for OPAL because it uses -Werror=sign-compare. Src/C_ParticleLib/Particles.H commit 60a7ed700a34840b8c2c56c81bc4a926c78141a4 Author: Weiqun Zhang Date: Tue Nov 15 10:33:05 2016 -0800 fix more int and unsigned comparisons for OPAL because it uses -Werror=sign-compare. Src/C_ParticleLib/Particles.H commit 9267833f64a7dd780b652c0739501566e9148977 Author: Weiqun Zhang Date: Tue Nov 15 09:07:48 2016 -0800 fix a number of typos; fix a number of int and unsigned comparison for OPAL Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp Src/C_BaseLib/FabArray.H Src/C_ParticleLib/Particles.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H commit 47d19b9966ca602c4582a7c68d15308f3e406c83 Author: vince Date: Mon Nov 14 16:17:43 2016 -0800 more code for nfiles and blprof. Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit b78cfd7e2e8f0e8aef926b0660abaee946535801 Author: Weiqun Zhang Date: Sun Nov 13 17:29:57 2016 -0800 fix signature of function average_down_faces Src/C_BaseLib/MultiFabUtil.cpp commit d04f8c27393c1b2582c42a9b356126c9d0ec5f7c Author: Weiqun Zhang Date: Sun Nov 13 10:17:31 2016 -0800 fix new bug in last commit Src/C_BaseLib/Array.H commit 517a53140eb9023a1bae17d00becd09554519347 Author: Weiqun Zhang Date: Sun Nov 13 08:27:18 2016 -0800 more consistent style Src/C_BaseLib/Array.H Src/C_ParticleLib/Particles.H Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PIC_C/Make.package Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp commit 0392339692680d18e80cc5e0288e0b46f0aa3f6d Author: Weiqun Zhang Date: Sat Nov 12 12:47:43 2016 -0800 turn on C++11 in F_mk Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/gfortran.mak commit 031940ce20bcaae498f7c7516cb7103794e069cb Author: Weiqun Zhang Date: Sat Nov 12 12:28:49 2016 -0800 fix tutorials Tutorials/GettingStarted_C/GNUmakefile Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp Tutorials/README_C Tutorials/Tiling_Heat_C/main.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp commit db0b6f16aaed2e6037cfb482b7c6aba6f307d3c5 Author: vince Date: Fri Nov 11 17:17:14 2016 -0800 use NFilesIter for profiling output. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/NFiles.H commit e9d92f7ed3824260d09336b02e9c0121674217f6 Author: Weiqun Zhang Date: Fri Nov 11 15:14:19 2016 -0800 fix compilation of a number of tests Tests/C_BaseLib/GNUmakefile Tests/FillBoundaryComparison/main.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp commit 04fd580fc0ce3bd1ddb9fe80dd75fb84e3370023 Author: vince Date: Fri Nov 11 14:46:04 2016 -0800 add support for appending nfiles set. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 47a56e3353dc8dac2874303837fce3ae469a7577 Author: Weiqun Zhang Date: Fri Nov 11 14:30:00 2016 -0800 add const Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 52a813079d02d2669315cd1513060ddca47df6b5 Author: vince Date: Fri Nov 11 13:30:16 2016 -0800 output for verbose only, remove unused var. Src/C_AMRLib/Amr.cpp commit 84aec263556074f931aae8c6e0b6c991c32cff3c Author: vince Date: Fri Nov 11 13:29:01 2016 -0800 test for zero grids, output for debug only. Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.cpp commit c4ae192af235eb58f707d74f3723ce9fe4f61b35 Author: Weiqun Zhang Date: Fri Nov 11 13:23:05 2016 -0800 rm Rose Tests/RoseTests/CPP/NullTransTest/GNUmakefile Tests/RoseTests/CPP/NullTransTest/PROB_3D.F Tests/RoseTests/CPP/NullTransTest/PROB_F.H Tests/RoseTests/CPP/NullTransTest/README Tests/RoseTests/CPP/NullTransTest/RoseNullTest.cpp Tests/RoseTests/F90/Readme Tests/RoseTests/F90/test1/GNUmakefile Tests/RoseTests/F90/test1/main.f90 Tests/RoseTests/F90/test2/GNUmakefile Tests/RoseTests/F90/test2/main.f90 Tests/RoseTests/F90/test3/GNUmakefile Tests/RoseTests/F90/test3/bc.f90 Tests/RoseTests/F90/test4/GNUmakefile Tests/RoseTests/F90/test4/main.f90 Tests/RoseTests/F90/test5/GNUmakefile Tests/RoseTests/F90/test5/main.f90 Tests/RoseTests/F90/test6/GNUmakefile Tests/RoseTests/F90/test6/main.f90 Tests/RoseTests/F90/test6/omp.f90 Tests/RoseTests/F90/test7/GNUmakefile Tests/RoseTests/F90/test7/main.f90 Tests/RoseTests/F90/test7/probin.f90 Tests/RoseTests/F90/test7/runtime.f90 Tests/RoseTests/F90/test8/GNUmakefile Tests/RoseTests/F90/test8/init_data.f90 Tests/RoseTests/F90/test8/main.f90 commit 2a0467c8920b5cc1c08b8dc88553e7b3f46d2519 Author: Weiqun Zhang Date: Fri Nov 11 12:59:41 2016 -0800 rm C_TowerLib with Marc's permission Src/C_TowerLib/Layout.H Src/C_TowerLib/Layout.cpp Src/C_TowerLib/MFTower.H Src/C_TowerLib/MFTower.cpp Src/C_TowerLib/MFTower_2D.F Src/C_TowerLib/MFTower_3D.F Src/C_TowerLib/MFTower_F.H Src/C_TowerLib/Make.package Tutorials/AMR_PETSc_C/Exec/Make.PETSc Tutorials/AMR_PETSc_C/Exec/UniformVelocity/.gdbinit Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Make.package Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_2lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_3lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_PETSc_C/README Tutorials/AMR_PETSc_C/Source/Darcy.H Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F Tutorials/AMR_PETSc_C/Source/DarcySNES_F.H Tutorials/AMR_PETSc_C/Source/Darcy_2D.f90 Tutorials/AMR_PETSc_C/Source/Darcy_F.H Tutorials/AMR_PETSc_C/Source/MLBoundary.H Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp Tutorials/AMR_PETSc_C/Source/Make.package Tutorials/AMR_PETSc_C/Source/extern_probin.template Tutorials/AMR_PETSc_C/Source/interpolate.f90 Tutorials/AMR_PETSc_C/Source/main.cpp Tutorials/README_C commit 9e252f1397e4780329bdf2cac4b76f0d2c9b2976 Author: Weiqun Zhang Date: Fri Nov 11 12:55:04 2016 -0800 add const to MultiFabUtil functions Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_F.H Tutorials/PIC_C/solve_for_accel.cpp commit ee0a76a72a141145220b5499998b1c0fb480d3aa Author: Weiqun Zhang Date: Fri Nov 11 12:34:56 2016 -0800 add a few functions for converting array of (unique) pointers to array of (const) pointers Src/C_BaseLib/Array.H commit 08abd3caf3aa3d6f65530198d3861fa1c51e825d Author: vince Date: Fri Nov 11 12:45:40 2016 -0800 change function name. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit db98ecfcaba24215b00edb3f0578d6d7c1a1baf1 Author: Weiqun Zhang Date: Fri Nov 11 12:29:20 2016 -0800 fix in make Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 60283fa6f6b80ccf49f07ea6062121736bee581c Author: Weiqun Zhang Date: Fri Nov 11 11:33:41 2016 -0800 rm PArray from ParticleLib and LinearSolver Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_ParticleLib/Particles.H Src/C_ParticleLib/TracerParticles.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp commit 3ee3b4376103e73c73742e8c7fdc5c53097ce5aa Author: Weiqun Zhang Date: Thu Nov 10 13:46:02 2016 -0800 remove PArray Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp Src/C_AmrCoreLib/AmrCore.cpp Src/C_AmrCoreLib/ErrorList.H Src/C_AmrCoreLib/ErrorList.cpp Src/C_AmrCoreLib/FillPatchUtil.H Src/C_AmrCoreLib/FillPatchUtil.cpp Src/C_AmrCoreLib/TagBox.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_F.H Src/C_BaseLib/PArray.H Src/C_BaseLib/iMultiFab.cpp Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp commit f3b6d4bf865bd7815333caf5397e57f54c419056 Author: Michael Zingale Date: Wed Nov 9 19:54:49 2016 -0500 report for each variable in a plotfile if there is a NaN Tools/Postprocessing/F_Src/fnan.f90 commit e07e33a627e9c5ec4f8af4c49651e3979d025dd5 Merge: 3bb003f9e e7eba2fc5 Author: Michael Zingale Date: Wed Nov 9 19:37:30 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 3bb003f9eedb8d181b9f79d4a4e71997bc969938 Author: Michael Zingale Date: Wed Nov 9 19:37:13 2016 -0500 add a simple tool to dump data to the screen Tools/Postprocessing/F_Src/fdump.f90 commit 90595472a6fd20699036524aa0892336491db879 Merge: 1b80c5227 e7eba2fc5 Author: Weiqun Zhang Date: Wed Nov 9 10:27:46 2016 -0800 Merge branch 'development' into experimental commit e7eba2fc5fceb6019f1a866e720de365e530b16c Author: Weiqun Zhang Date: Wed Nov 9 10:27:16 2016 -0800 use size_t instead of int as loop index in a few places so that OPAL can compile Src/C_ParticleLib/Particles.H commit 1b80c5227eeec087b32d948b0b52d430613a1937 Author: Weiqun Zhang Date: Wed Nov 9 09:37:30 2016 -0800 use Array instead of vector for consistence and bound checking Src/C_BaseLib/PlotFileUtil.H Src/C_BaseLib/PlotFileUtil.cpp commit d96e70dcfd0f306520f75f99609c42ec407791a2 Author: Weiqun Zhang Date: Tue Nov 8 14:43:06 2016 -0800 rework on the Array class Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabConv.cpp Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Tools/C_mk/Make.defs commit 96c72c5b55b151eccff5598cbadd4c7857736ed0 Author: Weiqun Zhang Date: Tue Nov 8 14:41:21 2016 -0800 rm BL_CXX11.H because C++11 is now require; replace BL_OVERRIDE with override MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp Src/C_AMRLib/Amr.H Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/StateDescriptor.H Src/C_AmrCoreLib/Interpolater.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/BL_CXX11.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/CArena.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/PhysBCFunct.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/MacBndry.H Src/C_ParticleLib/Particles.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_TensorMG/DivVis.H Tests/C_BaseLib/BcastClasses/GNUmakefile Tests/C_BaseLib/GNUmakefile Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/MultiFabTests_C/GNUmakefile commit 11e41eed28cee8818b45dd3c7a2a6566fb7b2ffe Author: vince Date: Tue Nov 8 14:38:23 2016 -0800 change Array to vector to run with the intel compiler. Src/C_BaseLib/VisMF.cpp commit fc67a15c6ac869b04aeed4f9c57e79282d008939 Author: Weiqun Zhang Date: Tue Nov 8 14:21:30 2016 -0800 no longer need to specify FCOMP Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HelloWorld_C/GNUmakefile Tutorials/MultiColor_C/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiGrid_C/GNUmakefile Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PIC_C/GNUmakefile Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Tiling_C/GNUmakefile Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/TwoGrid_PIC_C/GNUmakefile commit 0f1ada142f095da780e6832dc6a9fd2d6f9ec3c5 Author: Weiqun Zhang Date: Tue Nov 8 14:12:28 2016 -0800 Src/C_AMRLib/Make.package doe not include C_AmrCoreLib anymore MiniApps/FillBoundary/GNUmakefile MiniApps/MultiGrid_C/GNUmakefile Src/C_AMRLib/Make.package Tests/C_BaseLib/BcastClasses/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/MKDir/GNUmakefile Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_PETSc_C/Exec/Make.PETSc Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/WaveEquation_C/GNUmakefile commit cbd753d3269e58e5af7c25a8526ca8009782533e Author: Weiqun Zhang Date: Tue Nov 8 13:34:44 2016 -0800 need to pass fincludes into MODDEP Tools/C_mk/Make.rules commit 07692755c815b3970e887efdf0f6330f51b4d521 Merge: 693988c97 7271aa170 Author: Weiqun Zhang Date: Tue Nov 8 12:24:12 2016 -0800 Merge branch 'development' into experimental Ray will have to add his make setup back to maybe Tools/C_mk/sites/Make.nrel. Conflicts: Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 693988c97bda8819ebf80205e1e0686194985b1c Author: Weiqun Zhang Date: Mon Nov 7 17:06:03 2016 -0800 try to detect mpich or openmpi Tools/C_mk/sites/Make.unknown commit 811597575f05d202c8da268e68a10782b2f1807f Author: Weiqun Zhang Date: Mon Nov 7 16:37:48 2016 -0800 more on README.md Tools/C_mk/README.md commit 62b462d61ffbc22f49a8c86e45982a59bf3c1e75 Author: Weiqun Zhang Date: Mon Nov 7 16:25:45 2016 -0800 minor Tools/C_mk/README.md commit 2ca7c52d7e09ebc7cf06c2d96447f541c910c046 Author: Weiqun Zhang Date: Mon Nov 7 16:22:08 2016 -0800 fix format Tools/C_mk/README.md commit 40facdd70b4cf0d61b4765c1feb400c2a550b678 Author: Weiqun Zhang Date: Mon Nov 7 16:17:57 2016 -0800 more on README.md for make Tools/C_mk/Make.defs Tools/C_mk/README.md commit 7271aa170436056f61ed76b9ce12b1fe13ddcae2 Author: Brian Friesen Date: Sun Nov 6 18:45:02 2016 -0800 C_mk: add workaround for compiling C++11 features using Intel compilers at NERSC This is a known but unfixed Cray bug. The workaround is to force Intel compilers to use compatible header files from GCC, specifically from GCC 4.9.3. The user can do this by loading the 'gcc/4.9.3' module. Tools/C_mk/Make.defs commit 5d4116587ac489ff6b8bd244ba8159117932dab9 Author: Brian Friesen Date: Mon Nov 7 08:16:54 2016 -0800 C_mk, F_mk: remove Babbage compiler hooks (it has been retired) Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit b8ca62f7c537c3f881313813e249668b1c61dc1a Author: Weiqun Zhang Date: Mon Nov 7 09:14:31 2016 -0800 MLSDCAmr: restrict --> Restrict to avoid name conflict. Although restrict is not a C++ keyword and it was used as a member function of class MLSDCAmrLevel, cray compiler is unhappy about it being used because it is a C keyword. Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/MLSDCAmr.cpp commit 7a9c305847768730e85ea114a7c394d6338d89ef Author: Weiqun Zhang Date: Sun Nov 6 12:08:51 2016 -0800 add python to build requirement Tools/C_mk/README.md commit de368e7090af91ce40a2621a983d2e90c1d735f4 Merge: 745216615 c10cf9a7e Author: Michael Zingale Date: Sat Nov 5 21:40:01 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 745216615e28fda97cda225f9a5720a75f3d8cfa Author: Michael Zingale Date: Sat Nov 5 21:39:38 2016 -0400 need to actually pass FPP_DEFINES to the dependency script Tools/F_mk/GMakerules.mak commit a20df7d9f49447f650a0a2ff3d55854bd5fc50a5 Author: Weiqun Zhang Date: Fri Nov 4 20:12:54 2016 -0400 do not exit due to compiler mismatch for goals like clean, realclean, etc. Tools/C_mk/Make.rules Tools/C_mk/sites/Make.nersc Tools/C_mk/sites/Make.olcf commit 63fd17bc896d8d36639e56d9a328dc0aad4e00fb Author: Weiqun Zhang Date: Fri Nov 4 16:39:21 2016 -0700 removed -fimplicit-none flag because we have some really old Fortran code Tools/C_mk/comps/gnu.mak commit 99b28139ae995d81f9e1eea2e22f790f9af3c0cc Author: Weiqun Zhang Date: Fri Nov 4 14:45:25 2016 -0700 Make.nersc: add -lmpichf90 Tools/C_mk/sites/Make.nersc Tools/C_mk/sites/Make.olcf commit 07e9f1825df97cc6b59d817491b107ea424ca59c Author: Weiqun Zhang Date: Fri Nov 4 12:58:20 2016 -0700 add intel.mak and Make.vtune Tools/C_mk/Make.defs Tools/C_mk/comps/cray.mak Tools/C_mk/comps/gnu.mak Tools/C_mk/comps/intel.mak Tools/C_mk/comps/pgi.mak Tools/C_mk/tools/Make.vtune commit 0ac4db369d75c03f49a539c78ce49e863b95149a Author: Weiqun Zhang Date: Fri Nov 4 11:21:58 2016 -0700 add Make.nersc and cray.mak Tools/C_mk/comps/cray.mak Tools/C_mk/comps/pgi.mak Tools/C_mk/sites/Make.nersc commit 7f797916e4f41352c5921b33209d9c36ae18e515 Author: Weiqun Zhang Date: Fri Nov 4 13:35:11 2016 -0400 Make.olcf: link to mpichf90 Tools/C_mk/sites/Make.olcf commit e2ba3f7b1304116698fa6f36a9ac93381c9c354c Author: Weiqun Zhang Date: Fri Nov 4 10:30:11 2016 -0700 fix missing $ in gnu.mak Tools/C_mk/comps/gnu.mak commit 057adabf2aef9737bcee377520d257b62d474038 Author: Weiqun Zhang Date: Fri Nov 4 13:11:30 2016 -0400 rename gcc.mak to gnu.mak to match Cray's convention for naming PrgEnv; add sites/Make.olcf Tools/C_mk/Make.defs Tools/C_mk/Make.local.template Tools/C_mk/comps/gnu.mak Tools/C_mk/sites/Make.olcf Tools/C_mk/sites/Make.unknown commit c352b65091fc2e4ebdf83bf346e448491e1b81e0 Author: Weiqun Zhang Date: Thu Nov 3 19:19:27 2016 -0400 add an example of filter-out in Make.local.template Tools/C_mk/Make.local.template commit 1c75381a16ce5ad5ad40b2fd0b7d910e7573dcf7 Author: Weiqun Zhang Date: Thu Nov 3 18:33:50 2016 -0400 In C++11, isnan and isinf are in std namespace Src/C_BaseLib/FArrayBox.cpp commit 11d4d5be73515b06dde315e765bd5c6e093d6a86 Author: Weiqun Zhang Date: Thu Nov 3 18:33:22 2016 -0400 add pgi.mak Tools/C_mk/Make.defs Tools/C_mk/comps/gcc.mak Tools/C_mk/comps/pgi.mak commit ceb2e1dd6d571eddc985f05e6aad0799cf65bf6c Author: Weiqun Zhang Date: Thu Nov 3 17:21:47 2016 -0400 add Make.unknown Tools/C_mk/Make.defs Tools/C_mk/Make.local.template Tools/C_mk/sites/Make.ccse Tools/C_mk/sites/Make.unknown commit 4e84ff39e74aa7a07939b4d437128fe3e10aa530 Author: Weiqun Zhang Date: Thu Nov 3 13:37:30 2016 -0700 another typo in README Tools/C_mk/README.md commit d054d348f506bda03cf4103df78b855ad1ee6dea Author: Weiqun Zhang Date: Thu Nov 3 13:34:43 2016 -0700 typo in README Tools/C_mk/README.md commit 08bea853a826f2b07e49860d8456f082a817ee46 Author: Weiqun Zhang Date: Thu Nov 3 13:27:43 2016 -0700 new Make system work in progress: gcc and CCSE are done Tools/C_mk/Make.AIX Tools/C_mk/Make.CYGWIN_NT Tools/C_mk/Make.Darwin Tools/C_mk/Make.FreeBSD Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.local.template Tools/C_mk/Make.machines Tools/C_mk/Make.mpi Tools/C_mk/Make.rules Tools/C_mk/Make.upcxx Tools/C_mk/README.md Tools/C_mk/comps/gcc.mak Tools/C_mk/packages/Make.hpgmg Tools/C_mk/sites/Make.ccse commit c10cf9a7e70bbbe04c0df806dc4939a3b0926326 Author: Grout Date: Thu Nov 3 09:22:38 2016 -0600 Revised Peregrine (NREL) configuration to use intel or gcc toolchains Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit e32cc3c503a6c91aa70cae9674a1d4f34220d5dd Author: vince Date: Wed Nov 2 15:34:12 2016 -0700 set default header formats. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.cpp commit dc31fcfa6396c0fbaf8be0345b07f27dc46d9fab Merge: 08425aebd 8360c56b5 Author: vince Date: Wed Nov 2 13:36:45 2016 -0700 fix merge conflicts. commit c3cd50d6fedf109dce2a35078b1d651d8c8d2ee0 Author: Grout Date: Wed Nov 2 13:11:20 2016 -0600 Add makefile defs for Peregrine (NREL cluster) Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 08425aebd7a37e581a70629de60c0610fedd4189 Author: vince Date: Wed Nov 2 12:08:34 2016 -0700 changes to doc and inputs. Docs/Readme.io Tests/IOBenchmark/inputs commit 8360c56b55f66506089cf4d32321f2712191d02d Author: Michael Zingale Date: Wed Nov 2 09:19:51 2016 -0400 add a runtime_params attribute for a test to override inputs Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit 3dc041cfdca767f52ea606cdb9686994d6800787 Author: vince Date: Tue Nov 1 16:37:18 2016 -0700 simplify file order reads. Src/C_BaseLib/VisMF.cpp commit 1ba883e6d99c561ba6d81b7d3d75d5d2d0c662fe Author: vince Date: Tue Nov 1 16:35:41 2016 -0700 function for items per bin. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit ddd49a238efedf1aa937499c4bbb219dda2d6034 Merge: 54c9457de 6a7cfb954 Author: Michael Zingale Date: Tue Nov 1 12:31:57 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 54c9457de4b623da0eb8a31cc431ca640bf1c334 Author: Michael Zingale Date: Tue Nov 1 12:28:26 2016 -0700 Intel doesn't seem to define __STDC__ for its Fortran preprocessor, so force it to take a particular branch for macro expansion Src/C_BaseLib/ArrayLim.H commit 6a7cfb954e1503f242828c06e8eae59016665c1b Merge: f801a8c0d 20ecaa152 Author: Weiqun Zhang Date: Tue Nov 1 09:17:51 2016 -0700 Merge branch 'development' commit f801a8c0dea4037d7785a71afe2d6a6522002df4 Author: Weiqun Zhang Date: Tue Nov 1 09:17:28 2016 -0700 Release Notes 16.11 ReleaseNotes/release-notes-16.11 commit 20ecaa152c51b436f8f560ced368daba4aa9ca80 Merge: 71e1cd7e7 b7a3db689 Author: Weiqun Zhang Date: Tue Nov 1 09:16:50 2016 -0700 Merge branch 'master' into development commit ccef5dc3add4bb814b0932b1e84de68c4d1b700f Author: Weiqun Zhang Date: Mon Oct 31 20:46:15 2016 -0700 fix a new bug in Fortran fillpatch for face data Src/F_BaseLib/fillpatch.f90 commit 71e1cd7e78ea5b633e43236d13913c7c0dd8c1ef Author: Michael Zingale Date: Mon Oct 31 13:59:36 2016 -0400 don't require probin -- this will be on the user to ensure it exists Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/test_report.py commit 57bd51ee71d2290e95442b9e92b50baca8756222 Author: Weiqun Zhang Date: Mon Oct 31 09:11:34 2016 -0700 fix some new bugs in Fortran fillpatch for face data Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 commit 73f548f64af7516a8ac3aea77d3cc8505b63cb9a Author: Weiqun Zhang Date: Fri Oct 28 14:56:59 2016 -0700 minor Src/C_BaseLib/Box.cpp commit 49b75e5ccfca6175cec4f3bae4ca9e50dd10edd6 Author: vince Date: Fri Oct 28 14:48:44 2016 -0700 optimize sync reads. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 25909ced2abd51d940a6951088ad5e9e450b5461 Author: Weiqun Zhang Date: Fri Oct 28 10:37:02 2016 -0700 fillpatch for face data Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 commit 66cb4d5f07e6fb616076d4495db73dcc964a727c Author: Weiqun Zhang Date: Fri Oct 28 10:35:35 2016 -0700 add some functions for nodal box coarsening Src/F_BaseLib/box_f.f90 Src/F_BaseLib/boxarray_f.f90 commit 08cc1ef82edcc462c9e39b2635cdb41fedf3e8c0 Author: Ann Almgren Date: Thu Oct 27 16:21:43 2016 -0700 Last one ... Tools/RegressionTesting/IAMR-tests.ini commit 6c9a0ab224d3ad5593108eadd356305ee318c9ac Author: Ann Almgren Date: Thu Oct 27 15:58:22 2016 -0700 Remove more app specific regression test files. Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/RNS-tests.ini Tools/RegressionTesting/SMC-tests.ini commit da41eabd3d23ca78d4e3a58ac9a3d71f4500a6a2 Author: vince Date: Thu Oct 27 15:43:39 2016 -0700 support for non-native format conversions. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 48f21a9f1268ce1af6492c2734a5d092caf9278a Author: vince Date: Thu Oct 27 15:39:37 2016 -0700 added const. Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp commit bb72844266cd2585caf4728341221ad51ee2edb4 Author: vince Date: Thu Oct 27 15:38:54 2016 -0700 correct comments. Src/C_BaseLib/FArrayBox.H commit 421bcdd8fae8f03a51ec6eade55f80fcbfff793c Author: Michael Zingale Date: Thu Oct 27 18:37:48 2016 -0400 move these to the application codes Tools/RegressionTesting/Castro-SBU-tests.ini Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/Microphysics-tests-pgi.ini Tools/RegressionTesting/Microphysics-tests.ini commit b657453bc32310c5e5d04e98f72b119872426c48 Author: Ann Almgren Date: Thu Oct 27 15:26:05 2016 -0700 Removed Nyx-tests.ini from the regression testing directory. Tools/RegressionTesting/Nyx-tests.ini commit 7c232dbda1d65b3c0364ec4864ac63ddb841f4b1 Author: vince Date: Wed Oct 26 12:26:21 2016 -0700 change to a more searchable name. Src/C_BaseLib/FArrayBox.cpp commit 75c119ea5ba10b60d292f6e6df9e2a645d406ed7 Author: Grout Date: Wed Oct 26 08:28:41 2016 -0600 Fix to make InitOnePerCell work in 2D Src/C_ParticleLib/ParticleInit.H commit 38d943e13df8bfb6ee6469d0d157334d41e73a89 Author: Weiqun Zhang Date: Mon Oct 24 15:33:45 2016 -0700 make sure grid id is valid Src/C_ParticleLib/Particles.cpp commit ed1661ecf453ce9f7fdadd1ca9a6118c7640474d Merge: 8b9027e09 eb58c46b0 Author: vince Date: Mon Oct 24 15:22:28 2016 -0700 Merge branch 'optio' of https://github.com/BoxLib-Codes/BoxLib into optio commit 8b9027e09e78b941437792f095adb5911af26fce Author: vince Date: Mon Oct 24 15:21:57 2016 -0700 dont copy data for single grid combined read, seek fix for persistent streams, secondary sort. Src/C_BaseLib/FabArray.H Src/C_BaseLib/VisMF.cpp commit 266526ba2e73a7d7c2caed249de6e1e822269ba4 Author: Weiqun Zhang Date: Mon Oct 24 12:17:17 2016 -0700 fix typo Src/C_BaseLib/PlotFileUtil.H Src/C_BaseLib/PlotFileUtil.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp commit 0a26ebb18a7547af985faafaafd918b5c6669a8c Author: Weiqun Zhang Date: Mon Oct 24 11:09:57 2016 -0700 Particles: add functions to clear particle boxarray and distribution map and some other minor changes Src/C_AmrCoreLib/AmrCore.cpp Src/C_AmrCoreLib/AmrParGDB.H Src/C_AmrCoreLib/AmrParticles.H Src/C_ParticleLib/ParGDB.H Src/C_ParticleLib/ParticleInit.H Src/C_ParticleLib/Particles.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit 47918e76854dd49b9a1041d09b4a347b38369f0e Author: Weiqun Zhang Date: Fri Oct 21 20:59:16 2016 -0700 AMR_Adv_C_v2 tutorial: fix bc in interp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 244df0549da85e73042d8f9bb959e2d515cdaaea Author: Weiqun Zhang Date: Fri Oct 21 12:27:17 2016 -0700 AMR_Adv_C_v2 tutorial: iteratively build fine levels in init Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 21211ca3dbaa97d9f5d82ccbd776e61d7d28bc49 Author: Weiqun Zhang Date: Fri Oct 21 11:52:46 2016 -0700 sync up time in post coarse timestep for all levels Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H commit f17fc95e78225aaf7aa347017e058bda6740f12f Author: Weiqun Zhang Date: Fri Oct 21 11:50:19 2016 -0700 AMR_Adv_C_v2 tutorial: put regrid_int, check_int, plot_int, etc. in amr parameter space Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit d25d213937381b12a183b71771b23b8715d0f2a7 Author: Weiqun Zhang Date: Fri Oct 21 09:37:07 2016 -0700 sync up time in post coarse timestep Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit fca81accb5297e8f02b33d302a41139fd4091825 Merge: f6585ee39 21459f95f Author: Weiqun Zhang Date: Thu Oct 20 16:43:52 2016 -0700 Merge branch 'development' into amrcore commit f6585ee3907461bd821cc984deae0504a6aca981 Author: Weiqun Zhang Date: Thu Oct 20 16:43:45 2016 -0700 minor Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit b7a3db689e02c83ab5804cffaa0ae9b3acdedd17 Author: Weiqun Zhang Date: Thu Oct 20 16:07:36 2016 -0700 add missing template parameter Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/MultiFab.cpp commit 21459f95f85876cd2b9c8136e3d1005fcb7e0f40 Author: Weiqun Zhang Date: Thu Oct 20 16:07:36 2016 -0700 add missing template parameter Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/MultiFab.cpp commit 301fb50c99f29b743b4d810a6da9b6f635904dc4 Merge: 0706bee8b 42e8f0468 Author: Weiqun Zhang Date: Thu Oct 20 16:03:18 2016 -0700 Merge branch 'amrcore' of github.com:BoxLib-Codes/BoxLib into amrcore commit 42e8f04687c0fdea16c228a270feb60156700dc5 Author: Ann Almgren Date: Thu Oct 20 15:06:59 2016 -0700 Getting the cmake stuff to work ... Src/CMakeLists.txt commit 1d5fb27d7515c02e05ffa3749fc0b75a84d9dded Author: Ann Almgren Date: Thu Oct 20 15:05:50 2016 -0700 Rename box_camr --> box_camrcore for C_AmrCoreLib. Src/C_AmrCoreLib/CMakeLists.txt commit 5d78e92b5813d7562ca541454261f8440eb74b56 Author: Ann Almgren Date: Thu Oct 20 15:00:46 2016 -0700 We want AmrParticles to depend on AmrCore not Amr Src/C_AmrCoreLib/AmrParticles.H commit fc261a8e712a1e57bfd0fa412950202d3678ff7b Author: Ann Almgren Date: Thu Oct 20 14:58:30 2016 -0700 Add new CMakeLists.txt for C_AmrCoreLIb and modify the ones in C_AMRLib and Source. Src/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_AmrCoreLib/CMakeLists.txt commit 0706bee8b46c0244413433fa4e9c4a285b26bf4f Author: Weiqun Zhang Date: Wed Oct 19 20:48:33 2016 -0700 minor Src/C_BaseLib/PlotFileUtil.cpp commit afa5d62ec08618f830bc56fe766d8c8d7e2cc199 Author: Weiqun Zhang Date: Wed Oct 19 16:58:10 2016 -0700 AmrAdv/AmrCore tutorial: write the last plotfile Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit 0064621bec870ca65702a201b131e2e8bc280525 Author: Weiqun Zhang Date: Wed Oct 19 16:43:13 2016 -0700 pass explicit distributionmap Src/C_AMRLib/FillPatchUtil.cpp commit 7b75876a82cc15a83b664558367dc634c6f4a21c Author: Weiqun Zhang Date: Wed Oct 19 16:41:46 2016 -0700 minor Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 5f6ad74268a48c7e4a37864af8da3e82e27608c4 Author: Weiqun Zhang Date: Wed Oct 19 16:34:50 2016 -0700 AmrAdv/AmrCore tutorial: flush distributionmap cache Src/C_AmrCoreLib/FillPatchUtil.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit b8f4404d0ef76a492df5fc2145d48ab903d505e9 Author: Weiqun Zhang Date: Wed Oct 19 16:15:46 2016 -0700 AmrAdv/AmrCore tutorial: add regrid Src/C_AmrCoreLib/AmrCore.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 89c4e0d6cbb09298cbc2fee1601b32947b61f022 Merge: 04bef474e db6bec872 Author: Michael Zingale Date: Wed Oct 19 17:16:29 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 04bef474ee99a39b3cf984e7eec33e9aa533c6de Author: Michael Zingale Date: Wed Oct 19 17:15:47 2016 -0400 since there can be many more system-provided modules, don't abort if a module is not found, but instead print a warning to STDERR Tools/F_scripts/dep.py commit db6bec8722e91854e57c32766c4d7f33df7ed817 Author: Weiqun Zhang Date: Wed Oct 19 10:28:55 2016 -0700 fix a typo Tools/Release/ppCleanup.py commit fda957069933072a9edc0eaea3c189cc085cb06b Author: Weiqun Zhang Date: Wed Oct 19 10:28:06 2016 -0700 wip Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit 8849d4ccf78b46a3a35a451d5ed3aa1a33a4cd86 Author: Weiqun Zhang Date: Wed Oct 19 09:47:18 2016 -0700 AmrAdv/AmrCore tutorial: add reflux Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit e4cbf5007c7257dd628750acb4dc630fcfe3b7d6 Author: Weiqun Zhang Date: Wed Oct 19 09:01:16 2016 -0700 AmrAdv/AmrCore tutorial: average down in post timestep Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit 06a364639f91f790ace3e81ba4ecc21ea5b3a5bd Author: Weiqun Zhang Date: Wed Oct 19 11:37:45 2016 -0400 fix isinf and isnan for PGI; it looks like PGI pretends to be __GNUC__ Src/C_BaseLib/FArrayBox.cpp commit d61a0d29fd79d6a8437b57b99ab10b2cd194954d Author: Weiqun Zhang Date: Tue Oct 18 17:06:10 2016 -0700 AmrAdv/AmrCore tutorial: write plotfiles Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 14ebd0aaf4a030872b36c2a163a1784c6aee821c Author: Weiqun Zhang Date: Tue Oct 18 16:50:39 2016 -0700 AmrAdv/AmrCore tutorial: add advect Fortran routines Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/Src_2d/Adv_2d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_2d/Make.package Tutorials/AMR_Adv_C_v2/Source/Src_2d/compute_flux_2d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_3d/Adv_3d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_3d/Make.package Tutorials/AMR_Adv_C_v2/Source/Src_3d/compute_flux_3d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_3d/slope_3d.f90 commit b273fcb66cca245ecb9da6705380467b06a612f0 Author: Weiqun Zhang Date: Tue Oct 18 16:12:55 2016 -0700 AmrAdv/AmrCore tutorial: FillPatch Src/C_BaseLib/PhysBCFunct.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/Make.package commit 6fde01d77bd8be674bc4d2aacf2a8b1dae7cefa8 Author: Weiqun Zhang Date: Tue Oct 18 16:12:32 2016 -0700 new BaseFab::make_alias function Src/C_BaseLib/BaseFab.H commit 83ec549869ad72a9932924299a1881a7531052c0 Author: Weiqun Zhang Date: Tue Oct 18 16:12:32 2016 -0700 new BaseFab::make_alias function Src/C_BaseLib/BaseFab.H commit 0be1ddcbf45e8d7b6a949b3e8ca0c077144a0deb Author: Weiqun Zhang Date: Tue Oct 18 13:29:34 2016 -0700 AmrAdv/AmrCore tutorial: compute dt; set up time stepping Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/main.cpp commit b4c9ebf3fbad40ffc1c98032a52cb938684c6a5e Author: Weiqun Zhang Date: Tue Oct 18 10:46:43 2016 -0700 AmrAdv/AmrCore tutorial: put tagging parameters in inputs Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/Src_nd/Make.package Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90 Tutorials/AMR_Adv_C_v2/Source/Src_nd/tagging_params.f90 commit dc5d97a5525f3ace538b00c128862204be9128e0 Author: Weiqun Zhang Date: Tue Oct 18 10:29:12 2016 -0700 AmrAdv/AmrCore tutorial: write plotfile Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 58ac3c505a7b1ceb0e03bbb4751377ad1cd8b3f1 Author: Weiqun Zhang Date: Tue Oct 18 10:28:36 2016 -0700 remove unused variables Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90 commit 4bdf1ed867dd0cfb56ea09e9ad9f6a73f8c45357 Author: Weiqun Zhang Date: Tue Oct 18 10:27:40 2016 -0700 PlotFileUtil: write multi-level plotfile Src/C_BaseLib/PlotFileUtil.H Src/C_BaseLib/PlotFileUtil.cpp commit d1c85af7b3b04a31050afe8354dbd58435261e75 Author: Michael Zingale Date: Mon Oct 17 19:26:43 2016 -0400 copy the string routines over from Castro Src/F_Interfaces/BaseLib/parmparse_fi.cpp Src/F_Interfaces/BaseLib/parmparse_mod.f90 commit ce704fee1c39a8b5b4d75746136647c49b56e502 Author: Weiqun Zhang Date: Sat Oct 15 22:07:39 2016 -0700 AmrAdv/AmrCore tutorial: implement ErrorEst Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/Src_nd/Make.package Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90 Tutorials/AMR_Adv_C_v2/Source/Src_nd/tagging_params.f90 commit 7bff01d7ab84f313bd26f4f6ed09588abfdca771 Author: Weiqun Zhang Date: Sat Oct 15 16:58:50 2016 -0700 AmrAdv/AmrCore tutorial: build fine grids and init data on fine levels; ErrorEst to be implemented Src/C_AmrCoreLib/AmrCore.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit a38877815f798d3c0d6326e64ca9696c453683fa Author: Weiqun Zhang Date: Sat Oct 15 11:59:18 2016 -0700 AmrAdv/AmrCore tutorial: init data on base level Src/C_AmrCoreLib/AmrCore.H Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/Make.package commit f5acabc46f0e56c809bed16a90832718536d8548 Author: Michael Zingale Date: Sat Oct 15 13:16:31 2016 -0400 change how we record COMP_VERSION and FCOMP_VERSION to be safer for Ubuntu Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit c6b5065dee41ebdb6758ba70635e77b5b9567625 Merge: 1444b7a12 75e72cb60 Author: Weiqun Zhang Date: Fri Oct 14 15:55:58 2016 -0700 Merge branch 'development' into amrcore commit 1444b7a121aeba84853a6afd3281a2cc5a3d1a0d Author: Weiqun Zhang Date: Fri Oct 14 13:36:40 2016 -0700 start AMR_Adv tutorial based on AmrCoreLib Src/C_AmrCoreLib/AmrCore.H Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/README Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp Tutorials/AMR_Adv_C_v2/Source/Make.package Tutorials/AMR_Adv_C_v2/Source/main.cpp Tutorials/README_C commit a9c7b9490195daa54eb919ddd75d699b852b219f Merge: eeba6f120 d120ef458 Author: Weiqun Zhang Date: Fri Oct 14 12:47:04 2016 -0700 Merge branch 'amrcore' of github.com:BoxLib-Codes/BoxLib into amrcore Conflicts: Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp commit eeba6f120b3e7ae4f9031bb48cb140d99a91473f Author: Weiqun Zhang Date: Wed Oct 12 14:22:29 2016 -0700 move part of the regrid function into AmrCore Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp commit 75e72cb60780d1b024787cee5b9c9900ee357ed0 Author: Weiqun Zhang Date: Thu Oct 13 16:00:06 2016 -0700 using std::isinf & std::isnan for GCC >= 5 Src/C_BaseLib/FArrayBox.cpp commit 4ab1e8b48aa385f68568427e1716fb8ff4238294 Author: Weiqun Zhang Date: Thu Oct 13 10:42:42 2016 -0700 Add PlotFileUtil for writing plotfiles; some functions in MultiFabUtil for averaging from face and edge to cell center Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/PlotFileUtil.H Src/C_BaseLib/PlotFileUtil.cpp commit 5640cef897b8492c4699792674369fc3105dfa31 Author: Michael Zingale Date: Thu Oct 13 14:59:52 2016 -0400 some updates on the suite Docs/UsersGuide/Regression/test_suite.tex commit 596212861108711ae600730de1b2342e5a2c06de Author: Marc Day Date: Thu Oct 13 08:32:43 2016 -0700 Minor mods to README to point user to BoxLib User Guide Tools/RegressionTesting/README commit d120ef4587340ff6b3469c1430b5fff70d56990b Author: Weiqun Zhang Date: Wed Oct 12 14:22:29 2016 -0700 wip Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp commit 30964d2bbcb8e9b3423f3039ba7a3b3f91c05187 Merge: f4f6da610 8b48742ed Author: Marc Day Date: Wed Oct 12 17:58:53 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit f4f6da610ba2b3da4c2f0e21a30a2d11f4a2e81c Author: Marc Day Date: Wed Oct 12 17:58:24 2016 -0700 Add more info in the RegTest README Tools/RegressionTesting/README commit 8b48742ed52415a461c78886617fdc4fdc2d7812 Author: Weiqun Zhang Date: Wed Oct 12 15:14:55 2016 -0700 cmake update CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Src/C_ParticleLib/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 2c5f4137a74d7cd3b5d83689c483e8164a16d335 Merge: 748303a9d a218db786 Author: vince Date: Wed Oct 12 15:12:13 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 748303a9d9b082b05b43a7365949c58914a63587 Author: vince Date: Wed Oct 12 15:11:33 2016 -0700 fix typo in profiling call. Src/C_BaseLib/ParallelDescriptor.H commit eb58c46b0b435215c5c12a5a38d8cc3520469fc0 Author: vince Date: Wed Oct 12 15:09:43 2016 -0700 fix typo in profiling call. Src/C_BaseLib/ParallelDescriptor.H commit 75df7175d785f41ade5d817cba22b2fe0b0d66e5 Merge: 76928bb02 a218db786 Author: Weiqun Zhang Date: Wed Oct 12 12:44:38 2016 -0700 Merge branch 'development' into amrcore commit 76928bb020df03b7191ed9cadc5c34d12398ebfc Author: Weiqun Zhang Date: Wed Oct 12 12:37:21 2016 -0700 fix particle grids and dmap; move the two grids stuff from AmrLevel to AmrParGDB Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp Src/C_AmrCoreLib/AmrParGDB.H commit c4a97398a9741e39e259246dc97a07bb38be4e1f Author: Weiqun Zhang Date: Wed Oct 12 11:02:03 2016 -0700 remove a number of unused and do-nothing functions Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit a218db786f054652d79c31565a206c4a29824028 Author: Michael Zingale Date: Wed Oct 12 11:16:54 2016 -0400 hook in preprocessing of the .F90 files -- some code bases need this Tools/F_mk/GMakerules.mak commit 0b045054fe2e0135cfb3576516107f4ee71bba34 Author: Michael Zingale Date: Wed Oct 12 11:16:43 2016 -0400 make the use of the f90_preprocessor optional Tools/F_scripts/dep.py commit 2c2a8f9bf73cae487bf5ff4bad7174746e2f728e Author: Michael Zingale Date: Wed Oct 12 10:33:20 2016 -0400 module matching needs to be case-insensitive Tools/F_scripts/dep.py commit cce15b1b7ed7402113d2a42a15657969e49b618a Author: Weiqun Zhang Date: Tue Oct 11 15:57:03 2016 -0700 AmrCore: finish particles Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp Src/C_AmrCoreLib/AmrParGDB.H Src/C_BaseLib/DistributionMapping.H Src/C_ParticleLib/ParGDB.H Src/C_ParticleLib/Particles.H Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp commit 592d596328ae42a39af3a0a14ebb4707a27fcc35 Author: vince Date: Tue Oct 11 16:27:40 2016 -0700 set checkpoint and plot header versions individually. Src/C_AMRLib/Amr.cpp commit a18e79aaf782eaa2e4bcc477874fedac4650e647 Author: Weiqun Zhang Date: Tue Oct 11 09:05:45 2016 -0700 move some data from Amr into AmrCore Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp Src/C_AmrCoreLib/AmrParGDB.H Src/C_AmrCoreLib/Make.package Src/C_BaseLib/Geometry.cpp Src/C_ParticleLib/ParGDB.H commit 3913650ac383456a3e3bc9396d444f4eb898b222 Author: vince Date: Tue Oct 11 14:20:29 2016 -0700 fix for dss for different nfiles for plots and checkpoints. Src/C_BaseLib/NFiles.cpp commit e55d5060b3e48f207a115166fc061e11185ea17a Author: vince Date: Tue Oct 11 13:05:29 2016 -0700 fix for faminmax header. Src/C_BaseLib/VisMF.cpp commit a31b1304fc0c3f1e24c862b107d4bc0fedb3edd1 Author: Weiqun Zhang Date: Tue Oct 11 11:19:10 2016 -0700 particle: minor Src/C_ParticleLib/ParticleInit.H Src/C_ParticleLib/Particles.H commit 244f7aa6d39b39d3ffccd9bb87d51da0ea33b72d Author: Michael Zingale Date: Tue Oct 11 13:38:00 2016 -0400 fix dupe Tools/F_mk/GMakerules.mak commit 22eeb6c4f68853a4b793e41cd1cc4e01cbb016e2 Author: Michael Zingale Date: Tue Oct 11 11:12:02 2016 -0400 capture the return code from dep.py and abort if it was not happy Tools/F_mk/GMakerules.mak commit e0ea0d6b38f2a6655d556e94457d86a18108376f Author: Michael Zingale Date: Tue Oct 11 09:48:56 2016 -0400 clarify where EXT_DIR data lives Src/C_BaseLib/BC_TYPES.H commit 4635fe720fed661abd0e2a7843baceb8e0996a94 Author: Michael Zingale Date: Tue Oct 11 09:44:58 2016 -0400 move the F90 BoxLib dependency checking over to the same dep.py that we use for C++ builds. Remove the old perl script. Note, for F90 BoxLib, we do not preprocess the files before the dependency checking. This is easy to add in, if necessary. Also remove the old deppairs target -- that does not seem to be used anywhere. Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_scripts/moddep.pl commit c2bdeb2eecd1ffe5640eaf915d188758050c3afa Author: Weiqun Zhang Date: Mon Oct 10 13:37:39 2016 -0700 move more files from C_AMRLib into C_AmrCoreLib Src/C_AMRLib/Make.package Src/C_AmrCoreLib/ErrorList.H Src/C_AmrCoreLib/ErrorList.cpp Src/C_AmrCoreLib/FLUXREG_1D.F Src/C_AmrCoreLib/FLUXREG_2D.F Src/C_AmrCoreLib/FLUXREG_3D.F Src/C_AmrCoreLib/FLUXREG_F.H Src/C_AmrCoreLib/FillPatchUtil.H Src/C_AmrCoreLib/FillPatchUtil.cpp Src/C_AmrCoreLib/FluxRegister.H Src/C_AmrCoreLib/FluxRegister.cpp Src/C_AmrCoreLib/INTERP_1D.F Src/C_AmrCoreLib/INTERP_2D.F Src/C_AmrCoreLib/INTERP_3D.F Src/C_AmrCoreLib/INTERP_F.H Src/C_AmrCoreLib/Interpolater.H Src/C_AmrCoreLib/Interpolater.cpp Src/C_AmrCoreLib/Make.package Src/C_AmrCoreLib/TagBox.H Src/C_AmrCoreLib/TagBox.cpp commit ee0259aadc9d7dc0a189b585c9b4967e468c4e5a Author: Weiqun Zhang Date: Mon Oct 10 13:13:54 2016 -0700 start C_AmrCoreLib Src/C_AMRLib/Make.package Src/C_AmrCoreLib/AmrParGDB.H Src/C_AmrCoreLib/AmrParticles.H Src/C_AmrCoreLib/Cluster.H Src/C_AmrCoreLib/Cluster.cpp Src/C_AmrCoreLib/Make.package commit 074030b29714f7a23769c2edf71c6470112a8e76 Merge: 7c9de23f6 44fdaef52 Author: Michael Zingale Date: Mon Oct 10 15:58:13 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 7c9de23f657018fd8ec21a1c250471933f704b67 Author: Michael Zingale Date: Mon Oct 10 15:58:00 2016 -0400 allow for no preprocessing if --cpp is not supplied Tools/F_scripts/dep.py commit 44fdaef527f32fb24855f4f83e199f8eba1fa5ca Author: Weiqun Zhang Date: Mon Oct 10 10:44:01 2016 -0700 Particle: template on container type, vector or deque Src/C_ParticleLib/AmrParticles.H Src/C_ParticleLib/ParticleInit.H Src/C_ParticleLib/Particles.H Src/C_ParticleLib/TracerParticles.H commit 95783ae2b2e16b60ca9b257539027a793bffb959 Author: Weiqun Zhang Date: Mon Oct 10 10:12:01 2016 -0700 Particle: reimplement removing particles so that we can use either deque or vector Src/C_ParticleLib/Particles.H commit 7a563eb4f6bc08b48b111e282907181b50f04b6b Author: Weiqun Zhang Date: Sun Oct 9 21:00:42 2016 -0700 Particle: send the new int data Src/C_ParticleLib/Particles.H commit fd3ad67166c1d2a75679995b0c5b2d5fc62cfcf0 Author: Weiqun Zhang Date: Sun Oct 9 20:29:21 2016 -0700 Particle: loop fusion Src/C_ParticleLib/Particles.H commit 70b1e6dd1f555e740446754b45edccbc59b74809 Author: Weiqun Zhang Date: Sun Oct 9 13:19:23 2016 -0700 Particle: fix my recent bug Src/C_ParticleLib/Particles.H commit c3e23ed429628b03e4ec4e3160e97d79eb02d62b Author: Weiqun Zhang Date: Sun Oct 9 13:09:22 2016 -0700 particle: a comment Src/C_ParticleLib/Particles.H commit 2f3f1463d23ae68a604743d2759c662c166f22d4 Author: Weiqun Zhang Date: Sun Oct 9 12:48:23 2016 -0700 Particle: skip PeriodicWhere if not periodic Src/C_ParticleLib/Particles.cpp commit 720d0dd92e0a4785703bc152d382cf4747ca8a5c Author: Weiqun Zhang Date: Sat Oct 8 22:57:56 2016 -0700 Particles: range for and auto Src/C_ParticleLib/Particles.H commit 3e03f970e0269e8b4e2199e14693b6208893aaee Author: Michael Zingale Date: Sun Oct 9 16:21:45 2016 -0400 skip dependency if a file provides the modules it needs on its own Tools/F_scripts/dep.py commit 932bfab3a29822c0bcd573ecd23eeb77df10a1c5 Merge: 052e6da5b 74d3f7181 Author: Michael Zingale Date: Sat Oct 8 19:37:53 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 052e6da5b9fb2d40e58b36c1c7072b0a23607f03 Author: Michael Zingale Date: Sat Oct 8 19:37:13 2016 -0400 we don't use Solaris anywhere in the make stuff Tools/C_mk/Make.defs Tools/C_mk/README.md commit 74d3f7181618c365b090e87aa4335bbc05bba9ee Author: Weiqun Zhang Date: Sat Oct 8 16:29:24 2016 -0700 Particles: move a few functions back Src/C_ParticleLib/Particles.H commit 06bb8e3471765f6af297b7f317c9032584488f0a Author: Weiqun Zhang Date: Sat Oct 8 15:07:39 2016 -0700 Particles: move a few functions back so that the tutorials can compile Src/C_ParticleLib/Particles.H Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp commit 15ab10ee79453e2e41a77bf23e22b846fc66a17f Author: Weiqun Zhang Date: Sat Oct 8 12:47:01 2016 -0700 Particles: towards losing weight by moving a lot of stuff into Nyx Src/C_ParticleLib/AmrParticles.H Src/C_ParticleLib/Particles.H Src/C_ParticleLib/Particles.cpp Src/C_ParticleLib/TracerParticles.H commit 054273b941f1aa65a5a77c959fbd25484c13bce4 Author: Michael Zingale Date: Sat Oct 8 15:12:18 2016 -0400 remove g77 support Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 82499fedcbd946ee54b72086c91f6c3b72ec8478 Author: Michael Zingale Date: Sat Oct 8 15:07:23 2016 -0400 fix endit Tools/C_mk/Make.Linux commit 68fecd45c828715b4a41332e565d79173212b804 Author: Michael Zingale Date: Sat Oct 8 15:06:53 2016 -0400 some machine clean-ups Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit bcec425a35fe65fd08a2720d68fff9fd9bc1588a Author: Michael Zingale Date: Sat Oct 8 11:19:58 2016 -0400 ppCleanup is obsoleted by Release Tools/ppCleanup/README Tools/ppCleanup/cleanWords.txt Tools/ppCleanup/ppCleanup.py commit 7fa7a5b6a41c496acd79a01774d9537f7bd9b7a5 Author: Michael Zingale Date: Sat Oct 8 11:18:26 2016 -0400 darter, lens, alphacluster, and pccluster are no more Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 507720caf254637c8b4c23afb178211849fadc32 Author: Weiqun Zhang Date: Fri Oct 7 21:43:54 2016 -0700 Add a new script that does macro cleanup on a directory Tools/Release/ppCleanupDir.py Tools/Release/release.py commit da9a34d46283f831e0e90bff063879eb3490c30e Merge: 241878fba 4700a1375 Author: Michael Zingale Date: Fri Oct 7 21:36:51 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 4700a1375c674fcd4bc70dd93bd47d62de97eeb0 Author: Weiqun Zhang Date: Fri Oct 7 13:39:43 2016 -0700 MultiFabUtil average_edge_to_cellcenter Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 98733f42117e6fe7e0446c2c346c2675a9287874 Author: Weiqun Zhang Date: Fri Oct 7 12:31:11 2016 -0700 add particlecontainer default constructor Src/C_ParticleLib/Particles.H commit 1ed1e9f3c02da3c7b6f8c408504ce29c035615e6 Author: vince Date: Fri Oct 7 11:14:06 2016 -0700 fixes for serial. Src/C_BaseLib/NFiles.cpp Tests/IOBenchmark/IOTest.cpp commit 10aeaa9759962bab4aca4ca66b56748d3d4d9c5f Author: vince Date: Fri Oct 7 10:36:25 2016 -0700 fix for serial. Src/C_BaseLib/NFiles.cpp commit 241878fba86ad31baa05c1a4db53b958fbdedd85 Author: Michael Zingale Date: Fri Oct 7 12:41:59 2016 -0400 we don't use the library building features for C++ BoxLib, so remove them to make the make stuff clearer and easier to read Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 90b7a3405b2e40892f9b35f7e863e53c1d004621 Author: Michael Zingale Date: Fri Oct 7 12:31:41 2016 -0400 compressor is a job management script -- it doesn't belong here Tools/F_scripts/compressor commit 46024f6bcc4ca6af7aa99f7fae2e1c6861857e43 Author: Michael Zingale Date: Fri Oct 7 12:31:28 2016 -0400 remove coco -- this is not used Tools/F_scripts/coco/coco.pl Tools/F_scripts/coco/coco_e.FF Tools/F_scripts/coco/e1.FF Tools/F_scripts/coco/e1.II commit 445307c60b2611bb11965f9e90f2a5cda1db18ed Author: Michael Zingale Date: Fri Oct 7 12:31:16 2016 -0400 require python 2.7 or later Tools/F_scripts/dep.py commit 98ec454f9c250d05182b1eb103e9171b87cfc27f Author: Michael Zingale Date: Fri Oct 7 09:35:07 2016 -0400 add a few comments Tools/F_scripts/dep.py commit 1aaab75fcc50cddc4cc5846054d9771a8ba3be4a Author: Michael Zingale Date: Fri Oct 7 08:58:54 2016 -0400 add some system modules to IGNORES, make things case insensitive Tools/F_scripts/dep.py commit 75a27de1c802d81c1e99d21905e3c89272f49506 Merge: 9d1d42292 dc389498f Author: Michael Zingale Date: Thu Oct 6 20:57:23 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 9d1d42292ef9f5d719aa98ad9826f3c18460c630 Author: Michael Zingale Date: Thu Oct 6 20:56:57 2016 -0400 add a readme, remove a very old submission script Tools/F_scripts/README.md Tools/F_scripts/dep.py Tools/F_scripts/ibm_sp_batch.poe commit dc389498f00cf85b6061511c6c77e6ab5b733c71 Author: Weiqun Zhang Date: Thu Oct 6 17:08:34 2016 -0700 Revert "FabArray: always respect the wish of nodal flag" This reverts commit d14adae93b0fb1e68e5cd2c34255eeaa276ea7f5. Src/C_BaseLib/FabArray.H commit e6ea768a6210141252fb3b6566518a73f99614e8 Merge: 9d7e9926b d14adae93 Author: Michael Zingale Date: Thu Oct 6 19:58:20 2016 -0400 Merge branch 'development' into preprocessing commit 9d7e9926b574c24378e524a19a97bd4f7950392d Author: Michael Zingale Date: Thu Oct 6 19:40:32 2016 -0400 add debugging option, make the "use module" be matched at the start of a line (perhaps with some whitespace) and test for key errors Tools/F_scripts/dep.py commit d14adae93b0fb1e68e5cd2c34255eeaa276ea7f5 Author: Weiqun Zhang Date: Thu Oct 6 16:33:01 2016 -0700 FabArray: always respect the wish of nodal flag Src/C_BaseLib/FabArray.H commit f08029f132f183f27ab29749bc122680e95db9ba Author: Michael Zingale Date: Thu Oct 6 15:16:52 2016 -0400 pylint + python 3 changes Tools/F_scripts/dep.py commit f425f06f45f856d6c048d33dae45b1af7ed071d3 Author: Michael Zingale Date: Thu Oct 6 15:00:04 2016 -0400 a little cleaning Tools/C_mk/Make.rules commit 28fe699a768f6b8f958b066e0827f1813af19877 Author: Michael Zingale Date: Thu Oct 6 14:40:57 2016 -0400 this seems to work -- .F90 files are now preprocessed for dependency checking only (using the new dep.py script to find module dependencies) and then these preprocessed files are ignored and the Fortran compiler is invoked on the .F90 file itself, doing the preprocessing internally. Tools/C_mk/Make.rules Tools/F_scripts/dep.py commit 0707181e3791c21e4bcd6216cb90bac7d78716b4 Author: Michael Zingale Date: Thu Oct 6 13:35:17 2016 -0400 a little cleaning Tools/F_scripts/dep.py commit 8c1c9cf88d6f16283dd15e35e79874ad5d880693 Author: Michael Zingale Date: Thu Oct 6 10:27:30 2016 -0400 prep for preprocessing Tools/F_scripts/dep.py commit 1eeaa041a28227e2d85c2faf501e4e59a15cd89d Author: Michael Zingale Date: Thu Oct 6 10:05:11 2016 -0400 make it classy Tools/F_scripts/dep.py commit cb218b88af5143b54da6fbe09de31f6332c5af56 Author: Michael Zingale Date: Wed Oct 5 23:04:29 2016 -0400 add runtime hooks for preprocessing Tools/F_scripts/dep.py commit dbc24d223622ae039476c587a82578e3c38a436c Author: Michael Zingale Date: Wed Oct 5 22:46:21 2016 -0400 remove dupes Tools/F_scripts/dep.py commit 0e5f45bac2624cd36a47e706fbb5c29e773604fb Author: Michael Zingale Date: Wed Oct 5 22:15:48 2016 -0400 switch in a python F90 dependency checker this works for Castro in the current way of doing things. Needs more testing and cleaning, and then needs an option for doing preprocessing Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/F_scripts/dep.py commit df1fcb6e286123c328d661c14104e51299236b9f Author: vince Date: Wed Oct 5 17:34:40 2016 -0700 multiple deciders for chained fabarray reads, clean up ignored messages. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Tests/IOBenchmark/IOTest.cpp commit 19380156a3dc20d516adc6300ab386bc6d32e25e Author: Weiqun Zhang Date: Wed Oct 5 16:34:13 2016 -0700 allow BaseFab change box type without changing size Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H commit fad05dfd8dc92e2372c64baa4abb4afde9317a7b Author: Michael Zingale Date: Wed Oct 5 19:17:30 2016 -0400 add support for OpenACC tests Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit 67b290a56e40fe0800167e37fb3debbf5f3a6ee3 Author: Weiqun Zhang Date: Wed Oct 5 15:30:30 2016 -0700 NodalDepositionSingleLevel: the new MultiFab must have the same index type as the MultiFab to be filled Src/C_ParticleLib/Particles.H commit 696c9778984b5b6dffe4dbc930ea8df457439c2d Merge: 2ee1d59bd 244e37fac Author: Weiqun Zhang Date: Tue Oct 4 17:08:07 2016 -0700 Merge branch 'master' into development Conflicts: Src/C_AMRLib/CMakeLists.txt commit 244e37fac9aadf3e8d0fa3907df1ab760068d085 Author: Weiqun Zhang Date: Tue Oct 4 17:07:03 2016 -0700 cmake Src/C_AMRLib/CMakeLists.txt commit 2ee1d59bd8513a95005ab0f2b64f37c0f7f18bdc Author: Weiqun Zhang Date: Tue Oct 4 17:01:55 2016 -0700 cmake Src/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_ParticleLib/CMakeLists.txt commit ef2e74c4e7b6d2b668ec96716432569135336a0f Author: Weiqun Zhang Date: Tue Oct 4 16:49:13 2016 -0700 include(PreprocessBoxLibFortran90) Src/CMakeLists.txt commit 878b5fdf6015063099a88889588812dcff4c8081 Merge: 0b9f600c8 e6065df1e Author: Weiqun Zhang Date: Tue Oct 4 16:30:38 2016 -0700 Merge branch 'master' into development commit e6065df1e63aa6319b46d1d9a45c1557f30b38ba Author: Weiqun Zhang Date: Tue Oct 4 16:30:25 2016 -0700 typo Src/C_BaseLib/CMakeLists.txt commit 0b9f600c899b1d5b07ee846198b7d37c82b1b83c Merge: e18f31eb9 87eb45695 Author: Weiqun Zhang Date: Tue Oct 4 16:29:17 2016 -0700 Merge branch 'master' into development commit 87eb456955106a1d16f15be48b5e5effb321cee5 Author: Weiqun Zhang Date: Tue Oct 4 16:28:42 2016 -0700 trying to fix cmake; not tested because I don't know how to run cmake CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Tools/CMake/PreprocessBoxLibFortran90.cmake commit b1262e615076ec8171d8cb117e69cf10a4a0b0d6 Author: Ann Almgren Date: Tue Oct 4 07:07:33 2016 -0700 FILCC* now live in C_BaseLib so remove them from C_AMRLib/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt commit e18f31eb9d4ca9aa081952f97908206e27a95a81 Author: Weiqun Zhang Date: Tue Oct 4 15:50:19 2016 -0700 clean up Tutorials/HelloWorld_C/GNUmakefile commit 2c67a85aab2d9bf781af305ad3f1caaca20a1d97 Author: Weiqun Zhang Date: Tue Oct 4 13:23:55 2016 -0700 move Timestamp function into TracerParticleContainer class Src/C_ParticleLib/Particles.H Src/C_ParticleLib/TracerParticles.H Src/C_ParticleLib/TracerParticles.cpp commit a9dc8ec1205437c4163ce961f78dcd8dad977d70 Author: Weiqun Zhang Date: Tue Oct 4 12:26:55 2016 -0700 move Particle stuff into C_ParticleLib; add TracerParticleContainer; note that cmake needs to be fixed Src/C_AMRLib/Make.package Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_ParticleLib/AmrParGDB.H Src/C_ParticleLib/AmrParticles.H Src/C_ParticleLib/Make.package Src/C_ParticleLib/ParGDB.H Src/C_ParticleLib/ParticleInit.H Src/C_ParticleLib/Particles.H Src/C_ParticleLib/Particles.cpp Src/C_ParticleLib/Particles_1D.F Src/C_ParticleLib/Particles_2D.F Src/C_ParticleLib/Particles_3D.F Src/C_ParticleLib/Particles_F.H Src/C_ParticleLib/TracerParticles.H Src/C_ParticleLib/TracerParticles.cpp Tutorials/PIC_C/GNUmakefile Tutorials/TwoGrid_PIC_C/GNUmakefile commit d98ee529b7845bb847829fb8a22ac24c5cd481d9 Author: Ann Almgren Date: Tue Oct 4 12:57:43 2016 -0700 Make 1d and 2d versions of NodalDeposition Src/C_BaseLib/Particles.H commit 7a27362978142ccbce6eb99dc1e311e3b058e1fe Author: Weiqun Zhang Date: Tue Oct 4 08:39:31 2016 -0700 NodalDepositionSingleLevel only works in 3d Src/C_BaseLib/Particles.H commit a74bfaa15c1a5c2d9ad1b2d807f05fd994bc8deb Author: Ann Almgren Date: Tue Oct 4 07:07:33 2016 -0700 FILCC* now live in C_BaseLib so remove them from C_AMRLib/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt commit 0773551bbd409590df55a44f8a3ac9e4f9a713a4 Author: vince Date: Mon Oct 3 17:30:18 2016 -0700 name barriers for profiling. Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit c6ebc0f24df89c31d677d615a2d224ecfc3e2e56 Author: Weiqun Zhang Date: Mon Oct 3 17:13:05 2016 -0700 some minor changes Src/C_BaseLib/Particles.H commit a8af51e4789163ae0d467824a4c8d695bd90ada1 Merge: 6a471e3cd 7c910574f Author: Ann Almgren Date: Mon Oct 3 16:34:12 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 6a471e3cd68a09f3a059aaad3779f0b90ab1cd61 Author: Ann Almgren Date: Mon Oct 3 16:34:01 2016 -0700 Add the single level nodal deposition routine here. Src/C_BaseLib/Particles.H commit 7c910574f88c13b18d7e83520d37a623c4906eea Author: Weiqun Zhang Date: Mon Oct 3 16:30:24 2016 -0700 elide some mpi reduce Src/C_BaseLib/Particles.H commit 5c1c23cb2a16151b3a8c4fa7d1489a7241191138 Author: Weiqun Zhang Date: Mon Oct 3 15:04:12 2016 -0700 Particle: use std::array for Real m_data Src/C_BaseLib/Particles.H commit 21bd8e0e5302ace97170397ec7cd2edff982e1f8 Merge: fe75db6f3 2858e4670 Author: Ann Almgren Date: Mon Oct 3 14:51:22 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit fe75db6f3964e254a5eb7d09c6283f3115aa25b0 Author: Ann Almgren Date: Mon Oct 3 14:50:58 2016 -0700 Get rid of everything to do with neutrinos / relativistic mass -- that all now lives in the Nyx repo. Src/C_BaseLib/Particles.H commit 7e65d8209ae02153043d7b9adf07b056ee7ed226 Author: vince Date: Mon Oct 3 14:21:03 2016 -0700 added option to provide coordinator processor number to VisMF::Read for chained fabarray reads. Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 2858e4670d08d9e428ac7f0218c497401b970a88 Author: Weiqun Zhang Date: Mon Oct 3 14:07:13 2016 -0700 update function parameter names Src/C_BaseLib/Particles.H commit b33cd4865f9c8e035c143a78c8ed5b79cdbf9d64 Merge: 1407161db b740ae256 Author: Weiqun Zhang Date: Mon Oct 3 13:58:24 2016 -0700 Merge branch 'development' into devel-particle Conflicts: Src/C_BaseLib/Particles.H commit b740ae25687b562e16f0d0c5c16b783c28c37d4b Author: Ann Almgren Date: Mon Oct 3 13:50:23 2016 -0700 1) Remove the versions of moveKick and moveKickDrift that took normal acceleration vectors on faces (keep the versions that use cell-centered accelerations) 2) Remove movePredict and moveCorrect -- no one is using those. 3) Remove AssignDensityAndVels -- that now lives in the Nyx repo. 4) Replace references to "gravity" by references to "acceleration" Src/C_BaseLib/Particles.H commit 1407161dba535ad9cfbc7d92abf1f3e65efcdc48 Author: Weiqun Zhang Date: Mon Oct 3 13:48:03 2016 -0700 white space Src/C_BaseLib/Particles.H commit 24f06a95aa801c781b71140c038a60dd2fb46c25 Author: Weiqun Zhang Date: Mon Oct 3 12:49:51 2016 -0700 Add number of intergers to Particle template Src/C_AMRLib/AmrParticles.H Src/C_BaseLib/Make.package Src/C_BaseLib/ParticleInit.H Src/C_BaseLib/Particles.H Tools/C_mk/Make.defs commit 1bfe38b37bdd641cfb2a118fb8b61ab8c5816c95 Merge: ea7e36e57 b78a92494 Author: Andy Nonaka Date: Mon Oct 3 09:08:45 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit ea7e36e57db669da0c5cba0f719ee23488bbb639 Author: Andy Nonaka Date: Mon Oct 3 09:08:27 2016 -0700 update readme_'s Tutorials/GettingStarted_F/main.f90 Tutorials/README_C Tutorials/README_F commit b78a92494d2ddba24cf795dbc87a20e43556819f Author: Weiqun Zhang Date: Mon Oct 3 08:56:32 2016 -0700 comment Src/C_BaseLib/FabArray.cpp commit d76809be838c705be7e347c3d84df202eb50f015 Author: Weiqun Zhang Date: Mon Oct 3 08:54:09 2016 -0700 Release Notes 16.10 ReleaseNotes/release-notes-16.10 commit 71d026f0528a4f31f69fd44ea99f226703130e63 Merge: 1027df993 4ed405e1f Author: Weiqun Zhang Date: Mon Oct 3 08:53:20 2016 -0700 Merge branch 'development' commit 1027df993c79d61512b46c7a48ba474d338221eb Author: Weiqun Zhang Date: Mon Oct 3 08:53:16 2016 -0700 fix a typo ReleaseNotes/release-notes-16.09 commit 4ed405e1f4338b137397373f4f2d869e31728ae9 Author: Ann Almgren Date: Sun Oct 2 16:13:26 2016 -0700 Move all of the ParticleContainer::InitCosmo... routines out of BoxLib and into Nyx because they are specific to cosmological applications Src/C_BaseLib/ParticleInit.H Src/C_BaseLib/Particles.H commit daf7b37ecc4b0279b27b4200aa4a42121b816c96 Author: vince Date: Thu Sep 29 16:43:34 2016 -0700 more preread headers. Tests/IOBenchmark/IOTest.cpp commit 49fbfba8927e720cf1c4ce80eac17adaf3ee366d Author: vince Date: Thu Sep 29 16:31:21 2016 -0700 workaround for intel compiler, preread mf headers. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit e9f173c6281e685551ac4b8d0dd75d148cc33ff7 Author: Andy Nonaka Date: Wed Sep 28 19:26:54 2016 -0700 cleanup of C++ tutorials. start bc documentation Docs/UsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex Docs/UsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex Docs/UsersGuide/GettingStarted/GettingStarted.tex Docs/UsersGuide/UsersGuide.tex Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/writePlotFile.cpp commit 328cadbc9bbf248f54f9a6ba7700fe2ad0a67c15 Author: Andy Nonaka Date: Wed Sep 28 18:49:03 2016 -0700 setup.cpp not needed Tutorials/HeatEquation_EX2_C/setup.cpp commit 5e2031cc65c021b8c7752b830d09720070f4748c Author: Andy Nonaka Date: Wed Sep 28 16:08:29 2016 -0700 implemented dirichlet and neumann conditions in HeatEquation_EX2_C. Results match HeatEquation_EX2_F Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/inputs_3d Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_F/inputs_2d Tutorials/HeatEquation_EX2_F/inputs_3d commit 05310503e1dab449c890e2ce1a5b8f0651f669dc Author: Andy Nonaka Date: Wed Sep 28 15:47:49 2016 -0700 index bugfix in bcs Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX5_F/advance.f90 commit dc7e29128399b38bb0e0d215ce5c4b6e82c23e2f Author: vince Date: Wed Sep 28 15:06:17 2016 -0700 remove init, more options. Docs/Readme.io Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.cpp commit 9a78426ae796ab24b66c98c0fe3a92aeaa634f34 Author: vince Date: Wed Sep 28 14:52:13 2016 -0700 tests to read and write multiple multifabs. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs.dssmf commit 21bbccd2bce6692e3a3d6a39b56aa0119768cba7 Author: vince Date: Wed Sep 28 12:35:47 2016 -0700 use single write for old format. Src/C_BaseLib/VisMF.cpp commit bc376e4d3643be3092ac7313cca575b7d40cfcf4 Author: Weiqun Zhang Date: Tue Sep 27 16:14:55 2016 -0700 fix comment Src/C_BaseLib/Box.H commit 83d64a9376a71ddc1ee516cf23f7f90faae1d28f Author: Weiqun Zhang Date: Tue Sep 27 16:02:28 2016 -0700 comment Src/C_BaseLib/Box.H commit 1b0d35b1de1adaef60d6ebec71913b94f08f1581 Author: Weiqun Zhang Date: Tue Sep 27 16:02:19 2016 -0700 minor Src/C_BaseLib/BoxArray.cpp commit ab4cf7286f50f2600fb342df0f32d8fb32f81f56 Author: vince Date: Tue Sep 27 15:42:11 2016 -0700 fix for combined transfer. Src/C_BaseLib/VisMF.cpp commit 936a2bae9687459b0cbad6152be18a2da55a2cfc Author: vince Date: Tue Sep 27 15:41:15 2016 -0700 separate options for plot and checkpoint formats. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 66243a74e51e5d4606e49a52b79e564ed8d8e66d Author: Weiqun Zhang Date: Tue Sep 27 08:15:17 2016 -0700 nodal SumBoundary: forgot to zero out the destination Src/C_BaseLib/MultiFab.cpp commit 825ab04f88eae6be8a5db21a0c3c434974b2c6ea Author: Weiqun Zhang Date: Mon Sep 26 22:22:57 2016 -0700 nodal SumBoundary: fix new bug Src/C_BaseLib/IntVect.H Src/C_BaseLib/MultiFab.cpp commit fea4f4b4532a94843b9bd2aa152008402eb0eaa2 Author: Andy Nonaka Date: Mon Sep 26 13:44:30 2016 -0700 pass in bc(:,:) and domlo/hi into compute_flux Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/myfunc_F.H commit 306094bec387971af24360efd26fd3a19ea1ffd2 Merge: 3eaa5ad09 437479d44 Author: Andy Nonaka Date: Mon Sep 26 13:08:33 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 3eaa5ad09aa7905f0c279ebbe0de821c5bd9ce2f Author: Andy Nonaka Date: Mon Sep 26 13:06:41 2016 -0700 starting to put Dirichlet BC's in. This doesn't work quite right yet, as compute_flux() in advance_xd.f90 needs to know to alter the stencil at the boundary for the EXT_DIR case, where the ghost cell stores the value on the boundary. Tutorials/HeatEquation_EX2_C/FILCC_2D.F Tutorials/HeatEquation_EX2_C/FILCC_3D.F Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/inputs_3d commit 437479d44dd7403fffe27e9a7673916976c3a997 Merge: 00c872cf2 b3c53e5c9 Author: Weiqun Zhang Date: Mon Sep 26 12:06:25 2016 -0700 Merge branch 'weiqun/SumBoundary' into development commit b3c53e5c9a696fefb9d719b4d35528d5fc320930 Author: Weiqun Zhang Date: Mon Sep 26 11:29:01 2016 -0700 SumBoundary: fix new bug Src/C_BaseLib/FabArray.H commit 9165bf3f819a1ae606e8b40c10fd3d72834f2a34 Author: Weiqun Zhang Date: Mon Sep 26 10:08:43 2016 -0700 make MultiFab::SumBoundary work for nodal Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 00c872cf2f252d996ec17d352bbfb41002bc27e0 Author: Andy Nonaka Date: Mon Sep 26 09:53:43 2016 -0700 C++ plotfiles now report the time and variable name properly Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/writePlotFile.cpp commit 2ad36906ca8303ba495ed44275de419d853f50e8 Author: Weiqun Zhang Date: Mon Sep 26 09:10:38 2016 -0700 MultiFab::AddProduct that computes dst += src1*src2 Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 233fcc71e7799bde75ef3e06ef0f3f2da1103696 Author: Weiqun Zhang Date: Mon Sep 26 08:37:50 2016 -0700 typos Src/C_BaseLib/IntVect.H commit eba7a6139ccb5728ebb8874db968e79e9d3f26f8 Author: Michael Zingale Date: Sun Sep 25 18:16:49 2016 -0400 add -Mbounds for PGI in debug mode Tools/C_mk/Make.Linux commit b3a425a303f4daceb45840806ced762cf61d9d0d Author: Ann Almgren Date: Sat Sep 24 15:19:34 2016 -0700 Add two more initialization routines for particles to ParticleInit.H Src/C_BaseLib/ParticleInit.H Src/C_BaseLib/Particles.H commit 7bba15f51b5a036a961cea206ff0cd9d83747afb Author: Ann Almgren Date: Sat Sep 24 14:48:43 2016 -0700 Moved the ParticleContainer::Init... routines into their own file. Src/C_BaseLib/Make.package Src/C_BaseLib/ParticleInit.H Src/C_BaseLib/Particles.H commit a2b076cc2238a42c81f242dc25c96bd50d5bc0cf Author: Andy Nonaka Date: Fri Sep 23 17:37:21 2016 -0700 added explicit array shaping to the C++ version and a note in the user's guide Docs/UsersGuide/GettingStarted/GettingStarted.tex Tutorials/GettingStarted_C/work_on_data_2d.f90 Tutorials/GettingStarted_C/work_on_data_3d.f90 Tutorials/GettingStarted_F/main.f90 commit 5142f6a914325329c6fc675fd73e54d2786f4dd8 Author: Andy Nonaka Date: Fri Sep 23 17:15:34 2016 -0700 finish updating chapter 2. looking pretty good now. next on the list is documenting the first 'advanced' C++ feature: boundary conditions Docs/UsersGuide/GettingStarted/GettingStarted.tex commit 479d10d8b3ebf53231691a3cd629f0776d81d445 Author: Andy Nonaka Date: Fri Sep 23 16:51:34 2016 -0700 created a fortran version of the GettingStarted tutorial, and the User's Guide links directly to the source code for a first example Docs/UsersGuide/GettingStarted/GettingStarted.tex Tutorials/GettingStarted_F/GNUmakefile Tutorials/GettingStarted_F/GPackage.mak Tutorials/GettingStarted_F/main.f90 Tutorials/GettingStarted_F/work_on_data.f90 commit 4d3864d00b830fa5263a3c5965d66a9366b9f8d4 Author: Andy Nonaka Date: Fri Sep 23 16:07:01 2016 -0700 created a new C++ tutorial, "GettingStarted_C", which is basically a 'hello-world' type program that builds multifabs, accesses the multifab data in an f90 routine, and fills interior/periodic boundaries. Bonus points is that the user's guide now directly links to the source code! I hope to do the same for fortran90 shortly. Docs/UsersGuide/GettingStarted/GettingStarted.tex Docs/UsersGuide/UsersGuide.tex Tutorials/GettingStarted_C/GNUmakefile Tutorials/GettingStarted_C/Make.package Tutorials/GettingStarted_C/main.cpp Tutorials/GettingStarted_C/work_on_data_2d.f90 Tutorials/GettingStarted_C/work_on_data_3d.f90 commit 8c90f88811d5081265671ea3b010cbb1ab05b18f Author: vince Date: Fri Sep 23 15:18:24 2016 -0700 added support for precreating plot file level directories. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 3b7184e0ad66183fd1ca936ea4557b7eadf06802 Author: vince Date: Fri Sep 23 15:15:12 2016 -0700 added io parameters. Docs/Readme.io commit fa7ce3765948c74fd69b940050256615f0cfd0d3 Author: vince Date: Fri Sep 23 14:09:21 2016 -0700 sync vismf vars for dsc. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.H commit eda28a3b589f2609e6c1d484714af24868cc1f35 Author: Andy Nonaka Date: Fri Sep 23 13:11:28 2016 -0700 remove the bl_abort statements when using the default EXT_DIR option. Some codes with mixed inflow + extrapolation (on different faces) boundary conditions rely on EXT_DIR being a null-op Src/C_BaseLib/FILCC_1D.F Src/C_BaseLib/FILCC_2D.F Src/C_BaseLib/FILCC_3D.F Src/F_BaseLib/multifab_physbc.f90 commit ca1806760a847d94eba9a73275f97f9a38817a8b Author: Andy Nonaka Date: Fri Sep 23 12:57:54 2016 -0700 now FILLCC has EXT_DIR options built in for C++, just like multifab_physbc.f90 for F90 however, both C++ and F90 will now abort if you use EXT_DIR as given - we are forcing users to supply their own Dirichlet values Src/C_BaseLib/FILCC_1D.F Src/C_BaseLib/FILCC_2D.F Src/C_BaseLib/FILCC_3D.F Src/F_BaseLib/multifab_physbc.f90 commit f073bd7bf9151e0c8edb12b53f85b9619dcf82c4 Author: vince Date: Fri Sep 23 12:15:24 2016 -0700 parmparse inputs, change defaults. Src/C_BaseLib/VisMF.cpp commit b293a7cd461657d0dba75cebc6a9b8850db61058 Author: vince Date: Fri Sep 23 11:03:11 2016 -0700 set passed options. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/inputs.dssmf commit 1895a7d839d465bce0f0e55a9c36e065b86b89b9 Author: Weiqun Zhang Date: Thu Sep 22 21:19:15 2016 -0700 This reverts commit 883a93f4365. PArray is fundamentally broken, we cannot fix it. When we switch to C++ 11, we should make PArray be purely non-owning and use Array of smart pointers when we need memory management. We should also add a PArray constructor that takes Array of smart pointers. Src/C_BaseLib/PArray.H commit b8e2b02d90e19da855234d8bc09e5b6a35146a49 Author: Ann Almgren Date: Thu Sep 22 18:12:55 2016 -0700 Cleaned up Tutorials/PIC_C/GNUmakefile. Tutorials/PIC_C/GNUmakefile commit 883a93f4365a6c5a109aadaf76d92abacb533461 Author: Weiqun Zhang Date: Thu Sep 22 16:06:42 2016 -0700 add PArray copy assignment operator so that we can assert that the sizes are zero Src/C_BaseLib/PArray.H commit 5da212d3f346d0a67479ce1dc9d2fc3b3b42b71d Author: vince Date: Thu Sep 22 11:51:57 2016 -0700 added setting for synchronous reads. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 3ab6ffd79a5d122eb6416d89fe6a7d990421c9d6 Author: Andy Nonaka Date: Wed Sep 21 15:21:14 2016 -0700 minor name changes to user's guide matches tutorial Docs/UsersGuide/GettingStarted/GettingStarted.tex Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX2_C/main.cpp commit 8463e3eabaeeb2d99d12a58ae9540e9525381e94 Author: Andy Nonaka Date: Wed Sep 21 14:47:07 2016 -0700 periodic and outflow working in 2d and 3d Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/inputs_3d commit 4f32d63b377fafdc35d1aa2fade12451c7203d91 Author: Andy Nonaka Date: Wed Sep 21 14:43:08 2016 -0700 outflow bcs working for HeatEquation_EX2_C Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/main.cpp commit 90a34123047fe94ab07031bfd9bc662ff4387b93 Merge: 1e966fa2a 5e80a9cbf Author: vince Date: Wed Sep 21 13:24:01 2016 -0700 merge fixes. commit 9f0225a9c44bdea6c2b9ce9a579c14b1eb42c22b Merge: eec445d27 f6990b16a Author: Andy Nonaka Date: Wed Sep 21 13:17:07 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit eec445d278dbff0f88cb9909d51a274f4ebdc27d Author: Andy Nonaka Date: Wed Sep 21 13:16:18 2016 -0700 HeatEquation_EX1_C to uses PArray now for the state and fluxes Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX2_C/main.cpp commit aeb5fdfd168a2b29ff05aac2cdc40630101a23bf Author: Andy Nonaka Date: Wed Sep 21 12:57:44 2016 -0700 updating HeatEquation_EX1_C to more closely match EX2_C. WIP Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_C/Make.package Tutorials/HeatEquation_EX1_C/advance_3d.f90 Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/Make.package Tutorials/HeatEquation_EX2_C/main.cpp commit f6990b16a6fdd8712785400726d736312593b6e2 Author: Weiqun Zhang Date: Wed Sep 21 09:06:28 2016 -0700 move User's Guide from Docs/ to Docs/UsersGuide/ Docs/UsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex Docs/UsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex Docs/UsersGuide/F_AdvancedTopics/bc_example1.eps Docs/UsersGuide/F_AdvancedTopics/bc_example1.fig Docs/UsersGuide/F_AdvancedTopics/bc_example2.eps Docs/UsersGuide/F_AdvancedTopics/bc_example2.fig Docs/UsersGuide/F_AdvancedTopics/bc_example3.eps Docs/UsersGuide/F_AdvancedTopics/bc_example3.fig Docs/UsersGuide/F_AdvancedTopics/subcycling_algorithm.eps Docs/UsersGuide/GNUmakefile Docs/UsersGuide/GettingStarted/GettingStarted.tex Docs/UsersGuide/GettingStarted/VisIt_2D.eps Docs/UsersGuide/GettingStarted/VisIt_3D.eps Docs/UsersGuide/GettingStarted/edison.run Docs/UsersGuide/GettingStarted/edison_omp.run Docs/UsersGuide/Introduction/AMR.eps Docs/UsersGuide/Introduction/Introduction.tex Docs/UsersGuide/Introduction/boxlib_directory_bw2.eps Docs/UsersGuide/Introduction/castro_scaling.eps Docs/UsersGuide/Introduction/data_loc.odg Docs/UsersGuide/Introduction/data_loc2.eps Docs/UsersGuide/Introduction/index_grid.odg Docs/UsersGuide/Introduction/index_grid2.eps Docs/UsersGuide/Introduction/lmc_scaling.eps Docs/UsersGuide/Introduction/maestro_scaling.eps Docs/UsersGuide/Introduction/varden1.eps.REMOVED.git-id Docs/UsersGuide/Introduction/varden2.eps.REMOVED.git-id Docs/UsersGuide/Introduction/varden3.eps.REMOVED.git-id Docs/UsersGuide/Introduction/varden4.eps.REMOVED.git-id Docs/UsersGuide/LinearSolvers/LinearSolvers.tex Docs/UsersGuide/Preface/Preface.tex Docs/UsersGuide/README Docs/UsersGuide/Regression/test_suite.tex Docs/UsersGuide/Regression/testsuite.eps Docs/UsersGuide/UsersGuide.tex commit 6f5f8d2d1ddc0496b60aafbffc3b821f6ae1006b Author: Weiqun Zhang Date: Tue Sep 20 21:08:47 2016 -0700 PhysBCFunct: for clarity, add empty destructor Src/C_BaseLib/PhysBCFunct.H commit e2b9670c0b7d654e2f5cb997b6590a8280ebe58d Author: Weiqun Zhang Date: Tue Sep 20 20:53:16 2016 -0700 HeatEquation_EX2_C: use preprocessing Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 commit 2c72ad5b274a4fc59c0dd7f22eb5bf331e52d37a Author: Weiqun Zhang Date: Tue Sep 20 17:44:06 2016 -0700 HeatEquation_EX2_C: fix call filcc Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 commit 629f9d65e89d8b3452c534ad5b848c232ee6eaff Author: Weiqun Zhang Date: Tue Sep 20 17:27:23 2016 -0700 HeatEquation_EX2_C: clean up make Tutorials/HeatEquation_EX2_C/GNUmakefile commit c5960321fd5b9f6a8f7b62dc2afb028b8867e28f Author: Weiqun Zhang Date: Tue Sep 20 17:26:16 2016 -0700 HeatEquation_EX2_C: almost done except the boundaries are still all periodic Src/C_BaseLib/PhysBCFunct.H Src/C_BaseLib/PhysBCFunct.cpp Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 Tutorials/HeatEquation_EX2_C/main.cpp commit f566a0961bf21827b9582192cc97e3996bc10ef1 Author: Weiqun Zhang Date: Tue Sep 20 16:13:03 2016 -0700 HeatEquation_EX2_C: move fortran function declarations to a file Tutorials/HeatEquation_EX2_C/Make.package Tutorials/HeatEquation_EX2_C/bc_F.H Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/myfunc_F.H commit 7583d0e264573ac7b4812d048f42dd493c5d037d Author: Weiqun Zhang Date: Tue Sep 20 16:07:29 2016 -0700 simplify bc_fill fortran function Tutorials/HeatEquation_EX2_C/Make.package Tutorials/HeatEquation_EX2_C/bc_F.H Tutorials/HeatEquation_EX2_C/bc_fill_2d.F90 Tutorials/HeatEquation_EX2_C/bc_fill_3d.F90 commit 1e966fa2a3335257411fb4608b78ed7f47b0e6ff Author: vince Date: Tue Sep 20 15:53:13 2016 -0700 just use sends for now. Src/C_BaseLib/NFiles.cpp commit 9626b05a3e62f3628862b385ca5411d64dbe4a30 Author: vince Date: Tue Sep 20 15:49:21 2016 -0700 make stream pointer so intel will compile. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 5e80a9cbff7fa0135c790335ca2ce33f5ae61530 Author: Weiqun Zhang Date: Tue Sep 20 15:38:40 2016 -0700 make PhysBCFunct concrete so that we can use it without StateData; move FILCC to C_BaseLib Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/Make.package Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/FILCC_1D.F Src/C_BaseLib/FILCC_2D.F Src/C_BaseLib/FILCC_3D.F Src/C_BaseLib/Make.package Src/C_BaseLib/PhysBCFunct.H Src/C_BaseLib/PhysBCFunct.cpp Src/C_BaseLib/bc_types.fi commit 815667c3639c89afc8831e403978ca01befd51db Author: vince Date: Tue Sep 20 15:34:22 2016 -0700 remove check from timed block, cleanup. Tests/IOBenchmark/IOTest.cpp commit b284379472a9d0ca256c22bd5107e75c18865231 Author: Weiqun Zhang Date: Tue Sep 20 12:37:22 2016 -0700 PhysBCFunct --> PhysBCFunctBase and doit --> FillBoundary Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FillPatchUtil.H Src/C_AMRLib/FillPatchUtil.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/PhysBCFunct.H commit e759bb23dbe6981b3857a764fc717e6927e676c8 Author: Ann Almgren Date: Tue Sep 20 12:12:45 2016 -0700 We don't actually need C_BndryLib for this example. Tutorials/HeatEquation_EX1_C/GNUmakefile commit 42b4d5cfebf6d5021057119019c0c658adec81f0 Author: Weiqun Zhang Date: Tue Sep 20 11:09:30 2016 -0700 make it compile Tutorials/HeatEquation_EX2_C/main.cpp commit fe789ad1326cebe880adea25988fe5697dc4d914 Author: Weiqun Zhang Date: Tue Sep 20 08:54:14 2016 -0700 minor Tutorials/HeatEquation_EX1_C/GNUmakefile commit d317c3c6fa404cc693183ac3d06256f3f4c7999b Author: Weiqun Zhang Date: Tue Sep 20 08:53:45 2016 -0700 add default EBASE Tools/C_mk/Make.defs commit 0e5e512f27d323ebf30ca702befce854b6f7f15d Author: Weiqun Zhang Date: Tue Sep 20 08:37:47 2016 -0700 simplify GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile commit 08bc2fa4d16a1096777294924a113ad06463e82b Author: Weiqun Zhang Date: Tue Sep 20 08:37:33 2016 -0700 move the rule for building executable to the top Tools/C_mk/Make.rules commit b327875ccacd642fd818551798ab5e7ebaf1f6eb Author: Ann Almgren Date: Mon Sep 19 21:05:25 2016 -0700 Making progress but this still doesn't quite work yet ... Tutorials/HeatEquation_EX2_C/Make.package Tutorials/HeatEquation_EX2_C/bc_F.H Tutorials/HeatEquation_EX2_C/bc_fill_2d.F90 Tutorials/HeatEquation_EX2_C/bc_fill_3d.F90 Tutorials/HeatEquation_EX2_C/bcfill_nd.f90 Tutorials/HeatEquation_EX2_C/main.cpp commit e3cc73088a06c7b72861a4b4dd2b9f343c5d3d3d Author: Ann Almgren Date: Mon Sep 19 20:20:44 2016 -0700 Move the source file names from GNUmakefile to Make.package Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HeatEquation_EX2_C/Make.package commit 19fce93e8fb498a97ac81303d3e2cca4e8e28ee2 Author: Michael Zingale Date: Mon Sep 19 22:18:24 2016 -0400 use bind(C) Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/COEF_2D.F90 Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_3D.F90 Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/Make.package Tutorials/MultiGrid_C/RHS_2D.F Tutorials/MultiGrid_C/RHS_2D.F90 Tutorials/MultiGrid_C/RHS_3D.F Tutorials/MultiGrid_C/RHS_3D.F90 Tutorials/MultiGrid_C/RHS_F.H Tutorials/MultiGrid_C/main.cpp commit 46aff0c05a9b950860c04d943a639392b738025e Author: Michael Zingale Date: Mon Sep 19 21:31:42 2016 -0400 use bind(C) Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/bcfill_nd.f90 Tutorials/HeatEquation_EX2_C/init_phi_2d.f90 Tutorials/HeatEquation_EX2_C/init_phi_3d.f90 Tutorials/HeatEquation_EX2_C/main.cpp commit 54298f5c2a276e88870a900639ff07ad0947097b Author: Michael Zingale Date: Mon Sep 19 21:16:05 2016 -0400 add new example Tutorials/README_C commit 081fc5bd48646d864c10b05ab2a3333061ee6f72 Author: Michael Zingale Date: Mon Sep 19 21:14:13 2016 -0400 get this compiling Tutorials/HeatEquation_EX2_C/GNUmakefile commit d1f475e00d3c92e3b392eb6edf51ad6a0f29513d Merge: 26c9fe2c9 71ed949e9 Author: Michael Zingale Date: Mon Sep 19 20:58:59 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 26c9fe2c91bd2f8659fc4bc598ad28b4c0466dbe Author: Michael Zingale Date: Mon Sep 19 20:58:47 2016 -0400 use bind(C) for Fortran interfaces Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_dt.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90 Tutorials/AMR_Adv_C/Source/Src_nd/Adv_nd.f90 Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90 Tutorials/Tiling_Heat_C/advance_3d.f90 Tutorials/Tiling_Heat_C/init_phi_3d.f90 Tutorials/Tiling_Heat_C/main.cpp Tutorials/WaveEquation_C/advance_2d.f90 Tutorials/WaveEquation_C/advance_3d.f90 Tutorials/WaveEquation_C/init_data_2d.f90 Tutorials/WaveEquation_C/init_data_3d.f90 Tutorials/WaveEquation_C/main.cpp commit 71ed949e9cfc3ddfe029b0dd5ab500c3eff9ae3f Merge: f6d608c76 23a1a89e5 Author: Ann Almgren Date: Mon Sep 19 17:49:51 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit f6d608c7605e3be2edae7283c68a60025d5d3351 Author: Ann Almgren Date: Mon Sep 19 17:49:18 2016 -0700 Add a new Tutorial example that demonstrates how to use StateData without Amr or AmrLevel -- this allows us to introduce boundary conditions in the C++ stuff without being multilevel. Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HeatEquation_EX2_C/Make.package Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/bc_F.H Tutorials/HeatEquation_EX2_C/bcfill_nd.f90 Tutorials/HeatEquation_EX2_C/init_phi_2d.f90 Tutorials/HeatEquation_EX2_C/init_phi_3d.f90 Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/inputs_3d Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/setup.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/writePlotFile.cpp commit 23a1a89e5c1d513969fa16d83fcd3b63d9ab01c7 Author: Michael Zingale Date: Mon Sep 19 20:30:12 2016 -0400 use bind(C) to make the Fortran interfaces cleaner Tutorials/HeatEquation_EX1_C/advance_2d.f90 Tutorials/HeatEquation_EX1_C/advance_3d.f90 Tutorials/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HelloWorld_C/main.cpp Tutorials/HelloWorld_C/work.f90 Tutorials/README_C Tutorials/Tiling_C/main.cpp Tutorials/Tiling_C/work.f90 commit bec03a11125757b7431930bef5830497edb8b74d Author: Ann Almgren Date: Mon Sep 19 17:25:48 2016 -0700 We don't need C_AMRLib to compile this example. Tutorials/HeatEquation_EX1_C/GNUmakefile commit ba276596d78f796054f9798b8fee3e9611e51508 Author: Weiqun Zhang Date: Mon Sep 19 14:44:41 2016 -0700 add FluxRegister::ClearInternalBorders Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit a1b58049c9fc5a96ef49a207f7db30a23f33fce6 Merge: 050533067 0e3ef31d6 Author: Andy Nonaka Date: Mon Sep 19 12:59:47 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 0505330672fc19e51146690f1d2690dd0f011dbd Author: Andy Nonaka Date: Mon Sep 19 12:59:30 2016 -0700 update info for running on NERSC Docs/F_AdvancedTopics/hopper_omp.run Docs/GettingStarted/GettingStarted.tex Docs/GettingStarted/edison.run Docs/GettingStarted/edison_omp.run Docs/GettingStarted/hopper.run Docs/UsersGuide.tex commit d5ecf0f5b68b715f9ee1513087755809a54b487d Author: vince Date: Mon Sep 19 12:48:17 2016 -0700 fix for special case. Src/C_BaseLib/NFiles.cpp commit 0e3ef31d62f17ee52374c027a2d4b307b753672f Author: Weiqun Zhang Date: Mon Sep 19 12:36:20 2016 -0700 FabSet::plusTo (a MultiFab) Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 5a6f5dcc4b829cfc33e2d8c5daf4dbec4949ac2c Author: vince Date: Mon Sep 19 11:49:06 2016 -0700 another test inputs file. Tests/IOBenchmark/inputs.dssmf commit 5e6a8d3dca5b494617dc00791f25f66e673b633f Author: vince Date: Mon Sep 19 11:42:31 2016 -0700 remove implied order. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 638f1743665c75e460a7dff6300363ef170c4ffd Author: vince Date: Mon Sep 19 11:39:54 2016 -0700 check that the written multifab is valid. Tests/IOBenchmark/IOTest.cpp commit 168746508383be9427ec1c8dfcf6d6d30931fd3c Author: Andy Nonaka Date: Mon Sep 19 11:20:43 2016 -0700 cleaning up users guide. no significant changes yet Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/Preface/Preface.tex commit f3bbed524a2d6ba10487fa71b28f71ed7c08a2f7 Author: Andy Nonaka Date: Mon Sep 19 09:36:12 2016 -0700 starting re-org or user's guide. Move linear solver text into its own chapter, not the introductory material Docs/GNUmakefile Docs/GettingStarted/GettingStarted.tex Docs/LinearSolvers/LinearSolvers.tex Docs/UsersGuide.tex commit 6540212ec285653c6d3c3882586782861fcf2e8c Author: Michael Zingale Date: Mon Sep 19 11:58:26 2016 -0400 finish documenting the tutorials, and list them in an order of complexity Tutorials/README_C commit 07d493e1e90ad05ce67a7a2464971033eef4e8ca Author: Michael Zingale Date: Mon Sep 19 11:30:24 2016 -0400 start documenting tutorials Tutorials/README_C commit bbf612cf9d0d73d07fa8ec92413036ba4315f6b8 Author: vince Date: Thu Sep 15 17:39:00 2016 -0700 new test flag. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 8bfca64f1ce83238733d51c89a3c7b102ce89da5 Author: vince Date: Thu Sep 15 17:38:24 2016 -0700 fixes for dss offsets. Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 15d8cc5c321344bde0e26c83292917ed76bb53f8 Author: vince Date: Thu Sep 15 14:59:22 2016 -0700 ifdef for serial. Src/C_BaseLib/NFiles.cpp commit c8cd2e329eca650c46c75c81290a7d539dccb840 Author: vince Date: Wed Sep 14 17:23:54 2016 -0700 add option for writing with dynamic set selection. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 12b6cad694eb07dd77340859b3d8af2e0e54b9d4 Author: vince Date: Wed Sep 14 17:22:11 2016 -0700 update test check for nonzero decider. Tests/IOBenchmark/IOTest.cpp commit 965e89ce4842f88ae082093939a7b1834cf69ac8 Author: vince Date: Wed Sep 14 17:20:36 2016 -0700 make sure the decider is not in set zero. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 26ec5295c301683bc86e969e0f84e7e8d9bec083 Author: vince Date: Wed Sep 14 14:26:37 2016 -0700 SetDynamic function instead of constructor. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Tests/IOBenchmark/IOTest.cpp commit 9e537ec5e0cef9ad3cf29269d79e921a0259b3c5 Author: vince Date: Wed Sep 14 14:11:01 2016 -0700 change names to be more correct. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Tests/IOBenchmark/IOTest.cpp commit a276aa69f05040e468ce852db68aa5682aceb0d8 Author: Weiqun Zhang Date: Wed Sep 14 12:41:45 2016 -0700 remove unused and misspelled variable Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit b8b234e22db5b06851f15b322d01d009a0a9f449 Author: Weiqun Zhang Date: Wed Sep 14 08:57:39 2016 -0700 use dot product to implement 2-norm Src/C_BaseLib/MultiFab.cpp commit 7c47ab7905e174c6852ecaa4b1c78c3ab07d996c Author: Weiqun Zhang Date: Wed Sep 14 08:57:16 2016 -0700 fix typos Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit da6b019f69a6cc0d5e388e2f7168556a82f803bd Author: Weiqun Zhang Date: Tue Sep 13 17:36:20 2016 -0700 clean up comments Src/LinearSolvers/C_CellMG/MG_3D.F commit a750459bb4c3891961eff0076cb4a7113fd27f8e Author: vince Date: Tue Sep 13 17:26:37 2016 -0700 more dss support. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit b83a274d34b8c8048fc9f04ceebd59ee14b361dc Author: Weiqun Zhang Date: Tue Sep 13 16:29:37 2016 -0700 more omp and tiling in linear solvers Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 1665be04d0048f7d924577c80f57c4385eff69b5 Author: Weiqun Zhang Date: Tue Sep 13 16:15:10 2016 -0700 C_TensorMG: tiling Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLO_3D.F Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 829337da3d5807bd2a653c78e8e4f7d2e8fe0518 Author: Weiqun Zhang Date: Tue Sep 13 16:07:09 2016 -0700 C_TensorMG: cleanup Src/LinearSolvers/C_TensorMG/DivVis_F.H commit 6f8ac889473eddc43d910aa621ce1e84e48fa207 Author: vince Date: Tue Sep 13 16:01:46 2016 -0700 fix the special case. Src/C_BaseLib/NFiles.cpp commit 1ddfcb11a698f70a1b3b23f1461bb7da120f28f4 Author: Weiqun Zhang Date: Tue Sep 13 15:57:36 2016 -0700 remove FArrayBox::norm functions Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/MultiFab.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit daf027da2a5b7896f25c6afeb0dcc2de85caa512 Author: vince Date: Tue Sep 13 15:51:42 2016 -0700 new iterator tests. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 97adf325b6475af591bcf18b9aa63825265334c1 Author: vince Date: Tue Sep 13 15:51:19 2016 -0700 make the test code into an iterator for dynamic set selection. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit b80c6d83022a61f49362e4612432919f65121c63 Author: Weiqun Zhang Date: Tue Sep 13 15:30:33 2016 -0700 C_TensorMG: remove omp from Fortran subroutines Src/LinearSolvers/C_TensorMG/DV_3D1.F Src/LinearSolvers/C_TensorMG/DV_3D2.F Src/LinearSolvers/C_TensorMG/DV_3D3.F Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit 3f8fd89d802fc9d7247344a96bcd74408ad9a290 Author: Weiqun Zhang Date: Tue Sep 13 15:17:18 2016 -0700 use MulitFab::Xpay in linear solvers Src/LinearSolvers/C_CellMG/LO_1D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_TensorMG/DivVis_F.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLO_3D.F Src/LinearSolvers/C_TensorMG/MCLO_F.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 22fd36f870ccaa86f6a61898b4b7d1dbb1c119c6 Author: Weiqun Zhang Date: Tue Sep 13 15:01:43 2016 -0700 MultiFab::Xpay and BaseFab::xpay that do y = x + a*y Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 6b058bbbfb391e384247ce6ff655aef7fa6f5b36 Author: Weiqun Zhang Date: Tue Sep 13 14:40:15 2016 -0700 omp in C_Tensor Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp commit dc102e6a4e8c7d6d51727f05768a56a1ce812f7b Author: Weiqun Zhang Date: Tue Sep 13 14:34:56 2016 -0700 omp in MCCGSolver Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit 924472b312fe755748dd683a3b1fd945636baccd Author: Weiqun Zhang Date: Tue Sep 13 14:31:47 2016 -0700 remove CG_?D.F and use BaseFab and MulitFab functions instead Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/CG_1D.F Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit 20e5dadb2838cf54960bf6d203930fef5ce7f23c Author: Weiqun Zhang Date: Tue Sep 13 14:16:03 2016 -0700 CGSolver and MCCgSolver: use BaseFab::dot and MultiFab::Dot Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit b5ee4df35b09f668f77752d33629c77161fd4ed7 Author: Weiqun Zhang Date: Tue Sep 13 14:03:55 2016 -0700 add MultiFab::Dot and use it in CGSolver Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 1beb3cb96f9ff97ea33acd2a07e1c208fd40ec7a Author: Weiqun Zhang Date: Tue Sep 13 13:22:41 2016 -0700 CGSolver: use MultiFab::linComb Src/LinearSolvers/C_CellMG/CGSolver.cpp commit f7bd663498fd5e183e8c5ea92ce843c829616c4d Author: Weiqun Zhang Date: Tue Sep 13 13:22:16 2016 -0700 add MultiFab::LinComb Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 1c008a6a82bf6b78edf02d088b4b3810436bd8d8 Author: Weiqun Zhang Date: Tue Sep 13 13:10:38 2016 -0700 BaseFab: make linInterp call linComb Src/C_BaseLib/BaseFab.H commit 03264b71f81c01d961945d7ecf3738f82b55feed Author: Weiqun Zhang Date: Tue Sep 13 13:06:48 2016 -0700 BaseFab: specialize linComb Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit e4e39cbcae03fe8412dc5877a504154761797a7f Author: Weiqun Zhang Date: Tue Sep 13 10:30:47 2016 -0700 BaseFab: fix new bug Src/C_BaseLib/BaseFab_nd.f90 commit 744c464d9fdd4b4a08921e70ad642d9e329c2cb8 Author: Weiqun Zhang Date: Tue Sep 13 10:11:38 2016 -0700 BaseFab: remove SPECIALIZE_?D.F Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 107afac74d906e1fe324c80ad5109f2fdbd95e22 Author: Weiqun Zhang Date: Tue Sep 13 10:08:32 2016 -0700 BaseFab: dimension agnostic minus, mult, divide, and invert Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit 3c824ce246476055eafcfd2a09fbff7ff497fe78 Author: Weiqun Zhang Date: Tue Sep 13 09:53:22 2016 -0700 BaseFab: dimension agnostic plus Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit 781feccde138a46b78a23668d645677c72470376 Author: Weiqun Zhang Date: Tue Sep 13 09:40:40 2016 -0700 BaseFab: dimension agnostic norm Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit 5b2704fe7efc1d69ba3d13f740d62be36573869f Author: Weiqun Zhang Date: Tue Sep 13 09:25:13 2016 -0700 BaseFab: dimension agnostic setval Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit 19f4f00ec60fe157aad5eb309cb99dfd689078e7 Author: Weiqun Zhang Date: Tue Sep 13 09:05:41 2016 -0700 BaseFab: dimension agnostic copyfrommem Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit 78155fd1d640f54bcf8ff2f69220f6ca7f201ddb Author: Weiqun Zhang Date: Tue Sep 13 08:51:40 2016 -0700 BaseFab: dimension agnostic copy Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit 53e21d532c32597498e3013a6a95db70cdfc7681 Author: Weiqun Zhang Date: Mon Sep 12 13:44:20 2016 -0700 move fortran saxpy routine to dimension agnostic BaseFab_nd.f90 Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package commit 6d83ab2ea61681d42160c999c4ae577bfc32db5d Author: vince Date: Mon Sep 12 13:21:24 2016 -0700 test implementation of nfiles dynamic set selection. Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/GNUmakefile Tests/IOBenchmark/IOTest.cpp commit f1d86c7f1fe4174c654d7866fd5df028bd858666 Author: Weiqun Zhang Date: Mon Sep 12 12:30:43 2016 -0700 add bl_fort_module.F90 Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/bl_fort_module.F90 commit 63fd9ba849da8f2315a34662666810c74182d924 Author: Weiqun Zhang Date: Mon Sep 12 12:14:12 2016 -0700 clean up some GNUmakefile MiniApps/PGAS_SMC/GNUmakefile Tools/C_mk/Make.defs Tutorials/AMR_Adv_C/Exec/Make.Adv commit e2a889500a06a6db3f060edf1e1f74a545fc0239 Author: Weiqun Zhang Date: Mon Sep 12 11:19:27 2016 -0700 add vpath %.fi Tools/C_mk/Make.rules commit bb2a46c463fec52bfa401a8cb35ba2e6aa444f34 Author: Weiqun Zhang Date: Mon Sep 12 11:10:43 2016 -0700 set up VPATH_LOCATIONS and INCLUDE_LOCATIONS in various Make.package and add vpath ... to Make.rules so that the user does not need to do it Src/C_AMRLib/Make.package Src/C_BaseLib/Make.package Src/C_BoundaryLib/Make.package Src/C_TowerLib/Make.package Src/Extern/amrdata/Make.package Src/Extern/hpgmg/Make.package Src/F_BaseLib/FParallelMG.mak Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG4/Make.package Src/LinearSolvers/C_TensorMG/Make.package Src/LinearSolvers/C_to_F_MG/Make.package Src/LinearSolvers/F_MG/FParallelMG.mak Tools/C_mk/Make.rules commit 67ab2c4a9e760c277d4d235f71c79c7e94c53e0c Merge: 676ceecae 67c7ad4a7 Author: Michael Zingale Date: Sun Sep 11 10:02:50 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 676ceecae61f744e45affc0b18825817d1f2b921 Author: Michael Zingale Date: Sun Sep 11 10:02:37 2016 -0400 new inputs for the merged castro + radiation Tools/RegressionTesting/Castro-SBU-tests.ini commit 67c7ad4a7e6ae8fbd27a62c3b8915378c3548471 Author: Weiqun Zhang Date: Fri Sep 9 14:52:51 2016 -0700 omp in TensorMG Src/LinearSolvers/C_TensorMG/DivVis.cpp commit 59ea9107416f88ff874d82a8440a92621f37f869 Author: Weiqun Zhang Date: Fri Sep 9 14:19:32 2016 -0700 omp in CellMG4 Src/LinearSolvers/C_CellMG4/ABec4.cpp commit 18c70c6ddd93d10629132f3a78890654b0d904c5 Author: Weiqun Zhang Date: Fri Sep 9 13:57:02 2016 -0700 omp in cg and remove XBLAS stuff Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 0127c59afeb6812cdb37bdd6eae85a8185389aae Author: Weiqun Zhang Date: Fri Sep 9 13:56:40 2016 -0700 remove nested omp parallel Src/LinearSolvers/F_MG/itsol.f90 commit cbfba005668367b3fbec4117a50d41f94f3bc85c Author: Weiqun Zhang Date: Fri Sep 9 13:43:42 2016 -0700 fix assertion Src/C_BaseLib/BoxArray.cpp commit eb8f20e89c6db6a6747d299bc44857d8e25a1834 Author: Weiqun Zhang Date: Fri Sep 9 09:45:40 2016 -0700 use BL_ASSERT for calls to contains_nan Src/LinearSolvers/C_CellMG/CGSolver.cpp commit eb68c7e79af10cebd47f14d9c62a447556167d74 Author: Weiqun Zhang Date: Fri Sep 9 09:21:01 2016 -0700 remove the fast version of contains function from Cluster.cpp and incorporate it into BoxArray class Src/C_AMRLib/Cluster.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 65d9210e53b0b2cff4bef5caa8a5e6f2631e9498 Author: vince Date: Thu Sep 8 17:57:51 2016 -0700 test implementation of nfiles dynamic set selection. not complete. Tests/IOBenchmark/IOTest.cpp commit 8c66c05e41773870079d88d9475ca7bbe5701afd Author: vince Date: Thu Sep 8 17:39:58 2016 -0700 more io notes. Docs/Readme.io commit 456e76ab2d2085f2b6792103a469dc326653e172 Author: vince Date: Thu Sep 8 17:39:27 2016 -0700 test inputs. Tests/IOBenchmark/inputs Tests/IOBenchmark/inputs.dss Tests/IOBenchmark/inputs.nft commit dc048754f9b7316ad078a9b53db87e8a33bd9537 Author: vince Date: Thu Sep 8 17:38:28 2016 -0700 test for nfiles dynamic set selection. Tests/IOBenchmark/IOTestDriver.cpp commit 935b57e75456d58edd10e40475113631cd212788 Author: Weiqun Zhang Date: Thu Sep 8 17:13:08 2016 -0700 cleanup Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 2ca099c9a9563e63a7a55c01079195bf23f20ab0 Author: Weiqun Zhang Date: Thu Sep 8 17:11:43 2016 -0700 comment Src/C_BoundaryLib/BndryData.cpp commit 1c8832e384b194a2806561dd2390de84dd99845c Author: Weiqun Zhang Date: Thu Sep 8 17:01:01 2016 -0700 tiling in FabArray::BuildMask Src/C_BaseLib/FabArray.H commit 97e01b756fc4ca247aad7ffd94c6de1536daeb14 Author: Weiqun Zhang Date: Thu Sep 8 16:57:06 2016 -0700 make MultiMask work with multiple component Src/C_BoundaryLib/MultiMask.cpp commit 8bd07844a78c13de7527ee714024dd5c8d0240d3 Author: Weiqun Zhang Date: Thu Sep 8 16:51:20 2016 -0700 fix a new bug in tensor solver Src/LinearSolvers/C_TensorMG/DivVis.cpp commit 6791d3c0c6eb8574b1e1c9622877696d33e35c87 Author: vince Date: Thu Sep 8 15:05:35 2016 -0700 added check for total nfiles. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit ce433a91841bf97ee3b5c5f8cc26b7865e754f40 Author: Weiqun Zhang Date: Wed Sep 7 17:05:02 2016 -0700 update 4th order linear solver to the new Mask Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp commit 3bbae688ff83cfaef47febc545784850d9320184 Author: Weiqun Zhang Date: Wed Sep 7 16:42:40 2016 -0700 reimplement Masks used by linear solvers with FabArray Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/MultiMask.H Src/C_BoundaryLib/MultiMask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 7bccdb48ce82a63755e6dcfd79950e1a77a54775 Author: vince Date: Wed Sep 7 12:19:46 2016 -0700 settable buffer size, option for synchronous reads. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit c3919dcc839a19aea8da80b97042488b2244161b Author: vince Date: Wed Sep 7 12:07:28 2016 -0700 use buffer size function. Src/C_AMRLib/Amr.cpp Src/Extern/amrdata/AmrData.cpp commit b2fe1d535ff779d78d2a9db3852290476366c9b7 Author: vince Date: Wed Sep 7 11:57:27 2016 -0700 use buffer size function. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/NFiles.cpp commit c7f2a90bc1549f3b0627134a1ac9b23741a10c5f Author: vince Date: Wed Sep 7 11:55:06 2016 -0700 use buffer size function. Src/C_BaseLib/Particles.H commit cd37c0f560925781eec8cf14b51d07f4de683bbf Merge: e47e3fb27 d9522a5d2 Author: Weiqun Zhang Date: Wed Sep 7 10:02:22 2016 -0700 Merge branch 'development' into weiqun/multimask commit d9522a5d2063e6995f3f04b6cac356b233a615aa Author: Weiqun Zhang Date: Wed Sep 7 09:53:14 2016 -0700 minor Src/C_BaseLib/BoxArray.cpp commit 0a142ab0d3da7cca6d9a13160adc6a262d77b736 Author: Weiqun Zhang Date: Wed Sep 7 09:10:33 2016 -0700 Cluster: if there is a tie, z-direction has the highest precedence whereas x-direction the lowest. This is more likely to generate boxes with the longest dimension in x. Src/C_AMRLib/Cluster.cpp commit 594e6680c7094867e4702eaca9101b604526e69e Author: Weiqun Zhang Date: Wed Sep 7 08:36:52 2016 -0700 clean up fpb Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 2c0b25b21f3fd6f7c4ca73517949ad799136cf04 Author: vince Date: Tue Sep 6 15:30:59 2016 -0700 long seeks and separate tags for reads and signals. Src/C_BaseLib/VisMF.cpp commit 3e956e409231d23a90c0176fd4083edcb43ba0a7 Author: vince Date: Tue Sep 6 15:28:41 2016 -0700 updated comment. Src/C_BaseLib/ParallelDescriptor.H commit c949ca597470cbc5aa2e5bd8855156e4a1151817 Author: Weiqun Zhang Date: Tue Sep 6 13:30:30 2016 -0700 fix the new FabSet::Copy: cannot use MultiFab::Copy Src/C_BoundaryLib/FabSet.cpp commit 4dd3dfb6afe70f7b9750d33695c1dbdd81657731 Author: Weiqun Zhang Date: Tue Sep 6 11:24:52 2016 -0700 add static local Copy function for FabSet and BndryRegister Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 342734b40a75296557d85eded35337f2cc4ef43e Author: Weiqun Zhang Date: Tue Sep 6 11:09:48 2016 -0700 BoxLib::match: shortcut when BoxArrays are equal (i.e., ==) Src/C_BaseLib/BoxArray.cpp commit f919ef4ce409138d029ba7c20bbf4ba05737feb4 Author: Weiqun Zhang Date: Tue Sep 6 10:17:17 2016 -0700 When provided with BoxArray, StateData::restart will use the provided one and make sure it matches the one in the istream. This helps reduce duplicated BoxArrays. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 7e7e8c2ce4384a11514a304f8343ac631554c87f Author: Weiqun Zhang Date: Tue Sep 6 09:51:53 2016 -0700 add BoxLib::match that returns ture if the boxes returned by operator[] in two BoxArrys match. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 9ad32e2310e22ffdd7a99b9dbaa46a593f144f81 Merge: 098acd48e 495341878 Author: Michael Zingale Date: Mon Sep 5 22:58:04 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 098acd48ea04d9127e68f733266febc57bbea46c Author: Michael Zingale Date: Mon Sep 5 22:57:23 2016 -0400 add the ability to put the point we slice through at the lower left instead of the center of the domain. Tools/Postprocessing/F_Src/fextract.f90 commit 49534187840c0ccf38473cf9fb1674c8da47c85f Author: Weiqun Zhang Date: Fri Sep 2 14:56:34 2016 -0700 FillCoarsePatch: call bc function to fill physical boundaries instead of interploating Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp commit 8e49c9c3730769bce3095dbf0779299dbbe1f1ad Author: Weiqun Zhang Date: Fri Sep 2 11:09:15 2016 -0700 minor clean up Src/C_BaseLib/Geometry.cpp commit a0117bc0fb1c3fb3850040f6c9fdf52818269342 Author: Weiqun Zhang Date: Fri Sep 2 11:06:16 2016 -0700 assertion Geometry::Setup is not called inside omp parallel Src/C_BaseLib/Geometry.cpp commit 7af78108e0d24d2c5f68e4296cb330f6c4094f9c Author: Weiqun Zhang Date: Fri Sep 2 10:50:09 2016 -0700 rm deprecated Geometry::FillPeriodicBoundary and Geometry::PeriodicCopy Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit ee69a8e2d264555069a48479a47079a9656291b5 Author: Weiqun Zhang Date: Thu Sep 1 10:16:49 2016 -0700 call various Initialize() in BoxLib::Initialize() to ensure thread safety Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IArrayBox.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp commit fa8f135ba0fefb6d639e54c7e31ad07fb4965e38 Author: Weiqun Zhang Date: Thu Sep 1 08:30:29 2016 -0700 Release Notes 16.09 ReleaseNotes/release-notes-16.09 commit 79a7b62a6d5a484e404df529d955d99e968fdef5 Merge: d728f4305 1846431b6 Author: Weiqun Zhang Date: Thu Sep 1 08:29:30 2016 -0700 Merge branch 'master' into development Conflicts: Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/FabArray.H commit 33471615ca3c99ad60779391a4cdcc61af9a165f Author: vince Date: Wed Aug 31 15:44:44 2016 -0700 close persistent streams before each test. Tests/IOBenchmark/IOTest.cpp commit 7fe9f4b4cfdf17c1c57e9a6f1783ff247eacb9a8 Author: vince Date: Wed Aug 31 14:57:50 2016 -0700 added more test options. Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit 2ff75ad886e75e993cde0fe392771bb48ebb99be Author: vince Date: Wed Aug 31 14:56:25 2016 -0700 implemented persistent streams for reading. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 5e1e78d476313e1de8d6be10325d13766ebb33a1 Author: vince Date: Wed Aug 31 14:54:54 2016 -0700 changed default buffer size. Src/C_BaseLib/ParallelDescriptor.cpp commit 99db2b99ffed1106724326495867a60671e6096d Author: vince Date: Wed Aug 31 10:54:26 2016 -0700 changed default buffer size. Src/C_BaseLib/FabConv.cpp commit d728f43054ff948f224450d775dd599f1dfc6955 Merge: 053128438 94d3f75f3 Author: Michael Zingale Date: Wed Aug 31 13:12:21 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 053128438351add4c4a8818d30ba5a0fc1758338 Author: Michael Zingale Date: Wed Aug 31 13:11:59 2016 -0400 print out zone info for the biggest error zone to make Dr. Katz happy :) Tools/Postprocessing/F_Src/fcompare.f90 commit 94d3f75f34a52397821b3bccd09affc81e39b01d Author: Weiqun Zhang Date: Tue Aug 30 20:31:58 2016 -0700 BoxLib::InterpFromCoarseLevel(): fix box type Src/C_AMRLib/FillPatchUtil.cpp commit f107760a8cf2c148c495fadcf41eafcea345b0b7 Author: Weiqun Zhang Date: Tue Aug 30 20:23:32 2016 -0700 fix BoxLib::InterpFromCoarseLevel() Src/C_AMRLib/FillPatchUtil.cpp commit 39281f23ba6d347550eaccab25d9722856122ab6 Author: Weiqun Zhang Date: Tue Aug 30 16:47:05 2016 -0700 add BoxLib::InterpFromCoarseLevel() Src/C_AMRLib/FillPatchUtil.H Src/C_AMRLib/FillPatchUtil.cpp commit 508cf269230cd7cc1dc2ea549c15bc503785de08 Author: Weiqun Zhang Date: Tue Aug 30 18:06:20 2016 -0400 Revert "protect FArrayBox::Initialize with omp single because it is not thread safe" This reverts commit 84a980833b5f781a829691721bbfd117a39d7ba3. Src/C_BaseLib/FArrayBox.cpp commit 2e24778a7a03c8bb849ee5dee740307dd82a1e52 Author: Weiqun Zhang Date: Tue Aug 30 17:37:22 2016 -0400 fix the fix (but I think it's compiler's fault): In MultiFab::Iniitialize, construct a FArrayBox so that the FArrayBox class will be properly initialized. Src/C_BaseLib/MultiFab.cpp commit 84a980833b5f781a829691721bbfd117a39d7ba3 Author: Weiqun Zhang Date: Tue Aug 30 16:42:37 2016 -0400 protect FArrayBox::Initialize with omp single because it is not thread safe Src/C_BaseLib/FArrayBox.cpp commit e2671b9ccf2f24eb91d1aa6158c4ea7e0fd36b82 Author: Weiqun Zhang Date: Tue Aug 30 13:14:03 2016 -0400 Insert flush() between writing header and data to get around a bug (?) on Titan. Src/C_BaseLib/FArrayBox.cpp commit ac5110e87663615a7d2e4f929f59faaf0b4cbe1b Author: Weiqun Zhang Date: Mon Aug 29 15:18:46 2016 -0700 given a MultiFab filled with weights, make a KnapSack DistributionMapping Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit d907a94a0b5b1328db81e9b4a12cb9876fad7e8e Author: vince Date: Thu Aug 25 18:35:18 2016 -0700 more support for persistent streams. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit edd6874ff543748e22c98c3abea064d4ea761acb Author: vince Date: Thu Aug 25 18:34:23 2016 -0700 level directory creation setting. Src/C_AMRLib/AmrLevel.H commit eb3207c6f55bc9efc2224fcd9b164caa81468877 Author: vince Date: Thu Aug 25 18:33:25 2016 -0700 add more parmparse options. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit dde3f250d7972d18718ddbcc484fd73f240fc941 Author: Weiqun Zhang Date: Thu Aug 25 17:41:17 2016 -0700 because the do_async_sends flag is ignored by FillBoundary now, we should not test that flag in WaitForAsyncSends Src/C_BaseLib/FabArray.H commit fbcd8606ebc9136c70e8e9b33effd9db1a7b388b Author: Weiqun Zhang Date: Thu Aug 25 17:21:59 2016 -0700 remove calls to BoxLib::fill_boundary because it is deprecated Tutorials/MultiFab_C_F/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp commit 186b4d3fdc223df74f850f51ecdc348a5f3c7795 Author: vince Date: Thu Aug 25 15:53:53 2016 -0700 more io tasks. Docs/Readme.io commit 3187ef9991fdbef345fdda700ad54e4f86862719 Author: vince Date: Thu Aug 25 12:24:07 2016 -0700 check for sufficient memory for single reads and writes. Src/C_BaseLib/VisMF.cpp commit c7f5a5291472493b1a4f83826e731a0f164caca1 Author: vince Date: Thu Aug 25 11:45:35 2016 -0700 format, set version for plot files. Src/C_AMRLib/Amr.cpp commit e03ab79146f54ad2f91d376a38900f2476a0e0aa Author: vince Date: Wed Aug 24 18:20:01 2016 -0700 added use single read and write code. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 073b42db47ab3edf92adf59277dd1268c5fe9f7e Author: Weiqun Zhang Date: Wed Aug 24 17:32:35 2016 -0700 remove Geometry::SumPeriodicBoundary Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit f462bae2a69fed8a0a4e92fa29f879c97468e14b Author: vince Date: Wed Aug 24 17:18:28 2016 -0700 add use single read and write parmparse variables. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 874927e02a18b0c50078bf10c414bde2d74db18e Author: Weiqun Zhang Date: Wed Aug 24 16:57:09 2016 -0700 use MulitFab::SumBoundary for periodic boundaries too. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Particles.H commit f186de8be9f772579bacdb739c114753ab861889 Author: vince Date: Wed Aug 24 16:11:37 2016 -0700 statedata support for prereading fabarray headers. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 38a2d3d666b96df44b2c01192969362166112092 Author: vince Date: Wed Aug 24 14:46:09 2016 -0700 fix for in file order. Src/C_BaseLib/VisMF.cpp commit 2221e2c49b4af713aa71a911d2572c48bd411b44 Author: Weiqun Zhang Date: Wed Aug 24 14:43:36 2016 -0700 fix MemProfiler by casting lambda functions into std::function with the correct type. Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/MultiFab.cpp Src/F_BaseLib/MemProfiler_f.cpp commit 2b09a9d61e0871ae8182e4d0b877110f5ad1fa74 Author: Weiqun Zhang Date: Wed Aug 24 13:18:26 2016 -0700 remove const from return type Tools/C_scripts/buildInfo.H Tools/C_scripts/makebuildinfo_C.py commit 9be851922301f09bf750c156afe497c7b2b12960 Author: Weiqun Zhang Date: Wed Aug 24 13:11:38 2016 -0700 Add template argument to BATBase otherwise some compilers are not happy. Src/C_BaseLib/BoxArray.H Src/C_BoundaryLib/BndryRegister.cpp commit a1ac2d1b8d7c6f57f75b479f0ec9bf27e35a2f6f Merge: 4115c6680 def51899d Author: Weiqun Zhang Date: Wed Aug 24 12:21:27 2016 -0700 Merge branch 'development' into weiqun/work Conflicts: Src/C_BaseLib/CMakeLists.txt commit 1846431b6328e62baceffd5442fde639b68008af Author: Ann Almgren Date: Wed Aug 24 09:55:48 2016 -0700 We need to add the line include_directories(${CBOXLIB_INCLUDE_DIRS}) to the CMakeLists.txt so that backtrace_c.cpp can find BLBackTrace.H (which is in C_BaseLib). Src/F_BaseLib/CMakeLists.txt commit def51899d7369b638c3943d7e2ee2c27b87eac03 Author: Ann Almgren Date: Wed Aug 24 09:55:48 2016 -0700 We need to add the line include_directories(${CBOXLIB_INCLUDE_DIRS}) to the CMakeLists.txt so that backtrace_c.cpp can find BLBackTrace.H (which is in C_BaseLib). Src/F_BaseLib/CMakeLists.txt commit 9f1a39e57c2dd14d7fff40f65b40434120e1de1d Author: Weiqun Zhang Date: Wed Aug 24 06:27:05 2016 -0700 fix assertion: the recvcount and disp vections are insignificant on non-root processes. Src/C_BaseLib/ParallelDescriptor.H commit 1051c11958514486d0dc2c3e259e7d4e9098729e Author: Weiqun Zhang Date: Tue Aug 23 21:57:57 2016 -0700 TagBoxArray::collate: use the long version of ParallelDescriptor::gatherv to avoid interger overflow. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit f890189d35dc1814ccb848790a7006527c4d0ec8 Author: Weiqun Zhang Date: Tue Aug 23 21:16:45 2016 -0700 add two version of ParallelDescriptor::gatherv: one takes int as offset and the other takes long. The int version calls MPI_gatherv. The long version uses MPI_Irecv and MPI_Send because MPI does not support using long as offset in MPI_gatherv. Src/C_BaseLib/ParallelDescriptor.H commit 2ecb4591042c9de7fb491fb26b8b6300cd6e23b6 Author: Weiqun Zhang Date: Tue Aug 23 20:56:43 2016 -0700 add a non-const version of IntVect::getVect Src/C_BaseLib/IntVect.H commit 5159303869afc1787d6f8b94a4c8033ce201376a Author: vince Date: Tue Aug 23 15:11:27 2016 -0700 added option to preread and broadcast all multifab headers to avoid synchronization during restart. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 4115c6680ea695e2387055fd5e38aa07b57ec309 Author: Weiqun Zhang Date: Tue Aug 23 12:42:28 2016 -0700 Extrapolater: should still use masks even after setting all crse cells to zero first because these cells get updated. Src/C_AMRLib/extrapolater_2d.f90 Src/C_AMRLib/extrapolater_3d.f90 commit cbc3917b26c1141e8be9a9b02312be8c6f4f0f49 Author: Weiqun Zhang Date: Mon Aug 22 17:32:14 2016 -0700 tidy Src/C_AMRLib/extrapolater_3d.f90 commit 2f5b7fb401b6fe0f6a194c237f667535c79e06cb Author: Weiqun Zhang Date: Mon Aug 22 17:30:48 2016 -0700 fix array bound in extraploater Src/C_AMRLib/extrapolater_3d.f90 commit 18e1ead7cd9301668c762532ac89a58bac8ec0b0 Author: Weiqun Zhang Date: Mon Aug 22 17:06:22 2016 -0700 EnforcePeriodicity cannot use ngrow to decide to skip jFillBoundary_finish Src/C_BaseLib/FabArray.H commit a52008b6a1495e16be8aabb34be3c5e30dce00d3 Author: vince Date: Mon Aug 22 15:25:18 2016 -0700 added support for prereading fabarray headers. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 2a1e8b8cb95ca0396f8194f232914b94bd803a3f Author: vince Date: Mon Aug 22 14:41:29 2016 -0700 restart fixes for new formats. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp Src/C_BaseLib/VisMF.cpp commit fb418321fa050f6076e0435f91fd1c254b9cd12d Author: Weiqun Zhang Date: Mon Aug 22 14:36:47 2016 -0700 FabArray::EnforcePeriodicity: make sure the source cells are always inside the periodic domain. Src/C_BaseLib/FabArray.cpp commit 55e5bcc8993b4c0c15be1417ad31d01c0803ecac Author: vince Date: Mon Aug 22 12:08:03 2016 -0700 remove old code. Src/C_AMRLib/Amr.cpp commit 78fa116b6913ed018afe76e856885d88e30d0666 Author: vince Date: Mon Aug 22 11:59:58 2016 -0700 formatting. Src/C_AMRLib/StateData.cpp commit 3a759fb86db7cfa41282dc815b15415ebe4349b0 Author: vince Date: Mon Aug 22 11:06:34 2016 -0700 formatting. Src/C_AMRLib/Amr.cpp commit 7b8d0ee54d69c6aebb5025cf7e347b13d11304b2 Author: Weiqun Zhang Date: Sun Aug 21 16:41:16 2016 -0700 FillBoundary: return immediately if there are no ghost cells Src/C_BaseLib/FabArray.H commit b6a622a7e61374c8401d0c9a04d54e58387e58cf Author: Weiqun Zhang Date: Sun Aug 21 16:32:51 2016 -0700 EnforcePeriodicity: return immediately if there is no periodic boundaries Src/C_BaseLib/FabArray.H commit c4f1e42a9139699b59bd514ac4633004e31c2aba Author: Weiqun Zhang Date: Sun Aug 21 16:20:36 2016 -0700 FabArray::BuildMask: treat ghost cells outside periodic boundaries as normal ghost cells not physical boundary cells Src/C_BaseLib/FabArray.H commit 63df991c4d3552a37b42d53b33ba715911a20c93 Author: Weiqun Zhang Date: Sun Aug 21 16:01:41 2016 -0700 minor name changes Src/C_BaseLib/FabArray.H commit 1b706db90a9830c757bb081218b4d718a236ed99 Author: Weiqun Zhang Date: Sun Aug 21 15:36:27 2016 -0700 move iMultiFab::buildMask to FabArray::BuildMask so that it becomes a template Src/C_AMRLib/Extrapolater.H Src/C_AMRLib/Extrapolater.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit 7a75f8f43cb51c81128a0f2f07d2954461b909bd Author: Weiqun Zhang Date: Sat Aug 20 12:46:11 2016 -0700 EnforcePeriodicity: allow ghost cells to be source Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 2326e9378d5a688063b9258bcc1d42338d40eff3 Author: Weiqun Zhang Date: Sat Aug 20 12:14:52 2016 -0700 Extrapolater: set coarse cells to zero first to ensure there are no NaNs Src/C_AMRLib/extrapolater_2d.f90 Src/C_AMRLib/extrapolater_3d.f90 commit 6e3f70065843796edde28f6d15b290f6480fea3d Author: vince Date: Fri Aug 19 15:52:28 2016 -0700 set relative path. Src/C_BaseLib/VisMF.cpp commit 079348613d750613bbe887cd731018652c1352b9 Author: vince Date: Fri Aug 19 15:51:57 2016 -0700 option to precreate checkpoint directories to avoid a barrier at each level. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit ad1f88cda9cf03ed8afae154cc0fcdff0fb40a5c Author: vince Date: Fri Aug 19 15:50:18 2016 -0700 more io notes. Docs/Readme.io commit cd5fc721d134d9e1110b018b43fa38a923d9e0ff Author: vince Date: Thu Aug 18 17:56:10 2016 -0700 add nstreams readers. Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit 4551fda2fb45fc1684a41ef2a3e8db471f95a79e Author: Weiqun Zhang Date: Thu Aug 18 15:42:48 2016 -0700 Extrapolater: fix bugs Src/C_AMRLib/extrapolater_3d.f90 commit 25ea870b1db44d0311a4956b145216b2913ce11b Author: Weiqun Zhang Date: Thu Aug 18 15:35:50 2016 -0700 Extrapolater: fix a bug Src/C_AMRLib/extrapolater_3d.f90 commit 8458b904401b820c01a922c1469a24e8b20470b6 Author: Weiqun Zhang Date: Thu Aug 18 15:07:08 2016 -0700 Extrapolater: fix index bug Src/C_AMRLib/extrapolater_2d.f90 commit 833b211bc7c5249043191ea8224f4ca1819ca583 Author: Weiqun Zhang Date: Thu Aug 18 14:54:43 2016 -0700 let Extrapolater build the mask Src/C_AMRLib/Extrapolater.H Src/C_AMRLib/Extrapolater.cpp commit e06a47b4fa985c642e73bf680995dba966772631 Author: Weiqun Zhang Date: Thu Aug 18 12:21:59 2016 -0700 Add Extrapolater to replace IAMR functions for extraploating viscout terms. Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/Extrapolater.H Src/C_AMRLib/Extrapolater.cpp Src/C_AMRLib/Make.package Src/C_AMRLib/extrapolater_1d.f90 Src/C_AMRLib/extrapolater_2d.f90 Src/C_AMRLib/extrapolater_3d.f90 Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit 23e80cbef88ea8d8b287324987b5a6841ea6b138 Author: vince Date: Thu Aug 18 13:55:23 2016 -0700 removed diagnostics, added timer. Src/C_BaseLib/VisMF.cpp commit 4f61204aa85c431b5a6beab6b592dff652590394 Author: vince Date: Thu Aug 18 13:32:41 2016 -0700 file order fabarray reads. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 1f704f246211b6460112d765cad9aa755acb53b7 Author: Ann Almgren Date: Thu Aug 18 11:54:05 2016 -0700 Update CMakeLists.txt to reflect the fact that Particles* have moved from C_AMRLib to C_BaseLib and also to include PhysBCFunct.H and ParGDB.H in C_BaseLib/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt commit 6321906784a339ea1935dc1feb5efbed98d744e6 Author: Ann Almgren Date: Thu Aug 18 11:54:05 2016 -0700 Update CMakeLists.txt to reflect the fact that Particles* have moved from C_AMRLib to C_BaseLib and also to include PhysBCFunct.H and ParGDB.H in C_BaseLib/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt commit f8ac7e39679cdad1e889b374e5cf1cae1ae22b14 Author: Weiqun Zhang Date: Wed Aug 17 16:35:42 2016 -0700 new function iMultiFab::buildMask Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit 16c3927c1f3dc39b68e9fa15bae587d65f9557d8 Author: vince Date: Wed Aug 17 14:35:35 2016 -0700 changed mf name. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 74f7554c548568a8fe75990d7698f9bb13ade4de Author: Weiqun Zhang Date: Wed Aug 17 14:31:09 2016 -0700 tweak FabArrayBase::TheFB interface Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit 9db6058baa94d53bea869d518a7306591e769bdd Author: vince Date: Wed Aug 17 14:15:41 2016 -0700 calculate header offsets. Src/C_BaseLib/VisMF.cpp commit 02f34b4d0b99ea41a26880769bfaabdbd25a80c1 Author: Weiqun Zhang Date: Wed Aug 17 13:58:59 2016 -0700 clean up iMultiFab Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit c0379574afdfc8a1b36866b61a98bfc0d33a0829 Author: Weiqun Zhang Date: Wed Aug 17 13:50:24 2016 -0700 FillPeriodicBoundary --> EnforcePeriodicity Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 5166b4261be7a55651d6b8b1dbf8fbd5a3acd5d1 Author: Weiqun Zhang Date: Wed Aug 17 13:42:47 2016 -0700 clean up outdated stuff Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 542ed1977a801196d47bb94e4f9d84a3a149f604 Author: Weiqun Zhang Date: Wed Aug 17 13:38:03 2016 -0700 simplify the way of filling boundary corners Src/LinearSolvers/C_CellMG4/ABec4.cpp commit 4d3fa63b672badb254a517ea47b48fd74725d09f Author: Weiqun Zhang Date: Wed Aug 17 13:09:36 2016 -0700 a number of small changes related to FillBoundary interface Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Tests/C_BaseLib/tFB.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp Tutorials/Tiling_Heat_C/main.cpp commit bcf79f114f09d8745f445a173b50a20fed679ba6 Author: Weiqun Zhang Date: Wed Aug 17 12:31:23 2016 -0700 assertion that FillBoundary's (cell-centered verions) BoxArray is non-overlapping Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 7252e25008c28e13a0e70c504a2c90545856f32b Author: Weiqun Zhang Date: Wed Aug 17 12:28:15 2016 -0700 add BoxLib::convert for BoxArray Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit e82a303c72c53d47cb12d1965b4be5e99a05cc70 Author: Weiqun Zhang Date: Wed Aug 17 12:14:32 2016 -0700 add assertion and comments Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/FabArray.cpp commit 4a6ac101cfdd4b4d2b4663ae4f1ff7f264e7c9bc Author: Weiqun Zhang Date: Wed Aug 17 11:20:36 2016 -0700 use FillBoundary for periodic boundaries MiniApps/PGAS_SMC/SMC_advance.cpp Src/F_Interfaces/BaseLib/multifab_fi.cpp commit a3a7b5ef348568d34a98b3a145f7835b5f55161c Author: Weiqun Zhang Date: Wed Aug 17 10:56:43 2016 -0700 fix thread safety for FabArray::EnforcePeriodicity Src/C_BaseLib/FabArray.cpp commit 711ab9b37aa7e3c6684826cabd6fbdd0a2248a7e Author: vince Date: Tue Aug 16 16:59:17 2016 -0700 removed old test function. Tests/IOBenchmark/IOTest.cpp commit d14246c427ef0d2563ab97ecf46ef88c15b7d840 Author: Weiqun Zhang Date: Tue Aug 16 16:52:34 2016 -0700 fix bind c name for PGI MiniApps/PGAS_SMC/chemistry_module.f90 MiniApps/PGAS_SMC/derivative_stencil.f90 MiniApps/PGAS_SMC/init_data.f90 MiniApps/PGAS_SMC/kernels.f90 MiniApps/PGAS_SMC/make_plot.f90 MiniApps/PGAS_SMC/transport_properties.f90 MiniApps/PGAS_SMC/variables.f90 commit 960cb8eaa811c744cbee0740fdea17e192f29a22 Author: vince Date: Tue Aug 16 16:48:43 2016 -0700 removed debugging diagnostics. Src/C_BaseLib/VisMF.cpp commit c9e168b465ed77fe3dbe0881d0ee386e24a54348 Author: vince Date: Tue Aug 16 16:45:25 2016 -0700 added NFiles. Src/C_BaseLib/CMakeLists.txt commit d7158f2b5b436601f075aff96b392c5ec4433d4c Author: vince Date: Tue Aug 16 16:27:01 2016 -0700 removed test functions. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 6cc92dc53812ec4467f5ef2a1617c954fce74d7d Author: vince Date: Tue Aug 16 16:26:28 2016 -0700 more notes. Docs/Readme.io commit 87b105f550ddde355f8617e4b4143b24f0017caf Author: vince Date: Tue Aug 16 16:21:51 2016 -0700 consolidate write functions for all formats. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 391aa74f1d4dcb5d7d37fce1f997682da607ae69 Author: vince Date: Tue Aug 16 16:20:40 2016 -0700 consolidate nfiles write tests for the new formats. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit abbe43d1d5d9bcda411c6220c505ee999effc2ad Author: vince Date: Tue Aug 16 15:06:42 2016 -0700 calculate offsets for old version without communication. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit ca0dc717542a16b999da8a49419d0dc6a857beba Author: vince Date: Tue Aug 16 11:20:20 2016 -0700 change names to be more general. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit f1d27e5ba22a2c81c92bd203b35028c3aad888f6 Author: Weiqun Zhang Date: Tue Aug 16 07:42:31 2016 -0700 FabArray::EnforcePeriodicity: use a bool flag instead of a domain box Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Periodicity.H Src/C_BaseLib/Periodicity.cpp commit 1af6129e044a152b35400885e7ac22a86b62accf Author: Weiqun Zhang Date: Mon Aug 15 23:23:12 2016 -0700 fix EnforcePeriodicity function Src/C_BaseLib/FabArray.H commit e7b92b0c045923e8b92f4e8262219a71f6118c9e Author: Weiqun Zhang Date: Mon Aug 15 23:14:43 2016 -0700 FabArray::EnforcePeriodicity() Src/C_BaseLib/Box.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit 4e6bb4697568e76a7e049e2469732a0eb3692bc7 Author: vince Date: Mon Aug 15 19:01:44 2016 -0700 combine write functions. Tests/IOBenchmark/IOTest.cpp commit dd00429afcd5913b915863e722ebe6b272fe05bd Author: vince Date: Mon Aug 15 19:01:09 2016 -0700 combine write functions. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 112e1e110613a147986d793487dacea69994f4c0 Author: Weiqun Zhang Date: Mon Aug 15 16:11:27 2016 -0700 remove FabArrayBase::SetSendTag and SetRecvTag because IAMR SyncRegister no longer needs them Src/C_BaseLib/FabArray.H commit 1443ec9fbbb11a11bd7ba99ee91dcf07fad5170d Author: Ann Almgren Date: Fri Aug 12 16:01:12 2016 -0700 Add an option for setting constant coefficients for a nodal solve. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit b344fcfce73a6ab66b103f415ca19a363bcd6f3f Author: Weiqun Zhang Date: Fri Aug 12 13:13:33 2016 -0700 remove nested omp parallel. they seem to cause some problems. Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_3D.F commit c7f118dd4e43d9fbcae1b2d1d6458e23f087daf9 Author: Brian Friesen Date: Thu Aug 11 21:45:56 2016 -0700 Remove last bits of old sidecar implementation. The new stuff doesn't need it. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/F_BaseLib/parallel.f90 commit f6a272bf798bcbf9a61aecfa1d85a1833698ca8c Author: Brian Friesen Date: Tue Aug 9 12:57:01 2016 -0700 C_mk: add SDE ifdef for using Intel SDE for FLOP counting Tools/C_mk/Make.defs commit c55e378b3a60aed3f5c2e0c5d1945e7dd8a9b4f2 Author: Weiqun Zhang Date: Thu Aug 11 21:53:48 2016 -0700 remove unused variable Src/C_BaseLib/CArena.cpp commit 5c8d5b840b844bffc4d6fa4530f6e504bb4fe37d Author: vince Date: Thu Aug 11 17:22:57 2016 -0700 native reads, fixes for vis with no min max values in the header. Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit a285a9e63eebfc72ea7af5916cdcc28a2ba158c2 Author: Weiqun Zhang Date: Thu Aug 11 12:40:02 2016 -0700 Fabset::plusFrom takes Periodicity argument Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit e29258d8bc310b495cfa5d11794b69b195aa10b9 Author: vince Date: Wed Aug 10 18:26:54 2016 -0700 implemented new vismf reads for file order reads. not finished yet. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 9f4d5b9dc1accc6102279692d17a33ebbdc60320 Author: vince Date: Wed Aug 10 18:24:30 2016 -0700 added consts. Tests/IOBenchmark/IOTest.cpp commit eebcb07ef730d0aa1fd189e960ad0414bc964eb3 Author: vince Date: Wed Aug 10 16:49:48 2016 -0700 added functions for reading. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 4c928c624410d8cc3e1d41bbaa8f8f59fc8e755c Author: vince Date: Wed Aug 10 16:46:23 2016 -0700 added more inputs. Tests/IOBenchmark/inputs commit 45d1cde65c5a42435dcdcac0e843d818a16691f6 Author: Andy Nonaka Date: Wed Aug 10 15:45:47 2016 -0700 you can pass in an optional argument to ml_cc_solve, ok_to_fix_singular=.false. (default true). If false, the multigrid solver will not subtract off the average of the RHS for singular matrices. Useful for debugging singular problems if you want to see, e.g., if S integrates to zero for low mach codes, or if total charge integrates to zero for electrostatic potential solves. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 4eaeb90e7f34fafed23a119c38a3b7296d05e102 Merge: fad98e200 ea55a29a3 Author: Weiqun Zhang Date: Wed Aug 10 14:23:38 2016 -0700 Merge branch 'development' into weiqun/work commit fad98e200146f95ab41029700906ef457b08db7c Author: Weiqun Zhang Date: Wed Aug 10 13:22:53 2016 -0700 minor Src/C_AMRLib/FillPatchUtil.cpp commit ef16f80d1618c0575189061c54e7b78c35f93ab2 Author: Weiqun Zhang Date: Wed Aug 10 13:06:08 2016 -0700 add static function Periodicity::NonPeriodic() for clarity Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Periodicity.H Src/C_BaseLib/Periodicity.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit b68d5f70cb2b0e85478e13ec351775ba0b157e4d Author: Weiqun Zhang Date: Wed Aug 10 12:55:56 2016 -0700 use FabArray::copy for periodic copy Src/C_AMRLib/FillPatchUtil.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit ea55a29a33578330f22ef035b92c85e4bb45befb Author: Andy Nonaka Date: Wed Aug 10 12:51:08 2016 -0700 call parallel reduce only on elements in an array which are initialized. Otherwise code would crash Src/LinearSolvers/F_MG/ml_cc.f90 commit 10592c49d1d92891e37b087a8add0c1762daabdc Author: Weiqun Zhang Date: Wed Aug 10 12:45:27 2016 -0700 FabArray::copy does periodic copy too Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 87dfbb82b002258f00467184c1ce089fcdd52f01 Author: vince Date: Wed Aug 10 12:31:33 2016 -0700 more io tests. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit b177e928f23aad9b01206243c3d8999b43a35126 Author: Weiqun Zhang Date: Wed Aug 10 11:11:50 2016 -0700 FabArray::copy: add a new Periodicity argument Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BoundaryLib/FabSet.cpp commit d5eda63c2773749b49eb7831db8e010d35c765b2 Merge: 605539b05 44b476d93 Author: Weiqun Zhang Date: Wed Aug 10 10:53:40 2016 -0700 Merge branch 'development' into weiqun/work Conflicts: Src/C_BaseLib/FabArray.H commit 605539b05bd39655a8ae64c59d8fda8981fc4f70 Author: Weiqun Zhang Date: Tue Aug 9 21:16:33 2016 -0700 minor optimization Src/C_BaseLib/FabArray.cpp commit e5caa196e3abaaef2a6904c50f4428d61c14abb4 Author: Weiqun Zhang Date: Tue Aug 9 18:13:39 2016 -0700 fix new bug Src/C_BaseLib/FabArray.cpp commit 5314a873d329c1a15522b164dc93f52edc6b1407 Author: Ann Almgren Date: Tue Aug 9 17:55:17 2016 -0700 Needed to move the computation of coeff_sum and coeff_max ahead of the singular test on rh -- this meant separating back out the parallel reductions. Src/LinearSolvers/F_MG/ml_cc.f90 commit 6e19e4aa7011ab5f845fe6f4922f192dad6ea9d7 Merge: 9d4ba6d93 44b476d93 Author: Ann Almgren Date: Tue Aug 9 17:42:52 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 9d4ba6d930e36825d2cfabcfb67d5622c83ace6a Author: Ann Almgren Date: Tue Aug 9 17:42:24 2016 -0700 Impose solvability on rh not res at the start of ml_cc -- we need to do this because res is recomputed as rh - L(full_soln) after each cycle. Src/LinearSolvers/F_MG/ml_cc.f90 commit 7ca723b816fa685ddaf63293dc09c7065f311164 Author: vince Date: Tue Aug 9 17:29:50 2016 -0700 started implementing new FabArray reads. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/GNUmakefile commit 882ee5f1d99d7d357c3cab55c4bddabbda219e47 Author: vince Date: Tue Aug 9 17:22:50 2016 -0700 more io notes. Docs/Readme.io commit 44b476d93da6ff76c498ae7d9748f9b68432d853 Author: Weiqun Zhang Date: Tue Aug 9 16:13:19 2016 -0700 update the regtest clean script Tools/RegressionTesting/reg_test_gc.py commit 40a069a9c115576ac28c73a5bfa3b14a8a8724ef Author: vince Date: Tue Aug 9 15:47:09 2016 -0700 first part of code for persistent streams. Src/C_BaseLib/VisMF.cpp commit 4113091d52eaf59ded9759d454a41f9e97d8cd0b Author: vince Date: Tue Aug 9 15:45:28 2016 -0700 more notes. Docs/Readme.io commit 916533c55fda7cb87dbc5c6651c5549d035f0b83 Author: Weiqun Zhang Date: Tue Aug 9 14:37:14 2016 -0700 fix new bugs Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Periodicity.cpp commit e9707dc03ed487d58bb4b593eb19ee557c182543 Author: Weiqun Zhang Date: Tue Aug 9 14:30:46 2016 -0700 remove MultiFab::FillBoundary because it blocks FabArray::FillBoundary Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/MultiFabUtil.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 527d8bda4a4245d5815ec4a8fa6e3db02d87bba0 Author: Weiqun Zhang Date: Tue Aug 9 13:18:42 2016 -0700 start to use FillBoundary for periodic boundaries Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/MultiFabUtil.cpp Src/C_TowerLib/Layout.cpp Src/C_TowerLib/MFTower.cpp commit 92f2b106d12de0123e1cfc2a2c3bb9cb09882df6 Author: Weiqun Zhang Date: Tue Aug 9 13:03:57 2016 -0700 add Geometry::periodicity Src/C_BaseLib/Geometry.H commit 65c6a801092778129a3e9ebdcfa3839660dcb744 Author: Weiqun Zhang Date: Tue Aug 9 12:58:31 2016 -0700 tweak FillBoundary interface Src/C_BaseLib/FabArray.H commit f49596144b1d83c94b0db2709d7cb1e0702f2f28 Author: Weiqun Zhang Date: Tue Aug 9 12:47:07 2016 -0700 make FabArray::FillBoundary fill periodic boundaries too Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Periodicity.H Src/C_BaseLib/Periodicity.cpp commit 97cb8e9055c1c4a3129ba5ce0640850037adbff7 Merge: 4a3a088ed b3124150e Author: Brian Friesen Date: Tue Aug 9 11:19:27 2016 -0700 Merge branch 'VTune_fixes' into development commit b3124150ed1849afb3ec2a4a8796610a9cd190a9 Author: Brian Friesen Date: Tue Aug 9 11:16:45 2016 -0700 C_mk: add -DVTUNE and -DITTNOTIFY defines for USE_VTUNE and USE_ITTNOTIFY Tools/C_mk/Make.defs commit 83f906ca5b328005fbec310c6daae2e7c2af3ea2 Author: Brian Friesen Date: Tue Aug 9 11:13:11 2016 -0700 C_mk: move Intel compiler flag "-parallel-source-info=2" into USE_VTUNE Tools/C_mk/Make.defs commit a5768416349d5e68219f59ea858a399b913badb2 Author: vince Date: Mon Aug 8 16:30:30 2016 -0700 read tests for raw native format. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit c92069dae5a474938be090cf381bf4b4b1998898 Author: vince Date: Mon Aug 8 16:28:44 2016 -0700 add read functions for raw native format. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 13827e9c36a612a5576e30f34ce3475b62aa6eac Author: vince Date: Mon Aug 8 14:48:21 2016 -0700 remove BL_VISMF_MSGCHECK code. Src/C_BaseLib/VisMF.cpp commit 3e42f57eadb17bb4d4324b6a7ee4a7a4990c9c51 Author: vince Date: Mon Aug 8 14:45:31 2016 -0700 combine write code. Src/C_BaseLib/VisMF.cpp commit e2900990f41491d8c3dbd1e50028289000f4b96e Author: vince Date: Mon Aug 8 11:57:00 2016 -0700 change path Tests/IOBenchmark/GNUmakefile commit dcd7dda35cc4480644a943498c97e8ea688b07bc Author: vince Date: Mon Aug 8 11:14:30 2016 -0700 some cleanup. Src/C_BaseLib/VisMF.cpp commit 4a3a088ed95bdc7aa05d178287fd5e03abc6ced0 Author: Weiqun Zhang Date: Mon Aug 8 07:45:59 2016 -0700 promote FabArrayBase::CpOp to public Src/C_BaseLib/FabArray.H commit 17d599cb4d29dce3a3cad3a82909cb3d54e615cd Author: Weiqun Zhang Date: Mon Aug 8 07:29:59 2016 -0700 Add optional argument Periodicity to FillBoundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Periodicity.H commit 40d05e139e603429a88641e408ed53af6104c2a1 Author: Weiqun Zhang Date: Fri Aug 5 22:40:47 2016 -0700 fixed a bug in last commit Src/C_BaseLib/FabArray.H commit 722aff30ad4af00214a66f5a5437d0e19f9b40fb Author: Weiqun Zhang Date: Fri Aug 5 18:12:23 2016 -0700 prepare CopyComTag for periodic fill boundary and copy Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Periodicity.H commit 42893ce0b15bca1af865c55e58b54dd9a71344a3 Author: vince Date: Fri Aug 5 17:51:51 2016 -0700 some cleanup. Src/C_BaseLib/VisMF.cpp commit 2a95b997581929799950fb46c9640fee37692fd9 Author: vince Date: Fri Aug 5 17:13:19 2016 -0700 more io notes. Docs/Readme.io commit 0cafc8b05c975909834135c2d22c087f1b0171fb Author: vince Date: Fri Aug 5 17:12:18 2016 -0700 update tests for new vismf versions. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit cf3698a600b45ad585a0a618683f00c5132ce16b Author: vince Date: Fri Aug 5 17:11:10 2016 -0700 new header versions, calc famin famax values. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit dcf49422337ac3315378b49de4a52d57243fa023 Author: Weiqun Zhang Date: Fri Aug 5 15:14:58 2016 -0700 add ngrow to FabSet::copyTo Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit dd262ee7b85100a55627c68dd85ec8d911f20ca1 Author: Weiqun Zhang Date: Fri Aug 5 14:48:31 2016 -0700 FabSet: new version of plusFrom that add two FabSets together Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit af215d7f360f37ecc7d64fb35d4ac3af66b6df89 Merge: f13114f46 b14bfcfd2 Author: Weiqun Zhang Date: Fri Aug 5 14:03:53 2016 -0700 Merge branch 'development' into weiqun/boxarrayconverter Conflicts: Src/C_BaseLib/FabArray.H commit f13114f46458cb7280a0f84c478a2ec1b5ba8deb Author: Weiqun Zhang Date: Fri Aug 5 13:53:23 2016 -0700 Abort if FabSet::AddProcsToComp is called. Src/C_BoundaryLib/FabSet.H commit 7ed4485543cc62954819fd4ab9ae6861601c3bdf Author: Weiqun Zhang Date: Fri Aug 5 13:20:37 2016 -0700 indexMap --> indexArray Src/C_BaseLib/FabArray.cpp commit c2bc245b13989fd7400d3ebf4212dc46b36f2466 Merge: f8ba5fa0a b14bfcfd2 Author: Michael Zingale Date: Thu Aug 4 21:09:46 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit f8ba5fa0aaaa75ff581645636275a90dc1d86f79 Author: Michael Zingale Date: Thu Aug 4 21:08:46 2016 -0400 add another color to the summary pages black = test crashed (as determined by backtrace files) the compile and crash failures now also show on the summary page for the entire run Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit 68e3ba7becce5b39e0847e30921a67261179978a Author: vince Date: Thu Aug 4 17:27:53 2016 -0700 filename fix for ungrouped sets for VisMF::Write. Src/C_BaseLib/VisMF.cpp commit c5727deb18444972feea77cbb133002f1b447d85 Author: vince Date: Thu Aug 4 17:27:09 2016 -0700 simplify code. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit b14bfcfd215560eead13466dede5b074ed924a50 Author: Weiqun Zhang Date: Thu Aug 4 17:12:51 2016 -0700 Changed the behavior of bdryLo and bdryNode (for the lower face) when len>1. With the old code the returned node box is obtained by growing inwards. With the new code the returned node box is obtained by growing outwards, just like bdryHi. Not sure the old one is a bug or feature. Marc and I agree that the old behavior is unexpected and undesired. It should be noted as far as I know these functions have never been called with len>1. For len=1, the results do not change. Src/C_BaseLib/Box.cpp commit 764ddea8886ed00014fe2d5462b3614384656303 Author: Weiqun Zhang Date: Thu Aug 4 16:58:08 2016 -0700 FabSet: remove aliasing in linComb Src/C_BoundaryLib/FabSet.cpp commit 8c3eaaeb734da4c465efbbe3f8d794211230d654 Author: Weiqun Zhang Date: Thu Aug 4 16:35:38 2016 -0700 FabSet: reimplement linComb Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 65ca3dc1b70e486625d1ed9baafa9be1bb8ad5d0 Author: Weiqun Zhang Date: Thu Aug 4 16:17:44 2016 -0700 fix linComb that was temporarily disabled because only castro radiation uses it Src/C_BoundaryLib/FabSet.cpp commit 2244db057ae01527b5c28df8a8b1a04f3afe3df6 Author: vince Date: Thu Aug 4 16:10:35 2016 -0700 use NFilesIter. Src/C_BaseLib/VisMF.cpp commit 574a77fbd4bd4de3535de3b82d139e9faa643ecd Merge: 80cd11b41 6632bb42a Author: vince Date: Thu Aug 4 15:37:41 2016 -0700 change mf to FabArray. commit 807c830360e5352df280f3724de5a2f7419f54f0 Author: Weiqun Zhang Date: Thu Aug 4 15:01:48 2016 -0700 BoxArray: clear hash bin whenever the boxes change Src/C_BaseLib/BoxArray.cpp commit e1dd2e43466c5064d6d0e351a1f4c4a64e43dff2 Author: Weiqun Zhang Date: Thu Aug 4 14:33:59 2016 -0700 remove calls to clear_hash_bin() Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 851c3b65914693ca60e2598dc08bb02c96b80447 Author: Weiqun Zhang Date: Thu Aug 4 14:17:41 2016 -0700 clean up BoxArray::intersections functions Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/Particles.H Src/C_BaseLib/Particles.cpp Src/C_BoundaryLib/FabSet.cpp commit 88f6b087a0e16b09013a8e195e193b6f85f22317 Author: Weiqun Zhang Date: Thu Aug 4 13:47:29 2016 -0700 minor tweak of TINY_PROFILE in make Tools/C_mk/Make.defs commit 6632bb42a0d739e8bf8db9c60fce76ebfed65033 Author: vince Date: Thu Aug 4 13:09:07 2016 -0700 fixec calls to bl_fortran_set_nprocs_sidecar Src/C_BaseLib/ParallelDescriptor.cpp commit 0710e73cb5d20d87de4cfb5f9f7d12e1d7c5fa0b Author: vince Date: Thu Aug 4 13:07:53 2016 -0700 allocate arrays for set_nprocs_sidecar. needs some error checking. Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 27b4e17953bdff9d6ff3cde7783c2586fb803748 Author: Weiqun Zhang Date: Tue Aug 2 15:00:02 2016 -0700 add optional no_assertion argument to a number of functions in FabArray because they might get called in situations the assertion for BDKey fails Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 80cd11b41f1bddf9ad950a2db63944b66c608a5a Author: vince Date: Wed Aug 3 15:52:49 2016 -0700 more notes. Docs/Readme.io commit 84de84e5240cc1277785eb973e870abde0eb2ed5 Author: vince Date: Wed Aug 3 15:52:03 2016 -0700 move remove out of timed block. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit f2fdf17541bad805166b86e98408126ac87df3cb Author: Brian Friesen Date: Wed Aug 3 17:46:40 2016 -0400 Tutorials: write correct number of component names in plotfile header in writePlotFile() The plotfile header file should list the same number of component names as there are components. This was already done correctly in a few versions of writePlotFile() in other tutorials, but not in these. Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/PGAS_HEAT/writePlotFile.cpp Tutorials/Tiling_Heat_C/writePlotFile.cpp commit 0bb103fd15f41ed78d948af3fcedb1fbd7deb11b Author: Ann Almgren Date: Wed Aug 3 14:06:37 2016 -0700 Also want to change the comments in HeatEquation_EX*F/main.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX4_F/main.f90 commit 8cba628f0e2e266c550d60f4c5200cf7ed863629 Author: Ann Almgren Date: Wed Aug 3 14:05:22 2016 -0700 Analogous changes to those just made in the other HeatEquation_EX*F Tutorials/HeatEquation_EX5_F/define_bc_tower.f90 Tutorials/HeatEquation_EX5_F/inputs-rt Tutorials/HeatEquation_EX5_F/inputs-rt-expl Tutorials/HeatEquation_EX5_F/inputs-rt-impl Tutorials/HeatEquation_EX5_F/inputs_2d Tutorials/HeatEquation_EX5_F/inputs_3d Tutorials/HeatEquation_EX5_F/main.f90 Tutorials/HeatEquation_EX5_F/multifab_physbc.f90 commit 1681fbec12c3391242db4d1a86527990271e7a07 Author: Ann Almgren Date: Wed Aug 3 13:54:31 2016 -0700 Analogous changes in HeatEquation_EX4_F to the most recent changes in HE*2_F and HE*3_F Tutorials/HeatEquation_EX4_F/define_bc_tower.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/multifab_physbc.f90 commit ab6091d9a5e4bba9c131b86084e7e7098ad8f829 Author: Ann Almgren Date: Wed Aug 3 13:51:17 2016 -0700 Update HeatEquation_EX2_F and HeatEquation_EX3_F so that we include local versions of define_bc_tower.f90 and multifab_physbc.f90 so that we can allow for a larger range of bc types in the inputs files and so that it more clear where to set the Dirichlet values of phi if we are using INLET. Tutorials/HeatEquation_EX2_F/define_bc_tower.f90 Tutorials/HeatEquation_EX2_F/inputs_2d Tutorials/HeatEquation_EX2_F/inputs_3d Tutorials/HeatEquation_EX2_F/multifab_physbc.f90 Tutorials/HeatEquation_EX3_F/define_bc_tower.f90 Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/multifab_physbc.f90 commit 456be8632638281620b4c04eb0a6997df2e80d32 Author: Weiqun Zhang Date: Tue Aug 2 23:28:08 2016 -0700 fix bounding box bug in the new BoxArray intersection function Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp commit a5757e2f18afd2b596e4af1b19fff6352a8ea6f7 Author: Weiqun Zhang Date: Tue Aug 2 15:00:02 2016 -0700 add optional no_assertion argument to a number of functions in FabArray because they might get called in situations the assertion for BDKey fails Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 675942631a297fb6510b32c808e4b0154d1671b1 Author: Weiqun Zhang Date: Tue Aug 2 15:00:02 2016 -0700 add optional no_assertion argument to a number of functions in FabArray because they might get called in situations the assertion for BDKey fails Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 0f1f4480c2d13f2258c357a0c565233ccf1f0b1d Author: Weiqun Zhang Date: Tue Aug 2 14:38:57 2016 -0700 assertion and minor cleanup Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit a0dfd42a3fe6ff66e1d0bcc3997c3ecfe9f3af95 Author: Michael Zingale Date: Tue Aug 2 10:13:27 2016 -0400 fix benchmade link Tools/RegressionTesting/test_report.py commit 899c2732ff5bdf155e904e8959f50d48ad98eb75 Author: vince Date: Mon Aug 1 16:18:49 2016 -0700 forgot the header. Src/C_BaseLib/VisMF.H commit b36219cb22bdf6157fecc4a40bc641b8fbeb9a0b Author: vince Date: Mon Aug 1 16:14:59 2016 -0700 test remove nfiles. Tests/IOBenchmark/IOTest.cpp commit cf18248aba427c8956da832a7398ce555c081416 Author: vince Date: Mon Aug 1 16:14:33 2016 -0700 tweak set groups. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 551579d7704886ff0a025f785ffc27d58c6879b5 Author: vince Date: Mon Aug 1 16:13:42 2016 -0700 added function to remove nfiles. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 0ddfbfb7d35cab80134827d295f9f39c8a1098fa Author: vince Date: Mon Aug 1 12:23:12 2016 -0700 test group set option. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit fe997f010ce7d3a4e85995c327f331829588ccc1 Author: vince Date: Mon Aug 1 12:22:56 2016 -0700 propagate group set option. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 6f21c30aebc81107ddb81d0d1646fcc9ec33787f Author: vince Date: Mon Aug 1 12:22:15 2016 -0700 added option to group sets. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 1455716cd3fda7b69e70ba5d4fefb5376ddfa7d5 Author: Weiqun Zhang Date: Mon Aug 1 07:26:59 2016 -0700 Release Notes 16.08 ReleaseNotes/release-notes-16.08 commit 88371d5d0696e5e84a91a92b4f727d806b79bf35 Merge: fdaefde95 b6f3ba865 Author: Weiqun Zhang Date: Sun Jul 31 15:07:46 2016 -0700 Merge branch 'development' Conflicts: Src/C_BaseLib/FabArray.H commit a40563883d951a5a8e976c43c47e02b0516deae8 Author: Weiqun Zhang Date: Sun Jul 31 07:15:24 2016 -0700 BoxArray: In some special cases, the internal reference counted cell-center boxes may look empty. Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp commit a350a9a98db208faa6bb995c0caabb7dd18544a5 Author: Weiqun Zhang Date: Sat Jul 30 22:12:32 2016 -0700 FabSet::periodicCopyTo Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit c9225927f71508795f82ee0dc60ddb428a1e7d4c Author: Weiqun Zhang Date: Sat Jul 30 16:49:29 2016 -0700 use doi (domain of influence) in BoxArray intersection Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.cpp commit 163b553d468d5b80aee26a7861b6209cf1d8c2e9 Author: Weiqun Zhang Date: Sat Jul 30 13:47:53 2016 -0700 BoxArray Transformer: add doi (domain of influence) Src/C_BaseLib/BoxArray.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit f5c756b6bba9dcb42f8595624c3932c3368426e4 Author: Weiqun Zhang Date: Sat Jul 30 10:38:00 2016 -0700 Revert "refactor BoxArray Transformer" This reverts commit 02ff0022cf98f0ab2a443e28ba29a6b89472b9a0. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 02ff0022cf98f0ab2a443e28ba29a6b89472b9a0 Author: Weiqun Zhang Date: Sat Jul 30 08:21:48 2016 -0700 refactor BoxArray Transformer Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 1686b08a45cb0a9e2de03938c4b0dcce1fceecf4 Author: Weiqun Zhang Date: Fri Jul 29 23:03:53 2016 -0700 FabSet::copyTo interface Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 7c93dd62c33f7012d3889e9584bc8b10622fd91e Author: Weiqun Zhang Date: Fri Jul 29 22:40:41 2016 -0700 update CPC due to that type plus reference key is no longer sufficient for BoxArray comparison Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 94c339dc61b76f816dcdff76ebbd5b6e5ca92741 Author: Weiqun Zhang Date: Fri Jul 29 18:13:44 2016 -0700 WIP: FabSet copy wip Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 23c2f3c81fda672eace5daa9408e58782c6e41fc Author: Weiqun Zhang Date: Fri Jul 29 17:44:05 2016 -0700 WIP: more clean up of FabSet Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 83826fc05eea9959646d170f52d7555e818bd66e Author: vince Date: Fri Jul 29 16:48:15 2016 -0700 updated readme. Tests/IOBenchmark/README commit 234d36b8adcfa1e5ff6c2bb3c29ee63430b7c4bd Author: vince Date: Fri Jul 29 16:42:35 2016 -0700 command line option for writeminmax. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 0b621ffb1477e97d9c50362230089cea4a4a956c Author: vince Date: Fri Jul 29 16:27:35 2016 -0700 calc offsets without communication, option to write minmax. Src/C_BaseLib/VisMF.cpp commit e195c63b318fb366f335dfe8bb8d2816ccf62292 Author: vince Date: Fri Jul 29 16:26:29 2016 -0700 util function, enforce proc range. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 40ff35c308716308503e3c4ae4f1c677f7661323 Author: Weiqun Zhang Date: Fri Jul 29 16:10:34 2016 -0700 add a new version of FabSet::setVal Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 46ce3dc9c7d4ad66d65fc6916171fe188a1b10ac Author: vince Date: Fri Jul 29 14:22:35 2016 -0700 added stream buffer option. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit b4eb8c717891bd7c0b9d06b118ad75bdcf53363d Author: Weiqun Zhang Date: Fri Jul 29 11:24:45 2016 -0700 WIP: get it to compile be commenting out a lot of codes in FabSet Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit b6f3ba865d0007beb998d647aa67f44ee4db6998 Author: Michael Zingale Date: Fri Jul 29 10:16:46 2016 -0400 testnew.py -> regtest.py Docs/Regression/test_suite.tex commit c6447196eed5992bc39693acd355adf3314897aa Merge: 3259e717e 47fde68ec Author: Michael Zingale Date: Fri Jul 29 10:11:34 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 3259e717e029e92463d0e1dceaac429a95dec366 Author: Michael Zingale Date: Fri Jul 29 10:11:18 2016 -0400 remove the older suite -- use regtest.py now Tools/RegressionTesting/testnew.py commit 47fde68ec62a7b133f1ec9d6e0665c30a0bb3d82 Merge: e2e6629e2 ee11b4c50 Author: Michael Zingale Date: Fri Jul 29 09:44:42 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit e2e6629e2dee415480c5b5760d7c39111aa7874c Author: Michael Zingale Date: Fri Jul 29 09:44:30 2016 -0400 update to point to regtest.py Tools/RegressionTesting/README commit 143417ba2c6862db6ca524f9175225021e9d2e84 Author: Weiqun Zhang Date: Thu Jul 28 22:11:33 2016 -0700 WIP: reimplement FabSet with MultiFab as member instead of base class; this allows more control over hiding MulitFab methods from FabSet Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit a4995648adddd1b56a517b4c274a84ca0db40cec Author: Weiqun Zhang Date: Thu Jul 28 21:04:09 2016 -0700 define BndryRegister with BoxArray with special transformer Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 9b66aef73b366db891dc38dd1e25f9d0c2923540 Author: vince Date: Thu Jul 28 17:22:21 2016 -0700 continue write raw native wirtes. Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/GNUmakefile commit 6da270eb466ffc113a778eefc019848f82949510 Author: vince Date: Thu Jul 28 16:54:13 2016 -0700 test write minmax to raw native mf. Tests/IOBenchmark/IOTest.cpp commit 65662ac3ff673891d8a25ea6e2a955d7f0b90c53 Author: vince Date: Thu Jul 28 16:24:51 2016 -0700 add option to write fab minmax to the data. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 137e5e2f48a57d4760efedf676fe970c219426a1 Author: vince Date: Thu Jul 28 16:04:52 2016 -0700 added comments and an example. Src/C_BaseLib/NFiles.H commit 78d3141718b93f6e08fc1666cda25e33c50b19aa Author: Weiqun Zhang Date: Thu Jul 28 15:02:15 2016 -0700 BoxArray: add transformer that transforms internally stored and possibly shared boxes into boxes of the public interface Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 7019df10602b1e404f1c920f108c6da110bd8775 Author: vince Date: Thu Jul 28 14:04:14 2016 -0700 change defaults. Src/C_AMRLib/AmrLevel.H commit ee11b4c50529bc9412f64342039ac1d2efdc5568 Author: Michael Zingale Date: Thu Jul 28 13:00:54 2016 -0400 a little cleaning Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit a93c26d4dcc713a01b420163d87ecc61494bc17d Author: Michael Zingale Date: Thu Jul 28 12:39:19 2016 -0400 highlight a compilation failure in a different color (purple) than regular failure (comparison) Tools/RegressionTesting/test_report.py commit cbf5937014593f813d94b105b98552e9aa374d6f Author: Michael Zingale Date: Thu Jul 28 11:31:57 2016 -0400 fix stderr output when we aren't sending it to its own file Tools/RegressionTesting/test_util.py commit fdaefde950254111540718baf3933148baddf5b4 Author: Weiqun Zhang Date: Wed Jul 27 22:43:53 2016 -0700 add libquadmath Tools/C_mk/Make.defs commit 09be8c41cc1d2de838d8696c884e99dda952349c Author: Weiqun Zhang Date: Wed Jul 27 22:43:53 2016 -0700 add libquadmath Tools/C_mk/Make.defs commit 6b186be99eace20291c4f29eaeeadabbc86cbebb Author: vince Date: Wed Jul 27 17:19:15 2016 -0700 test functions for VisMF::WriteRawNative. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 9bac42bfb0d354220d53a9ca91c26145961da16e Author: vince Date: Wed Jul 27 17:18:33 2016 -0700 added WriteRawNative function. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit ab0015bc2b6cece92a715e04ddb4027790212334 Author: vince Date: Wed Jul 27 17:17:32 2016 -0700 added file name functions. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit a6ebbe8dbd0bc77e2abb167c93669367cb8b7915 Author: Brian Friesen Date: Wed Jul 27 13:30:10 2016 -0700 C_mk: add some extra compiler flags when using VTune This adds support for the GNUmakefile options USE_VTUNE and USE_ITTNOTIFY when using the Intel compilers. USE_VTUNE adds some extra debugging output during compilation which allows VTune to resolve more information about the code during profilng, while USE_ITTNOTIFY provides support for manual code instrumentation with VTune to profile only certain regions instead of the entire thing. Tools/C_mk/Make.defs commit 4551bcf5a908fab61f93f8a7d38da49af067304d Author: Brian Friesen Date: Thu Jul 7 13:15:31 2016 -0700 C_mk, HPGMG: rename DUNLIMIT_FMG_VCYCLES -> DUNLIMIT_FMG_ITERATIONS Sam renamed this in HPGMG so we need to follow suit in our compilation scripts. Tools/C_mk/Make.defs commit 73674a94704e010d8a427257a11459fe05d073e9 Author: vince Date: Wed Jul 27 12:12:27 2016 -0700 change how default, some cleanup. Src/C_AMRLib/Amr.cpp commit 77be0ced915d86a197f6fee294f42b12e6967f25 Author: Weiqun Zhang Date: Wed Jul 27 07:07:49 2016 -0700 fix assertion Src/C_BaseLib/Geometry.cpp commit 2eac7f1ddc93149a2ffb910eca791e5e9a4dfa97 Author: Weiqun Zhang Date: Tue Jul 26 22:28:52 2016 -0700 explicit Src/C_BaseLib/BoxArray.H commit 9318856692b74e851e88b07aa1ce0a7416eb467c Author: Weiqun Zhang Date: Tue Jul 26 21:02:46 2016 -0700 reimplement fillperiodicboundary cache using boxarray-distributionmap key Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit c974b138d4dbb4984a943d25f76d674b8d61f991 Author: Weiqun Zhang Date: Tue Jul 26 16:12:45 2016 -0700 clean up FB Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 205ef3b3c0cc6288893be664eb4f80926b6e9ce5 Author: Weiqun Zhang Date: Tue Jul 26 15:06:33 2016 -0700 reimplement parallel copy cache using boxarray-distributionmap key Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d9c0c3b647cf7158f0ee83096a3844d974e4442d Author: Weiqun Zhang Date: Tue Jul 26 10:55:13 2016 -0700 MemPool: static_assert Src/C_BaseLib/MemPool.cpp commit 7dd68040cba6f108e3aca24905e2d5094c4be5fb Author: Weiqun Zhang Date: Tue Jul 26 07:51:00 2016 -0700 reimplement fillboundary cache using boxarray-distributionmap key Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit 891ff3b1ce41942567d5760309c5e1c0fe372e7a Author: vince Date: Tue Jul 26 17:55:19 2016 -0700 packaged nfiles writing. Src/C_BaseLib/Make.package Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit ca8de6591fbc41d831576e392f43116a69959f0e Author: Ann Almgren Date: Tue Jul 26 14:57:44 2016 -0700 Enable us to call fourth_order interpolation without having to define the stencil_width to 2 independently -- affects multifab_fill_ghost_cells and fillpatch. Also fix the fourth_order_interp routine so that it can fill some but not all fine cells in a coarse cell. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 9a135acc413e314278d7d130d372b5689a6a0368 Author: vince Date: Tue Jul 26 14:44:12 2016 -0700 limit buffer size. Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabConv.cpp commit 14e7404b56a493175f5a1f58c19e56379f7706f7 Author: vince Date: Tue Jul 26 13:01:32 2016 -0700 added directory creation tests. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 2af3056c664f185099925540f94f224656889596 Author: vince Date: Tue Jul 26 12:58:00 2016 -0700 updated UtilCreateDirectory Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit aa34f5afc8ff47c6f29566caec35e0a13b9af3fb Author: Weiqun Zhang Date: Mon Jul 25 15:53:54 2016 -0700 fix tilearray memory profiling counter Src/F_BaseLib/layout.f90 commit ab9359bcddec42aa559e088dba6ad75465d5cd4e Author: Weiqun Zhang Date: Mon Jul 25 15:48:56 2016 -0700 nullify fortran pointer in bl_deallocate Src/C_BaseLib/mempool_f.f90 commit fd6b92bd8da33099757b0be76d479542223ebef4 Author: Weiqun Zhang Date: Mon Jul 25 15:10:33 2016 -0700 use constexpr Src/C_BaseLib/MemProfiler.cpp commit 0aeeac80408e4f9c34bcf249e9aac4252c937cc0 Merge: 21d7ae832 c4bba0063 Author: Weiqun Zhang Date: Mon Jul 25 14:50:33 2016 -0700 Merge branch 'development' into weiqun/coarsenboxarray Conflicts: Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit c4bba00639df0a32bde27b809b0f033280642bf1 Author: Weiqun Zhang Date: Mon Jul 25 14:41:49 2016 -0700 MEM_PROFILE: keep track of the number of BoxArrays and MultiFabs Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 21d7ae832362585f2d473954f4be6af3a9fcdd78 Author: Weiqun Zhang Date: Sun Jul 24 18:57:48 2016 -0700 update because BoxArray::define(const BoxArray&) is gone Tests/LinearSolvers/ComparisonTest/main.cpp commit 4490ba0903fea6beba177c5cd97786fd37ca8a29 Author: Weiqun Zhang Date: Sun Jul 24 17:35:17 2016 -0700 cache coarse BoxArrays Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/Pointers.H commit 2bd66e6c577ae8b1641c95512f852bc66ddbb5f7 Author: Michael Zingale Date: Sun Jul 24 17:33:22 2016 -0400 'make file_locations' will printout where in the VPATH each source file is found as well as indicate which files are not found Tools/C_mk/Make.rules commit 320ff827777a7ea8e0e26c9b711699a60f4e9bb8 Author: Michael Zingale Date: Sun Jul 24 17:26:58 2016 -0400 'make file_locations' will output where each source file is found by make this will also indicate which files make cannot find Tools/F_mk/GMakerules.mak commit 516f9ba39b58704ad5ec67d52f19eadc1d91b4c6 Author: Michael Zingale Date: Sun Jul 24 17:23:39 2016 -0400 a useful tool for makefile debugging -- this script will print out where files are found in the vpath and which files are not in the vpath Tools/F_scripts/find_files_vpath.py commit 773fd439ea740c235c517584eb493f3f40980bfc Author: Weiqun Zhang Date: Sat Jul 23 12:55:15 2016 -0700 remove BoxArray::define(const BoxArray& bs) because it is equivalent to the assignmeent operator Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit d0e40ebb741ecf047b9e59361c681baf51f2f6ed Author: Weiqun Zhang Date: Sat Jul 23 11:14:17 2016 -0700 use BoxArray assignment operator instead of define function because I plan to remove the define fucntion Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StateData.cpp Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/BndryRegister.cpp commit ab110a98a847378b94c26ae891118e77d96ca933 Author: Weiqun Zhang Date: Sat Jul 23 07:33:28 2016 -0700 make ~FabArrayBase just in case Src/C_BaseLib/FabArray.H commit 32c412616f1274b91ec08f265a5f5562889f0e16 Author: Weiqun Zhang Date: Fri Jul 22 17:03:04 2016 -0700 virtualize a few functions in FabArray and make VisMF a class for FabArray instead of MultiFab Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 7300dab04b8257f2dd7f1447d195de95c69e4782 Author: vince Date: Fri Jul 22 14:29:40 2016 -0700 added dir tests. Tests/MKDir/MKDir.cpp commit 4d060fa0ca4bfe4c664880ea9738e45189425692 Author: vince Date: Thu Jul 21 16:30:16 2016 -0700 code cleanup. Src/C_BaseLib/VisMF.cpp commit e47e3fb27cc5c0bd1b1c7637330ad4318221b167 Author: Weiqun Zhang Date: Thu Jul 21 14:45:00 2016 -0700 wip Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MultiMask.H Src/C_BoundaryLib/MultiMask.cpp commit a4fd02c25bc3136f709da80471847ba012e101ce Author: vince Date: Thu Jul 21 14:33:22 2016 -0700 some code cleanup. Src/C_BaseLib/FArrayBox.cpp commit f0e99d9f53eb8edc5669485392b527d567fc4721 Author: Weiqun Zhang Date: Thu Jul 21 12:58:12 2016 -0700 start MultiMask class Src/C_BoundaryLib/CMakeLists.txt Src/C_BoundaryLib/Make.package Src/C_BoundaryLib/MultiMask.H Src/C_BoundaryLib/MultiMask.cpp commit f159374cc1a4936151afbf73a248181536f50bb2 Author: Weiqun Zhang Date: Thu Jul 21 12:48:04 2016 -0700 add alloc and shared as optional arguments to Mask class in preparation for new MultiMask class Src/C_BoundaryLib/Mask.H Src/C_BoundaryLib/Mask.cpp commit 74e9f3d86e739460aec3ea0ba5722438629fc03f Author: vince Date: Thu Jul 21 12:38:27 2016 -0700 added functions to set buffer sizes. Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp commit 866cb3b29f70d78b5c2d9dac369568e306085044 Author: Weiqun Zhang Date: Thu Jul 21 11:14:30 2016 -0700 remove edge_restriction.f90 because all its functions are already duplicated in cc_restrition_module and the edge restriction functions are called by functions in ml_cc_restriction_module (since there is no ml_edge_restriction_module Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/edge_restriction.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit 506def2a25948116dc92e879fb39a1c29b9eab43 Author: vince Date: Thu Jul 21 11:14:01 2016 -0700 added test files and io doc. Docs/Readme.io Tests/C_BaseLib/AMRPROFTEST_F.H Tests/C_BaseLib/AMRProfTestBL.cpp Tests/C_BaseLib/tRABcast.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp commit 9d70923d5dfdeafc7cfd9f6b66dce0cfd76f36ac Merge: ecd7d5f12 65d1c17ae Author: Michael Zingale Date: Thu Jul 21 12:28:13 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit ecd7d5f12e044e7637b9495d446288f43672b2b3 Author: Michael Zingale Date: Thu Jul 21 12:27:53 2016 -0400 move the return code logic to _after_ we do zone info Tools/Postprocessing/F_Src/fcompare.f90 commit 65d1c17ae5e0bcf680de584cc028efbb8e7e9c89 Author: vince Date: Wed Jul 20 16:46:53 2016 -0700 remove the word grok. Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit d7e20b171fa062b10615400d18039642f20070b4 Merge: 890ffa4a9 946125444 Author: Michael Zingale Date: Wed Jul 20 19:33:46 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 946125444910245cadbac69dab90194e6b3569cd Merge: e7db6b28e 0fb71cf83 Author: vince Date: Wed Jul 20 12:39:20 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit e7db6b28e8ec5e8fab51434057fc4ba79c222bc5 Author: vince Date: Wed Jul 20 12:39:15 2016 -0700 remove profile call. Src/C_BaseLib/ParallelDescriptor.cpp commit 0fb71cf836f7440c7b26ddaa8355cdfec48719e5 Author: Michael Zingale Date: Sun Jul 17 14:13:04 2016 -0400 the microphysics suite inputs Tools/RegressionTesting/Microphysics-tests-pgi.ini Tools/RegressionTesting/Microphysics-tests.ini commit 9aaf8fd58a7878331a6c70f9aab47ee1f12b4f34 Author: Michael Zingale Date: Sun Jul 17 13:07:59 2016 -0400 detect variable mismatch in comparison Tools/RegressionTesting/test_report.py commit 9dace46a53f7924281fcc738460728e85476666f Author: Michael Zingale Date: Sun Jul 17 12:28:40 2016 -0400 return error code if there are different / missing variables in the plotfiles Tools/Postprocessing/F_Src/fcompare.f90 commit 890ffa4a97a5c130b56bd4cb675d95a764d94255 Merge: c4f76ab2f c05ad7f7f Author: Michael Zingale Date: Thu Jul 14 10:03:17 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit c05ad7f7f2e1064d637c8d60043c6e45f25fdcfc Author: Weiqun Zhang Date: Wed Jul 13 13:42:15 2016 -0700 tweak Fortran make system to support codes relying on the programs variable Tools/F_mk/GMakerules.mak Tools/Postprocessing/F_Src/GNUmakefile commit 25242ae06013165a07bc80af80bb1b7e5141a9a3 Author: Weiqun Zhang Date: Wed Jul 13 12:51:32 2016 -0700 Fortran random: add more static_assert Src/F_BaseLib/bl_random_c.cpp commit 6eb28b7b6c0e4e8a8bac2cefa6fccb1630eee746 Author: Weiqun Zhang Date: Tue Jul 12 18:30:01 2016 -0700 Fortran random: add single precision Src/F_BaseLib/bl_random_c.cpp commit ba3e7d3568e056cf5987dc05bff2f472ffc27446 Merge: 8a4270773 00dbb2d78 Author: vince Date: Tue Jul 12 16:33:44 2016 -0700 refix name change. commit c4a1fadd3ecd22b9dbba39ddd2b8176ba8358164 Author: Weiqun Zhang Date: Tue Jul 12 16:10:48 2016 -0700 promote IndexMap() and localindex() to public so that some codes can use Src/C_BaseLib/FabArray.H commit 00dbb2d78d170ee314146c97d382d391fb4ecf5f Author: Weiqun Zhang Date: Tue Jul 12 16:10:48 2016 -0700 promote IndexMap() and localindex() to public so that some codes can use Src/C_BaseLib/FabArray.H commit 8a427077355b0c94ec1e9f24660852c804dbfe5a Merge: c210f8bfb 2c360a04b Author: vince Date: Tue Jul 12 16:03:09 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit c210f8bfb581f4ae7654641a419401a795b8fecf Author: vince Date: Tue Jul 12 15:59:38 2016 -0700 add a default real function. Src/C_AMRLib/LevelBld.H commit 2290151b05c40fb3706bd8a024c51b061d686541 Author: vince Date: Tue Jul 12 15:41:32 2016 -0700 dont free the comm from fortran for intransit. Src/C_BaseLib/BoxLib.cpp commit fab1628430f7934766a9365c05c1b1686c773eee Author: vince Date: Tue Jul 12 14:32:32 2016 -0700 flush another cache for MoveFabs. Src/C_BaseLib/FabArray.H commit 56cca713393e8366dbd7ea9dc4f5ee4fcd28911a Author: vince Date: Tue Jul 12 14:28:03 2016 -0700 flush another cache for MoveFabs. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit e82f50a64c1bcd77787393f1dd41c153512e1bef Author: vince Date: Tue Jul 12 14:26:08 2016 -0700 remove unused vars. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/FillPatchUtil.cpp commit c4f76ab2f61bbe7533436f6c435d6faaa0e38037 Merge: e5cfdc37d 2c360a04b Author: Michael Zingale Date: Tue Jul 12 14:55:37 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit dab6ce481f7a17bab90f465934162cd2c24b8eff Author: vince Date: Mon Jul 11 14:07:46 2016 -0700 merge fix. Src/C_AMRLib/Amr.cpp commit 2c360a04b643a378831acba2ec72ad037a890384 Author: Weiqun Zhang Date: Mon Jul 11 14:02:55 2016 -0700 Fortran random: allow using FluctHydro/HydroGrid distribution Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 commit 1448aa9da18a5c945017298c35a2bc199185ccc5 Author: vince Date: Mon Jul 11 13:33:32 2016 -0700 fix for serial. Src/C_BaseLib/ParallelDescriptor.cpp commit 04b0ae9716c36aa9c1264e1c164a947537c1b012 Merge: fcaef3d35 e194b5995 Author: vince Date: Mon Jul 11 12:19:05 2016 -0700 merge fix. commit e5cfdc37dfc750edca8939ed065d832dd3b33467 Author: Michael Zingale Date: Mon Jul 11 09:55:21 2016 -0400 minor formatting Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit acb2b01d1f921ed17aa32babb842aaf35c65430f Author: Michael Zingale Date: Mon Jul 11 09:48:46 2016 -0400 replace redefined name Tools/RegressionTesting/regtest.py commit fcaef3d358e76bac55e075f552564d7294bf47c1 Merge: 664efb5f5 61d4401a2 Author: Michael Zingale Date: Sun Jul 10 16:59:48 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 664efb5f5350363edec0bf21feb0d3f1fad77376 Author: Michael Zingale Date: Sun Jul 10 16:59:21 2016 -0400 a little cleaning Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit 61d4401a2660becc3f59ce11bd2925a46c629098 Author: Michael Zingale Date: Sun Jul 10 12:01:08 2016 -0400 a little more PEP-8 Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/repo.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit ba7b56589e98d73b26868ac3d523691f44dd8c3f Merge: bcf16ec7f 3f0c5a64f Author: Michael Zingale Date: Sun Jul 10 11:55:47 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit bcf16ec7f8842738bbb7a131095a13b3c21ed1ec Author: Michael Zingale Date: Sun Jul 10 11:55:32 2016 -0400 use is to compare to None Tools/RegressionTesting/regtest.py commit 3f0c5a64f070e5ad233007b2f6a070e654fde294 Author: Michael Zingale Date: Sun Jul 10 11:51:20 2016 -0400 actually check whether the user-specified compareFile exists Tools/RegressionTesting/regtest.py commit 7bac53b6c6b262878deb33cef10d09b1fa13854a Author: Michael Zingale Date: Sat Jul 9 19:53:01 2016 -0400 rely on the return code from fcompare to determine if the comparison was successful Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit e0417dc5a19cec8f6a6550d40c6a75038d600782 Author: Michael Zingale Date: Sat Jul 9 15:08:17 2016 -0400 explicitly send return codes of success or failure Tools/Postprocessing/F_Src/fcompare.f90 commit 797a236127ca5555e7375c36cdcda8eee03d1c75 Merge: 8b2e6296f 08ec9292b Author: Michael Zingale Date: Sat Jul 9 14:55:58 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 8b2e6296fa37a41b149d13bc9a6f9142b55950a9 Author: Michael Zingale Date: Sat Jul 9 14:55:41 2016 -0400 two new functions for sending return codes from Fortran Src/F_BaseLib/system_util_c.c commit 08ec9292bbb31a7ca64352cef9901a917bddb126 Author: Max Katz Date: Sat Jul 9 14:49:44 2016 -0400 Write a plotfile on demand with plot_and_continue Src/C_AMRLib/Amr.cpp commit bc467c27d62634b407d5c2290b0fa964817b52ec Author: Michael Zingale Date: Sat Jul 9 13:27:41 2016 -0400 use the return code to determine if compilation was successful consolodate the main copying code Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit 8c7d0064bbd56d96b3ea785f33c7378a82bc8b17 Author: Michael Zingale Date: Sat Jul 9 12:55:31 2016 -0400 no really, .pyc .gitignore commit cc794366b19e3c06c1fa54907f4b739f0f6087a3 Author: Michael Zingale Date: Sat Jul 9 12:55:04 2016 -0400 add .pyc .gitignore commit 720e31371c35cacdfcaf78ec50b00e84179db739 Author: Michael Zingale Date: Sat Jul 9 12:27:47 2016 -0400 use the return code from make to determine if the tools built Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit e194b599510623d799c3ac623ad72e86be8a3592 Author: vince Date: Fri Jul 8 17:47:36 2016 -0700 copy more vars for comp resize. Src/C_AMRLib/Amr.cpp commit a79be09935b32be56c6fde68886ee763b552af24 Author: Weiqun Zhang Date: Fri Jul 8 17:17:30 2016 -0700 IBM compiler does not like 'using FabArray::setVal' because FabArray is templated. Src/C_AMRLib/TagBox.H commit a116d261e1c2c39348ec026de7aa972070cbd597 Author: Marc Day Date: Fri Jul 8 15:59:11 2016 -0700 Copy autogen files into repo as well...a bad idea that these were added in the first place... Src/Python/boxlib/bl1.py Src/Python/boxlib/bl2.py Src/Python/boxlib/bl3.py Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id commit 64b5350f74346749fc507cc7453f352f5ab5b95e Author: Marc Day Date: Fri Jul 8 15:55:46 2016 -0700 Remove interface to mf->fab function from swig i file Src/Python/swig/boxlib.i commit ceaa7dbe83dea3d32101e14f75e6eba1931896f8 Merge: c2d5e9090 4f366a1e8 Author: Michael Zingale Date: Fri Jul 8 18:37:18 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit fbf09d2389f3ec25460e2b8636eb2c01ad6cf842 Author: vince Date: Fri Jul 8 15:23:54 2016 -0700 some changes for sidecars and teams. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit f005a4654b5a5c09f8440c66821095f5260649d7 Author: vince Date: Fri Jul 8 15:21:12 2016 -0700 remove test output. Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit ff870b9ecf3cb8a827d72cebbaac5a79163267df Author: vince Date: Fri Jul 8 15:20:28 2016 -0700 option to print unique set. Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 4f366a1e8adca1f6b4dbd8384d6d0c0adcfd6360 Author: vince Date: Fri Jul 8 13:31:12 2016 -0700 added serial initializations. Src/C_BaseLib/ParallelDescriptor.cpp commit a9b53226adc108deb1930bf8e782b06a565520b0 Merge: 19e9b5993 5d9d854a5 Author: Michael Zingale Date: Fri Jul 8 10:40:13 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 19e9b59932d2ffcb9da8a93e8d5d0e77e01da06b Author: Michael Zingale Date: Fri Jul 8 10:38:45 2016 -0400 don't process _parameters until we ask for a net or eos Tools/Postprocessing/F_Src/GNUmakefile commit 5d9d854a5a5d82248b7e7a490462b24313e6d76c Author: Weiqun Zhang Date: Fri Jul 8 07:35:08 2016 -0700 fix make Tools/Postprocessing/F_Src/GNUmakefile commit 2b1e20486dae3f2eb8fbdf776b59a63e620e5697 Author: Weiqun Zhang Date: Fri Jul 8 07:22:24 2016 -0700 fixed a typo Tools/F_mk/GMakedefs.mak commit c977f137a8cbc62b749bbe37e3bb0459a32c3317 Author: Weiqun Zhang Date: Thu Jul 7 16:13:41 2016 -0700 add F_mk/Readme and some minor tweaks Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_mk/Readme commit 5aebced28e910b96ecc71eab6c0cdc4942e1025e Author: Weiqun Zhang Date: Thu Jul 7 12:13:56 2016 -0700 Make: -include Make.local allowing users to reset variables; add ccache and f90cache to speed up compilation Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/F_mk/GMakedefs.mak commit e5c2586179e00a9164a03a68b15426e4b7826681 Merge: 998e6153a 27acb1c23 Author: Michael Zingale Date: Wed Jul 6 22:09:35 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 998e6153afe58a243b44c29a638159a7b11de580 Author: Michael Zingale Date: Wed Jul 6 22:09:11 2016 -0400 split stdout/err and save stderr from the run, if present Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit c2d5e90908eaa0d841ae9624b5b84caa0569405e Merge: 66b6b4326 27acb1c23 Author: Michael Zingale Date: Wed Jul 6 18:45:49 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 27acb1c235718ce05a6f7e9e91790e04833a1399 Author: Michael Zingale Date: Wed Jul 6 16:45:56 2016 -0400 copy -> move for executable Tools/RegressionTesting/regtest.py commit 09beea8211ad90c9454161139a6ecbb6f802986e Author: Michael Zingale Date: Wed Jul 6 09:57:45 2016 -0400 clean-up memory to quiet memory sanitizer Tools/Postprocessing/F_Src/fcompare.f90 commit 66b6b4326854bfc478d4ca8a382a6d18bfded99e Merge: d9d9d208f 41f180385 Author: Michael Zingale Date: Tue Jul 5 18:48:33 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit d9d9d208f209d8fea4f2394b3e9e30de2514ef3c Author: Michael Zingale Date: Tue Jul 5 18:48:24 2016 -0400 remove trailing blanks Tools/RegressionTesting/suite.py commit 41f18038583cc6c1779728ab83e820bb8583f500 Author: Michael Zingale Date: Tue Jul 5 13:52:26 2016 -0400 add a warning if we are running on a non-default branch Tools/RegressionTesting/regtest.py commit 50248a43a0e8971344e5b292d373a54aea27c41b Author: Weiqun Zhang Date: Tue Jul 5 07:00:43 2016 -0700 Release Notes 16.07 ReleaseNotes/release-notes-16.07 commit 5176359566ae51b52926682e0ae8a969c3dae6f0 Merge: d975c9b24 67df9e613 Author: Weiqun Zhang Date: Tue Jul 5 06:59:44 2016 -0700 Merge branch 'development' commit 67df9e613a7403df7e879122259a73a7aef0aee8 Author: Michael Zingale Date: Mon Jul 4 21:56:37 2016 -0400 add an indicator if we are running on a non-default branch + bug fix now we add an '*' next to the date on the master page if any of the git repos are not on "suite.default_branch". This helps delineate the normal tests from those we run occassionally on feature branches. Also fix a crash if we ran with only self-tests (no output file is ever defined) Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit 2f5bfbf7bb0b97effcc0b4bc8fadc2e2b1f304d2 Author: Michael Zingale Date: Mon Jul 4 13:05:02 2016 -0400 remove legacy comma warning Tools/Postprocessing/F_Src/fcompare.f90 commit 5a46b3f376822177f6e3c9f608cbba7c2b292974 Author: Michael Zingale Date: Mon Jul 4 12:51:25 2016 -0400 fcompare no longer needs --infile1/2 Tools/RegressionTesting/regtest.py commit 9e202fcb36e2113176ba047e60b25b3b53c62918 Author: Weiqun Zhang Date: Tue Jun 28 21:44:56 2016 -0700 Only test skewed for the current level Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 commit a7e81bdc1bafcfc30c7d6a336f3a54539b9d143f Author: Weiqun Zhang Date: Tue Jun 28 14:09:09 2016 -0700 Turn off tiling for skewed stencil Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 commit e33ded935a32211dfc05df536a0235c72dd80d65 Author: Weiqun Zhang Date: Tue Jun 28 11:04:42 2016 -0700 function to turn on fpe trapping in Fortran BoxLib Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 commit d5ce692a406ce5da64b862f22f439f1645a50463 Author: Weiqun Zhang Date: Tue Jun 28 10:51:07 2016 -0700 indentation Tutorials/Tiling_Heat_F/advance.f90 commit 57776ec86d9e60940a8a766f710cda6ab46c1869 Merge: 922a2af85 f50fb564e Author: Michael Zingale Date: Tue Jun 28 14:02:53 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 922a2af85a0f75219ef5d4d596e71180af98bd5c Author: Michael Zingale Date: Tue Jun 28 14:02:40 2016 -0400 latest version Tools/RegressionTesting/Maestro-tests.ini commit f50fb564ed2f4eb88d85e78947a65e4b58383901 Author: Michael Zingale Date: Tue Jun 28 14:00:45 2016 -0400 latest version Tools/RegressionTesting/Castro-SBU-tests.ini commit c69903ea01d329f6dcd4d444f47f9b9e609d5f9c Author: Weiqun Zhang Date: Mon Jun 27 19:29:06 2016 -0400 removed my accidental changes in makefile Tools/C_mk/Make.mpi commit a575b1b933d528acf69cd57cd21a28eda84c6331 Author: Michael Zingale Date: Mon Jun 27 19:28:10 2016 -0400 fix typo Tools/RegressionTesting/suite.py commit 1e62439b37e07eb322db5793b99659cdc43b582a Author: Weiqun Zhang Date: Mon Jun 27 19:13:53 2016 -0400 use subroutine instead of function to get around a gcc 6.1.1 bug Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 Tools/C_mk/Make.mpi commit bf6ea460193dd4961d4c03246fbd3a1c3104682c Author: Michael Zingale Date: Mon Jun 27 15:46:09 2016 -0400 remove some debug prints Tools/F_scripts/write_probin.py commit ee2eab864dac38654137fcf7a85a0e5311ace36d Author: Michael Zingale Date: Mon Jun 27 15:40:48 2016 -0400 sanitize apostrophes in the slack Tools/RegressionTesting/suite.py commit a1706641f1962c30ec062e877f10dbf1aaf20dd6 Merge: 9a4c92f64 1896a06f0 Author: Michael Zingale Date: Mon Jun 27 15:39:04 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 9a4c92f643de4bdbd87db4d3eeadaf57413c4be3 Author: Michael Zingale Date: Mon Jun 27 15:38:54 2016 -0400 add future Tools/RegressionTesting/suite.py commit 1896a06f03798d05a76028ebc8dcb9acd8dce4e1 Author: Weiqun Zhang Date: Mon Jun 27 11:24:06 2016 -0700 missed omp end parallel Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 commit a81c1319d28b9b1e57168361109c9a349edded63 Author: Weiqun Zhang Date: Mon Jun 27 11:18:50 2016 -0700 turn off tiling for 1d and 2d because they are not ready; fix MS_SMOOTHER_EFF_RB Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 commit 599a72f719b760b082591fe406e99c0759b037e7 Author: Weiqun Zhang Date: Mon Jun 27 11:10:26 2016 -0700 turn off tiling for 1d, 2d and nodal because they are not ready Src/LinearSolvers/F_MG/mg.f90 commit 4df3d5abf31e3226cbc029760517759a1389bbc0 Author: Michael Zingale Date: Mon Jun 27 10:01:26 2016 -0400 using std::isinf for __GNUC__ >= 6 Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 3df3891af93548eedf34ba7e4529df7a4fd70539 Merge: ea0e54dfc 03087b72c Author: Brian Friesen Date: Sun Jun 26 17:10:15 2016 -0700 Merge branch 'fix_tiled_CC_F_MG_2D' into development commit ea0e54dfc4bdbb963d709bdd8acd06aa78640738 Author: Brian Friesen Date: Sun Jun 26 11:56:32 2016 -0700 C_BaseLib: make Box::isSquare() always return false in 1-D Src/C_BaseLib/Box.cpp commit 03087b72c3b364b3b5d2f7e470d56005653ea0cf Author: Brian Friesen Date: Sun Jun 26 12:01:24 2016 -0700 F_MG: set dim of tile box indicies "tlo" and "thi" to mgt%dim In commit 59ab377 ("F_MG: tile the cell-centered restriction") I hard-coded the dimension of tlo and thi to 3, anticipating that tiling will only benefit 3-D problems and not so much 2-D. However this breaks 2-D problems which need to use Fortran multigrid, so instead we set the dim of tlo and thi to whatever dim is set to in the mgt object. Src/LinearSolvers/F_MG/mg.f90 commit febaf8efab78f3f311d10d839b3dd1afa33d5264 Author: Michael Zingale Date: Sun Jun 26 10:12:40 2016 -0400 got g++ 6.1, we need use std::isnan and std::isinf Src/C_BaseLib/FArrayBox.cpp commit 370db4549cd018832c7e093082e50f5f529ed316 Merge: b70dd38fa c5c5312c4 Author: Andy Nonaka Date: Fri Jun 24 16:47:38 2016 -0700 Merge branch 'weiqun/random' into development commit c5c5312c486fa42a331e6dfeb7ad4519805fa6ad Author: Weiqun Zhang Date: Fri Jun 24 16:34:26 2016 -0700 fix pmask in ml_layout Src/F_BaseLib/ml_layout.f90 commit b70dd38faa4758ee54d3b2ad40df485fb9a827b1 Author: Brian Friesen Date: Fri Jun 24 14:55:39 2016 -0700 F_MG: add line wraps to long OpenMP directive The Cray compiler quits when encountering OpenMP directives with line lengths with > 128 characters. Src/LinearSolvers/F_MG/mg.f90 commit e834d18786d81ca206a1943fcd3540c4106f4e7a Author: Weiqun Zhang Date: Fri Jun 24 14:30:15 2016 -0700 Fortran random: in restore, destroy first if the ptr is already associated. Src/F_BaseLib/bl_random_f.f90 commit 58c6d2dad696021971bd82cc73a1645d2b3df1ce Author: Weiqun Zhang Date: Fri Jun 24 13:39:38 2016 -0700 add initialization flag to IArrayBox.cpp Src/C_BaseLib/IArrayBox.cpp commit 495a0275459322abb81a2f76e7829633adaa5618 Merge: 7b3d70d36 59e72db9f Author: Brian Friesen Date: Fri Jun 24 10:55:47 2016 -0700 Merge branch 'tile_MultiGrid_C_tutorial' into development These commits add tiling to setup_rhs() and setup_coeffs() in the MultiGrid_C tutorial. These are just initialization routines specific to this tutorial and thus the speedup from these commits does not benefit any other BoxLib code. commit 7b3d70d36424c7d517e38fee50ca0c448a7a2d73 Merge: cf971954d 06e1efb38 Author: Brian Friesen Date: Fri Jun 24 10:52:01 2016 -0700 Merge branch 'tile_CC_F_MG' into development These commits add OpenMP tiling to the cell-centered GSRB smooths and restrictions in F_MG. The prolongation is not as simple as replacing the nfabs() loop with a next_tile() loop so that will be done in a different series of commits. Using the MultiGrid_C tutorial with a 512^3 grid decomposed into 8 256^3 boxes, these changes yield a roughly 8% speedup on both Ivy Bridge (using 2 MPI x 12 OpenMP) and pre-production Knights Landing (using 1 MPI x 64 OpenMP). commit 06e1efb38bf9db5c9a853962f8f1fe200daa03b7 Author: Brian Friesen Date: Thu Jun 23 22:34:47 2016 -0700 F_MG: tile the cell-centered restriction Src/F_BaseLib/cc_restriction.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/LinearSolvers/F_MG/mg.f90 commit 3449e68be4e1e9e7c5d2301564f0043b5827979e Author: Brian Friesen Date: Thu Jun 23 22:32:32 2016 -0700 F_MG: tile the cell-centered GSRB smoothers Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 commit cf971954d51d9e2f64fed8b782dc7deffc022ad7 Author: Max Katz Date: Thu Jun 23 21:50:15 2016 -0400 Add dimension agnostic version of BL_FORT_IFAB_ARG Src/C_BaseLib/BLFort.H commit 59e72db9fcd69af01682686d6066989fb80ec203 Author: Brian Friesen Date: Wed Jun 22 17:23:46 2016 -0700 Tutorials: tile setup_rhs() in MultiGrid_C Tutorials/MultiGrid_C/main.cpp commit 10e9f5929f2761e195816b5afecda6a7f73332d2 Author: Brian Friesen Date: Wed Jun 22 17:22:40 2016 -0700 Tutorials: tile setup_coeffs() in MultiGrid_C Tutorials/MultiGrid_C/main.cpp commit 2af8c8ad5f8bed0a2cc7fd93f3c54e7ce972a17f Author: vince Date: Wed Jun 22 14:34:51 2016 -0700 fixes for merge. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit 7217dc28864b2d95d608c0051b3908dc52a32d40 Merge: 27fd748f3 b874f10fc Author: vince Date: Wed Jun 22 14:15:09 2016 -0700 fixed merge conflicts. commit 5f26211bca2dfe1417c9e6954e4abe9bacf4199f Author: Weiqun Zhang Date: Wed Jun 22 13:24:18 2016 -0700 Fortran random: consistent names Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit 635abc30a74c8d5834f59db4463d5818a4b0fb21 Author: Weiqun Zhang Date: Wed Jun 22 12:13:13 2016 -0700 Fortran random: minor cleanup Src/F_BaseLib/bl_random_c.cpp commit ca0877e908a22f79abedb3965279813e552b73fb Author: Weiqun Zhang Date: Wed Jun 22 11:05:16 2016 -0700 Fortran random: refactor Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp commit 6916538e8c9e4e3a2454a83afa3b9ff3f2264dc8 Author: Weiqun Zhang Date: Wed Jun 22 07:36:24 2016 -0700 Fortran random: template save and restore Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp commit c28104f21c5d558b1b34f7ad6cd4c21cb42e7283 Author: Weiqun Zhang Date: Wed Jun 22 06:55:19 2016 -0700 Fortran random: minor Src/F_BaseLib/bl_random_c.H commit b874f10fc1ed9744e410b8a1e13b85932049ce99 Author: Michael Zingale Date: Tue Jun 21 22:46:54 2016 -0400 fix the zone_info functionality we were not resetting the current zone error Tools/Postprocessing/F_Src/fcompare.f90 commit dce720e6482d4d524088bcffe42c4779999edd87 Author: Michael Zingale Date: Tue Jun 21 22:25:54 2016 -0400 remove "use f2kcli" -- our compilers support the F2003 command line stuff that module was a compatibilty-layer module for codes before Fortran 2003 was commonplace Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsource.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/frhdshocktube.f90 Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fgaussianpulse.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlcompare.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlconverge.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fnorm.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fad_excess.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fconv_slopes.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/frates.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspec_total_mass.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspeciesmass.f90 Tools/Postprocessing/F_Src/faverage.f90 Tools/Postprocessing/F_Src/fboxinfo.f90 Tools/Postprocessing/F_Src/fcoarsen.f90 Tools/Postprocessing/F_Src/fcompare.f90 Tools/Postprocessing/F_Src/fdumpdata2d.f90 Tools/Postprocessing/F_Src/fextract.f90 Tools/Postprocessing/F_Src/fextrema.f90 Tools/Postprocessing/F_Src/ffdcompare.f90 Tools/Postprocessing/F_Src/fintgvar2d.f90 Tools/Postprocessing/F_Src/fsnapshot2d.f90 Tools/Postprocessing/F_Src/fsnapshot3d.f90 Tools/Postprocessing/F_Src/ftime.f90 Tools/Postprocessing/F_Src/fvarnames.f90 Tools/Postprocessing/F_Src/old_flame/fbubble_position.f90 Tools/Postprocessing/F_Src/old_flame/fbubble_position_3d.f90 Tools/Postprocessing/F_Src/old_flame/fcusp.f90 Tools/Postprocessing/F_Src/old_flame/fcylflame.f90 Tools/Postprocessing/F_Src/old_flame/fflamelength.f90 Tools/Postprocessing/F_Src/old_flame/finteg.f90 Tools/Postprocessing/F_Src/old_flame/fturbkin.f90 Tools/Postprocessing/F_Src/old_flame/fwidth.f90 Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90 Tools/Postprocessing/F_Src/tutorial/fwrite2d.f90 commit f5fea3b1d04273fb0ea232b11cde3deee4aa3508 Author: Weiqun Zhang Date: Tue Jun 21 15:53:46 2016 -0700 Fortran random: clean up Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp commit 6e8a29b09cc6574e4b0698c4c34de2f9771c58cb Author: Weiqun Zhang Date: Tue Jun 21 15:41:58 2016 -0700 Fortran random: update tutorial Tutorials/Random_F/main.f90 commit e373d15a9f28d02677fc2998323dd3d8c3f65391 Author: Weiqun Zhang Date: Tue Jun 21 15:40:05 2016 -0700 Fortran random: remove change_distribution Src/F_BaseLib/bl_random_f.f90 commit 0965ad5f880aba1cfb49e2b4d1bc58dd7ad8a4ce Author: Weiqun Zhang Date: Tue Jun 21 15:32:21 2016 -0700 Fortran random: separate engine from distribution just like C++ standard Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit 27fd748f3a74d6d435980ae70244da396d931cde Author: vince Date: Tue Jun 21 13:57:18 2016 -0700 add new test to makefile. Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/Make.package commit 25310bc471cc3b4999f7eb93b6a85a02e62d3477 Author: Michael Zingale Date: Tue Jun 21 16:41:39 2016 -0400 remove debug print Tools/F_scripts/write_probin.py commit 95b0faf8f1898ce06603ad16f5aa79eea29c30aa Author: Michael Zingale Date: Tue Jun 21 16:40:32 2016 -0400 fix priorities Tools/F_scripts/write_probin.py commit 558017cc88efb0cff9aca1038fdbbad3a92729c0 Author: Michael Zingale Date: Tue Jun 21 12:58:44 2016 -0400 add some help Tools/F_scripts/findparams.py commit 5499ea061248be39d996bbe0d3bd9650d6229159 Author: Michael Zingale Date: Mon Jun 20 21:38:46 2016 -0400 some cleaning -- no change in functionality Tools/F_scripts/write_probin.py commit 37eb0206073a53e68136b6e1f9ac15f1e83f1c80 Author: Weiqun Zhang Date: Mon Jun 20 14:35:44 2016 -0700 remove extra MultiFabUtil.H and .cpp. Src/C_BaseLib/Make.package commit 5e122194f4045ecb18f18d20fcd32d45ecadbae0 Author: Weiqun Zhang Date: Mon Jun 20 13:40:26 2016 -0700 FabArrayBase::FPC --> FabArrayBase::FPinfo to avoid confusion with class FPC Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d2223259d0e3f46d8ac951418596a63926eb42e5 Merge: efc4e29b2 0ba5886de Author: Michael Zingale Date: Mon Jun 20 18:58:41 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit efc4e29b2a5a8eb7444dac31d187b2f2b11ce645 Author: Michael Zingale Date: Mon Jun 20 18:57:47 2016 -0400 add the ability to inspect the zone where the largest error (for a given variable) is set Tools/Postprocessing/F_Src/fcompare.f90 commit 44604c533d3b615abfe69b8c5e82f962ffd26f22 Author: vince Date: Mon Jun 20 15:30:10 2016 -0700 add check for ranks moving both from and to comp during sidecar resize. this is currently disallowed. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp commit d975c9b241e08760771e0867cdba1afc94559351 Author: Weiqun Zhang Date: Mon Jun 20 14:35:44 2016 -0700 remove extra MultiFabUtil.H and .cpp. Src/C_BaseLib/Make.package commit 0ba5886de5ed733f9c3deb0f95e31c7b96ed34da Merge: ca3cbb644 ee6aa25a0 Author: Michael Zingale Date: Sat Jun 18 16:20:19 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit ca3cbb644603395a66a917eeb923b375823f3192 Author: Michael Zingale Date: Sat Jun 18 16:20:02 2016 -0400 only consider the base name of the aux files when copying Tools/RegressionTesting/regtest.py commit ee6aa25a085b6dc07976359063c65dd6a738aba0 Author: Weiqun Zhang Date: Thu Jun 16 15:15:45 2016 -0700 GCC option for fsantizer Tools/F_mk/comps/gfortran.mak commit 7836266d70e05004152e4372265dbc9e68f9433e Author: Weiqun Zhang Date: Thu Jun 16 15:15:12 2016 -0700 Fortran BoxLib: respect do_init_fabs parameter Src/F_BaseLib/fab.f90 commit 575d22c038041f09c8962454ea6e8897dbb12afe Author: vince Date: Thu Jun 16 14:12:15 2016 -0700 added file to test resizing sidecars with disallowed rank sets. Tutorials/Sidecar_EX1/TestRankSets.cpp commit 32f55632ba6f10a7289b7c5b3cc2c48caae8247d Author: vince Date: Thu Jun 16 12:29:19 2016 -0700 random sidecar ranks test. Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit fb1041e9e06d33939cfcc0747534b1d23ee5132a Author: vince Date: Thu Jun 16 12:26:56 2016 -0700 clarified comments. Src/C_BaseLib/Utility.H commit 7423e78268790314060294e52657186103440187 Author: Michael Zingale Date: Wed Jun 15 19:52:16 2016 -0400 this scripts are obsolete things should be switched over to to the python version, makebuildinfo.py See Maestro's GMakestro.mak and the rule for build_info.py for an example of using that. Tools/F_scripts/make_build_info Tools/F_scripts/make_build_info2 commit fa74cc7ffaeae809a185c0561f39b6664c9a90fd Author: Michael Zingale Date: Wed Jun 15 19:51:46 2016 -0400 clean this up and switch to argparse this now requires python 2.7 or later Tools/F_scripts/makebuildinfo.py commit 57448b122d08df477237dcf0479b26aaed1fdda9 Author: Michael Zingale Date: Wed Jun 15 10:58:51 2016 -0400 port the job_info_field3 stuff over from this point forward, new features will only go into regtest.py and co, testnew.py will not be updated with new features Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit 41682fa34d0447660366943f77dff08b48886fe1 Merge: 291c76e93 a6e7aa4d6 Author: Michael Zingale Date: Wed Jun 15 10:37:30 2016 -0400 Merge branch 'master' into development commit 291c76e93edc04c02fb704acfed7842233dc6555 Author: Andy Nonaka Date: Mon Jun 13 16:36:14 2016 -0700 if generating a random seed, print out the seed Src/F_BaseLib/bl_random_f.f90 commit f6618caee69ea1e717189e5e0fae3e67d2b41ae1 Author: Andy Nonaka Date: Mon Jun 13 15:18:00 2016 -0700 seed verbosity Src/F_BaseLib/bl_random_f.f90 commit 062fb7c01c42e8b01b6c8a87fc3662d1583845b1 Merge: ac92fa0fd 47be9e054 Author: Andy Nonaka Date: Mon Jun 13 14:04:49 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit ac92fa0fd61828bd1a72d7e9e0442232c05447d5 Author: Andy Nonaka Date: Mon Jun 13 14:04:32 2016 -0700 print out the random seed info Src/F_BaseLib/bl_random_f.f90 commit 47be9e0545183e93bd7c778253e804bb9cb1b152 Author: Ann Almgren Date: Mon Jun 13 13:07:26 2016 -0700 Fix spelling in comment. Tutorials/PIC_C/solve_with_f90.cpp commit a6e7aa4d64b2b0e1126c9468f8ec360eae0d61d9 Author: Michael Zingale Date: Mon Jun 13 16:01:05 2016 -0400 add 3rd job_info field + allow for bigger name length in tables Tools/RegressionTesting/testnew.py commit 2aa52b1b303fe30169d4bf028d3d5f8dcc1f6b5a Author: Weiqun Zhang Date: Mon Jun 13 10:55:05 2016 -0700 OpenMP is very picky. Have to use it < end() instead of the idomatic it != end() as the for loop predicate. Src/C_BaseLib/Particles.H commit d6a86a5991e92fc3cabfd724d5d309172091e232 Merge: 7e552ef3f ca636444e Author: Andy Nonaka Date: Mon Jun 13 10:37:16 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 7e552ef3f3fba4842443452f98318d60b4fde465 Author: Andy Nonaka Date: Mon Jun 13 10:35:56 2016 -0700 mpi settings for laptop Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit ca636444e485c3356395a9801e5c87d2f54ddaa7 Author: Michael Zingale Date: Mon Jun 13 13:31:09 2016 -0400 saner default -- for 1 plotfile, give each var its own line Tools/Postprocessing/F_Src/fextrema.f90 commit 47722fdee3b6e91d8e3de44fe256c61d0cbec339 Author: Michael Zingale Date: Mon Jun 13 09:13:30 2016 -0400 add integrator Tools/F_scripts/makebuildinfo.py commit bbdd424b3748bc8ab94e306a67a6365bb5175af5 Author: Max Katz Date: Sat Jun 11 23:35:19 2016 -0400 Add Cray compiler version variables to C_mk Tools/C_mk/Make.Linux commit c57e7b420101f312d51ec1de1615dda3a75cf69d Author: Michael Zingale Date: Sat Jun 11 16:45:43 2016 -0400 the stub version of parallel_tag needs reset Src/F_BaseLib/parallel_stubs.f90 commit 7db522defa12fc8a7d6cdcff1b4287e719b5b80e Author: Max Katz Date: Sat Jun 11 11:38:33 2016 -0400 Permit disabling of forced plotfile on checkpoint Presently the code writes a plotfile when we force a checkpoint with the dump_and_stop or dump_and_continue capability. We can now disable this behavior by setting amr.write_plotfile_with_checkpoint = 0. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit f55ace29319a65f1715a64f7524172a6a606f0bc Author: Weiqun Zhang Date: Fri Jun 10 16:45:02 2016 -0700 Fortran BoxLib: reset mpi tag after fancy bottom solve Src/F_BaseLib/parallel.f90 Src/LinearSolvers/F_MG/mg.f90 commit 8ee7b179236913cec2dbd478c9e3672ee07f4752 Author: vince Date: Fri Jun 10 12:21:13 2016 -0700 new mpi location for naphta. Tools/C_mk/Make.mpi commit 09c2f644a0483c6497d53ed4dffe80c67e50f7d3 Author: vince Date: Fri Jun 10 12:19:07 2016 -0700 more testing of multiple sidecars. Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit 865abcb54ba22c92339d773d119a5e0fba5dab72 Author: vince Date: Fri Jun 10 12:18:20 2016 -0700 added commBoth, removed default whichSidecar. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 6f9b83efbb0aa52815325b64c2a81ea2be156a61 Author: vince Date: Fri Jun 10 12:11:46 2016 -0700 more documentation. Docs/Readme.sidecars commit e3770d3a1ef8a73e0f6bc76c9e43672e6a9da402 Author: vince Date: Fri Jun 10 11:39:25 2016 -0700 add copyInter support for multiple sidecars. Src/C_BaseLib/FabArray.H commit 2d3d113c24d000254b03c9af06969fb95d23ac7f Merge: bd8cf0336 18a6f6353 Author: Brian Friesen Date: Fri Jun 10 09:26:59 2016 -0700 Merge branch 'particle_threading' into development These commits slightly change the way OpenMP parallelizes over particles to improve thread scaling when using a small number of boxes with a large number of threads per MPI process. commit 18a6f63530dbda4d7a18e1b5893adb7f5ed9f8ef Author: Brian Friesen Date: Fri Jun 10 09:12:52 2016 -0700 ParticleContainer: add TODO about tiling over grid loop in AssignCellDensitySingleLevel() Src/C_BaseLib/Particles.H commit d533b9885a697b222c3aca07f23f101cf1e63750 Author: Brian Friesen Date: Fri Jun 10 09:11:36 2016 -0700 ParticleContainer: add comment suffix to #endif for NEUTRINO_PARTICLES for clarity Src/C_BaseLib/Particles.H commit 864f23c237e467f17536b1063aa826e56f894af6 Author: Brian Friesen Date: Thu Jun 9 18:37:21 2016 -0700 ParticleContainer: move OpenMP parallel region from grid loop to PBox loop in AssignCellDensitySingleLevel() If the OpenMP region parallelizes over grids, and if we have a small number of large grids and a large number of OpenMP threads (which is the typical Nyx use case), then this routine scales extremely poorly. So instead we parallelize threads over PBoxes within each grid, which leads to much better thread scaling. Src/C_BaseLib/Particles.H commit 4225a1539fbc41c09495aa6680e1466a3036bbb0 Author: vince Date: Thu Jun 9 16:34:01 2016 -0700 update for multiple sidecars. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 2dcff9ff20712f7674ac3ab10ca67fad31f6728b Author: vince Date: Thu Jun 9 16:33:34 2016 -0700 update for multiple sidecars. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 2231b5073fb51340cfaae5fc63f502e690bca375 Author: vince Date: Thu Jun 9 16:03:29 2016 -0700 remove send to sidecar function. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit e1ad1a19cb3e8d229d957172c99ae884d96b9a30 Author: vince Date: Thu Jun 9 15:56:34 2016 -0700 remove SendMultiFabToSidecars function, use FabArray::copyInter instead. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit bd8cf03364268d971b3a4275674d16f22c93d225 Merge: 2fa49bc30 49dc5dcaa Author: Adam M. Jacobs Date: Thu Jun 9 18:13:14 2016 -0400 Merge upsteam 'development' into Adam's local 'development' commit 2fa49bc30e13e4b458c9c12fddc8d993cb6e8f0b Author: Adam M. Jacobs Date: Thu Jun 9 18:09:00 2016 -0400 Add a comment to particle_where noting it sets particle properties. I found this to be quite unexpected, so I wanted to document in the code that particle_where doesn't just indicate a particle's position is valid within the grid heirarchy but also sets a found particle's level, grid, and cell properties. Src/F_BaseLib/particles_f.f90 commit 7ce049c8d637ea1e12f08ebc98dc10b3a6acef52 Author: vince Date: Wed Jun 8 13:44:37 2016 -0700 include both local and global ranks in filename. Src/C_BaseLib/BLBackTrace.cpp commit 358810991db833b0dce1d42cc379a3537c8ce94c Author: vince Date: Tue Jun 7 16:47:54 2016 -0700 started documenting the sidecars. Docs/Readme.sidecars commit 49dc5dcaa1a625fae52739f176df482df7656a19 Author: Ann Almgren Date: Tue Jun 7 16:30:29 2016 -0700 Put in error statement if we try to call create_umac_grown with factor 4 refinement since we don't currently support that Src/F_BaseLib/create_umac_grown.f90 commit 7e810b7f5c3e3d64e88169ad7d62b72293582b72 Merge: de1bf457d 11de56b7f Author: Ann Almgren Date: Tue Jun 7 15:08:43 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit de1bf457d7d0c943cb22545a5841dac6d9ace52d Author: Ann Almgren Date: Tue Jun 7 15:08:27 2016 -0700 Oops -- was printing the wrong times in my print statement! Tutorials/PIC_C/single_level.cpp commit 11de56b7f28d01c7b6d08ade45728edc98c4a0a1 Merge: 430ad9eab 635d53bab Author: Michael Zingale Date: Tue Jun 7 14:24:29 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 430ad9eab276a5afe5e08b8432603ec4e156082e Author: Michael Zingale Date: Tue Jun 7 14:23:23 2016 -0400 add a module flexibilty way of specifying build components now you can use --module to send in key=value for the different components, e.g., as: "EOS=helmeos NETWORK=triple_alpha" and get them through the module name and value functions Tools/C_scripts/buildInfo.H Tools/C_scripts/makebuildinfo_C.py commit 635d53bab94d3e349b477d0a1f60913a469782f3 Author: Weiqun Zhang Date: Mon Jun 6 21:24:40 2016 -0700 make sure mpi tags in Fortran and C++ do not overlap Src/F_BaseLib/parallel.f90 commit 6ae39b1cbba98b26e31e69709d454035f81a9708 Author: Weiqun Zhang Date: Mon Jun 6 17:06:04 2016 -0700 Fortran BoxLib: add a function that returns mpi tag just like C++ BoxLib; don't call mpi_wait unless the size mpi statuses is greater than 0 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 1959ba3515fcc837ee7be144a949ff4a06e8b703 Author: vince Date: Mon Jun 6 17:04:24 2016 -0700 write proc number to abort message. Src/C_BaseLib/BoxLib.cpp commit 99e591e3af14891118b14cfbec67e378e137e206 Author: vince Date: Mon Jun 6 15:33:51 2016 -0700 write proc number to abort message. Src/C_BaseLib/BoxLib.cpp commit df8d49d1ea3b73038eb66ec7c64992b8a29f3273 Author: Weiqun Zhang Date: Sat Jun 4 13:34:06 2016 -0700 Release Notes 16.06 ReleaseNotes/release-notes-16.06 commit a22746e2d58fe747fee2a1d7c4db3674d569e9ff Merge: e2d57c490 aa91fe863 Author: Weiqun Zhang Date: Sat Jun 4 12:54:54 2016 -0700 Merge branch 'development' Conflicts: Tools/C_mk/Make.defs commit aa91fe863d1926941b2702a74b42f10941a3811c Author: Michael Zingale Date: Fri Jun 3 21:00:31 2016 -0400 remove ALCF intrepid and all bits of Intel < 13 Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 40cadff396baaea8f7d031744172be0f9b342084 Author: Michael Zingale Date: Fri Jun 3 20:24:37 2016 -0400 remove OSF1 and Intel 11,12 support -- they're old Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/osf1.mak commit 9e68577ebeb1a0728e08eaacab8fd7d549486f7f Author: Michael Zingale Date: Fri Jun 3 16:26:37 2016 -0700 define intel versions so they appear in job_info Tools/C_mk/Make.defs commit 0a966798c78ec96d0c73383d5567c1a811ad0345 Author: Weiqun Zhang Date: Thu Jun 2 22:17:50 2016 -0700 PIC_C: fix memory leak Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/two_level.cpp commit 07d0da75ee0113e51f236f294e83bfa7c8435acf Author: Ann Almgren Date: Thu Jun 2 18:31:07 2016 -0700 This verison of PIC_C is designed for doing timing studies. There is also now an inputs file rather than hard-wiring the size of the problem into main.cpp Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/README Tutorials/PIC_C/inputs Tutorials/PIC_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp commit 0ab81b7c8f10e2c9d75cb9ee2080a4220eb996ca Author: Weiqun Zhang Date: Thu Jun 2 09:50:58 2016 -0700 Make: option to use fsanitizer for debug build too Tools/C_mk/Make.defs commit efb2ac48ac758eb23d42ee4a9e3d16c4c9a2638f Author: Michael Zingale Date: Wed Jun 1 22:39:35 2016 -0400 some cleaning Tools/RegressionTesting/test_report.py commit b068d158ec9a49e6e7e69c215365eaa8732d455b Author: Michael Zingale Date: Wed Jun 1 22:39:27 2016 -0400 simplify run() Tools/RegressionTesting/test_util.py commit 688bf010224d985411e8f0b1ad7aacb543c9a26d Author: Michael Zingale Date: Wed Jun 1 21:09:53 2016 -0400 clean up the warnings Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit 5fe08a729c75c362b66c97386eb3fa249f179144 Author: Michael Zingale Date: Wed Jun 1 20:33:31 2016 -0400 a little more clean-up Tools/RegressionTesting/regtest.py commit bcb607e70de2f211080aeaa31f56e666100684c2 Author: Michael Zingale Date: Wed Jun 1 19:47:31 2016 -0400 more refactoring Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit 0f062c84ebdd442365d6f88b90ec37253f11ece1 Author: Michael Zingale Date: Wed Jun 1 15:19:11 2016 -0400 start of some refactoring split up the main test suite into separate files to make it easier to maintain. regtest.py is now the entrypoint. Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/repo.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit e707f9246dcb05b376665225c990a4df59eb41eb Author: Weiqun Zhang Date: Tue May 31 10:55:16 2016 -0700 Fortran bl_random: use 0 as a special flag for using random device to generate a seed Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 commit 04f68f9dc5bb7a7c818e32fdd495dc5d68ab2998 Author: Michael Zingale Date: Tue May 31 12:34:43 2016 -0400 need to rename job_info when copying to the web dir this prevents job_info from being overwritten by the next test Tools/RegressionTesting/testnew.py commit a8e385293e0381c8110be1ad3ae7beb66d2316d8 Merge: 0106641af c9b620ff0 Author: Michael Zingale Date: Tue May 31 12:29:41 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit c9b620ff03ab4335623cda458a9b3d0e43e33454 Author: Weiqun Zhang Date: Mon May 30 20:44:45 2016 -0700 MultiColor_C: minor Tutorials/MultiColor_C/main.cpp commit 7d9f9450b154f54048bbd2c4b4da61a309dfc8f0 Author: Weiqun Zhang Date: Mon May 30 18:10:12 2016 -0700 MultiColor_C test: add a ne fortran file Tutorials/MultiColor_C/ff.f90 commit 3a988c180de88aa3605e60789c92cc2ce6a28d0b Author: Weiqun Zhang Date: Mon May 30 18:09:24 2016 -0700 Color C_CellMG Src/C_BoundaryLib/BndryRegister.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Tutorials/MultiColor_C/Make.package Tutorials/MultiColor_C/inputs Tutorials/MultiColor_C/main.cpp commit 38f219f94977fbfd6eeaa51b91d1769b768a0569 Author: Weiqun Zhang Date: Mon May 30 16:29:26 2016 -0700 color InterpBndry and MacBndry Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/MacBndry.H Src/C_BoundaryLib/MacBndry.cpp commit 44c822616e84db1a01acbcb8bb29c09ced9ead6e Author: Weiqun Zhang Date: Mon May 30 13:38:31 2016 -0700 color BndryData Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 638afa32a9b69ea8a5d5ad9fd8c6c74c759ccc21 Author: Weiqun Zhang Date: Mon May 30 13:28:44 2016 -0700 color BndryRegister Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 66b4fd2109a259d30e92445724071e6945b1c615 Author: Michael Zingale Date: Mon May 30 11:27:16 2016 -0400 if a restart test produces backtraces -- abort previously we didn't look for backtraces on the first run of a restart test. Now we do and abort if they are produced. Tools/RegressionTesting/testnew.py commit 0106641af906ade6e6f7d576753f0ecd6611f7f4 Merge: b2c6cd8ee 83a3b07c7 Author: Michael Zingale Date: Sun May 29 22:28:59 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 83a3b07c766a1079a6aa6bfdb0f3edbcdeb913f2 Author: Max Katz Date: Sun May 29 22:17:06 2016 -0400 Turn off PGI Fortran debug symbols if using OpenACC Tools/C_mk/Make.Linux commit 71d56153f5c8ec88f6af32256150c17116cf5739 Author: Weiqun Zhang Date: Sun May 29 17:30:02 2016 -0700 Color FabSet Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 240d4253bdf045bfda790c7cda0154e79e0a3cb1 Author: Weiqun Zhang Date: Sun May 29 09:59:13 2016 -0700 Fortran bl_random: more assertion and make sure no duplicates in parallel seeds Src/F_BaseLib/bl_random_c.cpp commit e0ef836bd726fa81d9a85482df7bd4ff783955b0 Author: Weiqun Zhang Date: Sun May 29 09:47:45 2016 -0700 Fortran bl_random: assert seed >0 Src/F_BaseLib/bl_random_f.f90 commit 79321e07d4190113f999dd9b3eec8d9e564bf3a6 Author: Weiqun Zhang Date: Sat May 28 23:20:38 2016 -0700 Fortran bl_random: Use random numbers instead of seed_seq as parallel seed. The latter has a high chance of collision. Src/F_BaseLib/bl_random_c.cpp commit 57df48650326f5d7d0fe2396fe7fbfab5c45b51f Author: Michael Zingale Date: Sat May 28 21:58:06 2016 -0400 fix formatting of the job_info summary fields Tools/RegressionTesting/testnew.py commit a8b80ef2f1f7fc6a6a47fc8243043dcd0bb067f1 Author: Michael Zingale Date: Sat May 28 21:11:07 2016 -0400 if we produce backtraces, we fail Tools/RegressionTesting/testnew.py commit b2c6cd8ee764879e390d97128ade7ad8fc361686 Author: Michael Zingale Date: Sat May 28 20:32:17 2016 -0400 shorten some headings Tools/RegressionTesting/testnew.py commit 1f4fac74fbe0d889667dd23bef36621cc4a0dc1d Author: Michael Zingale Date: Sat May 28 18:58:19 2016 -0400 initialize the job_info fields Tools/RegressionTesting/testnew.py commit d34eb8f5a037fe6a2f6dabec4777afbaa906fe8d Merge: 51c29633e 76414711a Author: Michael Zingale Date: Sat May 28 16:02:43 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 51c29633e2e79700b7345ab7796c43e3d6f00ea4 Author: Michael Zingale Date: Sat May 28 16:02:22 2016 -0400 cleaning + copy job_info to web output Tools/RegressionTesting/testnew.py commit 76414711acec9c8e3b9b91b737e67bc8aeca3ec8 Author: Michael Zingale Date: Sat May 28 14:56:34 2016 -0400 update prototypes Tools/C_scripts/buildInfo.H commit 5356f2ed7f03d5f3c6af362fb64d5954cddc553c Author: Michael Zingale Date: Sat May 28 14:41:42 2016 -0400 hook in the compiler versions Note: we cannot quote the shell output because we quote it when passing to the makebuildinfo_C.py routine, and trouble ensues. Also make the names consistent Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_scripts/makebuildinfo_C.py commit 38a1b17cbcf3a4577357c7ccff486137ba85e23e Merge: 4548bc602 e765dd946 Author: Michael Zingale Date: Sat May 28 14:27:26 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 4548bc6023416e1899d1da035e8e8c1f79976a0c Author: Michael Zingale Date: Sat May 28 14:27:01 2016 -0400 add FCOMP_VERSION and CCOMP_VERSION for gfortran and PGI THis mirrors the F_mk stuff Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit e765dd946cf9c795421559dd7b12877fc12580be Author: Michael Zingale Date: Sat May 28 13:43:59 2016 -0400 robustify the summary table Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/testnew.py commit 9a38dc70452c73e0b48a3de52343ec83e6dacf0e Author: Weiqun Zhang Date: Fri May 27 21:46:51 2016 -0700 Fortran bl_random: minor tweak Src/F_BaseLib/bl_random_c.cpp commit acc76ed2e8a6d73ccd5aa2d60e375ccb5ac4e5ef Author: Michael Zingale Date: Fri May 27 21:41:27 2016 -0400 updated test file Tools/RegressionTesting/Castro-SBU-tests.ini commit a0c76cb74d7f3cd43224b600cda500925e52831d Author: Michael Zingale Date: Fri May 27 21:36:01 2016 -0400 add custom fields to the summary table Now we can define special fields to appear in the suite summary table. These fields should appear in the job_info file, and we split on a ":", and store the result in the table (we also remove anything before the last "/" to handle paths) Tools/RegressionTesting/testnew.py commit 4142c040f5d58975e3929a109bfdb2ecba57df64 Merge: a0f155b9c 2ed6e324b Author: Michael Zingale Date: Fri May 27 20:03:20 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit a0f155b9cef645fd5390297b48955ff6debf0c58 Author: Michael Zingale Date: Fri May 27 20:02:44 2016 -0400 add network, EOS, and conductivity for easy parsing in the test suite Tools/F_scripts/makebuildinfo.py commit 2ed6e324b5bfc2dc529447cf5e0523202e348442 Author: Weiqun Zhang Date: Fri May 27 17:01:06 2016 -0700 Fortran bl_random: add bl_rng_change_distribution for poisson and binomial Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit 3e50d6d40f34ef90557552434921f8d62233ca70 Author: Weiqun Zhang Date: Fri May 27 16:17:48 2016 -0700 Fortran bl_random: add binomial Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit e7fd43d0cfe8dff6f79d056fcba73b3d5c622b50 Author: Weiqun Zhang Date: Fri May 27 15:55:15 2016 -0700 Fortran bl_random: add poisson Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit 7db735dc6e3c534edacc86fb162d4f95ec909cd8 Author: Weiqun Zhang Date: Fri May 27 15:40:52 2016 -0700 forgot to add a file Src/F_BaseLib/bl_random_c.H commit 0de91cb6d82c86e90ccdca6f3fb0382f25cae980 Author: Weiqun Zhang Date: Fri May 27 15:19:02 2016 -0700 Fortran: use C++11's random number generators Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/gfortran.mak Tutorials/Random_F/GNUmakefile Tutorials/Random_F/GPackage.mak Tutorials/Random_F/main.f90 commit 2c06bb2e97b315077928b053f4420bfb3e268a3d Author: vince Date: Thu May 26 17:34:43 2016 -0700 working test code with three sidecars. Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit 2cceba7532eee61f2363ed99908dcc4054ace6e9 Author: vince Date: Thu May 26 17:30:15 2016 -0700 fix for multiple sidecars. Src/C_BaseLib/ParallelDescriptor.cpp commit 0486cf2016e3c1beed026ddf4d50d83c27b73ccc Author: vince Date: Thu May 26 17:29:17 2016 -0700 added more error checking. Src/C_BaseLib/ParallelDescriptor.H commit 19ef58bf58fd61966962bce9596e5e1e76ba6c76 Author: vince Date: Thu May 26 14:48:05 2016 -0700 added function for which sidecar. Src/C_BaseLib/ParallelDescriptor.H commit 54f16b5ba5e3556047238b5427ed2ce9fb64260a Merge: cadc60886 4612d963b Author: Michael Zingale Date: Thu May 26 12:07:07 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit cadc6088693d77361b87fb652c7b956975e9de03 Author: Michael Zingale Date: Thu May 26 12:06:52 2016 -0400 make this work with python3 Tools/C_scripts/makebuildinfo_C.py commit 4612d963bc02915df9a7d5cf28b5c81ecad3b156 Author: Max Katz Date: Wed May 25 22:24:55 2016 -0400 The write_probin script now has a hook for updating GPU data Tools/F_scripts/write_probin.py commit b4500698df7b502d5341a53ee393d995009a9d27 Author: vince Date: Wed May 25 13:20:16 2016 -0700 free extra groups. Src/C_BaseLib/ParallelDescriptor.cpp commit aa384a7e488320c3aa24151eebacd07ce2824c55 Author: Michael Zingale Date: Wed May 25 13:27:08 2016 -0400 add FPP_DEFINES for .F90 preprocessing Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit b9366981a1b768bd87463d4ae48eb090bc356278 Author: Michael Zingale Date: Wed May 25 13:01:49 2016 -0400 no need to have 2 copies of moddep.pl The C++ build now uses the version in the F_scripts Tools/C_mk/Make.defs Tools/C_scripts/moddep.pl commit 4b4b1cf80ead03e92305ad5f0a0f9200e1e844d3 Author: Michael Zingale Date: Wed May 25 12:45:36 2016 -0400 sync up with the version in C_scripts Tools/F_scripts/moddep.pl commit 92b0fd4c86c48b28648da3084eace9192ae82ea6 Author: Max Katz Date: Wed May 25 11:49:42 2016 -0400 Conditionally disable -g on PGI when using OpenACC Tools/F_mk/comps/Linux_pgi.mak commit 846d028af506dda96cf5677ee2915c5661745155 Merge: f6b8f86d6 8a2be1b6f Author: Max Katz Date: Wed May 25 11:42:37 2016 -0400 Merge branch 'development' into openacc commit 8a2be1b6faca30b71c0c913ef51864b36d52f88f Author: Michael Zingale Date: Wed May 25 11:16:41 2016 -0400 add support for .F90 files -- these will be preprocessed. We adopt the convention that the Fortran compiler is smart enough to handle the preprocessing, recognizing the .F90 (caps) means preprocess Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit b733abc82324bba5f9ad133f78e8f564ea44128a Author: Michael Zingale Date: Wed May 25 11:15:28 2016 -0400 make the Fortran dependency script recognize .F90 too Tools/F_scripts/moddep.pl commit 5fae1c1bfad5becf17c53c21be54fb4e73b6452e Merge: c3a2342df fa7d358d1 Author: Michael Zingale Date: Wed May 25 10:40:59 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit c3a2342dfc6c82a1071a0fa3b91f1e52138c2949 Author: Michael Zingale Date: Wed May 25 10:40:37 2016 -0400 fix the permissions so this is executable so 'make doc' works Tools/F_scripts/f90doc/f90doc commit fa7d358d17d2cf5c79d36f5b7080ce15b34fb47b Merge: b41da6f56 36e123746 Author: Ann Almgren Date: Wed May 25 07:04:45 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development Conflicts: Src/F_BaseLib/ml_nd_restriction.f90 commit b41da6f56faec60c25ce75cdb561901aba5a5992 Author: Ann Almgren Date: Wed May 25 07:03:25 2016 -0700 Oops -- should have removed mp_crse, mp_fine Src/F_BaseLib/ml_nd_restriction.f90 commit 36e123746ad04ff043aef2e8ac8179e3a599174b Author: Michael Zingale Date: Wed May 25 08:40:46 2016 -0400 fix the OMP here Src/F_BaseLib/ml_nd_restriction.f90 commit 388e6900303025a525a1124c1362b35ee263c542 Merge: 85494791d 6d91ad6f8 Author: Michael Zingale Date: Tue May 24 20:42:45 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 85494791dc8990e52af384eb509a24d6d0a96b42 Author: Michael Zingale Date: Tue May 24 20:42:22 2016 -0400 cause why not ... define FIVE12TH and FIVE32ND Src/F_BaseLib/bl_constants.f90 commit ec9bc9ae5627fa5d4af31beaa8a62557eddf22d0 Author: vince Date: Tue May 24 16:13:07 2016 -0700 added a new test. Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit 8f0cd72f3948c321f1558f5260a376d50eb78818 Author: vince Date: Tue May 24 16:12:47 2016 -0700 added a new test. Tutorials/Sidecar_EX1/Make.package commit 1f07d0048595dc8c355d557069752501d0742bfe Author: vince Date: Tue May 24 16:12:23 2016 -0700 update test for latest boxlib dsc. Tutorials/Sidecar_EX1/DestMFTest.cpp commit 07a07b992421d2703b1dd9cd4ac722026eb226b2 Author: vince Date: Tue May 24 16:11:37 2016 -0700 fix group free for zero sidecars. Src/C_BaseLib/ParallelDescriptor.cpp commit 6d91ad6f8401e5b91866a376ed628cfaf54070c4 Merge: 944b6f7fc beb27117f Author: Ann Almgren Date: Tue May 24 15:26:30 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 944b6f7fc2f292d424484565dd43d105d8d270ab Author: Ann Almgren Date: Tue May 24 15:26:11 2016 -0700 Add nodal injection (in addition to nodal restriction) Src/F_BaseLib/ml_nd_restriction.f90 Src/F_BaseLib/nodal_restriction.f90 commit 7e4d1c9ca1ee553199c3b47d8195991bd653a9a7 Author: vince Date: Tue May 24 14:21:35 2016 -0700 fix for serial. Src/C_BaseLib/ParallelDescriptor.cpp commit cd24478d22b46b9c3038dca5f97fb01947ab7e2c Author: vince Date: Tue May 24 14:11:18 2016 -0700 default arg. Src/C_BaseLib/ParallelDescriptor.H commit ea9c5153ad65f237ca6b97fb24bfda4db0a1629d Author: vince Date: Tue May 24 13:58:30 2016 -0700 fix for zero sidecars. Src/C_BaseLib/ParallelDescriptor.H commit 12bec56ccb4525cb09252a5c0a7011c8554beba8 Author: vince Date: Tue May 24 13:45:15 2016 -0700 additions for multiple sidecars. fortran interface needs testing. Src/F_BaseLib/parallel.f90 commit 3019826768e39d16fedc906fc7313ad66c77fee8 Author: vince Date: Tue May 24 13:44:17 2016 -0700 additions for multiple sidecars. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit beb27117f6960445928789a179760e9e31186f12 Author: Michael Zingale Date: Tue May 24 14:35:45 2016 -0400 fix convert_type wrapper for None Tools/RegressionTesting/testnew.py commit 148865d1711564e0a82182f2314786e55bcb0db8 Merge: 3ac02be02 272987f15 Author: Michael Zingale Date: Tue May 24 14:32:10 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 3ac02be02873029cf8553da648bf36c37626f349 Author: Michael Zingale Date: Tue May 24 14:31:58 2016 -0400 a little clean-up Tools/RegressionTesting/testnew.py commit 272987f151e40156339162249d164520f3a94d09 Author: Michael Zingale Date: Tue May 24 11:01:42 2016 -0400 gracefully handle the "grids don't match" error from fcompare Tools/RegressionTesting/testnew.py commit fd4a01e133556f61d78e3f38990ada8f70595f30 Merge: a37b66cbf dea56bcbe Author: Michael Zingale Date: Sun May 22 16:39:23 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit dea56bcbea105c1c1b99610c96df71e435509f4a Author: Weiqun Zhang Date: Fri May 20 22:56:01 2016 -0700 a multi-color test Tutorials/MultiColor_C/GNUmakefile Tutorials/MultiColor_C/Make.package Tutorials/MultiColor_C/inputs Tutorials/MultiColor_C/main.cpp commit 8f46ca6a3f8e15e4447988565a0165c60b308c7f Author: Weiqun Zhang Date: Fri May 20 17:14:55 2016 -0700 fix non-parallel build Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 3887750f2dc4cb6843dd5d23ccfd1df2815d089b Author: Weiqun Zhang Date: Fri May 20 16:51:34 2016 -0700 make reduce work with color Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/iMultiFab.cpp commit 7be4e57e09dda03fb2e68016e65b1314f7ee124b Author: Weiqun Zhang Date: Fri May 20 13:49:13 2016 -0700 update SeqNum functions for multi-color Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 1731e5f6e8af6ff50cd28b54ca559ce73cfce46d Author: Weiqun Zhang Date: Thu May 19 21:52:18 2016 -0700 operator<< for ParallelDescriptor::Color Src/C_BaseLib/ParallelDescriptor.H commit bc90c129a9dfbc43a80b4ae0106243d97b6f5ba0 Author: Weiqun Zhang Date: Thu May 19 21:15:33 2016 -0700 DistributionMapping: finished coloring Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 79868ff52604d884dbde0f4f404179b9302b7bcd Author: Weiqun Zhang Date: Thu May 19 10:56:41 2016 -0700 DistributionMapping: use color as part of the key Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit be247b8267b3c6eaf78435a45c18ff38290cbf22 Author: Weiqun Zhang Date: Thu May 19 10:34:59 2016 -0700 replace int type color with ParallelDescriptor::Color class for type safety Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 3f3da43f251dfdfbc33844955ef97085ec780ec4 Author: Weiqun Zhang Date: Thu May 19 07:13:36 2016 -0700 remove useless 'explicit' Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 2e5cda993b1cf0258cb5ff4f55f33c8933a8fed8 Author: Weiqun Zhang Date: Wed May 18 22:30:44 2016 -0700 start sub-communicators controlled by boxlib.ncolors Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/MultiGrid_C/GNUmakefile commit 04409561fe724d6cdb5554129c02b38760f8cfb4 Author: Weiqun Zhang Date: Fri May 20 17:01:19 2016 -0700 clean up an unused template for parallel reduce Src/C_BaseLib/ParallelDescriptor.H commit e2d57c49096b07211bf4dd8cc42d6bac2ed4f8de Author: Weiqun Zhang Date: Fri May 20 11:21:42 2016 -0700 update make for CCSE machines because of new MPI installation Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 6568e0f28bb6662a0cc46bc98c0a281e33c587e6 Author: Weiqun Zhang Date: Fri May 20 10:38:15 2016 -0700 update make for battra and baragon Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit b0747b1dd7036a03549c3f896ce89adbdd944c03 Author: Weiqun Zhang Date: Fri May 20 11:21:42 2016 -0700 update make for CCSE machines because of new MPI installation Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 43b64bc6fe1aedb093ad808b485dd5d22ca17a54 Author: Weiqun Zhang Date: Fri May 20 10:38:15 2016 -0700 update make for battra and baragon Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit ec60aab8754353bbd93ffe52c14772375457122e Author: Max Katz Date: Thu May 19 19:51:30 2016 -0400 Permit disabling of PGI OpenACC Tools/C_mk/Make.Linux commit b902d7e224d536ac69d5cefed3d979e1f58eb1cd Author: vince Date: Thu May 19 14:58:13 2016 -0700 additions for multiple sidecars, check bl_fortran_set_nprocs_sidecar. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 840c9703c61af757f3891157cf0710948d52afaf Author: vince Date: Thu May 19 14:56:56 2016 -0700 fixes for multiple sidecars. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit b84ed6de5ac93e8984732cefe152a347fe2940fd Author: Weiqun Zhang Date: Thu May 19 08:24:11 2016 -0700 fix bug in my last commit Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 4b0428572e32b554992c0c7a3f1db7d62a348641 Author: vince Date: Wed May 18 18:00:04 2016 -0700 dont need arrays for sidecar groups or comm. made simple interface function for one sidecar case. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c5f27284fd10c6a5eb9457add642e37e721ff5dd Author: vince Date: Wed May 18 16:03:46 2016 -0700 update NProcsSidecar for multiple sidecars. Src/C_BaseLib/ParallelDescriptor.H commit 3b38b6860c4946b6b48126f0f28824fd77103d4c Author: vince Date: Wed May 18 15:43:36 2016 -0700 update SetNProcsSidecars to support multiple sidecars. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 77e7c135e0b0803c9aaa98ddf551483946c8817a Author: Weiqun Zhang Date: Wed May 18 13:36:55 2016 -0700 MultiFab::norm0 add nghost optional argument Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit cdde4241d2f66a60724e616596e57099f6721f75 Author: Weiqun Zhang Date: Tue May 17 12:25:10 2016 -0700 typo Src/C_BaseLib/ParallelDescriptor.H commit 527cc3142fe6fe38bacb0b74bd731af58ed23223 Author: Weiqun Zhang Date: Tue May 17 12:19:02 2016 -0700 runtime parameter team.reduce Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 5974164d2cf1e5c98e45ada3b2b495fe9b6c414a Author: Weiqun Zhang Date: Tue May 17 12:05:39 2016 -0700 keep track of UPC++ and MPI mode Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 035f9e67aa71c1b104136bee3e3f8150921ad5f7 Author: Weiqun Zhang Date: Mon May 16 17:01:45 2016 -0700 Reduce: do team reduce first, then team lead reduce, and finally team bcast Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit f74a9b55f6544afc303d44a13dfcbf24838814c4 Author: Weiqun Zhang Date: Mon May 16 15:06:38 2016 -0700 Team: create team lead communicator Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit f25f95ccda7910e510ae0663fb02155220ea2344 Author: vince Date: Mon May 16 14:04:43 2016 -0700 updated error string and comments. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 2b7ef6580dcbf8b3b6671a0baa635798be2ef779 Author: Weiqun Zhang Date: Mon May 16 12:24:13 2016 -0700 FMultiGrid: add const Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 3ab188637b03480eed831e6510890fa78e76dcc0 Author: vince Date: Thu May 12 12:19:21 2016 -0700 only print error messages if abortOnError. these may not be errors during transient states. Src/C_BaseLib/FabArray.H commit ea0144aab5ed938d1c509d1ac53ad9593ff5c38b Author: vince Date: Thu May 12 12:14:32 2016 -0700 removed cout. Src/C_AMRLib/Amr.cpp commit a37b66cbf3bd9bcc8d8d3215391bbcee8bf92ef8 Merge: 6476208b6 17e50770e Author: Michael Zingale Date: Wed May 11 22:24:33 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 17e50770ef916d91d324daf51939b57e92260c40 Author: Weiqun Zhang Date: Wed May 11 12:42:15 2016 -0700 Array: removed the disallowed copy assignment so that C++11 compilers could auto-generate move constructor and move assignment Src/C_BaseLib/Array.H commit 1e24aa1edfdf82e74c2608179fbb53d965e64940 Author: Weiqun Zhang Date: Wed May 11 12:18:46 2016 -0700 tweak IntVect comparison functions to make it consistent with Fortran convention. Src/C_BaseLib/IntVect.cpp commit f0b2b23be39f1a0198f17662a06d58a84637986f Author: Weiqun Zhang Date: Tue May 10 20:50:30 2016 -0700 FillPatch: turn off omp for nodal. This is actually a benign race. Src/C_AMRLib/FillPatchUtil.cpp commit 1baf471049e34c07eb251de3ba0543ce237ee2dd Author: Weiqun Zhang Date: Tue May 10 20:35:05 2016 -0700 FillBoundary: avoid writing to valid region Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit a77390fd2427f49d397679bfcfdd6b275deae0b8 Author: Weiqun Zhang Date: Tue May 10 15:57:53 2016 -0700 FillPeriodicBoundary: avoid writing to valid regions Src/C_BaseLib/Geometry.cpp commit e1222ac52f525b6d288d049b7878a10c1fb9c8a4 Author: Weiqun Zhang Date: Tue May 10 10:38:03 2016 -0700 add BoxLib::shift function returning a shifted box Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit cbd5b06167af862532482a1996a8f24c1e40d540 Author: Weiqun Zhang Date: Mon May 9 21:48:48 2016 -0700 FluxRegister: make it behave exactly the same as before Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.cpp commit f6b8f86d64db4b69529a2e8750ad66887d8d54f0 Merge: 9c65a5314 dd098ef6a Author: Adam Jacobs Date: Mon May 9 18:35:11 2016 -0400 Merge branch 'development' into openacc commit dabc831daa1908f574dad1e1af0ec46742c1dacc Author: Weiqun Zhang Date: Mon May 9 14:07:19 2016 -0700 baragon makefile Tools/C_mk/Make.defs commit dd098ef6a1ced34f33200683764d2559ebe0ffee Author: Michael Zingale Date: Sun May 8 18:55:09 2016 -0400 some more OpenACC PGI flags Tools/C_mk/Make.Linux commit 6784f980b15a639e67079a89ce2715dc2647383b Author: Weiqun Zhang Date: Sat May 7 17:33:24 2016 -0700 update make for baragon Tools/C_mk/Make.defs commit 309e0d67b47a29d6650ed916a4e39ea4674d3fdd Author: Weiqun Zhang Date: Sat May 7 07:15:33 2016 -0700 fix some minor data race Src/C_BaseLib/MemPool.cpp commit 9d110831c4a50535669d348f1ecb89bf857f1120 Author: Weiqun Zhang Date: Sat May 7 07:06:00 2016 -0700 add MultiFab::Saxpy Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 35e3004e237746c85dc8433372b8e10d9cfe0a21 Author: vince Date: Fri May 6 15:29:09 2016 -0700 dont abort on CheckFAPointers. Src/C_AMRLib/Amr.cpp commit 3511de3304c399a058fdf5265aec18d2ff802ea8 Author: vince Date: Fri May 6 15:17:28 2016 -0700 added option to not abort on errors in CheckFAPointers. Src/C_BaseLib/FabArray.H commit c345b712953743445e6117415594ce4fe03a2b82 Author: vince Date: Fri May 6 13:36:17 2016 -0700 cleanup diagnostics. Src/C_BaseLib/FabArray.H commit 02b8e4d1e06996e1fd1026c1fe2e46c0d3c182c1 Author: vince Date: Fri May 6 13:35:21 2016 -0700 add call to fabarray internal check. Src/C_AMRLib/Amr.cpp commit b7574101b7ac590130ec5e5c3c6c7cc324b80cf5 Author: Weiqun Zhang Date: Fri May 6 08:57:33 2016 -0700 add source ghost cell option to periodicCopy Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 44d47f14c43f85a55cc6897f37460c0b3629523e Author: Weiqun Zhang Date: Fri May 6 08:44:27 2016 -0700 fix a new bug: need to update BD key Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d69e618d3d60fa4bce70ecb946394f6e91f7df36 Author: Weiqun Zhang Date: Thu May 5 23:14:28 2016 -0700 use ADD instead of COPY in mapPeriodic Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 1ce4d9b3c9e5b1fc2fd5c3988221d15d3a5c3d76 Author: Weiqun Zhang Date: Thu May 5 22:19:51 2016 -0700 simplify TagBoxArray::mapPeriodic Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit fcd065353d70235ddf3353ab922f1afe8cb2b685 Author: Weiqun Zhang Date: Thu May 5 17:07:26 2016 -0700 fix logic in new BoxArray::complement Src/C_BaseLib/BoxArray.cpp commit 7749d3177f417a32ecfac33723ac65202a43d88a Merge: dab69d918 8fd5701a6 Author: Weiqun Zhang Date: Thu May 5 14:38:37 2016 -0700 Merge branch 'development' into weiqun/complement commit 8fd5701a66ae9f4c03f6801bd41a1e59cdc89125 Merge: 0b280a511 9bafaf848 Author: Weiqun Zhang Date: Thu May 5 14:01:39 2016 -0700 Merge branch 'new_reflux' into development commit 9bafaf848264140c99460dc2857fe5d8f74a7ffa Author: Weiqun Zhang Date: Thu May 5 13:23:54 2016 -0700 clean up Src/C_AMRLib/FluxRegister.cpp commit 0b280a511e61401c3180f07c0b71750d4fd44227 Author: Michael Zingale Date: Thu May 5 15:35:58 2016 -0400 output more usage defails Tools/Postprocessing/F_Src/fcompare.f90 Tools/Postprocessing/F_Src/ffdcompare.f90 commit bbc8d63134affec16bfd7c07d9f52699483350e1 Author: vince Date: Thu May 5 12:35:30 2016 -0700 another check for data integrity. Src/C_BaseLib/FabArray.H commit dab69d918dbe49bc4dada116d382ea935e8755a1 Author: Weiqun Zhang Date: Thu May 5 11:18:48 2016 -0700 new complement list Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.cpp commit c68acd5493f30e4e7362906cb9588080d37fb4e4 Author: Max Katz Date: Thu May 5 01:57:54 2016 -0400 Update the probin script to handle OpenACC declarations Tools/F_scripts/write_probin.py commit 431d9473dab20a84a0459de3f715c865d86a4588 Author: Weiqun Zhang Date: Wed May 4 18:12:50 2016 -0700 fix some errors in last commit Src/C_AMRLib/FLUXREG_3D.F commit baa75c4c884d5b5015ba56b0ac80694ed346e367 Author: Weiqun Zhang Date: Wed May 4 18:10:29 2016 -0700 FluxRegister: no longer use CollectData Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H commit b4fb6d2af795f8821057102b84c341c7e70de001 Author: Weiqun Zhang Date: Wed May 4 15:15:42 2016 -0700 omp in FluxRegister Src/C_AMRLib/FluxRegister.cpp commit c7c482b68e356407186ddedac9c2a040e4304362 Author: Weiqun Zhang Date: Wed May 4 13:53:26 2016 -0700 omp in BndryRegister Src/C_BoundaryLib/BndryRegister.cpp commit e52c2a9e3c2047a1be76379295fa0956da0f0c0d Author: Weiqun Zhang Date: Wed May 4 12:46:34 2016 -0700 comment Src/C_BoundaryLib/FabSet.cpp commit ed19ae38e5a7ab09d9dd33741621d3be07b6c82b Author: Weiqun Zhang Date: Wed May 4 12:19:44 2016 -0700 Switch FillCoarsePatch to using the new FillPatch Src/C_AMRLib/AmrLevel.cpp commit 9bdd5c92c67bfe0b14ffce18229bfafaa81194b4 Author: Weiqun Zhang Date: Wed May 4 11:24:08 2016 -0700 fix the new FillCoarsePatch Src/C_AMRLib/AmrLevel.cpp commit fedf1b3cc13e15ee2cdf552301fa4d92d65f3936 Author: Weiqun Zhang Date: Wed May 4 10:40:14 2016 -0700 If the boxarray for a level does not change during regrid, assign the previous boxarray to the current to avoid making a duplicate with the same boxes but different reference id. This will help preserve caches associated with the previous boxarray. Src/C_AMRLib/Amr.cpp commit 490297221f3280a0fe3a621c9bf334e4bdb030cf Author: Max Katz Date: Wed May 4 12:50:44 2016 -0400 Use pgcc for compiling C code with PGI Tools/C_mk/Make.Linux commit 6fcc0a6559044bb88c05e38093f0d1b6221d52a2 Author: Weiqun Zhang Date: Tue May 3 17:54:48 2016 -0700 FillPatchIterator: switch to the point-to-point version. This may break some regression tests with nodal data and periodic boundaries. Src/C_AMRLib/AmrLevel.cpp commit bcd94568cac51df183eb0e7aa97a5904e4abece8 Author: Weiqun Zhang Date: Tue May 3 14:58:36 2016 -0700 FillCoarsePatch: optimization Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FillPatchUtil.H Src/C_AMRLib/FillPatchUtil.cpp commit ba982ad9c2e1181402864781599923dc68ea2754 Author: vince Date: Tue May 3 12:20:56 2016 -0700 mpi_require. Src/C_BaseLib/FabArray.H commit 2660a1fb2efde53033ba0b56cd1cf5b4859d74f2 Author: Weiqun Zhang Date: Tue May 3 12:06:22 2016 -0700 FillPatchCache: fix a bug Src/C_BaseLib/FabArray.cpp commit 3bf953ce5e9c1e2fadfa689811ef99f713e00e32 Author: Weiqun Zhang Date: Tue May 3 09:19:39 2016 -0700 FillPatch: optimization Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 764e0e6c5035e08187e42fc6fe8052b44fd736eb Author: Weiqun Zhang Date: Tue May 3 08:29:36 2016 -0700 FillPatchCache: fix some bugs Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/FabArray.cpp commit 53996ab05263e6b53ed127d4441b39f40da8d467 Author: Weiqun Zhang Date: Mon May 2 16:53:22 2016 -0700 FillPatch cache stats Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 6476208b66d7b6d8ad1fc3757051a2cd0e765520 Merge: 8be09b4be 026785fcf Author: Michael Zingale Date: Mon May 2 19:15:30 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 1cf641ee4bf3703788bb988236399634994f154d Author: Weiqun Zhang Date: Mon May 2 15:36:45 2016 -0700 FillPatch cache Src/C_AMRLib/FillPatchUtil.cpp Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.H Src/C_BaseLib/Box.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 026785fcf05b52b7ee44b7f36bbb6d7a9bd8fb0f Author: Weiqun Zhang Date: Mon May 2 10:40:50 2016 -0700 Release Notes 16.05 ReleaseNotes/release-notes-16.05 commit 494152762e8ec62f679d0be0996495e4a68c7a2b Merge: ae86a6f79 68d33340c Author: Weiqun Zhang Date: Mon May 2 10:13:10 2016 -0700 Merge branch 'master' into development commit ae86a6f79d7e3cbdd0194ff5f12d7930865e6fd3 Author: Weiqun Zhang Date: Sat Apr 30 13:37:45 2016 -0700 add ghost cell option to PeriodicCopy Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 90e2ac171379792ecc5ef1dfa101cf93dddbba2b Author: Weiqun Zhang Date: Fri Apr 29 18:34:44 2016 -0700 fix leastuseteam forUSE_MPI=FALSE Src/C_BaseLib/DistributionMapping.cpp commit 5a2f9635d7299e91ed8da1c39cd3e4ecd2fbb008 Author: Weiqun Zhang Date: Fri Apr 29 17:48:24 2016 -0700 clean up unused CPC constructor Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 52c8d0f75ebd53462850b1fda2f5bd5522b2b7c2 Author: Weiqun Zhang Date: Fri Apr 29 17:21:34 2016 -0700 fix a bug in paralle copy to ghost cells Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 0cebc798e10de83d8d39efb1849f8d0888d374d2 Author: Weiqun Zhang Date: Fri Apr 29 15:23:22 2016 -0700 new runtime parameter DistributionMapping.node_size that allows knapsack within a node and SFC at the node level Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 2577ca57b59e31203d0bbe30dc472348aed3779e Author: vince Date: Fri Apr 29 15:09:27 2016 -0700 const refs. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 8b3f69a9a80c10640919eadca457978aa6b52fc9 Author: vince Date: Fri Apr 29 15:08:36 2016 -0700 const refs. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 7f8cde7146d9d94251f4184e82edf647f891d867 Author: vince Date: Fri Apr 29 15:08:07 2016 -0700 const refs. Src/C_BaseLib/FabArray.H commit dddd2886c4530854feafab08a674e32ad0c11def Author: vince Date: Fri Apr 29 15:07:17 2016 -0700 delete dm cache. Src/C_AMRLib/Amr.cpp commit e667b6085b6fccb9dd4ad3bd080a5f6d2ae1759d Merge: 45a34fec7 7cde88b0b Author: Weiqun Zhang Date: Fri Apr 29 10:35:59 2016 -0700 Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development commit 7cde88b0bdbf2a49a1bb4667cd97e55703084025 Author: Weiqun Zhang Date: Fri Apr 29 10:05:30 2016 -0700 Profiling reduce Src/C_BaseLib/ParallelDescriptor.cpp commit ec970ab1e3ed8f90f134fd03164599315244325f Author: Weiqun Zhang Date: Fri Apr 29 10:03:50 2016 -0700 TinyProfiler: setfill Src/C_BaseLib/TinyProfiler.cpp commit d11048d2f5f968b3438646f18bbd1e15421d2435 Author: Brian Friesen Date: Thu Apr 28 12:42:45 2016 -0700 Tutorials: revert changes to inputs file in MultiGrid_C Commit 49f3551 ("4th order in progress...") changed some default values of the "inputs" file. This changes them back. Tutorials/MultiGrid_C/inputs commit 9c65a531443c372694aa0c18cdea8acee180d2d0 Merge: 9aea7776e 4a228c2f9 Author: Adam M. Jacobs Date: Tue Apr 26 15:26:44 2016 -0400 Merge branch 'development' into openacc commit 9aea7776ed84da8ea706618875e89560888cf371 Merge: 4d61f3b26 0086b0e30 Author: Adam M. Jacobs Date: Tue Apr 26 15:26:32 2016 -0400 Merge branch 'openacc' of ssh://github.com/BoxLib-Codes/BoxLib into openacc commit 8be09b4be1c6f4120e731e1e09376f5a56d22083 Merge: 3945a6862 4a228c2f9 Author: Michael Zingale Date: Mon Apr 25 18:05:08 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit babde0d9467ba2637ec090bd10901f67107fd855 Author: vince Date: Mon Apr 25 12:59:25 2016 -0700 delete distmap cache function. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 45a34fec7e4420476be85c77354bfaea8ed794b2 Author: Weiqun Zhang Date: Mon Apr 25 12:32:18 2016 -0700 Start Tutorials/AMR_Adv_CF Tutorials/AMR_Adv_C/README Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_CF/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_CF/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_CF/README Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/fmain.f90 commit 4a228c2f92cc1232fc7fbc95d4d187b5064cf354 Author: Weiqun Zhang Date: Mon Apr 25 11:18:46 2016 -0700 runtime parameter boxlib.use_collectdata=1; to use the new fillpatch, set it to 0. Src/C_AMRLib/AmrLevel.cpp commit ce5a99f4bc10c3ccf03ce7614f1a5dadc5e8f44f Author: Weiqun Zhang Date: Mon Apr 25 11:09:56 2016 -0700 move FillPatchUtil to C_AMRLib Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/FillPatchUtil.H Src/C_AMRLib/FillPatchUtil.cpp Src/C_AMRLib/Make.package Src/C_BaseLib/Make.package commit cb4d2cd5c1b1e1a5c293cbc5bbbece16d77217bf Author: Weiqun Zhang Date: Mon Apr 25 11:01:26 2016 -0700 Revert "move Interpolator from AMRLib to BaseLib" This reverts commit 4a0cc8dc9c792ee7bce1b8075f63046641384919. Src/C_AMRLib/ARRAYLIM_1D.F Src/C_AMRLib/ARRAYLIM_2D.F Src/C_AMRLib/ARRAYLIM_3D.F Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/Make.package Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package commit beaf399e077cf9c41462e8560c0127695e477811 Merge: eaf418958 2f24be4fc Author: Weiqun Zhang Date: Mon Apr 25 10:23:26 2016 -0700 Merge branch 'development' into fp2 Conflicts: Src/C_BaseLib/Geometry.H commit 2f24be4fcbc3ba2f87206c96a7de2f8e4c0e9cc7 Author: Weiqun Zhang Date: Mon Apr 25 09:54:21 2016 -0700 Tutorials: heat equation sovler using the Fortran interfaces of C++ BoxLib Src/F_Interfaces/BaseLib/multifab_mod.f90 Tutorials/HeatEquation_EX1_CF/Make.package Tutorials/HeatEquation_EX1_CF/advance.f90 Tutorials/HeatEquation_EX1_CF/fmain.f90 Tutorials/HeatEquation_EX1_CF/inputs commit e807a2467a22e238c1fd3284050cee61561bb8ae Author: Weiqun Zhang Date: Sun Apr 24 21:32:38 2016 -0700 FI: add optional nodal argument to multifab_build Src/F_Interfaces/BaseLib/boxlib_mod.f90 Src/F_Interfaces/BaseLib/multifab_fi.cpp Src/F_Interfaces/BaseLib/multifab_mod.f90 commit 4e13031086119185fe6cfc55dd3247ce632b2093 Author: Weiqun Zhang Date: Sun Apr 24 16:33:59 2016 -0700 FI: add fill boundary Src/F_Interfaces/BaseLib/multifab_fi.cpp Src/F_Interfaces/BaseLib/multifab_mod.f90 Tutorials/HeatEquation_EX1_CF/Make.package Tutorials/HeatEquation_EX1_CF/fmain.f90 Tutorials/HeatEquation_EX1_CF/init_phi.f90 commit cf6ad5015bea82c4a25648e62f66d8c4477ae13b Author: Weiqun Zhang Date: Sun Apr 24 15:20:43 2016 -0700 FI: rename baselib module to boxlib module Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/baselib_mod.f90 Src/F_Interfaces/BaseLib/geometry_mod.f90 Tutorials/HelloWorld_CF/fmain.f90 commit 0ddcbf3f2925308d4c8e5d9cababb4253d98fc81 Author: Weiqun Zhang Date: Sun Apr 24 14:56:41 2016 -0700 FI: start heat equation Tutorials/HeatEquation_EX1_CF/GNUmakefile Tutorials/HeatEquation_EX1_CF/Make.package Tutorials/HeatEquation_EX1_CF/fmain.f90 Tutorials/HeatEquation_EX1_CF/inputs commit fad1d7432f730b00009c0c34af37a0cd5b8ec4fd Author: Weiqun Zhang Date: Sun Apr 24 14:56:10 2016 -0700 FI: geometry module Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/baselib_mod.f90 Src/F_Interfaces/BaseLib/geometry_fi.cpp Src/F_Interfaces/BaseLib/geometry_mod.f90 Src/F_Interfaces/BaseLib/multifab_mod.f90 commit 2c8aa8a445995439eee1083512455c76c8144af6 Author: Weiqun Zhang Date: Sun Apr 24 11:15:03 2016 -0700 FI: ParmParse module Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/baselib_mod.f90 Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/multifab_mod.f90 Src/F_Interfaces/BaseLib/parmparse_fi.cpp Src/F_Interfaces/BaseLib/parmparse_mod.f90 Src/F_Interfaces/BaseLib/string_mod.f90 Tutorials/HelloWorld_CF/GNUmakefile commit aaf93a1b75c8e67e3b8e706bfb583e5d3219173c Author: Weiqun Zhang Date: Sun Apr 24 06:54:24 2016 -0700 FI: add string module Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/omp_mod.F90 Src/F_Interfaces/BaseLib/string_mod.f90 commit 273dfa5e61c7673cc56055f7512863d830899905 Author: Weiqun Zhang Date: Sun Apr 24 06:42:32 2016 -0700 FI: prefer default intent Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/multifab_mod.f90 commit 50ad5d08702d0a9c010a8e6782401520c59818ba Author: Weiqun Zhang Date: Sat Apr 23 22:42:43 2016 -0700 FI: intent(out) => intent(inout) to avoid a strange gfortran behavior. gfortran 5.2 calls destructor on threadprivate mfiter when OMP is used. What's even worse is it does not initialize threadprivate mfiter properly, resulting in error in the initial destructor. Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/multifab_mod.f90 commit bb0afe1c8ded916c99b11d4652ccb79ed2f4414b Author: Weiqun Zhang Date: Sat Apr 23 22:11:11 2016 -0700 FI: parallel and omp module Src/C_BaseLib/BoxLib.cpp Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/baselib_mod.f90 Src/F_Interfaces/BaseLib/boxarray_fi.cpp Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/main.cpp Src/F_Interfaces/BaseLib/multifab_fi.cpp Src/F_Interfaces/BaseLib/multifab_mod.f90 Src/F_Interfaces/BaseLib/parallel_fi.cpp Src/F_Interfaces/BaseLib/parallel_mod.F90 Tutorials/HelloWorld_CF/fmain.f90 commit 3945a6862af29c53a417eb31d53fad0420051271 Merge: 8981ec7f2 c4b27c49d Author: Michael Zingale Date: Sat Apr 23 17:47:54 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 2ca626ad4041101a3f315aca4491c53bcb1ad317 Author: Weiqun Zhang Date: Sat Apr 23 14:05:36 2016 -0700 FI: more works Src/F_Interfaces/BaseLib/boxarray_fi.cpp Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/multifab_fi.cpp Src/F_Interfaces/BaseLib/multifab_mod.f90 Tutorials/HelloWorld_CF/GNUmakefile Tutorials/HelloWorld_CF/fmain.f90 commit 103f9004de9e8966fe04a4a8fcb0c10eea4a95a0 Author: Weiqun Zhang Date: Sat Apr 23 07:13:35 2016 -0700 FI: remove fab because Fortran pointer is kind of like fab Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/baselib_mod.f90 Src/F_Interfaces/BaseLib/fab_mod.f90 Src/F_Interfaces/BaseLib/multifab_mod.f90 Tutorials/HelloWorld_CF/fmain.f90 commit c4b27c49d5cb641a341d3971cccf247780871fea Author: Weiqun Zhang Date: Sat Apr 23 00:12:26 2016 -0700 Start F_Interfaces/BaseLib that provides Fortran interfaces to C++ BoxLib Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/baselib_mod.f90 Src/F_Interfaces/BaseLib/bl_space_mod.F90 Src/F_Interfaces/BaseLib/box_mod.f90 Src/F_Interfaces/BaseLib/boxarray_fi.cpp Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/fab_mod.f90 Src/F_Interfaces/BaseLib/main.cpp Src/F_Interfaces/BaseLib/multifab_fi.cpp Src/F_Interfaces/BaseLib/multifab_mod.f90 Tutorials/HelloWorld_CF/GNUmakefile Tutorials/HelloWorld_CF/Make.package Tutorials/HelloWorld_CF/fmain.f90 commit eaf418958ea0464de6381743182a400c9b3e4d87 Author: Weiqun Zhang Date: Fri Apr 22 14:44:33 2016 -0700 minor changes in profiling Src/C_AMRLib/AmrLevel.cpp commit 69609251d09767df2487d9887192b0a114b39b2a Author: Weiqun Zhang Date: Fri Apr 22 14:40:26 2016 -0700 make echo-x will print out the value of x Tools/C_mk/Make.rules commit e6a7d34a8c8846566ffe1d73cc27c934d9d8582b Author: Weiqun Zhang Date: Fri Apr 22 12:32:00 2016 -0700 fix periodiccopy when the periodic length is very very short (say <= 4 cells) Src/C_BaseLib/Geometry.H commit e9438b1f1bb3c5c712f3622bd0b81738d5e1dd77 Author: Michael Zingale Date: Fri Apr 22 10:01:37 2016 -0400 add navigation links to the top of the test result page Tools/RegressionTesting/testnew.py commit d7e9242410dab629ee35c5ac403d42e4418e4e79 Author: Weiqun Zhang Date: Thu Apr 21 22:29:38 2016 -0700 more general periodic copy Src/C_BaseLib/Box.H Src/C_BaseLib/Geometry.H commit 522f2cb6a5fef6676ab4b20e6ff77964e77ac195 Author: Weiqun Zhang Date: Thu Apr 21 17:57:36 2016 -0700 BoxArray: need to update type after constructing from boxlist Src/C_BaseLib/BoxArray.cpp commit 7b3fe3feeae926b8f95430fa34efd3126740d88e Author: Weiqun Zhang Date: Thu Apr 21 21:41:31 2016 -0700 fillpatch: clean up Src/C_BaseLib/FillPatchUtil.cpp commit bf029c4a4cdde16cc941ed0693646e72bbf63c36 Author: Weiqun Zhang Date: Thu Apr 21 21:36:45 2016 -0700 periodic copy: bug fix Src/C_BaseLib/Geometry.H commit 07f3511ae33d266bae0163a9dc5b2199650a8510 Author: Weiqun Zhang Date: Thu Apr 21 17:57:36 2016 -0700 BoxArray: need to update type after constructing from boxlist Src/C_BaseLib/BoxArray.cpp commit cfdae6f6f9f2143e1a3d29eba5a771237ed6141e Author: Weiqun Zhang Date: Thu Apr 21 16:45:05 2016 -0700 new periodic copy: remove empty boxes from list Src/C_BaseLib/Geometry.H commit 046e8edaa04fea58aaded0f77644fada16487776 Author: Weiqun Zhang Date: Thu Apr 21 16:39:44 2016 -0700 profiling two levels fillpatch Src/C_BaseLib/FillPatchUtil.cpp commit 1ccda614d4894ee26a26284c6f7012fa24de5a69 Author: Weiqun Zhang Date: Thu Apr 21 16:39:07 2016 -0700 fix the new periodic copy Src/C_BaseLib/Geometry.H commit 61a3449aacb03fc5a344e9b09104bda01f066c05 Author: Weiqun Zhang Date: Thu Apr 21 13:36:29 2016 -0700 change default blocking factor from 2 to 8 Src/C_AMRLib/Amr.cpp commit 9f680585366f627c2d5a6cfb1b9eee8e9295f71f Author: Weiqun Zhang Date: Thu Apr 21 13:33:14 2016 -0700 new two levels fillpatch Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/Box.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FillPatchUtil.H Src/C_BaseLib/FillPatchUtil.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Interpolater.cpp commit 60e7f67b5276fa100909d4bd2edd16c00dd775a4 Author: vince Date: Wed Apr 20 18:11:04 2016 -0700 cleanup. Src/C_BaseLib/ParallelDescriptor.cpp commit e402a0a9be3fb62818222e2d8934717deb3212a0 Author: vince Date: Wed Apr 20 18:08:35 2016 -0700 redistribute particles when resizing sidecars. Src/C_AMRLib/Amr.cpp commit 95af6e8c4e21fa474e09a77fe3f8c6bcc11dd632 Author: vince Date: Wed Apr 20 18:07:44 2016 -0700 syncronize sequence numbers across groups. Src/C_BaseLib/FabArray.H commit 4a0cc8dc9c792ee7bce1b8075f63046641384919 Author: Weiqun Zhang Date: Wed Apr 20 14:17:21 2016 -0700 move Interpolator from AMRLib to BaseLib Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/Make.package Src/C_BaseLib/ARRAYLIM_1D.F Src/C_BaseLib/ARRAYLIM_2D.F Src/C_BaseLib/ARRAYLIM_3D.F Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/INTERP_1D.F Src/C_BaseLib/INTERP_2D.F Src/C_BaseLib/INTERP_3D.F Src/C_BaseLib/INTERP_F.H Src/C_BaseLib/Interpolater.H Src/C_BaseLib/Interpolater.cpp Src/C_BaseLib/Make.package commit 0591fe7fbd15a7c99b1254ae8ba670a47d330c11 Author: Weiqun Zhang Date: Wed Apr 20 11:14:33 2016 -0700 single level fillpatch: parallel copy ghost cells too Src/C_BaseLib/FillPatchUtil.cpp commit a8d4b16db8d3639eb97c5ef1a06fe0e0b36f54ca Author: Weiqun Zhang Date: Wed Apr 20 11:07:04 2016 -0700 single level fillpatch: support the case source and destination have different BoxArrays Src/C_BaseLib/FillPatchUtil.cpp commit 052bd63f1b72ae199462cf1f6726866696469383 Author: Weiqun Zhang Date: Wed Apr 20 10:43:45 2016 -0700 derive: fix box type and ghost Src/C_AMRLib/AmrLevel.cpp commit 52d65c9f1b9d744ecaf655fc0ecc24a59ca362e5 Author: Weiqun Zhang Date: Tue Apr 19 17:59:37 2016 -0700 new fillpatch: fix single level fillpatch Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/FillPatchUtil.H Src/C_BaseLib/FillPatchUtil.cpp Src/C_BaseLib/PhysBCFunct.H commit 998e2c9f2b9cba7e8fae8b52a39401d5ee321a46 Author: Weiqun Zhang Date: Tue Apr 19 15:38:29 2016 -0700 new fillpatch: omp Src/C_AMRLib/StateData.cpp commit 06a4967f67129232501dcd9ce13c5f82d31f20e9 Author: Weiqun Zhang Date: Tue Apr 19 15:37:46 2016 -0700 new fillpatch: linear interp in time for level 0 Src/C_BaseLib/FillPatchUtil.cpp commit b61b04a5fb76c7bc5f6214e422b4d1f8492ce496 Author: Weiqun Zhang Date: Tue Apr 19 14:41:33 2016 -0700 new fillpatch: add profiler and rm debug statements Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FillPatchUtil.cpp commit 9011c00bd7ba9463a6eb75fc7747bf1f31631ae2 Author: Weiqun Zhang Date: Tue Apr 19 14:06:50 2016 -0700 new fillpatch: use it on level 0 Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/FillPatchUtil.H Src/C_BaseLib/FillPatchUtil.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/PhysBCFunct.H commit 3d6b2e583a99ccf7b2319f78f6402f3e6819c393 Author: Weiqun Zhang Date: Mon Apr 18 14:56:50 2016 -0700 TinyProfiler: avg % --> max % Src/C_BaseLib/TinyProfiler.cpp commit 391f47018275e261ae480a6350482798deeeb7a0 Author: Weiqun Zhang Date: Mon Apr 18 14:53:35 2016 -0700 TinyProfiler: avoid finalizing twice Src/C_BaseLib/TinyProfiler.cpp commit 5c93a309c459d55a8bba6a6132e551fb6a151989 Author: vince Date: Mon Apr 18 11:12:30 2016 -0700 remove diagnostic. Src/C_BaseLib/FabArray.H commit 8981ec7f28875a388cb3a003c0d4309eac9095a8 Author: Michael Zingale Date: Sat Apr 16 21:35:30 2016 -0400 make this python3-aware Tools/F_scripts/findparams.py commit 084fa8c6229664a79703d43e0563d77e4a574a56 Author: vince Date: Fri Apr 15 18:11:59 2016 -0700 resolve Fab_noallocate fabarrays for MoveAllFabs. Src/C_BaseLib/FabArray.H commit 56d6b3ff6d339e2a9a81658eab04474d3825d7a1 Author: vince Date: Fri Apr 15 12:08:12 2016 -0700 removed reduction. Src/C_BaseLib/FabArray.H commit 05451ff4bc15b92349ed40e0feaec526a81e1388 Author: vince Date: Thu Apr 14 16:04:26 2016 -0700 fix for nyx. Src/C_AMRLib/Amr.cpp commit 06ab5cf4a2f0f7d98e34e4d07e5ee710a76cffc1 Author: vince Date: Thu Apr 14 15:07:06 2016 -0700 remove temporary diagnostics. Src/C_BaseLib/FabArray.H commit 1fb06310c257d713dc4d6618fdff0f3bda3d638e Author: vince Date: Thu Apr 14 14:25:24 2016 -0700 implemented BroadcastBoundaryPointList. Src/C_AMRLib/Amr.cpp commit 841c268b879325e7e2904c7d50f02011328694f9 Author: vince Date: Thu Apr 14 14:23:46 2016 -0700 implemented BroadcastBoundaryPointList. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit b9186ea0650625a66bde5f0ae39005f6f516f124 Author: Weiqun Zhang Date: Wed Apr 13 17:38:33 2016 -0700 TinyProfiler: fixed pop Src/C_BaseLib/TinyProfiler.cpp commit 8f322ea3e84fabd4d3b325ee3df5ded2eaa14a58 Author: Weiqun Zhang Date: Wed Apr 13 17:15:57 2016 -0700 TinyProfiler: fix OMP Src/C_BaseLib/TinyProfiler.cpp commit c064aa8b944848a8ba9f17b3061829141de5adf8 Author: Weiqun Zhang Date: Wed Apr 13 16:45:29 2016 -0700 TinyProfiler: warning about improperly nested timers Src/C_BaseLib/TinyProfiler.H Src/C_BaseLib/TinyProfiler.cpp commit ea8557b66393ada3cc3daa35a29ba0c1e99024b4 Author: Weiqun Zhang Date: Wed Apr 13 14:54:55 2016 -0700 TinyProfiler: fix inclusive time by keeping track of the depth of the call tree Src/C_BaseLib/TinyProfiler.H Src/C_BaseLib/TinyProfiler.cpp commit d5f8f40cd1e32d8f21b4e647f808a97d54b4cb37 Author: Weiqun Zhang Date: Wed Apr 13 13:59:18 2016 -0700 TinyProfiler: a tiny profiler that only supports a tiny fraction of what BLProfiler can offer. It does not need postprocessing. It shows inclusive and exclusive times. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/Make.package Src/C_BaseLib/TinyProfiler.H Src/C_BaseLib/TinyProfiler.cpp Tools/C_mk/Make.defs commit e24b668e5a098a0186c920868b35a9dfa964edd4 Author: vince Date: Wed Apr 13 12:57:25 2016 -0700 remove diagnostic. Src/C_BaseLib/Geometry.cpp commit c7222ed50bf32ccc9c26cdceb828f43393952ec3 Author: Brian Friesen Date: Wed Apr 13 12:12:32 2016 -0700 C_scripts: squash warning about "hdf5" module Tools/C_scripts/moddep.pl commit dc921e1adb071cc85323e6c43c01eb8193128a96 Author: Brian Friesen Date: Wed Apr 13 10:37:00 2016 -0700 C_scripts: squash warning about "iso_fortran_env" module Tools/C_scripts/moddep.pl commit a1c258184cacc4e850cbcb7f2864d88aafb4dc90 Author: Weiqun Zhang Date: Tue Apr 12 14:37:52 2016 -0700 update comments Src/C_AMRLib/Interpolater.cpp commit 18d2631868bbbe5c22a123fa8fc02e9037236d2e Author: Weiqun Zhang Date: Mon Apr 11 17:56:45 2016 -0700 remove unused variable Src/C_AMRLib/AmrLevel.cpp commit c3afed492981aa86f0f2dd7c929c0d33e36d4863 Author: Weiqun Zhang Date: Mon Apr 11 17:55:23 2016 -0700 FillBoundary: timer Src/C_BaseLib/FabArray.H commit b18d982e59b2abe3d8deac5471858c47024d40c2 Author: Weiqun Zhang Date: Mon Apr 11 17:53:15 2016 -0700 add fixediter option to MultiGrid_C tutorial Tutorials/MultiGrid_C/main.cpp commit d7b3bb0aa995717abe3ee0974418a2ca64305263 Author: Weiqun Zhang Date: Mon Apr 11 17:46:50 2016 -0700 comment out the mpi-3 fix recommended by NERSC Tools/C_mk/Make.Linux commit aef7569d0fe4006a4abd90cef3358c4b17dd66df Merge: ec0c5ec3a ec5fae567 Author: Weiqun Zhang Date: Mon Apr 11 16:29:10 2016 -0700 Merge branch 'development' into pgas Conflicts: Tools/C_mk/Make.defs commit 68d33340c25dd12815dee7f2f618679d68befe3f Author: Weiqun Zhang Date: Mon Apr 11 15:42:12 2016 -0700 release-notes-16.04 ReleaseNotes/release-notes-16.04 commit 519ff1b68b76095057645ee5650d2063ddf4a901 Author: vince Date: Mon Apr 11 15:33:26 2016 -0700 fixes for nyx. Src/C_AMRLib/Amr.cpp commit ec5fae567fe6417c9d5d307ac11528c978ed267c Merge: 28a724a62 9bc778cab Author: Weiqun Zhang Date: Mon Apr 11 14:38:33 2016 -0700 Merge branch 'master' into development commit 52c150536fa71e6af45475e3b798aee388481da9 Author: vince Date: Fri Apr 8 13:49:50 2016 -0700 clean up proximity maps. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 1d104764b522c6d9b019029ab43f69b26eae7dae Author: vince Date: Wed Apr 6 16:59:27 2016 -0700 additions for nyx dynamic sidecars. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/F_BaseLib/parallel.f90 commit fc144bb833aeaccb53e893d6ea294d3201b725e0 Author: vince Date: Wed Apr 6 16:45:39 2016 -0700 stubs for dynamic sidecars support. Src/F_BaseLib/parallel_stubs.f90 commit cb9b44744fe33e9b2e5c18a6d40dfcdbed476722 Author: vince Date: Wed Apr 6 16:06:57 2016 -0700 fix for non-mpi. Src/C_BaseLib/BoxArray.cpp commit d5b3b21ca5aeea3b204abba421ba82a259891657 Author: vince Date: Wed Apr 6 16:04:27 2016 -0700 fix for non-mpi. Src/C_BaseLib/FabArray.H commit 56a351116326662af0ecea8c1ffa75b9e92eb27b Author: vince Date: Wed Apr 6 14:38:54 2016 -0700 remove old SidecarProcess. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 28a724a62aadf9ef2221fb852cc37977a230da34 Author: Andy Nonaka Date: Wed Apr 6 10:56:37 2016 -0700 utility from Aleks that writes the contents of a 2d plotfile into a text file, one line per data point Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fwritecontents2d.f90 commit 43c0142c1244b00ba5296234c910a21560578439 Author: Andy Nonaka Date: Wed Apr 6 10:49:18 2016 -0700 works for all ref ratios now as long as the cells you are averaging down are on the same grid Tools/Postprocessing/F_Src/fcoarsen.f90 commit f517721af8dfbafa24fca37e8355a26b57e759bb Author: Weiqun Zhang Date: Wed Apr 6 09:41:24 2016 -0700 fine_flx now starts at level 1, not level 2. Tutorials/HeatEquation_EX5_F/advance.f90 commit a0a51ec257e84f36d4d943037ce825f5e616a8a7 Author: Andy Nonaka Date: Tue Apr 5 14:45:51 2016 -0700 get dx for plotfile write correct Tools/Postprocessing/F_Src/fcoarsen.f90 commit cbc4ff25c76b3acea8e2040371cc35d57082b126 Author: Andy Nonaka Date: Tue Apr 5 14:08:27 2016 -0700 updates from Aleks - add coarsening factor input Tools/Postprocessing/F_Src/fcoarsen.f90 commit 881dddfdb189cf5cca8fb5aef9d81e157b61d63b Author: Andy Nonaka Date: Tue Apr 5 13:22:24 2016 -0700 turn back on 3d coarsening of plotfiles Tools/Postprocessing/F_Src/fcoarsen.f90 commit 4dd7a312cb41580d9d93ab4b9f9d5c98cea0ac4e Author: Weiqun Zhang Date: Tue Apr 5 13:19:18 2016 -0700 add fcompiler option to f2py Tools/Py_util/GNUmakefile commit 551c0b366bbf61872073b71d502bea78c3db0597 Author: Andy Nonaka Date: Tue Apr 5 12:58:33 2016 -0700 revert accidental commit Tools/C_util/Convergence/GNUmakefile commit c8ba7ddeb07f3712bc0558912ca60e7680964a55 Merge: 668ab17e8 31532a042 Author: Andy Nonaka Date: Tue Apr 5 12:57:14 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 668ab17e89ee742fdd3aa6e2e87721cb15fa70ed Author: Andy Nonaka Date: Tue Apr 5 12:57:00 2016 -0700 forgot to add file Tools/Postprocessing/F_Src/fcoarsen.f90 commit 31532a0421791226551b6690d0528ff2d83fb221 Merge: 30add196f dd726272c Author: Ann Almgren Date: Tue Apr 5 12:39:25 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 30add196f04a23dd90cd48c8c4a55ae27ebb475d Author: Ann Almgren Date: Tue Apr 5 12:38:42 2016 -0700 The flux we pass into the F90 interface (in ml_solve.f90) for cell-centered solves now starts at the base level of the solve, not one level higher. Src/LinearSolvers/F_MG/ml_solve.f90 commit dd726272c245081ac7b22bcf452c9d79f498aa88 Merge: 37304cb0a ead716f18 Author: Andy Nonaka Date: Tue Apr 5 12:23:21 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 37304cb0a8d0b228e1e5faf856ca21eb24e83c83 Author: Andy Nonaka Date: Tue Apr 5 12:22:44 2016 -0700 utility that reads in a single level plotfile and writes out a coarsened plotfile (rr=2) Tools/C_util/Convergence/GNUmakefile Tools/Postprocessing/F_Src/GNUmakefile commit 339194b1243c7fcc293182aa1d8a658f0de29fbe Author: vince Date: Mon Apr 4 17:21:51 2016 -0700 check return of getcwd. Src/C_BaseLib/BoxLib.cpp commit ead716f182f1ef42f2433a7f48a05302a331dce0 Author: Ann Almgren Date: Mon Apr 4 16:35:49 2016 -0700 Add the option in the F90 interfaces to the cell-centered solver to have the base level have Dirichletboundary conditions at a distance away from the boundary, not just at the boundary. You make this happen by passing in base_level > 1 and crse_ratio = the ratio of dx between the coarsest level of the solve to the coarser AMR level outside the solve. Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 16bb6abd221a9a3f32d09677579b09e62735aa89 Author: vince Date: Mon Apr 4 12:05:19 2016 -0700 fix for particles. Src/C_AMRLib/AmrLevel.cpp commit 007b26e2b9fd2564d16ea82827db1f084b654bfc Author: Marc Day Date: Fri Apr 1 23:00:33 2016 -0700 Use gnu99 instead of c99 if using GNU compilers Tools/C_mk/Make.defs commit 4bda470332551ec0d5e8c463ce4f25373e9b4720 Author: Marc Day Date: Fri Apr 1 16:37:58 2016 -0700 Add USERSuffix to optionsSuffix to allow generalized suffix creation in app build. Should probably move app-specific suffix defs out of BoxLib....someday Tools/C_mk/Make.defs commit 0086b0e30847905818f0d2cca4f00b015e5970f4 Author: Adam Jacobs Date: Fri Apr 1 18:18:41 2016 -0400 Get PGI compilation working for OpenACC on titan Tools/F_mk/comps/Linux_pgi.mak commit 5cafbde658c219bf5c2767d2d9dd23cf2a04a04e Author: vince Date: Thu Mar 31 17:35:27 2016 -0700 fix for copyInter sidecar tutorial. Src/C_BaseLib/FabArray.H commit a7f81840d8786ad1f422a2db4b8586208bd53cdb Merge: 338053321 25bc646d3 Author: vince Date: Thu Mar 31 17:06:29 2016 -0700 merge with master. commit cbb8426e43b6d6b60902f762ffad28a61cc686f0 Author: Ann Almgren Date: Thu Mar 31 15:29:15 2016 -0700 Fix another typo in the latest changes to create_umac_grown. Src/F_BaseLib/create_umac_grown.f90 commit 130cd0e32df5c30b99bd0b118254feda93c6176e Author: Ann Almgren Date: Thu Mar 31 14:45:01 2016 -0700 Fix some oops from previous commit. Src/F_BaseLib/create_umac_grown.f90 commit ef453bcb0ffd4653845df30423d6120d5245b31a Author: Ann Almgren Date: Thu Mar 31 14:07:19 2016 -0700 Allow for factor 4 as well as factor 2 interpolation in create_umac_grown. Src/F_BaseLib/create_umac_grown.f90 commit 9bc778cab7654e83e0e22267aca476f9f10f3d86 Author: Weiqun Zhang Date: Wed Mar 30 16:02:34 2016 -0700 try to fix CMake for F_BaseLib; not tested because I don't even know how to use CMake Src/F_BaseLib/CMakeLists.txt commit 0b5ade1a306ea5caaaf64431bb6afa205a6f4e7e Author: Weiqun Zhang Date: Wed Mar 30 16:02:34 2016 -0700 try to fix CMake for F_BaseLib; not tested because I don't even know how to use CMake Src/F_BaseLib/CMakeLists.txt commit 5da4cbe59dfd4a2cc7842ba9e1d7aa815ba99b1c Author: Adam Jacobs Date: Wed Mar 30 16:02:19 2016 -0400 Use Cray compiler wrappers, even for PGI, on Titan Tools/F_mk/comps/Linux_pgi.mak commit 4f1128d1bbd13066824801f1e51f401ede951d98 Author: Adam Jacobs Date: Wed Mar 30 15:32:40 2016 -0400 For now, GPUs can't handle PGI's -gopt. Debug symbols break it with internal compiler errors. Tools/F_mk/comps/Linux_pgi.mak commit fa9a5e9a5c967aea2c5d57a2b589dbbc98a0e58d Merge: f1bae6c06 be70088b6 Author: Adam Jacobs Date: Wed Mar 30 15:31:00 2016 -0400 Merge branch 'development' into openacc commit f1bae6c065f2a21159e1f56933fd1a7d4b43c522 Merge: a4f3315c8 0d55d1400 Author: Adam Jacobs Date: Wed Mar 30 15:30:04 2016 -0400 Merge branch 'openacc' of ssh://github.com/BoxLib-Codes/BoxLib into openacc commit a4f3315c842a5e74c2c2d722f2fc928438fbeb61 Author: Adam Jacobs Date: Wed Mar 30 15:29:52 2016 -0400 fix indent Tools/F_mk/comps/Linux_cray.mak commit ec0c5ec3a449cc4123c9f8d80ed5cb1aeb1f470a Merge: 2f685a2ea 595b9e272 Author: Weiqun Zhang Date: Wed Mar 30 09:12:45 2016 -0700 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 595b9e272f0dc9b2464bdb9e8d3063634227f155 Merge: dd7694793 be70088b6 Author: Weiqun Zhang Date: Tue Mar 29 12:56:00 2016 -0700 Merge branch 'development' into pgas commit dd7694793f6ffddcc4f813ddd7db3748c98ef030 Merge: 2c3460136 25bc646d3 Author: Weiqun Zhang Date: Tue Mar 29 12:55:29 2016 -0700 Merge branch 'development' into pgas commit be70088b68aaf725d5b85303df147cfa260250cd Author: Regression Tester Date: Tue Mar 29 11:02:48 2016 -0700 regression test: option to use valgrind, --with_valgrind Tools/RegressionTesting/testnew.py commit 636e9d7e759cc881d9987ab9d107cf567295d90b Author: Weiqun Zhang Date: Tue Mar 29 10:56:24 2016 -0700 battra F_mk Tools/F_mk/GMakeMPI.mak commit a8747a8f403dc949144ca05805eb356cf226acc7 Author: Weiqun Zhang Date: Tue Mar 29 10:30:22 2016 -0700 battra: use rpath so that we do not need to bother with LD_LIBRARY_PATH Tools/C_mk/Make.mpi commit 1d6d554cb01b552eceb2a2b8e39f413dccd93bfb Author: Weiqun Zhang Date: Tue Mar 29 10:25:21 2016 -0700 battra: option to use valgrind friendly build of mpich at /usr/local Tools/C_mk/Make.mpi commit 9d0057bc1a6b7981abe334c9e00daea649f2b24f Author: Marc Day Date: Mon Mar 28 15:38:47 2016 -0700 Remove ifdefd code to set space-varying bcs. Was a remnant of debugging, and was incorrect anyway. Tutorials/MultiGrid_C/main.cpp commit 5b7c6fddce7586546624ccb88cdaaa843f10ccb2 Merge: dff697efd f22e9c951 Author: Adam M. Jacobs Date: Mon Mar 28 14:06:18 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit dff697efd60f69cc06fa544a2a47915638d8668e Author: Adam M. Jacobs Date: Mon Mar 28 14:06:12 2016 -0400 Add 5/6 to bl_constants Src/F_BaseLib/bl_constants.f90 commit f22e9c95174e974901abfff583a926e382803a58 Author: Weiqun Zhang Date: Fri Mar 25 17:21:34 2016 -0700 bndry_reg: fix a bug when the fine level has a single box and covers the entire non-periodic domain Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit 2f685a2ead420c8816aeb13e8a65b5a956ef9b33 Merge: 2c3460136 25bc646d3 Author: Weiqun Zhang Date: Fri Mar 25 14:48:08 2016 -0700 Merge branch 'development' into pgas commit 338053321ece9bde683c3816648177227c43c0cb Merge: 7e506d608 00d985aaf Author: vince Date: Fri Mar 25 12:46:05 2016 -0700 Merge branch 'master' into dynamicsidecars commit 7e506d60832131211c218853f3a5ba1f6f7d6535 Author: vince Date: Fri Mar 25 12:40:27 2016 -0700 premerge cleanup. Src/C_BaseLib/FabArray.cpp commit 6a84beefa0c1c370c4ed0ff1b3cde382c84f5ea7 Author: vince Date: Fri Mar 25 12:38:23 2016 -0700 added more profiling. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 905ddefee29e911fa48afee05d9f4840039a6e9b Author: vince Date: Fri Mar 25 12:37:53 2016 -0700 premerge cleanup. Src/C_AMRLib/Amr.cpp commit 2c3460136fe3e57624ca32164d0ccc62ed80e40d Author: Weiqun Zhang Date: Thu Mar 24 15:59:15 2016 -0700 PGAS_SMC: should use NTeams() MiniApps/PGAS_SMC/SMC_init.cpp commit 0b900065c59572d876f19746c5d18ceb0c405261 Author: Weiqun Zhang Date: Thu Mar 24 15:52:24 2016 -0700 PGAS_SMC: change defaults MiniApps/PGAS_SMC/SMC.cpp commit b24fbf7f89765f095c6bd42b6cd9578ad418314d Author: Weiqun Zhang Date: Thu Mar 24 15:47:01 2016 -0700 PGAS_SMC: chop box into small pieces so that each process has at least one box MiniApps/PGAS_SMC/SMC_init.cpp commit d91396251a95daa9639414721eb9b509e7bc467c Author: vince Date: Tue Mar 22 11:56:38 2016 -0700 add periodic to output. Src/C_BaseLib/Geometry.cpp commit 25bc646d3b3221c73eed13b8984dc08a206a9927 Author: Michael Zingale Date: Tue Mar 22 07:48:26 2016 -0400 fix typo Tools/RegressionTesting/testnew.py commit feb07da5ecfdf7bc5f70e0791a73ca33f7542544 Author: Brian Friesen Date: Mon Mar 21 12:34:13 2016 -0700 C_mk, F_mk: add optimization reports for Cray compilers Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_cray.mak commit 5043fc17d745196ed3c0cc5ef52a524de3b67e3d Author: Weiqun Zhang Date: Mon Mar 21 13:14:35 2016 -0700 update make for baragon Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit a2f5cd338c071f75af165c386567683067f928dc Author: Weiqun Zhang Date: Mon Mar 21 13:14:08 2016 -0700 free MPI_group Src/C_BaseLib/ParallelDescriptor.cpp commit b893afea3a9e5bdc24f03849f63bce638c76c6ed Merge: 2b0e17567 ea548ddb7 Author: Michael Zingale Date: Mon Mar 21 10:54:13 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 2b0e175678d2004d5425448f9ddb3e6f5a8ef52d Author: Michael Zingale Date: Mon Mar 21 10:53:58 2016 -0400 some slack cleaning Tools/RegressionTesting/testnew.py commit 4763a9a66f59ff423e9f49ee7023c51e749a313b Merge: 637267ee4 ea548ddb7 Author: Weiqun Zhang Date: Fri Mar 18 14:23:51 2016 -0700 Merge branch 'development' into pgas commit 637267ee4d245fa318923d6cacf180e45022df0d Author: Weiqun Zhang Date: Fri Mar 18 14:22:11 2016 -0700 add upcxx::barrier() before MPI reduce Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tests/FillBoundaryComparison/main.cpp Tutorials/PGAS_HEAT/main.cpp commit e5d2d979e387b530ff79acfc54c87ef13277b415 Author: vince Date: Fri Mar 18 13:10:51 2016 -0700 code cleanup. Src/C_AMRLib/Particles.H commit ea548ddb72c25761a7c283919d66ba2aafa84f1e Author: Weiqun Zhang Date: Fri Mar 18 12:26:43 2016 -0700 add 'class' because extended friend syntax is a C++11 feature Src/C_BaseLib/Box.H commit 8313e58ae4af5f2e501057f3bb372428c4807eeb Author: vince Date: Thu Mar 17 16:52:52 2016 -0700 added profiling, cleanup. Src/C_AMRLib/Particles.H commit 1e510bf82081617f54c0b703c7885bf486a1de19 Author: Emmanuel Motheau Date: Thu Mar 17 16:51:57 2016 -0700 Bug fix restricted_build Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 commit 8d4d04df36347cd299d172dd8ea0550bac0ff567 Author: Emmanuel Motheau Date: Thu Mar 17 16:50:21 2016 -0700 Add varan machine Tools/F_mk/GMakeMPI.mak commit ead9a714b43cf8569c0af3a9c560f25ad0a50217 Author: vince Date: Thu Mar 17 16:48:09 2016 -0700 added profiling, cleanup. Src/C_AMRLib/Particles.H commit fa4af7f32615b41bdfe91ed7bca18bc087f4ceb4 Author: vince Date: Thu Mar 17 16:47:17 2016 -0700 added profiling, cleanup. Src/C_AMRLib/Particles.H commit 909e7e8a9a7eea1ce98502468870eb64d1eee8e4 Author: Weiqun Zhang Date: Thu Mar 17 16:24:55 2016 -0700 new functions for doing shallow copies of ml_layout and ml_boxarray Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 commit 7975af61d884191cb29d390b145a3c11b24c31a5 Merge: b51578985 03cd46912 Author: Weiqun Zhang Date: Thu Mar 17 14:19:10 2016 -0700 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/Make.package Tools/C_mk/Make.defs commit 789f30b3c8f025b47346ac03b3c9b6e98fcb78bb Author: Weiqun Zhang Date: Thu Mar 17 12:36:25 2016 -0700 fix a memory leak: must call MPI_Wait to free resources even when we know for sure the messages have been sucessfully sent. Src/C_BaseLib/FabArray.H commit 03cd46912bc239a3e108cb2e69d3cf06ccc6ee0e Author: Weiqun Zhang Date: Thu Mar 17 12:36:25 2016 -0700 fix a memory leak: must call MPI_Wait to free resources even when we know for sure the messages have been sucessfully sent. Src/C_BaseLib/FabArray.H commit 18a336cb34231b6313d24b2de149a5c2e17f3ecc Merge: 2e0fe7dff 641f7a30c Author: Marc Day Date: Thu Mar 17 10:22:44 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 641f7a30caf9711b8f41673a590f48a87c5e9d84 Author: Weiqun Zhang Date: Thu Mar 17 08:41:01 2016 -0700 box_f: avoid using Huge(1) because it can cause integer overflow Src/F_BaseLib/box_f.f90 commit 6e7b4f5056fe101b6b651773649556ef8ccc37b4 Author: Marc Day Date: Wed Mar 16 21:34:14 2016 -0700 Add def for BL_PROFILE_VAR_NS when PROFILE=FALSE Src/C_BaseLib/BLProfiler.H commit 2e0fe7dffb4a1a94b068c8a482fca297340065b2 Author: Marc Day Date: Wed Mar 16 21:34:14 2016 -0700 Add def for BL_PROFILE_VAR_NS when PROFILE=FALSE Src/C_BaseLib/BLProfiler.H commit 1070b4a7ef4bb74fd8b923d7a83fce5d9670315a Author: vince Date: Wed Mar 16 13:08:17 2016 -0700 add section for start/stop. Docs/Readme.profiling commit 627c0da3deab3a6f527b774b3c8060f9981a2192 Author: vince Date: Wed Mar 16 12:23:36 2016 -0700 fort profiling fixes. Src/LinearSolvers/F_MG/mg.f90 commit f346af596126467f7d048aad673199c7c5f332ad Author: Weiqun Zhang Date: Wed Mar 16 10:37:26 2016 -0700 make: rm *.mod that could be left over because of wrong PrgEnv Tools/C_mk/Make.rules commit 5fca605fafa7e45ca2ffe922c7e64134d1109e2f Author: Weiqun Zhang Date: Wed Mar 16 10:35:15 2016 -0700 MemProfiler: add VmSize Src/C_BaseLib/MemProfiler.cpp commit b515789854f39d6d702a9e888fb11f6f76d47602 Author: yzheng Date: Wed Mar 16 09:24:42 2016 -0700 Add UPC++ version of CollectData, which needs the latest version of UPC++ Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H commit 876bdb37ab934e094368e3094788de0522ceb7e4 Author: Weiqun Zhang Date: Tue Mar 15 22:02:50 2016 -0700 reduce max # of copyassoc to 25 Src/F_BaseLib/layout.f90 commit 2b90e6b42092fff4bb18994afa59e13e3d82cd05 Author: Weiqun Zhang Date: Tue Mar 15 22:01:21 2016 -0700 MemProfiler: fix an index Src/C_BaseLib/MemProfiler.cpp commit 414660c9d5f755f88f0bac0acfb8235b4b55bfba Author: Weiqun Zhang Date: Tue Mar 15 21:13:00 2016 -0700 decrement copyassoc_cnt Src/F_BaseLib/layout.f90 commit 389c26451c837462b9cdb83a89d030eefbd5815e Author: Weiqun Zhang Date: Tue Mar 15 20:40:15 2016 -0700 cleanup Src/F_BaseLib/memprof.f90 commit 25b2da7dd46109b793350d497e4b9cf523129fa7 Author: Weiqun Zhang Date: Tue Mar 15 18:13:12 2016 -0700 MemProfiler: add data form /proc/pid/status Src/C_BaseLib/MemProfiler.cpp commit 2ed380df68b69804e18d5a08dc008f9874f2aee3 Author: Weiqun Zhang Date: Tue Mar 15 17:07:22 2016 -0700 add a header that Intel complains about missing Src/C_BaseLib/MemProfiler.cpp commit eeec9d0cae54887e75553405da6408182daba48c Author: Weiqun Zhang Date: Tue Mar 15 16:31:34 2016 -0700 flush fortran copyassoc after regrid Src/C_AMRLib/Amr.cpp Src/LinearSolvers/F_MG/FParallelMG.mak commit 9d2cc00e51a13ef005b098a4231e64ddb8ddd1dd Author: Weiqun Zhang Date: Tue Mar 15 16:18:39 2016 -0700 add the new counters to MemProfiler Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/memprof.f90 commit 63c9931a3432da2a116841991db3b737cdf647a7 Author: Weiqun Zhang Date: Tue Mar 15 16:05:47 2016 -0700 layout: add more memory counters Src/F_BaseLib/layout.f90 commit f67526abeab5fb19329e304a592142c75cc5b669 Author: Weiqun Zhang Date: Tue Mar 15 15:18:39 2016 -0700 better estimates of memory cost of fortran data structures Src/F_BaseLib/box_f.f90 Src/F_BaseLib/layout.f90 commit 76557b5e7f1a838fb934b13673a358dd0d410938 Author: vince Date: Tue Mar 15 14:26:00 2016 -0700 use max_level for size. Src/C_AMRLib/Amr.cpp commit a5c4b7079cb3d7f13c7dc78c612cf31008db06da Author: Weiqun Zhang Date: Tue Mar 15 13:28:44 2016 -0700 remove gcc-2 Tools/C_mk/Make.defs commit 807d9343ac842dce702b79f13f2db3691f92e6f3 Author: vince Date: Tue Mar 15 12:25:05 2016 -0700 some cleanup. Tutorials/Sidecar_EX1/DestMFTest.cpp commit 3f3997aa9bc0f7381200ad4e3e275fa4595b20e4 Author: Weiqun Zhang Date: Tue Mar 15 12:23:44 2016 -0700 fix an uninitialized value that affects the memory usage counter Src/F_BaseLib/layout.f90 commit 9ffc3909d615a4a6c9fc57d1666caf4b8359a4a5 Author: Weiqun Zhang Date: Tue Mar 15 12:17:06 2016 -0700 cleanup Src/F_BaseLib/layout.f90 commit b0399d2c273cfcfa3ff96c0ad336663f24d0dc7d Author: Weiqun Zhang Date: Tue Mar 15 10:13:35 2016 -0700 Fortran copyassoc: change the max # allowed Src/F_BaseLib/layout.f90 commit 17c99bf3d188fb85f8f86072873251d00dc89a37 Author: vince Date: Mon Mar 14 18:36:56 2016 -0700 added test to copy from sidecars to comp. Tutorials/Sidecar_EX1/DestMFTest.cpp commit 194b4ae0ec778cc178f9bb3e109379282dfab5ac Author: vince Date: Mon Mar 14 18:34:03 2016 -0700 allow copy from sidecars to comp. Src/C_BaseLib/FabArray.H commit ddee2168f7c21bdfebe6b1df1a1618305642137d Author: Weiqun Zhang Date: Mon Mar 14 18:32:18 2016 -0700 MemProfiler: minor mistake Src/F_BaseLib/layout.f90 commit 6c6fc2018fcb0c949c4f0433d5e2cf66bb04206c Author: Weiqun Zhang Date: Mon Mar 14 18:26:01 2016 -0700 MemProfiler: add fortran copyassoc and boxassoc Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/layout.f90 Src/F_BaseLib/memprof.f90 commit f5bef54bb3826ae2d588846a41924ec6e74b0977 Author: Weiqun Zhang Date: Mon Mar 14 17:50:00 2016 -0700 MemProfiler: skip print if high water mark is zero Src/C_BaseLib/MemProfiler.cpp commit e6e236ac5d1ae8b7f6b4806ce9631995641ee792 Author: Weiqun Zhang Date: Mon Mar 14 17:47:03 2016 -0700 MemProfiler: fortran boxarray Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/memprof.f90 commit b8d3576528a12b9dd1f3572b69102fb61cb7a490 Author: Weiqun Zhang Date: Mon Mar 14 17:29:15 2016 -0700 MemProfiler: add fortran fab Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/MemProfiler_f.H Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/memprof.f90 Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit f917a50ea3fac3d1de2036901567fd7197c42378 Author: Weiqun Zhang Date: Mon Mar 14 17:27:38 2016 -0700 MemProfiler: sort the output Src/C_BaseLib/MemProfiler.cpp commit a8d4f898862cc159f7062d4ef420ff64bd7670d4 Author: Weiqun Zhang Date: Mon Mar 14 15:59:23 2016 -0700 MemProfile: add cached memory Src/C_BaseLib/MemProfiler.cpp commit 094ecdfb7422a1ff559ab4d6503c9e72cb7ea6c7 Author: Weiqun Zhang Date: Mon Mar 14 15:25:00 2016 -0700 MemProfiler: use sysinfo instead of sysconf so that we can get memory used by buffers; we still don't have know about cached memory unless we are going to read /proc/meminfo directly. Src/C_BaseLib/MemProfiler.cpp commit 5d9f0c60fc31295ddb255db44ec6987333b6f218 Author: Weiqun Zhang Date: Mon Mar 14 11:24:57 2016 -0700 BoxArray: do nothing if size does not change in maxSize(); cleanup Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit a2a213589f87d39fb0eb834a8bf210f1e578ffde Author: Weiqun Zhang Date: Mon Mar 14 10:36:19 2016 -0700 fix a new bug in BoxArray I introduced yesterday Src/C_BaseLib/BoxArray.cpp commit 6ff4e17447fc6f4cc09988bd866c25bdd210a959 Author: Brian Friesen Date: Mon Mar 14 09:44:31 2016 -0700 C_mk: remove explicit "-lmpich" flag from link line on Edison/Cori The Cray wrappers resolve MPICH for us automatically, so we don't need to link this by hand. Also, Chris Daley discovered that using this link flag overwrites Darshan's MPI_Init() call with the native MPICH MPI_Init(), which means Darshan can't collect I/O profiling data for any BoxLib code. Tools/C_mk/Make.mpi commit f98fac1014cc49c7c886e78ea5641bd00480a0a1 Author: Weiqun Zhang Date: Sun Mar 13 20:55:18 2016 -0700 MemProfiler: fix BoxArray::removeOverlap Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit ae8a3e6a872f46a09fe2a458871183d1c96b21fb Author: Weiqun Zhang Date: Sun Mar 13 16:58:51 2016 -0700 MemProfiler: optimization Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 2cf3638280bf236b6b94e5f510a99c550bbc5cdc Author: Weiqun Zhang Date: Sun Mar 13 16:13:49 2016 -0700 MemProfiler: save the log in a file Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit 34c48606a1743e6ceeb7ace6e417f102434cb9ed Author: Weiqun Zhang Date: Sun Mar 13 12:58:45 2016 -0700 MemProfiler: pretty Src/C_BaseLib/MemProfiler.cpp commit 46b23adcf0dee9d594181660d43fb726ae1d4036 Author: Weiqun Zhang Date: Sun Mar 13 09:08:21 2016 -0700 BoxArray MemProfiler: split box and cache data Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit bfae3d52bffee45a8480c2c63d1ea781565b01fa Author: Weiqun Zhang Date: Sun Mar 13 09:03:21 2016 -0700 MemProfiler: Copy and FillBoundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit e3821a8904d8b12be96c3a92f4e30b610db9f84f Author: Weiqun Zhang Date: Sat Mar 12 22:52:58 2016 -0800 MemProfile: TileArrayCache Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 530bbce8f456e186bb3826679950a40691270e46 Author: Weiqun Zhang Date: Sat Mar 12 21:37:13 2016 -0800 MemProfiler: Geometry Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit eb14d2c6315ad7ab1487d7b0a39397e4f9608323 Author: Weiqun Zhang Date: Sat Mar 12 18:47:28 2016 -0800 Geometry & FabArray: use the new memory counting function. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit a026b8233a830ae1b71f9f19f736ad6070035bc4 Author: Weiqun Zhang Date: Sat Mar 12 17:56:48 2016 -0800 move memory counting functions into Utility.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp Src/C_BaseLib/Utility.H commit 68ce984235fe1a56cccab82bac2402f80b357d44 Author: Weiqun Zhang Date: Sat Mar 12 17:21:58 2016 -0800 MemProfiler: replace templates with specialized codes Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit 273b709ad561ecc2bd8475dc0c7f50258d2cf866 Author: Weiqun Zhang Date: Sat Mar 12 16:24:04 2016 -0800 MemProfiler: BoxArray and bytesOf for map Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit eb7dae20524a0dd7fc885bbc0463afa2aed90edd Author: Weiqun Zhang Date: Sat Mar 12 11:09:28 2016 -0800 MemProfiler: minor Src/C_BaseLib/MemProfiler.cpp commit fc1e667925759eafc22ebdef61093c9e10eb95b1 Author: Weiqun Zhang Date: Sat Mar 12 11:08:52 2016 -0800 MemProfiler: bytesOf function for std::vector and Array Src/C_BaseLib/MemProfiler.H commit 344f80674e52f06a05cc8a7018993982d5a00ed5 Author: yzheng Date: Fri Mar 11 22:49:07 2016 -0800 Use map instead of unordered_map in BLPgas because unordered_map would cause some linking errors when using the Intel compilers with a recent version of GCC (4.8 or newer) on Cray XC systems Src/C_BaseLib/BLPgas.cpp commit 915b89752d05a173e7ea5212a8747798e753bb45 Author: Weiqun Zhang Date: Fri Mar 11 21:28:45 2016 -0800 MemProfiler: cleanup Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit 8ff5f6aee2e30ca7fcadb9fd0ec7ff72a9b48d76 Author: Weiqun Zhang Date: Fri Mar 11 17:15:31 2016 -0800 MemProfiler: when adding, make sure the name does not exist Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit d4de32dc34099df1cfb219a88f28ec4e1ae87691 Author: Weiqun Zhang Date: Fri Mar 11 17:02:24 2016 -0800 Memory Profiler: first pass Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp Tools/C_mk/Make.defs commit fe6a8c807958b52a1a63c90c838401d1fc909c7a Author: Michael Zingale Date: Fri Mar 11 19:44:40 2016 -0500 latest inputs file -- this has the slack integration Tools/RegressionTesting/Maestro-tests.ini commit 292f634879e7be26825e17db7900a33a1490fac6 Author: vince Date: Fri Mar 11 15:55:05 2016 -0800 changed inputs. Tutorials/Sidecar_EX1/inputs_sc commit 81fabc8235ae7b1b6ec0cfcda6daf35054144d95 Author: vince Date: Fri Mar 11 15:54:16 2016 -0800 added several tests for shifted and grown multifab copies. Tutorials/Sidecar_EX1/DestMFTest.cpp commit 5b306ab00d0e6617b581cbec1db0c2cb762d316d Author: Michael Zingale Date: Fri Mar 11 18:00:00 2016 -0500 add slack integration using webhooks. Now, if you define the slack parameters it will post to the slack channel when the suite starts and post again when the suite ends, reporting the number of failures Tools/RegressionTesting/testnew.py commit 714364b805528a8c932c616cbfd14e0b20b1b3c1 Author: vince Date: Fri Mar 11 14:34:56 2016 -0800 reenable assertions, add more error checking. Src/C_BaseLib/FabArray.H commit 5922501e13efac28c3ca13f11612956f4cb61c7e Author: vince Date: Fri Mar 11 13:57:42 2016 -0800 remove unused variables. Src/C_BaseLib/Geometry.cpp commit 47509c6e05ca3361b167fddc15d88e18b8b5658d Author: vince Date: Fri Mar 11 13:57:25 2016 -0800 FabArray::copyInter seems to work. needs more testing. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit e727a5ba523aa74d086e12cb7c1e1ee0e13d9be1 Author: Michael Zingale Date: Thu Mar 10 22:04:18 2016 -0500 fix formatting when variables are not present Tools/RegressionTesting/testnew.py commit f0e9c409c5314f9f756a3265629f0a941fcbead4 Author: vince Date: Thu Mar 10 18:37:33 2016 -0800 testing the new FabArray::copyInter. Tutorials/Sidecar_EX1/DestMFTest.cpp commit 1397954f21caf1808c9f7737b1b003d5c757dddd Author: vince Date: Thu Mar 10 18:33:46 2016 -0800 copyInter function, TheCPC that takes IndexMaps, not yet complete. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 935772a0b37fb14169c8c7bb8d3a6c1b10ff9dfb Merge: 850cacf9a 72cc2fea7 Author: Andy Nonaka Date: Thu Mar 10 18:13:09 2016 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 850cacf9a778644042a8ca60d3700bf89f58560d Author: Andy Nonaka Date: Thu Mar 10 18:12:32 2016 -0800 added a routine to do a nodal sum and nodal volume, weighting faces, edges, and corners appropriately Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/nodal_sum.f90 commit d6a13d8242b048e3e5353f893cc207de73b2b859 Author: Weiqun Zhang Date: Thu Mar 10 14:05:46 2016 -0800 buildTileArray: fix reordering Src/C_BaseLib/FabArray.cpp commit cb2ce1fd359e70660d779a54cffe82e4e215c9c3 Merge: 26051f44c 72cc2fea7 Author: Weiqun Zhang Date: Thu Mar 10 10:58:32 2016 -0800 Merge branch 'development' into pgas commit 72cc2fea7ecf1f164e478596069d664d04c1bd2c Author: Weiqun Zhang Date: Thu Mar 10 10:58:12 2016 -0800 FillBoundary: remove empty messages in case of cross=true Src/C_BaseLib/FabArray.cpp commit e3828378d5c1523f8665c71740d135693eb5ea0f Author: vince Date: Wed Mar 9 18:30:20 2016 -0800 sync translated dist maps to all procs. Tutorials/Sidecar_EX1/DestMFTest.cpp commit 26051f44c099fd8812c533b2c9bc17ad6dd9bf7f Author: Weiqun Zhang Date: Wed Mar 9 16:25:36 2016 -0800 have to make some changes due to how Intel compiler handles C++11 Src/C_BaseLib/FabArray.cpp commit c1b0ca0c93c51dcabd62caca37334492891886cc Author: Weiqun Zhang Date: Wed Mar 9 16:15:04 2016 -0800 add headers Src/C_BaseLib/FabArray.cpp commit 788825914b4791e3cf02fc8b48abae39769e96b4 Merge: 1054284a7 8de6aaaaa Author: Ann Almgren Date: Wed Mar 9 16:06:31 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 1054284a7ade16e06a10d56d6a39bed9fa84d8ea Author: Ann Almgren Date: Wed Mar 9 16:06:03 2016 -0800 Need to define nlevs based on the mgt, not on the array of multifabs. Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90 commit 41f72b95ce18fa95350400e05c230c7c1706ede1 Merge: 887a14968 a5ba1ff38 Author: vince Date: Wed Mar 9 15:44:49 2016 -0800 resolve confilicts. commit 6abf9813b37b594ec78ffd10db9847fa201d0b1f Author: Weiqun Zhang Date: Wed Mar 9 15:43:37 2016 -0800 make sure that each team worker is more likely to work on its own fabs Src/C_BaseLib/FabArray.cpp commit 887a149681d38852f535d20c021667e4d896d19f Author: vince Date: Wed Mar 9 15:17:13 2016 -0800 copy setup test. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/Utility.H Tools/C_mk/Make.defs Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/inputs_sc commit a5ba1ff38b825123bd0313b0c04520d1fa6b97c4 Author: Brian Friesen Date: Wed Mar 9 15:07:57 2016 -0800 DestMFTest: add extra code showing how to translate DistributionMappings between groups Tutorials/Sidecar_EX1/DestMFTest.cpp commit 6ea0b1d2da5f1f7c8520b5698b082f092ee4c0fe Author: Brian Friesen Date: Wed Mar 9 15:05:46 2016 -0800 DistributionMapping: add static function TranslateProcMap() This function translates the processor map from a DistributionMapping on one MPI group into a map on another group. It currently does not set the sentinel rank, so this must be done manually after the call to this function. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit cd00a8d2c93c97eb107483bcd0514fd41880c1a5 Author: Brian Friesen Date: Wed Mar 9 15:05:07 2016 -0800 DestMFTest: add buzzard wings around cases to prevent variable cross-initialization Tutorials/Sidecar_EX1/DestMFTest.cpp commit af438f0f526865b74bd244f5b43fb893bd8f997a Merge: 6c4549897 8de6aaaaa Author: Weiqun Zhang Date: Wed Mar 9 14:05:38 2016 -0800 Merge branch 'development' into pgas commit 8de6aaaaac2c8775d0b5224b0cd2b88c2d80da01 Author: Weiqun Zhang Date: Wed Mar 9 14:02:42 2016 -0800 Renaming. C++ standard says, "Each name that contains a double underscore (__) or begins with an underscore followed by an uppercase letter (2.11) is reserved to the implementation for any use." Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FabConv.cpp Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 6ddc23702d4b5642c7eeb1645afe6f8e1eef3e9b Author: Brian Friesen Date: Wed Mar 9 13:11:13 2016 -0800 BoxArray: use new BoxArray serialization functions to reduce # of Bcasts() Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp commit be2e713ea19450336b1e71d1e99c37642b340f56 Author: Brian Friesen Date: Wed Mar 9 12:59:00 2016 -0800 BoxArray: split SendBoxArrayToSidecars() into SendBoxArray() and RecvBoxArray() Originally SendBoxArrayToSidecars() had separate logic for senders and receivers internally, but this was confusing because receiving processes would still call "SendBoxArrayToSidecars()" so it looked like they were actually sending something. Splitting this into two functions brings it more in line with point-to-point MPI function names. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp commit 43952b66a979bcc73d9a2f11bccdf909450935fe Author: Ann Almgren Date: Wed Mar 9 12:42:21 2016 -0800 Oops -- in ml_layout restricted build, only define ref ratio up to max_levs-1, not max_levs. Src/F_BaseLib/ml_layout.f90 commit 6c45498970709477f630831c6b4c16d436e10f65 Merge: b042813a2 ab80cc4b1 Author: Weiqun Zhang Date: Wed Mar 9 11:29:10 2016 -0800 Merge branch 'development' into pgas commit ddd126aadb987361d5773753ac662fd6e5074100 Author: Brian Friesen Date: Wed Mar 9 11:24:43 2016 -0800 Sidecars_EX1: add Marc's new test code for moving MultiFabs Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/Make.package commit ab80cc4b11569c4a3a6c4d5e4e871edb3800f476 Merge: 972ef2703 4fea8a5bc Author: Ann Almgren Date: Wed Mar 9 11:21:19 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 4fea8a5bcf7a456bb214a8e89ab75e6a94646a6a Author: Weiqun Zhang Date: Wed Mar 9 11:06:32 2016 -0800 Remove BLMap because (1) C++11 enhanced the thread safety of std::map (2) BLMap does not play well with FabArray in shared memory. Src/C_BaseLib/BLMap.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp commit 972ef27039f7461ecb124b8faf088abc26d71438 Author: Ann Almgren Date: Wed Mar 9 10:33:40 2016 -0800 Fix typo in comment in Tutorials/Tiling_C/main.cpp Tutorials/Tiling_C/main.cpp commit 15cb8a2a05cd05e56c02793a74ba23af538c4313 Author: Ann Almgren Date: Wed Mar 9 10:25:10 2016 -0800 Add a new version restricted build to ml_layout that takes a minimum and maximum level rather than just a new nlevs. Src/F_BaseLib/ml_layout.f90 commit b042813a2eecfe11830c780e6c06770cb3ad5eb1 Author: Weiqun Zhang Date: Wed Mar 9 09:43:48 2016 -0800 minor Src/C_BaseLib/Box.H Src/C_BaseLib/FabArray.H commit dea250cdae45074123c56c2eb1da25fa1d5e80ed Author: Weiqun Zhang Date: Tue Mar 8 18:29:52 2016 -0800 MultiGrid_C: put the main body into a scope so that local MultiFabs are destroyed before MPI_Finalize is called. Tutorials/MultiGrid_C/main.cpp commit 5a9675e20d582f20c100d93c6771ff4216690ac0 Author: Weiqun Zhang Date: Tue Mar 8 11:24:01 2016 -0800 fix typo Src/C_BaseLib/BLPgas.cpp Tools/C_mk/Make.Linux commit c0074be37baf873b78a33c6d293a73382687927b Author: Weiqun Zhang Date: Tue Mar 8 11:20:29 2016 -0800 TagBox::coarsen: disable OMP when team size is greater than 1 Src/C_AMRLib/TagBox.cpp commit 7430796982d9c8dd6eb2e15197951e0ab2108f38 Author: Weiqun Zhang Date: Tue Mar 8 08:36:37 2016 -0800 BLPgas::alloc: proctect against zero or negative size Src/C_BaseLib/BLPgas.cpp commit 9c249eceaa31a53fa9bd86fc45d8d885b0323d11 Author: Weiqun Zhang Date: Mon Mar 7 18:11:28 2016 -0800 0 --> nullptr Src/C_BaseLib/FabArray.H commit 2d838063425a036c49848316e397b37674793125 Author: Weiqun Zhang Date: Mon Mar 7 17:06:09 2016 -0800 FabArray::AllocFabs: for upc++, allocate one big chunk of memory for the whole mulitfab just like what we do now in mpi Src/C_BaseLib/FabArray.H commit 0b1178317fac19b31fd5f54c4264e7e21f2755e1 Author: Weiqun Zhang Date: Mon Mar 7 16:13:07 2016 -0800 FabArray: move shared memory stuff into a struct Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 14f10b196116412cedb61cdbecae19ace179c28f Author: Weiqun Zhang Date: Mon Mar 7 15:18:04 2016 -0800 MPI-3 shared memory: rewrite AllocFabs to reduce the number of shared memory allocation. There is a limit of 1024 sysv segments on Cori and Edison. Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 804372860060af4cfda01006811eec05107afbe2 Author: Weiqun Zhang Date: Mon Mar 7 10:36:48 2016 -0800 BaseFab: remove swap function because it is used and it could be unsafe in shared memory model Src/C_BaseLib/BaseFab.H commit 9dc2fcb0e98fc6b99a2c0dd353827309f67694d2 Author: Max Katz Date: Sat Mar 5 01:52:23 2016 -0500 Print out a more informative message if we crash because the user's Python is too old to support the print() command used in write_probin.py. Tools/F_scripts/write_probin.py commit 754bbd5c893a51503b140dd5f4c1b36f7a9e836d Author: Weiqun Zhang Date: Fri Mar 4 21:30:55 2016 -0800 Set MPI_Info for MPI_Win_allocate_shared to alloc_shared_noncontig Src/C_BaseLib/BaseFab.H commit 91763d71e42297fda7b970da74ef083e050ca2ea Author: Weiqun Zhang Date: Fri Mar 4 17:20:53 2016 -0800 Cray supports C++11 now. Tools/C_mk/Make.Linux commit 3a46158bfe1e5d6f9c55b5ec411d0442a7657ae1 Author: Weiqun Zhang Date: Fri Mar 4 17:20:53 2016 -0800 Cray supports C++11 now. Tools/C_mk/Make.Linux commit b324ba1f8f8d9c511aa5a3916378e3c23495ef15 Merge: 9cf221489 c24eca0ef Author: Weiqun Zhang Date: Fri Mar 4 17:09:05 2016 -0800 Merge branch 'development' into pgas commit c24eca0ef9c389bbcd550edca9cc0841963c03a0 Author: Brian Friesen Date: Fri Mar 4 16:28:46 2016 -0800 C_mk: turn off debug symbols for optimized code with Cray compilers Using "-g" or "-G2" significantly reduces code performance, even with "-O2". So disable all debug symbols to get the fastest code. Tools/C_mk/Make.Linux commit 9f76fcf7b77330806be6b841de4d1ef7895b6059 Author: vince Date: Fri Mar 4 16:16:38 2016 -0800 use new broadcast functions. Src/C_AMRLib/Amr.cpp commit 9cf221489afe3bf41ad5746337b613cb6404aec2 Author: Weiqun Zhang Date: Fri Mar 4 16:09:00 2016 -0800 fix LAZY for team Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c65ef7a279513f5ade5ad070ce72941bba9584fb Author: vince Date: Fri Mar 4 16:03:09 2016 -0800 move some code. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit a1e92c4d7db6d53ee484b0ad3a4e535c8b4032a6 Author: Brian Friesen Date: Fri Mar 4 15:20:05 2016 -0800 C_mk: remove "-debug all" from Intel compiler flags on Edison and Cori This flag emits the same debug information as "-g", which we already use, so it's unnecessary. This partially reverts commit 4c2d110. Tools/C_mk/Make.defs commit 1a05a04247bd9cd6997c1a05f49c9f7b4159c957 Merge: c56c58399 d413a1297 Author: Brian Friesen Date: Fri Mar 4 14:51:54 2016 -0800 Merge branch 'compiler_flag_fixes' into development This merge fixes a few logic bugs in Make.defs related to selecting Intel compiler flags on Edison, Cori, and Babbage at NERSC. commit d413a1297c56eda9a632d92c165e5d44d3e09982 Author: Brian Friesen Date: Fri Mar 4 14:34:49 2016 -0800 C_mk: add back "-fp-model source" to Intel compiler flags on Edison, Intel, and Cori Tools/C_mk/Make.defs commit a9620fbf588f85b02f418cc5603e9149aba6e819 Author: Brian Friesen Date: Fri Mar 4 14:33:05 2016 -0800 C_mk: removed another "else" from "if Edison then" clause when selecting Intel compiler flags Tools/C_mk/Make.defs commit d2827f4544ed47ad424014cdb78a0c041c914f0d Author: Brian Friesen Date: Thu Mar 3 13:27:11 2016 -0800 C_mk: add "-parallel-source-info=2" and "-debug all" to Intel compiler flags on Edison and Cori These emit more complete debug information than is emitted by default, which is useful when running VTune and other profiling tools on optimized code. Tools/C_mk/Make.defs commit bc57f2501f493c2b9b622c8f9b449e4fda0e572f Author: Brian Friesen Date: Fri Mar 4 14:22:58 2016 -0800 C_mk: remove "else" from "if Edison then ..." clause when setting Intel compiler flags Tools/C_mk/Make.defs commit 31cb043a8aa3e331e888a178ab5df0b13ab87f98 Author: Brian Friesen Date: Fri Mar 4 13:44:35 2016 -0800 C_mk: remove "-xHost" flag from Intel compiler flags on Edison and Cori The Cray compiler wrappers for the Intel compilers already contain the correct instruction set flags for both architectures ("-xCORE-AVX-I" on Edison and "-xCORE-AVX2" on Cori). Furthermore, "-xHost" uses the optimal instruction set on the architecture which hosts the compiler, which may be different than that of the compute nodes. This commit partially reverts commit 0088bae. Tools/C_mk/Make.defs commit 2d433a00877390e965b72df964363ebbdee52e6b Merge: 2e1d5e7b3 c56c58399 Author: Weiqun Zhang Date: Thu Mar 3 17:31:49 2016 -0800 Merge branch 'development' into pgas commit c56c583991314898db94d1c3c5ccf48810b1d600 Author: Weiqun Zhang Date: Thu Mar 3 17:31:33 2016 -0800 disable SIGFPE trapping by default because vectorized codes with if statement may have invalid floating point operations whose results are eventually masked out. Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp commit 99f1edbdae7b013913dc602535581656c91f8255 Author: vince Date: Thu Mar 3 14:03:32 2016 -0800 fix for starting with zero sidecar procs. Src/C_BaseLib/ParallelDescriptor.cpp commit 3de11e270bef67fae2f4a0854c731b97273792bc Author: vince Date: Wed Mar 2 17:20:57 2016 -0800 allow nSidecarProcs == 0 Src/C_BaseLib/ParallelDescriptor.cpp commit a7fb11e08ee4db4ba22ec3453bfb09b88b7c16d0 Author: vince Date: Wed Mar 2 16:58:43 2016 -0800 allow nSidecarProcs == 0 Src/C_AMRLib/Amr.cpp commit 5f88b7fac111bf7336e4ba537404db910518c57a Author: vince Date: Wed Mar 2 14:27:09 2016 -0800 some cleanup. Src/C_AMRLib/Amr.cpp commit 1e657ecc0e457ece3885358a4369876ff94c9dc4 Author: vince Date: Wed Mar 2 14:21:53 2016 -0800 first fully working version of dynamic sidecars. Src/C_AMRLib/LevelBld.H Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 185c0007a575ac33e9a03e9bd43b4cc69174dbe2 Author: vince Date: Wed Mar 2 14:10:55 2016 -0800 some cleanup. Src/C_AMRLib/AmrLevel.cpp commit 2e1d5e7b38ff71f89b9614d80fb752e594503ca4 Merge: 3a2e06532 531048693 Author: Weiqun Zhang Date: Wed Mar 2 13:40:29 2016 -0800 Merge branch 'development' into pgas commit 5310486939f299b418c86621094b7a47ca5ff291 Author: Weiqun Zhang Date: Wed Mar 2 13:39:49 2016 -0800 explicitly add noinline attribute for gcc Src/C_BaseLib/FabArray.cpp commit 3a2e065328be3c97a2be5aa184b3ab03a5b0c09f Author: Weiqun Zhang Date: Wed Mar 2 13:39:49 2016 -0800 explicitly add noinline attribute for gcc Src/C_BaseLib/FabArray.cpp commit e3332b5746ca4f371737ad4ca118964b13562cb3 Author: vince Date: Wed Mar 2 13:39:18 2016 -0800 reinitialize fortran data for new procs. Src/C_AMRLib/Amr.cpp commit 03760ca5ebafeeab3013caa81d23843d7380dd67 Merge: ec2b900a6 592f571d8 Author: Weiqun Zhang Date: Wed Mar 2 13:32:14 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit ec2b900a64d9c0b5954dd8f9e4bdf19ad927f557 Author: Weiqun Zhang Date: Wed Mar 2 13:19:45 2016 -0800 minor Src/C_BaseLib/FabArray.H commit 592f571d86017595ef4ab2176034d91163b54d83 Author: Weiqun Zhang Date: Wed Mar 2 16:13:31 2016 -0500 For whatever reason, gcc sometimes doesn't like some functions live in FabArray.H, unless '-fno-inline' is used. Moving them to .cpp file seems to solve the problem. And we can maybe remove the -fno-line from makefile. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Tools/C_mk/Make.defs commit 629ee12207c402460da1f4bac32a29f78c78b5ed Author: Weiqun Zhang Date: Tue Mar 1 14:15:34 2016 -0800 read into MultiFab directly so that it works with shared memory Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit b2eb10a748a678334f9f3640a4f6acf39f21a3f7 Author: Weiqun Zhang Date: Tue Mar 1 12:58:35 2016 -0800 define ownership even if fabs are not allocated so that mfite could work on empty multifabs Src/C_BaseLib/FabArray.H commit b61bb3f9d4bc85a60855c2907603a7efd78c33a7 Author: Weiqun Zhang Date: Tue Mar 1 12:15:40 2016 -0800 avoid setFab because it does not work with the new MFIter Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.cpp commit c4bd91fd5c1f89b97b0debb0179f98f09ef27fa7 Author: Weiqun Zhang Date: Mon Feb 29 18:02:27 2016 -0800 MemoryBarrier: add omp barrier before upcxx and mpi barrier; only master thread calls upcxx or mpi barrier Src/C_BaseLib/ParallelDescriptor.H commit 6fdf1a1fd547d47432d6c54426ad070b0184d0c4 Author: Weiqun Zhang Date: Mon Feb 29 17:27:01 2016 -0800 MFGhostIter: support for team and thread Src/C_BaseLib/FabArray.cpp commit 9a3071d27f1ba29e867d17ea2f6b1a6c3afb1fb0 Author: Weiqun Zhang Date: Mon Feb 29 17:06:49 2016 -0800 minor Src/C_BaseLib/ParallelDescriptor.H commit 91b1c63802a05be53b54f9aeab03ce19901df167 Author: Weiqun Zhang Date: Mon Feb 29 17:05:10 2016 -0800 team_for: rework on support for OMP Src/C_BaseLib/ParallelDescriptor.H commit 60a210b5e777374644f6c967982e0bc1e1c0e3a8 Author: Weiqun Zhang Date: Mon Feb 29 16:44:38 2016 -0800 MFIter: support both team and thread Src/C_BaseLib/FabArray.cpp commit 8f4028c4f0796c074a1ba1ced4dbd2c6955f2bcf Author: Weiqun Zhang Date: Mon Feb 29 15:53:20 2016 -0800 team_for: support for OMP Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 93969202cadd1301000896002831319cb3c5ed30 Author: Weiqun Zhang Date: Mon Feb 29 15:21:34 2016 -0800 Don't call free if not allocated Src/C_BaseLib/Geometry.H commit 2f5a1367d98e9c8f9efb566f675a0de994a671b2 Merge: 39b984e3c cde9f65b1 Author: Weiqun Zhang Date: Mon Feb 29 15:01:58 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit cde9f65b17c1b23cd86fc0ec4c792132b4e39f85 Author: Weiqun Zhang Date: Mon Feb 29 14:39:19 2016 -0800 fix BL_AMRPROF Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit 39b984e3cbc1cac317842c26c2d7db4395cb5583 Author: Weiqun Zhang Date: Mon Feb 29 14:20:04 2016 -0800 make mpi onesided a runtime parameter mpi.onesided Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tests/FillBoundaryComparison/main.cpp Tools/C_mk/Make.defs Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PGAS_HEAT/inputs_3d commit ad9a6269d6a6e5b8364d7beef9c6f50aaa148162 Author: vince Date: Mon Feb 29 13:27:39 2016 -0800 setVect function for broadcasts. Src/C_AMRLib/BCRec.H commit 033d947eedea191d33c39ca624a70988a4d9acee Author: vince Date: Mon Feb 29 13:15:07 2016 -0800 broadcast bcrec. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit b1e76f31c44811589e7024e1a0ad51d2305516fb Merge: d051b491e 3923a7587 Author: Weiqun Zhang Date: Mon Feb 29 10:52:13 2016 -0800 Merge branch 'development' into pgas commit 3923a758730de62d20bd17464a7259a9558037fd Author: Weiqun Zhang Date: Mon Feb 29 10:51:03 2016 -0800 removed an unsafe omp parallel I recently added Src/C_AMRLib/TagBox.cpp commit d051b491e29a260ea4838701ce54661362b668e5 Merge: 9fdf952c2 6eec68f52 Author: Weiqun Zhang Date: Mon Feb 29 10:24:47 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/ParallelDescriptor.H commit 6eec68f52e178529833f2e72625392f5f31c791a Author: Weiqun Zhang Date: Sun Feb 28 12:31:40 2016 -0800 BoxLib::Error and Abort: call BLBackTrace::handler instead of calling ParallelDescriptor::Abort directly so that it can be backtraced Src/C_AMRLib/StateData.cpp Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp commit cf6b90c76a5676d5536395583f3ffa557357b02d Author: Weiqun Zhang Date: Fri Feb 26 21:09:05 2016 -0800 ParallelDescriptor: clean up CommData, which is no longer used in CollectData Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 9fdf952c22b53194d899877566e6870d4dfd3d22 Merge: 5d69deb13 1185cd97b Author: Weiqun Zhang Date: Fri Feb 26 18:14:39 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H commit 1185cd97badecbd47a4622bb171273521040affc Author: Weiqun Zhang Date: Fri Feb 26 18:04:50 2016 -0800 protect IndexMap() function and thus preventing raw loops Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/FabSet.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 5d69deb1354ff73bc6cfc304e492d475d0498ffd Merge: fae165980 77528856b Author: Weiqun Zhang Date: Fri Feb 26 16:50:39 2016 -0800 Merge branch 'development' into pgas commit 77528856b9514f91f49b91205c434f812a47eba0 Author: Weiqun Zhang Date: Fri Feb 26 16:50:27 2016 -0800 remove deprecated functions Src/C_AMRLib/FluxRegister.cpp commit fae165980b897f6de4c1eb4a63f801c75e0c502a Author: Weiqun Zhang Date: Fri Feb 26 16:16:06 2016 -0800 remove the owneronly flag and make owneronly the default when tiling is off Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/FabSet.cpp commit 7bc1502d89a893763cd4f1231f7d2a55e650df74 Merge: 4b1340616 2c82e57ff Author: Weiqun Zhang Date: Fri Feb 26 13:07:45 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 2c82e57ff91eec775176d1af3a181a020ed0f83b Author: Weiqun Zhang Date: Fri Feb 26 13:04:44 2016 -0800 FillPatchIteratorHelper does not need to derive from MFIter Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 09aee65084bbdef356e281d58fab2857f5123cdb Author: Weiqun Zhang Date: Fri Feb 26 12:57:37 2016 -0800 TagBox: sync up with pgas branch Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 4b1340616f0f99f764bcf71bd6e2b9b793e417de Author: Weiqun Zhang Date: Fri Feb 26 12:43:35 2016 -0800 Fix TagBox for team Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit a933003921e8198411b1748ef4e2f7f617d5ef55 Author: Weiqun Zhang Date: Fri Feb 26 09:50:02 2016 -0800 minor Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FabArray.H commit e5819f55bf71388216b2ee25cac6717d2ed1e9eb Merge: 223eb19b9 d6a1727d7 Author: Weiqun Zhang Date: Thu Feb 25 16:27:18 2016 -0800 Merge branch 'development' into pgas commit d6a1727d77d35862a08756f29af1cc02e8af1c72 Author: Weiqun Zhang Date: Thu Feb 25 16:22:45 2016 -0800 rename the fabarray to fab copy function to copyTo and optimize it a bit Src/C_BaseLib/FabArray.H commit 1a164d187db1c24175639570d7e9e745d98e85ff Author: Weiqun Zhang Date: Thu Feb 25 16:21:06 2016 -0800 add BoxCommHelper that helps communicating boxes Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit d070a4114b37da526b5fb0747dd77254d8f6efad Author: Weiqun Zhang Date: Thu Feb 25 10:45:11 2016 -0800 remove some unused and potentially unsafe and inefficient functions Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit d0da8697d2452c8208c4acdce066bc08a657ab03 Author: Weiqun Zhang Date: Wed Feb 24 18:25:41 2016 -0800 remove some deprecated functions Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 223eb19b9a02f5fa00920a240fa2667f8d3be9db Author: Weiqun Zhang Date: Wed Feb 24 18:17:29 2016 -0800 Owner only in the parallel linComb Src/C_BoundaryLib/FabSet.cpp commit 03eb336694a3151a619a0b01c86b907a60dfc161 Author: vince Date: Wed Feb 24 18:14:06 2016 -0800 added min rank to random range map. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 9a9786c24f9c68c23d584a73d82a1b924675c3e3 Author: Weiqun Zhang Date: Wed Feb 24 17:47:40 2016 -0800 update FabSetIter constructor interface Src/C_BoundaryLib/FabSet.H commit 241fe0c5dcf7f8242cd362108709964d3279ed52 Author: vince Date: Wed Feb 24 17:07:51 2016 -0800 added grid redistribution. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 15ad3a488c7fd934e17efe16e72bfa588dad58c8 Author: vince Date: Wed Feb 24 17:06:20 2016 -0800 more broadcast variables. Src/C_BaseLib/MultiFab.cpp commit ad1ff2a3ca225ca87025357fefa7729006c76453 Author: vince Date: Wed Feb 24 17:05:52 2016 -0800 more broadcast variables. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 502fe417f8d2f90280ecff5db9a65157a4e2ac06 Merge: 8fdd438df c7c9c3ce3 Author: Weiqun Zhang Date: Wed Feb 24 15:24:13 2016 -0800 Merge branch 'development' into pgas commit c7c9c3ce31dd2e8d909305eaa7816f2f79fa130a Author: Weiqun Zhang Date: Wed Feb 24 15:23:54 2016 -0800 use quiet nans as initial values of some fabs Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/BndryRegister.cpp commit 8fdd438df042d43d6a2bd974436893b17a5cf83b Merge: 7b5f54fb8 843a7d007 Author: Weiqun Zhang Date: Wed Feb 24 15:15:05 2016 -0800 Merge branch 'development' into pgas commit 843a7d007f919e791bedda791d0fc6e8b47e39cf Author: Weiqun Zhang Date: Wed Feb 24 15:14:41 2016 -0800 No need to use bogus values since in debug and test modes farraybox is filled with snan Src/C_BaseLib/MultiFab.cpp commit 7b5f54fb8b77772628a1a2a7577ef726532ffb58 Author: Weiqun Zhang Date: Wed Feb 24 15:10:12 2016 -0800 comment Src/C_BaseLib/FabArray.H commit 3bc61f504ff6562509b77c85a95313b19fffced8 Author: Weiqun Zhang Date: Wed Feb 24 14:57:13 2016 -0800 Insert a memory barrier at the end of FillPatchIterator. Switch to MFIter in FillCoarsePatch Src/C_AMRLib/AmrLevel.cpp commit 22dc9f8c6fad9f466722edb9708b01049f07ea07 Author: Brian Friesen Date: Wed Feb 24 14:25:07 2016 -0800 C_AMRLib: change "include 'omp_lib.h'" to "use omp_lib" The IBM XL Fortran compiler does not support omp_lib.h. Also that header often includes non-standard OpenMP functions. Using the "omp_lib" module is standard and is supported by all compilers. Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_3D.F commit e65919dc28d4d0035626e349429bc341a7ab218d Author: Brian Friesen Date: Tue Feb 16 15:09:33 2016 -0800 MultiFab: update comment on using SendMultiFabToSidecars() Src/C_BaseLib/MultiFab.cpp commit c7760cffa8fa9f318132a96e040663cce05230b6 Author: Weiqun Zhang Date: Wed Feb 24 14:14:27 2016 -0800 FillPatchIterator: owner only in fill() Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H commit a038bee4db5589e6cdc6691708accfaf01813c65 Author: vince Date: Wed Feb 24 14:00:37 2016 -0800 added more vars to broadcast. Src/C_AMRLib/Amr.cpp commit 433770ebca0798b4dee806d4dde38d44068e04b8 Author: Brian Friesen Date: Wed Feb 24 10:00:19 2016 -0800 MultiFab::SendMultiFabToSidecars: remove redundant check for Box indices in a procmap This check always returns true, so remove it. Src/C_BaseLib/MultiFab.cpp commit 71376fb7dda44ef16b10e2ecc9ba674e0746c515 Author: Brian Friesen Date: Mon Dec 21 10:45:32 2015 -0800 C_mk: update library locations for new custom-built versions of GCC and MPICH on orga Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 82db2b742b67dd7c96a65b6990b42d74474c7155 Author: Weiqun Zhang Date: Tue Feb 23 22:32:56 2016 -0800 first pass of new fillpatch that avoid a mpi_alltoallv Src/C_BaseLib/FabArray.H commit bb7c48c02ae7581716f36dd6c9d1aafd0ec5a052 Author: Weiqun Zhang Date: Wed Feb 24 12:22:06 2016 -0800 BaseFab::swap: swap those new meta data too Src/C_BaseLib/BaseFab.H commit ef2baa91da745530e34ac49e7c57406813e9d8c8 Author: Weiqun Zhang Date: Wed Feb 24 12:20:06 2016 -0800 TagBox: should use local index instead of global index Src/C_AMRLib/TagBox.cpp commit 57bbfadec737aa1984e09e38d6ddbd4ef6ee4fc6 Author: vince Date: Wed Feb 24 11:29:30 2016 -0800 moved data declarations out of function area. Src/C_AMRLib/Amr.H commit cf14dc4f149845e1985e67db072557263ca3e5ad Author: Weiqun Zhang Date: Wed Feb 24 10:52:37 2016 -0800 BaseFab: need to give empty BaseFab's shared_memory variable an initial value, otherwise resize function will be using uninitialized shared_memory Src/C_BaseLib/BaseFab.H commit fe5c7e75d6358236a2d0ff5cd75efecf6f84120a Author: vince Date: Wed Feb 24 10:35:37 2016 -0800 handle zero size intvects. Src/C_AMRLib/Amr.cpp commit 13805647b5ba850cfa37d4680fff7b96f79ea8e8 Merge: 4212b32ae cdcef2aca Author: Weiqun Zhang Date: Wed Feb 24 09:52:20 2016 -0800 Merge branch 'new_fillpatch' into pgas commit cdcef2acabad8b5ed93eed7a68f2ebada727bf6b Author: Weiqun Zhang Date: Tue Feb 23 22:32:56 2016 -0800 first pass of new fillpatch that avoid a mpi_alltoallv Src/C_BaseLib/FabArray.H commit c40daaa6e2e89e3e71e623387fd911f9184496d5 Author: Michael Zingale Date: Tue Feb 23 10:46:17 2016 -0500 now that xrb_simple has a different default network, explicitly compile in rprox Tools/RegressionTesting/Maestro-tests.ini commit 1744bfd6096b21c09a3905903392f32f26320e87 Author: vince Date: Mon Feb 22 15:32:42 2016 -0800 pass flag to add distmap to cache on broadcast. Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 1cdf7600d61aab6fc251a3100a758f28a8e18d77 Author: vince Date: Mon Feb 22 15:15:10 2016 -0800 whichProc option for CacheStats. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 075753a124f85d9f59e95e77e2d79acf04e037e0 Author: vince Date: Mon Feb 22 15:09:01 2016 -0800 option to add map to cache when defining with Array. Src/C_AMRLib/ErrorList.H Src/C_BaseLib/FabArray.H commit 1ab47e74bf852c2ca7a2e8cfe1cf896e1d3c69e4 Author: vince Date: Mon Feb 22 15:07:07 2016 -0800 option to add map to cache when defining with Array. Src/C_BaseLib/Utility.cpp commit 4cc39a847435426649e06e5c11aa71552bbc832c Author: vince Date: Mon Feb 22 15:05:30 2016 -0800 option to add map to cache when defining with Array. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit c3860b584f0d1248762717294d1bf3e11e1c1180 Author: vince Date: Mon Feb 22 15:04:43 2016 -0800 code cleanup. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/StateData.cpp commit 4212b32ae18d5f4bc0569749130e679027feb5d1 Author: Weiqun Zhang Date: Mon Feb 22 12:24:51 2016 -0800 comments Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H commit 928a0f3a9c1280f375cfdd230f9e9d0a7f27b8de Merge: ac91482ac 8a67db181 Author: Weiqun Zhang Date: Mon Feb 22 12:20:33 2016 -0800 Merge branch 'development' into pgas commit 8a67db1811d1b08d5a83e2df72f55a99817012e6 Author: Weiqun Zhang Date: Fri Feb 19 18:02:14 2016 -0800 use quiet nan as safe bogus value Src/C_BoundaryLib/BndryRegister.cpp commit 18b182e0ed890980336aaf10eac41a0954c771ae Author: Weiqun Zhang Date: Fri Feb 19 17:51:42 2016 -0800 no longer need to set special bogus values in DEBUG because it is done in constructor of fab now Src/C_AMRLib/AmrLevel.cpp commit 3815f42e34b658db7d750f9ebc127586e1e511fc Author: Weiqun Zhang Date: Fri Feb 19 17:23:17 2016 -0800 tidy Src/C_AMRLib/AmrLevel.cpp commit ac91482ac4472996213d5027d1e0b734a267acb2 Author: Weiqun Zhang Date: Fri Feb 19 16:04:07 2016 -0800 DistributionMapping: Support for team in KnapSack Src/C_BaseLib/DistributionMapping.cpp commit a83baaf8ce9ed49662f4b18e1c433c5c378d593a Author: vince Date: Fri Feb 19 15:31:32 2016 -0800 set dmid for new procs. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Utility.cpp commit c48b5c3b920cf8be6f626fcd4c9066f1c88f2991 Author: Weiqun Zhang Date: Fri Feb 19 15:07:59 2016 -0800 DistributionMapping: Support for team in RoundRobin Src/C_BaseLib/DistributionMapping.cpp commit 8b249d1b626fd2b5158f92d838494fc8a16598ba Author: vince Date: Fri Feb 19 13:56:02 2016 -0800 print allocatedFAPtrs, remove unused maps. Src/C_BaseLib/FabArray.H commit 25001d29d7a8858aee4b3006072362205aa71582 Author: Weiqun Zhang Date: Fri Feb 19 13:38:41 2016 -0800 MPI one-sided FabArray::copy Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 90fef1bbfdec95fa30d28d2929ffae04f9e5704b Author: Marc Day Date: Thu Feb 18 18:15:45 2016 -0800 Uptick tag Tools/CMake/BoxLib_Version.cmake commit cda2e3959c26a3e358e7ec22482867ad7eca6c9d Author: Weiqun Zhang Date: Tue Feb 16 16:42:38 2016 -0800 add Team support in CPC Src/C_BaseLib/FabArray.cpp commit ab6a0ace1db7c8bdfa5363381626fd257c0485dc Author: Weiqun Zhang Date: Tue Feb 16 15:43:05 2016 -0800 UPC++ in FabArray::copy Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H commit f712e88202fcf00d62daf16764fb58b7ffe448dd Author: Marc Day Date: Wed Feb 17 10:26:08 2016 +1100 Initial changes for building on Australian machines Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 2d91b7b7da9c8d9567b78d3af2969065f4f94646 Merge: a432ea430 3f6b1f2e2 Author: Marc Day Date: Wed Feb 17 08:40:30 2016 +1100 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit a432ea43010737ddd5ca173026530c933cc1d631 Author: Marcus Day Date: Wed Feb 17 08:39:20 2016 +1100 PGI doesnt know about fegetexcept Src/F_BaseLib/backtrace_c.cpp commit ce45bed0f852d21fb3a95a5fddabeaac99ff77a6 Author: Weiqun Zhang Date: Tue Feb 16 13:30:55 2016 -0800 WIP for TagBox with team Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit c7aa17d20c126a20a65865904165e1b371043a16 Merge: d6c094516 3f6b1f2e2 Author: Weiqun Zhang Date: Tue Feb 16 12:40:09 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.cpp commit 3f6b1f2e24f797a901bfa3bf2b353bf9ac2f2b6b Author: Weiqun Zhang Date: Tue Feb 16 07:10:19 2016 -0800 Following up on parent commit, Fortran also likes to print 1.d99 as 0.1+100, so change the upper bound to 1.d98 Src/F_BaseLib/multifab_physbc_edgevel.f90 Tools/Postprocessing/F_Src/fcompare.f90 commit e032c7884f126e5f8a54578697b6401d937c599a Author: Michael Zingale Date: Tue Feb 16 09:56:25 2016 -0500 protect the prints at the high-end too -- if the error is larger than 1.d99, make it 1.d99, this avoids Fortran's habit of dropping the 'E' in the asci representation of numbers with 3-digit exponents. Tools/Postprocessing/F_Src/fcompare.f90 commit c0865fc52313efafbab2e96dcdf8e5584a814638 Author: Weiqun Zhang Date: Mon Feb 15 16:02:47 2016 -0500 Turn on floating point exception trapping for PGI 16 and later Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp commit 6381cbed7c0da85a8eee2e4f6aa56708131735e5 Author: Weiqun Zhang Date: Mon Feb 15 11:40:57 2016 -0800 Fortran fab build: skip memory allocation if box is empty. Src/F_BaseLib/fab.f90 commit dbdddf360200722c5b0108f4e1e970bf04d2ea50 Author: Max Katz Date: Mon Feb 15 13:09:50 2016 -0500 Only print warnings if we're on I/O processor Src/C_AMRLib/Amr.cpp commit 5c936eb4fce1adb9cab66da64f074b09fce321dc Author: Michael Zingale Date: Sun Feb 14 20:59:46 2016 -0500 some png tweaks Tools/RegressionTesting/testnew.py commit 0129205b3fc28dd5b23131b8d316f825a6ef9738 Author: Max Katz Date: Sat Feb 13 20:16:42 2016 -0500 Add two new member functions to StateData: copyOld and copyNew. These copy the old_data and new_data from a source StateData to a destination StateData, and set the time levels correspondingly. Additionally, add a static function StateData::Initialize. Given a StateData generated using the default constructor, set it up with the same characteristics as a source StateData object and do a deep copy of the data. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 964d37ef684689c00d7481ca29838fb1f8a8a248 Author: Michael Zingale Date: Sat Feb 13 18:55:06 2016 -0500 fix a few uninitialized vars Tools/RegressionTesting/testnew.py commit a491534655e93072e9b8571fcb38f99ad6b2cb53 Author: Michael Zingale Date: Sat Feb 13 18:17:14 2016 -0500 remove report_test_failure -- we can get that functionality from report_single_test now, with a failure_msg Tools/RegressionTesting/testnew.py commit 04bc9cd0f6e3ee5e237985666a43050f901dd31a Author: Michael Zingale Date: Sat Feb 13 15:53:22 2016 -0500 store the backtrace when we have failures during the benchmark creation Tools/RegressionTesting/testnew.py commit 7cf175b38d6b472fc3b7d974b6a80b7c4509afd7 Author: Michael Zingale Date: Sat Feb 13 15:21:52 2016 -0500 more error reporting Tools/RegressionTesting/testnew.py commit 46b5e7da7d112bc53356a3e0cf0429fbb46f1e30 Merge: 88d6287cf e501287f8 Author: Michael Zingale Date: Sat Feb 13 15:16:36 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 88d6287cf579bf0fea5dab3271c7f07d538bc594 Author: Michael Zingale Date: Sat Feb 13 15:16:29 2016 -0500 some failure reporting Tools/RegressionTesting/testnew.py commit e501287f8192cb6b7b16a7423b44ece7bdf6b39b Author: Michael Zingale Date: Sat Feb 13 14:52:19 2016 -0500 clean up some error messages Tools/RegressionTesting/testnew.py commit 27132492f897683ba8216a8596592f19876187cd Author: Michael Zingale Date: Sat Feb 13 11:46:18 2016 -0500 fix the early abort test report for restart tests, and also fix the wallclock time. Tools/RegressionTesting/testnew.py commit 3ea7eb06d572422f658e91f10d7ca776a3388b60 Author: Michael Zingale Date: Sat Feb 13 09:54:36 2016 -0500 remove some print debugs Tools/F_scripts/write_probin.py commit 0a507bcfd779aca7a688e2a7332a267842c65321 Author: Weiqun Zhang Date: Fri Feb 12 21:50:01 2016 -0800 Cray: use -G2 instead of -g for ndebug build Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_cray.mak commit f7f53910cf051376e05bebe0b4eeb216f86700c5 Author: Weiqun Zhang Date: Sat Feb 13 00:31:43 2016 -0500 PGI: use -gopt instead of -g for ndebug build Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_pgi.mak commit d6222c9c43c19d2af2ef8505726f0a4e89f51f11 Author: Michael Zingale Date: Fri Feb 12 18:35:31 2016 -0500 this isn't used anywhere Tools/C_mk/Make.bgl commit 2fb19d50eec7246821549f8bee260019dd062011 Author: Michael Zingale Date: Fri Feb 12 18:17:43 2016 -0500 remove carver Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 552f30ed7fc889328ec9881cfc06baa3522c0992 Author: Weiqun Zhang Date: Fri Feb 12 12:48:12 2016 -0800 no longer define BL_TESTING when DEBUG=TRUE to avoid confusion Src/F_BaseLib/backtrace_c.cpp Tools/C_mk/Make.defs Tools/F_mk/GMakedefs.mak commit a10a8b8784774fa8b3d99cfc7be29588c4113e27 Author: Weiqun Zhang Date: Fri Feb 12 12:38:23 2016 -0800 Linear Solver: set full_soln corner cells to quiet nans Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 3a2dcf2cb5d8cabd770c07665c2280fe3a6b3b2d Author: Michael Zingale Date: Fri Feb 12 15:10:19 2016 -0500 for the PGI compilers, we need to compile the C++ source with -O1 instead of -O. This eliminates some global optimizations. There is a compiler error that manifests itself at link time when we compile ParmParse.cpp with -O. Tools/C_mk/Make.Linux commit 1416cf3c710b4e01b7650ee1ba39c32c68c9c6c7 Author: Michael Zingale Date: Fri Feb 12 14:07:02 2016 -0500 Carver is no more Tools/F_mk/GMakeMPI.mak commit 03857d40bb5b32be8636479cf5a82892437a44f3 Author: Michael Zingale Date: Fri Feb 12 12:44:18 2016 -0500 update for PGI 16.1+ -- pgCC no longer exists. We now use pgc++. Also, we can use just -pgf90libs to get the F90 stuff linked Tools/C_mk/Make.Linux commit e96d71240e4ce3444cab07f3186c69c03f0b8652 Author: Weiqun Zhang Date: Thu Feb 11 23:01:01 2016 -0800 do not need to avoid PGI in getting exception flags Src/F_BaseLib/backtrace_c.cpp commit 31b0a97f4565ab5f279d16017cadbb99f0a5f6e7 Author: Weiqun Zhang Date: Thu Feb 11 22:52:49 2016 -0800 minor tweak of get_fpe_trap() Src/F_BaseLib/backtrace_c.cpp commit 3d217f714581f94d11224a528dea661641574557 Author: Weiqun Zhang Date: Thu Feb 11 22:43:01 2016 -0800 remove debug print statements Src/LinearSolvers/F_MG/ml_cc.f90 commit 221b06018c71f95dc5403e6ac218d140a03c0c32 Author: Weiqun Zhang Date: Thu Feb 11 22:04:10 2016 -0800 define BL_TESTING when DEBUG=TRUE Src/F_BaseLib/fab.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Tools/C_mk/Make.defs commit 259ddcc7059a827c55674e6f7ea9742baf5de402 Author: Weiqun Zhang Date: Thu Feb 11 18:19:40 2016 -0800 disable the new code because it does not work. Src/LinearSolvers/F_MG/ml_cc.f90 commit ad880fff1c4cc9c0a8aad18ec9dac1c7d9258560 Author: Weiqun Zhang Date: Thu Feb 11 18:13:38 2016 -0800 Setting corner cells in linear solver: do not set on the first level Src/LinearSolvers/F_MG/ml_cc.f90 commit 70c35851b62b4720b183d5bade843c54c444140c Author: Weiqun Zhang Date: Thu Feb 11 18:03:55 2016 -0800 add get_fpe_trap function; when it returns true, we need to set some corner ghost cells to valid values in linear solver to avoid being trapped by floating point exception Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 3a42f2e0247cb9b2e3dcb8d0c32b3284e4dbd7a8 Author: Weiqun Zhang Date: Thu Feb 11 16:57:07 2016 -0800 add new function mulitfab_set_corner to set corner cells not used in cross stencils; in linear solver call it on full_soln when cross stencil is used. Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 92791b4f142a3e0e946ff5b9b4440032ab9cf9f9 Author: Michael Zingale Date: Thu Feb 11 13:53:17 2016 -0500 for PGI 16.1, we need -pgc++libs instead of -pgcpplibs on the link line (and it should have always been an option, not a library, so I switch the make variable for this). This should hopefully still work on the 15.x compilers, since we are now using pgc++ Tools/F_mk/comps/Linux_pgi.mak commit 043f4041359da8fa0db89fd303be75f4688bc4cc Author: Michael Zingale Date: Thu Feb 11 13:27:00 2016 -0500 as of PGI 16.1, pgCC no longer exists. The new C++ compiler is pgc++ Tools/F_mk/comps/Linux_pgi.mak commit e01083a483aaaccdc64dc3d52e7111b0f56c890c Author: Michael Zingale Date: Wed Feb 10 20:08:26 2016 -0500 we have both compareFile and outputFile -- they serve slightly different purposes. Document that better and make copy_benchmarks know about outputFiles Tools/RegressionTesting/testnew.py commit 39164ade4bcd0ea6f114f423476c496778b6a695 Author: Marc Day Date: Wed Feb 10 14:00:05 2016 -0800 Add godzilla into the make system Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 9b71f603e825978cd7e57cf44ce4c4a7f3c1798e Author: Marc Day Date: Wed Feb 10 13:54:12 2016 -0800 Remove my debugging line in the GNUmakefile Tutorials/MultiGrid_C/GNUmakefile commit ab4541b1dbdd336c2119811bb45f2178015a76d8 Author: Weiqun Zhang Date: Wed Feb 10 12:27:25 2016 -0800 finally fixed my new bug in INTERPER_3D Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit 8923c439ed820e7c4c6df49878b46dc0b97da180 Author: Michael Zingale Date: Wed Feb 10 15:23:18 2016 -0500 fix boxlib-only runs Tools/RegressionTesting/testnew.py commit ae06c1140c1693800f69c7b5d0bb0d6dbe92db1a Author: Weiqun Zhang Date: Wed Feb 10 10:32:23 2016 -0800 latest regression test inputs files Tools/RegressionTesting/BoxLib-tests.ini Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/Nyx-tests.ini Tools/RegressionTesting/RNS-tests.ini Tools/RegressionTesting/SMC-tests.ini Tools/RegressionTesting/VARDEN-tests.ini commit b2d668e4ce4ba42a0db6101dee6d03376c01470d Author: Weiqun Zhang Date: Wed Feb 10 09:58:14 2016 -0800 fix a bug in my last commit: accidentally deleted a line Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit fcd0aa599febf4bcad719dcca928d962737f5e18 Author: Weiqun Zhang Date: Tue Feb 9 15:25:54 2016 -0800 avoid nans Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit 5eb0aaf148b47240498cc586dd2dae199bc6d438 Merge: 1e4d77a75 a880371e1 Author: Marc Day Date: Tue Feb 9 13:56:38 2016 -0800 Merge branch 'development' into 4thOrderMG commit 1e4d77a7500b08c1b593d82de91eea940e6ee11f Author: Marc Day Date: Tue Feb 9 13:56:08 2016 -0800 Change default Tutorials/MultiGrid_C/GNUmakefile commit 1e6bd7e55f927a35de9f9b4ec8db60cfa922ce4c Author: Marc Day Date: Tue Feb 9 13:51:37 2016 -0800 Final junk Tutorials/MultiGrid_C/main.cpp commit a880371e16e7aed5d641602f532adb8bf56729fb Author: Weiqun Zhang Date: Tue Feb 9 12:50:05 2016 -0800 avoid copying nans Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit e49f73f7dbe77f741d2b1b41539d964ffcaed238 Author: Michael Zingale Date: Tue Feb 9 11:56:30 2016 -0500 fix the backtrace links Tools/RegressionTesting/testnew.py commit 1cf2b8d024cc29ff4682d7f11ab36f2a2a4dd214 Author: Michael Zingale Date: Tue Feb 9 10:48:43 2016 -0500 fix name clashing on the backtrace files Tools/RegressionTesting/testnew.py commit 2f568e98327e2ac907285129dae02213c673a840 Author: Marc Day Date: Mon Feb 8 19:33:43 2016 -0800 Fix 3D bug in 4th order boundary stencil, remove some debugging output Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_CellMG4/ABec4_3D.F commit 114f47cf764afb70d6b7a38462ad60928c193c27 Merge: 8f5080f88 2690108c7 Author: Michael Zingale Date: Mon Feb 8 21:08:33 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 8f5080f8827732bfe12c1f26b9d1198efde2238f Author: Michael Zingale Date: Mon Feb 8 21:08:21 2016 -0500 add support for copying and posting the Backtrace files Tools/RegressionTesting/testnew.py commit 2690108c7187d5f97aa2c7d60fb5351dc20683a3 Author: Michael Zingale Date: Mon Feb 8 20:17:53 2016 -0500 enable TEST=TRUE in the tests Tools/RegressionTesting/Castro-SBU-tests.ini commit 8c883521a4e42cdf9f01d61afb631f69a883e6b3 Author: Michael Zingale Date: Mon Feb 8 19:58:39 2016 -0500 split C and F add stuff. Now we have: add_to_f_make_line add_to_c_make_line update the Maestro suite to run with TEST=t Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/testnew.py commit 3e692512afd348ad7d1d9f4e2247d474608b9870 Author: Marc Day Date: Mon Feb 8 16:56:02 2016 -0800 4th order in progress... Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG4/ABec2.H Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec2_3D.F Src/LinearSolvers/C_CellMG4/ABec2_F.H Src/LinearSolvers/C_CellMG4/ABec4.H Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_CellMG4/ABec4_2D.F Src/LinearSolvers/C_CellMG4/ABec4_3D.F Src/LinearSolvers/C_CellMG4/ABec4_F.H Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs Tutorials/MultiGrid_C/main.cpp commit 0698fc3fdb3f7dd037f8dde5ac25923bc65b3181 Author: Michael Zingale Date: Mon Feb 8 19:50:12 2016 -0500 add support for a global line to add to the make command Tools/RegressionTesting/testnew.py commit 899434b5e57f1c4a3421f8bc77d7aa45d3387772 Author: Weiqun Zhang Date: Mon Feb 8 14:28:54 2016 -0800 put abort_fortranboxlib back to module and add a c name for it Src/F_BaseLib/backtrace_f.f90 commit 4e53bda9e8d36a730d4dea36cb2fd7492d5c608d Author: Weiqun Zhang Date: Mon Feb 8 14:14:40 2016 -0800 disable SIGFPE trapping for PGI Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp commit f5b57f9a837742c87f96d4262f8a0258cf0bb604 Author: Weiqun Zhang Date: Mon Feb 8 13:40:47 2016 -0800 To make PGI happy, define _GNU_SOURCE for PGI on Linux Src/C_BaseLib/BLBackTrace.cpp commit b6baf8f4466f50b7f9917694dc3f402372e7e609 Author: Weiqun Zhang Date: Mon Feb 8 13:22:19 2016 -0800 To make PGI happy, define _GNU_SOURCE for PGI on Linux and move subroutine abort_fortranboxlib out of module. Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 commit 70d93ffb64d19accca48ef31bbba70f8afcf0b0c Author: Weiqun Zhang Date: Sun Feb 7 16:24:16 2016 -0800 Backtrace: fix calling handler from Linear Solver in C++ BoxLib codes Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/backtrace_c.cpp commit 4bcf94b9bbc087c2f61560d0c310088a0060ba5c Author: Weiqun Zhang Date: Sun Feb 7 13:16:59 2016 -0800 add write_to_stderr_without_buffering to BoxLib namespace Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp commit 65d7876800389509e641145d3b76f93860d0d471 Author: Weiqun Zhang Date: Sun Feb 7 12:17:02 2016 -0800 update Readme.backtrace Docs/Readme.backtrace commit 8205184b8e7da4b19fde1d51dfc2c570696f6dce Author: Weiqun Zhang Date: Sun Feb 7 10:46:50 2016 -0800 Backtrace: remove SIGTERM because MPI_Abort might use it; cleanup Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/bl_error.f90 commit 3f808881e3a0ab4a745938f407bff50ae18dbe81 Author: Weiqun Zhang Date: Sun Feb 7 00:41:57 2016 -0800 Fortran BoxLib: define BL_TESTING in DEBUG mode Tools/F_mk/GMakedefs.mak commit 711872bb7e20e3d156ca559315e4f5c8ecf9c8d6 Author: Weiqun Zhang Date: Sun Feb 7 00:36:29 2016 -0800 Backtrace: remove SIGABRT from backtrace because that's abort sends Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp commit 790436c5dbc76d157ceaf277d6dd64dab398a890 Author: Weiqun Zhang Date: Sun Feb 7 00:13:43 2016 -0800 Fortran BoxLib: remove the old backtrace Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_error_backtrace.f90 Src/F_BaseLib/bl_prof_backtrace.f90 commit 792a1d6f22f5db2722bb262583d21c433c23a11f Author: Weiqun Zhang Date: Sun Feb 7 00:10:02 2016 -0800 Fortran BoxLib bl_error: call backtrace before abort Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/bl_error.f90 commit 646c382e998ed5d2fc10fe0a225d2a10bbf687dc Author: Weiqun Zhang Date: Sat Feb 6 23:51:09 2016 -0800 Fortran fab: if DEBUG or TEST, initialize fab to snan. Src/F_BaseLib/fab.f90 commit 74115054adbbe913c60cd8bf9ab94ddf2bc23ac4 Author: Weiqun Zhang Date: Sat Feb 6 22:56:00 2016 -0800 Define BL_TESTING when BACKTRACE=TRUE Tools/C_mk/Make.defs commit 376f74696c252f0032d7f53d9f1d6fbafe2f2a4d Author: Weiqun Zhang Date: Sat Feb 6 22:53:25 2016 -0800 Move the setting of snan from FArrayBox to MemPool so that the bl_allocated array can use it and Fortran BoxLib can use it. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/MemPool.H Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/mempool_f.f90 commit d74b08026581e6f3610e854cf6c1164ab66bed22 Author: Weiqun Zhang Date: Sat Feb 6 20:43:48 2016 -0800 add -g to get useful information out of backtrace Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/gfortran.mak Tools/F_mk/comps/osf1.mak commit 9f6f773a269399fc5c31a1a1fa2011b3a4c3efb6 Author: Weiqun Zhang Date: Sat Feb 6 19:44:00 2016 -0800 add handler for SIGABGT Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp commit 4efb0d3ab4d7a674fe640942169bf5c6f314f3f2 Author: Weiqun Zhang Date: Sat Feb 6 19:33:21 2016 -0800 Backtrace in Fortran BoxLib: we now backtrace segfault in Fortran BoxLib. TEST=t or empty is added to the make system. Its purpose is similar to TEST in C++ BoxLib. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 Src/F_BaseLib/boxlib_f.f90 Tools/F_mk/GMakedefs.mak commit 7e7e1a0aa246d7de71d8ad731a5b859e22e10d28 Author: Weiqun Zhang Date: Sat Feb 6 19:30:33 2016 -0800 Add TEST=TRUE or FALSE to the make system. If TEST=TRUE, floating point execeptions will be trapped and MultiFabs will be initialized to snan. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.cpp Tools/C_mk/Make.defs commit a25e2d4eb2c404aa656130a93c6859d32d3edc45 Author: Weiqun Zhang Date: Sat Feb 6 19:21:24 2016 -0800 getcwd should work on any non-windows machines, so move it out of __linux__. Src/C_BaseLib/BoxLib.cpp Tutorials/Tiling_Heat_F/inputs_2d commit a4563bbeca87ab458c23bd7ab03b62d7ccd3138e Author: Weiqun Zhang Date: Fri Feb 5 18:13:52 2016 -0800 New runtime parameter fab.init_snan=0 or 1. The default is 0 when DEBUG=FALSE and 1 when DEBUG=TRUE. This controls initializing Fabs to snan. Note that one still needs to set boxlib.fpe_trap_invalid to trap snans. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit dbd011dc8c90b35099e3ce79aa83290cd0ae1f79 Author: Weiqun Zhang Date: Fri Feb 5 16:08:21 2016 -0800 Turn on the backtracing of segfault, interruption and assertion by default; Floating point exceptions are trapped when DEBUG=TRUE, and they can be turned on or off by runtime parameters, boxlib.fpe_trap_invalid, boxlib.fpe_trap_zero and boxlib.fpe_overflow. Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp commit ea64f0db0a1a74b4c7abb492a49f9dbc0b6bd440 Merge: e02c9a0c7 88b06ad12 Author: vince Date: Thu Feb 4 17:51:42 2016 -0800 Merge branch 'master' into development commit 88b06ad1218519f40c366269bcafe72c6330d02f Author: vince Date: Thu Feb 4 16:46:19 2016 -0800 i/o tests for the burst buffer. the read part needs to be finished. Tests/BBIOBenchmark/BBIOTest.cpp Tests/BBIOBenchmark/BBIOTestDriver.cpp Tests/BBIOBenchmark/GNUmakefile Tests/BBIOBenchmark/README commit e02c9a0c722f2ad5f37462396dbdee7429168f1f Author: Michael Zingale Date: Wed Feb 3 15:53:04 2016 -0500 add priority to runtime parameters. When two parameters are encountered with the same name, the value corresponding to the highest priority one will be kept. Also, a lot of source code cleaning a la PEP-8 Tools/F_scripts/write_probin.py commit d6c094516688675c80d4fb02492f29e47b8227a8 Author: Weiqun Zhang Date: Tue Feb 2 17:47:56 2016 -0800 In simple test codes, MultiFabs are still alive after MPI_Finalize() has been called. The dtor of BaseFab calls MPI functions when MPI shared memory is used. To avoid MPI complaining, we explicitly destroy these MultiFabs before BoxLib::Finalize(). Tests/FillBoundaryComparison/main.cpp Tutorials/PGAS_HEAT/main.cpp commit f6a1784ee64c54ac00521819ae2605aa0ffb37b6 Merge: 8459104cc a15566d94 Author: Weiqun Zhang Date: Tue Feb 2 17:22:31 2016 -0800 Merge branch 'development' into pgas commit 8459104cc2083720099a628d19800190b70e45b3 Author: Weiqun Zhang Date: Tue Feb 2 17:22:04 2016 -0800 clean up FillPeriodicBoundary Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 117ce93901657658553fc9d83f150cde4182cb74 Author: Weiqun Zhang Date: Tue Feb 2 16:18:14 2016 -0800 clean up FillBoundary Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 5c471e41f7d4f54fc7ec72a9d86d94b44e00aa30 Author: Weiqun Zhang Date: Tue Feb 2 14:27:21 2016 -0800 call MPI_Group_free to free the groups Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 0a7a0a05b56d05251ed35310a81f86da7bcd0195 Author: Weiqun Zhang Date: Tue Feb 2 14:11:37 2016 -0800 clean up Src/C_BaseLib/FabArray.H commit 062777023c8110ea28a550365064206f07189b96 Author: Weiqun Zhang Date: Tue Feb 2 13:26:27 2016 -0800 test-mpi3: write and read Tutorials/PGAS_HEAT/test-mpi3/main.cpp commit c12784bb0c8a7685fb3e69430d64581de7d38c07 Author: Weiqun Zhang Date: Tue Feb 2 13:25:43 2016 -0800 fix a typo Src/C_BaseLib/BaseFab.H commit bf457302fe6503eeb8fbd67dece91d2c59516df2 Author: Weiqun Zhang Date: Tue Feb 2 12:20:23 2016 -0800 fix typo Src/C_BaseLib/FabArray.H commit 4e90efbf9d70a669c559cd811b73c57324799c36 Author: Weiqun Zhang Date: Tue Feb 2 12:19:04 2016 -0800 minor change for consistence Src/C_BaseLib/Geometry.H commit d4f9a16997947408cc029b6f0efd2fa11ae61d19 Author: Weiqun Zhang Date: Tue Feb 2 12:18:50 2016 -0800 another BL_USE_UPCXX --> BL_USE_TEAM Src/C_BaseLib/FabArray.cpp commit a8db3dad656594d7581c882174da20b048c97041 Author: Weiqun Zhang Date: Tue Feb 2 11:23:13 2016 -0800 MFIter: BL_USE_UPCXX --> BL_USE_TEAM because of MPI3 team Src/C_BaseLib/FabArray.cpp commit ad7406acba7bdc8c4111d883026b7a3ba60488e7 Author: Weiqun Zhang Date: Tue Feb 2 11:22:22 2016 -0800 add more Memory Barriers Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 7ad50ec3f434f9a8dcf04a0fafcb34cc4969aa42 Merge: 85a7fec83 a15566d94 Author: Marc Day Date: Tue Feb 2 10:45:59 2016 -0800 Merge in process, mg tutorial does not yet build commit 85a7fec83b3b19230840d1d2d3c8afc0c08085a4 Author: Marc Day Date: Tue Feb 2 10:23:49 2016 -0800 Finish up 4th order implementation Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec2_2D.F Src/LinearSolvers/C_CellMG4/ABec2_3D.F Src/LinearSolvers/C_CellMG4/ABec2_F.H Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_CellMG4/ABec4_2D.F Src/LinearSolvers/C_CellMG4/ABec4_F.H Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/main.cpp commit 2fda6f06179cdf004f5c598d47ab52a8aafa0ea2 Author: Yili Zheng Date: Mon Feb 1 20:44:14 2016 -0800 Minor fix of test-mpi3 Tutorials/PGAS_HEAT/test-mpi3/main.cpp commit a99fd904e360c1a8c6ca233c0af7d2a633c41599 Author: Weiqun Zhang Date: Mon Feb 1 20:07:49 2016 -0800 no need to allocate a MPI_Win in the initialization of team; remove MPI calls in the dtor of team Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 1aa777395bbd2d327648581a94d8f0e5299406a4 Author: Weiqun Zhang Date: Mon Feb 1 19:57:23 2016 -0800 need to pass T** to MPI_Qin_allocate_shared Src/C_BaseLib/BaseFab.H commit 308e48cbf3b18836e59a57604bc712576dee6395 Author: Weiqun Zhang Date: Mon Feb 1 19:56:33 2016 -0800 update ifdef Src/C_BaseLib/Geometry.H commit cdaf982af7a3f49c25ef57d4fba5009caef48184 Author: Weiqun Zhang Date: Mon Feb 1 17:34:45 2016 -0800 testing mpi3 shared memory Tutorials/PGAS_HEAT/test-mpi3/main.cpp commit adec17b0fc8ec7284637a979ca0e0dc347cdb17d Author: Weiqun Zhang Date: Mon Feb 1 16:09:52 2016 -0800 fix ifdef Src/C_BaseLib/DistributionMapping.cpp commit 45bc25dab0f8ae872cfe0a4af029e150ef83b5d8 Author: Weiqun Zhang Date: Mon Feb 1 15:49:48 2016 -0800 rename the memory barrier Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H commit 3e49e3bd12d98ecfb961545983eeff4391077954 Author: vince Date: Mon Feb 1 15:38:42 2016 -0800 sync sequence number. Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp commit 6754588978144b12ca1001bb733a15c65d76e632 Author: vince Date: Mon Feb 1 15:04:45 2016 -0800 braces. Src/C_BaseLib/VisMF.cpp commit 185e249e5521bb6a3642e0303ec7b5422b43917c Author: vince Date: Mon Feb 1 15:02:37 2016 -0800 reset noutfiles. Src/C_AMRLib/Amr.cpp commit 3dde7aa2c4be28755de71663014bfddfe68ef682 Author: Weiqun Zhang Date: Mon Feb 1 14:45:47 2016 -0800 fix MFIter::OwnerOnly and NoSharing Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit cbce8adc5d85fad4ccdeec2dfb4e4f88023816b1 Author: Weiqun Zhang Date: Mon Feb 1 12:44:14 2016 -0800 add MPI3 team Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/IArrayBox.H Src/C_BaseLib/IArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/UArena.H Src/C_BaseLib/UArena.cpp Tools/C_mk/Make.defs commit b658304a8546ba4c56fb0c3166e276d1363366bf Merge: 8a79a498c 67280d532 Author: Weiqun Zhang Date: Mon Feb 1 12:41:09 2016 -0800 Merge branch 'mpi-onesided' into pgas commit 67280d5323d0f7f5d58ce983198ac03876964a7b Author: Weiqun Zhang Date: Mon Feb 1 09:07:39 2016 -0800 should be MPI_Group instead of MPI_Comm Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit a15566d9458ea3a780b333609907c532b2d82bf2 Author: Weiqun Zhang Date: Mon Feb 1 09:02:03 2016 -0800 fix assertion when DEBUG=FALSE Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 631d6036e9cb5d43c43ae4a25c6408e3acdffdc8 Merge: 5ee53014c 3a1bcbe1e Author: Michael Zingale Date: Sun Jan 31 20:36:28 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 76d138b1b460b0bb6d06aeb48ae6a037e24ca216 Author: vince Date: Fri Jan 29 19:05:03 2016 -0800 sync sequence numbers. Src/C_AMRLib/Amr.cpp commit 4c9192a9c4a673e8330edf34b38783e6af72efc8 Author: vince Date: Fri Jan 29 19:04:52 2016 -0800 sync sequence numbers. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c75bb371be62c016cdd5116abf4a8f246f130079 Author: vince Date: Fri Jan 29 16:56:53 2016 -0800 more code for the dynamic sidecars. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/Utility.cpp commit 3a1bcbe1ea5a8c497fe1d90501aace993b154eb3 Author: Ann Almgren Date: Fri Jan 29 12:16:53 2016 -0800 Remove unused variables. Src/C_BaseLib/Particles.H commit cd9ce2a2b644a28cc508f7d9fa0861a3f4d2a5ea Author: vince Date: Fri Jan 29 11:36:02 2016 -0800 some name changes. Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H commit 2ce1eb75bfb321d5ad1269e29f1f696c4f04f0f3 Author: vince Date: Fri Jan 29 11:35:08 2016 -0800 also bcast coordsys. Src/C_BaseLib/Geometry.cpp commit 535987a60ce7424d37cbf2ac073af97c12346e13 Author: vince Date: Fri Jan 29 11:33:34 2016 -0800 some name changes. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 9faed6b583f34cacbc4cdfd6be78585b87f183f7 Author: vince Date: Fri Jan 29 11:30:54 2016 -0800 sync distributionmap caches. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 83cd97f994517268882c1d73fc1329e83d0bb14e Author: vince Date: Fri Jan 29 11:29:59 2016 -0800 some name changes. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 8a79a498c5ee9f838cb56d42afa4f7a401f66210 Merge: ec30c0ae9 38cf0d0de Author: Weiqun Zhang Date: Thu Jan 28 14:49:46 2016 -0800 Merge branch 'development' into pgas commit bba796a8412e0d894227f5f1cb140f2533e0c41c Merge: df3c57ca0 38cf0d0de Author: Weiqun Zhang Date: Thu Jan 28 14:49:15 2016 -0800 Merge branch 'development' into mpi-onesided commit 38cf0d0debead77ecf5f8d04a94bd6c8f45f75bc Author: Weiqun Zhang Date: Thu Jan 28 14:02:31 2016 -0800 Particles: fix array index Src/C_BaseLib/Particles.H commit 7a5fe83656469f642c201bcb2ff9523f49e91b38 Author: Weiqun Zhang Date: Thu Jan 28 13:52:15 2016 -0800 TwoGridPIC: add min_grid_size, the smallest box size we can have Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp commit b3d3388d60ebd68b923f98cb73b577aac81bebe2 Author: Weiqun Zhang Date: Thu Jan 28 13:44:18 2016 -0800 Particles: add ParticleBoxArray() and ParticleDistributionMap() to container class Src/C_BaseLib/Particles.H commit 2fc9ba34c71f8f3ab53d2872f0acf74b8179979e Author: vince Date: Thu Jan 28 11:54:34 2016 -0800 func name changes. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit bb3fe9d1a6330207b1181cdd0c0079fdc322d5c7 Author: vince Date: Thu Jan 28 11:54:13 2016 -0800 func name changes. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit eb63aca2eb0810ff46450479ed315245bec48f28 Author: vince Date: Thu Jan 28 11:50:39 2016 -0800 func name changes. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 8d52b8fc90a82cb6128ea15531ff9c72c93d9f36 Author: vince Date: Thu Jan 28 11:16:51 2016 -0800 some cleanup. Src/C_AMRLib/TagBox.cpp commit 49a09958e952ac4ca432434b1e68e7ee7114c006 Author: vince Date: Thu Jan 28 11:15:51 2016 -0800 some cleanup. Src/C_AMRLib/StateData.cpp commit 1869d9441039c305952fb81d8eb6439017d8f2f0 Author: Weiqun Zhang Date: Thu Jan 28 11:11:57 2016 -0800 MemPool: minor clean up Src/C_BaseLib/MemPool.cpp commit 11047f90f7f468932d4a224fd8060014b1c5ec60 Author: Weiqun Zhang Date: Thu Jan 28 10:57:03 2016 -0800 turn off printing various cache statistics by default; to turn it on, use boxlib.v=1 Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 428fa49af4b21585d60db6aa21da9df610c5abfc Merge: c3822ac5a 177e881fb Author: Ann Almgren Date: Wed Jan 27 16:48:47 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit c3822ac5acb19c125cc15d39e0c881415aa4d824 Author: Ann Almgren Date: Wed Jan 27 16:46:08 2016 -0800 This version checks the actual new efficiency instead of just the approximate efficiency and re-distributes the grid if need be. Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp commit 0cfffcd4ca8badd1c887a9da105ab66750a2a42d Author: vince Date: Wed Jan 27 16:02:58 2016 -0800 tests for broadcasting and (un)serializing classes. Tests/C_BaseLib/BcastClasses/BcastClasses.cpp commit 669a4ebe7ee24afa7c2d989b2812cded38747e80 Author: vince Date: Wed Jan 27 16:02:01 2016 -0800 (un)serializeboxarray. Src/C_BaseLib/BoxArray.cpp Tests/C_BaseLib/BcastClasses/GNUmakefile commit ec30c0ae98035ec22e3f2fd0f8e612658f925e5c Merge: df3c57ca0 177e881fb Author: Weiqun Zhang Date: Wed Jan 27 13:19:22 2016 -0800 Merge branch 'development' into pgas commit df3c57ca00856e2347f369327d746474468ddec1 Author: Weiqun Zhang Date: Wed Jan 27 13:03:15 2016 -0800 not possible to have zero size message in the communication tags Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 177e881fb065a6c91730f62624bc17407127aa8d Author: Weiqun Zhang Date: Wed Jan 27 12:35:16 2016 -0800 Particles: replace ParticlesOnSameGrids with OnSameGrids that always does the comparison. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/AmrParGDB.H Src/C_BaseLib/ParGDB.H Src/C_BaseLib/Particles.H commit f7cfcc7b9d9c17878c73e63ef658d1fbdee46feb Author: Weiqun Zhang Date: Wed Jan 27 11:11:43 2016 -0800 BoxArray: new CellEqual function that returns true if the two BoxArrays are equal in enclosed cells. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit cdd5110058c80e8cb62f9224fa228fd21e61d0c3 Author: Weiqun Zhang Date: Wed Jan 27 06:20:03 2016 -0800 fix omp problem due to recent renaming Src/C_BaseLib/Particles.H commit 33d744c4ec7b79b83d49cf5b459490a59d8ef487 Merge: bab6fb8d8 085a5baae Author: hongzhang shan Date: Wed Jan 27 00:17:55 2016 -0800 one more timer commit bab6fb8d8f3ab48bd77bc9a6a35b55213972b279 Author: hongzhang shan Date: Tue Jan 26 22:33:31 2016 -0800 add profiling info Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tests/FillBoundaryComparison/main.cpp commit 02388659895e941516e055cd47e3e003c65a8f82 Author: Weiqun Zhang Date: Tue Jan 26 21:24:33 2016 -0800 fix AdvectWithUmac: (1) since umac is not cell-centered, we should not compare its boxarray with particle boxarray; (2) when we need to build new umac, we should build face-centered mf, not cell-centered Src/C_BaseLib/Particles.H commit 881bb52604688ef922f5c5deb25e10aa1d69e198 Author: Weiqun Zhang Date: Tue Jan 26 21:15:53 2016 -0800 TwoGrid PIC: leave the original ba untouched and fix a memory leak Tutorials/TwoGrid_PIC_C/main.cpp commit d99f1ad2a50a7758bc27f8e959b58d5fc571e7c2 Author: Weiqun Zhang Date: Tue Jan 26 21:14:21 2016 -0800 new MultiFab using Particle BoxArray should also use Particle DistributionMap Src/C_BaseLib/Particles.H commit ddbc06f4f1b460a66f2f321b7fa73bbc90118bfc Author: Weiqun Zhang Date: Tue Jan 26 20:33:43 2016 -0800 store a copy of Geometry, DistributionMapping & BoxArray in non-Amr particle containers Src/C_BaseLib/ParGDB.H commit 085a5baaeed2d132f1c9fa29dedf401fb6a5d077 Author: Weiqun Zhang Date: Tue Jan 26 16:24:39 2016 -0800 remove a barrier Src/C_BaseLib/FabArray.H commit 83d6a97766435dd5759bec3bd383cf6a770040bc Author: Weiqun Zhang Date: Tue Jan 26 16:23:41 2016 -0800 fix typo Src/C_BaseLib/FabArray.H commit 0e12224689f34e30f4dd12f8b01e81e44bca7a0d Author: Weiqun Zhang Date: Tue Jan 26 16:22:30 2016 -0800 fix a new bug; forgot that the address of vector element can be invalidate by push_back Src/C_BaseLib/FabArray.H commit e2903a9ceaa36dd6760506a4365cfd3a8a3ec8ac Author: Weiqun Zhang Date: Tue Jan 26 15:37:27 2016 -0800 Add recv_disp as a member of FabArray so that it is still alive when we exit from FillBoundary_nowai_MPI_Onesided, because it is possible that the sender has not received (or even posted recv for) the address stored in recv_disp yet. Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 96ee39eadd524720b941779d8c13855b3cea64b9 Author: Ann Almgren Date: Tue Jan 26 14:22:13 2016 -0800 Add a new Tutorial which uses a different boxArray for the particles than for the multigrid solve. This uses functions stolen from SedonaBox that split up boxes if they have a disproportionate share of the cost. Tutorials/TwoGrid_PIC_C/GNUmakefile Tutorials/TwoGrid_PIC_C/Make.package Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp commit 559ab6550b00a3d906028ea7094623bcececb046 Merge: 9b2e497d3 832ad1e5e Author: Ann Almgren Date: Tue Jan 26 14:15:16 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 9b2e497d315c9b0695abcac3dfe0453a496f77a5 Author: Ann Almgren Date: Tue Jan 26 14:13:05 2016 -0800 1) Put in placeholder for AssignDensity for nodal multifabs -- not fully implemented yet. 2) Enforce that mf in AssignDensitySingleLevel must have at least one ghost cell or we will lost part of the contribution of a particle near a fine-fine boundary! 3) Replace the "ParticlesOnSameGrids" flag by the actual test since that flag may not be set correctly when we are not calling it with an AMR. 4) Add NumberOfParticlesOnGrid so that we can count and return the number of particles per grid to use as a work estimate for load balancing. Src/C_BaseLib/Particles.H commit 832ad1e5e52a429dde9d3e531f790a76fda34616 Author: Marc Day Date: Tue Jan 26 13:10:46 2016 -0800 Add NumGrow as function to LinOp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit 8e694605ead59b1b8338d5b41b3786f2e3f277a0 Author: Ann Almgren Date: Mon Jan 25 17:11:56 2016 -0800 Let us use the "set" command to reassign a pointer within a PArray if PArrayManage is not true (i.e. PArrayNoManage is true) Src/C_BaseLib/PArray.H commit 74b9f54e6b37e88c769c27526769d8f3ba5a2757 Author: vince Date: Mon Jan 25 15:21:59 2016 -0800 broadcast functions. Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp commit 492df6d2a214d92ebfdd530e2b2757c5e0ddeb04 Author: Weiqun Zhang Date: Mon Jan 25 10:52:30 2016 -0800 Particles: add SetParticleBoxArray function to set a new Particle BoxArray for non-Amr particle containers. For Amr particle containers, users should set the Particle BoxArray in AmrLevel. Src/C_AMRLib/AmrParGDB.H Src/C_BaseLib/ParGDB.H Src/C_BaseLib/Particles.H commit cb06bf66dba5af0c0eadd7f8e7520e94a7b51f13 Author: hongzhang shan Date: Sun Jan 24 18:06:03 2016 -0800 remove 0 size messages, maybe not necessary Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit c4ec0862716f6e60abfe285f6b8000189beaf97d Author: hongzhang shan Date: Sun Jan 24 15:52:08 2016 -0800 fix isend error Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 5ee53014c8d3836a4f8c8db93242aee075043a6e Merge: 823a15878 58e3d531b Author: Michael Zingale Date: Fri Jan 22 19:39:13 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit ca38b66bc0339fdcca610cffc2262ad2d0a025af Author: vince Date: Fri Jan 22 15:16:41 2016 -0800 USleep function. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 74ef2185b5cd79dc6aa953cb7d7f04c847e74c2c Author: Weiqun Zhang Date: Thu Jan 21 17:34:07 2016 -0800 fixed assertion and a similar 'reserve' bug in Geometry Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 394a522444f9cda8c0597df69390d3ad4947474e Author: Weiqun Zhang Date: Thu Jan 21 17:10:31 2016 -0800 Calling reserve is not enough for send_disp. Need to actually allocate space by calling resize. Src/C_BaseLib/FabArray.H commit 58e3d531b12ecfa19b88759f2f9b54161334f889 Author: Ann Almgren Date: Thu Jan 21 15:52:57 2016 -0800 Change itsol_CG_Solve --> itsol_cg_solve to be consistent with the declaration at the top. Src/LinearSolvers/F_MG/itsol.f90 commit 183ad7c30a9cd89c7cbddc7ebde70ccf3b21b1ed Author: Ann Almgren Date: Thu Jan 21 14:43:56 2016 -0800 In itsol_CG_solve: removing the diagonalization and calling the preconditioner earlier dramatically reduces the number of CG iterations needed. Src/LinearSolvers/F_MG/itsol.f90 commit 671fb0c664bd49f080be2c732a0eea6d2cef602f Merge: 6aaaaf457 3c8bea4e8 Author: Ann Almgren Date: Thu Jan 21 14:28:19 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 2da45fd18e309073eb0e5324e229aad62a6c4671 Author: hongzhang shan Date: Wed Jan 20 18:36:14 2016 -0800 with finish function Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 3c8bea4e8610a1533b486f52781f5d7831821cef Author: vince Date: Wed Jan 20 17:32:44 2016 -0800 the makefile. Tutorials/DataServicesTest0/GNUmakefile commit ff3d4e049c4fd5945d9511bb82158233ad6462d6 Author: Hongzhang Shan Date: Wed Jan 20 17:19:57 2016 -0800 add finish functions Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 2ae22ce8d6dad00713dd0bdf7326989f4b09374b Merge: 896eaf6de 3d9629f1a Author: vince Date: Wed Jan 20 17:14:41 2016 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 896eaf6de91e2a0cb8caa722172e7902d95ca903 Author: vince Date: Wed Jan 20 17:02:35 2016 -0800 A simple tutorial for DataServices and AmrData. Tutorials/DataServicesTest0/DataServicesTest0.cpp commit 3d9629f1a9d60aa148be257346b4c2468465553f Author: Weiqun Zhang Date: Wed Jan 20 17:01:17 2016 -0800 fix a recent bug in FillPeriodicBoundary; it affected a special case in which there is a small box (size <= ngrow) near the corner of periodic and non-periodic boundary Src/C_BaseLib/Geometry.cpp commit 6aaaaf4575215ab31bf7c7b0fe437fa39159b819 Merge: 1a6024a2d ac054721f Author: Ann Almgren Date: Wed Jan 20 10:59:42 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit ac054721f1eee9bdf9e5c669af336a3782397bca Author: Michael Zingale Date: Wed Jan 20 11:19:42 2016 -0500 add plot of rad sphere Tools/RegressionTesting/Castro-SBU-tests.ini commit a842ab87d5e1077b9325ee5b85eedbf2911df6fa Author: hongzhang shan Date: Wed Jan 20 03:24:52 2016 -0800 version 1 Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit ab93588364efa75ff17f4e2c4f8547ebe87dc8dd Author: hongzhang shan Date: Tue Jan 19 17:46:09 2016 -0800 fix compiling error and process Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Tools/C_mk/Make.defs Tutorials/PGAS_HEAT/GNUmakefile commit b0ae3e0f69a8a7faa67c164d652330bf0657518a Author: Weiqun Zhang Date: Tue Jan 19 16:48:37 2016 -0800 relax an assertion in average_face_to_cellcenter for Castro Gravity where the cell-centered grad phi has 3 components independent of dimsionality Src/C_BaseLib/MultiFabUtil.cpp commit 6cc218095771aa18063eedafe80a3073d8bac6c1 Author: Hongzhang Shan Date: Tue Jan 19 15:50:11 2016 -0800 follow interface from main.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 1a6024a2dfbea4c846f72fc311b91c6c3e27c2ba Merge: 56efa4699 0092bb3b0 Author: Ann Almgren Date: Tue Jan 19 12:06:31 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 0092bb3b053e7278b7ce59a669c79d57a7c32f81 Author: Michael Zingale Date: Tue Jan 19 12:17:55 2016 -0500 use the Agg backend so that we can do plots when backgrounded Tools/RegressionTesting/testnew.py commit 0aa9734db0d3af35fe27f5e9928db67136803206 Author: Hongzhang Shan Date: Tue Jan 19 01:59:40 2016 -0800 add onesided BL_USE_MPI_ONESIDED Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 823a1587829f57a7fb6e867c55bb2659cb0e25e0 Merge: e09da8844 f9d784e66 Author: Michael Zingale Date: Mon Jan 18 13:27:17 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit f9d784e66639eee774f4f5503e71f6f4d492a9c1 Author: Michael Zingale Date: Sun Jan 17 16:47:51 2016 -0500 use font-awesome Tools/RegressionTesting/testnew.py commit da6c5e2dfecd67f784feb0ed4af2acec21be109b Author: Michael Zingale Date: Sun Jan 17 14:45:54 2016 -0500 add timing plots Tools/RegressionTesting/testnew.py commit f5d980710cae4b46f65e5d4f285104f6af718cf5 Author: Michael Zingale Date: Sun Jan 17 13:09:24 2016 -0500 fix complete_report_from_crash and isolate the code that parses all completed runs and tests to be a method of Suite Tools/RegressionTesting/testnew.py commit e09da8844abaff718c72fb88c87573b95825bdce Merge: c659fa7d9 1531accdc Author: Michael Zingale Date: Sun Jan 17 12:04:58 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 1531accdc87dd6d358aea785ba47f034eeb74e37 Author: Weiqun Zhang Date: Sat Jan 16 15:16:09 2016 -0800 more interfaces to bl_allocate Src/C_BaseLib/mempool_f.f90 commit c659fa7d9dc894bdb7ee1cbeae0a8a27ed9fd1d3 Merge: 0a6b64b78 df708547d Author: Michael Zingale Date: Fri Jan 15 09:37:48 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 27107ca70b785f46696b12aa9e1272e9879b3fce Author: Weiqun Zhang Date: Wed Jan 13 09:07:16 2016 -0800 Just like PostRcvs, no need to pass in RcvTags in PostRcvs_PGAS Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 2daa5d50cee4b18022a75007f033c19b879742d0 Author: Weiqun Zhang Date: Wed Jan 13 08:59:09 2016 -0800 fix the merge Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 8bf9c3ca82c7462c0cef5fadaf916d009a01ae1d Merge: ef8cdde00 df708547d Author: Weiqun Zhang Date: Wed Jan 13 08:47:12 2016 -0800 merge commit df708547dce1dafffc9a379d7d12c3a604e22523 Author: Weiqun Zhang Date: Wed Jan 13 08:31:39 2016 -0800 PostRcvs: no need to pass in RcvTags Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit d9f54ad3a7bef9817d20c9925622d4e24dc635af Author: Weiqun Zhang Date: Tue Jan 12 16:50:11 2016 -0800 add FabArrayBase::empty() Src/C_BaseLib/FabArray.H commit f743c4dd8cb42490d10df5d322f31f4cbe551f5c Author: Weiqun Zhang Date: Tue Jan 12 12:29:10 2016 -0800 add AdvectWithUcc that advects particles with cell-centered velocity Src/C_BaseLib/Particles.H commit 6007bc38586d7d510bc4eaaf5e01eab1a16e3868 Author: Weiqun Zhang Date: Tue Jan 12 11:30:14 2016 -0800 AdvectWithUmac: fix boundary Src/C_BaseLib/Particles.H commit c4f06fa2a0a13070257282ce9abf09be058720e8 Author: Weiqun Zhang Date: Mon Jan 11 18:12:48 2016 -0800 remove an assertion Src/C_BaseLib/Particles.H commit e692ad4387f42446acd32edf598bc960b5719b00 Merge: 06c5c31c1 719157e94 Author: Michael Zingale Date: Sun Jan 10 15:31:24 2016 -0500 Merge branch 'development' into preprocessing commit 719157e9434dedc94fd2d83d312142e517472a02 Author: Weiqun Zhang Date: Fri Jan 8 10:11:19 2016 -0800 Revert this for now because IAMR's SyncRegister actually needs these functions. Will need to fix SyncRegister. This reverts commit 4652df14803966b5be882529bd3720b9783b4b2f. Src/C_BaseLib/FabArray.H commit cb6eb363c105b863b9fb1204be4b75c704147abb Author: Weiqun Zhang Date: Fri Jan 8 10:07:14 2016 -0800 fix bug in my recent change to SumPeriodicBoundary Src/C_BaseLib/Geometry.cpp commit 5473fc1381dfc3afac0699ae8e1417d2378998a0 Author: Weiqun Zhang Date: Fri Jan 8 10:05:36 2016 -0800 fix bug in my recent change to SumPeriodicBoundary Src/C_BaseLib/Geometry.cpp commit 1f38b0f5c269be2f9f9a26aa6034a0ad46b152c7 Author: Weiqun Zhang Date: Thu Jan 7 21:10:46 2016 -0800 add comments and tweak Geometry::FPB::Operator< Src/C_BaseLib/Geometry.H commit 9a68c8e2ee50f0721b023c6035170fd6914e134c Author: Weiqun Zhang Date: Thu Jan 7 20:54:09 2016 -0800 comments Src/C_BaseLib/FabArray.H commit 4652df14803966b5be882529bd3720b9783b4b2f Author: Weiqun Zhang Date: Thu Jan 7 17:29:11 2016 -0800 no longer needed Src/C_BaseLib/FabArray.H commit 2720761a2a5613dc5139ec7d84093e827427de45 Author: Weiqun Zhang Date: Thu Jan 7 17:28:11 2016 -0800 Optimization of SumPeriodicBoundary by reusing the FillPeriodicBoundary cache Src/C_BaseLib/Geometry.cpp commit 25946aa27dcb8ac7a4ea3f5b180cc4dcb0affc51 Author: Weiqun Zhang Date: Thu Jan 7 15:57:47 2016 -0800 readablity Src/C_BaseLib/MultiFab.cpp commit ef8cdde00efdd66813f547aaced587700fdc5ffa Author: Weiqun Zhang Date: Thu Jan 7 12:34:37 2016 -0800 minor clean up Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 0cb90507526c0524d9d887bd407a30677ddf8b02 Merge: d229cb414 a4dc8a8fb Author: Weiqun Zhang Date: Thu Jan 7 11:16:19 2016 -0800 Merge branch 'development' into pgas commit d229cb414ecd7ea00c2bce9306825892bbfb9a21 Author: Weiqun Zhang Date: Thu Jan 7 11:16:03 2016 -0800 remove the option to break messages into smaller pieces Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit 0332ff2f97a887d822529e316d0a7257afd33944 Author: Weiqun Zhang Date: Wed Jan 6 18:08:16 2016 -0800 remove team sender and receiver because it does not perform Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 425090c0aa278c55b724c02de7a8d6573d36aa07 Author: Weiqun Zhang Date: Wed Jan 6 17:01:52 2016 -0800 started MPI-3 team Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tools/C_mk/Make.defs commit a4dc8a8fbadf24aca4d2f67be5e725d15a5d4cc8 Author: Changho Kim Date: Wed Jan 6 14:44:49 2016 -0800 f90 codes do now work on cori. Tools/F_mk/GMakeMPI.mak commit d80168e13faf878995c1653b83ed761c6fadd6d5 Author: Weiqun Zhang Date: Wed Jan 6 13:46:44 2016 -0800 TagBox: add optional alloc argument because of its base class BaseFab Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 35879beb87f08af0de9b10455ca328ef6b786c9f Merge: 605b9fece 68d3922cd Author: Weiqun Zhang Date: Wed Jan 6 12:58:13 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 68d3922cda50e1cf2aff2e05a9bf880931aef910 Author: Weiqun Zhang Date: Wed Jan 6 12:19:59 2016 -0800 new way of thread safety check in FillBoundary, FillPeriodicBoundary and parallel copy Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit a2c73b73ec2cde9a7a3897b6ab3f2fd27a15499f Merge: f3c631554 f7714e0cd Author: Andy Nonaka Date: Tue Jan 5 18:59:38 2016 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit f3c631554695373019424d0ba97cf240e8e85493 Author: Andy Nonaka Date: Tue Jan 5 18:58:58 2016 -0800 plug memory leak in multifab_sum_boundary_c Src/F_BaseLib/multifab_f.f90 commit f7714e0cd190f39e0173639276fd53381af0d5e8 Author: Weiqun Zhang Date: Tue Jan 5 16:39:35 2016 -0800 FabArray::shift: need to update BoxArray-DistributionMap key. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 8a710b199fbbd54dcc95c8243dc7c80744801be1 Author: Michael Zingale Date: Tue Jan 5 19:25:53 2016 -0500 update usage Tools/Postprocessing/F_Src/fextrema.f90 commit a0120dc11993a523b41838926d88fa3b3f3e4339 Author: Weiqun Zhang Date: Tue Jan 5 15:37:09 2016 -0800 clean up Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 605b9fece733ada8283d7eaa9a4cd5f7d073405a Merge: 183f00038 dfcc6a7cf Author: Weiqun Zhang Date: Tue Jan 5 15:08:12 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit dfcc6a7cfccae1653f47f7239fd1b4b9d0b42961 Author: Weiqun Zhang Date: Tue Jan 5 13:22:01 2016 -0800 new functions that copy from periodically shifted MultiFab to another MultiFab. This is useful for restriction of nodal/edge/face MultiFabs Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 899476117aee60139983234fe558c65e9fe3ba65 Author: vince Date: Tue Jan 5 13:21:11 2016 -0800 call bndryreg function. Src/C_AMRLib/FluxRegister.cpp commit 0a6b64b781d65f895719badfce08257a8790ac31 Merge: 06c5c31c1 a6fb893a8 Author: Michael Zingale Date: Tue Jan 5 10:45:14 2016 -0500 Merge branch 'development' into preprocessing commit 06c5c31c10b4c256d18b14b1533752aa3643fb10 Author: Weiqun Zhang Date: Mon Jan 4 21:17:04 2016 -0800 comment out rules for F90 and add VPATH for preprocessed F90 Tools/C_mk/Make.rules commit a6fb893a8791ca762675f78839298683d1a09d5e Merge: 6df1d6123 e5d6d0811 Author: Michael Zingale Date: Mon Jan 4 19:12:50 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 6df1d61239a5d0eb9d1b7dcc2360088194f7be7c Author: Michael Zingale Date: Mon Jan 4 19:12:40 2016 -0500 new source format Tools/RegressionTesting/Maestro-tests.ini commit e5d6d08117e165310858dbe9ff5b2b4f664db8a9 Author: Michael Zingale Date: Mon Jan 4 19:11:23 2016 -0500 add the Detonation test Tools/RegressionTesting/Castro-SBU-tests.ini commit 56efa4699d795047231d8bb643a6b648d18e2266 Author: Ann Almgren Date: Mon Jan 4 15:33:33 2016 -0800 Replace FillPeriodicBoundary by fill_boundary so we fill grad_phi on all ghost cells, not just periodic boundaries. Tutorials/PIC_C/solve_for_accel.cpp commit 33afb449cc0641308b8a79f58d7a940b9b9c1f46 Author: Michael Zingale Date: Mon Jan 4 14:15:51 2016 -0500 remove Intel compilers version 5 to 9.1 -- they are all more than 10 years old Tools/C_mk/Make.defs commit b803db0d09f0b4cb385ac73ea106de7a29c9234a Author: Michael Zingale Date: Mon Jan 4 11:30:35 2016 -0500 remove unneeded clause -- this now seems to work. The F90 files are preprocessed before the dependency checking is done. This eliminates spurrious warnings from the moddep script about modules that are ifdef-ed out not being found. Note: in your code's makefile, you need to add: $(f77TempDir) to the vpath %.f90 line Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 4a52f8b71bf950a5e7254ee87e87f086b7d5d039 Author: Michael Zingale Date: Mon Jan 4 09:59:58 2016 -0500 some work to get F90 preprocessed before the dependency checking Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit b32dcaea66b74586a1aea225d3d9793a13eb614f Author: Michael Zingale Date: Sun Jan 3 22:08:03 2016 -0500 remove homer Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit a19e8547b3327243e07489f83ca983cf7c7190d7 Author: Weiqun Zhang Date: Sun Jan 3 16:39:26 2016 -0800 PArray: add a new function to make it easy for PArray to be used in the 'resource acquisition is initialization' idiom. Src/C_BaseLib/PArray.H commit ae7f7562074df81a430da97e601bd673ff0dc095 Author: Weiqun Zhang Date: Sat Jan 2 20:51:36 2016 -0800 Remove the SumPeriodicBoundary that takes two mfs. I don't think it is used in any codes now. This will allows further optimization of the remaining version of SumPeriodicBoundary. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit f35790bd55c1b9b9f75cefb33bffaf835f8db150 Author: Weiqun Zhang Date: Sat Jan 2 13:52:46 2016 -0800 optimize box-box intersection for FillPeriodicBoundary Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit f40f445cbb4ea0979cec51dd29d074496f47de06 Author: Weiqun Zhang Date: Sat Jan 2 13:52:00 2016 -0800 keep boxarray hash Src/C_BaseLib/FabArray.cpp commit 0590d8e3e53a6a8d205c714d523be96f5b0bff86 Author: Weiqun Zhang Date: Sat Jan 2 08:19:15 2016 -0800 comments on filling periodic boundary Src/C_BaseLib/Geometry.H commit b6866b351d993845df1dec00f77f4f253e4b4646 Author: Weiqun Zhang Date: Sat Dec 26 20:28:40 2015 -0800 minor optimization Src/C_BaseLib/FabArray.cpp commit 63ecba7946da70c0e3772bf56fa5726799f1ab62 Author: Weiqun Zhang Date: Sat Dec 26 20:28:09 2015 -0800 make it more readable Src/F_BaseLib/layout.f90 commit 35c6f4865a266ef486c4bfa77109c8df32d4f0b1 Author: Michael Zingale Date: Sat Jan 2 16:34:07 2016 -0500 fix the make_realclean -- we need to be careful about whehter any build strings are None Tools/RegressionTesting/testnew.py commit 947fce5138fc723edd435d95cfe48cdf78f4002d Author: Michael Zingale Date: Sat Jan 2 12:53:46 2016 -0500 update to the new format + rad and wdmerger tests Tools/RegressionTesting/Castro-SBU-tests.ini commit e39edd3bcde1e1c3fae9a3cbd422afe2412616d9 Author: Michael Zingale Date: Sat Jan 2 12:51:57 2016 -0500 change the way source repos are defined -- they now all have their own block in the inputs file. See ./testnew.py -h for a description. This change makes it a lot easier to support multiple sources and define the desired branch for each. Tools/RegressionTesting/testnew.py commit d9b2c3b3c7a098bf6b0e419eaac6dbc2c4d5a80b Author: Weiqun Zhang Date: Sat Dec 26 13:46:52 2015 -0800 tiling in local copy Src/C_BaseLib/FabArray.cpp commit 67223b9ef823c18acae5e6563698b0de68faa87e Author: Weiqun Zhang Date: Sat Dec 26 12:40:34 2015 -0800 optimize box-box intersection for parallel copy Src/C_BaseLib/FabArray.cpp commit 0d0961e45be36e3a7e52a965371178267c8d5c68 Author: Weiqun Zhang Date: Sat Dec 26 11:59:59 2015 -0800 fix thread safety in FillPeriodicboundary Src/C_BaseLib/Geometry.cpp commit 16a9fdb825eb16a21c9279f82c9716bb96967a7d Author: Weiqun Zhang Date: Fri Dec 25 21:18:16 2015 -0800 have to make sure the intersection box is not empty Src/C_BaseLib/FabArray.cpp commit ff6644806212005d2caaf772276df7b6c1199032 Author: Weiqun Zhang Date: Fri Dec 25 20:57:32 2015 -0800 revert some changes in the last commit because of IAMR Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 6cc40c84f1114fa2f44bd425810ce38f4ea56a86 Author: Weiqun Zhang Date: Fri Dec 25 17:33:04 2015 -0800 optimize box-box intersection for Fillboundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 8a9b8b1862fed5fd4ded12895f823e6e2b287f41 Author: Max Katz Date: Wed Dec 23 02:37:22 2015 -0500 Change the logic for amr.check_per so that it is analogous to amr.plot_per: we write a checkpoint at the first timestep *after* the interval has passed, whereas before we wrote a checkpoint at the timestep *before* we got to the interval. Src/C_AMRLib/Amr.cpp commit 59d8a4ee5c955ed27c63e41e2bcc80c7da4b6b8f Author: Weiqun Zhang Date: Mon Dec 21 20:30:54 2015 -0800 Fortran layout: clean box hash to save memory Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_nd_restriction.f90 commit a3b65b36cfc13a11451db7c9249ee181aa915da6 Author: Weiqun Zhang Date: Mon Dec 21 17:09:46 2015 -0800 tidy Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_nd_restriction.f90 commit 8f8389382968d70aabec60e349a98a376d4a2421 Author: Weiqun Zhang Date: Mon Dec 21 13:12:52 2015 -0800 removed some temporary layouts Src/F_BaseLib/ml_nd_restriction.f90 commit 3a9437c64b61b45cca46abbb0793d15ce1238aae Author: Weiqun Zhang Date: Mon Dec 21 12:37:48 2015 -0800 Fortran layout: get rid of temporary layouts since now layout box intersector can handle nodal and ghost cells. Src/F_BaseLib/layout.f90 commit 5d21ab1d9b96faf43e8bea9f6e0190f709122474 Author: Weiqun Zhang Date: Mon Dec 21 11:21:11 2015 -0800 Fortran Box Intersector: make it work for nodal and ghost cell Src/F_BaseLib/layout.f90 commit b7d77a8140641fce54e3d9f2ccbbe7ae56bdcf01 Author: Max Katz Date: Sat Dec 19 14:17:02 2015 -0500 Fix incorrect query for small_plot_file_root Src/C_AMRLib/Amr.cpp commit a17dcabc1105035a0a18c28ec85b5c8b661b9e2d Author: Weiqun Zhang Date: Fri Dec 18 15:46:15 2015 -0800 move the setup of signal handler after MPI_Init Src/C_BaseLib/BoxLib.cpp commit b8a9d07d298ca6df4776a389ae212936394c67b1 Author: Weiqun Zhang Date: Fri Dec 18 15:35:14 2015 -0800 move the saving of the executable name after MPI_Init has a chance to propgate argv to all processes Src/C_BaseLib/BoxLib.cpp commit 9b22133d37da4fc7b8bc460319e17d54b90bccce Author: Weiqun Zhang Date: Thu Dec 17 17:52:05 2015 -0800 Particle: Use midpoint instead of predictor/corrector to advance particles with mac velocity. This requires only one instead of two ghost cells. Src/C_BaseLib/Particles.H commit 578acd0096c148426601b60849942c674fefbffb Author: Weiqun Zhang Date: Thu Dec 17 17:19:19 2015 -0800 make the output more readable Src/C_BaseLib/BoxLib.cpp commit a6a8b59799ee930de9425f42027259c9bb637c4b Author: Ann Almgren Date: Thu Dec 17 15:50:03 2015 -0800 Add is_nodal() test for MultiFab so we can easily test if a MultiFab is fully nodal or not. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/MultiFabUtil.cpp commit 3b6ed54e8af6ca0b5027642aef97746a7cae6e0f Author: Weiqun Zhang Date: Wed Dec 16 12:14:34 2015 -0800 Particle: change the minimal number of ghost cells of mac velocity from 2 to 1 in assertion Src/C_BaseLib/Particles.H commit 2902ffa331b1394226a567f158d66da7a3ee7b07 Author: Weiqun Zhang Date: Wed Dec 16 09:13:48 2015 -0800 tidy backtrace Src/C_BaseLib/BoxLib.cpp commit 80b907900f28a3d75128907fe15592839f802668 Author: Weiqun Zhang Date: Tue Dec 15 16:51:06 2015 -0800 print out more comments about addr2line Src/C_BaseLib/BoxLib.cpp commit 1cbc5366b04068ca84042c9181b9b411a18dea27 Author: Weiqun Zhang Date: Tue Dec 15 16:21:14 2015 -0800 Particles: fix a memory leak in AdvectWithUmac Src/C_BaseLib/Particles.H commit 3154f138bdbd1331668cfe0589a95d384abb6a81 Author: Weiqun Zhang Date: Tue Dec 15 16:07:51 2015 -0800 clean up Src/C_BaseLib/BoxLib.cpp commit 3fcb3593c57026fd6ef0169953f8563320ca0e14 Author: Weiqun Zhang Date: Tue Dec 15 16:04:47 2015 -0800 For backtracing, use addr2line, if available, to print out function names and line numbers Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Tools/C_mk/Make.defs commit 54534d33558192da21d937aeb95cdbad6f6568a5 Author: Weiqun Zhang Date: Tue Dec 15 14:03:51 2015 -0800 mfiter: allow growntilebox to have negative ng Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 57e0fc9efe9c3c60e1ba9e51cea3a31f2111fe37 Author: vince Date: Mon Dec 14 18:37:29 2015 -0800 MakeSidecarsSmaller function. Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 593d43b3bd7e351f131f5e2267a41a6904463f7d Author: vince Date: Mon Dec 14 17:08:05 2015 -0800 promote MultiFab::MakeSidecarsSmaller Src/C_BoundaryLib/FabSet.H commit c355f897b89427c8fd24b0540f195fceb7285a80 Author: vince Date: Mon Dec 14 17:05:01 2015 -0800 MakeSidecarsSmaller function. Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit fea6672ebeedf0101f8c3b75944e4668a586574f Author: vince Date: Mon Dec 14 17:04:19 2015 -0800 lock allocated fabarray pointers. Src/C_BaseLib/FabArray.H commit 349042ca0158f7fb37b64a1d0179d4bc53497c11 Author: vince Date: Mon Dec 14 17:03:06 2015 -0800 MakeSidecarsSmaller function. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit b6a350c3c2d5624cf3652902dbdbe49930f5beec Author: vince Date: Mon Dec 14 17:02:39 2015 -0800 multifab movement. Src/C_AMRLib/StateData.cpp commit a36771b6960f2b3011a127f8a2dac572eb2cc74a Author: vince Date: Mon Dec 14 17:01:29 2015 -0800 lock allocated fabarray pointers. Src/C_AMRLib/Amr.cpp commit 53f2d5a9015bc98d9a79c25996d24680d9c0b21b Author: Michael Zingale Date: Mon Dec 14 19:04:54 2015 -0500 no more hopper Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 183f00038caa3df9ae677839fe846543b7d6a9f7 Merge: ff3987e85 b6e44c2f2 Author: Weiqun Zhang Date: Mon Dec 14 11:24:19 2015 -0800 Merge branch 'development' into pgas commit b6e44c2f2ede1fc9694a77a86c007fe9f08a3152 Author: Weiqun Zhang Date: Mon Dec 14 11:23:11 2015 -0800 cleanup Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit ff3987e8536b2e0906187574fe35cacab343d6f7 Merge: 9d483e825 cc3bc8c97 Author: Weiqun Zhang Date: Mon Dec 14 11:06:58 2015 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit cc3bc8c979b0f65a181dd37245758b407b377f4f Merge: 5dcefeef4 8e1389994 Author: Michael Zingale Date: Mon Dec 14 11:45:53 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 5dcefeef4dce679760e23a8c4dae2590b4d7489b Author: Michael Zingale Date: Mon Dec 14 11:45:44 2015 -0500 goodbye hopper Tools/F_mk/GMakeMPI.mak commit 8e1389994802bf9f118a82f9fd7fda690e32f178 Author: Weiqun Zhang Date: Sun Dec 13 16:14:00 2015 -0800 clean up Src/C_BaseLib/FabArray.H commit 95e34c1153c628734c1d5b343f8023944baefe1d Author: Andy Nonaka Date: Fri Dec 11 08:21:10 2015 -0800 add gojira and kumonga to DEFAULT_MACHINES Tools/F_mk/GMakeMPI.mak commit 2a316b63d05f107d8ce2a0f894b52d9fed53292a Author: Michael Zingale Date: Thu Dec 10 20:58:43 2015 -0500 simplify a lot of entries in GMakeMPI.mak -- all these machines were doing the same thing, so we use a GNU make findstring() to simplify them. Tools/F_mk/GMakeMPI.mak commit 0acf5ad73ad2b76346883b74550caf63dc531114 Merge: 784dd19a6 c7e881f1d Author: Michael Zingale Date: Thu Dec 10 17:18:12 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 784dd19a6bb9c2d0ae31e17d7d42e0b4c5a14779 Author: Michael Zingale Date: Thu Dec 10 17:17:58 2015 -0500 update the build_info.f90 to allow for no modules Tools/F_scripts/makebuildinfo.py commit c7e881f1d0a8a928d3d4f058498a1edd9eba3e0f Author: Weiqun Zhang Date: Thu Dec 10 12:35:24 2015 -0800 use the new BoxArray intersect functions Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Particles.H Src/C_BoundaryLib/FabSet.cpp commit 5a65941fd946714322592a2ec678c15d6e205040 Author: Weiqun Zhang Date: Thu Dec 10 12:29:48 2015 -0800 fillpatch: remove the ngrow hack Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/AuxBoundaryData.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit baa115c268e94db694f842fa44a06c076dbd3f61 Author: Weiqun Zhang Date: Thu Dec 10 11:20:59 2015 -0800 Parallel copy: using the new BoxArray intersect function Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b9cfd782facfb87cac3b22b390ba09ef0fd4e746 Author: Weiqun Zhang Date: Thu Dec 10 11:07:01 2015 -0800 BoxArray: add ng argument to intersect functions. using it, we don't need to create temporary boxarrays in parallel copy Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 0867a7a5725e59cfac4830b514c5e16d07821387 Author: Michael Zingale Date: Thu Dec 10 12:40:16 2015 -0500 shut-up the iso_c_binding warning Tools/C_scripts/moddep.pl commit ff3ba9b99be38edb37eb92bb6cefa2a34f2e6deb Merge: 68f86948e 023ea8de3 Author: Michael Zingale Date: Thu Dec 10 12:26:26 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 68f86948e7fd5d460799c47bcb3868888b2af3ec Author: Michael Zingale Date: Thu Dec 10 12:26:13 2015 -0500 homer no longer exists Tools/C_mk/Make.defs commit 023ea8de37c959853c7f495bf76741310460c96c Author: Michael Zingale Date: Thu Dec 10 12:17:45 2015 -0500 inlining of C++ doesn't work with GCC 5 and the recent BoxArray stuff. Disable it for now until gcc is fixe.d Tools/C_mk/Make.defs commit caf810434369cc7ab293505bf7275ab0fe9787db Author: Weiqun Zhang Date: Wed Dec 9 20:44:32 2015 -0800 fix typo Src/C_BaseLib/BoxArray.cpp commit 4863c43c18be91260d57e14e9091f843cce659d9 Author: Weiqun Zhang Date: Wed Dec 9 18:04:22 2015 -0800 Since BoxArray has index type now, we can use it insetead of the type of Box 0 in the array Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_TowerLib/MFTower.cpp Src/Extern/amrdata/AmrData.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Tools/C_util/WritePlotFile.cpp Tutorials/AMR_PETSc_C/Source/Darcy.cpp commit af38aa5c36bf971470ab966b3722189670af2a85 Author: vince Date: Wed Dec 9 16:27:27 2015 -0800 broadcast array function. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit b3c80f60954af1c0c3591544b7424b04ed3221e2 Author: Weiqun Zhang Date: Wed Dec 9 14:00:12 2015 -0800 BoxArray: Add index type to BoxArray. This allows nodal and cell-centers BoxArrays share the same reference, which is now always stored as cell-centered boxes. Because of the change, the operator[] now returns Box on demand instead of const Box&. MFIter: Because of the changes in BoxArray, the tile arrays now always store cell-centered boxes. This will construct a nodal box on-demand. A number of other changes have to be made due to that BoxArray no longer provides a const_iterator and the change in return type of operator[]. Src/C_AMRLib/AmrLevel.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 55457294e743076643b629bcd53f74716b822fc2 Author: Weiqun Zhang Date: Wed Dec 9 10:10:35 2015 -0800 IndexType: functions testing cell or node given a direction Src/C_BaseLib/IndexType.H commit e1ba175d98faa92ddaa8f556009e20b9a5a59e6e Author: Weiqun Zhang Date: Wed Dec 9 09:54:40 2015 -0800 Box: add convert more functions and remove a const Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit e7f680cfc9fe08c932c78d28e8230d5af3170bf0 Author: Weiqun Zhang Date: Thu Dec 3 15:47:12 2015 -0800 add distributin mapping to cache even if it's a single process run so that the reference id could work Src/C_BaseLib/DistributionMapping.cpp commit 9d483e825022bde6de7e85824dadbaa5397f0cf3 Merge: 8008487a8 788ced409 Author: Weiqun Zhang Date: Wed Dec 9 09:39:14 2015 -0800 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 4d61f3b2658d60d09104f2e65459c36d2334ba4e Merge: 0d55d1400 9f4ac2bf9 Author: Adam M. Jacobs Date: Tue Dec 8 21:17:26 2015 -0500 Merge branch 'development' into openacc commit 3bf956694166255636357cee24e0f92d37143524 Author: vince Date: Tue Dec 8 18:03:45 2015 -0800 more broadcast functions. Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 58d662713377a35b154b2f85e52ac514fcf9d522 Author: vince Date: Tue Dec 8 16:27:37 2015 -0800 added virtual destructor. Src/C_BaseLib/MultiFab.H commit c0553172c7b260d5cab0e0f6d96665492183bc6b Author: vince Date: Tue Dec 8 16:26:49 2015 -0800 replaced code with broadcast functions. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp commit afd810c3eaaddd4e8b484d0577c0f000e8231f60 Author: vince Date: Tue Dec 8 16:05:16 2015 -0800 functions to broadcast boxes and boxarrays. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit e6532ea692e9a81be081b6b3a7666919ad93e6e2 Author: Max Katz Date: Tue Dec 8 16:01:32 2015 -0500 Add a small plotfile functionality to C++ BoxLib. The small plotfile is very similar to a normal plotfile, but it can be output at a different rate using amr.small_plot_int and amr.small_plot_per. The major difference is that it only accepts state variables, and you have to manually specify each one using amr.small_plot_vars. This is designed for output of a small number of variables at a high rate, for purposes like making movies of your simulations. Unlike the plotfile functionality, this is not implemented as a pure virtual function, so it is not required for derived classes of AmrLevels to implement this functionality. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 9f4ac2bf95d9816866f0d1b77f7525275d1afb48 Merge: 4050be6c2 ea6c230c0 Author: Michael Zingale Date: Tue Dec 8 12:55:40 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 4050be6c25cd60494d9b4e647c34b1ccf441515f Author: Michael Zingale Date: Tue Dec 8 12:55:23 2015 -0500 fix the flags for .F90 preprocessing with Linux Tools/C_mk/Make.Linux commit bd8b4a788739a047285b8de8307bb9c5a0d8f1aa Author: vince Date: Mon Dec 7 18:28:52 2015 -0800 added undefined strategy. Src/C_BaseLib/DistributionMapping.H commit a33501326da628c33fbd7fea9535e25c89840aa5 Author: vince Date: Mon Dec 7 17:56:04 2015 -0800 functions for making the sidecars smaller. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit faaa06ba223bd8d5334b5096263fba0ef7a69be3 Author: vince Date: Mon Dec 7 16:35:46 2015 -0800 FabArray pointer locks, mpi only sections. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit ea6c230c01a9da80433adb6ad582444b0e0b2b11 Merge: dae4872dc 3f6191b0b Author: vince Date: Mon Dec 7 14:11:29 2015 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit dae4872dc6bbfdfb2534aa636cc438c6c451437f Author: vince Date: Mon Dec 7 14:11:09 2015 -0800 added machine support for syrah. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 3f6191b0b7e0ef4112f13550813ccb5ebbca5cd8 Author: Weiqun Zhang Date: Fri Dec 4 15:51:22 2015 -0800 add optional argument to FillCoarsePatch to allow copy into ghost cells Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 9d6c1945320632d5971eaf5b9d2e197d0af0610d Author: Weiqun Zhang Date: Fri Dec 4 15:45:42 2015 -0800 copy from FabArray to fab: allow copying from the ghost regions Src/C_BaseLib/FabArray.H commit bc51aba591d3cae4661bb2e16286e750083e609a Author: Gunther H. Weber Date: Thu Dec 3 18:32:56 2015 -0800 Fix building with BL_NO_FORT for VisIt Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Make.package commit 1176fbc5363d9af2a788121aad70f3f5b4e778ac Author: Gunther H. Weber Date: Wed Dec 2 17:05:15 2015 -0800 Added BL_CXX11.H to CMakeList.txt Src/C_BaseLib/CMakeLists.txt commit 8e15ff8f354c0a3ae7a0337616bc1c4145ce821f Author: Weiqun Zhang Date: Wed Dec 2 14:33:06 2015 -0800 Copy Cache stats Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 158bbca81a2cccb90bb6980a353d0b31d5ce5b70 Author: Weiqun Zhang Date: Wed Dec 2 14:15:09 2015 -0800 tidy Src/C_BaseLib/FabArray.H commit 3031712e5213c4f50f3b486d84efb325b9201f17 Author: Weiqun Zhang Date: Wed Dec 2 14:04:06 2015 -0800 Fill Boundary Cache stats Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit f0b5f31d1ee31dfae530043358ec6c3ff19625f5 Author: Weiqun Zhang Date: Wed Dec 2 13:08:28 2015 -0800 rework on cache stats Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 771f00d76da181bd724b18c5485f07fd6e8110a2 Author: Marc Day Date: Wed Dec 2 14:11:22 2015 -0800 Fixup CMakeLists.txt to reflect that BCRec and BC_TYPES.H moved from C_AMRLib to C_BaseLib Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt commit a1fdef04640f7b9379d7473d35f710ed120b2f57 Author: Michael Zingale Date: Wed Dec 2 13:19:51 2015 -0500 hack in support for branches for the extra build directories Tools/RegressionTesting/testnew.py commit 788ced4092422574486032fe38094a9777ca2b41 Merge: b4ac11c33 06b284237 Author: Weiqun Zhang Date: Tue Dec 1 21:31:30 2015 -0800 Merge branch 'development' into pgas commit 06b284237ab5482b1ab7d2ff3afa393a816e5c1c Author: Weiqun Zhang Date: Tue Dec 1 21:28:55 2015 -0800 TileArrayCache: improve print() Src/C_BaseLib/FabArray.H commit b4ac11c333eaa6f17dd2d8c56181a9ef72789213 Author: Weiqun Zhang Date: Tue Dec 1 21:28:55 2015 -0800 TileArrayCache: improve print() Src/C_BaseLib/FabArray.H commit 498622edf79fb96582b61ee86db77ef259814862 Author: Weiqun Zhang Date: Tue Dec 1 21:27:38 2015 -0800 PGAS_SMC: limit the scope of SMC for more accurate stats MiniApps/PGAS_SMC/main.cpp commit 1615c5f5d5b39d768b81ca68a8e09221a1c8c4f9 Author: Weiqun Zhang Date: Tue Dec 1 20:50:11 2015 -0800 MFGhostIter: need to set various indices Src/C_BaseLib/FabArray.cpp commit a87bf7df09c6592fad8079f0a0e172c49488296f Merge: ca8613895 f07eb3a0d Author: Weiqun Zhang Date: Tue Dec 1 20:45:47 2015 -0800 Merge branch 'development' into pgas commit f07eb3a0d298e17639de8c9eddb46424627b539f Author: Weiqun Zhang Date: Tue Dec 1 20:45:07 2015 -0800 TileArrayCache: tidy Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 0a2825aa0a96633ff063708607b5714fb22b037d Merge: b32fc6c79 5353151f2 Author: Weiqun Zhang Date: Tue Dec 1 17:56:06 2015 -0800 Merge branch 'tilearraycache' into development commit 8008487a892e090954a095afe55227a44c454c45 Author: Weiqun Zhang Date: Tue Dec 1 17:18:20 2015 -0800 PGAS_SMC: change defaults MiniApps/PGAS_SMC/SMC.cpp commit ca8613895a7bac176d886cdbda682ece8f448824 Merge: f094d8fff 5353151f2 Author: Weiqun Zhang Date: Tue Dec 1 17:06:40 2015 -0800 Merge branch 'tilearraycache' into pgas commit 5353151f2f2d9899449841c4fa659a40f23c9c6c Author: Weiqun Zhang Date: Tue Dec 1 17:06:33 2015 -0800 FabArray stats: don't need to use long long because long is 8 bytes on 64-bit Unix systems. Src/C_BaseLib/FabArray.H commit f094d8fff21c11f91e83d577293d15c065ef111a Author: Weiqun Zhang Date: Tue Dec 1 17:03:24 2015 -0800 fixed MFGhostIter Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 732385539c824bedd12c37ce2e59f9b522f74539 Merge: 285066cf5 ab8483356 Author: Weiqun Zhang Date: Tue Dec 1 16:34:39 2015 -0800 Merge branch 'tilearraycache' into pgas Conflicts: Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit ab8483356897c7fe2522e609c7f2509e70bf634c Author: Weiqun Zhang Date: Tue Dec 1 16:21:54 2015 -0800 tidy Src/C_BaseLib/FabArray.H commit b707cd204d7f4dba0be92295909f6a3c7bed4b0b Author: Weiqun Zhang Date: Tue Dec 1 15:09:28 2015 -0800 FabArray: stats Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b57ffaab5dc36d25dba6e77af34936862da6cd38 Author: Weiqun Zhang Date: Tue Dec 1 14:40:54 2015 -0800 TileArray: add stats Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit f29903ea3fc4be9308534d978023af159a75f324 Author: Weiqun Zhang Date: Tue Dec 1 10:54:18 2015 -0800 new MFIter ctor taking TileArray ptr Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 9e8dfeb300ece8be4c19067b663b8ccde650e0fe Author: Weiqun Zhang Date: Tue Dec 1 10:42:51 2015 -0800 add MFIter dtor Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 6b32e86ba1f7163ae1dd5a14e7c6239ea6782234 Author: Weiqun Zhang Date: Tue Dec 1 10:40:53 2015 -0800 cleanup Src/C_BaseLib/FabArray.cpp commit 85aac227e6c2bca6d6892d2ea651e39877355dbf Author: Weiqun Zhang Date: Tue Dec 1 10:30:29 2015 -0800 TileArray: use pointer instead of reference in MFIter so that we can pass null ptr; use omp critical instead of single. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d6361e789be8c4bac1517c84aa661c1e77de8566 Author: Weiqun Zhang Date: Mon Nov 30 16:33:42 2015 -0800 FabArray: if it is never defined, do not need erase tile array Src/C_BaseLib/FabArray.H commit b32fc6c79f415acc49118b9b3387e04c88d10fba Author: Weiqun Zhang Date: Mon Nov 30 16:10:04 2015 -0800 more regression tests inputs Tutorials/MultiGrid_C/inputs-rt-c-neu Tutorials/MultiGrid_C/inputs-rt-c-ord2 Tutorials/MultiGrid_C/inputs-rt-c-ord3 Tutorials/MultiGrid_C/inputs-rt-f-neu Tutorials/MultiGrid_C/inputs-rt-f-ord2 Tutorials/MultiGrid_C/inputs-rt-f-ord3 commit ecb829d2c1102d9914b490b03674f161e465d329 Author: Brian Friesen Date: Mon Nov 30 15:49:10 2015 -0800 Tutorials/MultiGrid_C: fix contradictory comments about Dirichlet boundary order in HPGMG Tutorials/MultiGrid_C/inputs commit 9956c1e74f9df135d03f943ca84f96d436b4910d Author: Weiqun Zhang Date: Mon Nov 30 15:45:56 2015 -0800 Linear Solvers Comparison Test: add maxorder parameter and new inputs for regression tests Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord2 Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord3 Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp commit 4bc5612d19a8cfff83d4f90b74d20caeeef8dc83 Author: Brian Friesen Date: Mon Nov 30 15:39:56 2015 -0800 MultiFab: remove my inexplicable const_cast<> for getVect() pointers in MPI buffers in SendMultiFabToSidecars() I don't know what I was thinking here. Using const_cast<> sometimes sends nonsense data to the sidecars. Src/C_BaseLib/MultiFab.cpp commit dd26f41339d1a5b2ac9ff9d7a5a113de6113c2c0 Author: Weiqun Zhang Date: Mon Nov 30 15:37:17 2015 -0800 MultiGrid_C Tutorial: add inputs for new regression tests Tutorials/MultiGrid_C/inputs-rt-c-ord2 Tutorials/MultiGrid_C/inputs-rt-c-ord3 Tutorials/MultiGrid_C/inputs-rt-f-ord2 Tutorials/MultiGrid_C/inputs-rt-f-ord3 commit 7fd00753ae4c11cb2d49a1827a497f9a8f78bab8 Author: Weiqun Zhang Date: Mon Nov 30 15:32:10 2015 -0800 MultiGrid_C Tutorial: rename mg.stencil_order to mg.maxorder Tutorials/MultiGrid_C/inputs Tutorials/MultiGrid_C/main.cpp commit 285066cf50add11d0d4b2033eedb7d8316d482e5 Merge: cf38ae82e 1aa6ecc57 Author: Weiqun Zhang Date: Mon Nov 30 14:56:53 2015 -0800 Merge branch 'tilearraycache' into pgas Haven't fixed all conflicts yet! Conflicts: Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b007518b7c098748609da04b268f34c8e305e090 Author: Brian Friesen Date: Mon Nov 30 13:58:27 2015 -0800 Tutorials/MultiGrid_C: set default Dirichlet boundary condition order to 2 in inputs file HPGMG uses 2nd-order Dirichlet boundary conditions, so use that by default in the BoxLib solvers so that all 3 solutions match. Tutorials/MultiGrid_C/inputs commit 5cf2f8e4167e7e85485e8cec9b57267aafd14785 Author: Brian Friesen Date: Mon Nov 30 13:57:13 2015 -0800 Tutorials/MultiGrid_C: enable writing numerical solution plotfiles by default in inputs file Tutorials/MultiGrid_C/inputs commit 5a643f29d01553e0568070e2d8b5d4fb94379176 Author: Brian Friesen Date: Mon Nov 30 13:56:27 2015 -0800 Tutorials/MultiGrid_C: disable calculation of norms by default in inputs file Tutorials/MultiGrid_C/inputs commit f4ad864897310fe415f74c5c6b44c4e9654efe76 Author: Ann Almgren Date: Mon Nov 30 13:30:43 2015 -0800 We can now pass mg.stencil_order in through the inputs file to be used to set the max_order for the F90 solver through a set_maxorder call. Note that the "orders" must match (2 and 2, or 3 and 3) for the F90 and C++ solvers to give the same solution with Dirichlet boundaries. Tutorials/MultiGrid_C/inputs Tutorials/MultiGrid_C/main.cpp commit b09cfdd0185265179d0840813e12fec7ddd2c15f Author: Ann Almgren Date: Mon Nov 30 13:29:55 2015 -0800 Typo in comment. Tutorials/MultiGrid_C/RHS_3D.F commit e344d99ae60dd6d477b9fc802659d371b8f5a763 Author: Ann Almgren Date: Mon Nov 30 13:29:38 2015 -0800 Formatting changes so these are easier to read. Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/RHS_3D.F commit 40a33b507e7973b495a643aaa71accc570e3b0d8 Merge: 246801c3f 7ff8d7729 Author: Ann Almgren Date: Mon Nov 30 13:29:13 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 246801c3fe07cb46aa21bd6adf0fed244d1bf57f Author: Ann Almgren Date: Mon Nov 30 13:28:26 2015 -0800 We previously had the same RHS and the same exact solution in 2D and 3D. However, this is not analytically correct. We have modified the RHS in 2D so that it gives the 2D solution with the same magnitude as the 3D solution. Tutorials/MultiGrid_C/RHS_2D.F commit 1aa6ecc577a957a1170cba4ea1079c319e0b48a3 Author: Weiqun Zhang Date: Mon Nov 30 13:26:49 2015 -0800 TileArray: fix typo Src/C_BaseLib/FabArray.cpp commit 7ff8d772985e03b7447af9f34f9c14ef1d86008a Author: Michael Zingale Date: Mon Nov 30 16:23:02 2015 -0500 also fix fab_bind for 2-d w/ ghost-cells Src/F_BaseLib/plotfile.f90 commit 04dfa2f13bf1118893540ea9324dd6c4c243d847 Merge: 60a736faf a62fdc7ec Author: Ann Almgren Date: Mon Nov 30 13:07:38 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 60a736fafb8fd07dd932ff71a0de1b5b1df1db78 Author: Ann Almgren Date: Mon Nov 30 13:07:10 2015 -0800 Test on whether lo(3) = hi(3) -- if that is true then the data is really 2D so doesn't have ghost cells in the third direction. Src/F_BaseLib/plotfile.f90 commit a62fdc7ece80703697377da1526c3f9f53d04c02 Author: Weiqun Zhang Date: Mon Nov 30 12:40:12 2015 -0800 AMR_Adv: add some comments Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d commit 43ddf535035e69665e91a099b3a16b15f7865485 Author: Andy Nonaka Date: Mon Nov 30 12:33:10 2015 -0800 for each level advance, make sure we are not violating cfl since the time step is based on the velocity at t^n Tutorials/AMR_Adv_F/Source/advance.f90 commit f0ca002a945640c7f5cf9640dfb0bcc5a456a321 Merge: 95bd7b9de 19bf855b5 Author: Weiqun Zhang Date: Mon Nov 30 11:24:10 2015 -0800 Merge branch 'development' into tilearraycache commit 19bf855b52170d76970f4420c8706b2973011123 Author: Weiqun Zhang Date: Mon Nov 30 11:22:10 2015 -0800 AMR_Adv: change cfl to 0.7 for the single vortext problem Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d commit 95bd7b9de74b6b10aff49d3aaf58d55274f17d5d Author: Weiqun Zhang Date: Mon Nov 30 10:34:01 2015 -0800 FabArray: add some assertion making sure BoxArray and DistributionMapping do not change Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b02682e5fc2483f88030ad823aad23d15cb985a0 Author: Weiqun Zhang Date: Sun Nov 29 17:51:59 2015 -0800 FabArray & MFIter: cache tile array and use cached tile array in MFIter Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b0bafa6b05e3a6ef660a9503e07e24d4e2315463 Merge: 52dd14195 e99811ca8 Author: Ann Almgren Date: Sun Nov 29 17:26:07 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 52dd141954b02da46fad00990b6b201db2a33656 Author: Ann Almgren Date: Sun Nov 29 17:25:49 2015 -0800 See previous comments. Tutorials/MultiGrid_C/inputs commit c62d4cc48178c0442d23eeef358f9c86b2e63343 Author: Ann Almgren Date: Sun Nov 29 17:24:28 2015 -0800 1) We only need a single inputs file for 2d and 3d. 2) Change the tolerance from 1e-6 to 1e-10 3) Set the maxorder for the BoxLib_C solver to be 3 in the inputs file. The default is 2, but if we set maxorder = 3 then the Cpp results match the F90 results. Tutorials/MultiGrid_C/inputs Tutorials/MultiGrid_C/inputs.f90.3d commit f888a541df46bbec1ad0b42a248dc3790d694a5f Author: Ann Almgren Date: Sun Nov 29 17:23:53 2015 -0800 Have the default be not to test HPGMG. Tutorials/MultiGrid_C/GNUmakefile commit 132bafaa4c50157953202af85692e1fbae356d3c Author: Ann Almgren Date: Sun Nov 29 17:23:32 2015 -0800 Fix typo in comment. Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/COEF_3D.F commit 1c6797fe49d55c691bd62ec4f3d2675dbb387377 Author: Weiqun Zhang Date: Sun Nov 29 07:57:42 2015 -0800 DistributionMapping: ID Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 0ebdadf5de7ee771484802880f52ec66a4657b52 Author: Weiqun Zhang Date: Sun Nov 29 07:50:40 2015 -0800 BoxArray: ID Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit cf38ae82e1897a63f39892da98b9930cc153e8d6 Author: Weiqun Zhang Date: Fri Nov 27 20:12:00 2015 -0800 PGAS_SMC: tiling MiniApps/PGAS_SMC/SMC_advance.cpp commit c7e2880444134dd3b06c8db0ce9caed823b52e3f Author: Weiqun Zhang Date: Fri Nov 27 20:11:43 2015 -0800 MFGhostIter: update for UPC++ Src/C_BaseLib/FabArray.cpp commit eefef6d670e5914ed88e59500f3e2a0b3313f93b Author: Weiqun Zhang Date: Fri Nov 27 15:14:05 2015 -0800 PGAS_SMC: change default MiniApps/PGAS_SMC/SMC.cpp commit fc5813eb89355957d714253810b1f3a3383a3bba Author: Weiqun Zhang Date: Fri Nov 27 12:15:16 2015 -0800 PGAS_SMC: replication for weak scaling MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/init_data.f90 commit ac081902d4b6abfa264b203a07ed54ee8ee1fc6f Author: Weiqun Zhang Date: Fri Nov 27 07:40:53 2015 -0800 PGAS_SMC: make max_grid_size a vector MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_init.cpp commit 048de281ed1e129c8b843593cf9448d5b0039c4b Author: Weiqun Zhang Date: Thu Nov 26 15:53:39 2015 -0800 fix a bug and tidy Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H commit e99811ca8b3e2d1b78224fe6a9701282d5756383 Author: Max Katz Date: Thu Nov 26 09:37:50 2015 -0500 Only print out a warning on the I/O processor. Src/C_AMRLib/Amr.cpp commit b31c071bdfb7ccee76a6d520c665d1e8ef5be107 Author: Weiqun Zhang Date: Tue Nov 24 18:13:15 2015 -0800 add Team Free consisting of processes not involved in remote communication and use it for local copy in Fill Boundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H commit 873e0b44ef666823f72230774504aa95de07a8b2 Author: Weiqun Zhang Date: Tue Nov 24 16:35:28 2015 -0800 finished team message aggregation for periodic boundary Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 2a584940b01af4a91b4e1dbd60709c4c31c9947a Author: Weiqun Zhang Date: Tue Nov 24 16:15:23 2015 -0800 fixed bug Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H commit 47cedbbe192e4b9ad4e4db11ba89acef9728ca31 Author: Weiqun Zhang Date: Tue Nov 24 16:15:14 2015 -0800 added override Src/C_BaseLib/UArena.H commit b98bf0b9abef2c2109e9d0ed1ba7427f64a7154d Author: Weiqun Zhang Date: Tue Nov 24 15:28:34 2015 -0800 various message aggregation methods Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 7f43742bce66e998e3354ef32b57c2a5249053c7 Merge: 8584d1f53 099d18a6a Author: Weiqun Zhang Date: Tue Nov 24 13:47:31 2015 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/Make.package commit 8584d1f53fe9884c595ce7a5fc24de5af14a6dce Merge: ecd8c9e1d 116c55100 Author: Weiqun Zhang Date: Tue Nov 24 13:44:23 2015 -0800 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 099d18a6abc98a7feb787bc394559fd545e10630 Author: Weiqun Zhang Date: Tue Nov 24 11:14:11 2015 -0800 Geometry: new versions of GetVolume and GetFaceArea Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 307b2b48965a8b6a323344585f4310958583b05e Author: Weiqun Zhang Date: Tue Nov 24 11:07:32 2015 -0800 added edge boxarrays and nodal boxarray to AmrLevel. note that they are built on demand Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 92999a79a6b98f26cdde90c8b981d76337645b3d Merge: 2b1393e37 032226613 Author: Brian Friesen Date: Tue Nov 24 13:19:08 2015 -0800 Merge branch 'hpgmg_updates' into development This merge adds recent changes Sam made to the HPGMG code base, as well as significant reorganization of the HPGMG hooks in BoxLib. Specifically, the hooks (both headers and source files) have moved from MultiFab.{H,cpp} to Src/Extern/hpgmg/BL_HPGMG.{H,cpp}. commit 032226613bf95ae182ab5ef1adddf1f2fc97f651 Author: Brian Friesen Date: Tue Nov 24 13:12:26 2015 -0800 Tutorials, C_mk: move all HPGMG compile hooks from GNUmakefile into Make.defs This way we don't have to define the compile hooks in every GNUmakefile separately. Tools/C_mk/Make.defs Tutorials/MultiGrid_C/GNUmakefile commit 57b115f1d508751f5cb82a01229604edaf991c11 Author: Brian Friesen Date: Tue Nov 24 12:20:59 2015 -0800 MultiFab, HPGMG, Extern: move hooks for HPGMG from MultiFab to Extern Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/Extern/hpgmg/BL_HPGMG.H Src/Extern/hpgmg/BL_HPGMG.cpp Src/Extern/hpgmg/Make.package Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/main.cpp commit cba4dca2e67e78859133ff7da2b0b7677e846ad4 Author: Brian Friesen Date: Thu Nov 19 09:21:03 2015 -0800 MultiFab, HPGMG: fix weird comment text alignment Src/C_BaseLib/MultiFab.cpp commit c17675e1a2544abdf7e39ec69631736540250a1a Author: Brian Friesen Date: Thu Nov 19 09:20:09 2015 -0800 MultiFab, HPGMG: misc. fixes which mirror Sam's most recent changes in HPGMG Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit a99cb982810c0ce579f138d9a537c84044782c72 Author: Brian Friesen Date: Wed Nov 18 16:25:11 2015 -0800 MultiFab, HPGMG: minor fixes to boundary condition logic in MultiFab::CreateHPGMGLevel() Src/C_BaseLib/MultiFab.cpp commit 3b0e2a8d4f8c4a6f454121dea52e60e5ba76a513 Author: Brian Friesen Date: Wed Nov 18 16:14:43 2015 -0800 MultiFab, HPGMG: in MultiFab::CreateHPGMGLevel(), iterate the MFIter until we find one that's valid Src/C_BaseLib/MultiFab.cpp commit 2b1393e37f1ea2b027cda5a47c36342b77b5c4cf Author: Brian Friesen Date: Mon Nov 23 15:38:52 2015 -0800 Geometry: split retrieval of Box index int array into 2 steps in SendGeometryToSidecars() Doing Box.type().getVect() yields nonsense numbers. So instead we save the IntVect from type() as a temporary variable and then get the int array from it as a separate step. Src/C_BaseLib/Geometry.cpp commit b52c56864bd4346c239496d3fc7e3aff961fbaa8 Author: Weiqun Zhang Date: Mon Nov 23 16:13:36 2015 -0800 AMR_Adv_C: added override Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/AdvBld.cpp commit 8df6d4ac202aaa47229a0180ec137a9ed9af33ea Author: Weiqun Zhang Date: Mon Nov 23 15:52:17 2015 -0800 omp clean up Src/F_BaseLib/multifab_f.f90 commit 43d74e1d641135c4d9e9842352a9eb6e7724fc75 Author: Weiqun Zhang Date: Mon Nov 23 14:15:17 2015 -0800 added a new header file for C++ 11 stuff and added BL_OVERRIDE (which is preprocessed to override or space depending on BL_USE_CXX11) to overriding virtual functions. This can help virtual function sugnature mismatch bugs at compile time Src/C_AMRLib/AmrParGDB.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/MLSDCAmr.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BL_CXX11.H Src/C_BaseLib/CArena.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Particles.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/MacBndry.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_TensorMG/DivVis.H commit 89d3b258c49c65346dc2aa7f821d0dcaff71c48a Author: Weiqun Zhang Date: Mon Nov 23 11:18:02 2015 -0800 replaced omp critical with reduction Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 2f94661009f3c3b9109db80f6bf69025fcd03acb Author: Weiqun Zhang Date: Mon Nov 23 11:12:15 2015 -0800 replaced omp critical with omp atomic Src/F_BaseLib/bl_mem_stat.f90 commit ea66c657a05e894b806dcf182f0f11d266c3b3ed Author: Weiqun Zhang Date: Mon Nov 23 10:49:25 2015 -0800 replaced an omp critical with omp atomic Src/C_BaseLib/Particles.cpp commit 9f8f15d05f07a7aa43cf082a1e059a78e34c4aa1 Author: Weiqun Zhang Date: Fri Nov 20 06:01:48 2015 -0800 Revert "bndry_reg: save have_periodic_bloxes when doing rr_build" This reverts commit d24ee97bffc1fb31c4e2bddc2d8716907e17592a. Src/F_BaseLib/bndry_reg.f90 commit d24ee97bffc1fb31c4e2bddc2d8716907e17592a Author: Weiqun Zhang Date: Thu Nov 19 12:57:59 2015 -0800 bndry_reg: save have_periodic_bloxes when doing rr_build Src/F_BaseLib/bndry_reg.f90 commit f6c4252dc40dde801d0006cdace787b536f515b3 Author: vince Date: Wed Nov 18 18:28:53 2015 -0800 better names for allocated fabarray pointers. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 3af0aed911027df67c278e9b074eaf90cac6c0de Author: vince Date: Wed Nov 18 18:28:11 2015 -0800 more support for dynamic sidecars. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp commit ebfc7439aa20a9330808df59dc194c5ea696760a Author: vince Date: Wed Nov 18 18:26:43 2015 -0800 vectSize function. Src/C_AMRLib/BCRec.H commit af96d9ebaaa9fe83011cb670a71852110aee52a9 Author: Weiqun Zhang Date: Wed Nov 18 14:45:51 2015 -0800 RegressionTesting: rm reg_test_blame because it does work well and updated reg_test_gc Tools/RegressionTesting/reg_test_blame.py Tools/RegressionTesting/reg_test_gc.py commit 97afe8f4c557087d872209e24871ae27c22fe54c Author: vince Date: Wed Nov 18 14:31:38 2015 -0800 added virtual. Src/C_AMRLib/AmrLevel.H commit 8efd455ebe54e4d71efb8b438a7bf81c25679b77 Author: vince Date: Wed Nov 18 14:31:12 2015 -0800 duplicate the initial comm in case it is world. Src/C_BaseLib/ParallelDescriptor.cpp commit 31b0137169ed6c4ea0960b35fe1e85cae6397035 Author: Weiqun Zhang Date: Wed Nov 18 13:32:01 2015 -0800 Fixed a bug in bndry_reg_copy. The mf source usually has only one ghost cell, whereas the bndry_reg can have two cell beyond periodic boundary. Thank Ashish Pathak for pointing this out to us. Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit c1fd7c673c0272d103d83218eaaf613feb939d82 Author: Michael Zingale Date: Wed Nov 18 08:37:51 2015 -0500 allow test_suite to take a string of arguments to parse -- this allows it to be callable by other routines more easily Tools/RegressionTesting/testnew.py commit 7005add17b38eb29ed8095b90fa051c9a5bc08e0 Merge: 2e31681d2 b6dbb1f46 Author: Michael Zingale Date: Tue Nov 17 20:54:10 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 7b25368d9e427718215234787537c1ae640ace47 Author: vince Date: Tue Nov 17 17:52:01 2015 -0800 more sidecar copies on resize. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 2e31681d24be8e04297c5dbb2d8c8bbdf2747757 Author: Michael Zingale Date: Tue Nov 17 20:28:45 2015 -0500 clean up the parsing Tools/RegressionTesting/testnew.py commit b6dbb1f46cc7573f0bd857adf4a1989d47ebb937 Author: Weiqun Zhang Date: Tue Nov 17 15:56:34 2015 -0800 AMR_Adv_C: check CFL violation Tutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90 commit 4cda92cd6966374f69e76da8f59961b107a90b09 Author: Weiqun Zhang Date: Tue Nov 17 15:34:47 2015 -0800 AMR_Adv_F: fixed omp Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 commit f82cf35e262fae7663af92a8c99defb074136eb1 Author: Weiqun Zhang Date: Tue Nov 17 15:22:17 2015 -0800 AMR_Adv_C: added change_max for dt Tutorials/AMR_Adv_C/Source/Adv_dt.cpp commit 9856b802eed4e5a426dc379fec53e1b4d9547891 Author: Weiqun Zhang Date: Tue Nov 17 14:40:33 2015 -0800 AMR_Adv_C: updated SingleVortex Tutorials/AMR_Adv_C/Exec/SingleVortex/ACT_advection_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/amrvis.defaults Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.2d Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.3d Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/SingleVortex/probdata.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/probin Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.2d Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.3d Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 commit f714db5a352d84ff0354c54fb1a7e91aa72c7d27 Author: Weiqun Zhang Date: Tue Nov 17 13:52:45 2015 -0800 AMR_Adv_C: fixed 3d bug in scaling the flux Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90 commit 407d9eb04b4b998d1a80dc186ec5abbed829a03b Author: Weiqun Zhang Date: Tue Nov 17 13:47:53 2015 -0800 AMR_Adv_C: fixed tagging Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90 Tutorials/AMR_Adv_C/Source/Src_nd/tagging_params.f90 commit 769b7ef051b82ce93c98d710c341b7b355810629 Author: Weiqun Zhang Date: Tue Nov 17 13:11:44 2015 -0800 AMR_Adv_C: made the 2d consistent with AMR_Adv_F Tutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/compute_flux_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90 commit 5abbee36319ed58930c9e7b30a709143e3d2a8db Author: Andy Nonaka Date: Tue Nov 17 13:00:25 2015 -0800 cleanup temporary arrays Tutorials/AMR_Adv_F/Source/compute_flux.f90 commit f6c7fcb77aba8a03802435db8ce20e96026680ef Author: Andy Nonaka Date: Tue Nov 17 12:50:45 2015 -0800 change flux convention to positive (and flipped flux register sign convention) Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/update_phi.f90 commit f72be23e6a1853122ff78bc13e798c07967e9142 Author: Weiqun Zhang Date: Tue Nov 17 12:44:42 2015 -0800 AMR_Adv_C: finished 3d Tutorials/AMR_Adv_C/Source/Adv_dt.cpp Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Make.package Tutorials/AMR_Adv_C/Source/Src_3d/compute_flux_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/trans_3d.f90 commit d262215ba524e7765f57ba03d91dae27e7f38886 Author: Weiqun Zhang Date: Mon Nov 16 17:28:29 2015 -0800 AMR_Adv_C: clean up Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Make.package Tutorials/AMR_Adv_C/Source/Src_3d/React_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Tagging_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/bc_fill_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/ext_src_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/fill_diff_coeff_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/trans_3d.f90 commit 078f62d8015baf60a03b183ba7eefb58ea35a623 Author: Ann Almgren Date: Tue Nov 17 10:17:05 2015 -0800 Go back to the tagging that actually sees the phi blob. Tutorials/AMR_Adv_F/Source/tag_boxes.f90 commit 28c0337c92fd8281b049f925bf0104769151595a Merge: e43e7e847 67255e7be Author: Ann Almgren Date: Tue Nov 17 10:15:12 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 67255e7be651affe8d86b5969ffe4840c079de19 Author: Andy Nonaka Date: Tue Nov 17 08:11:25 2015 -0800 fixed crash issue when nlevs .ne. max_levs based on refinement criteria. the compute_dt routine was looping over max_levs, not nlevs Tutorials/AMR_Adv_F/Source/main.f90 commit 180075a4b537ea5c7d38b9c1610539a37a6cc60f Author: Andy Nonaka Date: Tue Nov 17 08:06:36 2015 -0800 move bubble to center of domain in 3d Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 commit e43e7e84736667cb508be26605328d9ea21add43 Author: Ann Almgren Date: Mon Nov 16 18:45:23 2015 -0800 Fix this GNUmakefile Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile commit 63da40e5d6fc707348318659b87cb918a211b784 Author: Ann Almgren Date: Mon Nov 16 18:44:25 2015 -0800 1) Renamed KotheRiderExample --> SingleVortex in AMR_Adv_C. 2) Copied tag_boxes.f90 into AMR_Adv_F/Source directory so it is easy to see how to set the refinement criteria. Tutorials/AMR_Adv_C/Exec/SingleVortex/ACT_advection_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/amrvis.defaults Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.2d Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.3d Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/SingleVortex/probdata.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.2d Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.3d Tutorials/AMR_Adv_F/Source/GPackage.mak Tutorials/AMR_Adv_F/Source/tag_boxes.f90 commit 93033267392a8378baa4854a0045de5dc0b0162c Merge: fdfabd90f 8db125192 Author: Ann Almgren Date: Mon Nov 16 18:10:23 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit fdfabd90f985ca063ec14689c2afaa25be90f1f2 Author: Ann Almgren Date: Mon Nov 16 18:09:21 2015 -0800 1) Add computation of dt based on time-n velocity at every coarse timestep. 2) Move the routines to set the velocity and initialize phi into the Exec/problem directories. 3) Set do_subcycling = T in the inputs files. Tutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_F/Exec/SingleVortex/GPackage.mak Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d Tutorials/AMR_Adv_F/Exec/SingleVortex/set_velocity.f90 Tutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_F/Exec/UniformVelocity/GPackage.mak Tutorials/AMR_Adv_F/Exec/UniformVelocity/init_phi.f90 Tutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_2d Tutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_3d Tutorials/AMR_Adv_F/Exec/UniformVelocity/set_velocity.f90 Tutorials/AMR_Adv_F/Source/GPackage.mak Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/main.f90 Tutorials/AMR_Adv_F/Source/slope.f90 commit 9b7b26c3913e5533438b7407f1334952b3f33f86 Author: vince Date: Mon Nov 16 17:42:18 2015 -0800 consolidate geometry broadcast functions. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit c50ad5ad2bf2af65a8374577bdd53750eb108647 Author: vince Date: Mon Nov 16 17:41:14 2015 -0800 consolidate geometry broadcast functions. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 8db1251923ad630867b2cbccce03ea51f7bda80f Author: Weiqun Zhang Date: Mon Nov 16 16:45:12 2015 -0800 AMR_Adv_C: fixed a bug in 2d slope. The 2D C++ version works now. Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90 commit 95290f2767d87d0354ec866a4f396f8606455bc5 Author: Weiqun Zhang Date: Mon Nov 16 16:44:25 2015 -0800 AMR_Adv: make the initial model consistent Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_F/Source/init_phi.f90 commit ef961ea5f3636ba341629fc27cc809d3d63a4286 Merge: 4d41f8d55 904372936 Author: Weiqun Zhang Date: Mon Nov 16 16:43:04 2015 -0800 Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development commit 9043729361342c9ebd9119b2336b6678f3d180df Author: Ann Almgren Date: Mon Nov 16 16:34:56 2015 -0800 Update the README_F to correctly describe AMR_Adv_F Tutorials/README_F commit 8c63a4bf16aa47339a6294794672b4210c59b598 Author: Andy Nonaka Date: Mon Nov 16 16:18:13 2015 -0800 cleanup only. 2d and 3d check out 2nd order for cfl=0.9 Tutorials/AMR_Adv_F/Source/compute_flux.f90 commit 8bca80a4e4b8a6ecc5f7b6a2675b0f9f60e79d16 Author: Andy Nonaka Date: Mon Nov 16 15:26:29 2015 -0800 3d advection complete. convergence testing underway Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/init_phi.f90 commit 4d41f8d55e1b71392b0e6d9d8fee3a9f6717dfc9 Merge: f9e0ecff6 e8b4b1d5b Author: Weiqun Zhang Date: Mon Nov 16 13:43:44 2015 -0800 Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development commit e8b4b1d5b5e24b5d8c0c184dc96b9181ba835c04 Author: Andy Nonaka Date: Mon Nov 16 12:54:37 2015 -0800 constant velocity test case. cfl enabled (assumes umax=1). stop_time enabled Tutorials/AMR_Adv_F/Exec/inputs_2d Tutorials/AMR_Adv_F/Exec/inputs_3d Tutorials/AMR_Adv_F/Source/compute_velocity.f90 Tutorials/AMR_Adv_F/Source/init_phi.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit 87673af99b4d6135c10fd72d13e06dced6af66a7 Author: Andy Nonaka Date: Mon Nov 16 12:49:43 2015 -0800 get compute_flux compiling again Tutorials/AMR_Adv_F/Source/compute_flux.f90 commit e9798ccbe4825ba9b6b76815c8d28215835cee73 Author: Andy Nonaka Date: Mon Nov 16 12:42:12 2015 -0800 updates so we can start comparing F90 and C Tutorials/AMR_Adv_F/Source/compute_flux.f90 commit f9e0ecff66d5c7720e36fe8ef18e718cdbec6009 Author: Weiqun Zhang Date: Mon Nov 16 12:32:51 2015 -0800 AMR_Adv_C: updated assuming div(u)=0 Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/flux_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90 commit 7616567e20283a10946d6644cca140b2534f6a78 Author: Andy Nonaka Date: Mon Nov 16 11:26:44 2015 -0800 start 3d flux routine - WIP Tutorials/AMR_Adv_F/Source/compute_flux.f90 commit 1c6316c8f8c74e489f7107e42e4213b3c1176f21 Author: Andy Nonaka Date: Mon Nov 16 11:26:33 2015 -0800 3d init match 2d init Tutorials/AMR_Adv_F/Source/init_phi.f90 commit a9c60ddc9f250f807cba396dcbfc4cc2f23bbfbc Author: Andy Nonaka Date: Mon Nov 16 11:08:44 2015 -0800 code clean up Tutorials/AMR_Adv_F/Source/GPackage.mak Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/main.f90 Tutorials/AMR_Adv_F/Source/prob.f90 commit b2184636f0b4c60b3b82d908c316c15263f3df4a Author: Andy Nonaka Date: Mon Nov 16 11:03:02 2015 -0800 clean up boundary conditions Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_flux.f90 commit 82e34a8abf981d76a2646d2b30758e2bfc7332f7 Author: Andy Nonaka Date: Mon Nov 16 10:59:34 2015 -0800 3d velocity field with w=1 and inputs file Tutorials/AMR_Adv_F/Exec/inputs_3d Tutorials/AMR_Adv_F/Source/compute_velocity.f90 commit f802afe45f6d3693443b973b19144e118f5b05d6 Author: Andy Nonaka Date: Mon Nov 16 10:36:20 2015 -0800 fixed hdtdx scalining / units bug Tutorials/AMR_Adv_F/Source/compute_flux.f90 commit 929658eda69d6155395e36a6f0a627003556fa31 Author: Andy Nonaka Date: Mon Nov 16 10:23:19 2015 -0800 get rid of abs(u) < eps cases. confusing and not needed since this is just conservative scalar advection Tutorials/AMR_Adv_F/Source/compute_flux.f90 commit 204f914306c5fc9da33d7ad7a24b3f75d4d2c613 Author: Andy Nonaka Date: Mon Nov 16 10:09:19 2015 -0800 2d advection complete. assumes div(u)=0. does the tracing in convective form, then forms the final fluxes in conservative form Tutorials/AMR_Adv_F/Source/compute_flux.f90 commit 747744cc5adb043ce5dbbc7dc2838fcdabaeb438 Author: Andy Nonaka Date: Mon Nov 16 08:25:53 2015 -0800 2d cross terms incorporated. runs now at cfl=0.9. 3d not written yet Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit 10eec4ca3d9bc4e91065c300cdeba86407414c49 Merge: 03181f43f 33bb9d939 Author: Andy Nonaka Date: Mon Nov 16 07:35:04 2015 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 33bb9d939a571be9175eab51af7a7601f21f54c3 Author: Weiqun Zhang Date: Sun Nov 15 15:49:07 2015 -0800 AMR_Adv_C: write final checkpoint and plotfile Tutorials/AMR_Adv_C/Source/main.cpp commit 4f266fdbe066803209785200f6a2156103a4fa24 Author: Weiqun Zhang Date: Sun Nov 15 11:37:00 2015 -0800 AMR_Adv_C: minor Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs commit d41ee00aefd4606db80d6669cb3262a382c2eda3 Author: Weiqun Zhang Date: Sun Nov 15 11:29:09 2015 -0800 AMR_Adv_C: change the default max_grid_size to 64 Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs commit 3ca6624c1730c9ab7ff22fa03c93eaf22e2f831f Author: Weiqun Zhang Date: Sun Nov 15 11:27:12 2015 -0800 AMR_Adv_C: tweak initial model Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin commit 2a10b1f87efbbdf2e62aa28f70840bab309daf5d Author: Weiqun Zhang Date: Sun Nov 15 11:20:47 2015 -0800 AMR_Adv_2d: added missing piece in transx Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90 commit 35825534806f66e3c588b11277766f0315e72b49 Author: Weiqun Zhang Date: Sun Nov 15 11:19:28 2015 -0800 AMR_Adv_2d: fixed some comments Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 commit 9137c1402007c2e9a203da469046dac538bb5c14 Author: Weiqun Zhang Date: Sun Nov 15 11:14:43 2015 -0800 AMR_Adv_2d: removed hard coded eps Tutorials/AMR_Adv_C/Source/Src_2d/flux_2d.f90 commit de7b85c902a9b5af4711094f30d32dd51b7cc834 Author: Weiqun Zhang Date: Sun Nov 15 10:22:59 2015 -0800 AMR_Adv_C: use contiguous Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90 commit 7d51f713428d1c56a7a28eb8d99b88203b0f5005 Author: Weiqun Zhang Date: Sun Nov 15 10:20:28 2015 -0800 AMR_Adv_C: minor Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90 commit b482e83ccceb5c81832e354f4a59575b159068e4 Author: Weiqun Zhang Date: Sun Nov 15 10:18:16 2015 -0800 AMR_Adv_C: added tagging Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90 commit 9b98051d1f90d10f75a43f2f2a7d082b3dcd6f81 Author: Weiqun Zhang Date: Sun Nov 15 10:04:06 2015 -0800 AMR_Adv_C: clean up Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_dt.cpp commit 2b09377dde647b2e154edef0b937435f981c46be Author: Weiqun Zhang Date: Sat Nov 14 20:10:49 2015 -0800 AMR_Adv_C: edge --> face Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_C/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_dt.cpp commit 6fc141d3d785819617d7026a2a56621643837cf4 Author: Weiqun Zhang Date: Sat Nov 14 20:05:21 2015 -0800 AMR_Adv_C: 2d finished not checked Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/advection_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/flux_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90 commit a06451214ddbb7803a1448bc893355f5f73a8b90 Author: Weiqun Zhang Date: Fri Nov 13 22:04:31 2015 -0800 AMR_Adv_C: WIP Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/advection_2d.f90 commit 66e22afa070bde2aaa8fcd2ff1a8789388afd8ed Author: Weiqun Zhang Date: Fri Nov 13 21:11:54 2015 -0800 AMR_Adv_C: rm some files Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/advection_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/fill_diff_coeff_2d.f90 commit ebe971fd5987532111d6622f13c85da0150d2f5c Author: Weiqun Zhang Date: Fri Nov 13 21:06:13 2015 -0800 AMR_Adv_C: compute dt Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/edge_velocity_2d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_dt.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/Make.package Tutorials/AMR_Adv_C/Source/Src_nd/Adv_nd.f90 Tutorials/AMR_Adv_C/Source/Src_nd/Make.package Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90 Tutorials/AMR_Adv_C/Source/Src_nd/tagging_params.f90 commit e5a310aa8a1f67225d1f717b6f8a27cf402fe801 Author: Weiqun Zhang Date: Fri Nov 13 18:07:22 2015 -0800 AMR_Adv_C: remvoed prob_hi from initdata Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H commit 6eee1fcd04fb74e95a17bdbb7cda0c6c465b5b20 Author: Weiqun Zhang Date: Fri Nov 13 17:56:22 2015 -0800 AMR_Adv_C: fixed boundary function Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_setup.cpp commit 03181f43ff75adb1e7a95ce596a3230c06ffbb5f Author: Andy Nonaka Date: Fri Nov 13 17:52:46 2015 -0800 now computing velocity and half-time for both subcycling and non-subcycling cases Tutorials/AMR_Adv_F/Exec/GNUmakefile Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_velocity.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit f01c12a2f8a11c99661e7b3c40eb7694fcba2c4a Author: Weiqun Zhang Date: Fri Nov 13 17:38:54 2015 -0800 AMR_Adv_C: clean up headers Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/main.cpp commit ebdd2e241e2685f25b3de61781796ce785b13ed8 Author: Weiqun Zhang Date: Fri Nov 13 17:32:18 2015 -0800 AMR_Adv_C: removed area and volume Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp commit 32229724c33bbeff9ffa144704dd8329ea5a1621 Author: Weiqun Zhang Date: Fri Nov 13 17:24:22 2015 -0800 AMR_Adv_C: clean up Adv::advance Tutorials/AMR_Adv_C/Source/Adv_advance.cpp commit be1f4ba73a128991a2186b9bf2819f95d2740082 Author: Weiqun Zhang Date: Fri Nov 13 16:44:23 2015 -0800 AMR_Adv_C: fixed 2d initdata Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 commit 2eb3ee01fdcff49912c7d2f72d7e9aa9b80a44fe Author: Weiqun Zhang Date: Fri Nov 13 16:39:40 2015 -0800 AMR_Adv_C: fixed initdata Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_F/Source/init_phi.f90 commit fbe65f1f4e01a64bcba6f84d3be06e8b730c4979 Author: Weiqun Zhang Date: Fri Nov 13 16:24:01 2015 -0800 AMR_Adv_C: WIP Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_error.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/Adv_nd.f90 Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/Derive_F.H Tutorials/AMR_Adv_C/Source/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/extern_probin.template Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C/Source/meth_params.f90 Tutorials/AMR_Adv_C/Source/prob_params.f90 commit 695e46938675616f6a8798e335e2f48b6b967ee6 Author: Weiqun Zhang Date: Fri Nov 13 11:25:13 2015 -0800 AMR_Adv_C: rm diffusion Tutorials/AMR_Adv_C/Source/ADR_diffusion.cpp Tutorials/AMR_Adv_C/Source/Diffusion.H Tutorials/AMR_Adv_C/Source/Diffusion.cpp Tutorials/AMR_Adv_C/Source/Make.package commit c3b5e58c0578e71e853e0678b9744bf0a8324c14 Author: Weiqun Zhang Date: Fri Nov 13 11:24:12 2015 -0800 AMR_Adv_C: ADR --> Adv Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_error.cpp Tutorials/AMR_Adv_C/Source/Adv_nd.f90 Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/Make.package commit 25249f697431acbab39f2407bd8c6b985c6a6446 Author: Weiqun Zhang Date: Fri Nov 13 11:21:06 2015 -0800 AMR_Adv_C: updated make Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile commit cf65996939e5bc833e3d85fc076b381985af9966 Author: Weiqun Zhang Date: Fri Nov 13 11:09:46 2015 -0800 AMR_Adv_C: updated README Tutorials/AMR_Adv_C/README commit 394ac1acedc82f760e97fc2601794c9e9f2855da Author: Weiqun Zhang Date: Fri Nov 13 11:09:30 2015 -0800 AMR_Adv_C: renamed file Tutorials/AMR_Adv_C/Exec/Make.Adv commit 21e3aab8d95e1182bfc7e69ff7f124895cd364bb Author: Andy Nonaka Date: Fri Nov 13 15:57:32 2015 -0800 more progress on test problem Tutorials/AMR_Adv_F/Exec/GNUmakefile Tutorials/AMR_Adv_F/Exec/inputs_2d Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/compute_velocity.f90 Tutorials/AMR_Adv_F/Source/init_phi.f90 Tutorials/AMR_Adv_F/Source/main.f90 Tutorials/AMR_Adv_F/Source/update_phi.f90 commit d919852804852a2934c9d5a6c7e2415209a633d3 Author: Andy Nonaka Date: Fri Nov 13 14:47:36 2015 -0800 compute_velocity routine... need to fold it into subcycling case properly (so it uses most current time) Tutorials/AMR_Adv_F/Source/GPackage.mak Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_velocity.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit 58ed60504e65e790618635b234389adc68f88935 Author: Andy Nonaka Date: Fri Nov 13 12:53:46 2015 -0800 comments, initialize fluxes to zero now that the diffusive fluxes are gone Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit 0a46e496beb72381dac242714eb4d078495da7d9 Author: Andy Nonaka Date: Fri Nov 13 12:27:56 2015 -0800 clean up namelist and inputs file Tutorials/AMR_Adv_F/Exec/inputs_2d Tutorials/AMR_Adv_F/Exec/inputs_3d Tutorials/AMR_Adv_F/Source/init_phi.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit 5e464e214a2d758950d0957a3d69d79dea11ae44 Author: Andy Nonaka Date: Fri Nov 13 11:11:57 2015 -0800 remove redundant inputs file Tutorials/AMR_Adv_F/Exec/inputs-rt commit 0268805e6577403e74a7ceb90e5ac9249d17cea5 Author: Andy Nonaka Date: Fri Nov 13 11:07:48 2015 -0800 remove some diffusion stuff re-org directories to make it look like the C version Tutorials/AMR_Adv_F/Exec/GNUmakefile Tutorials/AMR_Adv_F/Exec/inputs-rt Tutorials/AMR_Adv_F/Exec/inputs_2d Tutorials/AMR_Adv_F/Exec/inputs_3d Tutorials/AMR_Adv_F/Source/GPackage.mak Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/init_phi.f90 Tutorials/AMR_Adv_F/Source/main.f90 Tutorials/AMR_Adv_F/Source/prob.f90 Tutorials/AMR_Adv_F/Source/slope.f90 Tutorials/AMR_Adv_F/Source/update_phi.f90 Tutorials/AMR_Adv_F/Source/write_plotfile.f90 commit 58ce648ecae9364653481ad592a663b9a61389cc Author: Andy Nonaka Date: Fri Nov 13 11:01:55 2015 -0800 new amr advection examples from Ann's latest commit Tutorials/AMR_Adv_C/Exec/KotheRiderExample/ACT_advection_2d.f90 Tutorials/AMR_Adv_C/Exec/KotheRiderExample/GNUmakefile Tutorials/AMR_Adv_C/Exec/KotheRiderExample/Make.package Tutorials/AMR_Adv_C/Exec/KotheRiderExample/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/KotheRiderExample/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/KotheRiderExample/amrvis.defaults Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.2d Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.3d Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.rt Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/KotheRiderExample/probdata.f90 Tutorials/AMR_Adv_C/Exec/KotheRiderExample/probin.2d Tutorials/AMR_Adv_C/Exec/KotheRiderExample/probin.3d Tutorials/AMR_Adv_C/Exec/Make.ADR Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Adv_C/README Tutorials/AMR_Adv_C/Source/ADR.H Tutorials/AMR_Adv_C/Source/ADR.cpp Tutorials/AMR_Adv_C/Source/ADRBld.cpp Tutorials/AMR_Adv_C/Source/ADR_F.H Tutorials/AMR_Adv_C/Source/ADR_advance.cpp Tutorials/AMR_Adv_C/Source/ADR_diffusion.cpp Tutorials/AMR_Adv_C/Source/ADR_error.cpp Tutorials/AMR_Adv_C/Source/ADR_nd.f90 Tutorials/AMR_Adv_C/Source/ADR_setup.cpp Tutorials/AMR_Adv_C/Source/Derive_F.H Tutorials/AMR_Adv_C/Source/Diffusion.H Tutorials/AMR_Adv_C/Source/Diffusion.cpp Tutorials/AMR_Adv_C/Source/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/fill_diff_coeff_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Make.package Tutorials/AMR_Adv_C/Source/Src_3d/React_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Tagging_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/bc_fill_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/ext_src_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/fill_diff_coeff_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/trans_3d.f90 Tutorials/AMR_Adv_C/Source/extern_probin.template Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C/Source/meth_params.f90 Tutorials/AMR_Adv_C/Source/prob_params.f90 Tutorials/AMR_Adv_F/GNUmakefile Tutorials/AMR_Adv_F/GPackage.mak Tutorials/AMR_Adv_F/advance.f90 Tutorials/AMR_Adv_F/compute_flux.f90 Tutorials/AMR_Adv_F/init_phi.f90 Tutorials/AMR_Adv_F/inputs-rt Tutorials/AMR_Adv_F/inputs_2d Tutorials/AMR_Adv_F/inputs_3d Tutorials/AMR_Adv_F/main.f90 Tutorials/AMR_Adv_F/prob.f90 Tutorials/AMR_Adv_F/slope.f90 Tutorials/AMR_Adv_F/update_phi.f90 Tutorials/AMR_Adv_F/write_plotfile.f90 Tutorials/AMR_Advection_C/Exec/Make.ADR Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Advection_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt.3d Tutorials/AMR_Advection_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Advection_C/README Tutorials/AMR_Advection_C/Source/ADR.H Tutorials/AMR_Advection_C/Source/ADR.cpp Tutorials/AMR_Advection_C/Source/ADRBld.cpp Tutorials/AMR_Advection_C/Source/ADR_F.H Tutorials/AMR_Advection_C/Source/ADR_advance.cpp Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp Tutorials/AMR_Advection_C/Source/ADR_error.cpp Tutorials/AMR_Advection_C/Source/ADR_nd.f90 Tutorials/AMR_Advection_C/Source/ADR_react.cpp Tutorials/AMR_Advection_C/Source/ADR_setup.cpp Tutorials/AMR_Advection_C/Source/Derive_F.H Tutorials/AMR_Advection_C/Source/Diffusion.H Tutorials/AMR_Advection_C/Source/Diffusion.cpp Tutorials/AMR_Advection_C/Source/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/ACT_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ACT_sums_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/React_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/fill_diff_coeff_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/trans_2d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_sums_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Make.package Tutorials/AMR_Advection_C/Source/Src_3d/React_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Tagging_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/bc_fill_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ext_src_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/fill_diff_coeff_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90 Tutorials/AMR_Advection_C/Source/burner.f90 Tutorials/AMR_Advection_C/Source/extern_probin.template Tutorials/AMR_Advection_C/Source/main.cpp Tutorials/AMR_Advection_C/Source/meth_params.f90 Tutorials/AMR_Advection_C/Source/network.f90 Tutorials/AMR_Advection_C/Source/prob_params.f90 Tutorials/AMR_Advection_C/Source/sum_integrated_quantities.cpp commit 6371c9584c5e5b18b889b85dc2f8552416bdc4b8 Author: Ann Almgren Date: Fri Nov 13 10:17:13 2015 -0800 Add new Tutorial example -- AMR_Adv_Diff_C Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/ACT_advection_2d.f90 Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/GNUmakefile Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/Make.package Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/Prob_2d.f90 Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/Prob_3d.f90 Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/amrvis.defaults Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.2d Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.3d Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.rt Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.rt.3d Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/probdata.f90 Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/probin.2d Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/probin.3d Tutorials/AMR_Adv_Diff_C/Exec/Make.ADR Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.rt.3d Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Adv_Diff_C/README Tutorials/AMR_Adv_Diff_C/Source/ADR.H Tutorials/AMR_Adv_Diff_C/Source/ADR.cpp Tutorials/AMR_Adv_Diff_C/Source/ADRBld.cpp Tutorials/AMR_Adv_Diff_C/Source/ADR_F.H Tutorials/AMR_Adv_Diff_C/Source/ADR_advance.cpp Tutorials/AMR_Adv_Diff_C/Source/ADR_diffusion.cpp Tutorials/AMR_Adv_Diff_C/Source/ADR_error.cpp Tutorials/AMR_Adv_Diff_C/Source/ADR_nd.f90 Tutorials/AMR_Adv_Diff_C/Source/ADR_setup.cpp Tutorials/AMR_Adv_Diff_C/Source/Derive_F.H Tutorials/AMR_Adv_Diff_C/Source/Diffusion.H Tutorials/AMR_Adv_Diff_C/Source/Diffusion.cpp Tutorials/AMR_Adv_Diff_C/Source/Make.package Tutorials/AMR_Adv_Diff_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_Diff_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/fill_diff_coeff_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/trace_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/Make.package Tutorials/AMR_Adv_Diff_C/Source/Src_3d/React_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/Tagging_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/bc_fill_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/ext_src_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/fill_diff_coeff_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/trans_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/extern_probin.template Tutorials/AMR_Adv_Diff_C/Source/main.cpp Tutorials/AMR_Adv_Diff_C/Source/meth_params.f90 Tutorials/AMR_Adv_Diff_C/Source/prob_params.f90 commit ac37c9e19a869a0a914a311d52f0f4305339991d Author: vince Date: Thu Nov 12 17:55:25 2015 -0800 added function to broadcast a geometry. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit e8c686e4395304f3be53f40fe2f9eb7c911a76f1 Author: vince Date: Thu Nov 12 17:54:05 2015 -0800 added function for serialized box size. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit cc082d5127f4b2565f16df9bbd4c9b67c17ed6fc Author: vince Date: Thu Nov 12 17:52:40 2015 -0800 added function to send data to procs moved from the sidecars into comp. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 648268ef45ed7b6ddb92677db1056e72f0709aef Author: vince Date: Thu Nov 12 17:52:05 2015 -0800 added function to send data to procs moved from the sidecars into comp. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 116c55100f391a893bbbd4cfe2450dc25a848de7 Author: Weiqun Zhang Date: Thu Nov 12 16:04:58 2015 -0800 added a barrier after we finish advance Tutorials/PGAS_HEAT/main.cpp commit 9427c6884923c29f2f8796f04939657c9c945998 Author: vince Date: Thu Nov 12 11:16:44 2015 -0800 added switch default. Src/C_BaseLib/CoordSys.cpp commit f033a4ddf5eecdd2a0e99caac62301763ab1a62c Author: Weiqun Zhang Date: Thu Nov 12 11:16:20 2015 -0800 added more barriers when we switch between MPI and UPC++ Tests/FillBoundaryComparison/main.cpp commit 2c5faba058e6b9327d4f325300329856491717b3 Merge: d77ca089e cd2e7a17f Author: yzheng Date: Thu Nov 12 07:58:44 2015 -0800 Add a barrier before switching from UPC++ to MPI commit ecd8c9e1dd45de4f89e76a1bae9ac282204da79a Author: Weiqun Zhang Date: Wed Nov 11 16:24:18 2015 -0800 renamed parameter upcxx_team_size to team.size and added new parameter team.aggregate_message to control how to aggregate team messages Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 07064552212a55f66121e1438eac194748d52671 Author: Weiqun Zhang Date: Wed Nov 11 14:28:32 2015 -0800 change the default of comm_num_pieces to 1; it does not seem to help on cori Src/C_BaseLib/FabArray.cpp commit 0e55d132706fab9995d07a000da199e8c03e01f4 Author: Andy Nonaka Date: Wed Nov 11 11:08:22 2015 -0800 a separate version of fabio_ml_multifab_write_d that works when the input multifab is a single-level, non-array Src/F_BaseLib/fabio.f90 commit cd2e7a17ff39b6388f74de70fa3391815602c00e Author: Weiqun Zhang Date: Tue Nov 10 14:45:05 2015 -0800 MFIter: fixed the no sharing flag Src/C_BaseLib/FabArray.cpp commit 8edfe1e293d5594cf0dbca684a1cbd2d6641703b Author: Weiqun Zhang Date: Tue Nov 10 14:42:27 2015 -0800 auto: fixed Intel complaints Src/C_BaseLib/FabArray.H commit 4cd7b9cfeb08d1dfa242b546261d5fffdc558209 Merge: 44525e9c9 1535d1bfa Author: Weiqun Zhang Date: Tue Nov 10 14:32:16 2015 -0800 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 1535d1bfa2c195afc64edf6076ca7405d9ecfc22 Author: Weiqun Zhang Date: Tue Nov 10 14:28:40 2015 -0800 UArena: check nullptr Src/C_BaseLib/FabArray.H Src/C_BaseLib/UArena.cpp commit c78f4ad5e4e6a52691b5d240fdbac681564a9d39 Author: Weiqun Zhang Date: Tue Nov 10 13:47:49 2015 -0800 UPC++: use auto since we are using C++11. Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 004d378b29c6472d01ee2fb4a646438907a1a6cf Author: Weiqun Zhang Date: Tue Nov 10 13:31:25 2015 -0800 updated local copy in fill periodic boundaries Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 24dd2888b62ea71802f1c84bc5e3454a53e764b1 Author: Brian Friesen Date: Tue Nov 10 13:28:02 2015 -0800 C_BaseLib, F_BaseLib: don't try to free MPI_COMM_WORLD in parallel_finalize() In commit 18fc260 ("C_BaseLib, F_BaseLib: free only the "local" MPI communicator when calling parallel_finalize() from C++ code") I added the "local" communicator as an argument to bl_fortran_mpi_comm_free() and parallel_finalize(). This works fine if MPI_COMM_WORLD has been split, i.e., if one is using sidecars, because then only the newly formed communicator gets freed. But if not using sidecars, then the code tries to free MPI_COMM_WORLD, which causes MPI to abort with an error. To fix this, we remove the communicator argument from bl_fortran_mpi_comm_free() and put it instead in a new function bl_fortran_sidecar_mpi_comm_free(). If the IN_TRANSIT preprocessor macro is *not* defined, then we have only one communicator (MPI_COMM_WORLD), and we call bl_fortran_mpi_comm_free() with no arguments; this restores the original behavior before commit 18fc260. If the macro *is* defined, then we have multiple communicators, and we call bl_fortran_sidecar_mpi_comm_free() instead. Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/parallel.f90 commit b69dc94a61a15fbb52b0bf29f4e8d1be0e84b5df Author: Weiqun Zhang Date: Tue Nov 10 12:55:43 2015 -0800 UPC++ team: added implicit team barrier in fillboundary and MFIter Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/ParallelDescriptor.H Tutorials/PGAS_HEAT/main.cpp commit 8a830122d3145b0c1b864b4f2e06857bb117d610 Author: Weiqun Zhang Date: Tue Nov 10 11:21:01 2015 -0800 FillBoundary: use local copy for communication inside team Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 1face51b5f0769584446c466fa5ed5050879ed1a Author: Weiqun Zhang Date: Tue Nov 10 11:08:51 2015 -0800 DistributionMapping: use team_for Src/C_BaseLib/DistributionMapping.cpp commit e563ded7585f1da1d68e344e65923cdc2cb766a0 Author: Weiqun Zhang Date: Tue Nov 10 11:08:11 2015 -0800 ParallelDescriptor: another type of team_for Src/C_BaseLib/ParallelDescriptor.H commit 7b5d6a138c445d43b4a05ef2ce88c0b5e3957b82 Author: Weiqun Zhang Date: Tue Nov 10 10:49:17 2015 -0800 BLPgas: renamed DEBUG to UPCXX_DEBUG Src/C_BaseLib/BLPgas.cpp commit e889ae98358b532c7ff0bbf3ab96d37ab73a6716 Author: Weiqun Zhang Date: Tue Nov 10 10:48:29 2015 -0800 ParallelDescriptor: added team_range and team_for Src/C_BaseLib/ParallelDescriptor.H commit fde7bee8570161bf587deff4bec94afea2621903 Author: vince Date: Mon Nov 9 16:45:54 2015 -0800 low memory option for writing particles. Src/C_BaseLib/Particles.H commit 74c632365ad970e620d6cbaae96b71056a52ad98 Author: Weiqun Zhang Date: Mon Nov 9 15:06:50 2015 -0800 PGAS_HEAT: added a number of barriers Tutorials/PGAS_HEAT/main.cpp commit 9192e76c02f7167e275980f22a7b787d1776c1cc Author: Weiqun Zhang Date: Mon Nov 9 15:05:58 2015 -0800 added UPC++ team barrier. Src/C_BaseLib/ParallelDescriptor.H commit b70ba8e7175c9c69d51b753d08d4cfaed11b1745 Author: Weiqun Zhang Date: Mon Nov 9 13:20:06 2015 -0800 updated VisMF::Write for UPC++ team Src/C_BaseLib/VisMF.cpp commit deb5a85702fd31e4b87e28d2fc52e1d8c8b9a703 Author: Weiqun Zhang Date: Mon Nov 9 13:07:13 2015 -0800 rewrote AllocFabs using the new team distribution map Src/C_BaseLib/FabArray.H Src/C_BaseLib/UArena.cpp commit 957aa4a6c05a5c4e0baa3a146250852ff7396f89 Author: Brian Friesen Date: Mon Nov 9 12:48:24 2015 -0800 C_BaseLib, F_BaseLib: free only the "local" MPI communicator when calling parallel_finalize() from C++ code When running C++/F90 codes with multiple communicators (i.e., with sidecars), the code will crash on BoxLib::Finalize() because in parallel_finalize() the sidecars are trying to free the "compute" communicator. So now we supply the "local" communicator as an argument to parallel_finalize(). Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/parallel.f90 commit 562e992f098923b25bd4c0dee2912931b6a6ecbe Author: Weiqun Zhang Date: Mon Nov 9 12:23:07 2015 -0800 DistributionMapping: add LeastUsedTeams and for SFC split the works among teams first and then inside teams Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit e1cce37c7f368aa54127205eeee2a272a3af3a01 Author: Weiqun Zhang Date: Sat Nov 7 20:06:45 2015 -0800 MFIter: new owner_only flag Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit dcb2b373b80a0b344c4315778beeb265c9ad549d Merge: 4456e5920 4aa1c64f3 Author: Weiqun Zhang Date: Sat Nov 7 10:05:35 2015 -0800 Merge branch 'development' into pgas commit 4aa1c64f3d520eb8b1359cc85818ec7030d5d7fe Author: Weiqun Zhang Date: Sat Nov 7 10:05:15 2015 -0800 MFIter: use bitfield flags Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 4456e59209d7c58d274abe72d5543cad5ca9125e Author: Weiqun Zhang Date: Fri Nov 6 20:24:10 2015 -0800 added fab ownership Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit ca436aeb511d07e517a80b70ae10c1761c4ec221 Author: Weiqun Zhang Date: Fri Nov 6 19:58:40 2015 -0800 Added an Arena for UPC++ Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Make.package Src/C_BaseLib/UArena.H Src/C_BaseLib/UArena.cpp commit c1068028d948d1fd7854181cf92ce779d7d0c016 Author: Weiqun Zhang Date: Fri Nov 6 17:14:00 2015 -0800 first pass of UPC++ team Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IArrayBox.H Src/C_BaseLib/IArrayBox.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/PGAS_HEAT/GNUmakefile commit e5c357123b04d6be5576da8aacca57d110070bb0 Author: vince Date: Fri Nov 6 16:26:36 2015 -0800 return coord type as an int (esp. for mpi) Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp commit 9ff1b0a0a9701888fb47a3dd5851e537f1ae0a58 Author: vince Date: Fri Nov 6 16:01:53 2015 -0800 check for correct array size. Src/C_BaseLib/Box.cpp commit 53c4ce1cb6e8943b5043db68995ef501128e206a Author: vince Date: Fri Nov 6 16:01:12 2015 -0800 fixed comment. Src/C_BaseLib/FabArray.H commit 956a6e9a76fd0e3a79e40acd6c06b51099eb6363 Author: vince Date: Fri Nov 6 16:00:49 2015 -0800 (un)serialize functions for boxarray. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit d2c1a3221f889b381971860c2fa767b4d01a4da2 Author: Ann Almgren Date: Fri Nov 6 11:56:16 2015 -0800 BoxLib/Tutorials/AMR_Adv_Diff_F: Put higher order slopes into algorithm -- now there is a separate slope routine which is called from compute_fluxes. There are still no transverse derivatives though. Tutorials/AMR_Adv_Diff_F/GPackage.mak Tutorials/AMR_Adv_Diff_F/compute_flux.f90 Tutorials/AMR_Adv_Diff_F/slope.f90 commit d77ca089e61f98a0923fe3e4cee8900b5dc94a16 Merge: 904d803b4 f6889d7c9 Author: yzheng Date: Fri Nov 6 09:56:17 2015 -0800 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 905d1a56fb057e87cfc61cc7137e3f2ff74fa94d Author: Ann Almgren Date: Fri Nov 6 09:02:38 2015 -0800 Don't need interpolate.f90 in this example. Tutorials/AMR_Advection_C/Source/Make.package Tutorials/AMR_Advection_C/Source/interpolate.f90 commit ff72c305085a4721d25b2c6e4951d634cb69c0a8 Author: Ann Almgren Date: Fri Nov 6 07:35:54 2015 -0800 Clean up of Tutorials/AMR_Advection_C code -- 1) Convert to use BoxLib::average_down(... 2) Clean out unused "nspec" Tutorials/AMR_Advection_C/Source/ADR.cpp Tutorials/AMR_Advection_C/Source/ADR_F.H Tutorials/AMR_Advection_C/Source/Src_2d/ACT_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/trans_2d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90 commit 506981603255e6a4a0dd389e1408c17e2780a6e8 Author: Michael Zingale Date: Thu Nov 5 22:49:32 2015 -0500 don't print a warning about visualization if we are making benchmarks Tools/RegressionTesting/testnew.py commit 70062e3bd69da2ab6e8b276a7f5f2d7602fd22cd Author: vince Date: Thu Nov 5 16:03:51 2015 -0800 parmparse setting for particles.particles_nfiles. Src/C_BaseLib/Particles.H commit f6889d7c925e0fbeb69ac232ae24fc1b513e9c3a Merge: 759ae876d 079c2cb02 Author: Weiqun Zhang Date: Thu Nov 5 10:52:36 2015 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package commit 079c2cb0293b0901471ff5c8c2a674417ff574f3 Author: Weiqun Zhang Date: Thu Nov 5 10:02:49 2015 -0800 PIC tutorial: update to the FMultiGrid function name Tutorials/PIC_C/solve_with_f90.cpp commit de846815af572c9edec8b53f6198fd11d8ab3694 Merge: cd72ddc8d df9792908 Author: Weiqun Zhang Date: Thu Nov 5 09:51:16 2015 -0800 Merge branch 'development' into new_particle commit cd72ddc8d4a21a8175740d75f01442647e0146ef Author: Ann Almgren Date: Thu Nov 5 03:11:09 2015 -0800 Add versions of BoxLib::average_down that take an int rather than an IntVect for the refinement ratio. Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp commit a7486a693755a54909bf28bf599019873b2c2778 Author: Ann Almgren Date: Thu Nov 5 03:09:41 2015 -0800 This version does a level-0-then-level-1 solve as well as a multilevel 0-1 solve. It compiles and runs with the latest versions of BoxLib::new_particle branch. Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp commit 53cd9bcab749ba3e005f5de1bc0b5b1845a70d9e Author: vince Date: Wed Nov 4 16:13:49 2015 -0800 added functions to (un)serialize arrays of strings. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 3654493612818c8822b14ab3d8c84da82f1cad0d Author: vince Date: Wed Nov 4 14:53:36 2015 -0800 proc numbers for all. Src/C_BaseLib/ParallelDescriptor.H commit 72077db2ba84c25c45fbf459cf6649a2895b5855 Author: vince Date: Wed Nov 4 14:52:42 2015 -0800 (un)serialize box functions for communicating boxes. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 2810d4e9fb82be4fba285bdecab0ae761c2f0068 Author: vince Date: Tue Nov 3 15:37:01 2015 -0800 random multilevel distribution map for testing the sidecars. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 071dad7fecfad3f64592ba1c5f4855209c5bca25 Author: vince Date: Tue Nov 3 15:35:36 2015 -0800 added function to increase the number of processes in a sidecar. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 9ab7b1c582ce3b575dc6c0118b6d0c40f62c256f Author: vince Date: Tue Nov 3 15:34:02 2015 -0800 added a few diagnostics for dynamic sidecar development. Src/C_BaseLib/FabArray.H commit df979290812e1558e844239a1ff58e55a5556f04 Merge: 184fa1934 13a755cd6 Author: Regression Tester Date: Tue Nov 3 12:21:16 2015 -0800 Merge branch 'master' into development commit 184fa193482b42403c44168d7d26bbdb56bbbae8 Author: Weiqun Zhang Date: Mon Nov 2 16:27:42 2015 -0800 FMultiGrid: renamed get_grad_phi back to get_fluxes because the latter is more accurate. Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Tutorials/MultiGrid_C/main.cpp commit 075caf7ef6c672cba446bea34c9da4ec2d6ee028 Author: Weiqun Zhang Date: Mon Nov 2 16:03:08 2015 -0800 fixed comments thanks to Ashish Pathak of Umass Dartmouth Tutorials/HeatEquation_EX5_F/advance.f90 commit 1693e7f5b8c7983326a35e6224b4e49ebd5c9b1c Author: Brian Friesen Date: Mon Nov 2 15:27:46 2015 -0800 Revert "IntVect: move static variables returned by TheDimensionVector() to anonymous namespace" This reverts commit 7d380196bce8148af7544b5920af5ab01f0d059d. Src/C_BaseLib/IntVect.cpp commit f2e038351720492583c8120cf0f31adbea1660a6 Author: Brian Friesen Date: Mon Nov 2 15:27:45 2015 -0800 Revert "IntVect: move all remaining static variable declarations to anonymous namespace" This reverts commit eb4ea0d9b111bc2b5debb5199e09b12a418a4721. Src/C_BaseLib/IntVect.cpp commit 0bb3b85e865bcd7d829f734aacd8549fb9a2ef02 Author: Brian Friesen Date: Mon Nov 2 15:27:44 2015 -0800 Revert "Box: move static variable "Unit" (returned by TheUnitBox()) to anonymous namespace" This reverts commit 87f50a2d86e8a6bd6d71afeaf238bc277fe20d43. Src/C_BaseLib/Box.cpp commit 540445d64641d4ba4e4d9309100b572bae925a7b Author: Brian Friesen Date: Mon Nov 2 15:27:41 2015 -0800 Revert "IndexType: move static variables "Cell" and "Node" to anonymous namespace" This reverts commit 685ad5b30fbff794d69017051fb06f5addcb1401. Src/C_BaseLib/IndexType.cpp commit 685ad5b30fbff794d69017051fb06f5addcb1401 Author: Brian Friesen Date: Mon Nov 2 15:04:19 2015 -0800 IndexType: move static variables "Cell" and "Node" to anonymous namespace Src/C_BaseLib/IndexType.cpp commit 87f50a2d86e8a6bd6d71afeaf238bc277fe20d43 Author: Brian Friesen Date: Mon Nov 2 15:02:47 2015 -0800 Box: move static variable "Unit" (returned by TheUnitBox()) to anonymous namespace Src/C_BaseLib/Box.cpp commit eb4ea0d9b111bc2b5debb5199e09b12a418a4721 Author: Brian Friesen Date: Mon Nov 2 15:01:03 2015 -0800 IntVect: move all remaining static variable declarations to anonymous namespace Src/C_BaseLib/IntVect.cpp commit 7d380196bce8148af7544b5920af5ab01f0d059d Author: Brian Friesen Date: Mon Nov 2 14:33:51 2015 -0800 IntVect: move static variables returned by TheDimensionVector() to anonymous namespace This renders unnecessary (and partially reverts) the changes made in commit 3f16894 ("IntVect: added braces around cases of TheDimensionVector"). In C++11 the "static" qualifier is no longer necessary because variable declarations in anonymous namespaces are guaranteed to have internal linkage. However, in C++03, without the "static" qualifier they have external linkage. Src/C_BaseLib/IntVect.cpp commit 1dafc8239c6af1a87b3440dd68560dc8cab54872 Author: Weiqun Zhang Date: Mon Nov 2 14:41:21 2015 -0800 MultiFabUtil: fixed bug in my last commit Src/C_BaseLib/MultiFabUtil.cpp commit 78fafee5a832476c2e5e3dd848243b18478dc5b5 Author: Weiqun Zhang Date: Mon Nov 2 13:50:08 2015 -0800 FMultiFab: use crse mf to construct MFIter Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 572837c5de4ebe615d09c63f6a447a11b3f1d241 Author: Weiqun Zhang Date: Mon Nov 2 11:27:26 2015 -0800 MultiFabUtil: thread safety Src/C_BaseLib/MultiFabUtil.cpp commit a2fe131d50b6f09a009ccb94d6250041db4447ac Merge: 4bb03b719 2f8c5eaff Author: Ann Almgren Date: Mon Nov 2 11:25:43 2015 -0800 Merge branch 'development' into new_particle commit b10952cf76e7de85701ab7d632ff90654b52be05 Merge: 31cd7af4c 2f8c5eaff Author: Michael Zingale Date: Mon Nov 2 14:25:35 2015 -0500 Merge branch 'development' into plotfile_ghost commit 31cd7af4c222484e247cd2e22fd718d8075b00bb Merge: ca512a4fd 492754ab9 Author: Michael Zingale Date: Mon Nov 2 14:25:05 2015 -0500 Merge branch 'development' into plotfile_ghost commit ca512a4fdf48ab89711610af597aae3abf217a13 Author: Ann Almgren Date: Mon Nov 2 11:10:43 2015 -0800 Revert to writing the plotfiles with ghost cells -- the fcompare routine in Tools/PostProcessing/F_src is now able to handle plotfiles with ghost cells. Tutorials/MultiGrid_C/writePlotFile.cpp commit 2f8c5eaffcce8663752731f8c9004e2e237ae3a2 Author: Weiqun Zhang Date: Mon Nov 2 09:56:05 2015 -0800 MultiFabUtil: Removed bl_constants_module because it is in F_BaseLib, not C_BaseLib. Some codes may not include F_BaseLib. Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 commit 13a755cd6c7806f59a6a1c33c08d40ffbaa72d9d Author: Weiqun Zhang Date: Sun Nov 1 19:36:27 2015 -0800 fixed a bug in regrid.f90 thanks to Ashish Pathak of Umass Dartmouth Src/F_BaseLib/regrid.f90 Src/Python/F90/src/regrid.f90 commit 492754ab96a8285668931a02683aa613063c1093 Author: Weiqun Zhang Date: Sun Nov 1 19:43:14 2015 -0800 Make: flags for using fsanitizer with gcc Tools/C_mk/Make.defs commit 0378f7f1319e887828a55e6f31638b7cb533afea Author: Weiqun Zhang Date: Sun Nov 1 19:41:36 2015 -0800 C_CellMG: return immediately if the initial residual is already zero. this could happen for species diffusion when certain species is initially zero everywhere. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit c3a68fe8fb19099ab601e59a7adc506be1902c5a Author: Weiqun Zhang Date: Sun Nov 1 19:36:27 2015 -0800 fixed a bug in regrid.f90 thanks to Ashish Pathak of Umass Dartmouth Src/F_BaseLib/regrid.f90 Src/Python/F90/src/regrid.f90 commit e699ab9c81c30ea5e40d6bc22b80cd6553ddbbff Author: Michael Zingale Date: Sun Nov 1 17:46:02 2015 -0500 copy the diffDir if we do copy_benchmarks Tools/RegressionTesting/testnew.py commit a52461f53902541acc182dcac5b4feef682966c2 Author: Ann Almgren Date: Sun Nov 1 12:49:08 2015 -0800 Have two separate versions of BoxLib::average_down -- one which uses volume weighting and one which does not. Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 4299b1c5219acc01986bcaacd7139fd846457e93 Author: Ann Almgren Date: Sun Nov 1 11:17:47 2015 -0800 Use tileboxes in BoxLib::average_down, and fix an indexing error in MultiFabUtil_*d.f90 Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 commit dcf421d200602e3c6fea145fd7f92e92703b1209 Author: Michael Zingale Date: Sat Oct 31 18:39:09 2015 -0400 lots of compilation fixes Src/C_BaseLib/MultiFabUtil_1d.f90 commit 13513ef41d0e723be0116f883fba8fa09407e1eb Author: Ann Almgren Date: Fri Oct 30 15:44:21 2015 -0700 Add the average down routines to 1d and 2d. Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 commit 9e3990349c71ab0781cb11cccdc108231aa31006 Author: Weiqun Zhang Date: Fri Oct 30 15:16:15 2015 -0700 MultiFabUtil: fixed function arguments Src/C_BaseLib/MultiFabUtil.cpp commit fe62e3fd13777b57b1d5ca0d7b6dc9edd980a0f3 Merge: 404abd0c8 0932040bc Author: Ann Almgren Date: Fri Oct 30 15:02:21 2015 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 404abd0c80c9b6d899b36f8415b473221b1a0b90 Author: Ann Almgren Date: Fri Oct 30 15:01:48 2015 -0700 Put in first pass at generic routine in BoxLib namespace that averages a fine MultiFab onto a coarse MultiFab without having to be owned by an AmrLevel. Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 0932040bc99f96e4dc65357997f5feec38a47f78 Author: Marc Day Date: Fri Oct 30 13:13:16 2015 -0700 Update system for OSX 10.11.1 Tools/C_mk/Make.Darwin Tools/C_mk/Make.mpi commit 2ecabc668cc171d984493667b782bdd25263c15b Merge: 0102f402c b326eb957 Author: Marc Day Date: Fri Oct 30 13:08:06 2015 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 0102f402ce96017b58e2a61b04f4256d6bc89ace Author: Marc Day Date: Fri Oct 30 13:04:50 2015 -0700 Remove question make from define of CC and CXX if USE_GNU in Make.defs because make defaults CC=cc before anything else. On Linux machines, CC then gets redefined explicitly. On Darwin it does not, and the USE_GNU bit fails to set CC and CXX as it should. Tools/C_mk/Make.defs commit b326eb957ef4210b607fe6a19f86281cdc066e2f Author: Weiqun Zhang Date: Fri Oct 30 12:50:51 2015 -0700 FMultiGrid: added mac projection Src/C_BoundaryLib/MacBndry.H Src/C_BoundaryLib/MacBndry.cpp Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 4bb03b719af108738e00c6c27c5a5b7919d03f02 Merge: f776c3d00 ec1bffbd6 Author: Ann Almgren Date: Fri Oct 30 10:19:11 2015 -0700 Merge branch 'development' into new_particle commit f776c3d0084a2b69db48c6e8a2659e593cb28a58 Author: Ann Almgren Date: Fri Oct 30 10:18:28 2015 -0700 Latest versions ... still not soup yet. Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp commit a067b5bb71e22358baa9f3bf907d6947a9c1fcbd Author: Ann Almgren Date: Thu Oct 29 17:26:14 2015 -0700 This verison of Particles.H actually compiles after the latest change. Src/C_BaseLib/Particles.H commit eb54c104b4bdfaac88a3743687eef9e59f86ca5a Author: Ann Almgren Date: Thu Oct 29 17:24:03 2015 -0700 Modify ParticleContainer::InitRandom so that it can take an optional RealBox argument which allows you to constrain the particles to lie within a rectangular region. Src/C_BaseLib/Particles.H commit 49e667e45874bb857157317951fc7fdc04ea1d81 Merge: 94fd6c861 445e5a566 Author: Ann Almgren Date: Thu Oct 29 16:52:29 2015 -0700 Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle commit ec1bffbd6839c870319a907df58a501ffa852ac5 Merge: d6025300e d1a24616b Author: Changho Kim Date: Thu Oct 29 13:24:32 2015 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit d6025300e0625a2b3db127b19b7224863d7c2bd5 Author: Changho Kim Date: Thu Oct 29 13:14:50 2015 -0700 new utility added !! fdumpdata2d generates plain-text-formatted data files from plotfiles. !! !! usage: fdumpdata2d --pf (pfs) [--var (vars)] [--lev (levs)] [--separate] !! where (pfs) = list of plotfiles, !! (vars) = list of variables, !! (levs) = list of levels, !! --var, --lev, --seprate are optional. Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fdumpdata2d.f90 commit d1a24616b2fdd6c4405464a1ce270d9c81a189fa Author: Michael Zingale Date: Thu Oct 29 16:12:08 2015 -0400 missing contiue Tools/RegressionTesting/testnew.py commit a9f7d1be0e21e099e8b425808ff566c833511990 Merge: 25ffc60e4 be1efa629 Author: Michael Zingale Date: Thu Oct 29 15:59:15 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 25ffc60e4538ac767be94643e2a6ac0c4a6c6175 Author: Michael Zingale Date: Thu Oct 29 15:59:07 2015 -0400 fix the output of the diff Tools/RegressionTesting/testnew.py commit 445e5a566734d91cb2f197bfb5dab321b443de66 Author: Weiqun Zhang Date: Thu Oct 29 12:58:17 2015 -0700 PIC tutorial: use FMultiGrid Tutorials/PIC_C/solve_with_f90.cpp commit f9af5106972cef6776a712a623d6e754f1401d5d Merge: 6498f8a85 be1efa629 Author: Weiqun Zhang Date: Thu Oct 29 12:57:25 2015 -0700 Merge branch 'development' into new_particle commit be1efa629f9390dba81f1fed55f3778eb6d74977 Author: Weiqun Zhang Date: Thu Oct 29 12:57:05 2015 -0700 FMultiGrid: minor tweak Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 6498f8a852577998506af9e6e9ef102c9c9b2cfe Merge: 0c02e2b65 6f9753b09 Author: Weiqun Zhang Date: Thu Oct 29 10:48:32 2015 -0700 Merge branch 'development' into new_particle Conflicts: Tutorials/MultiGrid_C/main.cpp commit 9046bd671d748b44f9ad0b1df0d1556054dfad7f Author: Michael Zingale Date: Wed Oct 28 20:06:39 2015 -0400 replace lbound() and ubound() with lo and hi, since these are safer in the presence of ghost cells Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90 commit 78ac9c418fecb357ce7e589afe1f8724822d403e Merge: 7724c23d1 0bb054e13 Author: Michael Zingale Date: Wed Oct 28 19:23:07 2015 -0400 Merge branch 'development' into plotfile_ghost commit 7724c23d1d9c408237d2fdb0caaa8ce6c9f74b33 Author: Michael Zingale Date: Wed Oct 28 19:00:36 2015 -0400 get ghost cell support in here -- the size now refers to the size on disk, including ghost cells. There should be no difference at all for plotfiles without ghost cells Src/F_BaseLib/plotfile.f90 commit ab87088f846f93be074d2d8987bd5198db2bca12 Author: Michael Zingale Date: Wed Oct 28 19:00:13 2015 -0400 this works with ghost cells now Tools/Postprocessing/F_Src/fcompare.f90 commit 6f9753b09aa9b8385871279f66078325c0b36ea9 Merge: c4beaabf3 0bb054e13 Author: Weiqun Zhang Date: Wed Oct 28 14:19:23 2015 -0700 Merge branch 'development' into ctof commit c4beaabf3b29ff7e467961307444e811ef8ac54b Author: Weiqun Zhang Date: Wed Oct 28 14:17:54 2015 -0700 capability of sharing a multifab from C++ to Fortran without copying the data Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/MultiFab_C_F.H Src/F_BaseLib/MultiFab_C_F.cpp Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab_c.f90 Tutorials/MultiFab_C_F/GNUmakefile Tutorials/MultiFab_C_F/Make.package Tutorials/MultiFab_C_F/ff.f90 Tutorials/MultiFab_C_F/main.cpp commit 3037300d094af598d034a06804d9231227ff553e Author: Weiqun Zhang Date: Wed Oct 28 13:07:55 2015 -0700 moved the stuff that starts mpi for fortran form mgt_solver to c++ boxlib init function Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/parallel.f90 Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 0bb054e13d30bfe7230560f84df7f750333e4e04 Author: Brian Friesen Date: Tue Oct 27 10:51:08 2015 -0700 Tutorials: add "beta" to argument list of solve_with_HPGMG() in MultiGrid_C HPGMG internally calculates beta at cell faces from the cell-centered beta MultiFab because BoxLib and HPGMG store cell face data in very different ways. It's much easier to do the averaging by hand than it is to translate array indices. However, in order to be consistent with the sign conventions of the other solvers, we want to calculate grad(Phi) in the same way that they do. So we use an AbecLaplacian to calculate the gradients. But AbecLaplacian needs the beta at cell faces, not cell centers. So we add beta to the arguments list. This also fixes a compile-time error if running this tutorial with HPGMG: the variable "abec_operator" was never declared. Tutorials/MultiGrid_C/main.cpp commit 4bad12766203a47cbc7f94c2895116bec3af75d9 Author: Brian Friesen Date: Mon Oct 26 23:00:43 2015 +0000 C_BaseLib: remove "__LP64__" preprocessor macro from list of macros describing long pointers This macro does not uniquely describe long pointers. It leads to compile-time errors on Mira (BG/Q) because many variables in FPC.cpp are duplicately declared, since both "__ppc__" and "__LP64__" are defined. This removal should (hopefully) not affect any architectures we run on, since at least one of the other macros should be defined. Src/C_BaseLib/FPC.cpp commit 1e36c50889063fb0f3f5785d7acc5b304cd094dd Author: Brian Friesen Date: Tue Oct 20 23:21:34 2015 +0000 F_MG: include "get_dim()" explicitly from multifab_module in ml_prolongation.f90 The XL Fortran compiler on Mira complains about being unable to find this function. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 3f0b48be6b93765ed00d7f6cd85860810f4a2d7a Author: Brian Friesen Date: Tue Oct 20 23:20:19 2015 +0000 C_BaseLib: add FORT_FASTSAXPY definition to SPECIALIZE_F.H for BL_FORT_USE_LOWERCASE Found this bug when trying to compile the MultiGrid_C tutorial with the XL compilers on Mira. Src/C_BaseLib/SPECIALIZE_F.H commit fcb28d436ca44c07847b2aaa821f3ad0d251f775 Author: Brian Friesen Date: Thu Oct 15 22:07:14 2015 +0000 IntVect: added braces around cases of TheDimensionVector Cases share scope, so without braces the variables declared in the different cases percolate down through the entire switch statement. This can lead to uninitialized variables if a particular case is skipped. Adding braces around each case creates a unique scope for each of these variables, which protects against this possibility. The IBM XL compiler caught this error. Src/C_BaseLib/IntVect.cpp commit 0f550e3b297341c86ae224d3a6287c2840594dd0 Author: Brian Friesen Date: Thu Oct 15 21:56:55 2015 +0000 C_mk, F_mk: add support for IBM XL compilers on Mira, the BlueGene/Q at ALCF Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/bgq.mak commit 08c4f5da2561c273ff65d8ea549e88caab481bd0 Author: Weiqun Zhang Date: Tue Oct 27 10:14:34 2015 -0700 AMR_Advection_C Tutorial: consolidate diffusion code Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp Tutorials/AMR_Advection_C/Source/Diffusion.H Tutorials/AMR_Advection_C/Source/Diffusion.cpp commit c4cf10e981dd6e7ded363150488b9ba25832b7cd Author: Weiqun Zhang Date: Tue Oct 27 10:14:01 2015 -0700 FMultiGRid: added functions for diffusion operator Src/LinearSolvers/C_to_F_MG/FMultiGrid.H commit 94fd6c861223492c3578333a10db7dfd0bed6b59 Merge: 50d7b90ee 8aecad560 Author: Ann Almgren Date: Tue Oct 27 10:09:40 2015 -0700 Merge branch 'development' into new_particle commit 8aecad560000021e10e75866a5f2def1a33a2e5b Merge: 4990cf45b ba093b337 Author: vince Date: Tue Oct 27 09:45:38 2015 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 4990cf45bf2c7a25f3ea1a414ed4e561a712f116 Author: vince Date: Tue Oct 27 09:45:17 2015 -0700 added 1d file. some subroutines now working yet. Src/Extern/amrdata/FABUTIL_1D.F commit ba093b337c58b0006d32cad511a29243641dfe8d Author: Weiqun Zhang Date: Mon Oct 26 17:28:43 2015 -0700 AMR_Advection_C Tutorial: use FMultiGrid Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp Tutorials/AMR_Advection_C/Source/Diffusion.H Tutorials/AMR_Advection_C/Source/Diffusion.cpp commit 0b342a7edbf73455578452730b9b394d3d651a84 Author: Weiqun Zhang Date: Mon Oct 26 17:26:47 2015 -0700 FMultiGrid: added applyop functions Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 49055091ce52307d5690f8e2f5bc2ea9573d0f57 Author: vince Date: Mon Oct 26 17:01:06 2015 -0700 dont use the word signal. Src/C_BaseLib/ParallelDescriptor.cpp commit 045793488c2ac63be8cfd2968f1d44121dbe32f6 Author: Weiqun Zhang Date: Mon Oct 26 16:25:18 2015 -0700 update Linear Solver Comparison Test to use FMultiGrid Tests/LinearSolvers/ComparisonTest/COEF_1D.F Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit 5d0a945bf8e3e5e593f7077dce56659cafa57d5a Author: vince Date: Mon Oct 26 16:00:10 2015 -0700 make safer data broadcasts. Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 679f0220773816f3e809bdcb206076576c3c5b3a Author: Weiqun Zhang Date: Mon Oct 26 15:32:31 2015 -0700 minor cleanup Src/C_BaseLib/MultiFabUtil.cpp commit 82c75eeac3b76e6e6759194d1af6773a7fe02846 Author: Weiqun Zhang Date: Mon Oct 26 14:09:59 2015 -0700 MultiGrid Tutorial: use FMultiGrid instead of MGT_Solver directly Tutorials/MultiGrid_C/main.cpp commit 0f0ca5aa97fc660ef48a0cbd1f135f4fdcc0c289 Author: Weiqun Zhang Date: Mon Oct 26 14:01:02 2015 -0700 FMultiGrid: make the interface consistent with C++ ABecLaplacian class Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 8cbee5677d4c395e8c09741532ac0e43f0b699c8 Author: Weiqun Zhang Date: Mon Oct 26 13:50:59 2015 -0700 MultiGrid Tutorial: use the new BoxLib::average_face_to_cell_center function and use PArray for bcoeffs Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/main.cpp commit 500cca1ab3b1a9a47657409e862cc9910672250e Author: Weiqun Zhang Date: Mon Oct 26 13:45:09 2015 -0700 C_CellMG: added a new function that takes PArray as b coeffs Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 2e0feccdd375b92ad690582d5a86f77d553d0f73 Author: Weiqun Zhang Date: Mon Oct 26 13:43:52 2015 -0700 added a new function that averages from cell-centered to face MultiFabs Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 9e5fe738252c46730c2014b5146b6fa8892f33c7 Author: Weiqun Zhang Date: Mon Oct 26 12:40:21 2015 -0700 MultiGrid Tutorial: removed unnecessary ghost cells Tutorials/MultiGrid_C/main.cpp commit 911002caba28a8a6de39a03404fedcfcd0683b5f Author: Weiqun Zhang Date: Mon Oct 26 11:25:36 2015 -0700 update HyperABecLap that has been broken for 3 years due to changes in BndryData Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp commit 6b9b91bddf52a1191527aaa79c73b3d28c343c53 Author: Weiqun Zhang Date: Mon Oct 26 10:18:56 2015 -0700 FMultiGrid: cleanup Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit ec4803b32a99de323053402cf5ccde094b729b72 Author: Michael Zingale Date: Mon Oct 26 10:47:44 2015 -0400 fix the build git hash stuff Tools/C_scripts/makebuildinfo_C.py commit 1cb1499f3090343d4276aea2f83c10bc0ac246da Author: Weiqun Zhang Date: Sun Oct 25 18:04:50 2015 -0700 FMultiGrid: make it more general Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 9776f06aa763c9813f4499412e8e2fa3b9806b4b Author: Weiqun Zhang Date: Sun Oct 25 16:06:22 2015 -0700 FMultiGrid: bug fix Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 72f602a63c9aa045fc0a46a40c0d2ebf75c418ba Merge: a149254f4 a4211e592 Author: Weiqun Zhang Date: Sat Oct 24 22:12:38 2015 -0700 Merge branch 'development' into mlcc commit a149254f481447999a8b786e07b6dd63349e9399 Merge: 83e3c9408 5fa4d44a4 Author: Weiqun Zhang Date: Sat Oct 24 22:11:52 2015 -0700 Merge branch 'development' into mlcc commit 83e3c94085a0003a54702a57e80a8edbaae78e98 Author: Weiqun Zhang Date: Sat Oct 24 22:10:41 2015 -0700 minor Src/C_AMRLib/Amr.cpp commit 605ecaa9dcc22d9270ef46647831d71a0ae66e07 Author: Weiqun Zhang Date: Sat Oct 24 20:42:05 2015 -0700 fixed comments Src/LinearSolvers/C_to_F_MG/FMultiGrid.H commit 6a066990ed5422fdb423ccf40e2e4094937d6b7c Author: Weiqun Zhang Date: Sat Oct 24 20:10:46 2015 -0700 FMultiFab: comments and minor tweak Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 22cb6f69edf0ed75b2b4c40736f201a5e39c7afa Author: Weiqun Zhang Date: Fri Oct 23 17:35:49 2015 -0700 FMultiGrid: refactor Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 50d7b90ee0bc8f29deee6bb6dadcde366e3e2d7e Merge: 0c02e2b65 a4211e592 Author: Ann Almgren Date: Fri Oct 23 17:15:53 2015 -0700 Merge branch 'development' into new_particle commit a4211e592c887c11634594c283390928fe03623f Author: Ann Almgren Date: Fri Oct 23 17:14:47 2015 -0700 In Tutorials/MultiGrid_C, I hard-wired the new grad_phi stuff for BL_SPACEDIM = 3. This generalizes it to work for BL_SPACEDIM = 2 or 3. Tutorials/MultiGrid_C/main.cpp commit 0c02e2b658d5fd00e9409620485c67ab28630d9f Author: Ann Almgren Date: Fri Oct 23 17:14:47 2015 -0700 In Tutorials/MultiGrid_C, I hard-wired the new grad_phi stuff for BL_SPACEDIM = 3. This generalizes it to work for BL_SPACEDIM = 2 or 3. Tutorials/MultiGrid_C/main.cpp commit 6fd99675fbca026568931c98b7ebecd423cc85aa Author: Ann Almgren Date: Fri Oct 23 17:12:17 2015 -0700 Since the C++ MultiGrid solver uses only V-cycles, we want to hard-wire piecewise constant, not piecewise linear interpolation -- the PC interpolation works better for V-cycles while the piecewise linear works better for F-cycles. Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit cf2652fb873d655dbde0a95f198c7807198b366f Author: Ann Almgren Date: Fri Oct 23 17:12:17 2015 -0700 Since the C++ MultiGrid solver uses only V-cycles, we want to hard-wire piecewise constant, not piecewise linear interpolation -- the PC interpolation works better for V-cycles while the piecewise linear works better for F-cycles. Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit 2c02483923caead5987f7809852540c6e9541a61 Author: Michael Zingale Date: Fri Oct 23 16:42:53 2015 -0400 more safely get the box indicies Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90 commit b6a4247f6a1b6202604c27c6f817381c774b1b0d Author: Michael Zingale Date: Fri Oct 23 16:33:56 2015 -0400 eliminate lbound/ubound Tools/Postprocessing/F_Src/fsnapshot3d.f90 commit 5d0a2eda64c231e47f33f71bde009e324defe507 Author: Michael Zingale Date: Fri Oct 23 16:28:26 2015 -0400 remove lbound/ubound Tools/Postprocessing/F_Src/fextract.f90 commit e0bbe775156bee51889250c654cc089a51cdf6ba Author: Michael Zingale Date: Fri Oct 23 16:21:16 2015 -0400 add get_pbox Src/F_BaseLib/plotfile.f90 commit db3ba7ddce57e3bc10cb5c671a8130b2843fdb8b Author: Ann Almgren Date: Thu Oct 22 22:13:57 2015 -0700 Remove excess print statements from Particles.H Src/C_BaseLib/Particles.H commit e91e2ecaef08dacc9be6e88863317e3c3b3d7e6c Merge: 8d76fb01b 5fa4d44a4 Author: Ann Almgren Date: Thu Oct 22 22:13:36 2015 -0700 Merge branch 'development' into new_particle commit 00e46f979f1219ef7aed2968ea0f96a7d411197e Author: Weiqun Zhang Date: Thu Oct 22 21:52:32 2015 -0700 PArray: removed isConstPointer Src/C_BaseLib/PArray.H commit 5fa4d44a4b99814bbed60222e5a21f8d9e81d934 Author: Ann Almgren Date: Thu Oct 22 17:11:53 2015 -0700 After we compute the solution, use the operator to return the face-based fluxes, then average those onto cell centers using BoxLib::average_face_to_cellcenter and write the cell-centered gphi out into a plotfile just like we write out the solution. This allows us to test the gradient routines as well as the solver itself. Tutorials/MultiGrid_C/main.cpp commit 8d76fb01b6ecc957c9dfa7bbdd9e8fef963038fc Author: Ann Almgren Date: Thu Oct 22 17:11:53 2015 -0700 After we compute the solution, use the operator to return the face-based fluxes, then average those onto cell centers using BoxLib::average_face_to_cellcenter and write the cell-centered gphi out into a plotfile just like we write out the solution. This allows us to test the gradient routines as well as the solver itself. Tutorials/MultiGrid_C/main.cpp commit ff114ff8198fd025bbf43554ef704424dd4b8505 Merge: a1d31f5ff c60315a6d Author: Chris Malone Date: Thu Oct 22 19:16:31 2015 -0400 Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development commit bd223eaae91b79ac20b8c79ee112933dd08d3ad0 Author: Weiqun Zhang Date: Thu Oct 22 15:08:37 2015 -0700 FMultiGrid: more functions Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 6a9bcaa8cbb34062a4b050f6d8de1d7acdc0ecb7 Author: Michael Zingale Date: Thu Oct 22 16:20:43 2015 -0400 replace lbound and ubound with lwb and upb on the boxes -- this will be safe when we deal with ghostcells Tools/Postprocessing/F_Src/faverage.f90 commit c78af9314f58d91de38ea24bf75b3e61baf33aed Author: Weiqun Zhang Date: Wed Oct 21 21:59:33 2015 -0700 first pass of MultiLevelMultiGrid Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/Make.package commit 0d55d1400434a1bc6752f5b3e9f247ab78be851b Author: Adam Jacobs Date: Thu Oct 22 15:12:25 2015 -0400 Add ACC flags to fortran mk Tools/F_mk/comps/Linux_pgi.mak commit e92c35f6c981d4b4fe7b9fe3443662c96551b028 Author: Adam M. Jacobs Date: Thu Oct 22 15:00:04 2015 -0400 Start adding ACC to PGI build Tools/F_mk/comps/Linux_pgi.mak commit 4ddab485628015ba9909f8150aff545e9da9f7fd Author: Michael Zingale Date: Thu Oct 22 14:34:05 2015 -0400 some notes along the way Tools/Postprocessing/F_Src/TODO_GHOST commit 3fb9899d31bc1596632eb666c7888f4878a34cd0 Author: Michael Zingale Date: Thu Oct 22 14:21:57 2015 -0400 more simplification + add the --ghost (or -g) option -- it doesn't really work yet... Tools/Postprocessing/F_Src/fcompare.f90 commit 794d7dfd9e1eafbe1f1c2582c623a82ef6a03ce6 Author: Michael Zingale Date: Thu Oct 22 14:09:51 2015 -0400 remove unused lo and hi Tools/Postprocessing/F_Src/fcompare.f90 commit 4764009accee9e7a9bdf7002b4211f6b5cb005b7 Author: Michael Zingale Date: Thu Oct 22 14:06:12 2015 -0400 use box_equal() to simplify some stuff Tools/Postprocessing/F_Src/fcompare.f90 commit 0cde5f7b94758c5c2e67292d38798fbca8d204bc Author: Michael Zingale Date: Thu Oct 22 13:56:51 2015 -0400 use volume(get_pbox) in the isnan check Tools/Postprocessing/F_Src/fcompare.f90 commit 005782ff8c19963beacf3600a78a3b22c17db70b Author: Michael Zingale Date: Thu Oct 22 13:44:15 2015 -0400 more work on getting ghostcells into plotfile.f90 Src/F_BaseLib/plotfile.f90 commit c60315a6d3e12bf2551e8456ee680d9aeccd5a05 Author: Michael Zingale Date: Thu Oct 22 13:02:11 2015 -0400 some comments on what else to do to get the ghost cells to work Src/F_BaseLib/plotfile.f90 commit 476160da71e581c6b00f8a07cf1ba13f7f292252 Author: Michael Zingale Date: Thu Oct 22 12:49:37 2015 -0400 store ng and create a physical box (%pbx) for each of the fabs in the grid hierarchy -- this is to help out with supporting ghostcells in the plotfiles... Src/F_BaseLib/plotfile.f90 commit 0154618f88ae0ffbe61b34c3ab3e519265e2a1de Author: Michael Zingale Date: Thu Oct 22 10:48:54 2015 -0400 check the number of ghostcells in the header and abort if it is not 0 (for now) Src/F_BaseLib/plotfile.f90 commit 5f6d84e3a85ded8ab73e643df22a7ad82f8b95d7 Author: vince Date: Wed Oct 21 17:58:54 2015 -0700 Made loop to test multiple sidecar sizes. Tutorials/Sidecar_EX1/SidecarResizeTest.cpp commit b67748e3235d4c46ef92556cc7ba95b68e4be135 Author: vince Date: Wed Oct 21 17:34:56 2015 -0700 Support for dynamic sidecars. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit 248a0c9cf1b3a87855ec867247cb5f8e0042b59b Author: vince Date: Wed Oct 21 17:23:51 2015 -0700 resize to zero at the end. Tutorials/Sidecar_EX1/SidecarResizeTest.cpp commit 1b2413b3baf57a2d9dbc3fecac27c2375e7bf35b Author: vince Date: Wed Oct 21 17:21:05 2015 -0700 test with two sizes. Tutorials/Sidecar_EX1/SidecarResizeTest.cpp commit dfd041715d346ed82a17c83798829a47780c3fb5 Author: vince Date: Wed Oct 21 16:39:59 2015 -0700 sidecar resize test. Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/Make.package Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/inputs_sc commit 4f9e90edc62609e70847d7c5c75b98e0c45b97ae Merge: 4f7a8b4d4 635bea4a0 Author: Ann Almgren Date: Wed Oct 21 15:00:18 2015 -0700 Merge branch 'development' into new_particle commit 635bea4a061458c9ba2f14097dc0cea28d52c7b9 Merge: 7743c84a7 cce7df1d3 Author: Ann Almgren Date: Wed Oct 21 14:58:39 2015 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 7743c84a763dc56cfa01fffe3c71a4730dc8dd02 Author: Ann Almgren Date: Wed Oct 21 14:57:38 2015 -0700 Write the plotfile with 0 ghost cells, otherwise fcompare will misinterpret the arrays. Tutorials/MultiGrid_C/writePlotFile.cpp commit 4f7a8b4d42c2b7c02e4fe0e6e240ee73e0e9d182 Author: Ann Almgren Date: Wed Oct 21 14:57:38 2015 -0700 Write the plotfile with 0 ghost cells, otherwise fcompare will misinterpret the arrays. Tutorials/MultiGrid_C/writePlotFile.cpp commit a1d31f5ffd0f7d24e2881cf003d5dbdddd883b52 Merge: 5dacecd61 cce7df1d3 Author: Chris Malone Date: Wed Oct 21 17:23:01 2015 -0400 Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development commit cce7df1d353ce8049928101f76679bcc2bd2621a Author: Brian Friesen Date: Wed Oct 21 13:17:24 2015 -0700 Tutorials: add MPI communicator argument in call to MGBuild() in MultiGrid_C when building with HPGMG Tutorials/MultiGrid_C/main.cpp commit 5dacecd61c324c02782c09fd5264e7e60f7b62f3 Merge: 81473c26c 83a7ce0e0 Author: Chris Malone Date: Wed Oct 21 16:05:52 2015 -0400 Merge branch 'master' into development commit b91f298e7c8f3c242d1abc8969d985fdf33b9f44 Merge: 7d4e2155c 81473c26c Author: Ann Almgren Date: Wed Oct 21 13:03:50 2015 -0700 Merge branch 'development' into new_particle commit 81473c26c909802df8bd727b1608e4e39e07e5f6 Author: Ann Almgren Date: Wed Oct 21 12:44:58 2015 -0700 Modify the C++ solver in MultiGrid.{H,cpp} in order to correctly compute and use the initial residual. There was an issue before when a non-zero initial guess was passed in. This is now closer to the decision-making in the F90 solver. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 83a7ce0e09afcb551150100ad922d76aade67934 Author: Chris Malone Date: Wed Oct 21 16:01:34 2015 -0400 add support for my mac Tools/F_mk/GMakeMPI.mak commit 26816e65cc5f626f8c9996e33b3a1ffba742b3bb Author: Michael Zingale Date: Wed Oct 21 15:55:31 2015 -0400 when we do the first --make_benchmarks, the test on get_last_run() fails, but it isn't needed there (it is only needed for copy_benchmarks). Now we return None in this case. Tools/RegressionTesting/testnew.py commit 7d4e2155cbc2568b320dcf78440e7aac53e63106 Merge: 9c243b8e3 e699a84a1 Author: Ann Almgren Date: Wed Oct 21 12:55:10 2015 -0700 Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle commit 9c243b8e3fbfda75c4fa748b355618b9be6d0667 Author: Ann Almgren Date: Wed Oct 21 12:44:58 2015 -0700 Modify the C++ solver in MultiGrid.{H,cpp} in order to correctly compute and use the initial residual. There was an issue before when a non-zero initial guess was passed in. This is now closer to the decision-making in the F90 solver. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit e699a84a1726ec4e67aeedce4060737f097b3483 Author: Weiqun Zhang Date: Wed Oct 21 11:10:10 2015 -0700 use Array instead of PArray in constructing ParGDB Src/C_BaseLib/ParGDB.H Src/C_BaseLib/Particles.H Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp commit 8c6c54f33974864ef6f294278f2d241f2db2d3ad Merge: 4c39e0b27 4595d98e7 Author: Ann Almgren Date: Wed Oct 21 10:40:15 2015 -0700 Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle commit 4c39e0b2762ff0c23be4166b593e3e88a4acdf46 Author: Ann Almgren Date: Wed Oct 21 10:39:52 2015 -0700 Get rid of all the extra print statements in Particles.cpp Src/C_BaseLib/Particles.cpp commit 1715a9c223ec50bf584716781bbf6a713bbfb66f Author: vince Date: Mon Oct 19 11:10:37 2015 -0700 code cleanup. Src/C_BaseLib/ParallelDescriptor.cpp commit 0364348453fb1452f820b16f3831081b0edf6f73 Author: vince Date: Fri Oct 16 17:00:33 2015 -0700 moved group and comm initialization to SetNProcsSidecar function. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 657f7cff85415123e2a390605846f872894c7e13 Author: vince Date: Fri Oct 16 15:28:52 2015 -0700 fixed comment. Src/C_BaseLib/Utility.H commit 988e219d66f9c64316094438b12ce7edb28bd339 Author: vince Date: Tue Oct 13 13:51:25 2015 -0700 comments. Src/C_BaseLib/ParallelDescriptor.cpp commit 1c9058403d946106d37b200113c2ce7d5c4d697c Author: vince Date: Tue Oct 13 13:47:55 2015 -0700 comments. Src/C_BaseLib/ParallelDescriptor.H commit 6edd3cd4e600908ee914c75aeec6d2167a80a3dc Author: vince Date: Tue Oct 13 13:35:37 2015 -0700 comments. Src/C_BaseLib/ParallelDescriptor.cpp commit 4595d98e7e7130122cc7c2efee4e7a042eb1770f Merge: c7bcd6b17 9e2e4d8d6 Author: Weiqun Zhang Date: Wed Oct 21 10:27:42 2015 -0700 Merge branch 'development' into new_particle Conflicts: Src/C_BaseLib/Make.package commit 9e2e4d8d685832d468b936a5a59d3ffe0a242920 Author: Weiqun Zhang Date: Wed Oct 21 10:25:07 2015 -0700 BoxArray: added a new define function Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit c7bcd6b17e33e4f6b28ec27a54bc03c63d154f68 Author: Weiqun Zhang Date: Tue Oct 20 16:53:02 2015 -0700 only the I/O processor needs to do I/O Tutorials/PIC_C/solve_for_accel.cpp commit 3be6fa84225b6bae47eda7b0c4caf96593582ee8 Author: Weiqun Zhang Date: Tue Oct 20 16:41:52 2015 -0700 bug fixes in PIC tutorial Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp commit d971d2b046bed6e72d2c528e15e11468d467d95b Author: Weiqun Zhang Date: Tue Oct 20 16:40:13 2015 -0700 Particles: tweak constructors Src/C_BaseLib/PArray.H Src/C_BaseLib/ParGDB.H Src/C_BaseLib/Particles.H commit cd772d17dfd27bec5faa7d71f22a78f83cfa6df2 Author: Weiqun Zhang Date: Tue Oct 20 16:38:59 2015 -0700 BACKTRACE: don't have to sleep if there is only on processor Src/C_BaseLib/BLBackTrace.cpp commit a55ad14811a5d15ea0ce9e72baa2170617269b05 Author: Ann Almgren Date: Tue Oct 20 13:01:48 2015 -0700 This is my latest version of the PIC_C tutorial code and the changes in the Particle stuff needed to accomodate a multilevel box array coming into ParGDB. Src/C_BaseLib/ParGDB.H Src/C_BaseLib/Particles.H Src/C_BaseLib/Particles.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/work.f90 commit dc820ec80abe1322697b1d86fa3e5fb559e9b0df Author: Changho Kim Date: Tue Oct 20 09:49:55 2015 -0700 new utility to integrate a variable Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fintgvar2d.f90 commit 7f13c91daa38670cf5a15561c93efdd9f2e366b3 Author: Adam Jacobs Date: Tue Oct 20 11:02:35 2015 -0400 At the moment on OLCF machines, pgclibs does not work, so use libstdc++ Tools/F_mk/comps/Linux_pgi.mak commit fa96b7a1792f3939bdecffeb277b664df5b54151 Merge: a15b0f280 b66ae3553 Author: Chris Malone Date: Mon Oct 19 13:05:31 2015 -0400 Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development commit a15b0f280b454f0936fd0944888b92cb548ccc4e Author: Chris Malone Date: Mon Oct 19 12:57:03 2015 -0400 add support for fortran chester for development Tools/F_mk/GMakeMPI.mak commit b66ae3553ee5921e39f942c6791cb4d7a1c1ba92 Author: Max Katz Date: Mon Oct 19 12:25:18 2015 -0400 Add C_mk definition for Chester (XK7) development system at OLCF. Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 2e1bbccb97822a9fd7fa9a9202a15c982343d1c8 Author: Brian Friesen Date: Thu Sep 3 10:09:33 2015 -0700 C_BaseLib: glorious re-design of the sidecar interface (again) This is our glorious new interface to the sidecars. It obviates the need for abstract base "callback" analysis classes and replaces them with void pointers to blackbox functions. This allows the user to write arbitrary analysis workflows, rather than requiring her to define Initialize(), DoAnalysis(), and Finalize() functions, as was required with the previous interface. Marc Day was responsible for most of this work. I just did some peripheral cleaning afterwards. Src/C_BaseLib/Analysis.H Src/C_BaseLib/Analysis.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/InTransitAnalysis.H Tutorials/Sidecar_EX1/InTransitAnalysis.cpp commit a9099f8612b3de985e939797658c0399a93d19bc Author: Weiqun Zhang Date: Thu Oct 15 16:20:00 2015 -0700 BACKTRACE: catch SIGTERM Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp commit 44525e9c9f643e786e6bd5324bd6391016d75d72 Merge: 759ae876d 490a8f18a Author: Weiqun Zhang Date: Thu Oct 15 11:15:03 2015 -0700 Merge branch 'development' into pgas commit 490a8f18a3656a604350c5ba89124e72dd957410 Author: Weiqun Zhang Date: Wed Oct 14 15:13:04 2015 -0700 added flags for gcc thread sanitizer Tools/C_mk/Make.defs commit 389309984c4483833c060322996852b67c7565e7 Author: Weiqun Zhang Date: Wed Oct 14 14:29:28 2015 -0700 turned the just disabled omp back on and put it inside ifdef CRSEGRNDOMP, which has already been used to indicate derive functions are thread safe Src/C_AMRLib/AmrLevel.cpp commit 81cf6cba44fe604d91c1cc051a49a01eb408b40a Author: Weiqun Zhang Date: Wed Oct 14 14:00:02 2015 -0700 disable omp in FillPatchIterator::Initialize for some LMC problems Src/C_AMRLib/AmrLevel.cpp commit 845c81dc82e6f85dd99287cc5f0ad118b8cf84cc Author: Marc Day Date: Wed Oct 14 12:27:34 2015 -0700 Fixed bug in looping for 3D MFTower fortran Src/C_TowerLib/MFTower_3D.F commit 055be40a94de1fb78ab6a9eb2efde39e3338e511 Author: Ann Almgren Date: Tue Oct 13 14:29:15 2015 -0700 This version of Tutorials/PIC_C works with either the F90 or the HPGMG solver. Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp commit 23217ada81f0442f2e683844fe5945936e6fe948 Merge: 55158595c ca65bbfe4 Author: Ann Almgren Date: Tue Oct 13 13:04:43 2015 -0700 Merge branch 'new_particle' of https://github.com/BoxLib-Codes/BoxLib into new_particle commit ca65bbfe49487a375f1fde1c5fac562ef815e3d6 Author: Ann Almgren Date: Tue Oct 13 12:57:37 2015 -0700 Updated files for Tutorials/PIC_C. Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp commit 55158595c7db3bba15897a325a4fbaf436e77ebe Author: Ann Almgren Date: Tue Oct 13 11:37:22 2015 -0700 Starting to add the option for HPGMG to Tutorials/PIC_C. Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp commit 00d985aaf05c744317fb2e082e64b4822e95a43d Merge: 331baee1f 835e67628 Author: vince Date: Tue Oct 13 10:41:37 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 6581cef6833fd9ecdb355b5a4b1386b88cb6e7db Author: Ann Almgren Date: Tue Oct 13 10:33:15 2015 -0700 More changes to make the Particle stuff not require anything in C_AMRLib. * move BCRec* and BC_TYPES.H from C_AMRLib to C_BaseLib * add a "sum" function to MultiFab that sums up the values over all the valid region (analogous to the FArrayBox sum) * update the PIC_C Tutorial code so it actually computes the acceleration of each particle Src/C_AMRLib/Make.package Src/C_BaseLib/BCRec.H Src/C_BaseLib/BCRec.cpp Src/C_BaseLib/BC_TYPES.H Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/main.cpp commit 4cd9d4f0d91e2ede2b55d45235d9dbf8698cf391 Merge: fce0e5fda 9f4d2a5b7 Author: Weiqun Zhang Date: Sun Oct 11 22:16:40 2015 -0700 Merge branch 'new_particle' of github.com:BoxLib-Codes/BoxLib into new_particle Conflicts: Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp commit fce0e5fda81476d4b8374c11c1cff1ee140f8280 Merge: a84648782 006b5377d Author: Weiqun Zhang Date: Sun Oct 11 22:08:58 2015 -0700 Merge branch 'PIC_Tutorial' into new_particle commit 9f4d2a5b7dd89a1cb12dd93f0777d427b9c884a6 Author: Ann Almgren Date: Sun Oct 11 22:06:02 2015 -0700 Add AssignDensity Tutorials/PIC_C/main.cpp commit a84648782a5812618ff5c94592dc1394f8b93779 Merge: f39a10247 835e67628 Author: Weiqun Zhang Date: Sun Oct 11 22:05:14 2015 -0700 Merge branch 'development' into new_particle Conflicts: Src/C_BaseLib/Particles.H Src/C_BaseLib/Particles.cpp commit 5290f89c4eaae0e1b44faa916b30e46ed8e009a9 Author: Ann Almgren Date: Sun Oct 11 22:01:20 2015 -0700 Make this work without creating an AMR object. Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp commit 608f61cc7a40d418fbfc2993c582148d3cedafec Author: Ann Almgren Date: Sun Oct 11 22:00:48 2015 -0700 Fix for new gdb stuff. Src/C_BaseLib/Particles.H commit f39a102475b088067b9b5a91ba89021aca8371d6 Author: Weiqun Zhang Date: Sun Oct 11 20:59:55 2015 -0700 Particle: forgot a new file Src/C_BaseLib/ParGDB.H commit 0838241061893fab67eb8103de03e86057709117 Author: Weiqun Zhang Date: Sun Oct 11 20:55:37 2015 -0700 moved Amr independent particle files to C_BaseLib Src/C_AMRLib/Make.package Src/C_AMRLib/ParGDB.H Src/C_BaseLib/Make.package Src/C_BaseLib/Particles.H Src/C_BaseLib/Particles.cpp Src/C_BaseLib/Particles_1D.F Src/C_BaseLib/Particles_2D.F Src/C_BaseLib/Particles_3D.F Src/C_BaseLib/Particles_F.H commit 02452016ffa0ab25f894b632eecfc11e3f5a9409 Author: Weiqun Zhang Date: Sun Oct 11 20:49:38 2015 -0700 Particle: created AmrParticleContainer and some other minor tweak Src/C_AMRLib/AmrParticles.H Src/C_AMRLib/Make.package Src/C_AMRLib/ParGDB.H Src/C_AMRLib/Particles.H commit 0ab40db5f324e6c908e31844d9ec96ae518a723e Author: Weiqun Zhang Date: Sun Oct 11 20:02:09 2015 -0700 Particle: forgot to wrap particle stuff inside ifdef USE_PARTICLES Src/C_AMRLib/Amr.cpp commit 96e6d8fa4482e1c0c677008d83a5790698bdee05 Author: Weiqun Zhang Date: Sun Oct 11 19:05:59 2015 -0700 more on the Amr independent particle Src/C_AMRLib/ParGDB.H commit 21539354b75fba38093dca9e66d1d5055c63d401 Author: Weiqun Zhang Date: Sun Oct 11 18:34:07 2015 -0700 Particle: removed multiFab function, we can always build a tmp MF without allocating data. Src/C_AMRLib/AmrParGDB.H Src/C_AMRLib/ParGDB.H Src/C_AMRLib/Particles.H commit 351183c6fd9dcc89022985603af09c389ddba10f Author: Weiqun Zhang Date: Sun Oct 11 16:42:59 2015 -0700 forgor two new files Src/C_AMRLib/AmrParGDB.H Src/C_AMRLib/ParGDB.H commit c1f87e887b2314cf4ed253aa764febeaecdc9039 Author: Weiqun Zhang Date: Sun Oct 11 16:30:41 2015 -0700 make particles class independent of Amr class Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Make.package Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 835e67628f63709ca1d56470a56ec105ca81e8ba Author: Michael Zingale Date: Sun Oct 11 19:17:03 2015 -0400 take care of the case where the source is not under git-control Tools/C_scripts/makebuildinfo_C.py commit ad0226c79a54e3f5a8f1c3dc935f1b5c1f2041dd Author: Michael Zingale Date: Sun Oct 11 19:12:15 2015 -0400 put a try...except clause around the git stuff, just in case a user isn't using git-controlled source Tools/F_scripts/makebuildinfo.py commit 006b5377d6a38615451ae9e8078be49a0f05f9e4 Merge: ae22878fd d98e15cc4 Author: Ann Almgren Date: Sun Oct 11 15:44:46 2015 -0700 Merge branch 'development' into PIC_Tutorial commit d98e15cc4a273bb88dfa78952c356e6b7b60ac3f Merge: 87a94ac5b 2233dabba Author: Ann Almgren Date: Sun Oct 11 15:22:03 2015 -0700 Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development commit 87a94ac5be33bbf3611a3d83100f05db3f9abe58 Author: Ann Almgren Date: Sun Oct 11 15:21:47 2015 -0700 Fix a comment so that it is now correct. Src/C_AMRLib/AmrLevel.H commit 2233dabba7f4193b8775e9ab2e7d232204859203 Author: Brian Friesen Date: Sun Oct 11 09:53:30 2015 -0700 C_mk: added manual link to libmpichf90.a on Cori when linking code with F90 MPI calls using the C++ linker Tools/C_mk/Make.mpi commit fcec8cb676c85f0fc4f7ae18581ef1cf8867e325 Author: Brian Friesen Date: Sun Oct 11 09:07:56 2015 -0700 C_mk: added basic Makefile compiler flags for Intel compiler on Cori Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit c56a206be0faf809dffdcc9b95bba7a563f18d13 Author: Brian Friesen Date: Sun Oct 11 09:01:34 2015 -0700 ParallelDescriptor: added timer output showing how long sidecars wait for next data set Src/C_BaseLib/ParallelDescriptor.cpp commit 9b960bfe9ba7867d6dff06f80a14a8d264b433b7 Merge: 1ca2077c1 8ec2943b0 Author: Ann Almgren Date: Fri Oct 9 19:39:54 2015 -0700 Merge branch 'development' of github.com:BoxLib-Codes/BoxLib into development commit 1ca2077c16b02a5d143ce6555750bf09ddc8f66b Author: Ann Almgren Date: Fri Oct 9 19:39:33 2015 -0700 Pass geom instead of amr when possible. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 8ec2943b02e3b5aef0bfd60f5e60cba4fe42c331 Author: Weiqun Zhang Date: Fri Oct 9 17:17:06 2015 -0700 SFC: Fixed a bug affecting efficiency Src/C_BaseLib/DistributionMapping.cpp Src/F_BaseLib/knapsack.f90 commit 532bb3718aa9839c11eb925a843ef1b016b3ba39 Author: Weiqun Zhang Date: Fri Oct 9 17:13:01 2015 -0700 Nodal solver: Fixed a problem in my commit dba46939. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 4f1c4212c3390d54cc920a9a8bf55666c4ec36f5 Author: Weiqun Zhang Date: Fri Oct 9 16:18:16 2015 -0700 BACKTRACE: update Readme Docs/Readme.backtrace commit e54c7e4264f3daa1b9d1dec1296271b31e57590f Author: Weiqun Zhang Date: Fri Oct 9 15:48:02 2015 -0700 BACKTRACE: output to files instead stdout and stderr Src/C_BaseLib/BLBackTrace.cpp commit 1f77d00a6eea985634434c33a024a68467205d1c Author: Weiqun Zhang Date: Fri Oct 9 14:08:31 2015 -0700 some minor cleanups in F_MG Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit e9b3d27260653e82a2a00421e397d971b2f047be Author: Weiqun Zhang Date: Fri Oct 9 14:07:21 2015 -0700 BACKTRACE: capture user interrupt too Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp commit 4413df0f52fb90ac85731048e6f0f33309255231 Author: Weiqun Zhang Date: Fri Oct 9 14:06:00 2015 -0700 MGT_Solver: avoid omp critical if we can Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 0f3f148d1edb3f4f927542bc90eba7716b7ab09e Author: Weiqun Zhang Date: Fri Oct 9 14:02:41 2015 -0700 add verbose to MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 30bc5e20e0c16d197a21646894ff3505c86add4a Author: Weiqun Zhang Date: Fri Oct 9 13:44:10 2015 -0700 fixed a bug Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit ae22878fd230743212bc23f0ff1baf792289cf6f Author: Ann Almgren Date: Fri Oct 9 09:25:05 2015 -0700 Latest... Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp commit 244ced706c8f047a34107f3c0217fbf57ade48f0 Merge: 60a196bfe 788ce6db4 Author: Michael Zingale Date: Fri Oct 9 11:32:59 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 60a196bfef388175949ff5e8854ebd69aa16bc06 Author: Michael Zingale Date: Fri Oct 9 11:31:21 2015 -0400 this now works with python3 Tools/F_scripts/makebuildinfo.py commit 788ce6db4065c49ff28fe9470c81b372cf8d8a3e Author: Michael Zingale Date: Thu Oct 8 22:33:49 2015 -0400 more python3 fixes (__cmp__ is replaced by __lt__ for comparing) Tools/RegressionTesting/testnew.py commit 1eae17153aeca77687b03e590929a0a06055f3b7 Merge: b2c955e85 8c7a38b53 Author: Michael Zingale Date: Thu Oct 8 22:22:29 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit b2c955e85e268ab30f416967f53cd54c29d33023 Author: Michael Zingale Date: Thu Oct 8 22:22:01 2015 -0400 .keys() is an iterator in python3, so convert it to a list Tools/RegressionTesting/testnew.py commit 8c7a38b53fd1e68648d65c2d1a2e4cb32b5e7c02 Author: Michael Zingale Date: Thu Oct 8 22:07:54 2015 -0400 start of a port to python 3 -- this handles the prints now. We also have a new Log() object to make it easier to capture and format the output. Finally, fix a bug in the copy_benchmarks option when we are dealing with problems that define specific benchmark files instead of the last plotfile Tools/RegressionTesting/testnew.py commit c74e210f98194e01f4894028d13fcbc78f03bd87 Author: vince Date: Thu Oct 8 13:45:39 2015 -0700 fix for 1d amrvis. Src/Extern/amrdata/AmrData.cpp commit 1fb2a38708dcbcfdc464e1e37b3287385003d713 Merge: 5d4204e79 71e9c3963 Author: Michael Zingale Date: Thu Oct 8 12:25:05 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 5d4204e79fc112dc737b01da4fa712d9d26abef0 Author: Michael Zingale Date: Thu Oct 8 12:22:48 2015 -0400 start of restructing the log into a class so we can control its output Tools/RegressionTesting/testnew.py commit 71e9c396316cca8595dcd7f0359eb025f94fb8d4 Merge: e6e0f69b5 a1219e8d3 Author: vince Date: Wed Oct 7 15:57:45 2015 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit a1219e8d3da8d5f9c4214bce9a008c03fe74e749 Author: Michael Zingale Date: Wed Oct 7 09:34:01 2015 -0400 use 2 digits when the level > 10 in the header. This fix was contributed by Ryan Houim via e-mail. Src/F_BaseLib/fabio.f90 commit 4d51da07e68cdf694cd5844d944e7a8f268d396c Author: Ann Almgren Date: Tue Oct 6 14:59:33 2015 -0700 These are my first attempt at a PIC tutorial. Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp Tutorials/PIC_C/work.f90 commit 759ae876d5bb9beed92fbdd607aca6af92857966 Merge: c20eb5d89 4561e8c9d Author: Weiqun Zhang Date: Tue Oct 6 14:51:08 2015 -0700 Merge branch 'development' into pgas commit e6e0f69b5f91fa2a9de75fed1dcd6b105bb6f73e Author: vince Date: Mon Oct 5 13:33:16 2015 -0700 define constant for 1d. Src/Extern/amrdata/AmrvisConstants.H commit 4561e8c9d64336f4632f0cb0ea50e5dd7fe08eaa Author: Michael Zingale Date: Mon Oct 5 12:01:32 2015 -0400 we were appending to the changelog, not writing a new one. This caused it to get big, and not be very useful. Now run() takes an outfile_mode Tools/RegressionTesting/testnew.py commit c79143ca31564e206a2ec2e13595c6c1186d01a2 Merge: 988353b88 6df9d5fba Author: Weiqun Zhang Date: Mon Oct 5 08:58:58 2015 -0700 Merge branch 'poisson' into development commit 988353b888b6f9520404f4196c66351062fa81b7 Author: Weiqun Zhang Date: Sat Oct 3 11:45:33 2015 -0700 make BoxArray::boxList possible for return value optimization (RVO) Src/C_BaseLib/BoxArray.cpp commit e683a6638b2fcea1be57e96fdaf5263630ed2e84 Author: Weiqun Zhang Date: Sat Oct 3 11:26:48 2015 -0700 removed a number of const's so that the compiler can do 'copy elision' Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H commit 32316a4a2a5c70ea9200156c2e1e6853df19cca7 Author: vince Date: Fri Oct 2 16:50:37 2015 -0700 quiet compiler warnings. Src/Extern/amrdata/DataServices.cpp commit 3e01b5ff1e4a817cd8d1a96005c56bab2e05752d Author: vince Date: Fri Oct 2 16:48:14 2015 -0700 only print for special debug. Src/C_BaseLib/FabArray.H commit d0972d8158df2d52d38f68ef7b724dce4d76e522 Author: vince Date: Fri Oct 2 16:47:39 2015 -0700 quiet compiler warnings. Src/Extern/amrdata/DataServices.cpp commit 6df9d5fba63bd3bf18e200668178e53ab2e0e797 Author: Weiqun Zhang Date: Fri Oct 2 15:34:47 2015 -0700 bottom solver: use the simple stencil for interior boxes in the case of constant coefficients Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/stencil_util.f90 commit 5f914db12c031a990f02611d4dc09de85b682cfc Author: Weiqun Zhang Date: Thu Oct 1 20:30:34 2015 -0700 F_MG: fixed a new bug in my last commit optimizing box intersection Src/LinearSolvers/F_MG/cc_stencil.f90 commit a5360f755396e884f86dd971450b67b381d55e15 Author: Weiqun Zhang Date: Thu Oct 1 18:19:47 2015 -0700 optimization in stencil_set_bc Src/LinearSolvers/F_MG/cc_stencil.f90 commit c5389fa13a0fcee5870fffbe411e9d9795bcc2b5 Author: Weiqun Zhang Date: Thu Oct 1 18:08:15 2015 -0700 fixed bug in stencil_norm and stencil_set_bc in periodic case Src/LinearSolvers/F_MG/cc_stencil.f90 commit 9ca0c94addf2aac0aa0165c9b13197d7883b68d6 Author: vince Date: Wed Sep 30 15:12:38 2015 -0700 cxx11 setting. Tutorials/MultiFabTests_C/GNUmakefile commit 07a86bfa765bd674a8bd6854b5cd50b3490e902a Author: vince Date: Wed Sep 30 15:10:41 2015 -0700 added profiling to tFB. Tests/C_BaseLib/tFB.cpp commit 8ab60177f20e49c13ba51c50718696be69a9a9b2 Author: vince Date: Wed Sep 30 15:09:55 2015 -0700 cxx11 setting. Tests/C_BaseLib/GNUmakefile commit 37ef49d7cdd4f4ca42cef88355f57b166cced6c8 Author: vince Date: Wed Sep 30 15:08:17 2015 -0700 more tests for the profiler. Tests/C_BaseLib/tProfiler.cpp commit 03d6fe316bb3266951b17bf75dce30e7e8e16207 Author: vince Date: Wed Sep 30 14:57:01 2015 -0700 set n files for profiler, add comm names if not already called. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp commit 85d2730fcf1c54e264aa77e0b72396d95324a303 Author: Michael Zingale Date: Wed Sep 30 08:41:51 2015 -0400 fix NDEBUG -- it is the opposite of what people expect it should be Tools/RegressionTesting/testnew.py commit 974fc2fc1be3875ce8ba9aac4462eb7013a26833 Author: Michael Zingale Date: Sun Sep 27 09:58:53 2015 -0400 some more cleaning Tools/RegressionTesting/testnew.py commit 04a69c16585289cd7b3f3619e776550e48ea2cb3 Author: Weiqun Zhang Date: Fri Sep 25 13:27:49 2015 -0700 changed makefile for babbage Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_intel.mak commit 90665fb2928b439a0f594e19b5483d4d1e7a43f5 Author: Weiqun Zhang Date: Fri Sep 25 12:39:52 2015 -0700 use relative path for BOXLIB_HOME since these tutorials are inside BOXLIB_HOME already MiniApps/AMR_Adv_Diff_F90/GNUmakefile Tutorials/AMR_Adv_Diff_F/GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX2_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GNUmakefile Tutorials/MultiGrid_F/GNUmakefile Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/Tiling_Heat_F/GNUmakefile Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_F/GNUmakefile commit d945af5fa443614dd4ac3440ea2aaa73901861c4 Author: Michael Zingale Date: Fri Sep 25 15:34:27 2015 -0400 a little more reorg Tools/RegressionTesting/testnew.py commit 92e0b986cbed7e5d7b96d695f1e8c20e63fb1040 Author: Weiqun Zhang Date: Fri Sep 25 12:31:31 2015 -0700 F_MG: fixed name conflicts Src/LinearSolvers/F_MG/cc_stencil.f90 commit c20eb5d89612e4b3452558c144e0c5024ae396b1 Author: Weiqun Zhang Date: Fri Sep 25 11:10:56 2015 -0700 added a new fill boundary test Tests/FillBoundaryComparison/GNUmakefile Tests/FillBoundaryComparison/Make.package Tests/FillBoundaryComparison/ba.max Tests/FillBoundaryComparison/main.cpp commit 96e83f7651e1671512cfcbfa43601b7325fc846c Merge: 9589733b4 3943e34c8 Author: Weiqun Zhang Date: Fri Sep 25 10:55:04 2015 -0700 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/FabArray.cpp commit 3943e34c8d10a3e530f5e0fd71e0a8d7c0b70c39 Author: Michael Zingale Date: Fri Sep 25 12:41:43 2015 -0400 remove systemCall entirely in favor of run() Tools/RegressionTesting/testnew.py commit 6ea366ce151af8887b10d339dd75713e52aa8268 Author: Michael Zingale Date: Fri Sep 25 10:47:45 2015 -0400 default the normal direction to 1 Tools/Postprocessing/F_Src/fsnapshot3d.f90 commit 9f4d4803103cfc9f4051db5f7a8e3a723acd5d9a Author: Weiqun Zhang Date: Thu Sep 24 16:56:28 2015 -0700 Linear solver: for systems with constant coefficients, use simple stencils for interior boxes Src/F_BaseLib/fab.f90 Src/LinearSolvers/F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/stencil_util.f90 commit a452cf1902a214dd9d804097e10ff6e78c18c253 Author: Michael Zingale Date: Thu Sep 24 21:27:31 2015 -0400 fix some more missing close(), switch a lot of open's to 'with open as' Tools/RegressionTesting/testnew.py commit 39cf52a1fd4635dab1f4349c79663d97d70f194d Author: Marc Day Date: Thu Sep 24 17:58:53 2015 -0700 More typos in CMakeLists.txt Src/C_BaseLib/CMakeLists.txt commit 4881edaa811478e011e0b867280725f4f7b224da Merge: be13a7cfc 1ac3c074e Author: Marc Day Date: Thu Sep 24 17:01:31 2015 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit be13a7cfc78f9dc13d3a11d951e8003b707dbf30 Author: Marc Day Date: Thu Sep 24 17:01:25 2015 -0700 Fix typo in CMakeLists.txt and uptick release number Src/C_BaseLib/CMakeLists.txt Tools/CMake/BoxLib_Version.cmake commit 1ac3c074e1359ece42be01d69e297cd6e5f53fc3 Author: Michael Zingale Date: Thu Sep 24 19:49:31 2015 -0400 remove quotes from the branch name when creating the suite status file Tools/RegressionTesting/testnew.py commit 88f36e83f4e3d281a81f16553ec66d0353e7c328 Merge: 4bc8778f9 6b35f83cf Author: Michael Zingale Date: Thu Sep 24 16:57:29 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 4bc8778f96420ee40bad456b55206f0faa1a30e2 Author: Michael Zingale Date: Thu Sep 24 16:57:06 2015 -0400 fix the deletion of TEST_RUN if it doesn't already exist Tools/RegressionTesting/testnew.py commit 6b35f83cf6640fd6cb7849c36c329bf6bb7c91ed Author: Michael Zingale Date: Thu Sep 24 16:51:01 2015 -0400 clean up the compiling of the various tools -- no longer copy them to the run directory either Tools/RegressionTesting/testnew.py commit 37f78e1d51943f6539ef1a5352bc2ad36a13e4c3 Author: Michael Zingale Date: Thu Sep 24 14:53:08 2015 -0400 fix an unclosed file. Add the branch name to the test run status file Tools/RegressionTesting/testnew.py commit 9ded947220941fe7ce9c46f36aebc46c09b8c6b8 Author: Michael Zingale Date: Wed Sep 23 21:25:31 2015 -0400 fix the web output directory Tools/RegressionTesting/testnew.py commit 5c2da5479fd919911f79463356d393a7a75f171a Author: Michael Zingale Date: Wed Sep 23 20:38:14 2015 -0400 first cut at an easily parsable status for a run Tools/RegressionTesting/testnew.py commit 89ab39d25457c4ce3dcd46644caf3267c5343cec Author: Michael Zingale Date: Wed Sep 23 15:39:29 2015 -0400 restructure all of the git logic. Now there is a Repo class that has the methods for updates, change log, etc., and knows where the repo is, what the current hash is, etc. This allows us to simply loop over all the repos in the suite.repos dictionary and greatly simplify code. Tools/RegressionTesting/testnew.py commit a02aa83a9c14fd263ba9b2166d5d90926b491d31 Author: Michael Zingale Date: Wed Sep 23 10:42:28 2015 -0400 bold heading in list of git info Tools/RegressionTesting/testnew.py commit 7e73d966a1572f67688ad0cb5b2cbc557b57df81 Merge: 55f01c0d6 d29cf8e3d Author: Michael Zingale Date: Tue Sep 22 20:24:51 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 55f01c0d69576ce0eff052962104beb6208b3554 Author: Michael Zingale Date: Tue Sep 22 20:24:15 2015 -0400 add libstdc++ to get around an import error -- not sure why this is pulling in the C++ boxlib though... Tools/Py_util/GNUmakefile commit d29cf8e3d789376c959b792d095a2c3c86855d78 Author: Michael Zingale Date: Tue Sep 22 19:14:02 2015 -0400 updated version of our test suite inputs Tools/RegressionTesting/Maestro-tests.ini commit 3728f5947777bd6b6f0742ae22a18ef97165abcb Author: Michael Zingale Date: Tue Sep 22 19:10:45 2015 -0400 default to the development branch Tools/RegressionTesting/testnew.py commit 331baee1f65c9ebbadc40bbeefd1b015b7b3e050 Merge: 9bb17854c 85d30d4fd Author: vince Date: Tue Sep 22 15:46:15 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 85d30d4fd7fb773b96eab6b9ecf56f4efe60bb19 Merge: 485c09fab 7aa2dcc4e Author: Max Katz Date: Tue Sep 22 11:41:52 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 485c09fab63263ddd30e252cf1f8b4cd91f072dd Author: Max Katz Date: Tue Sep 22 11:37:25 2015 -0400 Add a dimension-agnostic version of the error function. Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit 7aa2dcc4e8c765aa1a5dba9c20160a8579a58dcf Author: Weiqun Zhang Date: Mon Sep 21 16:32:41 2015 -0700 OMP ml_interface Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit d6376c86bcbdf1198bed17c3e1bbcc66b680f479 Author: Weiqun Zhang Date: Mon Sep 21 12:55:25 2015 -0700 Revert "save a multifab build and copy" because the nodal solver relies on that the ghost cells of amr_coeffs are filled with zero. This reverts commit 0a1b902aafafb0121ca00fd53a6b0332ca9ae153. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 685dcfb73a0e8aaddbb9b6d4bf37e1a016091a6d Merge: 0a1b902aa 863795b86 Author: Weiqun Zhang Date: Mon Sep 21 12:08:41 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 863795b86b76373652553adc9ed0d9f4114c1246 Author: Michael Zingale Date: Mon Sep 21 14:27:41 2015 -0400 simplify convert_type Tools/RegressionTesting/testnew.py commit 0a1b902aafafb0121ca00fd53a6b0332ca9ae153 Author: Weiqun Zhang Date: Mon Sep 21 11:27:29 2015 -0700 save a multifab build and copy Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit b0240dcc55cba9717e8e2e739525f6ea7a917eee Author: Weiqun Zhang Date: Mon Sep 21 11:23:37 2015 -0700 MGT_Solver: rewrote the cell-centered coeffs stuff in a hopefully less confusing way that is also consistent with the approach in nodal solver Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 891c3e06c996b0a860afa3b637ed8bfd88c6dc3f Author: Michael Zingale Date: Mon Sep 21 09:41:01 2015 -0400 fix the OMP stuff in the run() Tools/RegressionTesting/testnew.py commit 6aefe5d0afa5cbf4503677540e6d215ac57bb340 Author: Weiqun Zhang Date: Fri Sep 18 15:39:19 2015 -0700 MGT_Solver: removed unused applybc function and two unnecessary FillBoundary Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 57c87bbb145fbb9ff2da5c6ff18b371536344cd4 Author: Weiqun Zhang Date: Fri Sep 18 13:52:54 2015 -0700 more coarse-grained OMP in MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 4f5b11840cb2f7a5efaed938c40ab4671f09c8f7 Author: Weiqun Zhang Date: Fri Sep 18 13:49:13 2015 -0700 add more nodal functions to MFIter Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/F_BaseLib/multifab_f.f90 commit fd627cd44894798e946cc1e2290703e98aec4079 Author: Michael Zingale Date: Sat Sep 19 23:02:07 2015 -0400 store the diff command Tools/RegressionTesting/testnew.py commit fa74a390fb25ea4f7ef16b55965dba23162e7f8b Author: Michael Zingale Date: Sat Sep 19 22:32:43 2015 -0400 switch the diff over to run() Tools/RegressionTesting/testnew.py commit 430adb224b6c0c317f758f02fa1c64f988402e8e Author: Michael Zingale Date: Sat Sep 19 22:14:54 2015 -0400 switch to using subprocess.Popen() to run the tests instead of os.system(). THis is safer, and allows us to capture the stdout/err and return code. Note: for OMP, we need to pass a dictoionary of environment variables. Tools/RegressionTesting/testnew.py commit 4e9a6578cfafebf0852584212214daf844aa7946 Author: Weiqun Zhang Date: Thu Sep 17 17:03:03 2015 -0700 tiling in nodal MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 9bb17854c7e0255ca10b387fc039d4530ba69588 Author: vince Date: Thu Sep 17 15:11:24 2015 -0700 added profiling. Tests/C_BaseLib/tFB.cpp commit 5714a6beec4b5eccf2503a1fb7d08b85e7a8b9dd Author: Weiqun Zhang Date: Thu Sep 17 15:06:39 2015 -0700 added assertion Src/C_BaseLib/PArray.H commit ae87e3777b6085784ecbf6d7cb0b4a066f42adfa Author: Weiqun Zhang Date: Thu Sep 17 13:49:44 2015 -0700 fixed assertion Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tutorials/MultiGrid_C/main.cpp commit a422e4d8a28c372fe985b2b640f1cf257cf639e7 Merge: 0400519cf a16c81433 Author: vince Date: Thu Sep 17 11:35:47 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 0400519cf27408a64150d67da6cbdfe6808eb605 Author: vince Date: Thu Sep 17 11:31:14 2015 -0700 unique set. Tutorials/MultiFabTests_C/GridMoveTest.cpp commit a16c81433509066dd5b282b7e94ca909c4143090 Author: Weiqun Zhang Date: Wed Sep 16 17:31:38 2015 -0700 fixed a typo Src/C_BaseLib/IntVect.cpp commit 6ad510156ef4f259505a6f0fcdc6faf2cf2891cd Author: Weiqun Zhang Date: Wed Sep 16 16:56:42 2015 -0700 clean up MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tutorials/AMR_Advection_C/Source/Diffusion.cpp Tutorials/MultiGrid_C/main.cpp commit 520c6434749db26a65314200a121b896fd6c0c41 Author: Weiqun Zhang Date: Wed Sep 16 16:14:36 2015 -0700 Added a member function that takes a const * and removes the const. use it with care. Src/C_BaseLib/PArray.H commit e6ec0dc17a5d195bc92ad388fd4c23a62e7613c3 Author: Weiqun Zhang Date: Wed Sep 16 14:06:27 2015 -0700 added IntVect::TheDimensionVector for convenience Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp commit 8d729f7e5b81d1e2a53a87a84977778df46c2c20 Author: Weiqun Zhang Date: Wed Sep 16 13:40:08 2015 -0700 optional nodal argument for MultiFab and FabArray constructors Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit d1c10399a44acf8ec34d71283e4b24cb7ccb4921 Author: Weiqun Zhang Date: Tue Sep 15 18:23:44 2015 -0700 tiling in cc MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 0195828a1d966b318ffe2c0b8391c837120981c0 Author: Weiqun Zhang Date: Mon Sep 14 12:52:45 2015 -0700 In tiled tab_boxes, only the current tile should be touched. Src/F_BaseLib/tag_boxes.f90 commit 767dd2f81febd02cac07a7e6e60972aa559f5ae3 Merge: cd069a744 39fbaa885 Author: Max Katz Date: Mon Sep 14 15:38:45 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit cd069a744a0e626ec4af26a2a7cff6ecbd341e23 Author: Max Katz Date: Mon Sep 14 15:38:41 2015 -0400 Add a function to StateData that accepts a pointer to a new MultiFab and replaces the old_data or new_data with it, then deletes the old copy of old_data or new_data. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 39fbaa8856d5e6006ffd098f8e1b92038457d03c Author: Weiqun Zhang Date: Mon Sep 14 11:10:31 2015 -0700 fixed a new bug in tag_boxes Src/F_BaseLib/tag_boxes.f90 commit c4c37e2e545e5f73b64cd8c88d35b36f6f16aa27 Author: Michael Zingale Date: Mon Sep 14 12:10:46 2015 -0400 need to define last_run earlier Tools/RegressionTesting/testnew.py commit e7718fc28e2fc0b4e76173e997e6f91bd938edab Author: Weiqun Zhang Date: Sat Sep 12 12:14:01 2015 -0700 modified Cray C++ compiler option to make it work with a C99 feature we use. Tools/C_mk/Make.Linux commit 3b22c203b891570124bcbb4bf2a8a510b0c02611 Author: Weiqun Zhang Date: Sat Sep 12 11:25:03 2015 -0700 tweak flags for .F90 files Tools/C_mk/Make.rules commit cc6593854fd918ae6b1515f92cbbb2c0ada09810 Author: Max Katz Date: Sat Sep 12 02:45:14 2015 -0400 Don't actually need a separate FILCC_ND.F file to do dimension agnostic boundary filling Src/C_AMRLib/FILCC_ND.F Src/C_AMRLib/Make.package Src/C_AMRLib/StateDescriptor.cpp commit 98d1ed502703c87b4f2e4a925333f54fa822c92b Merge: 86b047fe5 eb53dada2 Author: Max Katz Date: Fri Sep 11 23:53:13 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 86b047fe555cd2892d80addb42f89e3fc75492c7 Author: Max Katz Date: Fri Sep 11 23:53:09 2015 -0400 Dimension agnostic boundary fill routine Src/C_AMRLib/FILCC_ND.F Src/C_AMRLib/Make.package Src/C_AMRLib/StateDescriptor.cpp commit eb53dada2a4f8a8d7c4d4617c072e9135080b46a Author: Brian Friesen Date: Fri Sep 11 13:43:04 2015 -0700 MultiFab: use local communicator with HPGMG instead of MPI_COMM_WORLD This lets us use the HPGMG solver in runs where we have multiple MPI groups/communicators. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 97fc24ba900968b6ddbbb2d7580810f7595f5893 Author: Brian Friesen Date: Thu Sep 10 13:05:52 2015 -0700 MultiFab: remove commented-out debugging print statement during HPGMG run Src/C_BaseLib/MultiFab.cpp commit b1263b6f9ce833ab0c860686c5d3be0936b57a19 Author: Brian Friesen Date: Thu Sep 10 13:05:17 2015 -0700 MultiFab: minor clean up of status output during HPGMG runs Src/C_BaseLib/MultiFab.cpp commit 430a2c2f187ba27cbb7c35c3b828741e00a32765 Author: Brian Friesen Date: Tue Sep 8 15:40:47 2015 -0700 C_mk: added compile-time options for smoothing behavior of HPGMG Tools/C_mk/Make.defs commit 204dc717e1f752f3e2d9cb2de4a37c849d4ae56f Author: Weiqun Zhang Date: Fri Sep 11 10:33:10 2015 -0700 tiling in tag_boxes Src/F_BaseLib/tag_boxes.f90 commit 78c1b2fbc3241f35836597a51a47917271fb4f5f Author: Weiqun Zhang Date: Fri Sep 11 10:24:04 2015 -0700 added omp paralle do Src/F_BaseLib/multifab_physbc_edgevel.f90 commit f92d73be340fb2f2732126b6c0517c3c520a692d Author: Michael Zingale Date: Fri Sep 11 10:06:45 2015 -0400 fix a bug in calling list for reportSingleTest Tools/RegressionTesting/testnew.py commit 46e0e1f7f74a6a4eae9b7dc518343ecc000192ba Author: Weiqun Zhang Date: Thu Sep 10 21:16:30 2015 -0700 trap floating-point exceptions in BACKTRACE Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp commit 7f4015c86b663e53c219674694ceafd242ca9f12 Author: Michael Zingale Date: Thu Sep 10 20:02:32 2015 -0400 define FCOMP_VERSION for intel so we can get the compiler version in the job_info files Tools/F_mk/comps/Linux_intel.mak commit 11953d442a9de0eb01189b7b9291a1d9511885a1 Author: Michael Zingale Date: Thu Sep 10 16:21:32 2015 -0400 fix a few bugs Tools/RegressionTesting/testnew.py commit 94246bc6b30c72ba7f08cc523fbe391b33742111 Author: Michael Zingale Date: Thu Sep 10 15:58:34 2015 -0400 a little more cleaning Tools/RegressionTesting/testnew.py commit 9cc0c1af0c38ca54b4b17db69773f59ec2b2a2cb Author: Michael Zingale Date: Thu Sep 10 12:34:02 2015 -0400 centralize the logic of how we select the tests to run into a method of the suite object. Tools/RegressionTesting/testnew.py commit c0633e5f7bb5ce77a55d2311721149097a081c4e Author: Michael Zingale Date: Thu Sep 10 11:59:34 2015 -0400 let the HTMLTable take a list of div elements Tools/RegressionTesting/testnew.py commit a0fa9a873024c5f4d6a3a27445e85573170f016b Author: Michael Zingale Date: Thu Sep 10 11:03:31 2015 -0400 fix missing ] Tools/RegressionTesting/testnew.py commit 93b7456c65b78445c90045a27262e2c80063d817 Author: Michael Zingale Date: Thu Sep 10 10:20:43 2015 -0400 fix the handling of NaNs present in the compare table Tools/RegressionTesting/testnew.py commit 148701c600d8b6378455eeaa9b9b8508f58241d4 Merge: 9360b4be8 acd1b8a1d Author: Weiqun Zhang Date: Wed Sep 9 21:03:30 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 9360b4be8229a61678456c1b3526e6d34717a637 Author: Weiqun Zhang Date: Wed Sep 9 16:55:09 2015 -0700 tiling in nodal restriction Src/F_BaseLib/ml_nd_restriction.f90 Src/F_BaseLib/nodal_restriction.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90 commit acd1b8a1d8d3bdb24fbd109b3f5cba2ba04ea8d0 Author: Michael Zingale Date: Wed Sep 9 20:39:34 2015 -0400 be careful -- if a test did not produce any output and we used --copy_benchmarks, then there it can erase the entire benchmark directory (d'oh). This is fixed now by checking that the last plotfile found is not "" Tools/RegressionTesting/testnew.py commit ad85a4e4da615e75ec4d9bef0d64de58ae4073f3 Author: Weiqun Zhang Date: Wed Sep 9 10:59:16 2015 -0700 reduced number of parallel reduce Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab_f.f90 commit bb7dc4f2cb7c7c65fc49877c14c07789c1d0b394 Author: Michael Zingale Date: Wed Sep 9 10:47:56 2015 -0400 add a copy_benchmarks functionality -- this does what make_benchmarks + redo_failed does, without rerunning any tests -- it simply copies all the benchmarks from the last runs that failed. Tools/RegressionTesting/testnew.py commit 9589733b4d55237aa9343e8f0d91af2977f97ef3 Author: Weiqun Zhang Date: Tue Sep 8 16:34:07 2015 -0700 Split MPI calls in FillBoundary and FillPeriodicBoundary into multiple pieces. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit e8a659fef488788087bb19d3766e2a6fb6c53550 Author: Michael Zingale Date: Tue Sep 8 13:12:03 2015 -0400 some css tweaks Tools/RegressionTesting/testnew.py commit d699f0e647384291cad5491ae9ea46586fd4b518 Merge: 3df1493aa d0a252915 Author: Weiqun Zhang Date: Tue Sep 8 09:58:47 2015 -0700 Merge branch 'master' into pgas Conflicts: Tools/C_mk/Make.defs commit d0a25291552cad8554271de1e0c4c2f8ddccb493 Author: Michael Zingale Date: Tue Sep 8 12:54:58 2015 -0400 use a new HTMLList() object to make the single test output more readable Tools/RegressionTesting/testnew.py commit 64ca8c3dd90cb0c55686dd24ea1df01492bc7361 Author: Michael Zingale Date: Tue Sep 8 09:42:32 2015 -0400 fix ordering of hash and branch in output Tools/RegressionTesting/testnew.py commit 5783b8e293997d60cf384f6789994406272e86a5 Author: Weiqun Zhang Date: Fri Sep 4 15:08:20 2015 -0700 Added next_tile function that also returns current fab index. Using next_tile instead of more_tile is recommended. MiniApps/SMC/advance.f90 MiniApps/SMC/init_data.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/F_BaseLib/multifab_f.f90 Tutorials/Tiling_Heat_F/advance.f90 commit ac351708d870211189cfaaac08d2cc1e4e7b9155 Author: Weiqun Zhang Date: Fri Sep 4 14:46:51 2015 -0700 more tiling Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/ml_cc_restriction.f90 commit 9a546c6f2b10cc6de920373e6c44185bf6cf5792 Author: Michael Zingale Date: Sun Sep 6 20:49:34 2015 -0400 print the branch and hash for the code on the summary page Tools/RegressionTesting/testnew.py commit 8cbbc5e55650a2216597062392b5af30888ebac9 Author: Weiqun Zhang Date: Sat Sep 5 14:23:07 2015 -0700 always include sstream Src/C_BaseLib/BLBackTrace.H commit 00a829d55a1cedeec1b750f78c5ef8e933d812f5 Author: Ann Almgren Date: Fri Sep 4 17:23:22 2015 -0700 Don't include bl_constants_module since that lives on F90 side. Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 commit 2a6b23af902f4c05f5c34bec0e7b9fc423d1a02d Author: Ann Almgren Date: Fri Sep 4 17:02:26 2015 -0700 Add the functionality to average down face-based MultiFabs as long as the crse BoxArray is a coarsened version of the fine BoxArray. Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 5205f255d9a32dcb06db10f55e00c60aad20591b Author: Weiqun Zhang Date: Fri Sep 4 13:45:23 2015 -0700 command line option for sending no email when regression tests fail Tools/RegressionTesting/testnew.py commit b91a875aebb398af34355d00c3a0cd84fbc5a14a Author: Weiqun Zhang Date: Fri Sep 4 13:19:19 2015 -0700 a bit of hack to get consistent answer with OMP Src/F_BaseLib/multifab_f.f90 commit debdf669d12937bf1b1dbbb70aed110c7d1e53e9 Author: Weiqun Zhang Date: Fri Sep 4 11:57:56 2015 -0700 minor changes that can cause roundoff errors Src/F_BaseLib/multifab_f.f90 commit 904d803b483ab48834b60c39977c42ad81065a6e Author: yzheng Date: Fri Sep 4 11:08:23 2015 -0700 Make async slightly more efficient without the need of reply Src/C_BaseLib/BLPgas.cpp commit 7d2b445bb1168391c96f1846f2d072d689bcbceb Merge: ce4f203b0 3df1493aa Author: yzheng Date: Fri Sep 4 11:05:09 2015 -0700 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 94f012e97bba08a6db6aa5a6782fe3c15392b071 Author: Michael Zingale Date: Fri Sep 4 11:03:41 2015 -0400 fix a link + pretty up some CSS Tools/RegressionTesting/testnew.py commit 580d3e436cab2feab6ab8750d83140550624b4e2 Merge: 6f95411c9 7f42a9ab8 Author: Michael Zingale Date: Fri Sep 4 10:01:36 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit 6f95411c9b7aae340c33a3b640baff402030ab64 Author: Michael Zingale Date: Fri Sep 4 10:01:16 2015 -0400 switch the test run overview talbe to HTMLTable Tools/RegressionTesting/testnew.py commit 7f42a9ab8319cd8fb5e64d6df987618f9a881ba3 Author: Michael Zingale Date: Fri Sep 4 09:28:36 2015 -0400 wrong indentation in the MPI call Tools/RegressionTesting/testnew.py commit da0f3db8cae6fce289f0ffccb9a69b9a2059af28 Author: Michael Zingale Date: Fri Sep 4 08:27:55 2015 -0400 catch when boxes don't match in fcompare Tools/RegressionTesting/testnew.py commit 62f9a373360a9bdfb829488e8ceff652abbc1a1c Author: Weiqun Zhang Date: Thu Sep 3 20:53:44 2015 -0700 tiling Src/C_BaseLib/MultiFabUtil.cpp commit 51e0397b80e4d6008d860faad5b04ed9743c2957 Author: Max Katz Date: Thu Sep 3 23:38:33 2015 -0400 Fix minor bug in assertion Src/C_BaseLib/MultiFabUtil.cpp commit c2396538bce911835532675d67b865eb964f53e1 Author: Michael Zingale Date: Thu Sep 3 21:17:33 2015 -0400 a bit more restructuring -- moving things into the suite class Tools/RegressionTesting/testnew.py commit 78f64921acfce03f9476f29141d9341460ecae64 Author: Weiqun Zhang Date: Thu Sep 3 16:11:53 2015 -0700 save local index in communication and local copy descriptors to avoid repeated calls to local_index Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_interface_stencil.f90 commit 2b2d1c34095d126f7d40e5b9092db4106c1317c0 Merge: 2381d1f32 fab266b5c Author: Weiqun Zhang Date: Thu Sep 3 14:47:27 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit fab266b5c6d851b26552f3aaade1693c0061e5fc Author: Brian Friesen Date: Thu Sep 3 13:15:59 2015 -0700 C_mk: updated Makefile flags for HPGMG to allow both pure V-cycles and pure F-cycles Tools/C_mk/Make.defs Tutorials/MultiGrid_C/GNUmakefile commit 2381d1f32a50c7ebecfeb2f51128f729080ae391 Author: Weiqun Zhang Date: Thu Sep 3 13:08:17 2015 -0700 Added a few new utility functions to BoxLib namespace. Src/C_AMRLib/AmrLevel.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 51b28936fe593c710004e7c7a10dd7221cb05dd4 Author: Michael Zingale Date: Thu Sep 3 09:57:49 2015 -0400 start of what will become some basic unit tests -- nothing to see here now. Src/F_BaseLib/unittests/GNUmakefile Src/F_BaseLib/unittests/gr0_3d.1level Src/F_BaseLib/unittests/tests.f90 commit 25d97ca2bf344f54394abfbba2b58e510dca9402 Merge: 7cabf2fa2 b63875baf Author: Michael Zingale Date: Thu Sep 3 09:57:35 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit 3df1493aa128c9cfd7527beaab91f8ed77017324 Author: Weiqun Zhang Date: Wed Sep 2 20:40:23 2015 -0400 added bl_profiler MiniApps/PGAS_SMC/main.cpp commit b63875bafbab0bd618a0a89b36fe73f053a66833 Author: Weiqun Zhang Date: Wed Sep 2 10:44:38 2015 -0700 minor bug: used optional argument without checking Src/F_BaseLib/make_new_grids.f90 commit cc3f5dce464410f00e3af47ad3a2ebc56c234892 Merge: 62159ed0c ff0ab2af9 Author: Brian Friesen Date: Tue Sep 1 16:13:26 2015 -0700 Merge branch 'port_hpgmg' This series of commits adds the ability to call the HPGMG multigrid solver written by Sam Williams. It is designed to be more or less a drop-in replacement for the in-house multigrid solver. There are a few caveats to using it, however: 1.) It is single-level only. No AMR. 2.) It is not nodal. 3.) It requires a cubic domain with cubic boxes. 4.) It does not support Neumann boundary conditions. Only periodic or Dirichlet. In addition, the version of HPGMG which Sam maintains will not work with this. You must use my "port" of it, which contains the necessary hooks. commit ff0ab2af993f633409b38395db30dea5ab99565b Author: Brian Friesen Date: Tue Sep 1 14:21:55 2015 -0700 MultiGrid_C: add HPGMG as an example multigrid solver in the tutorial Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/README Tutorials/MultiGrid_C/main.cpp commit bf78f385ccd893b0037b61410719aadbbc97d283 Author: Brian Friesen Date: Tue Sep 1 12:29:38 2015 -0700 MultiFab: add static functions and hooks for using the HPGMG linear solver Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Tools/C_mk/Make.defs commit 67e538a29045a64c9ac95460d0fa09c232c7089f Author: Brian Friesen Date: Tue Sep 1 12:17:21 2015 -0700 Box: add static function isSquare() Checks that a Box is square (or cubic in 3-D). This is a convenient function to have when using the HPGMG solver, which requires cubic Boxes. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 62159ed0c9f62b0acca61eb28570c93ee0d529da Author: Weiqun Zhang Date: Tue Sep 1 17:46:04 2015 -0700 fixed intel compiler macro in last commit Src/C_BaseLib/BLBackTrace.H commit b3e63dbc2eb263d32c4980131b4e17d341a8f2ca Author: Weiqun Zhang Date: Tue Sep 1 17:44:51 2015 -0700 Cannot get threadprivate static class memeber work in Cray and Intel, so let's turn it off. Note that this would not cause race conditions unless we use BL_BACKTRACE_PUSH and POP for debugging. In that case, we have to use gcc. Src/C_BaseLib/BLBackTrace.H commit be48bd18ef98e6f5aacc3607bcf3c03434bc1b3d Author: Weiqun Zhang Date: Tue Sep 1 17:38:58 2015 -0700 option to turn on assertion if compiled with USE_ASSERTION=TRUE enven when DEBUG is FALSE. Src/C_BaseLib/BLassert.H Tools/C_mk/Make.defs commit 74210f40657801d2afb961f1da477624a67682ea Author: Weiqun Zhang Date: Tue Sep 1 17:24:38 2015 -0700 added -g to Cray Tools/C_mk/Make.Linux commit 7cabf2fa24208783db5360fcd20470a2a4f8bf47 Merge: 932ca949c 766af0030 Author: Michael Zingale Date: Tue Sep 1 19:35:39 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit 932ca949cdd90833839c5577c819dc74b6466fd4 Author: Michael Zingale Date: Tue Sep 1 19:35:15 2015 -0400 change multifab_equal to a function and check the layouts Src/F_BaseLib/multifab_f.f90 commit f9bef06ec97c27c76412cf21f0057036b24ad506 Author: Weiqun Zhang Date: Tue Sep 1 14:19:46 2015 -0700 make Intel compiler happy MiniApps/PGAS_SMC/SMC_advance.cpp commit 766af00305c49fb746293f9df25625a4efecaad1 Author: Weiqun Zhang Date: Tue Sep 1 11:21:00 2015 -0700 Finished tiling in multifab_f. Roundoff errors are expected because this commit changes the order of sum. Src/F_BaseLib/multifab_f.f90 commit 8edc219f6ee9dc4b3f6fea1f895684c55a8489d7 Author: Weiqun Zhang Date: Tue Sep 1 10:25:04 2015 -0700 added an assertion in mfiter Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/multifab_f.f90 commit 88b1c8d723628e2433d420ebe718b2d852cb0a0e Merge: e2e9fd784 de4c922c2 Author: Michael Zingale Date: Tue Sep 1 12:05:09 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit de4c922c2bbb9724f5efeaeec0d19a5517d5d9e4 Author: Michael Zingale Date: Tue Sep 1 12:00:24 2015 -0400 if there is no png file produced, then skip the copy Tools/RegressionTesting/testnew.py commit e2e9fd784bf181a4bcd23c3563560ace54c44085 Merge: 2153858be 2a93890bf Author: Michael Zingale Date: Tue Sep 1 11:50:05 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit 2153858bec97c2f4f969fe628aed2ca39c768f00 Author: Michael Zingale Date: Tue Sep 1 11:49:56 2015 -0400 add an equal method Src/F_BaseLib/multifab_f.f90 commit 2a93890bf79989ddded14c9d8f83416f4db3f6bf Author: Weiqun Zhang Date: Tue Sep 1 08:30:27 2015 -0700 fixed a new bug: forgot to build mfiter Src/F_BaseLib/multifab_f.f90 commit cb4507ae0569f594e5fece158a142e9c11a448b1 Author: Weiqun Zhang Date: Mon Aug 31 17:44:20 2015 -0700 more tiling in multifab_f Src/F_BaseLib/multifab_f.f90 commit 0d7799486e32063af89e483b7f5689c6a36a52ba Merge: b326f8e33 925293f5d Author: vince Date: Mon Aug 31 17:19:02 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit b326f8e336ab2ee0b5cf6fb6f67e133468c3de77 Author: vince Date: Mon Aug 31 17:18:59 2015 -0700 some code cleanup. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/FabArray.H commit 737460393b340568891459c569a9c542c0608f66 Author: Weiqun Zhang Date: Mon Aug 31 16:02:54 2015 -0700 Fixed a very old in multifab_div_s_c. Fortunately, I don't think it is ever used by any codes. Src/F_BaseLib/multifab_f.f90 commit 925293f5dea714816c7dcf1f37f391118201e456 Author: Weiqun Zhang Date: Sat Aug 29 23:41:43 2015 -0700 fixed a new omp bug and cleanup Src/F_BaseLib/multifab_f.f90 commit 3a61fb4611958792a536d7e586d20d5830cf7b3f Author: Weiqun Zhang Date: Sat Aug 29 22:30:54 2015 -0700 fixed typo Src/F_BaseLib/multifab_f.f90 commit b8717d8f14d73d0071772651adf2c3173d660f63 Author: Weiqun Zhang Date: Sat Aug 29 22:15:21 2015 -0700 more tiling and forgot to build mfiter Src/F_BaseLib/multifab_f.f90 commit 97e6bec7794cf2c230e0da4414ccde13ff8ad38f Author: Weiqun Zhang Date: Sat Aug 29 21:53:48 2015 -0700 Multifab_fab_copy is serial only and I oon't think any codes are it, so it is removed. If it turns out some codes need to call it, we should implement a parallel version. Src/F_BaseLib/multifab_f.f90 commit 7fb914a180ca380d9c328e964461b879c95f70b9 Author: Weiqun Zhang Date: Sat Aug 29 21:46:48 2015 -0700 tiling in multifab_min Src/F_BaseLib/multifab_f.f90 commit 27606743940d5b0c455c0c29c569ac9b48602a59 Author: Weiqun Zhang Date: Sat Aug 29 21:37:02 2015 -0700 tiling in multifab_val and removed allow_empty argument because mfiter skips empty box already Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_f.f90 commit f2726b8b2dc312f763baa65b980bd9876cda61fc Author: Weiqun Zhang Date: Sat Aug 29 21:06:55 2015 -0700 It shouldn't be fab's responsibility to check if the caller passes in a box in fab_max_val and fab_min_val. Also note that in practice only the multifab module is supposed to call fab_max_val and fab_min_val. Src/F_BaseLib/fab.f90 commit 520816116d581a1bacfd494b9c0e5a65dc3ef881 Author: Weiqun Zhang Date: Fri Aug 28 17:01:48 2015 -0700 more tiling Src/F_BaseLib/multifab_f.f90 commit be38cd9128f13a1f019d4c8322dc167305f0c888 Author: Weiqun Zhang Date: Fri Aug 28 16:54:48 2015 -0700 no longer need to test empty box because mfiter will not hand out an empty box Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_f.f90 commit 76924f077532784446baa5dd4c56d815ad23c770 Author: Weiqun Zhang Date: Fri Aug 28 16:52:02 2015 -0700 handle empty box in mfiter Src/F_BaseLib/layout.f90 commit 0b12c3377131cbb9732f1606b08ed25de1e4ebbd Author: Weiqun Zhang Date: Fri Aug 28 16:18:13 2015 -0700 tiling and omp in multifab_f Src/F_BaseLib/multifab_f.f90 commit a8647e336dac8d6eaa8f513e354f84f5a819988a Author: Weiqun Zhang Date: Fri Aug 28 15:16:32 2015 -0700 removed omp in fab.f90 because we are going to do it in multifab_f.f90 Src/F_BaseLib/fab.f90 commit ce4f203b0c05d2293fca73845ed03eb54047d2b5 Merge: 6b979ae3a 6d8e6311c Author: yzheng Date: Sat Aug 29 15:55:46 2015 -0700 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit bc5d1ae30f26a43344f3a6d3e4b3a279d4209ec7 Merge: e197ff7d0 f4dbf9dee Author: Max Katz Date: Sat Aug 29 01:51:10 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit e197ff7d0f5d38bee579509ca9a33b7465b212fe Author: Max Katz Date: Sat Aug 29 01:51:07 2015 -0400 Add a DIMENSION_AGNOSTIC variable to the makefile/defines; we'll use it in some cases for determining whether to call dimension agnostic Fortran functions. Also add a dimension agnostic version of the boundary function routines, similar to how we did this for the derive class. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Make.package Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Tools/C_mk/Make.defs commit f4dbf9dee534a23dcd4d8899a6a943b7e7ed8c9b Author: Brian Friesen Date: Fri Aug 28 15:45:09 2015 -0700 ParallelDescriptor: put include of Analysis.H inside IN_TRANSIT ifdef Src/C_BaseLib/ParallelDescriptor.cpp commit 37f9e57f977342049c3bf06b8dcc3b7841fefcdc Author: Brian Friesen Date: Fri Aug 28 15:42:52 2015 -0700 F_BaseLib: derive world_group communicator from m_comm instead of MPI_COMM_WORLD in parallel_create_communicator() This routine ultimately just wants the "parent" communicator from which to build sub-communicators. It shouldn't care whether the parent communicator is actually MPI_COMM_WORLD or anything else. Src/F_BaseLib/parallel.f90 commit 6d8e6311ccf6aa5bb71a5031b142cf57d0ac3e79 Author: Weiqun Zhang Date: Fri Aug 28 13:15:31 2015 -0700 split FillPeriodicBoundary_finish into two versions: MPI and UPCXX Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 75f268c744479802e9ef6c494801cdb81293d9ad Author: Brian Friesen Date: Fri Aug 28 12:10:16 2015 -0700 F_BaseLib: change parent communicator from MPI_COMM_WORLD to m_comm in parallel_create_communicator() Using MPI_COMM_WORLD breaks code which uses more than one MPI group. "m_comm" should be the correct pseudo-global communicator anyway, so this should work for any number of MPI groups. Src/F_BaseLib/parallel.f90 commit dc5e1a915d1ee2ebec1eec096435f5faf0a5e6b5 Author: Brian Friesen Date: Fri Aug 28 10:44:27 2015 -0700 F_BaseLib: remove assignment of m_comm to MPI_COMM_WORLD in parallel_finalize() This breaks the multigrid solver when running with the sidecars because the solver invokes many MPI collective routines which hang due to this. Src/F_BaseLib/parallel.f90 commit f6c070e69e6169ffeee0c55a2d31cbbdaa3f076f Author: Brian Friesen Date: Fri Aug 28 09:24:57 2015 -0700 ParallelDescriptor: move creation of InTransitAnalysis variable outside if/else section in SidecarProcess() Every type of analysis will use an InTransitAnalysis object, so rather than duplicating this line in every if/else case, just do it once at the beginning. Src/C_BaseLib/ParallelDescriptor.cpp commit 99496596a8b2702446ccaebf9e159b59486f47c4 Author: Brian Friesen Date: Fri Aug 28 07:21:37 2015 -0700 ParallelDescriptor: break out of while() loop immediately after sidecars receive quit signal Src/C_BaseLib/ParallelDescriptor.cpp commit 309f0e4fee068b0fb916bf5c965a752a62a68215 Author: Brian Friesen Date: Fri Aug 28 07:16:18 2015 -0700 ParallelDescriptor: use automatic allocation instead of new[] and delete[] in SidecarProcess() There's no reason to use pointers and allocate objects by hand. Let them come into and go out of scope automatically. Src/C_BaseLib/ParallelDescriptor.cpp commit b5f83b75fce4cfcbc790940f6e62b74ea95daee4 Author: Brian Friesen Date: Fri Aug 28 07:06:16 2015 -0700 ParallelDescriptor: move sidecar completion message outside the signal if/else section This way we don't have to duplicate that message inside every if/else case. Src/C_BaseLib/ParallelDescriptor.cpp commit 4497ff5c4ca1a8bde5a85b1ba65c4695a5ca860f Author: Weiqun Zhang Date: Thu Aug 27 17:13:41 2015 -0700 split FillBoundary_finish into two versions: MPI and UPCXX Src/C_BaseLib/FabArray.H commit 6b979ae3a6cec0e76a244305d1d05a00849f392f Merge: 99f9ddfbd 7cb292106 Author: yzheng Date: Thu Aug 27 16:42:55 2015 -0700 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 99f9ddfbdac2f03eefa76e7d95c7a2fd42e8b03f Author: yzheng Date: Thu Aug 27 16:42:52 2015 -0700 Use UPC++ barrier for the UPC++ version MiniApps/PGAS_SMC/SMC.cpp commit 49224fb30b9e2e4f7d4eb4d834a0f03e55a9a508 Merge: 7cb292106 60ff15d3e Author: Weiqun Zhang Date: Thu Aug 27 16:24:34 2015 -0700 Merge branch 'master' into pgas commit 7cb292106971b9624e2e2d1af5a94831a8636649 Author: Weiqun Zhang Date: Thu Aug 27 15:22:44 2015 -0700 tweak the output of timing results MiniApps/PGAS_SMC/SMC.cpp commit 60ff15d3e566e8c49c5d986de7bb1a236a9af60a Author: Brian Friesen Date: Thu Aug 27 14:37:23 2015 -0700 Geometry: add forgotten assignment of is_periodic in SendGeometryToSidecars() Src/C_BaseLib/Geometry.cpp commit b2c37a6b21ae0dc11942daeaf35591254af3f0dc Author: Weiqun Zhang Date: Thu Aug 27 12:43:48 2015 -0700 PGAS_SMC: use blocking fill boundary when overlap is false MiniApps/PGAS_SMC/SMC_advance.cpp commit d02a4c821f89b57a2caed54e24cf8a690cbb6079 Author: Weiqun Zhang Date: Thu Aug 27 12:43:06 2015 -0700 blocking fill boundary function can also use upc++ now Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp commit 1c867275bb1466b8072259816f9a92286269556b Author: yzheng Date: Thu Aug 27 10:28:53 2015 -0700 Poll UPC++ progress engine more aggressivelly right after making send requests Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 7766022a50a9beb61406d628769506cf80e0d555 Author: Michael Zingale Date: Thu Aug 27 09:37:19 2015 -0400 fix the fix -- keep 0.0 if that is printed :) Tools/Postprocessing/F_Src/fcompare.f90 commit 2581e79f9561a339470f514bf0acd06d08f77f87 Merge: 93df2931f e94d7fd85 Author: Michael Zingale Date: Thu Aug 27 09:16:15 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit 93df2931f2201c134a2fd14015ea920b5021ed44 Author: Michael Zingale Date: Thu Aug 27 09:15:16 2015 -0400 Fortran prints numbers with 3-digit exponents without the 'E' (i.e., 0.3979676757-175) Python/C don't know how to interpret this. Now we floor things with 1.d-99 Tools/Postprocessing/F_Src/fcompare.f90 commit e4c3989431184471cdae26bd6209a2e0240fcf95 Merge: 901ee7de1 e94d7fd85 Author: Weiqun Zhang Date: Wed Aug 26 15:05:06 2015 -0700 Merge branch 'master' into pgas Conflicts: Src/C_BaseLib/BoxLib.cpp commit e94d7fd859abc65dcf42982704eef6fe271608ac Author: Weiqun Zhang Date: Wed Aug 26 15:02:46 2015 -0700 trying to keep x-direction long in creating box list of the compliment of a box in another Src/C_BaseLib/BoxList.cpp Src/F_BaseLib/list_box.f90 commit 901ee7de184d9d3a75bef58e2e322322a721df8a Author: Weiqun Zhang Date: Wed Aug 26 14:58:28 2015 -0700 adjusted timers MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_advance.cpp commit d0bc0708570d7dace9b5a1322cf21f3eaa3a0bf6 Author: Weiqun Zhang Date: Wed Aug 26 11:03:53 2015 -0700 PGAS_SMC: use the same initial guess for T MiniApps/PGAS_SMC/make_plot.f90 commit d82efe1d18c59aad082bef64a4784088f06fabda Author: Weiqun Zhang Date: Wed Aug 26 11:01:53 2015 -0700 PGAS_SMC: changed the default max_grid_size MiniApps/PGAS_SMC/SMC.cpp commit 3a4332fbba81aec4f26bf908db79009ff7a245ed Author: Weiqun Zhang Date: Wed Aug 26 10:25:50 2015 -0700 tidy MiniApps/PGAS_SMC/SMC.cpp commit 4e8f5888e1770352fa74a8f14e732e7213fe763b Author: Weiqun Zhang Date: Wed Aug 26 10:19:50 2015 -0700 added some timers and some minor changes MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_advance.cpp commit bccdc7dc0015c2a4dd76fd4943d49cc548d15d7e Author: Weiqun Zhang Date: Tue Aug 25 17:31:04 2015 -0700 first version of PGAS_SMC MiniApps/PGAS_SMC/Make.package MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_F.H MiniApps/PGAS_SMC/SMC_advance.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/init_data.f90 MiniApps/PGAS_SMC/kernels.f90 MiniApps/PGAS_SMC/make_plot.f90 MiniApps/PGAS_SMC/transport_properties.f90 MiniApps/PGAS_SMC/variables.f90 commit d4e367a55050efae1e736fc5a8fd3451a1069c6f Author: Weiqun Zhang Date: Tue Aug 25 17:29:41 2015 -0700 added MFGhostIter that iterates over ghost cells only Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 0a991ff34e0c307ce17ab0db6d80bf46d29fc39c Author: Brian Friesen Date: Tue Aug 25 16:21:49 2015 -0700 Analysis: started adding virtual Initialize() stubs for different kinds of analysis classes Different types of analyses require different types of input data, and at some point the compiler must know *something* about which data an analysis class requires. But we don't want to put the entire analysis code into BoxLib itself. Since we can't have virtual constructors, the compromise is to enumerate all the possible input sets via unique, virtual Initialize() stubs. BoxLib will not invoke a callback to Initialize() because it doesn't know which one to use. So the analysis class itself invokes its own Initialize(), and BoxLib will then invoke DoAnalysis() and Finalize(), since it is much easier to implement those functions for any analysis class with no arguments. Src/C_BaseLib/Analysis.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/Sidecar_EX1/InTransitAnalysis.H Tutorials/Sidecar_EX1/InTransitAnalysis.cpp commit cea925810acdc4c9a0a525ded7da38208081b910 Author: Brian Friesen Date: Tue Aug 25 15:57:08 2015 -0700 Analysis: created namespace "Analysis" and moved most stuff there from ParallelDescriptor Src/C_BaseLib/Analysis.H Src/C_BaseLib/Analysis.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp commit e4605fffaf60dd27b8a711627b34db2f2e49e1d6 Author: Brian Friesen Date: Tue Aug 25 15:41:16 2015 -0700 Analysis: renamed generic class "Analysis" to "AnalysisContainer" Src/C_BaseLib/Analysis.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 31c1a6f37aeef00a012e1e4b521f0c2c45249d15 Author: Brian Friesen Date: Tue Aug 25 14:26:56 2015 -0700 ParallelDescriptor: compactify pointer allocation syntax in SidecarProcess() Src/C_BaseLib/ParallelDescriptor.cpp commit cfe2e9de9429e07a8cb79c75ac48e409d1620371 Author: Weiqun Zhang Date: Tue Aug 25 13:19:09 2015 -0700 fixed typos Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp commit e4409f6f263bfd64a20e05165fc4fdd99d4d9e27 Author: Brian Friesen Date: Tue Aug 25 12:49:39 2015 -0700 Tutorials: added #ifdef IN_TRANSIT to relevant parts of Sidecar_EX1 We want the code to run with or without sidecars. It's just that if you don't use the sidecars in this example, the code doesn't do anything interesting. Tutorials/Sidecar_EX1/GridMoveTest.cpp commit 739741677e63e1188d9a1855ae075c84c63caeee Author: Amir Kamil Date: Tue Aug 25 15:38:01 2015 -0400 Split Send interface into Send and Request. Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 8aee68f63a835d923e6da21600acd28a3da6c6f6 Merge: 18ebf70e9 114f37dba Author: Brian Friesen Date: Tue Aug 25 12:35:07 2015 -0700 Merge branch 'add_sidecar_analysis' With these commits we return to a signal-based system for interacting with the sidecar MPI group. We have also moved to a callback-based system for performing the analysis so that the process of "registering" and executing a user-defined analysis routine with the sidecars can remain fairly generic. commit 114f37dbab8aacbc0ad12249cd02c4a1cf253da5 Author: Brian Friesen Date: Tue Aug 25 11:29:06 2015 -0700 Tutorials: removed Sidecar_EX2 example since Sidecar_EX1 has the same features Tutorials/Sidecar_EX2/GNUmakefile Tutorials/Sidecar_EX2/InSituAnalysis.H Tutorials/Sidecar_EX2/InSituAnalysis.cpp Tutorials/Sidecar_EX2/Make.package Tutorials/Sidecar_EX2/inputs_3d Tutorials/Sidecar_EX2/main.cpp commit 1b7d57d31ac7abcc63f93e72b37b6742ff4442d8 Author: Brian Friesen Date: Tue Aug 25 09:13:48 2015 -0700 Sidecars: changed sidecar implementation back to signal-based, and updated Sidecar_EX1 tutorial accordingly Src/C_BaseLib/Analysis.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/InTransitAnalysis.H Tutorials/Sidecar_EX1/InTransitAnalysis.cpp Tutorials/Sidecar_EX1/Make.package commit a183b158447201bd5bccc4eb54f0be26ce0e78e3 Author: Weiqun Zhang Date: Mon Aug 24 17:23:27 2015 -0700 flesh out PGAS_SMC MiniApps/PGAS_SMC/Exec/ToyFlame/GNUmakefile MiniApps/PGAS_SMC/Exec/ToyFlame/Make.package MiniApps/PGAS_SMC/Exec/ToyFlame/Prob_3d.f90 MiniApps/PGAS_SMC/GNUmakefile MiniApps/PGAS_SMC/LiDryer.c MiniApps/PGAS_SMC/Make.package MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_F.H MiniApps/PGAS_SMC/SMC_advance.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/Source/Make.package MiniApps/PGAS_SMC/Source/SMC.H MiniApps/PGAS_SMC/Source/SMC.cpp MiniApps/PGAS_SMC/Source/SMCBld.cpp MiniApps/PGAS_SMC/Source/SMC_advance.cpp MiniApps/PGAS_SMC/Source/SMC_io.cpp MiniApps/PGAS_SMC/Source/SMC_setup.cpp MiniApps/PGAS_SMC/Source/main.cpp MiniApps/PGAS_SMC/chemistry_module.f90 MiniApps/PGAS_SMC/derivative_stencil.f90 MiniApps/PGAS_SMC/init_data.f90 MiniApps/PGAS_SMC/main.cpp MiniApps/PGAS_SMC/variables.f90 commit 18ebf70e9591773a3fe5905ba027ec37db725fc1 Author: Weiqun Zhang Date: Sat Aug 22 23:33:02 2015 -0700 align memory arena allocation to 16 bytes Src/C_BaseLib/Arena.H Src/C_BaseLib/Arena.cpp Src/C_BaseLib/CArena.cpp commit 49f13ec43c94465041661c837e941ada4aa7c3d7 Author: yzheng Date: Sat Aug 22 15:45:33 2015 -0700 Update BLPgas.cpp to use the latest version of UPC++ signaling put interface Src/C_BaseLib/BLPgas.cpp commit 92f4d995f0f95c601fb5aa2f7df00f304e10e001 Author: Weiqun Zhang Date: Fri Aug 21 17:08:25 2015 -0700 fixed wrong index Src/LinearSolvers/F_MG/cc_stencil_apply.f90 commit 8efc771a9fd8d20505eecab983776560835f2689 Author: Weiqun Zhang Date: Fri Aug 21 17:07:49 2015 -0700 build edge multifab for flux instead of cell-centered with ghsot cells Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit a0dfedfe903c8d0c74398af5544baf2c71fe5f1f Merge: dbe86f9db 54d54ff99 Author: Brian Friesen Date: Fri Aug 21 10:26:09 2015 -0700 Merge branch 'sidecar_improvements' This adds a few new static functions for sending various objects to the sidecars processes, and cleans up a few things as well. commit 54d54ff9916cbe00a96a820aa3be595f4cfd01c6 Author: Brian Friesen Date: Wed Aug 12 12:51:38 2015 -0700 MultiFab: change memcpy() to std::memcpy() in SendMultiFabToSidecars() memcpy() is a C function. To be consistent let's use the C++ version in STL. Src/C_BaseLib/MultiFab.cpp commit 074413902d21664e9c8553c9957fde9cffae1942 Author: Brian Friesen Date: Wed Aug 12 12:04:18 2015 -0700 MultiFab: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast() Src/C_BaseLib/MultiFab.cpp commit 91f8dbfc631369e8f0aab51abb222a9301bfe0a0 Author: Brian Friesen Date: Wed Aug 12 12:03:42 2015 -0700 Geometry: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast() Src/C_BaseLib/Geometry.cpp commit e9c4513ba13a6de93904286e6dc435b48239e7a2 Author: Brian Friesen Date: Wed Aug 12 12:02:43 2015 -0700 DistributionMapping: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast() Src/C_BaseLib/DistributionMapping.cpp commit 03c9f99baa1323d00ddfde11e36b471733ffba4a Author: Brian Friesen Date: Wed Aug 12 12:01:48 2015 -0700 BoxArray: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast() Src/C_BaseLib/BoxArray.cpp commit 4bb5f8295cfed8938d487ce43dfe9dfc5fde5328 Author: Brian Friesen Date: Tue Aug 11 13:49:15 2015 -0700 BoxArray, Geometry, MultiFab: change regular cast to const_cast in Bcast() The buffer in a Bcast() must not be a const, but some functions return consts. So const_cast them to be non-const wen we do the Bcast(). It's not pretty but it works. Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit aef3549b3064257e3241072ada11910289875202 Author: Brian Friesen Date: Tue Aug 11 13:06:59 2015 -0700 DistributionMapping: add static function SendDistributionMappingToSidecars() When we move distributed data sets between the compute and MPI groups we send the FAB data using point-to-point communication, so each MPI group needs to know the distribution of FABs on the other group so that it knows who to Send() and Recv() from. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 3f45184dad6d20f7dbfc5cf1a3d7c971f69106dc Author: Brian Friesen Date: Tue Aug 11 11:15:03 2015 -0700 DistributionMapping: added define() to build a DM out of an Array This is useful if a DM is initialized with the default constructor and one wants to populate with a plain ol' array of ints. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 32755003c7aa4172d11bdbe41fe07c4fd255f7d6 Author: Brian Friesen Date: Tue Aug 11 09:49:29 2015 -0700 BoxArray: added static function SendBoxArrayToSidecars() This clones a BoxArray onto the sidecar MPI group. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit fa379456cd67662cdb2b7352f824d40fecf869ca Merge: bb64f9c64 dbe86f9db Author: Weiqun Zhang Date: Wed Aug 19 17:53:36 2015 -0700 Merge branch 'master' into pgas Conflicts: Src/C_BaseLib/FabArray.H Src/C_BaseLib/Make.package Tools/C_mk/Make.defs commit dbe86f9dbb5a98c138d71217de169c88cf9f8237 Merge: d0f43cea6 6ba81d4e3 Author: Weiqun Zhang Date: Wed Aug 19 17:45:47 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit d0f43cea62fa715083aee665f3968c8cb1b14515 Author: Weiqun Zhang Date: Wed Aug 19 17:22:47 2015 -0700 clean up MGT_Sover Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tutorials/MultiGrid_C/main.cpp commit 6ba81d4e361d2bc8f1147a31172d1b26e1bcf7a0 Merge: 2c822c57a 9123c7cb7 Author: Brian Friesen Date: Wed Aug 19 16:01:40 2015 -0700 Merge branch 'add_analysis_abstract_base_class' This provides an abstract base class "Analysis" for doing data analysis during BoxLib simulations. It also provides a simple example of in-situ data processing executed on the sidecars. The actual analysis routines themselves must be provided by the user. commit 9123c7cb74adff8c30e8eac3ab3b9574dd053994 Author: Brian Friesen Date: Wed Aug 19 12:45:01 2015 -0700 Tutorials: added example "Sidecar_EX2" demonstrating use of Analysis class on sidecars Tutorials/Sidecar_EX2/GNUmakefile Tutorials/Sidecar_EX2/InSituAnalysis.H Tutorials/Sidecar_EX2/InSituAnalysis.cpp Tutorials/Sidecar_EX2/Make.package Tutorials/Sidecar_EX2/inputs_3d Tutorials/Sidecar_EX2/main.cpp commit 9c041ec4a52e69414631ac2069129f3c63651231 Author: Brian Friesen Date: Wed Aug 19 12:24:30 2015 -0700 C_BaseLib: added abstract base class "Analysis" This class provides a platform for the user to do data analysis during BoxLib simulations. A class derived from Analysis should contain both functionality for doing the analysis itself, as well as storage for the results. Src/C_BaseLib/Analysis.H Src/C_BaseLib/Make.package commit 2c822c57a3530b463a59ef9b875bcc585417e661 Author: Brian Friesen Date: Tue Aug 18 15:39:40 2015 -0700 C_mk: added missing "-mmic" flag for compiling Fortran files on MIC in debug mode Tools/C_mk/Make.Linux commit bb64f9c64c254e431dcbc84e400125b5fa209bbe Author: Weiqun Zhang Date: Tue Aug 18 17:37:03 2015 -0700 started PGAS_SMC MiniApps/PGAS_SMC/Exec/Make.SMC MiniApps/PGAS_SMC/Exec/ToyFlame/GNUmakefile MiniApps/PGAS_SMC/Exec/ToyFlame/Make.package MiniApps/PGAS_SMC/Exec/ToyFlame/Prob_3d.f90 MiniApps/PGAS_SMC/Source/Make.package MiniApps/PGAS_SMC/Source/SMC.H MiniApps/PGAS_SMC/Source/SMC.cpp MiniApps/PGAS_SMC/Source/SMCBld.cpp MiniApps/PGAS_SMC/Source/SMC_advance.cpp MiniApps/PGAS_SMC/Source/SMC_io.cpp MiniApps/PGAS_SMC/Source/SMC_setup.cpp MiniApps/PGAS_SMC/Source/main.cpp commit aea6d0134be2bfe6eb87a89615b1c48e0d06115e Author: Michael Zingale Date: Tue Aug 18 09:55:56 2015 -0400 add a subtitle to the main test page Tools/RegressionTesting/testnew.py commit 54914befc12ddf0960a12c992c7d961d5d29eb6c Author: Yili Zheng Date: Mon Aug 17 22:34:36 2015 -0700 Rewrite the PGAS version to use non-blocking signaling put and event-based point-to-point synchronization; thus removing the need of global barriers Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 285eaa1f15b3ebff5bf4e090562ff82b3738af1e Author: Michael Zingale Date: Mon Aug 17 16:02:19 2015 -0400 turn off inlining for pure PGI -- this generates an internal compiler error for knapsack.f90. Also drop down to -O2. This brings us more in line with what we use on the Cray's when we come in via the ftn wrapper. Tools/F_mk/comps/Linux_pgi.mak commit 8056e83ef5ef4b27472ac7328bb67de571bbc066 Merge: 0f9f73299 1247255a2 Author: Michael Zingale Date: Mon Aug 17 15:04:58 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit 0f9f73299607056c7bf3fcefe4363f6bfffeb34e Author: Michael Zingale Date: Mon Aug 17 15:04:45 2015 -0400 get the compiler version working for pure PGI Tools/F_mk/comps/Linux_pgi.mak commit 1247255a2fe037844fcb5a3e7b2ee2a2614765c4 Author: Michael Zingale Date: Mon Aug 17 13:48:11 2015 -0400 make the tol 1.e-6 for highlighting Tools/RegressionTesting/testnew.py commit 43e5351103c978400a1712c5051c8736118497e6 Author: Michael Zingale Date: Mon Aug 17 13:31:39 2015 -0400 new test comparison table with highlighting Tools/RegressionTesting/testnew.py commit c0e3244b73427e2bf30dc6e764e108c6e3650976 Author: Michael Zingale Date: Mon Aug 17 10:53:31 2015 -0400 close an HTML header Tools/RegressionTesting/testnew.py commit cb6fc77310f6c7d6d69300e9075804db04dcaa6c Author: Michael Zingale Date: Sat Aug 15 18:56:04 2015 -0400 update comment Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 8262c309a796a54591c1083f5345ab421b9db03c Author: Ann Almgren Date: Sat Aug 15 08:36:41 2015 -0700 Enable mgt.cycle_type = MG_FVCycle in nodal as well. Src/LinearSolvers/F_MG/ml_nd.f90 commit 09271dc8359284a38c83b711734f069246922424 Author: Ann Almgren Date: Fri Aug 14 13:59:10 2015 -0700 1) Add the functionality to do 1 F-cycle followed by V-cycles 2) Force the interpolation to be piecewise constant for V-cycles and piecewise linear for F-cycles, regardless of the input values. Src/LinearSolvers/F_MG/ml_cc.f90 commit 00450cd94822fe557d70f7578efbd60f6859d0b8 Merge: 881163a88 a54624c9e Author: Ann Almgren Date: Fri Aug 14 10:29:43 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 881163a8849150da239844c2adae2115aeddce3a Author: Ann Almgren Date: Fri Aug 14 10:28:24 2015 -0700 Add another cycle type -- MG_FVCycle -- which is 1 F cycle followed by V cycles Src/LinearSolvers/F_MG/mg_tower.f90 commit a54624c9e828f9b5de38f5bdd82abce2a2b63547 Author: Weiqun Zhang Date: Thu Aug 13 11:32:21 2015 -0700 fixed periodic boundary and a local index bug Src/F_BaseLib/bndry_reg.f90 commit 7bfaa02c267e9b102f2f5fbd4f443a07127341be Author: Weiqun Zhang Date: Thu Aug 13 06:45:39 2015 -0700 delete removed variable 'id' from omp private Src/F_BaseLib/bndry_reg.f90 commit d583e5c50ded96627ab5ffde5c97d73ec41542ec Author: Weiqun Zhang Date: Wed Aug 12 22:37:45 2015 -0700 avoid covered coarse cells in ml_interp_bcs; in order to to do that, mask is built in bndry register Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_nd.f90 commit 29e2fa82c4af54cb150e94d033ad91a9e10df6ce Author: Weiqun Zhang Date: Wed Aug 12 11:11:27 2015 -0700 print more information Src/LinearSolvers/F_MG/ml_cc.f90 commit 942d9df692368d7c26436ea160bcf364d4986a63 Author: Max Katz Date: Thu Aug 13 16:14:23 2015 -0500 Make Titan consistent with other Cray machines we're using by adding -lmpichf90. Tools/C_mk/Make.mpi commit 26f6fe4c55e04ae054feb8fa9ba75f2d81e0b1ff Author: Ann Almgren Date: Thu Aug 13 13:27:21 2015 -0700 Oops -- committed the wrong expression for the stencil. Now works with Dirichlet as well as periodic. Src/LinearSolvers/C_CellMG/ABec_3D.F commit b570e08d17135f36e61e65556e5ec2f497d4ac16 Author: Ann Almgren Date: Thu Aug 13 13:00:08 2015 -0700 I have modified the 3D GSRB relaxation to use an over-relaxation factor of 1.15. This makes it the same as the smoother used in the F90 solver, and seems to consistently reduce the number of V-cycles needed. Src/LinearSolvers/C_CellMG/ABec_3D.F commit 42647c0490242453ad02fac7cc5b3951857edfb8 Author: Weiqun Zhang Date: Tue Aug 11 11:37:55 2015 -0700 use std::pair instead of std::make_pair because the latter does not work in C++11 due to template type deduction rules Src/C_BaseLib/FabArray.H commit b276dfbe0d520044c4dc6bdd5bc807d72dfe9514 Merge: 9b377ff08 8c5156991 Author: Weiqun Zhang Date: Mon Aug 10 17:43:43 2015 -0700 Merge branch 'weiqun' commit 9b377ff086a0d113237f85dfece53ae57158c133 Author: Weiqun Zhang Date: Mon Aug 10 17:43:35 2015 -0700 allocate at lease 1 element if asked size is zero Src/C_BaseLib/mempool_f.f90 commit 2bee6466f85ee2353959aea178cb6cd02c2ad5d3 Author: Weiqun Zhang Date: Mon Aug 10 17:17:52 2015 -0700 fixed bugs in vector_i function that has never been used Src/F_BaseLib/vector_i.f90 commit ad307f80f9387b2a66935d7ac1aea418ea1b5f73 Merge: e75f50d1d 0d6131fee Author: vince Date: Mon Aug 10 12:58:10 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit e75f50d1d8c8bb5b9aba45407132cb3ee79004ef Author: vince Date: Mon Aug 10 12:57:33 2015 -0700 code cleanup. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.cpp commit 0d6131fee9bbeb6f9bae7540fad4ca76106552f3 Author: Brian Friesen Date: Mon Aug 10 11:24:49 2015 -0700 MultiFab: clean up SendMultiFabToSidecars() interface Now the only argument to MultiFab::SendMultiFabToSidecars() is a MultiFab pointer. In the Compute group this will point to a MultiFab with actual data filled in, whereas in the Sidecar group this will point to a MultiFab which is allocated but uninitialized prior to this function call. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp commit bf56ef46b7aac0d249a593f5838aafc22cff278a Author: Brian Friesen Date: Mon Aug 10 11:02:34 2015 -0700 Geometry: clean up SendGeometryToSidecars() interface Now the only argument to Geometry::SendGeometryToSidecars() is a Geometry pointer. In the Compute group this will point to a Geometry with actual data filled in, whereas in the Sidecar group this will point to a Geometry which is allocated but uninitialized prior to this function call. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp commit 84d0e64a6783c3f7e57a7628596599aab44c8c23 Merge: 76b6e96f2 0a20a9d80 Author: vince Date: Mon Aug 10 11:03:06 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 8c5156991340aa926ccbcff863a3751060d8842f Author: Weiqun Zhang Date: Mon Aug 10 10:59:04 2015 -0700 Avoided allocating temporary multifab in multifab parallel copy Src/F_BaseLib/multifab_f.f90 commit 16f369c9bf8a848eb491e40b37579bdd7f2e58a9 Author: Yili Zheng Date: Fri Aug 7 15:13:35 2015 -0700 Added SeqNum (tag) matching in BLPgas::Send; Changed map to multimap; Use unordered_multimap if C++11 is available; Enabled non-blocking UPC++ code in Geometry.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/Geometry.H commit 484aef11bd079d28f6af420f6ac8318468ffa969 Author: Weiqun Zhang Date: Thu Aug 6 14:57:48 2015 -0700 fixed typo Src/C_BaseLib/Geometry.H commit eb5a660942118aef1c9e4779d4e7b532259407d2 Author: Weiqun Zhang Date: Thu Aug 6 14:38:27 2015 -0700 nonblocking version of FillPeriodicBoundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Tutorials/PGAS_HEAT/main.cpp commit b7f2e33fd4d6bb6862c3c9c8b7e349b12ffc1d4e Author: Weiqun Zhang Date: Thu Aug 6 11:15:57 2015 -0700 moved pgas send into new files Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Make.package commit 3f516f87ca49dee750ee02221b816969932e8617 Author: Weiqun Zhang Date: Wed Aug 5 12:36:50 2015 -0700 added USE_UPCXX to makefile Tools/C_mk/Make.defs Tools/C_mk/Make.upcxx Tutorials/PGAS_HEAT/GNUmakefile commit d6f4ef7b44c2f664e2ac7253aae6a3a2a4fca13b Author: Weiqun Zhang Date: Wed Aug 5 12:22:33 2015 -0700 fixed merge Src/C_BaseLib/BoxLib.cpp commit 1e18ae957fe083f09a35977ea59e1c80453d020f Merge: 02dfda140 0a20a9d80 Author: Weiqun Zhang Date: Wed Aug 5 10:37:11 2015 -0700 Merge branch 'master' into pgas commit 0a20a9d80f2554bacc537ca394063c3699fe8520 Author: Weiqun Zhang Date: Wed Aug 5 06:42:16 2015 -0700 fixed undefined reference to 'boxarray_build'. Src/F_BaseLib/fabio.f90 commit b1316b8e65f6dbed07367550eabbe02329399617 Author: Weiqun Zhang Date: Tue Aug 4 18:08:48 2015 -0700 minor change for consistence; note that nboxes(tagboxes%la) is the same as nfabs(tagboxes) because tagboxes is a special mf that has all fabs on io processor. Src/F_BaseLib/cluster_f.f90 commit 845a173c4c1505c87ee7af6d4fa6fdb7a8ebbcb7 Author: Weiqun Zhang Date: Tue Aug 4 17:16:55 2015 -0700 simplify parallel copy in bndry_reg Src/F_BaseLib/bndry_reg.f90 commit a5950023951a6f268d39d5e6dc7573cdbc4ba046 Author: Weiqun Zhang Date: Tue Aug 4 17:02:03 2015 -0700 added omp parallel do in bndry_reg Src/F_BaseLib/bndry_reg.f90 commit 292cbd1baf7cf4b741909ee02de42641830f3b57 Author: Weiqun Zhang Date: Tue Aug 4 15:52:56 2015 -0700 use bl_allocate in vector_i module Src/F_BaseLib/vector_i.f90 commit f045f1ee6ed9c231478b96ba1342f3def0c7101f Author: Weiqun Zhang Date: Tue Aug 4 15:46:33 2015 -0700 replaced a lot of generic calls with explicit calls so that grep and etags can work properly. Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/ml_nd_restriction.f90 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/nodal_stencil_bc.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_applyop.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 81ebd286281a1d33237bd2bd0634ade3b74ef888 Author: Marc Day Date: Tue Aug 4 15:32:15 2015 -0700 Fix the PyTools GNUmakefile for C++, and bump the tag number Tools/CMake/BoxLib_Version.cmake Tools/Py_util/GNUmakefile commit 76b6e96f2320992378b252eb26a1fe51a805595f Author: vince Date: Tue Aug 4 12:15:36 2015 -0700 itac suffix. Tools/C_mk/Make.defs commit 8e0907150a89f81ef4b97915a705ffdbb8bf4fae Merge: 50205de55 5e5409fae Author: vince Date: Tue Aug 4 12:14:07 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 02dfda14016d7649565371720471a7b0d7d1ec30 Merge: 36c11c695 5e5409fae Author: Weiqun Zhang Date: Mon Aug 3 18:18:56 2015 -0700 Merge branch 'master' into pgas Conflicts: Src/C_BaseLib/BoxLib.cpp commit 5e5409faedac02787bcaabde9d4b3936e135260e Author: Weiqun Zhang Date: Mon Aug 3 18:11:15 2015 -0700 Set HOST in Fortran BoxLib's make system if it is not defined. Tools/F_mk/GMakedefs.mak commit 36c11c69562c23a16bdc3e8f11213bbffae4ede5 Author: Yili Zheng Date: Mon Aug 3 13:02:49 2015 -0700 Add the first UPC++ version Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 976abbd5c3cabc93ec3b235962a9c07fd5d4c009 Author: Weiqun Zhang Date: Mon Aug 3 11:18:34 2015 -0700 update url in users's guide and test mailing list Docs/Introduction/Introduction.tex commit c0ee6417a6c8d1c1ee909bbbae66793431b5e139 Author: Weiqun Zhang Date: Fri Jul 31 15:21:10 2015 -0700 made 1d gsrb truly rb Src/LinearSolvers/F_MG/cc_smoothers.f90 commit b1979641e3bf4d7a7c1401f88bb73171310b1935 Merge: 5e8cc7a28 51b026562 Author: Marc Day Date: Fri Jul 31 12:26:02 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 5e8cc7a28320186c7244a8b46b420aed590baa78 Author: Marc Day Date: Fri Jul 31 12:24:57 2015 -0700 Update release tag ID Tools/CMake/BoxLib_Version.cmake commit 51b02656299912ff397abc6113d5129945f888a6 Author: Weiqun Zhang Date: Fri Jul 31 11:06:39 2015 -0700 mfiter: fixed a special case in which there is no local boxes at all Src/F_BaseLib/layout.f90 commit 4cdc323aaa455ffeb2dc47138c4b14c5bdc72c40 Author: Michael Zingale Date: Fri Jul 31 13:17:12 2015 -0400 sometimes if there is a crash before output, then our check on the number of levels fails and we get a wordy error message in the overview table. Now we check if the result is an integer to prevent this Tools/RegressionTesting/testnew.py commit 26696ce0bd92af118484e3ed99dd603d24d019a2 Author: Michael Zingale Date: Fri Jul 31 13:01:09 2015 -0400 fix the storing of the diffDir if it paradoxically is a file Tools/RegressionTesting/testnew.py commit 25eef79fa6c133d5eefb65733326b127f986a86b Author: Michael Zingale Date: Fri Jul 31 10:50:30 2015 -0400 fix the --complete_report_from_crash functionality Tools/RegressionTesting/testnew.py commit 2f29d89ccbaeba92967b558b13b81f9d3933774b Author: Marc Day Date: Thu Jul 30 13:13:22 2015 -0700 If the domain at level i is not divisible by blocking_factor[i], a regrid could generate new fine grids outside the allowable domain. Rather than enforcing the restriction on bf, we intersect the resulting grids with the domain and warn the user that the new grids do not satisfy the specified bf. Src/C_AMRLib/Amr.cpp commit 712152814163e579169a0839d14106facb6ed2a8 Author: Marc Day Date: Wed Jul 29 18:13:37 2015 -0700 Increment index of blocking_factor array used to build bf_lev in grid_places so that grids at level i have blocking factor i when all is said and done Src/C_AMRLib/Amr.cpp commit 4824384033d70b474510fa67ba46374535ad8b9c Author: Weiqun Zhang Date: Wed Jul 29 14:31:54 2015 -0700 touch the memory pool in mempool_init() Src/C_BaseLib/MemPool.cpp commit c7539972a3a61bed1664603fdcf22655d49dcd44 Author: Weiqun Zhang Date: Tue Jul 28 18:07:46 2015 -0700 always pre-allocate some memory in memory pool when boxlib is initialized Src/C_BaseLib/MemPool.H Src/C_BaseLib/MemPool.cpp Src/F_BaseLib/boxlib_f.f90 commit 70aebcb5054bb0ca2e4c08cb811cdfa74f9cf026 Author: Brian Friesen Date: Tue Jul 28 16:21:31 2015 -0700 MultiFab, Geometry: add #ifdefs so that sidecar functions won't compile without MPI The whole notion of sidecars and in-transit processes is ill-defined without MPI, so make the compiler skip them altogether if we're not using MPI. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit a45adf905e8f68eb173e4ea400413cd17cdab4cc Author: Weiqun Zhang Date: Tue Jul 28 16:57:09 2015 -0700 fixed 2D tilearray_build Src/F_BaseLib/layout.f90 commit 816cced9cbafd5ed1fdf76edc116b7a7e4d1638e Author: Weiqun Zhang Date: Tue Jul 28 16:29:35 2015 -0700 PGI: link to cpplib Tools/F_mk/comps/Linux_pgi.mak commit fc578d5d45ecaf0bfe2e5abd7448a01b94a105bc Merge: 382b7ad75 f42c1c77e Author: Weiqun Zhang Date: Tue Jul 28 15:32:31 2015 -0700 Merge branch 'mempool' of gamera.lbl.gov:/usr/local/gitroot/BoxLib into mempool commit 382b7ad751b2af60f6760d715fc421cc31dd9b61 Merge: edde99b79 e804efc82 Author: Weiqun Zhang Date: Tue Jul 28 15:32:07 2015 -0700 Merge branch 'master' into mempool Conflicts: Src/F_BaseLib/multifab_f.f90 commit f42c1c77ec298b9f4a3c878e189b432a4a47043e Merge: 25a3ca1e1 edde99b79 Author: Weiqun Zhang Date: Tue Jul 28 15:29:57 2015 -0700 Merge branch 'mempool' of gamera:/usr/local/gitroot/BoxLib into mempool commit edde99b79fc6a012081d98f63da261ac528ec411 Author: Weiqun Zhang Date: Tue Jul 28 13:26:36 2015 -0700 added CXX and CXXFLAGS to some make files Tools/C_mk/Make.defs Tools/F_mk/comps/Darwin_ibm.mak Tools/F_mk/comps/Darwin_intel.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_lahey.mak Tools/F_mk/comps/Linux_nag.mak Tools/F_mk/comps/Linux_pathscale.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/Linux_sunstudio.mak Tools/F_mk/comps/g95.mak Tools/F_mk/comps/xlf.mak commit bee5e8a258a57a6340619ad4aca2d0af22e51d2d Author: Weiqun Zhang Date: Tue Jul 28 11:31:27 2015 -0700 cleanup Make Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_catamount.mak Tools/F_mk/comps/Linux_xt4.mak Tools/F_mk/comps/crayx1.mak Tools/F_mk/comps/irix64.mak commit 2bd2cda64dbbccbfc17b79ec3f86e8a622863818 Author: Weiqun Zhang Date: Tue Jul 28 11:03:23 2015 -0700 removed some retired systems and added CXX to some systems Tools/F_mk/GMakeMPI.mak commit 25a3ca1e153901d0ba92205c2ed207c06b3ce337 Merge: 8ee18bbf7 e804efc82 Author: Weiqun Zhang Date: Mon Jul 27 17:06:58 2015 -0700 Merge branch 'master' into mempool Conflicts: Src/F_BaseLib/multifab_f.f90 commit 8ee18bbf7201e762a190953b7d66a4539b49cabc Author: Weiqun Zhang Date: Mon Jul 27 16:42:39 2015 -0700 include C_BaseLib whenever F_BaseLib is included Src/F_BaseLib/GPackage.mak Tutorials/Tiling_Heat_F/GNUmakefile commit e804efc820af5daa83e7fb970d0f3031ae8178b4 Author: Weiqun Zhang Date: Mon Jul 27 16:36:24 2015 -0700 ability to handle restarting from and old checkpoint that does have the same number of states Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit b91e52e6640022b04eba3dd89f4d2f876a7e0bcc Merge: 31b89d835 0f63e3608 Author: Brian Friesen Date: Mon Jul 27 13:11:40 2015 -0700 Merge branch 'sidecar' This series of commits expands Vince's original stubs for in-situ performance monitoring framework. It introduces the notion of "sidecars", which are a set of MPI processes in a second, non-overlapping MPI group. They do not perform the "main" grunt work of the application -- this is undertaken by the "Compute" MPI group -- but rather can perform auxiliary tasks such as in-situ post-processing of MultiFab data, dynamic optimization and regridding strategies, etc. One annoying feature of this implementation is that the number of sidecars must be specified at compile time, not run time. This is because of the complicated initialization procedures in BoxLib and ParallelDescriptor which prevent the use of a ParmParse before MPI initialization has completed. This should definitely be fixed in the future if the sidecars become a popular tool. commit 0f63e3608ea96aef45c1529d427aa2d6de4a66e7 Author: Brian Friesen Date: Fri Jul 24 15:31:47 2015 -0700 Tutorials: added example "Sidecar_EX1" to show how to send data to "sidecar" MPI group Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/Make.package Tutorials/Sidecar_EX1/inputs_3d Tutorials/Sidecar_EX1/run.sh commit 708feb26be031e7d675c28b1f9aaafc589eea970 Author: Brian Friesen Date: Fri Jul 24 15:16:17 2015 -0700 Geometry: add static function SendGeometryToSidecars() This clones a Geometry from the compute MPI group onto the "sidecar" MPI group. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 7cdf868c82e84f6e39f525de8e33370ee5552665 Author: Brian Friesen Date: Fri Jul 24 15:15:15 2015 -0700 MultiFab: add static function SendMultiFabToSidecars() This clones a MultiFab from the compute MPI group onto the "sidecar" MPI group. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 93a366321f6bdac21163667b7c5727f664f8a4f4 Author: Brian Friesen Date: Fri Jul 24 15:39:25 2015 -0700 ParallelDescriptor: add static function InCompGroup() This function is analogous to InSidecarGroup(). Src/C_BaseLib/ParallelDescriptor.H commit f530c49466373c20d4d39cb98b61ac4471a25bd5 Author: Brian Friesen Date: Tue Jul 21 13:45:12 2015 -0700 ParallelDescriptor:: remove some roll-call print statements Src/C_BaseLib/ParallelDescriptor.cpp commit e2187c9c47fd3650aeb301d7ae47857ce76efc4d Author: Brian Friesen Date: Fri Jul 24 15:29:55 2015 -0700 ParallelDescriptor: Communicator(), MyProc(), and NProcs() return values in the "local" communicator A large number of funtions assume the existence of only a single, global communicator, even though they operate on local objects. This approach worked fine until we introduced the notion of distinct MPI groups for computation and in-transit analysis. These MPI functions frequently break when operating on the in-transit processes because they request the computation communicator, which is undefined on those processes. Rather than introducing a million if-else's to all these functions, forcing them to explicitly return CommunicatorComp() or CommunicatorInTransit(), we just let Communicator() pick the correct communicator automatically. Src/C_BaseLib/ParallelDescriptor.H commit 5c3ff4fe589c5a21ba4fa4f5701a92eb6bf0156a Author: Brian Friesen Date: Fri Jul 24 15:12:55 2015 -0700 ParallelDescriptor:: rename "perfmon" -> "sidecar" Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 362bf9bdd2a43ddcfa3ca896bd7e55a03d6c598a Author: Brian Friesen Date: Tue Jul 21 13:37:10 2015 -0700 BLProfiler: remove perfmon stubs Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.cpp commit 31b89d83528e0cbe6878d174146c92a4ac277244 Author: Michael Zingale Date: Mon Jul 27 10:07:54 2015 -0400 remove the old compareToolDir -- it is now part of BoxLib Tools/RegressionTesting/Maestro-tests.ini commit bf5aef306e5e9370f3533b0eaaa8d1fc1af7e72f Author: Michael Zingale Date: Sat Jul 25 21:59:57 2015 -0400 add e-mail to the maestro-development group upon failure Tools/RegressionTesting/Maestro-tests.ini commit 3c6888bb4b550dd113591d7b577a73bffc7f4286 Merge: c7ba23a7d 9cacd2b87 Author: Andy Nonaka Date: Fri Jul 24 12:59:08 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c7ba23a7ddd8ae2cf917aac82e374a58985a5c2e Author: Andy Nonaka Date: Fri Jul 24 12:54:39 2015 -0700 created a fortran get_allnodaltilebox for nodal-in-all-dimensions boxes Src/F_BaseLib/multifab_f.f90 commit 6922bbbb9b4967ea97e932e47efcc7dcc2f7ce07 Author: Weiqun Zhang Date: Wed Jul 22 17:07:14 2015 -0700 minor tweaks Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/multifab_f.f90 Tools/F_mk/comps/Linux_intel.mak commit abe0a20dddfb7cd0a915661eae34d7a535ad3a68 Author: Weiqun Zhang Date: Wed Jul 22 15:04:30 2015 -0700 added CXXFLAGS for Intel in Fortran makefile Tools/F_mk/comps/Linux_intel.mak commit 5e629d517b209217c24869a0e7215618cd988f83 Author: Weiqun Zhang Date: Wed Jul 22 14:59:05 2015 -0700 each thread must destroy its own memory Src/F_BaseLib/layout.f90 commit 0207cc9d70a7adbd74adeb545966f668a98535d0 Author: Weiqun Zhang Date: Wed Jul 22 14:06:25 2015 -0700 new makefile for Fortran Src/C_BaseLib/GPackage.mak commit 3b47b226b7feb035535e31c50dd6fc5428f2b264 Author: Weiqun Zhang Date: Wed Jul 22 14:00:37 2015 -0700 started a branch that can use memory pool in Fortran BoxLib codes Src/C_BaseLib/BLassert.H Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/mempool_f.f90 Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_mk/comps/gfortran.mak Tutorials/Tiling_Heat_F/GNUmakefile commit 9cacd2b872fa4a1090a3712677123a85d32361d9 Author: Weiqun Zhang Date: Tue Jul 21 23:30:54 2015 -0700 Fortran mfiter: only let master do memory allocation and deallocation Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 3cdc26f3fc6abf2f982d217f0efd2642f431a2a4 Author: Weiqun Zhang Date: Tue Jul 21 17:27:42 2015 -0700 Fortran mfiter: save tilearray in layout Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 28c9cf564a3ac570b93ed218e5f4894c9da2df8f Author: Weiqun Zhang Date: Tue Jul 21 12:24:12 2015 -0700 Fortran mfiter: fixed a bug in tilearray checking and return the head if a tilearray is found. Src/F_BaseLib/layout.f90 commit 10a09b8580dfecb8e1d2aa86343ba85b702b95dd Author: Weiqun Zhang Date: Tue Jul 21 09:50:56 2015 -0700 rewrote Fortran mfiter; hopefully it's faster with multiple threads Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 43c635035b8c1ff42db3a1192e7f43909bd586d7 Author: Weiqun Zhang Date: Mon Jul 20 20:53:32 2015 -0700 identation Src/C_BaseLib/FabArray.cpp commit 33404a026ca7592ffbb04598391ac364b855f9f8 Author: Marc Day Date: Mon Jul 20 18:51:55 2015 -0700 Move .H and .cpp listings in the CMakelists.txt in C_Baselib Src/C_BaseLib/CMakeLists.txt commit cf128bb98f02aca46ebfa4ae746667a1cf6b8c2a Merge: 2536a2ac2 10b25a707 Author: Marc Day Date: Mon Jul 20 18:49:52 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 50205de555dc5bea99fe144dcb65a89643abc143 Author: vince Date: Mon Jul 20 16:45:19 2015 -0700 swap pair test. Src/C_AMRLib/Amr.cpp commit 10b25a7078f20f5649b6b52cf2ab5308cf2c3442 Author: Jessica Kawana Date: Mon Jul 20 16:19:04 2015 -0700 Included timing files and run script Tutorials/Tiling_Heat_F/results/babbage_omp.run Tutorials/Tiling_Heat_F/results/results.txt Tutorials/Tiling_Heat_F/results/t1a.txt Tutorials/Tiling_Heat_F/results/t1b.txt Tutorials/Tiling_Heat_F/results/t2a.txt Tutorials/Tiling_Heat_F/results/t2b.txt Tutorials/Tiling_Heat_F/results/t3a.txt Tutorials/Tiling_Heat_F/results/t3b.txt Tutorials/Tiling_Heat_F/results/t4a.txt Tutorials/Tiling_Heat_F/results/t4b.txt Tutorials/Tiling_Heat_F/results/t5a.txt Tutorials/Tiling_Heat_F/results/t5b.txt Tutorials/Tiling_Heat_F/results/t6a.txt Tutorials/Tiling_Heat_F/results/t6b.txt Tutorials/Tiling_Heat_F/results/t7a.txt Tutorials/Tiling_Heat_F/results/t7b.txt commit 7001eeb557fdda3ee37bf384c83f4e10ccb268da Author: Jessica Kawana Date: Mon Jul 20 16:09:21 2015 -0700 Changed configuration to match tests on Babbage, includes some results Tutorials/Tiling_Heat_F/advance.f90 Tutorials/Tiling_Heat_F/inputs_3d Tutorials/Tiling_Heat_F/results.txt commit 95de324e255b809a94ae466a7d1da4aa8b290653 Author: Jessica Kawana Date: Mon Jul 20 13:18:05 2015 -0700 Added timer Tutorials/Tiling_Heat_F/advance.f90 commit 0bf633f84bb93fb1ee671987ba49557019268a89 Merge: f3fc9318a 7761f0e4a Author: vince Date: Mon Jul 20 12:09:59 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7761f0e4a37b0d8c1f44766af257eb1548a402ed Author: Weiqun Zhang Date: Mon Jul 20 10:54:53 2015 -0700 fixed uninitialized values to quiet valgrind; added some comments Src/F_BaseLib/layout.f90 commit e4b1a441d37f18add4b4dd0a88248a9e98b1016b Author: Andy Nonaka Date: Mon Jul 20 10:51:00 2015 -0700 end if -> endif Tools/F_mk/GMakedefs.mak commit 7aef0b5d8ccca54cfb091e0f37813d8d3c3d1327 Author: Andy Nonaka Date: Mon Jul 20 10:48:39 2015 -0700 if compiled with MIC=t, add .mic to executable Tools/F_mk/GMakedefs.mak commit f3fc9318a6d4fe98268742388a60c9eed3610aeb Merge: 5f45ec05c 223afd83a Author: vince Date: Mon Jul 20 10:45:49 2015 -0700 merge conflict. commit 223afd83a2a0ed1fd5b4c260a3699e856ce46ed5 Author: Weiqun Zhang Date: Mon Jul 20 10:26:21 2015 -0700 fixed a new bug in FabSet: wrong source index Src/C_BoundaryLib/FabSet.cpp commit 8424a15cbd152cb5c4cf31d1cfbd44a8cafef523 Author: Weiqun Zhang Date: Mon Jul 20 06:56:16 2015 -0700 fixed another new bug in parallel copy Src/C_BaseLib/FabArray.H commit 883c4d5171e20a6a5fbdfb2aad86861a7d80d9fc Merge: 0194fdd4d bef075c62 Author: Weiqun Zhang Date: Mon Jul 20 06:16:52 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0194fdd4d6d7b56c5b558171686610d66826307a Author: Weiqun Zhang Date: Mon Jul 20 06:16:42 2015 -0700 fixed a new bug in parallel copy: shouldn't set n_grow twice Src/C_BaseLib/FabArray.H commit bef075c62034958a04f4682e34c868ec24235fc2 Author: Brian Friesen Date: Sun Jul 19 17:48:36 2015 -0700 Make: updated Babbage detection to work on any of the login nodes when selecting compiler flags in F_mk Tools/F_mk/comps/Linux_intel.mak commit cb8b11f15fda04fc7b0e4152789ca339ea9adc30 Author: Brian Friesen Date: Mon Jun 29 14:06:51 2015 -0700 Make: added Makefile variable "ITAC_TRACE" to define compiler flags and libs used with Intel Trace Analyzer and Collector Tools/C_mk/Make.Linux commit 9e38bee0c40b86cfcc2cf59cc2c646aa9d73d6e4 Author: Brian Friesen Date: Mon Jun 29 13:51:10 2015 -0700 Make: added "-xHost" flag to Intel compiler when compiling for Edison or the Xeon host on Babbage This flag generates the highest available instruction set on the native architecture. Without it, the compiler defaults to SSE2, while many newer instruction sets exist, including AVX, AVX2, SSE3, and SSE4.1/4.2. However, when compiling code for the MIC we can't use "-xHost" or any other instruction set request flag, hence all the logic around Babbage in this commit. Tools/C_mk/Make.defs Tools/F_mk/comps/Linux_intel.mak commit cd32992bbf19839acc67ec1e2c7d5b4e23647ee7 Author: Brian Friesen Date: Mon Jun 29 13:56:04 2015 -0700 Make: added Makefile variable "MIC" for compiling native code for Intel MIC This adds the "-mmic" flag to the Intel compiler if the MIC variable is defined. Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_intel.mak commit 36e8f785e1d54a22ba41bccf90d9610a5f05d93f Author: Brian Friesen Date: Tue Jun 9 12:20:25 2015 -0700 Make: use MPI compiler wrappers on orga No need to specify include/library directories by hand. Let the wrappers do all the work. Tools/C_mk/Make.mpi commit 56cec70ec483f75a24d30b1edc099709eb5dc41f Author: Weiqun Zhang Date: Sun Jul 19 10:52:10 2015 -0700 Option to call dimension agnostic Fortran subroutines in deriving. Note that it is OK to mix the two types Fortran functions in the derive list. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_BaseLib/ArrayLim.H commit 1193f2069cc2bdda71cf0974c3076226e436ee6e Merge: 1c9af9c57 c66c00fc4 Author: Weiqun Zhang Date: Sun Jul 19 06:55:19 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c66c00fc461b2cb020d2db310bc10b215a01a436 Author: Jessica Kawana Date: Fri Jul 17 17:21:59 2015 -0700 Swaps pointers between phi_old and phi_new instead of using actual multifab_copy to avoid allocating and de-allocating data. Tutorials/Tiling_Heat_F/advance.f90 commit f8139c4e886804db5c22380a04f5625d32693813 Author: Jessica Kawana Date: Fri Jul 17 16:59:06 2015 -0700 Combined compute_flux and update_phi subroutines into advance_phi. Tutorials/Tiling_Heat_F/advance.f90 Tutorials/Tiling_Heat_F/main.f90 commit 1c9af9c578cf1384def1e40a6a81a56a4991e3ac Author: Weiqun Zhang Date: Fri Jul 17 15:37:55 2015 -0700 Parallel copy can now include ghost cells for both source and destination. Note that it will not handle periodic boundary properly if the desitnation box includes ghost cells because MultiFab does not even know about periodicity. Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/FabSet.cpp commit 0b4d7bb4c8c13558a21fa170726b7d5fc0da6386 Author: Weiqun Zhang Date: Fri Jul 17 14:50:11 2015 -0700 comment Src/C_BaseLib/MultiFab.H commit 4364fe05ec8b0c517ddafc095a03132c980226f6 Merge: df2e4ff77 2071e53e1 Author: Jessica Kawana Date: Fri Jul 17 13:08:16 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit df2e4ff776c5075cd1cdf5c73a3427c59245b4fe Author: Jessica Kawana Date: Fri Jul 17 13:07:30 2015 -0700 Starting off Tiling_Heat_F as a copy of HeatEquation_EX1_F Tutorials/Tiling_Heat_F/GNUmakefile Tutorials/Tiling_Heat_F/GPackage.mak Tutorials/Tiling_Heat_F/advance.f90 Tutorials/Tiling_Heat_F/init_phi.f90 Tutorials/Tiling_Heat_F/inputs_2d Tutorials/Tiling_Heat_F/inputs_3d Tutorials/Tiling_Heat_F/main.f90 Tutorials/Tiling_Heat_F/write_plotfile.f90 commit a4811dca751ebfefd5faa287f79c9477c2da990c Author: Weiqun Zhang Date: Thu Jul 16 21:37:42 2015 -0700 added optional argument for number of ghost cells in parallel copy; this relieve the user's burden and avoids creating a temporary mulitfab. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BoundaryLib/FabSet.cpp commit 2071e53e18da05f994fccb09eeeb035d5d4844cd Author: Weiqun Zhang Date: Thu Jul 16 20:49:59 2015 -0700 added a new macro BL_TO_FORTRAN_N_3D provide by Max K. and moved ZFILL to ArrayLim.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BLFort.H commit 15db178dd4572e5f9679494f647b07d5117f1d86 Author: Weiqun Zhang Date: Thu Jul 16 15:34:44 2015 -0700 fixed a new bug Src/C_BaseLib/FabArray.cpp commit e72c670eb8fc70801df2a6dc94961ef1e0f6bf8a Author: Weiqun Zhang Date: Thu Jul 16 15:11:04 2015 -0700 FillPatchIterator now interally has a normal MulitFab with non-overlapping grids Src/C_AMRLib/AmrLevel.cpp commit 23076025dbca3c4fe1fd7f1cb5ad39db4b82ddc6 Author: Weiqun Zhang Date: Thu Jul 16 14:52:29 2015 -0700 allow MultiFab change n_grow without changing the data; this is useful for avoiding too local MultiFab to MultiFab copies in parallel copy, which only copies from valid to valid regions; Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b8094d0e05c72d57db3fb5668e9b6848f2d5112a Author: Weiqun Zhang Date: Thu Jul 16 14:14:20 2015 -0700 Fortran mfiter: added get_grownnodaltilebox Src/F_BaseLib/multifab_f.f90 commit 5a8d872e57e12b2a4b6e503a826cba4e55acfd43 Author: Weiqun Zhang Date: Thu Jul 16 13:33:43 2015 -0700 don't think boxarray in FabArray needs to be mutable Src/C_BaseLib/FabArray.H commit 5f45ec05c9a68971aa6ecd59f8816bd697dc35f0 Author: vince Date: Thu Jul 16 13:06:59 2015 -0700 more random cluster tests. Src/C_BaseLib/DistributionMapping.cpp commit 470c103a0cd424422161820871ba73f3db486938 Author: vince Date: Thu Jul 16 12:23:49 2015 -0700 random cluster distribution test. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit d57c8abcf7178f280900c331580bd1c900734b27 Author: Weiqun Zhang Date: Thu Jul 16 10:47:27 2015 -0700 added a new macro ZFILL that in 1D and 2D take a real array like dx, make it three elements long, and fill the new elements with zero; it won't do anything in 3D Src/C_BaseLib/BLFort.H commit 5ace37d5d9f176c8417e319a484d8cc1eccd9c5d Author: Weiqun Zhang Date: Wed Jul 15 20:47:12 2015 -0700 MemPool: tidy Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/MemPool.H Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/mempool_f.f90 commit cf89d0cc6591de2d235f7228ae14898be4f764d5 Author: Weiqun Zhang Date: Wed Jul 15 17:36:40 2015 -0700 revert my accident commit Tutorials/Tiling_Heat_C/advance_3d.f90 Tutorials/Tiling_Heat_C/init_phi_3d.f90 commit b2155f78ddbad46ecdb03f21aaa23256f3ad7737 Author: Weiqun Zhang Date: Wed Jul 15 17:21:27 2015 -0700 modified some macros to pass 3d integer index arrays right-filled with zeros in cased of 1d or 2d Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BLFort.H commit 93efab8f8b597bbe2d8a8067fe8154d532e602ee Author: Weiqun Zhang Date: Wed Jul 15 16:07:46 2015 -0700 Max's change that increases the optimization level of Cray compiler Tools/C_mk/Make.Linux Tutorials/Tiling_Heat_C/advance_3d.f90 Tutorials/Tiling_Heat_C/init_phi_3d.f90 commit a26bcb6ac760e4e6ae83830c2cecea986f132df6 Author: Marc Day Date: Wed Jul 15 13:57:07 2015 -0700 Add kumonga to make system Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 13b54e1b53dff612bd4590a4d2c8c87c1ca3495b Author: vince Date: Tue Jul 14 15:03:13 2015 -0700 staggered cluster test. Src/C_BaseLib/DistributionMapping.cpp commit 96e63113c795faec71f1ceb728caa9b64fad5123 Author: Andy Nonaka Date: Tue Jul 14 10:20:33 2015 -0700 initialize the timers Tutorials/HeatEquation_EX1_F/main.f90 commit c17d858699c6135dea523326b585623cd020722e Author: Andy Nonaka Date: Tue Jul 14 09:44:29 2015 -0700 add some timers Tutorials/HeatEquation_EX1_F/advance.f90 commit d3f900316567ccc65438e062c5a0a1150c919e8a Author: vince Date: Mon Jul 13 16:56:22 2015 -0700 more staggered grids. Src/C_BaseLib/DistributionMapping.cpp commit b50973ff688de92f4d03deb33546c78b5f8a6581 Author: vince Date: Mon Jul 13 16:52:36 2015 -0700 more staggered grids. Src/C_BaseLib/DistributionMapping.cpp commit 9d41bd7eadfec962d2749c8581ad8b5e526ebd8f Author: Weiqun Zhang Date: Mon Jul 13 16:27:28 2015 -0700 revert 'always use cray wrappers' because it causes problems for vtune Tools/C_mk/Make.Linux commit 5596501d7e3267a3376bb0e38922a2691846d36a Author: vince Date: Mon Jul 13 13:52:52 2015 -0700 added stagger option for mlpfc. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit c442c6b4a051f5e5f946a910c143db9c355804a2 Author: Weiqun Zhang Date: Sun Jul 12 22:27:05 2015 -0700 allow Intel compiler more memory and time Tools/C_mk/Make.defs commit a9ec1a9382dd53205f6b875aa112c3fe888a82f4 Author: Weiqun Zhang Date: Sun Jul 12 22:23:26 2015 -0700 always use cray wrappers Tools/C_mk/Make.Linux commit 388df1111bb96f8a59d0b2f6ae33cae361830d7c Merge: 1c037ec09 0daf98b14 Author: Weiqun Zhang Date: Sun Jul 12 22:22:09 2015 -0700 Merge branch 'mempool' commit 0daf98b14b2277b8b78e71f8ff5acb4aa1aa0150 Author: Weiqun Zhang Date: Sun Jul 12 20:33:15 2015 -0700 implemented a thread friendly memory pool that can be used in both C++ and Fortran to increase the speed of allocating and deallocating arrays inside OMP. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/MemPool.H Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/mempool_f.f90 commit 1c037ec099ea278fad0f1c7dbdbe9d8b0a8b2997 Author: Andy Nonaka Date: Thu Jul 9 08:57:42 2015 -0700 works on any babbage login node now Tools/F_mk/GMakeMPI.mak commit 83b7805f116931bb41548055393bae674420c335 Author: vince Date: Tue Jul 7 15:15:11 2015 -0700 some cleanup. Src/C_BaseLib/FabArray.H commit 993cd56b9c1c0a7a72f541c0dc3c44ee7be3e541 Author: vince Date: Tue Jul 7 13:46:00 2015 -0700 more multilevel distribution maps for moveallfabs. we now have full control. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit 0a9c9404d29b265f5197f4780a8e261778875e13 Author: Weiqun Zhang Date: Tue Jul 7 12:50:02 2015 -0700 starting a new branch for PGAS and split FillBoundary into two functions Src/C_BaseLib/FabArray.H Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PGAS_HEAT/Make.package Tutorials/PGAS_HEAT/advance_3d.f90 Tutorials/PGAS_HEAT/init_phi_3d.f90 Tutorials/PGAS_HEAT/inputs_3d Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.H Tutorials/PGAS_HEAT/writePlotFile.cpp commit 705e5e5f9af762379444b8855a35facb3ade7c49 Author: Michael Zingale Date: Tue Jun 30 12:56:15 2015 -0400 remove debugging prints Tools/RegressionTesting/testnew.py commit 0e150b11fdbb74b9a8541a3e165ef6fc9bb4e943 Author: Michael Zingale Date: Tue Jun 30 12:55:27 2015 -0400 catch AttributeError for the compilation failure too Tools/RegressionTesting/testnew.py commit 3cf40930565d2945445f0ecb5b6c66607149e75f Merge: bc11c7f0d 0e91fb26f Author: Adam Jacobs Date: Tue Jun 23 15:21:52 2015 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit bc11c7f0d3b4faa11580789139c3b1b8dbea6fc5 Author: Adam Jacobs Date: Tue Jun 23 15:21:21 2015 -0500 Add OpenMP to sub-chandra postprocessing Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 commit 0e91fb26fcb9989e055a1ce669f5934557d5c06a Author: Jessica Kawana Date: Mon Jun 22 13:30:10 2015 -0700 Changed path Tools/F_mk/GMakeMPI.mak commit afee0b7188c7e21b4908c205be6d8a55cc95aa07 Author: Ann Almgren Date: Thu Jun 18 17:20:18 2015 -0700 Add 3D UniformVelocity test. Tools/RegressionTesting/BoxLib-tests.ini commit 2f68afe8fa9e68a1ecbd6c304fec4d460ab953e3 Merge: 1d14256b9 85cf744c6 Author: Ann Almgren Date: Thu Jun 18 17:19:23 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 1d14256b9524ff3260e735c6616a0f4125a92fdd Author: Ann Almgren Date: Thu Jun 18 17:18:52 2015 -0700 1) Make the blobs less discontinuous so we don't deal with undershoot. 2) Make 3d regression test. Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt.3d commit 85cf744c696639fb5770dff15304ad5307c5c7c8 Merge: d3384e7b0 7faaba1dd Author: Jessica Kawana Date: Thu Jun 18 14:31:16 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d3384e7b0ce3d5fecd0375c52a11129cec747abb Author: Jessica Kawana Date: Thu Jun 18 14:30:43 2015 -0700 Turned off Intel compiler runtime warnings. Tools/F_mk/comps/Linux_intel.mak commit 7faaba1dd8f3b747e48d4ab0aafbb9f870e84fe0 Author: Michael Zingale Date: Thu Jun 18 11:49:37 2015 -0400 fix a bug I recently introduced that makes tests that were not run show up as failures in the suite overview webpage Tools/RegressionTesting/testnew.py commit ad645b062c6e99c559580c2ab31a284fe8d0ac3e Merge: 4575c7bdd c7e07a89f Author: Ann Almgren Date: Tue Jun 16 14:06:06 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 4575c7bddfd3d565da1fac1dbd5bad3059f54471 Author: Ann Almgren Date: Tue Jun 16 14:05:14 2015 -0700 Make the default velocities be completely diagonal. Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90 commit 88fbc7422d7ed0681a8456539e6e14376016e164 Author: Ann Almgren Date: Tue Jun 16 14:04:21 2015 -0700 Change plt file names for 2d vs 3d. Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.3d commit 9a94f3964d5e4822e4bb196e19b81f8a1e770c33 Author: Ann Almgren Date: Tue Jun 16 13:37:18 2015 -0700 Fix bug -- wrong dimensioning of uin in consup. Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 commit 72872c0ed81f1eb87f360e1843f3f65ebec899c5 Author: Ann Almgren Date: Tue Jun 16 13:37:00 2015 -0700 Reformat warning to look more like 2d. Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90 commit f42524199757feaa5151c89d922cafa33f4d7b55 Author: Ann Almgren Date: Tue Jun 16 13:04:14 2015 -0700 Remove print statement Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90 commit 24e1972c4bc6fde3381051259866930a530f9886 Author: Ann Almgren Date: Tue Jun 16 12:56:58 2015 -0700 Fix bug in calling transxy. Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 commit c7e07a89fb488d571d13c2e88193a5c5ae158b2a Author: Weiqun Zhang Date: Tue Jun 16 10:48:46 2015 -0700 SMC miniapp: added collapse to loop-level omp MiniApps/SMC/kernels.f90 Tools/C_mk/Make.defs commit a65d192a633089466d68d2c992ff719c86ccd1a5 Author: Ann Almgren Date: Tue Jun 16 09:55:09 2015 -0700 Fixed misuse of j for k. Tutorials/AMR_Advection_C/Source/Src_3d/React_3d.f90 commit 04d7ee1cde3433b93bb5d47bd8186248a1146890 Author: Jessica Kawana Date: Mon Jun 15 17:10:58 2015 -0700 Fixed various indexing errors. Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90 commit 68a5a4fe0f9debc86af8d3ff3a5ec7783d95eeb9 Merge: 5dea14ee2 b0aee021f Author: vince Date: Mon Jun 15 13:17:36 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5dea14ee213af0701d9211790013aef0b8f124a8 Author: vince Date: Mon Jun 15 11:53:30 2015 -0700 added function to move fabs to a new distribution map for all fabarrays sharing the same distribution map. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp commit 681f7db621b3d35e4cd26131e764b4a91d4f062a Author: vince Date: Wed Jun 10 14:19:19 2015 -0700 added id for distmaps. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit b0aee021fb1c5b8636c9cc4bfea101cc53204a5f Author: Weiqun Zhang Date: Tue Jun 9 13:39:49 2015 -0700 update the comments Tutorials/Tiling_Heat_C/results/run-babbage.sh commit 41c17cfaa199ee144ca269e768e87bb2bba34286 Author: Weiqun Zhang Date: Tue Jun 9 13:27:44 2015 -0700 SMC: extra optimization flags for babbage MiniApps/SMC/GNUmakefile commit ff7b4f7b98b196b806deebe8025b0d0a1b3dc333 Author: Weiqun Zhang Date: Tue Jun 9 13:26:52 2015 -0700 added babbage to make system in Fortran Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_intel.mak commit 66066ded4134afc61ca0070773ddc2193c976062 Author: Weiqun Zhang Date: Tue Jun 9 13:23:48 2015 -0700 fixed a new 2D bug Src/F_BaseLib/list_box.f90 commit 04b8d8ddf6cbdb26152cf52984c9d8c35a258efb Author: Weiqun Zhang Date: Tue Jun 9 13:07:01 2015 -0700 SMC: added thte original loop-level omp for comparison MiniApps/SMC/_parameters MiniApps/SMC/advance.f90 MiniApps/SMC/inputs_SMC MiniApps/SMC/kernels.f90 commit 874cec177b3b9c9ea41cd4ed3122125b1846320e Author: Weiqun Zhang Date: Mon Jun 8 20:59:02 2015 -0700 tiling in fill_boundary Src/F_BaseLib/layout.f90 Src/F_BaseLib/list_box.f90 commit bb45a1318b22a63dd9d6dd84554760a355a9e8c2 Merge: b223fa023 9c2d8b0f7 Author: Michael Zingale Date: Mon Jun 8 13:16:22 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit b223fa023557a42b9c7b5a433f03e1e99eea090e Author: Michael Zingale Date: Mon Jun 8 13:15:15 2015 -0400 if we are using BOXLIB_USE_MPI_WRAPPERS=1, then explicitly add -lmpichf90 to the libraries, some machines seem to need this, and it doesn't seem to mess up the others. Tools/C_mk/Make.mpi commit 9c2d8b0f7d310b1ed6b3e954676f7d6fe157d30f Author: Weiqun Zhang Date: Sun Jun 7 16:33:39 2015 -0700 Fortran mfiter: fix the fix Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 110effc6cdb364001d2203c37929dc083dca6d5e Author: Weiqun Zhang Date: Sun Jun 7 16:25:24 2015 -0700 Fortran mfiter: fixed a bug when grid cannot be split evenly into tiles Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 3ff1f2ac04e16208229f50309b237b9bc040da95 Author: Weiqun Zhang Date: Sun Jun 7 14:36:58 2015 -0700 Fortran mfiter: fixed nodal bug Src/F_BaseLib/multifab_f.f90 commit 8baba9cce6219731fd36029c8ca781f06d38e912 Author: Weiqun Zhang Date: Sun Jun 7 13:57:24 2015 -0700 Fortran mfiter: add a reset subroutine and rename get_tile to more_tile MiniApps/SMC/advance.f90 MiniApps/SMC/init_data.f90 Src/F_BaseLib/multifab_f.f90 commit 2b3a9eb5bfce349acba5a2f207e83caf2917e8c2 Author: Weiqun Zhang Date: Sun Jun 7 10:36:08 2015 -0700 added SMC as a mini app for playing with tiling MiniApps/SMC/GNUmakefile MiniApps/SMC/GPackage.mak MiniApps/SMC/LiDryer.c MiniApps/SMC/_parameters MiniApps/SMC/advance.f90 MiniApps/SMC/chemistry_module.f90 MiniApps/SMC/derivative_stencil.f90 MiniApps/SMC/init_data.f90 MiniApps/SMC/initialize.f90 MiniApps/SMC/inputs_SMC MiniApps/SMC/kernels.f90 MiniApps/SMC/main.f90 MiniApps/SMC/make_plotfile.f90 MiniApps/SMC/probin.template MiniApps/SMC/smc.f90 MiniApps/SMC/smcdata.f90 MiniApps/SMC/time.f90 MiniApps/SMC/transport_properties.f90 MiniApps/SMC/variables.f90 commit d9784556406a03cac4666844acdee422a3050bff Author: Weiqun Zhang Date: Sun Jun 7 10:33:47 2015 -0700 tiling in Fortran multifab copy Src/F_BaseLib/multifab_f.f90 commit cfd100b2e3a63e54b8511d4ebe5c66203112ecd3 Author: Weiqun Zhang Date: Sun Jun 7 10:11:19 2015 -0700 Fortran mifter: fixed a bug and tiled setval Src/F_BaseLib/multifab_f.f90 commit 57665917ca2b01816d899943fb5d2d13c7e495d1 Author: Weiqun Zhang Date: Sun Jun 7 09:33:13 2015 -0700 Fortran mfiter: changed the default to match C++ version Src/F_BaseLib/multifab_f.f90 commit 206be04df693231ea6ffcced6f136738dd911871 Author: Weiqun Zhang Date: Sun Jun 7 07:56:45 2015 -0700 Fortran mfiter: added optional argument, tiling Src/F_BaseLib/multifab_f.f90 commit c0b2ae1001e96cd7a167f1265448b30cefc1b622 Author: Weiqun Zhang Date: Sun Jun 7 07:38:30 2015 -0700 Fortran mfiter: minor renaming Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit c6a51ea197a5fe6f1c579ed663acf97c290b3e89 Author: Weiqun Zhang Date: Sat Jun 6 13:50:00 2015 -0700 Fortran mfiter: can change tile size Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 429c04468d06f4f5c57e247aba95525f15cf7681 Author: Weiqun Zhang Date: Sat Jun 6 10:33:39 2015 -0700 Fortran mfiter: added more functions Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 77d5318304d589adf89ca55120074558d0eb1678 Author: Weiqun Zhang Date: Sat Jun 6 09:41:34 2015 -0700 minor cleanup of mfiter Src/F_BaseLib/multifab_f.f90 commit 3c596615b21b19f01fa0857f09c518cd0ffb3f72 Author: Weiqun Zhang Date: Fri Jun 5 23:24:01 2015 -0700 started working on tiling in Fortran Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 3669e78b7bf6ba4b0e48bf51b8a6f1b93c9dd86f Author: Weiqun Zhang Date: Wed Jun 3 20:15:53 2015 -0700 rename FabArrayBase::fpb_boxarray_max_size to FabArrayBase::comm_tile_size (communication tile size) Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Tutorials/Tiling_Heat_C/inputs_3d commit 942ed06140050cd8eaa26b5e61c102bffbce901f Author: Weiqun Zhang Date: Wed Jun 3 17:40:38 2015 -0700 changed defaults Src/C_BaseLib/FabArray.cpp Tutorials/Tiling_Heat_C/inputs_3d commit 3bb782118f56460d9bd57f773799da2c61124e6a Author: Weiqun Zhang Date: Wed Jun 3 12:11:52 2015 -0700 removed an unnecessary std::max Src/C_BaseLib/BoxList.cpp commit 38233d6f46efb30aa6724446fda1dbcc92f1bf2f Author: Weiqun Zhang Date: Wed Jun 3 11:28:14 2015 -0700 It turns out maxSize is not suitable for chopping a nodal box into small chunks in the recent changes in FabArray because maxSize() returns overlapping nodal boxes. So a new function is added to chop a box into a list of non-overlapping tile boxes. Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 8e121f227ba1fdfc1ec9fff9c174c44f2686485e Author: Weiqun Zhang Date: Tue Jun 2 17:31:09 2015 -0700 no need to build boxarray if it's not used Src/C_BaseLib/FabArray.cpp commit 1a237057789bc03499cc48ecaef5d2aed2db8d49 Author: Michael Zingale Date: Tue Jun 2 20:16:42 2015 -0400 fix a bug with --single_tests pointed out by Ann Tools/RegressionTesting/testnew.py commit b83a93df608b5d95450c6c5e02b1c1a1ab8f6a05 Merge: a06a53d3a 4fb9f9044 Author: Brian Friesen Date: Tue Jun 2 16:13:45 2015 -0700 Merge branch 'fpb_thread_friendly' These commits improve thread efficiency when updating periodic boundary conditions by splitting Boxes which intersect domain edges into BoxArrays of smaller Boxes. Each individual thread then copies data from each smaller Box to the corresponding region elsewhere on the domain, rather than a single thread copying the entire intersecting Box while all the other threads spin idly. Preliminary tests using 120 threads on Babbage at NERSC have indicated a ~20x speedup for the boundary value update step, compared to the same number of threads updating boundary values using the old method. On systems with less concurrency the performance gain from these changes will likely be smaller. commit 4fb9f9044391af2c932f11adbfb89ac0d7d8198a Author: Brian Friesen Date: Wed May 27 11:14:11 2015 -0700 FabArrayBase: split Boxes into BoxArrays in TheFB() for thread friendliness Src/C_BaseLib/FabArray.cpp commit 3c5f2ec2f9685821f3b828da5a7c8a5119d5803d Author: Brian Friesen Date: Wed May 27 11:13:22 2015 -0700 FabArrayBase: split Boxes into BoxArrays in TheCPC() for thread friendliness Src/C_BaseLib/FabArray.cpp commit 4a31da5ad073b5b4e6bc78236e8e970bf75ca9e1 Author: Brian Friesen Date: Wed May 27 10:44:03 2015 -0700 Tiling_Heat_C: added timers to FillPeriodicBoundary() to test threading performance improvement Tutorials/Tiling_Heat_C/main.cpp commit 7babc0e4061e7fbecc21be46f2ce09565d29f6e4 Author: Brian Friesen Date: Tue May 26 14:45:47 2015 -0700 Geometry: changed box boundaries with periodic BCs to box arrays to improve performance with lots of threads Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Tutorials/Tiling_Heat_C/inputs_3d commit a06a53d3a32e1a23d0d1d16668c099c5eb15bfcf Author: Andy Nonaka Date: Mon Jun 1 14:30:36 2015 -0700 remove broken links in doc Docs/GettingStarted/GettingStarted.tex commit 806c0f535c41448281d164f82c4a112138c23739 Merge: d70e110b9 1c01a851c Author: Jessica Kawana Date: Mon Jun 1 14:03:29 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d70e110b9115614615821a86f26d153a2c7709e4 Author: Jessica Kawana Date: Mon Jun 1 14:02:44 2015 -0700 Fixed typos Docs/GettingStarted/GettingStarted.tex commit 1c01a851c2f056dd40a09486402eac817237e055 Author: Weiqun Zhang Date: Mon Jun 1 13:50:26 2015 -0700 added macros for calling dimension agnostic Fortran code Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BLFort.H commit 5ece0aecace987dc44acf5bd64b0a5b0825df23b Merge: e0844ee91 b53e16d91 Author: Jessica Kawana Date: Mon Jun 1 10:12:20 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e0844ee9161a8915f01d01a84a7b165482e00776 Author: Jessica Kawana Date: Mon Jun 1 10:10:55 2015 -0700 fixed a typo Docs/GettingStarted/GettingStarted.tex commit b53e16d9123ab3a18bf38eba8b80dda0baf2606b Author: Ann Almgren Date: Fri May 29 18:29:22 2015 -0700 Further fixes for the 3d version of AMR_Advection_C. Tutorials/AMR_Advection_C/Exec/Make.ADR Tutorials/AMR_Advection_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90 commit 9ea83131067fbdc1564fa2b2347b7a815fed53ee Author: Andy Nonaka Date: Fri May 29 11:49:43 2015 -0700 if plot_int <= 0, don't print any plotfiles Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX5_F/main.f90 commit 2b2822b9a3e14cefe58747a80289657e833d7eae Author: vince Date: Thu May 28 18:28:43 2015 -0700 movegrid tests, random copy from movedgrid mf. Tutorials/MultiFabTests_C/GridMoveTest.cpp commit 22221b3702fe1341f0ac66d11eb0bb3fb7471afd Author: vince Date: Thu May 28 14:10:11 2015 -0700 added function to move fabs in a fabarray given a new processor map. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/GridMoveTest.cpp commit cbb561ddeb71c5adac48baaa2f96d5980e7c9d0d Merge: ec83007f6 86a04a261 Author: Ann Almgren Date: Sun May 24 15:24:54 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ec83007f6230d8ea753584fd1bfbe8cdfd9f9bce Author: Ann Almgren Date: Sun May 24 15:24:36 2015 -0700 More changes for 3d plus cleaning up 2d. Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90 commit 58cda477006d557ce7305d8f3f501e2ca44773af Author: Ann Almgren Date: Sun May 24 15:24:04 2015 -0700 Fixing 3d source files ... Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90 commit a2e3658dfe160ce8602ba7e76fbddb91ed64216d Author: Ann Almgren Date: Fri May 22 18:29:05 2015 -0700 This version compiles in 3d (and fixes a small bug in the transverse stuff in 2d) Tutorials/AMR_Advection_C/README Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/trans_2d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_sums_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Make.package Tutorials/AMR_Advection_C/Source/Src_3d/React_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Tagging_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/bc_fill_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ext_src_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/fill_diff_coeff_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90 commit 86a04a261837641a57fecb333a08b845cd7b0f86 Author: Brian Friesen Date: Fri May 22 17:55:58 2015 -0700 profiling: added Babbage run script for tiled version of heat solver Tutorials/Tiling_Heat_C/results/run-babbage.sh commit 20deeaa2ca49a8cb01ae54e4f22b54537b7ecb34 Author: Weiqun Zhang Date: Fri May 22 16:49:37 2015 -0700 added Intel 15 to make Tools/F_mk/GMakerules.mak Tools/F_mk/comps/Linux_intel.mak commit ecc4865c9b3b1000e2e8877611e7a2482cb22bdb Author: Weiqun Zhang Date: Fri May 22 16:23:21 2015 -0700 crayftn --> ftn, craycc --> cc Tools/C_mk/Make.Linux commit d2a7723fb8e5d49a6a4e6f07aa25c64bd7ef92aa Author: Weiqun Zhang Date: Fri May 22 15:57:50 2015 -0700 checked in job script and timing result Tutorials/Tiling_Heat_C/results/results.org Tutorials/Tiling_Heat_C/results/run-edison.sh commit 957fbef4d043a2452306ea5d0b96c1cbfd4e4695 Author: Weiqun Zhang Date: Fri May 22 15:45:11 2015 -0700 Revert "use allocatable arrays in the non-tiling version so that it does not cause stack overflow" because this made the non-tiling version much slower. This reverts commit 288e893057a10503a5c0ad46a01739cf4d985ef8. Tutorials/Tiling_Heat_C/advance_3d.f90 commit 288e893057a10503a5c0ad46a01739cf4d985ef8 Author: Weiqun Zhang Date: Fri May 22 12:32:33 2015 -0700 use allocatable arrays in the non-tiling version so that it does not cause stack overflow Tutorials/Tiling_Heat_C/advance_3d.f90 commit 379511ed09b59bcdcb11cfc9b1f2fb071c85d0ae Author: Weiqun Zhang Date: Fri May 22 12:31:39 2015 -0700 default USE_MPI to FALSE Tutorials/Tiling_Heat_C/GNUmakefile commit 6447e71eeab9df5fc646c86d252577ec50f38879 Author: Brian Friesen Date: Thu May 21 14:43:05 2015 -0700 make: added support for Babbage, the Intel MIC testbed at NERSC This assumes you will be running natively on the MIC card, not on the Xeon host. NERSC recommends this approach since Cori will have a native MIC architecture with no co-processors. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 771776cf0aaf1bc0c783b38bd11c31a20882f6a6 Author: Weiqun Zhang Date: Thu May 21 14:14:18 2015 -0700 change default compilers to Intel in makefile Tutorials/Tiling_Heat_C/GNUmakefile commit 37cf1209e6b41b86957fdf899ce8d06aaa1663ff Author: Weiqun Zhang Date: Thu May 21 14:00:28 2015 -0700 added nowait for the omp on loops version Tutorials/Tiling_Heat_C/advance_3d.f90 commit e3226f09704255a2a98e504f3cac58ba1d9f9be4 Author: Weiqun Zhang Date: Thu May 21 13:47:48 2015 -0700 a new tutorial code for tiling Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/Tiling_Heat_C/Make.package Tutorials/Tiling_Heat_C/advance_3d.f90 Tutorials/Tiling_Heat_C/init_phi_3d.f90 Tutorials/Tiling_Heat_C/inputs_3d Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.H Tutorials/Tiling_Heat_C/writePlotFile.cpp commit 7f3548be22b6bd94d410eecc36cb920a015b0b43 Merge: fe12ff02a 06bf62978 Author: Weiqun Zhang Date: Tue May 19 17:45:34 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit fe12ff02a30855c01dfe98b8f19a7bed8bbb6572 Author: Weiqun Zhang Date: Tue May 19 17:45:25 2015 -0700 use MultiFab's norm function because it's threaded Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 06bf62978759ea93b656fa60fc99ecb5ff33beee Author: vince Date: Tue May 19 16:21:47 2015 -0700 test performance of mkdir and rename. Tests/MKDir/GNUmakefile Tests/MKDir/MKDir.cpp commit 64c27475843946cc09e535174a195d23085e99c7 Author: vince Date: Tue May 19 16:00:01 2015 -0700 test for random grid copies. Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/Make.package Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit e2505fa979eeb293b15b039a0996fdfb6a0cc65a Merge: f4f152790 1150498b8 Author: vince Date: Tue May 19 15:58:56 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 1150498b8ded461b593cd2e673a062344d1450ff Author: Weiqun Zhang Date: Tue May 19 10:57:15 2015 -0700 added -lmpichf90 to bluewaters. Tools/C_mk/Make.mpi commit 58a6b255dc1a873ec448c9902d927f86abe37e7b Author: Michael Zingale Date: Tue May 19 12:17:03 2015 -0400 more cleaning Tools/RegressionTesting/testnew.py commit 88268d4e4b006c34ec5d27d88cb1b961584312ba Author: Michael Zingale Date: Tue May 19 10:27:24 2015 -0400 return the compilatoin string in the build_f method Tools/RegressionTesting/testnew.py commit d1d21c076d9e5019fe66aad2e90277055f61705c Author: Michael Zingale Date: Mon May 18 22:09:45 2015 -0400 some pyflakes fixes Tools/RegressionTesting/testnew.py commit c33217f3cfb4218574b662417a61ed337afd8dd6 Author: Michael Zingale Date: Mon May 18 22:05:50 2015 -0400 remove the hack we used to encode the extra build directory in the build directory list by instead storing a tuple in the list. Tools/RegressionTesting/testnew.py commit 8c7f84bf70d93bb5ca15be6e41e2d906f2b0e130 Author: Michael Zingale Date: Mon May 18 21:09:15 2015 -0400 rename classes to be more PEP-8-y Tools/RegressionTesting/testnew.py commit 30876874f1808117f0897630b17d016ead83b11b Author: Michael Zingale Date: Mon May 18 21:06:53 2015 -0400 add build_f() and make_realclean() methods to the suiteObj class. Tools/RegressionTesting/testnew.py commit fd2909ce267c095aa163c8041bc639ee8cfbe64d Merge: f4a5d26fe edafbda56 Author: Andy Nonaka Date: Mon May 18 14:52:55 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f4a5d26fe702f875ecf2d4ed20bb2e17f9fef0c1 Author: Andy Nonaka Date: Mon May 18 14:52:02 2015 -0700 print out # of MPI processes and # of threads, even with there is only 1 MPI proc (still useful info for OpenMP on one node) Src/F_BaseLib/boxlib_f.f90 commit edafbda56ca07ab3bd2a500ea8aa02b5bf01a9b4 Author: Weiqun Zhang Date: Mon May 18 13:22:16 2015 -0700 Heat equation: fixed bug Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX5_F/main.f90 commit 435262d80a977cf299d60c036a48688695b19df2 Author: Weiqun Zhang Date: Mon May 18 13:06:00 2015 -0700 fixed heat equation ex5 Tutorials/HeatEquation_EX5_F/main.f90 commit 90390fca7fb8024f7de015957de304af9862d457 Author: Weiqun Zhang Date: Mon May 18 12:55:46 2015 -0700 quiet valgrind Src/F_BaseLib/vector_i.f90 commit 05622bf0e25303f0f2966dc452fca42d6ff38f21 Author: Weiqun Zhang Date: Mon May 18 12:54:56 2015 -0700 comment Tutorials/HeatEquation_EX4_F/main.f90 commit 9fc9f7bf697cfb9e99160889fb36f758d7087c3b Author: Weiqun Zhang Date: Mon May 18 12:32:00 2015 -0700 Fill ghost cells if tagging needs ghost cells Tutorials/HeatEquation_EX4_F/main.f90 commit c441bde6246e18df0f61caae7f93c3aec35863e3 Author: Weiqun Zhang Date: Mon May 18 12:30:23 2015 -0700 fixed number of component. removed duplicated multifab_fill_boundary and physbc calls Src/F_BaseLib/regrid.f90 commit ec6e11039f12c0c355f2e63033d8084656e9bff9 Author: Andy Nonaka Date: Mon May 18 10:17:28 2015 -0700 the 'tagging_needs_ghost_cells' option now has a call to multifab_fill_ghost_cells. fixes some problems where tagging is done with a gradient, but valgrind still complaining so no promises yet... Src/F_BaseLib/regrid.f90 commit f4f152790bf204b62e44103a44d71a7f07b4150f Merge: d7d2ada16 595449168 Author: vince Date: Thu May 14 13:51:57 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2536a2ac21d598a0104c63813abab4c2b2cece86 Author: Marc Day Date: Mon May 11 17:48:01 2015 -0700 Add f90 file pattern to VPATH for f90 files in C_BaseLib. Probably should be a better way to do this... Tools/C_util/AmrDeriveTecplot/GNUmakefile commit 595449168c5c595e83e89e91127636d735e38e9f Author: Michael Zingale Date: Fri May 8 15:03:10 2015 -0400 switch from getopt to argparse -- this is self-documenting and cleaner. Also fix the make_benchmark stuff -- the switch to shutil requires me to remove an existing benchmark before copying in the updated one. Tools/RegressionTesting/testnew.py commit 31511481b2977a0db94430c1a1f57f3ca2de9b3b Author: Michael Zingale Date: Fri May 8 10:44:54 2015 -0400 some more simplifications Tools/RegressionTesting/testnew.py commit e016090b7b7256e6b33c024228471cde51283177 Merge: cbd37a0a6 17987ed45 Author: Michael Zingale Date: Fri May 8 08:44:31 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit cbd37a0a6940ed50eb3e35367c14f6e171dad152 Author: Michael Zingale Date: Fri May 8 08:44:09 2015 -0400 fix num_threads -> numthreads for pure OMP Tools/RegressionTesting/testnew.py commit 17987ed454a053739319019b85a60d1759b0b9d6 Author: Michael Zingale Date: Thu May 7 20:03:30 2015 -0400 fix the hydrostatic_adjust case Tools/RegressionTesting/Castro-SBU-tests.ini commit 309ffb56690707c6e0db9714c90a28c6c881ef72 Merge: 089b96741 e10ddf2c8 Author: Michael Zingale Date: Thu May 7 14:12:13 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 089b96741898724c414a283eb3bdb3ecfbc08bb4 Author: Michael Zingale Date: Thu May 7 14:11:39 2015 -0400 sometimes we might encounter a plotfile with boxes that begin at negative indices -- this handles that now. Src/F_BaseLib/bl_stream.f90 commit e10ddf2c8c271e76a68f11233011c54ecf1e87f8 Author: Michael Zingale Date: Thu May 7 12:50:10 2015 -0400 we were constructing the actual form of the command to run (w/ or w/o MPI/OMP) in 4 separate places. Consolodate that into a function Tools/RegressionTesting/testnew.py commit d7d2ada16256688520a5d40db16b418d00d7fb83 Merge: d1e7d25e1 53328b8b8 Author: vince Date: Wed May 6 17:33:17 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 53328b8b8281e2d33f4dc009ca9ef49fbbc2bc28 Author: Michael Zingale Date: Wed May 6 09:32:54 2015 -0400 update the sub_chandra build location Tools/RegressionTesting/Maestro-tests.ini commit d92a3a3707d27099622da00058cbe486d2db6b67 Author: Michael Zingale Date: Wed May 6 09:18:35 2015 -0400 our check on whether the compilation was successful was not correct Tools/RegressionTesting/testnew.py commit 26f0d0fc268530b6e16e2d03af9eff46dfd67000 Author: Michael Zingale Date: Tue May 5 19:21:23 2015 -0400 more simplification of the run commands Tools/RegressionTesting/testnew.py commit c098a66ac9c1b7bf6a26d6345fa7d4d61dc7a88c Merge: ce5db33bd 115000cbf Author: Michael Zingale Date: Tue May 5 17:19:13 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit ce5db33bd43f5d8c4ddd7ed03493d658744ba0fb Author: Michael Zingale Date: Tue May 5 17:18:53 2015 -0400 remove redundant code Tools/RegressionTesting/testnew.py commit 115000cbf9bd76fa983c61d63e2384d25355854f Author: Weiqun Zhang Date: Tue May 5 13:11:41 2015 -0700 OMP'd GetVolume and GetFaceArea Src/C_BaseLib/COORDSYS_1D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.cpp commit 8f501bbba5336540744e2e92309bd75d0a2fec85 Author: Michael Zingale Date: Tue May 5 15:04:12 2015 -0400 fix typo Tools/RegressionTesting/testnew.py commit 9b57b0bb8290539313a7664cd25564f39c716020 Author: Michael Zingale Date: Tue May 5 14:59:00 2015 -0400 some more cleaning / modernization Tools/RegressionTesting/testnew.py commit cdb61a0ebb09f987dd0bd213c063b34bd22199e5 Author: Michael Zingale Date: Tue May 5 14:13:42 2015 -0400 some more modernization with list comprehensions Tools/RegressionTesting/testnew.py commit bccc00a68fe6de181d422443068e5922af3376e2 Merge: d403ac2f3 471529dfb Author: Michael Zingale Date: Mon May 4 20:43:20 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d403ac2f3da76244fae2c94d681f42b08ae51b1f Author: Michael Zingale Date: Mon May 4 20:43:02 2015 -0400 more systemCall -> run() replacement Tools/RegressionTesting/testnew.py commit 471529dfb2d2f3e854ec0f7d671f6808ecd8010d Author: Marc Day Date: Mon May 4 17:33:52 2015 -0700 Remove underflow protection code in LINCCINTERP. Was using a hardwired number, and overwrote crse data. Bad enough, but then appears to be totally unnecessary anyway. Let me know if this breaks someones code. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 2557e17f7d3f1364a83f3fc392d781959f369bcb Merge: b72267227 215f3bb35 Author: vince Date: Mon May 4 14:58:04 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b7226722728908e721007962d9f63435d4c808d7 Author: vince Date: Mon May 4 14:57:57 2015 -0700 ensure intermediate flushed database is complete. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp commit 098a42e815b24a87570d98031e94eff1e4dd2dce Author: vince Date: Mon May 4 11:34:56 2015 -0700 nostart option for var. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp commit 215f3bb351b65058d6aa4d2b42c043b58cb6c0f7 Author: Andy Nonaka Date: Mon May 4 08:05:47 2015 -0700 f90 mpi on atragon Tools/F_mk/GMakeMPI.mak commit c1a0cc9903f2b93014e50cb6aa3bf857c9bb07ef Author: vince Date: Fri May 1 15:05:34 2015 -0700 removed buf size restriction in Concatenate. Src/C_BaseLib/Utility.cpp commit db2adae4696ef513181bf7f6bb763dbf198d59e3 Merge: 084e0bae8 f11a0b44c Author: Adam Jacobs Date: Fri May 1 15:35:09 2015 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 084e0bae8208bda0fe79601b92944a6c6c1554ed Author: Adam Jacobs Date: Fri May 1 15:34:54 2015 -0500 Enable OpenACC for Cray compiling, remove obsolete target flag Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_cray.mak commit f11a0b44c61473add43f280dc6a0b70705b8fd59 Merge: aab98d928 e7beb6e61 Author: Andy Nonaka Date: Thu Apr 30 15:40:05 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit aab98d928a8a960f17c7f1f3e3a1ce8cfcc85597 Author: Andy Nonaka Date: Thu Apr 30 15:39:47 2015 -0700 mpi on orga Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit d1e7d25e1a87aec8227e85f8d5add71cbdb7ab3a Merge: 57db8fc04 e7beb6e61 Author: vince Date: Thu Apr 30 15:30:54 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e7beb6e611d182a8a3a80b335d5ec03fce999072 Author: vince Date: Thu Apr 30 15:01:13 2015 -0700 another Bcast interface, additions for serial. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 57db8fc04339c9e2109e03de5e09168f6e4576a4 Merge: 3dba3eb25 fe79c41e3 Author: vince Date: Tue Apr 28 16:51:14 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit fe79c41e3bc14c5e966bacb2f01f02e3747ab367 Author: Weiqun Zhang Date: Tue Apr 28 14:42:35 2015 -0700 define BL_ALIGN_BYTE and BL_SIMD_LEN Tools/C_mk/Make.defs commit 9e042cd328388d5ed324cfd430f0b922f09e612e Author: Michael Zingale Date: Tue Apr 28 12:58:29 2015 -0400 some more cleaning -- run() can now optionally output to a file Tools/RegressionTesting/testnew.py commit e861c07f60b63a4020d523ef9356ba37f6bce6d0 Author: Michael Zingale Date: Sun Apr 26 20:48:07 2015 -0400 we no longer need to store stderr separately, since run now pipes stderr into stdout Tools/RegressionTesting/testnew.py commit a10d37b94673eed1aecd120499189cc78f5557ab Author: Michael Zingale Date: Sun Apr 26 20:46:01 2015 -0400 switch all the git stuff to the run() function instead of doing their own subprocess stuff. Tools/RegressionTesting/testnew.py commit a89a72a1276c629baa91bd50fa51a83478a6dc6a Author: Weiqun Zhang Date: Sun Apr 26 11:17:45 2015 -0700 add BL_ALIGN_? to make for array alignment Tools/C_mk/Make.defs commit f609f9b903bfbcc3503fa283ce054c2d7ce766d1 Author: Weiqun Zhang Date: Fri Apr 24 23:07:21 2015 -0700 support F90 that will be preprocessed Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/C_scripts/moddep.pl commit 92eeb8ce8000db3441957fc927df9eae8ea0b2fa Merge: 8b92bf520 d18fb9a05 Author: vince Date: Wed Apr 22 17:21:18 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8b92bf52024f20e961ad9006ad1c4665401a3660 Author: vince Date: Wed Apr 22 17:21:09 2015 -0700 nesting fix. Src/C_BaseLib/BLProfiler.cpp commit d18fb9a0596a42e47c31c74bcc8b065f0710ccc9 Author: Weiqun Zhang Date: Wed Apr 22 16:42:16 2015 -0700 removed -target=linux for hopper Tools/C_mk/Make.Linux commit 16c06a4541d7997430ad0614105115e557569289 Author: Weiqun Zhang Date: Wed Apr 22 16:40:04 2015 -0700 added -lmpichf90 for edison and hopper. may need to do this for some other machines too, especially ones with cray mpich. Tools/C_mk/Make.mpi commit a8c27e19846b6c812a4ce6a7b871d018e380d6a0 Author: Michael Zingale Date: Tue Apr 21 19:21:02 2015 -0400 some more clean-ups Tools/RegressionTesting/testnew.py commit ed67104f24b91d3a0d69a9dcfe8317dc617b1667 Author: Weiqun Zhang Date: Tue Apr 21 15:23:46 2015 -0700 Fixed a problem on Windows. I do not have access to any Windows machines. But I believe the new overloaded functions in parallel module would not compile on Windows because c_long is the same as normal Fortran integer and the overloaded functions inside interface must have different kind. This also means the lastest BoxLib would not compile in the unlikely case that the compiler does not support long integer. Src/F_BaseLib/parallel.f90 commit c91b0127c63838ed0a60c453f5139be23c868993 Author: Weiqun Zhang Date: Tue Apr 21 12:31:47 2015 -0700 Let codes tell BoxLib the boundary functions are thread-safe. By default, BoxLib assumes that EXT_DIR is not thread safe, whereas other types are. Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit c9d7d4ad2020c9ff0a20abf357156122a3a8442c Author: Michael Zingale Date: Tue Apr 21 13:37:08 2015 -0400 more clean-ups -- eliminate some functions/logic in favor of list comprehensions Tools/RegressionTesting/testnew.py commit 8e6a0c52680a9f8c5aa8ebcc750bbec0f942aabf Author: Michael Zingale Date: Tue Apr 21 12:46:05 2015 -0400 some more cleaning -- especially to the restart execution string Tools/RegressionTesting/testnew.py commit e86b6c8e3457fc4ac8dc2423c1b862f7de5cc17d Merge: edff26f6f af317ca82 Author: Michael Zingale Date: Tue Apr 21 12:05:52 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib Conflicts: Tools/RegressionTesting/testnew.py commit edff26f6f2c55895efac96bcf866e96c67d59163 Author: Michael Zingale Date: Tue Apr 21 12:03:00 2015 -0400 more clean-up -- now the run commands are greatly simplified (since aside from the MPI and OMP stuff, the command is the same in all cases). Also fix the single suite run output page (columns were mixed) Tools/RegressionTesting/testnew.py commit af317ca82fbfec9c8bdd668acce866e260266127 Merge: d95f67bed 348fa66ad Author: Weiqun Zhang Date: Mon Apr 20 21:51:32 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d95f67bed6acdb20975eb13d89e56eb73bf3adb9 Author: Weiqun Zhang Date: Mon Apr 20 21:50:04 2015 -0700 Inflow boundary in IAMR and LMC is too complicated to be made thread safe. So an OMP critical region is added for EXT_DIR. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 348fa66ad1c5a46a78f379f664193d8aa7aae83f Author: Michael Zingale Date: Mon Apr 20 20:20:37 2015 -0400 remove some os.system() calls with shutil -- this is safer Tools/RegressionTesting/testnew.py commit 77543ff2d9f631723888f5db1011d35b54f1fd17 Author: Weiqun Zhang Date: Mon Apr 20 16:55:28 2015 -0700 changes OMP approach in FillPatchIterator Src/C_AMRLib/AmrLevel.cpp commit 5a0598f43ee3766001361365a6b06e421636b683 Author: Weiqun Zhang Date: Sun Apr 19 20:36:32 2015 -0700 tidy Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c commit 46f24a16691733507a9f07317bc714003028de75 Author: Weiqun Zhang Date: Sun Apr 19 17:28:48 2015 -0700 change user function in MPI_Op_create from fortran function to subroutine because it has no return value Src/F_BaseLib/parallel.f90 commit 7dcf39b773ecc0b7b085d1ec36052b8d906c0872 Author: Weiqun Zhang Date: Sun Apr 19 15:45:05 2015 -0700 create MPI_SUM, MIN and MAX for c_long in Fortran Src/F_BaseLib/parallel.f90 commit d6a2579c8e23529c0f332217e07f3ba67ab404d8 Author: Michael Zingale Date: Sun Apr 19 18:25:38 2015 -0400 call MPI_Type_create_f90_integer with 'r', not '5' -- fixes typo Src/F_BaseLib/parallel.f90 commit 1530aaf7ff4b5ce9e85389898276d05134847e68 Author: Weiqun Zhang Date: Sun Apr 19 14:28:17 2015 -0700 use (C) long integer for offset and size in fabio so that i can handle large files Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/particles_f.f90 Src/F_BaseLib/plotfile.f90 commit 3a9a99e2aaadf0ee23ab5482e148f978eef59863 Author: Weiqun Zhang Date: Sun Apr 19 14:24:16 2015 -0700 typo in comment Src/F_BaseLib/bl_types.f90 commit e45b9fdbe6ded9f3074205b4aef356a010f65735 Author: Weiqun Zhang Date: Sun Apr 19 14:23:47 2015 -0700 add MPI support for (C) long integer in Fortran Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 3dba3eb253a343cb12ca8b630415a05a6ec4e5d6 Merge: 2f49ffb5d a10baeab5 Author: vince Date: Thu Apr 16 15:21:38 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit a10baeab50a849611081f9bb6127d83bfe1dcbfe Author: Andy Nonaka Date: Thu Apr 16 11:07:17 2015 -0700 fix a print statement Src/F_BaseLib/fab.f90 commit ab03951c126f2439022f0b638b9af300e3f2258d Merge: 70ba120d7 7cb6274cc Author: vince Date: Wed Apr 15 14:42:58 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 70ba120d7a7b630a74f34ce2bf8134c88e5f89b9 Author: vince Date: Wed Apr 15 14:42:48 2015 -0700 more support for amrprof. Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 2f49ffb5dd52bc93532c9fc95f091da40df36472 Merge: 3f7291f49 7cb6274cc Author: vince Date: Wed Apr 15 10:36:00 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 7cb6274cc87771e8d7478ef092841fd6bf259f6f Author: Michael Zingale Date: Wed Apr 15 13:14:09 2015 -0400 if the last plotfile output was plotfile 0, then we give a warning and don't do the comparison. Also output the name of the file we used to compare to in the test output table. Finally, some clean-ups. Tools/RegressionTesting/testnew.py commit c40d4c0cd3f68263eeb5b7d197f5674bee4afef5 Merge: bac731a1f 555b76896 Author: Michael Zingale Date: Tue Apr 14 18:55:31 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 555b768969963710ffbd123b27f7b6f21f5ba830 Author: Michael Zingale Date: Tue Apr 14 18:54:52 2015 -0400 switch fboxinfo over to run() Tools/RegressionTesting/testnew.py commit bac731a1fe4e5dbd51a00de2834ae5bc37c1458e Merge: b5a9bff4d 3d3f2221e Author: Michael Zingale Date: Tue Apr 14 14:10:48 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit b5a9bff4d0116641e929abe120c15dfa0cbb16fc Author: Michael Zingale Date: Tue Apr 14 14:10:38 2015 -0400 some more run() Tools/RegressionTesting/testnew.py commit 3d3f2221e5eb21dec855ae58388bc2b3c6375595 Merge: 8173ca8ca f544ca56c Author: vince Date: Thu Apr 9 15:52:13 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f544ca56c82aa88c9e282741c66b1a5ca13c1150 Author: Weiqun Zhang Date: Wed Apr 8 11:45:56 2015 -0700 clean up Intel's optimization reports Tools/C_mk/Make.rules commit 29c8e84164cacb36ccc78646311023bb655fa1e3 Author: Weiqun Zhang Date: Wed Apr 8 09:31:39 2015 -0700 For Intel on Edison, add vectorization report Tools/C_mk/Make.defs commit 53101cc8b546a10f75664f88be30c83cbd3571ad Author: Weiqun Zhang Date: Tue Apr 7 12:37:35 2015 -0700 save stdout and strerr of make in make.out Tools/RegressionTesting/testnew.py commit 8173ca8cacf3bd5bbe8ac63452058e60ab65cb61 Author: vince Date: Mon Apr 6 14:01:08 2015 -0700 some perfmon cleanup. Src/C_BaseLib/ParallelDescriptor.cpp commit e683857ffb1f214d5da0b608d48e275305a55546 Author: vince Date: Mon Apr 6 13:21:11 2015 -0700 some cleanup for perfmon. Src/C_BaseLib/ParallelDescriptor.cpp commit 178844985c1b743c02a0094753e0677480590ed0 Author: vince Date: Mon Apr 6 13:20:35 2015 -0700 fix for serial. Src/C_BaseLib/ParallelDescriptor.H commit b9b8b1b311f44ea1ddd05853852a1c39cf04ee85 Merge: 4980a2e01 fa615023f Author: Michael Zingale Date: Mon Apr 6 10:25:27 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 4980a2e0168b405010c87ed44632fe846c98cf3d Author: Michael Zingale Date: Mon Apr 6 10:25:06 2015 -0400 update xrb_mixed location and aprox13 test to use MICROPHYSICS_DIR Tools/RegressionTesting/Maestro-tests.ini commit fa615023f0f9e3d0df61d9d3b04eac2d1f10c885 Author: Michael Zingale Date: Mon Apr 6 10:20:29 2015 -0400 take another git hash directory to accomodate MICROPHYSICS_DIR Tools/F_scripts/makebuildinfo.py commit 2414f8c37cb2c6ab42da878650e9b799beed2f4e Author: Michael Zingale Date: Sun Apr 5 20:57:50 2015 -0400 turns out that when we specified an alternate location in the .ini file for a microphysics routine, like: addToCompileString = NETWORK_TOP_DIR='$ASTRODEV_DIR/networks' NETWORK_DIR=aprox13 it was not using the ASTRODEV_DIR that was set via extSrcDir = /home/zingale/gfortran-testing/AstroDev/ extSrcCompString = ASTRODEV_DIR but instead was using whatever the value was through the system. This is because we were using os.system() and bash to do the make. Now we instead switch all of the build stuff from os.system() to subprocess -- this is a lot more flexible. As a result, we now have access to stdout, stderr, and the return value Tools/RegressionTesting/testnew.py commit 2e5bb828ac799d07af82e1d87ea60a0a7a984a74 Author: Weiqun Zhang Date: Sat Apr 4 21:50:31 2015 -0700 Allow check_int and check_per coexist in inputs files (submitted by Max Katz) Src/C_AMRLib/Amr.cpp commit ad11d6f89d10fdfb8e23f4f2306576ea031a2b2c Author: Marc Day Date: Thu Apr 2 14:45:12 2015 -0700 Uptick tagged version number Tools/CMake/BoxLib_Version.cmake commit a97cc244f5d701eb6a7c93138fffb2ab291e79e3 Merge: bb239a93d 2806f6b60 Author: Marc Day Date: Thu Apr 2 14:41:34 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2c565299d21e18ce994c9d602f19356be1f2fb2d Author: vince Date: Wed Apr 1 18:22:11 2015 -0700 support for multiple perfmonproc processes. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit d0d428c90d753daa38043f867c7d3932c792fcc3 Author: vince Date: Wed Apr 1 18:18:45 2015 -0700 support for multiple perfmonproc processes. Src/C_BaseLib/BLProfiler.cpp commit 2806f6b60ca7c6f5b39634ce4fdb6027500963d3 Author: Weiqun Zhang Date: Wed Apr 1 17:14:58 2015 -0700 Warn rather than Abort when both plot_int and plot_per are set Src/C_AMRLib/Amr.cpp commit 7d5b856958807f0cce0f7984646c42d876739552 Author: Weiqun Zhang Date: Wed Apr 1 17:11:03 2015 -0700 fixed a couple of things so that we can compile with PRECISION=FLOAT Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit e87bd00807309b6ee428be13287eecfd50679331 Author: Regression Tester account Date: Fri Mar 27 12:26:32 2015 -0700 update make file for battra again Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit ecb7d270be4b91df93919ddf886beffc96b53877 Author: Weiqun Zhang Date: Thu Mar 26 11:05:25 2015 -0700 updated makefile for battra Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit c0d485fa28da258eaccd488face342593214d4a0 Author: vince Date: Wed Mar 25 11:48:43 2015 -0700 added more profiling. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 9067de54d40cc29bd559cb38493fe8bf60a69b9c Author: vince Date: Wed Mar 25 11:47:52 2015 -0700 checks for zero size arrays, percent for cov. Src/C_BaseLib/BLProfiler.cpp commit 79ae9d79cee62c9b404a30cbbdbccd4d0fb82aa0 Author: vince Date: Thu Mar 19 12:49:12 2015 -0700 added coefficient of variation. Src/C_BaseLib/BLProfiler.cpp commit 3f7291f493dc7eea75dbfd7f4f085f86cc19b201 Merge: ffcd18897 685bdfdcb Author: vince Date: Wed Mar 18 15:33:11 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 685bdfdcba169be3b1ea64d8fb42c306e9a9f2e1 Merge: f8b699ae1 41fe36541 Author: vince Date: Wed Mar 18 15:31:19 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f8b699ae1f2f34c2e4435c0df9b2443f6df42481 Author: vince Date: Wed Mar 18 15:30:56 2015 -0700 showpoint to avoid 0 parse. Src/C_BaseLib/BLProfiler.cpp commit 41fe365414ca73770fe7272c84994779b6dc114b Author: Adam Jacobs Date: Mon Mar 16 14:39:05 2015 -0500 Update rules for Blue Waters compiling Tools/F_mk/GMakeMPI.mak commit 9fc7d040e738e516b5e829c4fdd519f86c6585d5 Merge: d7c93f4a1 c4b21a7f0 Author: Adam Jacobs Date: Mon Mar 16 13:04:53 2015 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 42d448e3b11c2def1e21fc534b5c0ec54074fa6f Author: vince Date: Thu Mar 12 17:43:27 2015 -0700 makefile update. Tests/IOBenchmark/GNUmakefile commit c4b21a7f00b37627b638db122a012ef271e8ec42 Author: Weiqun Zhang Date: Thu Mar 12 17:20:20 2015 -0700 better name for turning on c++11 support Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit e0d2e54956000d8d088b0aa00eba6790b8b869f6 Author: Weiqun Zhang Date: Thu Mar 12 17:16:35 2015 -0700 make c flags immediate so that we can later add c++ only flags Tools/C_mk/Make.defs commit 27e5fc004071d964bbd18b7b969f115de10597f5 Author: Weiqun Zhang Date: Thu Mar 12 17:14:52 2015 -0700 increased buffer size for backtracing Src/C_BaseLib/BLBackTrace.cpp commit 39f4752e70f4dff7b093842a995cd4e987ccaf44 Author: Michael Zingale Date: Tue Mar 10 15:27:09 2015 -0400 add a comment based on a question from a student Tutorials/WaveEquation_F/advance.f90 commit bb239a93d100ae8b116f347939d01a535b8cbf8f Merge: b40b7e086 6c4cec0da Author: Marc Day Date: Mon Mar 9 17:41:12 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d80767ebb62ca6c595f8186c33b04f6602a7aa67 Author: vince Date: Fri Mar 6 17:35:41 2015 -0800 extra send interface with comm. Src/C_BaseLib/ParallelDescriptor.H commit 6c4cec0da4d2bc5ccdc48af65f3bae4436eb9fb7 Author: Weiqun Zhang Date: Thu Mar 5 22:13:30 2015 -0800 use range based for in Lazy Src/C_BaseLib/Lazy.cpp commit f5e41ea6ef1cb724e2c1f1c6b76b0a14be88a04a Author: Weiqun Zhang Date: Thu Mar 5 14:18:56 2015 -0800 added laziness in a number of places where messages are printed when verbosity is on; added optional argument to a number of functions to allow for local reduction Src/C_AMRLib/AuxBoundaryData.cpp Src/C_AMRLib/Particles.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit b40b7e086fed9bb64d83d8cacf4c4bea674a0a5b Merge: 5dce185f6 2993fd2f8 Author: Marc Day Date: Thu Mar 5 14:17:01 2015 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2993fd2f8601d75b3f06de1317e5e9add4c221f3 Author: Weiqun Zhang Date: Thu Mar 5 13:55:28 2015 -0800 fixed a typo that made the high water mark of FAB wrong Src/C_BaseLib/BaseFab.H commit 27a2cf1f359ef53c73c705c4cbbc30b2f9a39ccc Author: Weiqun Zhang Date: Wed Mar 4 21:24:50 2015 -0800 added parameter amr.message_int to control how often to check messages touched by user Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 43277faec5a05c97ca830c6ec94990ed186ec607 Author: Weiqun Zhang Date: Wed Mar 4 17:30:20 2015 -0800 optional argument for contains_nan and contains_inf to control reduction Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit a4d97fc7b38eeed7b16e9804c4d9ce98bb2f0b77 Merge: cbb5871d5 38364677e Author: Weiqun Zhang Date: Wed Mar 4 17:20:06 2015 -0800 Merge branch 'lazy' commit cbb5871d5d7351e266b4fc9602cc54ebe7f7141a Merge: a062b389e d69a6e3e6 Author: Weiqun Zhang Date: Wed Mar 4 17:16:22 2015 -0800 Merge branch 'lazy' commit 38364677e3bc63529e56756282005971e521b530 Author: Weiqun Zhang Date: Wed Mar 4 13:58:54 2015 -0800 fixed it for Intel Src/C_BaseLib/Lazy.H commit d69a6e3e680f52594490f36eeeaec4b58ef69ab4 Author: Weiqun Zhang Date: Wed Mar 4 13:55:23 2015 -0800 forgot to add new files Src/C_AMRLib/Make.package Src/C_BaseLib/Lazy.H Src/C_BaseLib/Lazy.cpp Src/C_BaseLib/Make.package commit 8da3dfcafc4369ef82d89dce7d6573364f5681af Author: Weiqun Zhang Date: Wed Mar 4 13:42:40 2015 -0800 implemented prototype lazy evaluation that can delay MPI bulk synchronization till it hits a necessary bulk synchronization Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Make.package Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tools/C_mk/Make.defs commit 5dce185f60d1e95d8f014a423d5c1f29eb88d111 Merge: 12aa2b080 a062b389e Author: Marc Day Date: Wed Mar 4 13:15:52 2015 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d7c93f4a1409ce116409ed2c8fe8d9bc07328105 Merge: b5d48ea6a a062b389e Author: Adam Jacobs Date: Wed Mar 4 10:53:34 2015 -0600 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit a062b389e1fe6ff229a0c20332c34ec7062a8e65 Merge: 70e236e7e 6028ca963 Author: vince Date: Tue Mar 3 12:46:16 2015 -0800 commit merge. Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 70e236e7e69434ef630168ef65e577f13a4448a5 Author: vince Date: Tue Mar 3 12:46:06 2015 -0800 update the profiling doc. Docs/Readme.profiling commit 6028ca963b5f0cd15fe113401ddc8e21946a5b94 Author: Michael Zingale Date: Tue Mar 3 09:39:02 2015 -0500 update some problem locations Tools/RegressionTesting/Maestro-tests.ini commit 12aa2b080e89d414ab3615e6065077aa7e025231 Merge: e4a52bc5a a827762bc Author: Marc Day Date: Mon Mar 2 16:43:13 2015 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e4a52bc5a7c7ae64a473e6aa05bf13ffcac001b2 Author: Marc Day Date: Mon Mar 2 16:42:53 2015 -0800 For gfortran and g95, prefer -ffixed-line-length-0 over -ffixed-line-length-132 to avoid padding of character strings to col 132 when the string is split across continued lines. Tools/C_mk/Make.defs commit a827762bcc00798b2315cf103dcec9743d12190d Merge: 195cd03d9 55db75df7 Author: vince Date: Mon Mar 2 11:59:47 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 55db75df71d2e286ec4a34a18dcd17355c2ab38b Author: Andy Nonaka Date: Sat Feb 28 05:56:22 2015 -0800 mpi on gamera Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit ffcd188979033b783e3675efce10d08ad6b9b41b Merge: e464d797f 195cd03d9 Author: vince Date: Fri Feb 27 15:33:46 2015 -0800 rename dir test. Merge branch 'master' of naphta.lbl.gov:Development/BoxLib commit 195cd03d9cd1b119098c88efb2f6686db7d8fe87 Author: vince Date: Fri Feb 27 15:33:32 2015 -0800 rename directory function. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 94e390213aabf926660219054556dd0c9b980f53 Author: Marc Day Date: Fri Feb 27 12:53:41 2015 -0800 Propagate change to use BLMap in linop stuff Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp commit 6feb196f94173f8648d89df379b1b1dd4a2a585e Merge: 800a7be06 1fc9480e4 Author: Marc Day Date: Fri Feb 27 12:49:51 2015 -0800 Merge master commit 1fc9480e47713447747b7f037090eb82dddb67d6 Author: Weiqun Zhang Date: Thu Feb 26 14:25:36 2015 -0800 minor change to slient compiler warning Src/C_AMRLib/Particles.H commit 4eeb0d3d59175ba3b603f3c599495111fbaa0460 Author: Andy Nonaka Date: Wed Feb 25 16:13:53 2015 -0800 mpi on battra Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit a76e7d73f9b4a36061d6adc1cc1537ea3bd92340 Author: Michael Zingale Date: Tue Feb 24 09:23:07 2015 -0500 a little more cleaning Tools/RegressionTesting/testnew.py commit 006e9588ba75ba1bc1699a24ba6ea4630c293b4a Author: Michael Zingale Date: Mon Feb 23 14:16:57 2015 -0500 more clean-up, remove some redundant/unused modules are reported by pyflakes Tools/RegressionTesting/testnew.py commit 3077d4849a124b8cee9cb38985491be0ce6c9c48 Author: Michael Zingale Date: Mon Feb 23 12:52:19 2015 -0500 some more cleaning and PEP-8ing Tools/RegressionTesting/testnew.py commit fca030bfa67df3851140c58ad9c619679fa47092 Author: Michael Zingale Date: Mon Feb 23 11:09:48 2015 -0500 a little bit of clean-up -- use setattr to set a lot of the suite-wide parameters instead of needing a separate elif for each. Still need to do this for the test stuff. Also add a purge_output option to delete all but the comparison plotfile from the output directory. Finally do a little PEP-8 cleaning. Tools/RegressionTesting/testnew.py commit 350097cf6200929664b967909aa2124bfb6b496b Author: ajnonaka Date: Fri Feb 20 10:51:21 2015 -0800 gimantis MPI for f90 boxlib Tools/F_mk/GMakeMPI.mak commit 31944457c5be8fe3b9bbde4066d627fcfd88b9a3 Author: vince Date: Fri Feb 20 10:36:20 2015 -0800 changes for gimantis. Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 5af5997551d8317b47affa47ade08b689f69f132 Author: Michael Zingale Date: Wed Feb 18 10:14:15 2015 -0500 add some latex ignores .gitignore commit b5e39d9cb68972fe9f1feea80e4402ed56ce6a0d Author: Michael Zingale Date: Wed Feb 18 10:08:49 2015 -0500 remove stray } Tools/C_scripts/makebuildinfo_C.py commit f0f89067ac86a37e4946b7e23e0c0814c2af775e Author: Michael Zingale Date: Wed Feb 18 10:06:20 2015 -0500 update header with new functions Tools/C_scripts/buildInfo.H commit 0b572423fc982f9ad59af26c1db9127a7b5aaa01 Author: Michael Zingale Date: Wed Feb 18 09:58:19 2015 -0500 add a build_git_name and build_git_dir for problems that are built in special places... Tools/C_scripts/makebuildinfo_C.py commit f3e2ce5a4e5f6597b879acbac1533d7b0916e857 Author: Michael Zingale Date: Tue Feb 17 18:50:23 2015 -0500 if we set the extra directory (ASTRODEV_DIR for MAESTRO) and the directory doesn't actually exist, then handle this gracefully and still make a build_info.f90. Tools/F_scripts/makebuildinfo.py commit 536be1ec5c2717ab92f44b4aefde76d5b4ff88aa Author: ajnonaka Date: Tue Feb 17 15:08:27 2015 -0800 gigan MPI Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit c8a85f7b7b572d0a091f59e86af49ee3e336d1da Author: Michael Zingale Date: Sun Feb 15 11:05:11 2015 -0500 update to reflect new locations of test2 -> reacting_bubble and hydrostatic_adjust. Also fix the analysis hooks for the Sod_stellar stuff by passing sourceDir as the argument now. Finally, make sure that we run hydrostatic_adjust with the right network (we were doing it wrong all this time...) Tools/RegressionTesting/Castro-SBU-tests.ini commit 498ef39e57f5578383378d25442fe4da696102b3 Author: Michael Zingale Date: Wed Feb 11 15:13:11 2015 -0500 update to reflect fcompare.f90 now lives in BoxLib. Docs/GNUmakefile Docs/Regression/test_suite.tex commit 0bff6352bbcc09c907cf79462b5b1510025c758f Author: Michael Zingale Date: Wed Feb 11 15:10:58 2015 -0500 we no longer need to specify the compareToolDir, since it lives in BoxLib/ now Tools/RegressionTesting/Castro-SBU-tests.ini Tools/RegressionTesting/testnew.py commit 72bc645f9533a15407473485af4d56714c4d5534 Author: Michael Zingale Date: Wed Feb 11 15:04:17 2015 -0500 make BOXLIB_HOME relative Tools/Postprocessing/F_Src/GNUmakefile commit dbd9cad003ae51e7da490c32f24f40b76691bffc Author: Michael Zingale Date: Wed Feb 11 14:50:39 2015 -0500 move these from AmrPostprocessing Tools/Postprocessing/F_Src/CASTRO_radiation/GNUmakefile Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsource.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/frhdshocktube.f90 Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra.f90 Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_tests/fgaussianpulse.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlcompare.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlconverge.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fnorm.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo_driver.py Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_xrb/fad_excess.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fbuoyancy.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fconv_slopes.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/frates.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspec_total_mass.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspeciesmass.f90 Tools/Postprocessing/F_Src/Palette Tools/Postprocessing/F_Src/faverage.f90 Tools/Postprocessing/F_Src/fboxinfo.f90 Tools/Postprocessing/F_Src/fcompare.f90 Tools/Postprocessing/F_Src/fextract.f90 Tools/Postprocessing/F_Src/fextrema.f90 Tools/Postprocessing/F_Src/ffdcompare.f90 Tools/Postprocessing/F_Src/fsnapshot2d.f90 Tools/Postprocessing/F_Src/fsnapshot3d.f90 Tools/Postprocessing/F_Src/ftime.f90 Tools/Postprocessing/F_Src/fvarnames.f90 Tools/Postprocessing/F_Src/old_flame/GNUmakefile Tools/Postprocessing/F_Src/old_flame/fbubble_position.f90 Tools/Postprocessing/F_Src/old_flame/fbubble_position_3d.f90 Tools/Postprocessing/F_Src/old_flame/fcusp.f90 Tools/Postprocessing/F_Src/old_flame/fcylflame.f90 Tools/Postprocessing/F_Src/old_flame/fflamelength.f90 Tools/Postprocessing/F_Src/old_flame/finteg.f90 Tools/Postprocessing/F_Src/old_flame/fturbkin.f90 Tools/Postprocessing/F_Src/old_flame/fwidth.f90 Tools/Postprocessing/F_Src/python/README Tools/Postprocessing/F_Src/python/column_depth.py Tools/Postprocessing/F_Src/python/conv_slopes.py Tools/Postprocessing/F_Src/python/dumpparthistory.py Tools/Postprocessing/F_Src/python/eos_data.txt Tools/Postprocessing/F_Src/python/helmeos.py Tools/Postprocessing/F_Src/python/parseparticles.py Tools/Postprocessing/F_Src/python/test_helmeos.py Tools/Postprocessing/F_Src/python/test_parseparticles.py Tools/Postprocessing/F_Src/python/timestamp_00.REMOVED.git-id Tools/Postprocessing/F_Src/python/timestamp_02.REMOVED.git-id Tools/Postprocessing/F_Src/tutorial/GNUmakefile Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90 Tools/Postprocessing/F_Src/tutorial/fwrite2d.f90 commit 48f9f90d367aa63ff5e277546dbc6128232b9464 Merge: 8d5d28bc1 30e224f5b Author: Michael Zingale Date: Wed Feb 11 14:49:31 2015 -0500 Merge branch 'master' of /home/zingale/temp/AmrPostprocessing commit 30e224f5b9923ce6b6b68ba6cf483f8e1434290e Author: Michael Zingale Date: Wed Feb 11 14:47:12 2015 -0500 moving F_Src/CASTRO_radiation/GNUmakefile F_Src/CASTRO_radiation/fgaussianpulse.f90 F_Src/CASTRO_radiation/flgt_frnt1d.f90 F_Src/CASTRO_radiation/fradshock.f90 F_Src/CASTRO_radiation/fradsource.f90 F_Src/CASTRO_radiation/fradsphere.f90 F_Src/CASTRO_radiation/frhdshocktube.f90 F_Src/GNUmakefile F_Src/MAESTRO_sub_chandra/GNUmakefile F_Src/MAESTRO_sub_chandra/fsubchandra.f90 F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 F_Src/MAESTRO_tests/GNUmakefile F_Src/MAESTRO_tests/fgaussianpulse.f90 F_Src/MAESTRO_tests/fmlcompare.f90 F_Src/MAESTRO_tests/fmlconverge.f90 F_Src/MAESTRO_tests/fnorm.f90 F_Src/MAESTRO_wdconvect/GNUmakefile F_Src/MAESTRO_wdconvect/feint.f90 F_Src/MAESTRO_wdconvect/fthermo.f90 F_Src/MAESTRO_wdconvect/fthermo_driver.py F_Src/MAESTRO_wdconvect/fwdconvect.f90 F_Src/MAESTRO_xrb/GNUmakefile F_Src/MAESTRO_xrb/fad_excess.f90 F_Src/MAESTRO_xrb/fbuoyancy.f90 F_Src/MAESTRO_xrb/fconv_slopes.f90 F_Src/MAESTRO_xrb/frates.f90 F_Src/MAESTRO_xrb/fspec_total_mass.f90 F_Src/MAESTRO_xrb/fspeciesmass.f90 F_Src/Palette F_Src/faverage.f90 F_Src/fboxinfo.f90 F_Src/fcompare.f90 F_Src/fextract.f90 F_Src/fextrema.f90 F_Src/ffdcompare.f90 F_Src/fsnapshot2d.f90 F_Src/fsnapshot3d.f90 F_Src/ftime.f90 F_Src/fvarnames.f90 F_Src/old_flame/GNUmakefile F_Src/old_flame/fbubble_position.f90 F_Src/old_flame/fbubble_position_3d.f90 F_Src/old_flame/fcusp.f90 F_Src/old_flame/fcylflame.f90 F_Src/old_flame/fflamelength.f90 F_Src/old_flame/finteg.f90 F_Src/old_flame/fturbkin.f90 F_Src/old_flame/fwidth.f90 F_Src/python/README F_Src/python/column_depth.py F_Src/python/conv_slopes.py F_Src/python/dumpparthistory.py F_Src/python/eos_data.txt F_Src/python/helmeos.py F_Src/python/parseparticles.py F_Src/python/test_helmeos.py F_Src/python/test_parseparticles.py F_Src/python/timestamp_00.REMOVED.git-id F_Src/python/timestamp_02.REMOVED.git-id F_Src/tutorial/GNUmakefile F_Src/tutorial/fspeciesmass2d.f90 F_Src/tutorial/fwrite2d.f90 commit 8d5d28bc16445f9c0cc2557b86310bf3ff9b5f7f Author: Michael Zingale Date: Wed Feb 11 14:38:52 2015 -0500 update to reflect mainline Sod_stellar Tools/RegressionTesting/Castro-SBU-tests.ini commit e464d797f5706141c35da2438a00ccda5491d7cf Merge: 90116106a f97a0ae57 Author: Michael Zingale Date: Tue Feb 10 19:43:12 2015 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 90116106a5ce7a4756c04f1cace30f0767ed4e8d Author: Michael Zingale Date: Tue Feb 10 19:42:49 2015 -0500 test.py is the old version -- should not be used anymore Tools/RegressionTesting/test.py commit f97a0ae5702c1abf4780071635aac9ad8dc5f306 Author: Michael Zingale Date: Tue Feb 10 14:08:48 2015 -0500 update for helmeos stuff Tools/RegressionTesting/Castro-SBU-tests.ini commit 7cb72cacc218098dffe2934febc93fd7b0e6cf7d Merge: 90d6d44c6 dfbf164d4 Author: Michael Zingale Date: Tue Feb 10 14:01:23 2015 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 90d6d44c64e33df87921e244f835c5b994a4b7f5 Author: Michael Zingale Date: Tue Feb 10 14:01:01 2015 -0500 update docs on test suite to reflect removal of helmeos stuff Docs/Regression/test_suite.tex commit dfbf164d47fa8da8b009a3f91df3901c9380f7d4 Author: Michael Zingale Date: Tue Feb 10 13:59:35 2015 -0500 remove special treatment for helm_table.dat -- now we should specify it as a link?File parameter to a problem Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/testnew.py commit 9447670f1bbfa12c361bc5bd7e6d008be827582a Author: Michael Zingale Date: Tue Feb 10 13:21:54 2015 -0500 move the regression test suite info from Maestro Docs to here, and update it. Docs/Regression/test_suite.tex Docs/Regression/testsuite.eps Docs/UsersGuide.tex commit e16258f9b6ab9e1fdb1733ee60c22981a156be79 Author: Weiqun Zhang Date: Fri Feb 6 23:31:37 2015 -0800 clean up BACKTRACE and update Reame Docs/Readme.backtrace Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Tools/C_mk/Make.defs commit aa8d5b2a8c60a52180985fbe924ac992a40a079a Author: Weiqun Zhang Date: Fri Feb 6 14:20:46 2015 -0800 fixed typo Docs/Readme.backtrace commit c1f6360a7b362b51532365da118199dc7d4cd4c7 Author: Weiqun Zhang Date: Fri Feb 6 13:59:12 2015 -0800 updated Reame.backtrace Docs/Readme.backtrace commit 9a53025754ce5fc7ed3c0be06e480ae95763c9d6 Author: Weiqun Zhang Date: Fri Feb 6 13:48:55 2015 -0800 updated Readme.backtrace Docs/Readme.backtrace commit e85c006c8a0e983c101f0359fac64ae327b69c39 Author: Weiqun Zhang Date: Fri Feb 6 13:24:22 2015 -0800 better support of threads in BLBackTrace Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BLBackTrace.cpp commit 5652d3501ae54914cc4b23c7a1955806dce23f72 Merge: cc73dfc06 a8c89543b Author: Weiqun Zhang Date: Fri Feb 6 13:22:25 2015 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit a8c89543b4d236ce008a5cc6020f4307196add22 Author: Anuj Chaudhri Date: Fri Feb 6 10:33:19 2015 -0800 Rodan MPI Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit cc73dfc06439563a5ad2036b8c0b834fc201d4cd Author: Weiqun Zhang Date: Fri Feb 6 10:32:19 2015 -0800 moved -rdynamic flag to LDFLAGS Tools/C_mk/Make.defs commit 7b94bbf5550ca83bc3b4105c2bbba92975af6ff2 Author: Weiqun Zhang Date: Fri Feb 6 09:48:51 2015 -0800 fixed multithreading in BLBackTrace Src/C_BaseLib/BLBackTrace.cpp commit a3db40bfe542e53c4bd174b0d4deb52429f16e4e Author: Weiqun Zhang Date: Thu Feb 5 21:09:14 2015 -0800 Implemented backtrace capability in case of segfault. See Docs/Readme.backtrace for details. Docs/Readme.backtrace Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Tools/C_mk/Make.defs commit 74311dc6e80d80be6b4bd2665eeda0aecbe584fd Author: ajnonaka Date: Thu Feb 5 13:21:25 2015 -0800 mothra MPI Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 2f88232f9cbc96f9192bde66f163dd9e7de9b42b Author: Michael Zingale Date: Mon Feb 2 16:12:15 2015 -0500 in debug mode, switch from a nan to an snan (signaling NaN). This can be caught at runtime and help us find places we are using uninitialized variables. This should be good for gfortran >= 4.5. Tools/F_mk/comps/gfortran.mak commit acc5289235a6946e55979cee1cac899c27463fca Author: Weiqun Zhang Date: Mon Feb 2 10:51:33 2015 -0800 Added Amr::DataLogName to return the file names. Changed datalog from ofstream to fstream per Max's request. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit abbd4490e84689585b8b9d203cab53b6bad72261 Merge: 69e109c2e 34627e982 Author: Weiqun Zhang Date: Fri Jan 30 16:42:49 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 69e109c2e70ed0b84963f7e489e254ad0e54d116 Author: Weiqun Zhang Date: Fri Jan 30 16:42:42 2015 -0800 added a version of ParticleBase::NexID that does not contain omp critical Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 34627e982a0ea3afc5a0856071fd267c6818f1be Merge: 6e901d7e6 6d73495b2 Author: Michael Zingale Date: Fri Jan 30 10:12:38 2015 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 6e901d7e63b92757f040c20eeb46c7bdbfc86f5d Author: Michael Zingale Date: Fri Jan 30 10:12:20 2015 -0500 switch titan over to using whichlinux Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 6d73495b25a4d4655968eb0c3dd4d73bd6e954f6 Author: Weiqun Zhang Date: Thu Jan 29 17:06:00 2015 -0800 removed some omp critical Src/C_BaseLib/MultiFab.cpp commit 2c778298f4550b4ac86399059a4c10dbc1461e73 Author: vince Date: Thu Jan 29 15:38:38 2015 -0800 defs for new os. Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 48910b75706c37723d104dc9dbc6a91b3e742f35 Author: ajnonaka Date: Thu Jan 29 12:33:44 2015 -0800 update atragon mpi library directories lijewski no longer exists Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 505ee88c7ab52e7a8fce05bf7759617966175330 Author: Weiqun Zhang Date: Thu Jan 29 10:56:38 2015 -0800 update makefile per Andy's suggestion after os upgrade Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 81001b61e24e116545943622fbc722376e9c929d Author: Marc Day Date: Wed Jan 28 15:49:16 2015 -0800 Modify make config per Andy suggestion Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 8b02edb0da776c40cd9ee15ffbc76598ca4f659c Merge: d72171122 75974a2f6 Author: Matthew Emmett Date: Wed Jan 28 13:53:17 2015 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d721711229211fa3771a5be90c2bdf1bb792fb73 Author: Matthew Emmett Date: Wed Jan 28 13:52:43 2015 -0800 PyBoxLib: Fix fboxlib build and fix memory error. Src/Python/F90/Makefile Src/Python/F90/src/fboxlib.f90 commit 75974a2f6797c488c4596c1fdfe7e7d4a83fc6e8 Author: Weiqun Zhang Date: Wed Jan 28 12:45:41 2015 -0800 fixed assertion Src/F_BaseLib/multifab_f.f90 commit ed4150f4c27942da93250eae89d164d029ab4ea8 Merge: 4451852a3 1a9df61e2 Author: Matthew Emmett Date: Wed Jan 28 12:33:40 2015 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 1a9df61e2f3b62e035e63d957c3d4d030fef411d Author: Weiqun Zhang Date: Tue Jan 27 22:13:31 2015 -0800 fixed a bug in my last commit Src/C_BaseLib/FabArray.cpp commit d8d206559b4739e2201ef87a3f7886444ae8eb20 Author: Weiqun Zhang Date: Tue Jan 27 15:00:03 2015 -0800 minor cleanup Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Utility.cpp commit 2c03e67829b7ad923916c6383a97b726ef70b2b7 Author: Weiqun Zhang Date: Mon Jan 26 10:35:41 2015 -0800 set the type of nodaltilebox correctly to satisfy assertions Src/C_BaseLib/FabArray.cpp commit cd6b5802b5ac0f862b1cfc18166579dc668fe334 Author: Weiqun Zhang Date: Sat Jan 24 21:00:58 2015 -0800 added an optional argument, chunksize, to MFIter that can be used to fine tune work sharing Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit f35c4b8feec4d1ce1b5a5816c37d28ddcc86ca68 Author: Weiqun Zhang Date: Fri Jan 23 10:47:15 2015 -0800 converted to tiling in two places Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 960b4695a64c05c65915ece619b29656117e3998 Author: Weiqun Zhang Date: Fri Jan 23 10:09:26 2015 -0800 removed an extra endif Tools/C_mk/Make.mpi commit 78285d85c42c8ed087e5844024126c8238339057 Author: Weiqun Zhang Date: Fri Jan 23 10:04:43 2015 -0800 take a shortcut in make_particle_dmap Src/C_AMRLib/AmrLevel.cpp commit 4a6f57b190addb0df22105ef0254dec912e9eb1d Author: Ann Almgren Date: Fri Jan 23 09:48:21 2015 -0800 Make the manda options identical to the megalon options. Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 7fefe724ae57fe86a39ce7bea95acc751ccbfa75 Merge: 6ab3afa08 ec813843e Author: Weiqun Zhang Date: Wed Jan 21 13:54:09 2015 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 6ab3afa08e6ded07966ca8b25a6a0baa610b0a6f Author: Weiqun Zhang Date: Wed Jan 21 13:52:31 2015 -0800 fixed a bug in Particle and optimization for non-periodic case Src/C_AMRLib/Particles.cpp commit ec813843e5fdc51cacb7a659e62becb13c3fb571 Author: ajnonaka Date: Tue Jan 20 17:43:50 2015 -0800 point ebirah to correct MPI installation after upgrade to Ubuntu 14.04 Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 7e6f568b44b174bf9189d2b686a142f69023b141 Author: Weiqun Zhang Date: Tue Jan 20 17:11:19 2015 -0800 nodalbox -->> nodaltilebox Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp commit 9e9f856918047c3007cbb28c2a7430b917af76ec Author: Weiqun Zhang Date: Mon Jan 19 16:36:07 2015 -0800 backtrace when BL_ASSERT fails Src/C_BaseLib/BoxLib.cpp Tools/C_mk/Make.defs commit 635a125f9635936b974cab5e7ea8d61e4b4d4ca4 Author: Weiqun Zhang Date: Sun Jan 18 11:57:07 2015 -0800 merged RRKS into KnapSack Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 5ddedfd9a3fcfb1de7c9c4a7c0224d69efe41c15 Author: Weiqun Zhang Date: Thu Jan 15 17:06:30 2015 -0800 print put the number of particles too Src/C_AMRLib/Particles.H commit fa4238ad89f46458fe881ea504fc37842fdcb606 Author: Weiqun Zhang Date: Thu Jan 15 16:36:19 2015 -0800 fixed a typo Src/C_BaseLib/DistributionMapping.cpp commit bac2a1c764f2c022358e33956517f42dde40b415 Author: Weiqun Zhang Date: Thu Jan 15 16:30:03 2015 -0800 A new distribution mapping strategy called RRKS, which combines RoundRobin with KnapSack. It's not as greedy as KnapSack. It tries to keep the number of boxes balanced while considering box weights. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit ebef6242f9017c4e15a6f6a57e2d1c71515a815a Author: Weiqun Zhang Date: Thu Jan 15 13:41:41 2015 -0800 fixed a bug in regression test script Tools/RegressionTesting/testnew.py commit 85deb13a02f207b6dcc3f3edcc6fbb07bb477a19 Author: Weiqun Zhang Date: Thu Jan 15 12:57:37 2015 -0800 regression test: link file can be a directory Tools/RegressionTesting/testnew.py commit 71250f05d848cf468c56bcb883b16a24de57300a Author: Weiqun Zhang Date: Wed Jan 14 20:52:16 2015 -0800 single quote to double Src/C_AMRLib/Particles.H commit 10178750df02a7bae02e9cc2779a860ddabbbecc Author: Weiqun Zhang Date: Wed Jan 14 20:50:10 2015 -0800 new function that put distribution map in cache Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit e9c66745d45e71efd971f4032d9ea0d6de34f1a4 Author: Weiqun Zhang Date: Wed Jan 14 20:49:41 2015 -0800 added extra \n Src/C_AMRLib/Particles.H commit 1fd56f32e03ecdf49f0ec688e566be840955e3e3 Author: Weiqun Zhang Date: Wed Jan 14 20:11:17 2015 -0800 added new Amrlevel constructor and StateData::define that take distribution map Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit cf72682b38b5a6e6302836466fdfcf6697927971 Author: Michael Zingale Date: Wed Jan 14 22:18:15 2015 -0500 when writing the auxFiles to the webpage, remove the root. Also some neighboring pep-8 fixes Tools/RegressionTesting/testnew.py commit 8c81c46a5db005d1de2dfb88eeaff9a15c1666a0 Author: Weiqun Zhang Date: Wed Jan 14 09:59:55 2015 -0800 fixed typo Src/C_AMRLib/MLSDCAmrEncap.cpp commit 1964b55af20a47f95721fa682d1c88d3c78e5489 Merge: 92355251b cc6aa0b41 Author: vince Date: Tue Jan 13 15:01:07 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit cc6aa0b414090684a1df071cb54d3b083c89df86 Merge: f995f51f0 7070f543c Author: Weiqun Zhang Date: Tue Jan 13 14:57:19 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f995f51f0ff58fc71549c22c538eba6a8330a56c Author: Weiqun Zhang Date: Tue Jan 13 14:57:11 2015 -0800 more openmp Src/C_AMRLib/TagBox.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 7070f543ce0b7d5fc94bd9005c6f20897b8cddd6 Merge: ebca90c77 5d1f0e1ea Author: Andy Nonaka Date: Tue Jan 13 13:23:10 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ebca90c77240c06f53540b9b57c1ecef2c6161dd Author: Andy Nonaka Date: Tue Jan 13 13:22:30 2015 -0800 point to mpich on megalon... I can compile but get n instances of the program running Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 5d1f0e1eae8f2715efea2a550c5943388b30204c Author: Weiqun Zhang Date: Tue Jan 13 13:04:11 2015 -0800 fixed typo Src/C_BaseLib/iMultiFab.cpp commit 278a203ab6688c51c2cccd20c6e6de2bc62316fe Author: Weiqun Zhang Date: Tue Jan 13 13:01:40 2015 -0800 added OMP to iMultiFab::min, max, and norm Src/C_BaseLib/iMultiFab.cpp commit 0d63263c4055b5c70f7a06625453c39f96a496de Author: Weiqun Zhang Date: Tue Jan 13 12:48:19 2015 -0800 fixed new bugs Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp commit cb3c0a11d0b2a9d7d466e4caec54163bf75bc7f5 Author: Weiqun Zhang Date: Tue Jan 13 12:41:54 2015 -0800 fixed a new bug Src/C_BaseLib/MultiFab.cpp commit 90b5127129e180776eaba6ddaeb4046d69b8d33a Author: Weiqun Zhang Date: Tue Jan 13 11:25:28 2015 -0800 added OMP to MultiFab norm, min, and max.... Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F commit 34d53e23441d40f48e92afa9020d7a21801f6252 Author: Weiqun Zhang Date: Mon Jan 12 15:28:01 2015 -0800 removed an unstarted BL Profiler Src/LinearSolvers/F_MG/ml_cc.f90 commit 92355251b8a85d5a2aa7b2c2da874933059a192d Merge: 238cd9054 4c50a257c Author: vince Date: Mon Jan 12 14:50:09 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 238cd90541bccfb8ee5d3f7a2e458228f0aaae43 Author: vince Date: Mon Jan 12 14:49:48 2015 -0800 test code. Tests/C_BaseLib/TPROFILER.F Tests/C_BaseLib/tProfiler.cpp commit b822ef019ffacdf6a11bccce6b3d11a60f8b7b04 Author: vince Date: Mon Jan 12 14:49:01 2015 -0800 trace optimizations, flushing Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp commit 9d5e8cb53316cffcb84b10fe299fb1f43eaf4b1d Author: vince Date: Mon Jan 12 14:45:42 2015 -0800 added FAB_NATIVE_32 format for faster conversions. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabConv.cpp commit 4c50a257c55c102ecf0b8353e25a3943ade80ec3 Author: Weiqun Zhang Date: Mon Jan 12 14:42:30 2015 -0800 fixed an unmatched profiler Src/LinearSolvers/F_MG/ml_cc.f90 commit bd1477e967ad0e448c7b54fea8de3815a61fd24d Author: Weiqun Zhang Date: Mon Jan 12 14:34:25 2015 -0800 make BL Profilers in F90 codes work again for C++ codes Src/F_BaseLib/BLProfiler_f90.f90 Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_prof_stubs.f90 commit e14f69871479063c5a2f48560c05f32db107cd6b Author: Weiqun Zhang Date: Mon Jan 12 10:27:53 2015 -0800 commented out BL_PROFILE in BoxArray::intersections Src/C_BaseLib/BoxArray.cpp commit 8080b99c0f8865ab253be35f357df6361cb0e140 Author: Michael Zingale Date: Sat Jan 10 12:33:56 2015 -0500 latest version Tools/RegressionTesting/Maestro-tests.ini commit 3ef67f1765f5b979787ad20faf8fcf15414d125e Author: Weiqun Zhang Date: Fri Jan 9 20:16:54 2015 -0800 For tiling version of derive, set xlo to the lower left corner of the tilebox Src/C_AMRLib/AmrLevel.cpp commit 41f38cebeebbaf1907fb13fa246c0072681ef845 Author: Weiqun Zhang Date: Fri Jan 9 16:55:45 2015 -0800 in the new tiled derive, we should use the dst mf to initilize MFIter Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/MultiFab.cpp commit f97a42dfc6453885054744d1d0118da765544d3e Author: Weiqun Zhang Date: Fri Jan 9 15:39:32 2015 -0800 If CRSEGRNDOMP is defined, tile AmrLevel::derive. Src/C_AMRLib/AmrLevel.cpp commit 27c44a381eb00511f9e442fe187b405ff3235f85 Author: Weiqun Zhang Date: Fri Jan 9 15:28:55 2015 -0800 fixed a bug in my last commit Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit d9dfb12dcf630ede881d527987a604f669935ed3 Author: Weiqun Zhang Date: Fri Jan 9 15:06:19 2015 -0800 use the new FillPatch function Src/C_AMRLib/AmrLevel.cpp commit 8027859381e1ff0e83d6f93b5ee9c44c20d6f30c Author: Weiqun Zhang Date: Fri Jan 9 13:34:42 2015 -0800 Eliminated a few OMP critical directives by having threadprivate copies of variables like total_bytes_allocated_in_fabs. The trick is we can delay the summation of the numbers till we need them. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/DistributionMapping.cpp commit aa285634dfdd5c96fd74b8fdb7a7223585a69124 Author: Weiqun Zhang Date: Thu Jan 8 13:36:37 2015 -0800 fixed new bug Src/C_AMRLib/TagBox.cpp commit 1b2abd179a07cfa883be4e171ef0b78db5f73614 Author: Weiqun Zhang Date: Thu Jan 8 13:09:34 2015 -0800 added tiling functionality to TagBox Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 3c8183d0ffba16bbef47456ece64c01d9f53d414 Author: Weiqun Zhang Date: Tue Jan 6 12:22:04 2015 -0800 fixed a bug I introduced two weeks ago Src/C_AMRLib/Particles.cpp commit 5eb4e754c23737d062d2ecea0c2fdd706fea2087 Author: Weiqun Zhang Date: Mon Jan 5 21:32:07 2015 -0800 added an assertion Src/C_AMRLib/AmrLevel.cpp commit edde48f7196fdf54fd5ba71775cf52302f5fae81 Author: Weiqun Zhang Date: Mon Jan 5 20:53:51 2015 -0800 Added a static member function FillPatch to AmrLevel. This function takes the same argument as FillPatchIterator, but unlike FillPatchIterator, it fills the MultiFab. For example FillPatch(amrlevel,S_new,0,cur_time,State_Type,0,NUM_STATE); will fill-patch the MultiFab S_new. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/MultiFab.cpp commit ab4ff09e65ff5bd2055eb7677a526cbbe5c13209 Author: Weiqun Zhang Date: Sat Jan 3 07:58:32 2015 -0800 MFIter: rename fluxbox nodalbox for consistence Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp commit d249fc64c4c8f816881ab21a647105bfa3e96132 Author: Weiqun Zhang Date: Wed Dec 31 19:59:16 2014 -0800 added a new member function to FillPatchIterator t return the filled temporary MultiFab; this is useful for tiling loops that used to use FillPatchIterator Src/C_AMRLib/AmrLevel.H commit 293377fe50a3548e2ff39845854f6de5b400c3ac Author: Weiqun Zhang Date: Wed Dec 31 14:22:47 2014 -0800 print out the smallest and biggest grid on each level after regrid if verbose > 0 Src/C_AMRLib/Amr.cpp commit 6fba3555c2d20f145223c6ba71f3338df532d777 Author: Weiqun Zhang Date: Sun Dec 28 21:06:55 2014 -0800 minor: use a more meaningful name Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 86eb32ac95ca94875e6e62898c84b37b2115b3c6 Author: Weiqun Zhang Date: Sun Dec 28 20:36:45 2014 -0800 fixed a new bug Src/C_BoundaryLib/FabSet.cpp commit c7f7db7c7b50f85483bcae9c487067e12a916373 Author: Weiqun Zhang Date: Sun Dec 28 16:00:29 2014 -0800 added OMP to MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 2ca268e6226f45a84cd8c73e7df6c52aff286a69 Author: Weiqun Zhang Date: Sun Dec 28 15:13:10 2014 -0800 added tiling and OMP in serveral palces Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/InterpBndryData.cpp commit 52bfbf7875867d01c98e0e69646816cdfcc5da05 Author: Weiqun Zhang Date: Wed Dec 24 15:35:06 2014 -0800 fixed similar OMP issue in C++ Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 55341540cce4e2c919ff387cc63c00bb8a9012fb Author: Weiqun Zhang Date: Wed Dec 24 10:37:22 2014 -0800 Fixed an omp bug in F90 fill_boundary of nodal multifab with periodic boundary. In this case, fill_boundary actually copyies from valid cells to valid cells. Src/F_BaseLib/layout.f90 commit 03973aee21ae485bb716f86e5ab8504e33ccd700 Author: Weiqun Zhang Date: Tue Dec 23 14:12:42 2014 -0800 removed an unintended nested OMP parallel region Src/C_BaseLib/MultiFab.cpp commit 6ad38a1ca9e9fa9201c4928133af10b423ee30d6 Author: Weiqun Zhang Date: Tue Dec 23 13:16:32 2014 -0800 cleanup Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 6c850e723c5246e256702d35363109fa1507b8ef Author: Weiqun Zhang Date: Tue Dec 23 11:25:22 2014 -0800 implemented OMP in packing and unpacking for MPI Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 948a0177276fb1ff85060422d15b2dd0392f7b28 Author: Weiqun Zhang Date: Mon Dec 22 20:06:25 2014 -0800 minor shortcuts Src/F_BaseLib/layout.f90 commit 45c1b8ea266d8572d4ac5349f03d5f67eab4c142 Author: Weiqun Zhang Date: Mon Dec 22 16:35:01 2014 -0800 C++: work in progress: refactor OMP in packing and unpacking for MPI Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 15915756edf746017d45d22eb19c91e8e8e659e3 Author: Weiqun Zhang Date: Mon Dec 22 15:50:33 2014 -0800 fixed a new bug Src/F_BaseLib/layout.f90 commit 60f0456b186eb9ccb76fe1ff1e46c931f6747efc Author: Weiqun Zhang Date: Mon Dec 22 15:09:03 2014 -0800 F90: Added thread safety flags for multifab copy and fill_boundary, and fixed a 2-year old OMP bug in multifab copy. Added OMP to sum_boundary. This might break some regression tests. Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit ec2a379ac017310821c7e312fa75312d39d7c61e Author: Weiqun Zhang Date: Mon Dec 22 12:49:29 2014 -0800 fixed OMP data races introduced today Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit cce3104c9464f27c4ed549e82f78587695190a1c Author: Weiqun Zhang Date: Mon Dec 22 11:16:41 2014 -0800 removed random shuffle from FabArray because it is no longer used Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 4f2d1bda977382421244c2ca73009fdb508fcb65 Author: Weiqun Zhang Date: Mon Dec 22 11:14:00 2014 -0800 OMP in SumBoundary Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit d9dcfa7cacd10a7bb7b67279f979685b5b76ade6 Author: Weiqun Zhang Date: Fri Dec 19 14:28:55 2014 -0800 added a new distribution method, RRSFC, which do roundrobin on space filling curve. This is good for job balance in the case where the amount of work is correlated with position, such as Sedona. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 0905363b5ecc371520647108ed81c7a272ad556b Author: Weiqun Zhang Date: Fri Dec 19 11:53:17 2014 -0800 moved memory allocation out of OMP parallel region Src/C_AMRLib/AmrLevel.cpp commit 0265ec1a5f2615a5386a6a4c77b0ea97f68e70b7 Author: Weiqun Zhang Date: Thu Dec 18 16:05:12 2014 -0800 minor optimization and clean up Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.cpp commit 0a8b947a83221f5cea51a14c400a97550a490e98 Merge: 9b5c4771f 0f37aea00 Author: Weiqun Zhang Date: Thu Dec 18 11:23:53 2014 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 9b5c4771f4a9be550ed6faa84adb84c7447cc894 Author: Weiqun Zhang Date: Thu Dec 18 11:23:50 2014 -0800 added timers Src/C_BaseLib/FabArray.cpp commit 0f37aea007dff4584123cec30ef680742549953c Author: Weiqun Zhang Date: Wed Dec 17 16:42:42 2014 -0800 fixed a new bug in parallel copy Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit d75d71ad8a26bb0412f99040329ab932157deafd Author: Weiqun Zhang Date: Wed Dec 17 15:06:57 2014 -0800 OMP parallel copy Src/C_BaseLib/FabArray.H commit 17a3a47c4d21d77e2557b116e5c48a65ebacd55c Author: Weiqun Zhang Date: Wed Dec 17 13:57:52 2014 -0800 more OMP in FillPeriodicBoundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit b8a31db3cb10597a5a13c1420ea98bfef4f695dc Author: Weiqun Zhang Date: Wed Dec 17 13:05:40 2014 -0800 added OMP to FillPeriodicBoundary Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit c95df9000524695c24391fa844c9468283850d1f Author: Weiqun Zhang Date: Wed Dec 17 12:48:54 2014 -0800 option to turn off nested threading in MFIter Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 4e3d470d6516bc3c8323aa472e1055c9bb8cac5d Merge: ab8037bb7 05e5a0b52 Author: Weiqun Zhang Date: Wed Dec 17 10:38:41 2014 -0800 Merge branch 'master' into commopt commit ab8037bb7bcb737e69ea1dc6aaa01678d49ebe78 Author: Weiqun Zhang Date: Wed Dec 17 10:37:53 2014 -0800 more OMP in FillBoundary Src/C_BaseLib/FabArray.H commit 05e5a0b5216124cf0b934150174d8ce9a91fb1ce Author: Weiqun Zhang Date: Tue Dec 16 21:19:12 2014 -0800 fixes for gcc 4.8 and above Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp commit 3c95337cdd5ffd76e410b11fa693cf011231a3b7 Author: vince Date: Tue Dec 16 17:20:10 2014 -0800 typo. Src/C_BaseLib/BLProfiler.cpp commit 575e894c6daea765eb08bbb486c9d7dc69e707b7 Author: Weiqun Zhang Date: Tue Dec 16 14:24:59 2014 -0800 OMP two loops in FillBoundary Src/C_BaseLib/FabArray.H commit ecd04b908a7a7482260c0b1b2978c8cb4c3c0a09 Author: vince Date: Tue Dec 16 13:42:48 2014 -0800 array size. Src/C_BaseLib/BLProfiler.cpp commit 13c622525d0bc8f87db12c88d732e1fd63ab21e0 Merge: 1bf21680c a9325afda Author: Weiqun Zhang Date: Tue Dec 16 12:35:02 2014 -0800 Merge branch 'master' into commopt commit a9325afdabf5a78f4aa89811353921220e005463 Author: Weiqun Zhang Date: Tue Dec 16 12:27:36 2014 -0800 removed the update argument and optimized Where() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 6194d99ca5ad65c5ade409f54100e9da1828c9f3 Author: Weiqun Zhang Date: Tue Dec 16 10:10:12 2014 -0800 Since particle can intersect with only one grid, we can set first_only=true in serveral calls to BoxArray::intersections Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 1bf21680cbdab5f62175fe1812170e7fe5923d2a Author: Weiqun Zhang Date: Tue Dec 16 09:51:37 2014 -0800 minor Src/C_BaseLib/FabArray.cpp commit 8e34447dc2580547b4503fad5bc373533f93da8e Author: Weiqun Zhang Date: Fri Dec 12 14:13:00 2014 -0800 removed using std::isinf for Cray compiler on Hopper Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 76a9e0f71b3c5df3b6234f0e3d802bbfd06baa44 Author: Weiqun Zhang Date: Fri Dec 12 14:12:08 2014 -0800 removed tgmath.h and added std:: to sqrt for PGI on Hopper; tests show that it works for all compilers on Hopper and Edison, and my desktop with gcc 4.4.3 Src/C_BaseLib/BLProfiler.cpp commit f54294d8fe7cda83b4f44147cf637bfb0c3f77d8 Author: vince Date: Fri Dec 12 13:58:04 2014 -0800 fix for sqrt, ioproc parens. Src/C_BaseLib/BLProfiler.cpp commit f6aceb6899c063e4a2ea6d82851011480dc522e1 Merge: e95303fa0 301757f03 Author: vince Date: Fri Dec 12 11:56:31 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e95303fa00a6f8ccefec9adebec9578fc2d23116 Author: vince Date: Fri Dec 12 11:56:16 2014 -0800 changed double to Real in SumPeriodicBoundary so PRECISION=FLOAT will compile. Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 301757f0372228b069a8a530d54c4ef576513ac5 Author: Weiqun Zhang Date: Thu Dec 11 17:25:07 2014 -0800 reverted my last change because it created new problems Tools/C_mk/Make.defs commit 4a973a84200a0c8680c0c01c00259914078e80c0 Author: Weiqun Zhang Date: Thu Dec 11 16:30:39 2014 -0800 added -std=c++0x to gcc as needed by the new BLProfiler Tools/C_mk/Make.defs commit 6867fc9015a6fb86cc75131a316e4e7c0a227062 Author: vince Date: Thu Dec 11 11:04:02 2014 -0800 another donev machine. Tools/C_mk/Make.defs commit 32cfd40caef422600efe24641c7dac2d28280e18 Author: vince Date: Wed Dec 10 15:35:21 2014 -0800 renamed Profiler to BLProfiler (class and files). Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/iMultiFab.cpp Src/C_BoundaryLib/FabSet.cpp Src/C_TowerLib/Layout.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp commit 97bfed1c0b5026ccf30c04456fcde721d20e79e7 Merge: 1cdf3bcb9 5b87ef250 Author: vince Date: Tue Dec 9 14:33:23 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1cdf3bcb974c47659ed7f208bc4c509fc5c64631 Author: vince Date: Mon Dec 8 16:59:41 2014 -0800 added more statistics. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 5b87ef2503faa677dfece61c3d3ca4af068b12bc Author: Weiqun Zhang Date: Fri Dec 5 13:05:57 2014 -0800 fixed 2 new errors Src/C_AMRLib/Particles.cpp commit ef7c6a70123659ca2e0c6863a7fb7c10c4ab71e5 Author: Weiqun Zhang Date: Fri Dec 5 13:03:18 2014 -0800 fixed a new error Src/C_AMRLib/Particles.H commit 988c2b844d472987af7a2105e6146b7b27aef1dc Author: Weiqun Zhang Date: Fri Dec 5 12:51:50 2014 -0800 more const T -->> const T& Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/WaveEquation_C/main.cpp commit 1ff8db4980f313309e8ecb8f44a7eef7c8a2f566 Author: Weiqun Zhang Date: Fri Dec 5 12:27:09 2014 -0800 more const T -->> const T& Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/MacBndry.cpp Src/C_TowerLib/Layout.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/ViewMF/viewMFdiff.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tutorials/AMR_Advection_C/Source/ADR.cpp Tutorials/AMR_Advection_C/Source/Diffusion.cpp Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp commit fa9c35776fe71c819328ad101df25ad963dbbf29 Merge: f27233702 83b90f00c Author: Weiqun Zhang Date: Thu Dec 4 21:55:58 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f272337029a0b94fcc7d1fbc169700bc5cf15617 Author: Weiqun Zhang Date: Thu Dec 4 21:06:07 2014 -0800 minor optimization using a nice feature of C++: temporary variable created as the rhs of assignment to const T& lhs has the same lifetime as the lhs variable. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/AuxBoundaryData.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/C_TowerLib/Layout.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Tests/C_BaseLib/tBA.cpp commit 83b90f00cd6c751fc544b7db144b1c79803cc156 Author: Weiqun Zhang Date: Thu Dec 4 06:13:04 2014 -0800 added -lquadmath for gcc 4.9 Tools/C_mk/Make.Linux commit 72efff827fe903f6f0499146a1bbdcc39ae941e5 Merge: e24f58bc6 e4a318184 Author: Weiqun Zhang Date: Tue Dec 2 21:15:44 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e24f58bc613c0cc74570c4147f127a7ddd390138 Author: Weiqun Zhang Date: Tue Dec 2 21:02:00 2014 -0800 minor optimization Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp commit e4a31818427bfed89e5715c111354e1fe3029a4c Author: Weiqun Zhang Date: Tue Dec 2 16:58:22 2014 -0800 OMP'd part of FabArray::copy Src/C_BaseLib/FabArray.H commit adc736adf00d8d423a5f416c9cfc113c77e60850 Author: Weiqun Zhang Date: Tue Dec 2 16:21:51 2014 -0800 added a timer to BoxArray::intersections Src/C_BaseLib/BoxArray.cpp commit 1333ac2e7ba4e95250908424ce49d3b2f408d373 Author: Weiqun Zhang Date: Tue Dec 2 15:59:41 2014 -0800 added a timer to FabArray::copy from a Fab Src/C_BaseLib/FabArray.H commit 2c6d3e5d46f62ab99d014b97c68353c6142a15ed Merge: d23f402ca 83f33cd75 Author: Weiqun Zhang Date: Tue Dec 2 15:44:39 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d23f402cad00ca4dd46efb32c0b6fc7a566233be Author: Weiqun Zhang Date: Tue Dec 2 15:40:28 2014 -0800 removed OMP from BaseFab saxpy so that we can do OMP on MultiFab Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_BaseLib/SPECIALIZE_3D.F commit 7375dcb7a164742e4f93c7158c806cc05f7f6710 Author: Weiqun Zhang Date: Tue Dec 2 15:31:59 2014 -0800 add tiling to FabSetIter and use it in FluxRegister::SumReg Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BoundaryLib/FabSet.H commit 09fc9aed10427d7a09afc364f56a1b041147e4cb Author: Weiqun Zhang Date: Tue Dec 2 15:25:13 2014 -0800 cleanup Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 3de88036bae7a864d2ca66912ef5266f96c9b277 Author: Weiqun Zhang Date: Tue Dec 2 15:05:31 2014 -0800 tiled MultiFab::contains_inf and contains_nan Src/C_BaseLib/MultiFab.cpp commit 76c9647e218fcdd60937c6fc60be7b7465828f4e Author: Weiqun Zhang Date: Tue Dec 2 14:49:27 2014 -0800 tiled a number of MultiFab functions Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/iMultiFab.cpp commit 7561402089db70c6f0b3340a4cdc335fae9ae994 Author: Weiqun Zhang Date: Tue Dec 2 14:19:31 2014 -0800 minor optimization by moving omp critical out of MFIter loop Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 83f33cd757b014bd39889ea6bd549812956a2fea Author: Weiqun Zhang Date: Tue Dec 2 12:31:25 2014 -0800 minor Src/C_BaseLib/BaseFab.H commit c8b548ed04604cdaa659878f4727ec0e188db1e8 Author: Weiqun Zhang Date: Tue Dec 2 12:04:53 2014 -0800 tiled setVal Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d6b572ef2051c9c5be99e97135600a0b263c4d30 Author: Weiqun Zhang Date: Tue Dec 2 11:51:15 2014 -0800 Added MFIter::growntilebox that returns the tile box grown to include ghost cells; cleanup Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit af0f7127e02bfc0cbb7de66537059ed74c7c9a0d Author: Weiqun Zhang Date: Mon Dec 1 17:01:38 2014 -0800 Do not set initialized to false in CGSolver and MultiGrid::Finalize so that we don not have to query ParmParse again and again. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit b2b16cb83e66286cc68918dd4dd877ff9e5341a6 Author: Weiqun Zhang Date: Mon Dec 1 16:56:17 2014 -0800 Do not set initialized to false in LinOp::Finalize so that we don not have to query ParmParse again and again. Src/LinearSolvers/C_CellMG/LinOp.cpp commit 65544a61b0124310c40ca1972c7952342f53f860 Author: Weiqun Zhang Date: Mon Dec 1 15:57:42 2014 -0800 more tiling in C_CellMG Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LP_1D.F Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/MG_3D.F Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit cf3bc4c6ea1cbea3cf84b4a26558bae0a96353d4 Author: Weiqun Zhang Date: Mon Dec 1 15:16:36 2014 -0800 fixed a new bug Src/LinearSolvers/C_CellMG/ABec_2D.F commit e57c7f7eb4d1f2b92d4a620362cc64b1c830da03 Author: Weiqun Zhang Date: Mon Dec 1 14:56:35 2014 -0800 more tiling in C_CellMG Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_1D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/LO_1D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LinOp.cpp commit 6cf35951da4e26df78fabb2f4e32dd37d2044bb5 Author: Weiqun Zhang Date: Mon Dec 1 14:56:16 2014 -0800 added fluxbox to MFIter Src/C_BaseLib/FabArray.H commit 0241f72b95eedda23865220b00677870c45b4eea Author: Weiqun Zhang Date: Fri Nov 28 14:39:54 2014 -0800 BLMap: tidy Src/C_BaseLib/BLMap.H commit 2b1720ce9fac976c5410d216f36f9e55305fd72a Author: Weiqun Zhang Date: Fri Nov 28 14:15:53 2014 -0800 added local_size() function to FabArray.H; added reserve() to BLMap.H; fine tune BLMap::operator[] Src/C_BaseLib/BLMap.H Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/FabSet.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit 5e45246eda11b7f1b54eaa2192a76398eef4afe2 Author: Weiqun Zhang Date: Thu Nov 27 23:30:56 2014 -0800 comments Src/C_BaseLib/BLMap.H commit 10c6fcb0f2cf08bcacb486719d6998414dc0970c Author: Weiqun Zhang Date: Thu Nov 27 23:22:39 2014 -0800 comments Src/C_BaseLib/BLMap.H commit 880c5364021c8ed03d4d250a0d59803d8d6270d2 Author: Weiqun Zhang Date: Thu Nov 27 23:16:53 2014 -0800 added more comments Src/C_BaseLib/BLMap.H commit 76f61044ef3333336688d5dc727f2935c2db8fd5 Author: Weiqun Zhang Date: Thu Nov 27 22:19:03 2014 -0800 added BLMap, a lightweight and thread-safe (in reading) class with some features of std::map; use BLMap instead of std::map in LinOp Src/C_BaseLib/BLMap.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit be98d7267ed905a2cfdcc43f0c0d20a85ce11a8c Author: Weiqun Zhang Date: Wed Nov 26 20:47:49 2014 -0800 use std::lower_bound in local index search Src/C_BaseLib/FabArray.H commit acdb6a691a3965a5c3673c6ece7176aa6149d88b Author: ajnonaka Date: Wed Nov 26 08:57:45 2014 -0800 plug a memory leak for the case when you try to use bottom_solver_type=4 but the grid layout isn't appropriate Src/LinearSolvers/F_MG/mg.f90 commit 9e3dda83667c4b45de63d675306a217373e53627 Author: Weiqun Zhang Date: Wed Nov 26 07:00:00 2014 -0800 tiled C_CellMG/GSRB Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H commit 4e9afa22993202bed86db68b316dc54c379fdb0f Author: Ann Almgren Date: Tue Nov 25 13:41:23 2014 -0800 Add profiling to particle moveKick and moveKickDrift routines. Src/C_AMRLib/Particles.H commit dd5a57ddaa8397796b092b08da2fe023e72671eb Author: Weiqun Zhang Date: Mon Nov 24 10:22:29 2014 -0800 more mf[mfi.index()] --> mf[mfi] Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tutorials/AMR_Advection_C/Source/ADR.cpp Tutorials/AMR_Advection_C/Source/ADR_advance.cpp Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/main.cpp commit e3895129400adfe59f10ce2ba60e174c1b9fb5c5 Author: Weiqun Zhang Date: Mon Nov 24 09:43:46 2014 -0800 more mf[mfi.index()] --> mf[mfi] Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id Src/Python/swig/boxlib.i commit 807786eaf76dd4c26d803b0c5bb6f0f99f608c1a Author: Weiqun Zhang Date: Sun Nov 23 21:35:00 2014 -0800 fixed tiling bug in MFIter when inside OMP parallel region Src/C_BaseLib/FabArray.H commit a936f17600d7d8e785ecf05690690f8683290d37 Author: Weiqun Zhang Date: Sun Nov 23 20:43:47 2014 -0800 adde an omp atomic to fix a race condition Src/C_BaseLib/BaseFab.H commit adf02cdc413f26cb3591e222e73564fe8cdf3eda Author: Weiqun Zhang Date: Sun Nov 23 14:52:54 2014 -0800 clean up Src/C_BaseLib/FabArray.H commit 3651bdc5643988b16ab8ef449919123755027c83 Author: Weiqun Zhang Date: Sat Nov 22 22:07:02 2014 -0800 use binary search for local index Src/C_BaseLib/FabArray.H commit b3f3e1488accc54739807e5e7e308d1a7aad2bf0 Author: Weiqun Zhang Date: Sat Nov 22 20:34:51 2014 -0800 added a local index array that maps thread private index into local index of fab vectors Src/C_BaseLib/FabArray.H commit 84d695bca0c1aa946a0f0f9a877961cf6c59d477 Author: Weiqun Zhang Date: Fri Nov 21 22:27:21 2014 -0800 defensive programming: changed the name of the variable storing FAB* from m_fabs to m_fabs_v. we recently changed the variable type from map to vector for thread safety. So the meaning of operator[] has changed. Changing the name can prevent that variable being used directly be other classes. The last new bug I just fixed was due to direct use of the varible (i.e., not through member function) in TagBox (). Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H commit be0fd779a8de6995a7df23a995cd470546afef0f Author: Weiqun Zhang Date: Fri Nov 21 22:10:07 2014 -0800 fixed another new bug Src/C_AMRLib/TagBox.cpp commit b43045203c7f8b21386eaf28e422482b8cb4160e Author: Weiqun Zhang Date: Fri Nov 21 21:01:51 2014 -0800 fixed a new bug Src/C_AMRLib/AmrLevel.H commit 11da6250b4a504bef73844d8747684ffaf36404b Author: Weiqun Zhang Date: Fri Nov 21 19:17:21 2014 -0800 fixed a bug in localindex of the new vector based FabArray Src/C_BaseLib/FabArray.H commit 512a8c5c1555d898d80c3f05b54e16c94475cc5e Author: Weiqun Zhang Date: Fri Nov 21 17:01:39 2014 -0800 In many palce, use mfi instead of mfi.index() to access fab. This is now the preferred way because it is more efficient. MiniApps/MultiGrid_C/main.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit abae665a00efc01d69f74a8d3e6fce616550ffa5 Author: Weiqun Zhang Date: Fri Nov 21 15:59:51 2014 -0800 In FabArray, use vector instead of map to store fab pointers. Src/C_BaseLib/FabArray.H commit a93f8ee5695b83fdca4d9b73a0f3b2f8756ef0ff Author: Weiqun Zhang Date: Fri Nov 21 13:16:57 2014 -0800 Revert "tiled GSRB in C_CellMG" because of thread safety. The problem is C++ std::map::find is not thread safe. This reverts commit 7b452ac3e3eb9e1834fa8e8b4be8fce8ab7ded62. Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H commit f075d6a603172ebfd6b9536132616ca6a6af8d08 Merge: 7b452ac3e c5fc3205e Author: Weiqun Zhang Date: Fri Nov 21 11:29:32 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c5fc3205efedc9227ef8d7eaa33975df37fa95fd Author: vince Date: Fri Nov 21 11:19:23 2014 -0800 removed some debugging output. Src/C_BaseLib/DistributionMapping.cpp commit 9b577a0b32e3fdfa950a96afbdfd4842eddb410a Author: vince Date: Fri Nov 21 11:11:48 2014 -0800 removed unused vars. Src/C_BaseLib/DistributionMapping.cpp commit 7b452ac3e3eb9e1834fa8e8b4be8fce8ab7ded62 Author: Weiqun Zhang Date: Fri Nov 21 10:47:17 2014 -0800 tiled GSRB in C_CellMG Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H commit f356e494665d45067c992cb6a4dfbbc034f60eb4 Author: Weiqun Zhang Date: Fri Nov 21 10:18:14 2014 -0800 added some timers to C_CellMG Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 2768bd22a34164c214fcb551e26eb6d19602d683 Author: Weiqun Zhang Date: Thu Nov 20 20:45:00 2014 -0800 added tilebox function to MFIter; added a parameter for controlling tile size via ParmParse; another MFIter constructor that used the default tile size. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Tutorials/Tiling_C/main.cpp commit f4383963a99320815b2ca6c8f3690ad897d626e1 Author: Weiqun Zhang Date: Thu Nov 20 20:02:21 2014 -0800 fixed un-deleted heap memory to quiet valgrind MiniApps/MultiGrid_C/main.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tutorials/AMR_Trilinos_C/driver.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/WaveEquation_C/main.cpp commit 01943697212463e9f8bcf92cd88daa0f960b11d0 Merge: 05950d7b2 942074565 Author: vince Date: Thu Nov 20 17:23:35 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 05950d7b2cfb0196e6ca02f58c54afd13663b868 Author: vince Date: Thu Nov 20 17:23:25 2014 -0800 binary format for individual proc prof data. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 942074565e6c31fd1cb2d2e7a91707e5c6c71bd0 Author: Weiqun Zhang Date: Thu Nov 20 13:01:32 2014 -0800 validbox in MFIter must have the correct indexing type Src/C_BaseLib/FabArray.H commit 800a7be06fee2b8afa49b1e977ee2c1273b55526 Merge: ef6771baf d6f0727ec Author: Marc Day Date: Thu Nov 20 10:39:49 2014 -0800 Merge branch 'master' into 4thOrderMG commit d6f0727ece932becc9903790d59be47a888a7c02 Author: Weiqun Zhang Date: Thu Nov 20 10:38:42 2014 -0800 added a tutorial code showing how tiling version of MFIter can be used. Tutorials/Tiling_C/GNUmakefile Tutorials/Tiling_C/Make.package Tutorials/Tiling_C/main.cpp Tutorials/Tiling_C/work.f90 commit ef6771baf402ad1f5a8b0cee34ed070f42eaf30a Author: Marc Day Date: Thu Nov 20 10:37:58 2014 -0800 Initial commit of branch for 4th order mg Src/C_BaseLib/BLFort.H Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG4/ABec2.H Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec2_2D.F Src/LinearSolvers/C_CellMG4/ABec2_3D.F Src/LinearSolvers/C_CellMG4/ABec2_F.H Src/LinearSolvers/C_CellMG4/ABec4.H Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_CellMG4/ABec4_2D.F Src/LinearSolvers/C_CellMG4/ABec4_3D.F Src/LinearSolvers/C_CellMG4/ABec4_F.H Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_CellMG4/Make.package Src/LinearSolvers/C_CellMG4/OpenSource.txt Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Tools/C_mk/Make.mpi Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit e3aad315d19cf8361c0cd020fa0a1103db46d534 Author: Weiqun Zhang Date: Thu Nov 20 10:20:23 2014 -0800 Implemented a tiling version of MFIter. This should not affect the results of any codes unless a tiling version of MFIter is actually used. Src/C_BaseLib/FabArray.H commit ae9018b0141247ffc9a7387916053dcb5f401d2e Author: Weiqun Zhang Date: Wed Nov 19 16:19:10 2014 -0800 commented out a cout Src/C_BaseLib/DistributionMapping.cpp commit be3a3b06363d4f04312d216df9baf8c6b84e1367 Author: vince Date: Wed Nov 19 14:54:58 2014 -0800 moved readBoxArray from StateData to BoxArray, removed dependencies in DistributionMapping. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/DistributionMapping.cpp Tests/C_BaseLib/GNUmakefile commit 5412143cd81176440cebb52dfadcb69bdb93e237 Author: vince Date: Wed Nov 19 14:48:54 2014 -0800 added to the docs. Docs/Readme.profiling commit cb61af8f51b7a3fa933a0bf893773204bd12b276 Merge: 98e661c43 e82350f56 Author: Weiqun Zhang Date: Wed Nov 19 13:30:48 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Src/C_BaseLib/DistributionMapping.cpp commit 98e661c4373ac5aeb264a25c646cdaab1d8fec92 Author: Weiqun Zhang Date: Wed Nov 19 13:19:46 2014 -0800 Tutorials/HelloWorld_C: changed domain size Tutorials/HelloWorld_C/main.cpp commit 2ea6a56f9610834d7e7fc0d00ebc76d5f83ada1d Author: Weiqun Zhang Date: Wed Nov 19 09:30:41 2014 -0800 removed an unused variable Src/C_BaseLib/threadbox.f90 commit e82350f5638d42fb0f2b827dececdbf9f54f3cb8 Merge: be8cb5dc4 c83298cc6 Author: vince Date: Tue Nov 18 14:28:02 2014 -0800 more merge cleanup. commit be8cb5dc49e6bfa366f913f56b50b4d17c25fca4 Merge: 3a0dc1f2c dd4da37c2 Author: vince Date: Tue Nov 18 14:12:31 2014 -0800 merge resolution. commit 9b6897a0257ba448c7e84619ef16c94dd60554f8 Author: Weiqun Zhang Date: Tue Nov 18 13:57:54 2014 -0800 minor Src/C_BaseLib/DistributionMapping.cpp commit c83298cc633919448f3831d2f8d52a1a7a80c0f6 Author: Weiqun Zhang Date: Tue Nov 18 13:23:08 2014 -0800 Removed the long long int stuff I recently committed and the long long int stuff in Particles I did a while ago. But I added a warning about the size of long int, if it is too small. I give up because: (1) there are many places that have to be changed if we really want to make sure BoxLib can handle really big runs on systems like Windows where long int is only 4-byte wide; (2) on most if not all Unix systems, long int is 8-byte wide. Src/C_AMRLib/Particles.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 5a602e79816cb90b6ec55c113886f12dbb8813fc Author: Weiqun Zhang Date: Tue Nov 18 11:16:29 2014 -0800 minor cleanup: std::map::insert checks if the element to be inserted already existed, so we do not have to do it ourselves Src/C_BaseLib/DistributionMapping.cpp commit 3a0dc1f2c1fcbdd48255420233b5cb12e3332f85 Author: vince Date: Tue Nov 18 10:25:25 2014 -0800 some fortran profiling tests. Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/TPROFILER.F Tests/C_BaseLib/TPROFILER_F.H Tests/C_BaseLib/tProfiler.cpp commit 68f11eb7a13df2fe5d263e5dfa2de1eead8ee0ff Author: vince Date: Tue Nov 18 10:24:03 2014 -0800 made regular profiling for ParallelDescriptor functions a special profiling option. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 90b22c61f2837a2cf66db311fe021f2be7e61a51 Author: vince Date: Tue Nov 18 10:22:21 2014 -0800 some cleanup before the merge. Src/C_AMRLib/Amr.cpp commit c46cdf96bb3d9072cda72a8fec452045f52569e8 Author: vince Date: Tue Nov 18 10:21:44 2014 -0800 added faster fortran interface for functions with a large number of calls. Src/C_BaseLib/BLProfiler_F.f Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit dd4da37c2064776fed6460b44080d6ebc88d3505 Author: Weiqun Zhang Date: Tue Nov 18 06:26:45 2014 -0800 fixed typo and made it compile again. added comment on long long int. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/DistributionMapping.cpp commit 9febb8d587cb796657bc1f832edb12b975b40b7d Author: Weiqun Zhang Date: Mon Nov 17 16:43:13 2014 -0800 Make stable sort in LeastUsedCPUs truly stable. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 15d47dc36a0c06f328a8bea93e807186fa00eed7 Author: Weiqun Zhang Date: Mon Nov 17 16:33:39 2014 -0800 Use long long int for storing the total bytes allocated. The maximum value of long int is only slightly larger than 2e9, whereas a compute node of Edison has 64 GB memory. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/DistributionMapping.cpp commit ed546a3fb9322a3996453fad2f57817d6fc0e45a Author: Weiqun Zhang Date: Mon Nov 17 15:17:51 2014 -0800 comment Src/C_BaseLib/DistributionMapping.H commit 2954e0eca64dcbe9219573c8aa9100ce48734966 Author: Weiqun Zhang Date: Mon Nov 17 15:05:03 2014 -0800 Added one more digit to a few constants to achieve machine accuracy. For example, (1.d0/6.d0 .eq. 0.1666666666666667d0) is false, whereas (1.d0/6.d0 .eq. 0.16666666666666667d0) is true, if IEEE 754 is used. Src/C_BaseLib/CONSTANTS.H commit 6c6be22973915863be5fef531e00dc11ba8fa428 Merge: 716d8e27b b12571515 Author: Weiqun Zhang Date: Mon Nov 17 12:07:35 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 716d8e27be9a80e063175415bdf1a3fe90fb8622 Author: Weiqun Zhang Date: Mon Nov 17 12:05:54 2014 -0800 Fixed Box::isEmpty(). The old version would abort on an empty box in DEBUG mode because of an assertion. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 22b2aa16a05773b5fe404e83dc92f0bc1cac0c3b Author: Weiqun Zhang Date: Mon Nov 17 11:04:59 2014 -0800 minor cleanup Src/C_BaseLib/Box.H commit 24e3d0b53fabdaafa048528e9eb174509e939162 Author: Weiqun Zhang Date: Fri Nov 14 13:26:02 2014 -0800 added long long type for number of points in a BoxArray Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit e6df95f8e8bebcca2f4375b7a9465c35807d2ff7 Author: Weiqun Zhang Date: Fri Nov 14 13:25:07 2014 -0800 modified comment Src/C_BaseLib/Pointers.H commit f1e61ecb6cb97f9992eb75dd15211c8bd6d3a3ef Author: Weiqun Zhang Date: Thu Nov 13 17:08:18 2014 -0800 clean up USE_F90_SOLVERS Tests/LinearSolvers/C_CellMG/GNUmakefile Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini commit ad8c5100a156826d74e617bcda78c01292d6f3fe Author: Weiqun Zhang Date: Thu Nov 13 16:29:13 2014 -0800 removed an old obsolete file Src/C_BaseLib/std/limits commit 4209fbf4ab1bf553d311e051b522e860470bddc9 Author: Matthew Emmett Date: Fri Nov 14 00:25:10 2014 +0300 PyBoxLib: Tidy a lot and use relative imports. Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/boxarray.py Src/Python/F90/fboxlib/fab.py Src/Python/F90/fboxlib/fabutils.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/fboxlib/multifab.py Src/Python/F90/fboxlib/plotfile.py Src/Python/F90/fboxlib/regrid.py Src/Python/F90/fboxlib/utils.py Src/Python/F90/tests/regrid.py commit 48a0809280d010a63cc0419e6906a8e56d78e7c8 Author: Matthew Emmett Date: Fri Nov 14 00:05:59 2014 +0300 PyBoxLib: Update README files and add test script. Src/Python/F90/README Src/Python/F90/setup.py Src/Python/F90/test.py Src/Python/README commit 067ecf979a2e954d14652696886243c0d8d1c26d Author: Matthew Emmett Date: Thu Nov 13 23:56:02 2014 +0300 PyBoxLib: Flesh out new wrapper, regridding works. Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/base.py Src/Python/F90/fboxlib/fab.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/fboxlib/multifab.py Src/Python/F90/fboxlib/pybl.py Src/Python/F90/fboxlib/regrid.py Src/Python/F90/src/boxlib_numpy_c.c Src/Python/F90/src/boxlib_numpy_f.f90 Src/Python/F90/src/fboxlib.f90 Src/Python/F90/src/fboxlib_c.c Src/Python/F90/src/make_new_grids.f90 Src/Python/F90/src/tag_boxes.f90 commit 6166cbc4c27592bac8712c72a8440e743638dc94 Author: Matthew Emmett Date: Thu Nov 13 16:27:04 2014 +0300 PyBoxLib: Begin new wrapper. Src/Python/F90/Makefile Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/boxarray.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/src/fboxlib.f90 Src/Python/F90/src/fboxlib_c.c commit 3632ee5185d0eb232daf620cef54a5f0383df90f Author: Matthew Emmett Date: Thu Nov 13 12:21:31 2014 +0300 PyBoxLib: Add tagging callback throughout. Src/Python/F90/fboxlib/regrid.py Src/Python/F90/src/fboxlib.f90 Src/Python/F90/src/make_new_grids.f90 Src/Python/F90/src/regrid.f90 Src/Python/F90/src/tag_boxes.f90 commit 22607336e4a317554643c4f368dadf7afc5ee46a Author: Matthew Emmett Date: Thu Nov 13 10:47:11 2014 +0300 PyBoxLib: Mandatory boxes when creating a box array. Src/Python/F90/fboxlib/boxarray.py Src/Python/F90/fboxlib/pybl.py commit 1479f6d446dc71920cd8491960e0721549c1c1cb Author: Matthew Emmett Date: Thu Nov 13 10:46:43 2014 +0300 PyBoxLib: Add preliminary regrid capabilities. Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/regrid.py Src/Python/F90/src/fboxlib.f90 commit bbb501972895e5080448d8fbc4120cd9d131949a Author: Matthew Emmett Date: Thu Nov 13 10:45:51 2014 +0300 PyBoxLib: Try to be a bit more defensive in `base.py`. Src/Python/F90/fboxlib/base.py commit 5b504c66ee7ab9c738bc1964e91ad7d7a38dff2c Author: Matthew Emmett Date: Thu Nov 13 10:02:01 2014 +0300 regrid: Change an inout to an in, set nlevs_old properly. Src/F_BaseLib/regrid.f90 commit 80ccfebb33f6be3a70889159c7e4e5d536ac8e0c Author: vince Date: Wed Nov 12 18:04:56 2014 -0800 some profiling test codes. Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/TPROFILER.F Tests/C_BaseLib/TPROFILER_F.H Tests/C_BaseLib/tProfiler.cpp commit 6ef851f63f9601dcd8ec7e21da0844102c5d088b Merge: 5f7586482 f32674690 Author: vince Date: Wed Nov 12 16:11:33 2014 -0800 Merge branch 'master' into commprof in ParallelDescriptor.cpp, readded the deleted BL_COMM_PROFILE calls before the calls to mpi functions, they are required. left the BL_PROFILE calls in the code but commented out. some after merge cleanup. Conflicts: Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/F_BaseLib/bl_prof.f90 commit 5f75864824656f59b300d8555f6a0fe02ebf6fc4 Author: vince Date: Wed Nov 12 15:24:07 2014 -0800 cleanup before merge. Tests/C_BaseLib/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit f326746902c11ddc679e4550a4d4f2aeb9a9a912 Author: Matthew Emmett Date: Wed Nov 12 23:13:32 2014 +0300 PyBoxLib: Fix installation of fboxlib. Src/Python/F90/Makefile Src/Python/F90/fboxlib/fab.py Src/Python/F90/fboxlib/pybl.py Src/Python/F90/setup.py commit b4baf63c9d654bd88bf768d1007cfb18a94d9fdd Author: Matthew Emmett Date: Wed Nov 12 17:25:43 2014 +0300 PyBoxLib: Tidy. Src/Python/GNUmakefile_F90.mak Src/Python/fsrc/blobjects.f90 Src/Python/fsrc/blobjects.py Src/Python/fsrc/boxlib_numpy_c.c Src/Python/fsrc/boxlib_numpy_f.f90 Src/Python/fsrc/fboxlib.f90 commit 8aa1b7c40369fd2d61abeecad5c9ac95cef03f7d Merge: 6190502b7 cc4785f2c Author: Matthew Emmett Date: Wed Nov 12 17:21:10 2014 +0300 Merge branch 'master' of gamera.lbl.gov:/home/CCSE/gitroot/BoxLib commit 6190502b73f7e8f9805ced0a5eb2aa354d2ade41 Author: Matthew Emmett Date: Wed Nov 12 17:20:46 2014 +0300 PyBoxLib: Restore Fortran version in Src/Python/F90. Src/Python/F90/Makefile Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/base.py Src/Python/F90/fboxlib/boxarray.py Src/Python/F90/fboxlib/fab.py Src/Python/F90/fboxlib/fabutils.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/fboxlib/multifab.py Src/Python/F90/fboxlib/plotfile.py Src/Python/F90/fboxlib/pybl.py Src/Python/F90/fboxlib/utils.py Src/Python/F90/setup.py Src/Python/F90/src/blobjects.f90 Src/Python/F90/src/blobjects.py Src/Python/F90/src/boxlib_numpy_c.c Src/Python/F90/src/boxlib_numpy_f.f90 Src/Python/F90/src/fboxlib.f90 commit cc4785f2c29e6d06fc2d19a98e780649578474fc Author: Weiqun Zhang Date: Tue Nov 11 12:55:22 2014 -0800 removed xHost from intel compiler options because the executable may run on different processors than the host processor where it is compiled Tools/C_mk/Make.defs Tools/F_mk/comps/Linux_intel.mak commit d3e8dcf35fa1eccb6ee2646c2189d5a15c9b66af Author: Weiqun Zhang Date: Tue Nov 11 10:35:25 2014 -0800 added a fortran module that can do domain decomposition for threads Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/threadbox.f90 commit e081696a1f506998e2f2127054d7595d1de91211 Author: Matthew Emmett Date: Tue Nov 11 16:43:55 2014 +0300 PyBoxLib: Bring back Fortran version of PyBoxLib. Src/Python/GMakerules.mak Src/Python/GNUmakefile_F90.mak Src/Python/GPackage.mak Src/Python/fsrc/blobjects.f90 Src/Python/fsrc/blobjects.py Src/Python/fsrc/boxlib_numpy_c.c Src/Python/fsrc/boxlib_numpy_f.f90 Src/Python/fsrc/fboxlib.f90 commit dec7bcb702e46c3201efb9c702a726cf72ad0ff7 Author: Matthew Emmett Date: Tue Nov 11 16:11:47 2014 +0300 PyBoxLib: Another fix for libgfortran. Src/Python/GNUmakefile_CXX.mak commit b16328852b1dece9580e706d13a0c23df9d73cc3 Author: Matthew Emmett Date: Tue Nov 11 09:58:08 2014 +0300 PyBoxLib: Better gfortran detection (from Aron Ahmedia). Src/Python/GNUmakefile_CXX.mak commit efc2229c2913dd525092b4bf544eaeb66afeeacc Author: Matthew Emmett Date: Tue Nov 11 09:57:21 2014 +0300 PyBoxLib: Revert back to distutils instead of setuptools. Src/Python/setup.py commit d62b7b8698d983ccb5542408c5314a72fec6167f Author: Matthew Emmett Date: Sun Nov 9 22:26:57 2014 +0300 PyBoxLib: Fix BOXLIB_HOME for hashdist. Src/Python/GNUmakefile_CXX.mak commit 4451852a3552b063944acf000a86cb70d026bb2c Author: Matthew Emmett Date: Sun Nov 9 07:10:06 2014 -0800 PyBoxLib: Tweak BOXLIB_HOME. Src/Python/GNUmakefile_CXX.mak commit b5681298a91e29f23b6e0459bfdbfeff74eefdec Author: Matthew Emmett Date: Sun Nov 9 05:15:30 2014 -0800 PyBoxLib: Get 'python setup.py develop' working. Src/Python/setup.py commit 4f0a09e09e2cacb6d3234a5c1c0939593872edad Author: vince Date: Fri Nov 7 16:35:22 2014 -0800 typo, removed old code. Src/C_BaseLib/Profiler.cpp commit f4c2e8c5509b25082a9cc79d4092c123b705f7a1 Author: Weiqun Zhang Date: Fri Nov 7 12:49:56 2014 -0800 put the new mpi_waitall code inside 'if' so that it won't break assertion in BaseFab Src/C_BaseLib/FabArray.H commit 147b64e4be6cacc25f52f08fac6d5a9908affb30 Author: Weiqun Zhang Date: Fri Nov 7 08:16:14 2014 -0800 fixed OMP in Jacobi smoother Src/LinearSolvers/C_CellMG/ABec_3D.F commit 2db23654823f105eddb576995fae71f3fe1df48c Author: Weiqun Zhang Date: Thu Nov 6 16:59:18 2014 -0800 C++: Use isend instead of send and replace waitsome with waitall. This makes fill boundary noticeably faster just we have observed in F90 codes. Note that MPI_Waitsome is always slower than MPI_Waitall because the former does a lot more testing, and unpacking the data is much cheaper than the overhead of waitsome. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 1acde6d06951c4befd2ca8a5a0686e47a1fd146f Author: Weiqun Zhang Date: Thu Nov 6 16:46:43 2014 -0800 shut down compiler warning by removing some unnecessary const prefixes to functions return plain numbers Src/C_BaseLib/Profiler.H commit 3589f957d00211f264b8173535e9b3d7a66799e3 Author: Weiqun Zhang Date: Thu Nov 6 16:43:34 2014 -0800 removed BL_PROFILE (not BL_COMM_PROFILE) from ParallelDescriptor because (1) there is already commprof; (2) this reduces clutter in the profiling report and gives a better idea about the cost of fill boundary and copy. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit f6c6fddfb9d51840d5e6c941125f0b79dd97eae6 Author: ajnonaka Date: Thu Nov 6 13:21:38 2014 -0800 call applyBC before calling jacobi smoother (now mirrors GSRB) Src/LinearSolvers/C_CellMG/LinOp.cpp commit 0141cebb0749026ac21372b81315a52b78d2b9d9 Author: ajnonaka Date: Thu Nov 6 13:20:27 2014 -0800 properly implement jacobi smoothing in 2d and 3d Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F commit 6ad37e7a908f301357bc9914667d0fe4842bf899 Author: Weiqun Zhang Date: Wed Nov 5 20:39:14 2014 -0800 F90: send -> isend. We used to call irecv's followed by send's. Changing to isend makes multifab_copy and multifab_fill_boundary 20+% faster. Src/F_BaseLib/multifab_f.f90 commit eb5d1a780e2a978f822299f0569ffff551840435 Author: Weiqun Zhang Date: Wed Nov 5 09:35:54 2014 -0800 F90: removed "intent(in)" from parallel_bcast because (1) it currently causes seg fault on Edison when compiled with gfortran; (2) it is incorrect: only for root rank that argument has intent(in), whereas it should be intent(out) for other MPI ranks. Src/F_BaseLib/parallel.f90 commit fa7626269a1dfa0ec2193648f8dee4730354dec8 Author: ajnonaka Date: Wed Nov 5 09:21:37 2014 -0800 cims.nyu.edu Tools/C_mk/Make.defs commit 812acd140d830ede903f2cc651866d49bb764b2d Author: Weiqun Zhang Date: Tue Nov 4 20:14:35 2014 -0800 make Cray compiler on edison happy Src/F_BaseLib/layout.f90 commit 852696a18b412c8d78055710885013cfd940952b Author: Weiqun Zhang Date: Tue Nov 4 11:32:08 2014 -0800 wrap up ml layout strategy stuff Src/F_BaseLib/ml_layout.f90 commit eb49fdc55aa78d5608314dbc17fd7cf705091730 Author: Weiqun Zhang Date: Mon Nov 3 16:38:37 2014 -0800 more work on multi-level strategy 2 Src/F_BaseLib/ml_layout.f90 commit ec2c2e9d009c6c158489bdfb56851a1893698457 Author: Adam Jacobs Date: Mon Nov 3 19:02:01 2014 -0500 Further increase maximum pathname size, and get rid of magic numbers. Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/ppm_util.f90 Src/F_BaseLib/ppm_util_c.c commit 3472e1f923779615876b93a0d737a0665c21eb64 Author: ajnonaka Date: Mon Nov 3 14:08:41 2014 -0800 Donev updates Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit becc8e9c4be3cf60cf5f314105049c1161ffff3c Merge: d302b3b9d 5c7d22417 Author: Michael Zingale Date: Sat Nov 1 19:39:46 2014 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit 35715c3fd2335ce103123413f98fa181a89d8678 Author: Weiqun Zhang Date: Fri Oct 31 14:46:03 2014 -0700 added comments Src/F_BaseLib/create_umac_grown.f90 commit e3c13fdb6a0edcc4398ef44da2cdbb350ddc6927 Author: Weiqun Zhang Date: Fri Oct 31 14:30:26 2014 -0700 fixed the fix Src/F_BaseLib/create_umac_grown.f90 commit d9840f8060b20a4299afc4b8c018e82f50de4cf8 Merge: 042067fe7 35260a88f Author: Weiqun Zhang Date: Fri Oct 31 14:21:51 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 042067fe72c0368fc566b684e1be817538e507a6 Author: Weiqun Zhang Date: Fri Oct 31 14:21:46 2014 -0700 fixed a new bug in create_umac_grown Src/F_BaseLib/create_umac_grown.f90 commit 35260a88f166c9e8e1e41c9b917e94084dfb1b85 Author: Ann Almgren Date: Fri Oct 31 14:20:38 2014 -0700 Add InitCosmo1ppcMultiLevel for IAG folks. Src/C_AMRLib/Particles.H commit 25e55d893e12ad4243b908b739ad9a5cbc9ef318 Merge: 004bd5c47 2609dcefe Author: Weiqun Zhang Date: Thu Oct 30 17:35:27 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 004bd5c471d273b97c9c7c1a081386873b306ad2 Author: Weiqun Zhang Date: Thu Oct 30 17:05:03 2014 -0700 removed one parallel copy from fill ghost cells Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit f661d72b6803af2f8bbcc898c763e8168ad72cff Author: Weiqun Zhang Date: Thu Oct 30 16:35:19 2014 -0700 added argument to create_umac_grown to tell whether we need to fill fine boundaries Src/F_BaseLib/create_umac_grown.f90 commit c2334f4665a2f7cfbb98a29370737c5e595f20ab Author: Weiqun Zhang Date: Thu Oct 30 16:29:03 2014 -0700 cleanup Src/F_BaseLib/create_umac_grown.f90 commit e5bcb7c45be1401f2f721bdd93ff731fe87b3908 Author: Weiqun Zhang Date: Thu Oct 30 16:06:06 2014 -0700 removed a parallel copy and fill_boundary from create_umac_grown Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/layout.f90 commit 657b439bd84bf1da3c360628d3928d0b8cb7aa45 Author: Weiqun Zhang Date: Thu Oct 30 10:03:59 2014 -0700 merge ghstassoc with fgassoc Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/layout.f90 commit 0e59aa042a44cc24dad9eafa4ee359a24731ddb7 Author: Weiqun Zhang Date: Thu Oct 30 09:55:42 2014 -0700 simplify the boxarray in ghstassoc Src/F_BaseLib/layout.f90 commit 1b2970a6a21e41c9d6edd8ca5eaea181f7297730 Author: Weiqun Zhang Date: Wed Oct 29 17:53:34 2014 -0700 work in progress for ghstassoc, which is intended to replace fgassoc Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/layout.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 0a159b682f2e3f116db702b12cbadb2478f9ea16 Author: vince Date: Wed Oct 29 13:53:54 2014 -0700 put all output into one directory, bl_prof (or user specified name). write inclusive times option. trace flush threshold. directory creation cleanup. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 0ff5c471c44122a341ea13f6e3db5bcf052129fd Author: vince Date: Wed Oct 29 13:49:57 2014 -0700 optional barrier in ccd. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit edcf4c51d6f653a049acb163f075eebfe1023b75 Author: vince Date: Wed Oct 29 12:51:23 2014 -0700 clean up directory creation. Src/C_AMRLib/Amr.cpp commit ea99ba554c46fd1eb91d571a09694c4132c10219 Author: Weiqun Zhang Date: Wed Oct 29 12:14:50 2014 -0700 make ml layout strategy 1 more load balanced Src/F_BaseLib/fab.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/sort_i.f90 commit 68d38d08e031c3f1f6660aea2a062ace89439a5f Author: vince Date: Wed Oct 29 11:49:41 2014 -0700 create clean directory function. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit b5d48ea6ad5111abef8de7dc1cbe10c687d95182 Merge: 6ca23d19c 2609dcefe Author: Adam Jacobs Date: Wed Oct 29 10:56:57 2014 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2609dcefe467d1eefe5a34fad981aafa130448d3 Author: Weiqun Zhang Date: Tue Oct 28 20:34:29 2014 -0700 removed some includes Tutorials/HelloWorld_C/GNUmakefile commit e4ab59d0346867db81453b10bb485683ba040f48 Author: Weiqun Zhang Date: Tue Oct 28 17:34:10 2014 -0700 Added a "hello world" type program for people to try tiling. Tutorials/HelloWorld_C/GNUmakefile Tutorials/HelloWorld_C/Make.package Tutorials/HelloWorld_C/main.cpp Tutorials/HelloWorld_C/work.f90 commit d302b3b9dc2cc1d045ca919b9a994b1208b256f9 Author: Michael Zingale Date: Tue Oct 28 20:21:51 2014 -0400 add a trim() fvarnames.f90 commit 5c7d224176b06eb1b46d6de83df514fc4ab8ba7f Author: Adam Jacobs Date: Tue Oct 28 17:10:52 2014 -0400 Add comparison temp histograms using the EoS. MAESTRO_sub_chandra/GNUmakefile MAESTRO_sub_chandra/fsubchandra.f90 MAESTRO_sub_chandra/fsubchandra_mod.f90 commit 4d8d58e9cc520ece0736a35fcf86f8b1d4cc94c8 Author: Weiqun Zhang Date: Tue Oct 28 14:06:33 2014 -0700 F90 ml layout strategy 1: use prefilled version of knapsack for unassigned boxes. Src/F_BaseLib/ml_layout.f90 commit 2490dbf547a444e097195acbd5ddf3c560fc7f2f Author: Weiqun Zhang Date: Tue Oct 28 14:05:40 2014 -0700 F90: new knapsack that can have processors prefilled with boxes Src/F_BaseLib/knapsack.f90 commit 04ef81cfc8915bb56ac792edfd54b81a6aedea77 Author: vince Date: Mon Oct 27 15:38:12 2014 -0700 added call trace data flushing. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 79106b16218ef782ccafaed6f21b4a90ecc7d73c Author: Weiqun Zhang Date: Mon Oct 27 15:17:18 2014 -0700 F90: fine tune ml layout strategy 2 Src/F_BaseLib/ml_layout.f90 commit 0f79fe02a18b8067f728830cb077199826f61e1a Author: Weiqun Zhang Date: Mon Oct 27 14:59:56 2014 -0700 F90: fine tune ml layout strategy 2 Src/F_BaseLib/ml_layout.f90 commit 100e9e66a6823fd5d371a01059a220d0207699c5 Author: Weiqun Zhang Date: Mon Oct 27 14:20:28 2014 -0700 F90: implemented ml layout strategy 2 Src/F_BaseLib/ml_layout.f90 commit 1e873a181478c9f2d0c2d31d38e61658e99f5295 Author: Weiqun Zhang Date: Sun Oct 26 21:36:48 2014 -0700 cleanup Tutorials/HeatEquation_EX7_F/GNUmakefile commit 23fdc8b4b82e083e4ae88da81ae78ce10b8852d8 Author: Weiqun Zhang Date: Sun Oct 26 21:29:15 2014 -0700 update comments Src/F_BaseLib/ml_layout.f90 commit 5dc6f66c4d44cc5dca4962ce46738243cf2476d1 Author: Weiqun Zhang Date: Sun Oct 26 21:27:56 2014 -0700 F90: use the simple version for tutorial Tutorials/HeatEquation_EX5_F/main.f90 commit 4cf6808de2162dad96b911dba4e747cddf2cb743 Author: Weiqun Zhang Date: Sun Oct 26 21:20:25 2014 -0700 minor Tutorials/AMR_Adv_Diff_F/main.f90 commit 81e7332be666dae1610ad5da0231ad3143a74da1 Author: Weiqun Zhang Date: Sun Oct 26 21:19:28 2014 -0700 fixed a bug in Tutorials/AMR_Adv_Diff_F Tutorials/AMR_Adv_Diff_F/compute_flux.f90 commit 9b3014acbef3da122f826776f9acec0c4b8da6bb Author: Weiqun Zhang Date: Sun Oct 26 19:38:01 2014 -0700 F90: destroy unused layouts Src/F_BaseLib/ml_layout.f90 commit 6d015082d8df1b834b2f426968230f333761ab63 Author: Weiqun Zhang Date: Sun Oct 26 15:15:18 2014 -0700 F90: back to use lower corner of boxes in sfc for testing, and some other minor changes MiniApps/AMR_Adv_Diff_F90/main.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/ml_layout.f90 commit 6aa0c987205848e719fa79be1303833504e31b3a Author: Weiqun Zhang Date: Sun Oct 26 14:01:51 2014 -0700 F90: implemented the ignore_fine_in_layout_mapping strategy in ml_layout.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_layout.f90 commit a7df7dc62a1a2e9102bc43f2d2084121319d4c18 Author: Weiqun Zhang Date: Sun Oct 26 11:37:57 2014 -0700 F90: moved ml layout optimization stuff into ml_layout module, and do it when building ml_layout MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/write_plotfile.f90 Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/GPackage.mak Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_optimization.f90 Src/F_BaseLib/ml_remap.f90 Src/F_BaseLib/regrid.f90 Tutorials/HeatEquation_EX5_F/main.f90 commit 95e959dfb9dc44400065e43f7085a970aff1b31a Author: Weiqun Zhang Date: Sat Oct 25 21:37:18 2014 -0700 renaming: ml_layout_remap --> ml_remap; and flesh out more interfaces Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/GPackage.mak Src/F_BaseLib/ml_layout_remap.f90 Src/F_BaseLib/ml_optimization.f90 Src/F_BaseLib/ml_remap.f90 commit 8b22442d14c2d5e846738bc1747500594b8fb8b2 Author: Weiqun Zhang Date: Sat Oct 25 20:36:13 2014 -0700 F90: cleaned up layout by removing obsolete pn_children Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_layout.f90 commit b256351283fb329eb85f5f43448965fe3e5dee1f Author: Michael Zingale Date: Sat Oct 25 20:50:03 2014 -0400 add a 1-d routine, in prep for the Maestro flame problem. Also some styling syncing with that version Src/F_BaseLib/multifab_physbc.f90 commit 3c33fa93410f0c42f03245df91bdf30bd94a8a94 Author: Weiqun Zhang Date: Fri Oct 24 21:18:03 2014 -0700 F90: flesh out ml layout remapping Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/GPackage.mak Src/F_BaseLib/ml_layout_remap.f90 Src/F_BaseLib/ml_optimization.f90 Src/F_BaseLib/regrid.f90 commit 7061443c2396c3f415e2b95bf38d6d299d4630af Author: Weiqun Zhang Date: Fri Oct 24 17:17:36 2014 -0700 F90: use center of boxes instead of lower corner in sfc Src/F_BaseLib/knapsack.f90 commit 934530bcd9388daf4ed264de2bff2bd6d5bd10bd Author: Weiqun Zhang Date: Fri Oct 24 16:35:31 2014 -0700 F90: split sfc_i into two functions, and save sfc order in layout Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 commit b2e823c45b9c4539849b9534de24d388f61dec03 Merge: ada8195be f83d67e3a Author: Adam Jacobs Date: Wed Oct 22 17:40:11 2014 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing Conflicts: F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 commit ada8195beb70d0cf0fed7ebffc84fb6ba1dd58dc Author: Adam Jacobs Date: Wed Oct 22 17:38:02 2014 -0500 Add ability to handle full star geometries to sub-Chandra analysis routine. MAESTRO_sub_chandra/fsubchandra.f90 MAESTRO_sub_chandra/fsubchandra_mod.f90 commit f83d67e3a025012755c42df235fe6ae74a07b864 Merge: 04a1bde19 9d49ed7ea Author: Adam Jacobs Date: Wed Oct 22 18:35:45 2014 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit 04a1bde19337fea4f5c940673d7f3cf520bd5fe8 Author: Adam Jacobs Date: Wed Oct 22 18:35:07 2014 -0400 Add caclulation of temperature histogram data for the lengthscale of each level of refinement. MAESTRO_sub_chandra/fsubchandra.f90 MAESTRO_sub_chandra/fsubchandra_mod.f90 commit 6ca23d19c4d28c385cdf55a13fa74f1995014e57 Merge: 74cae01e9 a710adc26 Author: Adam Jacobs Date: Tue Oct 21 15:37:49 2014 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib Conflicts: Tools/F_mk/comps/Linux_intel.mak commit 74cae01e93529fe385cd5c5067859a00a7a5f95f Author: Adam Jacobs Date: Tue Oct 21 15:34:15 2014 -0500 Add version 15 of the Intel compiler to Linux_intel.mak. This is the version on Blue Waters. Tools/F_mk/comps/Linux_intel.mak commit a710adc2677cc775866842fdc541a94909e2372f Author: Matthew Emmett Date: Tue Oct 21 12:48:25 2014 -0700 MLSDCAmr: Use AmrLevel constructors for MLSDCAmrLevel. Src/C_AMRLib/MLSDCAmr.H commit 7a7d585389b18315af009182e4abbd55e5e39e6d Author: Matthew Emmett Date: Tue Oct 21 12:42:39 2014 -0700 Add MLSDCAmr. Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/MLSDCAmr.cpp Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_AMRLib/Make.package commit 893a1ff11679a2f13c8110ed6edad761e5dee4c7 Author: vince Date: Tue Oct 21 11:16:01 2014 -0700 added file Src/C_BaseLib/BLProfiler_F.f commit b5304da1a09954588c75af84de0f73f65c4145f1 Author: vince Date: Tue Oct 21 10:50:12 2014 -0700 added proffort interface to master branch. Src/C_BaseLib/Make.package Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_prof_stubs.f90 commit d081130b301f101175f877a55fd983e36dfddd01 Author: vince Date: Mon Oct 20 13:37:54 2014 -0700 added step regions. Src/C_AMRLib/Amr.cpp commit 831e0ca4c5d29dc531a5dfd87c8c74e39b2e0bbc Merge: 97a909929 e31c68669 Author: Weiqun Zhang Date: Mon Oct 20 10:16:50 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 97a909929b67b795acef20ca2a681e995e012478 Author: Weiqun Zhang Date: Mon Oct 20 10:12:57 2014 -0700 When printing fab byte spread information, let's us MB as units for avoiding integer overflow and readablity Src/F_BaseLib/fab.f90 commit e31c686698610167a7831207e1cc1484fda05cf7 Author: Michael Zingale Date: Sun Oct 19 15:50:39 2014 -0400 add "tooltips" when you hover over a test's cell in the master table of all the runs. Tools/RegressionTesting/testnew.py commit 4b7c1180bac396265f384ee84bfa9af7e7e4b5e6 Merge: fe652a729 e3d58afc0 Author: Michael Zingale Date: Sun Oct 19 06:20:16 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit fe652a729500d7753310ade92b834a44636605ea Author: Michael Zingale Date: Sun Oct 19 06:19:48 2014 -0700 remove support for Intel versions 8 and 9 -- these are about 10 years old and unlikely to work (or to be found anywhere) Tools/F_mk/comps/Linux_intel.mak commit e1f41c11d09995b284446c1cc7efdfd883ea7ec2 Author: Michael Zingale Date: Sun Oct 19 06:19:25 2014 -0700 kraken no longer exists (RIP...) Tools/F_mk/GMakeMPI.mak commit e3d58afc017b17ed1618421e6a1d7ee7685e434f Author: Weiqun Zhang Date: Sat Oct 18 07:42:26 2014 -0700 F90: tweaked the copyassoc_check to make it go much faster; now we can afford to increase the maximum count of the copyassoc allowed Src/F_BaseLib/layout.f90 commit 1d449c1d702d97c7ad6e5948c5516efa5f539620 Author: Weiqun Zhang Date: Fri Oct 17 21:02:16 2014 -0700 F90: added OMP to sfc Src/F_BaseLib/sort_i.f90 commit 4938e68747bb592963ed55fb67e787a1de06cb1f Author: Weiqun Zhang Date: Fri Oct 17 17:56:41 2014 -0700 F90: added a timer to find out how much time is spent in copyassoc checking Src/F_BaseLib/layout.f90 commit 309b02a119ee787d61bb55e59e0278ce945a1f73 Author: Weiqun Zhang Date: Fri Oct 17 15:58:30 2014 -0700 F90 profiler: print warning to the profiling result file instead of stdout Src/F_BaseLib/bl_prof.f90 commit f1b58f09c33557bf6067a7c5511269ebd5b8e529 Author: Weiqun Zhang Date: Fri Oct 17 15:56:58 2014 -0700 F90: added OMP to multifab copy Src/F_BaseLib/multifab_f.f90 commit d3fe9d7fdfc12bbf275a12953cb363644cba3769 Author: Weiqun Zhang Date: Fri Oct 17 08:48:02 2014 -0700 F90 profiler: print out profiling results for each individual processor even if the call trees are different Src/F_BaseLib/bl_prof.f90 commit c7d7b2625c2ae4a777defd4f7061d7c59725765d Author: Weiqun Zhang Date: Thu Oct 16 17:53:56 2014 -0700 F90 profiler: to help debug, print out more information when the call trees are not identical. Src/F_BaseLib/bl_prof.f90 commit d18d35d6b35f4f84810f3c9e658fee855888104d Author: Weiqun Zhang Date: Thu Oct 16 17:23:20 2014 -0700 F90 linear solver: fixed bl_prof_timer issue arisen from MPI communicator that does not include all ranks Src/LinearSolvers/F_MG/itsol.f90 commit b6a89471f07d134f110f505d9d79bad08167c230 Author: Weiqun Zhang Date: Thu Oct 16 16:33:04 2014 -0700 F90 ml_cc_solve: no need to build fine mask here becuase we have one already in ml_layout Src/LinearSolvers/F_MG/ml_solve.f90 commit 174c466f4c5772ccc27fc60873fdcaddbecb7f8c Author: Weiqun Zhang Date: Thu Oct 16 14:41:28 2014 -0700 removed a few unsafe bl_prof_timers because they might be inside OMP parallel region Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 1ba4035f52f3519cb09a181e114b8c0710b85503 Author: Weiqun Zhang Date: Thu Oct 16 14:16:09 2014 -0700 F90 linear solver: made the number of ghost cells of cell and edge coefficients consistent with alpha and beta passed in; there is no reason to always have one ghost cell Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 6100020bfb854f1da904cf75d0c9d78ec0ce9eda Author: vince Date: Thu Oct 16 11:55:18 2014 -0700 macros from the commprof branch. Src/C_BaseLib/Profiler.H commit ee53eba2f1b2f7e416d0a479c463fb8a33477587 Author: Adam Jacobs Date: Wed Oct 15 14:58:48 2014 -0500 Increase the maximum filename and full pathname from 128 character to 256 for the Fortran codebase. Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/ppm_util.f90 Src/F_BaseLib/ppm_util_c.c commit 5937f521e8cdedae5d15d7bbf12adac460852c56 Author: Weiqun Zhang Date: Wed Oct 15 11:15:04 2014 -0700 F90 linear solver: use the 8-byte integer versions of volume functions to find out if we cover the entire domain (if supported) Src/LinearSolvers/F_MG/mg.f90 commit ac8bcef08e42c79e955056e74fe36d7f7318f757 Author: Weiqun Zhang Date: Wed Oct 15 11:13:01 2014 -0700 F90: added a 8-byte integer version of box volume function, and used it in boxarray volume function Src/F_BaseLib/box_f.f90 Src/F_BaseLib/boxarray_f.f90 commit f1f3555a6d6d58f9529c7f53b1abf5c89cc13e86 Author: Weiqun Zhang Date: Wed Oct 15 11:11:37 2014 -0700 F90: added query functions that return whether or not quad precision or 8-byte integer is supported Src/F_BaseLib/bl_types.f90 commit 47287f33ad4c2554f9c8ef18d9a49c94949b30ef Author: Weiqun Zhang Date: Tue Oct 14 20:33:14 2014 -0700 clean up the new ml_layout_build_la Src/F_BaseLib/ml_layout.f90 commit 958b2a45bb0efb2d9156f9887ca105f12925d9d8 Author: Weiqun Zhang Date: Tue Oct 14 17:41:23 2014 -0700 new ml_layout_build that copies another layout Src/F_BaseLib/ml_layout.f90 commit e172dad694404461ef6c885d65900fdba32772b3 Author: vince Date: Tue Oct 14 16:11:51 2014 -0700 better bounds checking for debug. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 1bb399d8a993ed54a19c84e004755670c4b84607 Author: Weiqun Zhang Date: Tue Oct 14 15:43:43 2014 -0700 made the meaning of sfc_threshold in F90 consistent with C++ Src/F_BaseLib/layout.f90 commit e77cdb8c40e52ef75feb95539bf7ff82040fc509 Author: Weiqun Zhang Date: Tue Oct 14 15:30:55 2014 -0700 F90: only allow sfc to not sort in the least_used_cpus function Src/F_BaseLib/fab.f90 Src/F_BaseLib/layout.f90 commit 651d3340f57c15d900f59f381ec257c0841916e0 Author: Weiqun Zhang Date: Tue Oct 14 15:20:13 2014 -0700 F90: removed an unused function that was recently added Src/F_BaseLib/fab.f90 commit 340996c0e4a8e1d219791de09f1a9372fb7002ef Merge: 3903414d3 fcbd126d2 Author: Matthew Emmett Date: Tue Oct 14 11:11:17 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3903414d3cdf65439c43f59c74c7033d5a55c48b Author: Matthew Emmett Date: Tue Oct 14 11:09:46 2014 -0700 Add GetParticles method to ParticleContainer. Src/C_AMRLib/Particles.H commit fcbd126d2ccd068662926ec002dbc05026f270bb Author: Michael Zingale Date: Tue Oct 14 13:59:12 2014 -0400 add a description provided by Weiqun` Src/F_BaseLib/cluster_f.f90 commit 620361827b169d5115fc037739e088be7f201553 Author: Weiqun Zhang Date: Tue Oct 14 10:18:31 2014 -0700 F90: check allocation status of imask Src/F_BaseLib/cluster_f.f90 commit 4585b8731d0e243f0c61e70af6058a1cd1297b09 Author: Weiqun Zhang Date: Mon Oct 13 17:15:30 2014 -0700 fixed comments Src/LinearSolvers/F_MG/ml_solve.f90 commit eaebbec608ca9b63152141019af0be09bedd7d4d Author: Weiqun Zhang Date: Mon Oct 13 17:14:13 2014 -0700 F90: updated OMP for non-blocking multifab_fill_boundary so that it can be used for nodal mfs. Src/F_BaseLib/multifab_f.f90 commit 28408dd293673983a70e9ecfe4f66932139fbadd Author: Weiqun Zhang Date: Mon Oct 13 13:26:50 2014 -0700 F90: speed up cluster a little bit Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/fab.f90 commit be77cbc85e6d67b9075583de1ca5f7a9db3d37ee Author: vince Date: Mon Oct 13 12:21:44 2014 -0700 added several regions. Src/C_AMRLib/Amr.cpp commit 0969346955358e3811e640e15a0af79bea8e8158 Author: vince Date: Mon Oct 13 12:15:46 2014 -0700 more regions and trace profiling, allow regions for commprof without traceprof. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 8dd9b8b49612b0ee08967384e03ed37a773b65b6 Author: vince Date: Mon Oct 13 12:12:03 2014 -0700 added TRACE_PROFILE and new prof suffix and defs. Tools/C_mk/Make.defs commit e76ca5fea08a25c6406bb672cb2a7f289e519bb3 Author: Weiqun Zhang Date: Fri Oct 10 20:59:33 2014 -0700 F90: use merge sort rather than heap sort in SFC for speed Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/sort_i.f90 commit 2c099e34c4b6712ba8d6ae7dbf37494833d54981 Author: vince Date: Fri Oct 10 17:06:04 2014 -0700 some reorg, relative minmax calltimes. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 902ee7d318d247a09791f973c104d72d1c7485ce Author: Weiqun Zhang Date: Fri Oct 10 16:02:27 2014 -0700 fixed indentation Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 commit 3a098deb1f70cad80d58e8ecac295cabaf3a72c2 Author: Weiqun Zhang Date: Fri Oct 10 12:11:24 2014 -0700 added timer to create_nodal_mask Src/LinearSolvers/F_MG/nodal_mask.f90 commit 7046c241c07cb6f676a69ae3142f0f43f55a7a09 Author: Weiqun Zhang Date: Fri Oct 10 11:22:20 2014 -0700 removed a duplicated copy of create_nodal_mask Src/LinearSolvers/F_MG/ml_solve.f90 commit 0791d9591f828063aeba0b952ccd1e5f180570d1 Author: Michael Zingale Date: Fri Oct 10 13:34:46 2014 -0400 fix the summary table for when we make benchmarks Tools/RegressionTesting/testnew.py commit 603f48c42f71ca6df39d3e7409117d237b26ce88 Author: Michael Zingale Date: Fri Oct 10 12:19:55 2014 -0400 add the wall time to the summary table Tools/RegressionTesting/testnew.py commit dcea25ffcea0965b7924627b7bcdf177b98bb797 Author: Weiqun Zhang Date: Thu Oct 9 18:10:21 2014 -0700 F90: option to keep cpu order in providing the list of least used cpus Src/F_BaseLib/fab.f90 Src/F_BaseLib/regrid.f90 commit f1ed215fc0f9d88772aa60b9c0b10feedc0e7595 Author: vince Date: Thu Oct 9 16:46:38 2014 -0700 added const. Src/Extern/amrdata/AmrData.H commit 2395dcba90abb0c6c502cb6058d0a361674699a9 Author: vince Date: Thu Oct 9 16:36:37 2014 -0700 added const. Src/Extern/amrdata/AmrData.H commit 8cb847a7c79cdab08deff48aac9507c01cc200f6 Author: Weiqun Zhang Date: Thu Oct 9 16:32:13 2014 -0700 F90: incresed maximum # of copyassocs from 25 to 50 Src/F_BaseLib/layout.f90 commit 3b8afda46b5371c7f7d30005991c14f3c81a58e6 Author: Weiqun Zhang Date: Thu Oct 9 14:55:53 2014 -0700 F90: rebuild fine layout too when not properly nested Src/F_BaseLib/regrid.f90 commit e926d47a7bf668f86e0ace334f76f860483d4b38 Author: Weiqun Zhang Date: Thu Oct 9 14:42:02 2014 -0700 F90: new strategy for which item to remove when the copyassoc list is full Src/F_BaseLib/layout.f90 commit 39bc961bcd625349fd3cdcdbf9e316f304fd4f38 Author: Michael Zingale Date: Thu Oct 9 16:45:37 2014 -0400 prettification Tools/RegressionTesting/testnew.py commit 0e9f83d09934626aa89316c54a08a8e74fa1cfb8 Author: Michael Zingale Date: Wed Oct 8 22:28:57 2014 -0400 make the test run summary more informative Tools/RegressionTesting/testnew.py commit d8bfca92cc3b3a8f3f445de4cf0d812a92c503e4 Author: Michael Zingale Date: Wed Oct 8 21:32:57 2014 -0400 keep track of the number of levels by running fboxinfo on the output -- this is stored in the test object Tools/RegressionTesting/testnew.py commit 252cac246afea514935ce1e001564be6f5c02768 Merge: 2c7b1a202 74e22b36e Author: Michael Zingale Date: Wed Oct 8 20:38:31 2014 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2c7b1a2024acc8a9fa9addbc81e3ce290ab3e343 Author: Michael Zingale Date: Wed Oct 8 20:38:14 2014 -0400 latest version Tools/RegressionTesting/Maestro-tests.ini commit 9d49ed7ea5dada415d6e2969768b5b6694c5c856 Author: Michael Zingale Date: Wed Oct 8 20:25:22 2014 -0400 fix compilation fboxinfo.f90 commit b9844a45c96e73942c80b57326884e7c8762fbbe Author: Michael Zingale Date: Wed Oct 8 20:24:06 2014 -0400 add a -l option that only prints the number of levels -- I'm going to use this in the test suite shortly... fboxinfo.f90 commit 74e22b36e2957bb967fe2098f9065c12371b20bb Author: Weiqun Zhang Date: Wed Oct 8 16:34:43 2014 -0700 F90: ignore fine in layout mapping Src/F_BaseLib/regrid.f90 commit 31415a1ef7d24d57804b223f1750ffa9969ce8a9 Author: Weiqun Zhang Date: Wed Oct 8 16:27:32 2014 -0700 F90: We now have more control on the least used cpus function. This can be used by regrid to ignore fine in layout mapping Src/F_BaseLib/fab.f90 Src/F_BaseLib/layout.f90 commit 36b12d038748f203f2eb6d3d89b85011c94c088e Author: Weiqun Zhang Date: Wed Oct 8 13:32:03 2014 -0700 tidy Src/F_BaseLib/regrid.f90 commit e637ca5998105171134e36b2734d9b8dca7a6ba4 Author: vince Date: Wed Oct 8 13:21:33 2014 -0700 made profiler output functions generic. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 467b28c54243df740ff4be32ce6c7dd4ee7181f3 Author: Weiqun Zhang Date: Wed Oct 8 13:15:11 2014 -0700 Do not fill ghost cells in regrid unless told so by tag_boxes module. Do not call fillpatch if the new grids are the same as the original ones because a simple multifab copy is sufficient in this case. Src/F_BaseLib/regrid.f90 Src/F_BaseLib/tag_boxes.f90 commit 2ac6e9941608b5604c7602ecc5673d4d1f4241da Author: vince Date: Wed Oct 8 10:21:57 2014 -0700 moved text call tree to postprocessing. Src/C_BaseLib/Profiler.cpp commit 038a10222481b0095f536495212b0f49e4d86df6 Author: Weiqun Zhang Date: Wed Oct 8 09:49:58 2014 -0700 fixed a bug in miniapp MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 commit 90155764a8a76125c012e3b773c38ce126996380 Author: Weiqun Zhang Date: Wed Oct 8 09:41:03 2014 -0700 fixed a new bug in index slicing in ml_boxarray Src/F_BaseLib/ml_boxarray.f90 commit f07dc7457e2daf0ec73ac3678ade280f5b034f66 Author: vince Date: Tue Oct 7 16:05:12 2014 -0700 moved html output to postprocessor. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit d75cc277b981275a57d354b48b3c1b233b21e42f Author: Weiqun Zhang Date: Tue Oct 7 14:20:16 2014 -0700 added optional argument ref_ratio to cluster routine Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/make_new_grids.f90 commit c86401a5a47756ac7ea50e8e5fb07b91bc45ab73 Author: Weiqun Zhang Date: Tue Oct 7 14:04:11 2014 -0700 added arm_ref_ratio to ml_boxarray_module to make regrid easier to get that information MiniApps/AMR_Adv_Diff_F90/main.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/regrid.f90 Tutorials/AMR_Adv_Diff_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX4_F/main.f90 commit 7f176edab4c2254fa35508b87b5b037325ab5ea1 Merge: f4729fca5 0aed1d30b Author: Michael Zingale Date: Tue Oct 7 14:01:49 2014 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit f4729fca5b4fb4f794256cf153ad51cdb26aaa4a Author: Michael Zingale Date: Tue Oct 7 14:01:02 2014 -0400 have the list of active tests be what is defined in the .ini file -- this way we still see all the old active tests in the web report when we run with --redo_failed Tools/RegressionTesting/testnew.py commit 0aed1d30b914e62a8364f91718cbf9e12f6cc8b0 Author: Weiqun Zhang Date: Tue Oct 7 10:43:05 2014 -0700 make regrid use ref ratio stored in the mla argument Src/F_BaseLib/regrid.f90 commit 53c9396a32c39b270191c7acbe5374831205b16f Author: Ann Almgren Date: Tue Oct 7 10:02:38 2014 -0700 Remove unused variables. Src/F_BaseLib/ml_nd_restriction.f90 Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 2f35ab8786be07e6d42e11e0f1b7f934ebd88617 Author: Michael Zingale Date: Tue Oct 7 10:42:30 2014 -0400 add the --redo_failed option. This will automatically find all the tests that failed when the suite was last run and only rerun those. Tools/RegressionTesting/testnew.py commit 40e3477e70332e468f2a54758dae703e3de70816 Author: vince Date: Mon Oct 6 17:05:51 2014 -0700 sync names function into output, organized some code. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit ef9ef08c8e16faa651692ce65b38476248492bfb Author: Weiqun Zhang Date: Mon Oct 6 15:42:15 2014 -0700 moved the new regid subroutine that does not change the base level into F_BaseLib MiniApps/AMR_Adv_Diff_F90/GPackage.mak MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/regrid.f90 Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/GPackage.mak Src/F_BaseLib/regrid.f90 Tutorials/AMR_Adv_Diff_F/GPackage.mak Tutorials/AMR_Adv_Diff_F/main.f90 Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/HeatEquation_EX4_F/GPackage.mak Tutorials/HeatEquation_EX5_F/GPackage.mak Tutorials/HeatEquation_EX5_F/regrid.f90 commit 1ff038a97b62e2fd32a2f78d2ee653b3d2ba8fca Author: Weiqun Zhang Date: Mon Oct 6 14:59:38 2014 -0700 option to keep coarse layout when destroying multi-level layout Src/F_BaseLib/ml_layout.f90 commit 73d60856a0aae989f4dc116b593c262cb27d80af Author: Weiqun Zhang Date: Mon Oct 6 14:57:19 2014 -0700 added a new line in printf Src/C_AMRLib/Amr.cpp commit b5e86adad1e6fa27c73c88d7c0143b44dedc4688 Author: vince Date: Mon Oct 6 14:10:51 2014 -0700 fix for serial. Src/C_BaseLib/Utility.cpp commit d97a2ce359f16198217df4e74016bc06cfd0e58d Author: Ann Almgren Date: Mon Oct 6 13:39:22 2014 -0700 Update to work with new restrictions files... Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 commit fd311a48ba8024504deb60f8877362bdac10eb66 Author: Ann Almgren Date: Mon Oct 6 13:02:53 2014 -0700 Initialize variable so we don't get compiler warning. Src/F_BaseLib/box_f.f90 commit 1e8747412169bdd5b5523450339bb2b679334c21 Author: Ann Almgren Date: Mon Oct 6 12:59:20 2014 -0700 Remove unused variable. Src/F_BaseLib/fabio_c.c commit 5d56b18105fb6cfebaffc375ce260cb4ba096808 Author: Ann Almgren Date: Mon Oct 6 12:47:40 2014 -0700 Remove unused variable. Src/F_BaseLib/layout.f90 commit 76e0148cefc7f31066528835683337cebebeeadd Author: Ann Almgren Date: Mon Oct 6 11:22:01 2014 -0700 Add test on plot_int < 0 so we can turn off plotfiles by setting plot_int negative in the inputs file MiniApps/AMR_Adv_Diff_F90/main.f90 commit 75db8a8b43e6d64ffc6c3c9ec28d1d19ee102bea Author: vince Date: Fri Oct 3 12:52:03 2014 -0700 added function to sync sets of strings over procs. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 94cdb670f5f75d9a118534ae40d7d5035c0d9df8 Author: vince Date: Thu Oct 2 11:10:40 2014 -0700 mask for NoRegion region. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 1df7bcbab00a66056659d1af9cb46887c364490c Author: vince Date: Wed Oct 1 14:46:29 2014 -0700 added time values and NoRegion to region prof. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 37061ed37e840ea9245432bbc232ce797ab43632 Author: vince Date: Mon Sep 29 16:07:18 2014 -0700 streamlined binary callstats format. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 9f18b8e899f8fe63e21d82328da48df17b5e280e Author: Ann Almgren Date: Mon Sep 29 09:05:29 2014 -0700 Replace HeatEquation_EX6_F by AMR_Adv_Diff_F in documentation - this now correctly reflects what is in the code itself. Please enter the commit message for your changes. Lines starting Docs/F_AdvancedTopics/F_AdvancedTopics.tex commit d5862ceb1f3d2059981fa22f26208df6467bb59c Author: vince Date: Thu Sep 25 16:12:30 2014 -0700 binary format for trace data. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 27e89d06697ae9b059fd3625abaac2cd3e30e38b Author: Marc Day Date: Wed Sep 24 17:47:02 2014 -0700 Set default for tecplot tool to not require tecplot bin libraries Tools/C_util/AmrDeriveTecplot/GNUmakefile commit c89ed40571ff86ec5eec542823e8ead5eb3b6c1a Author: Marc Day Date: Wed Sep 24 17:39:38 2014 -0700 Add script to generate flattened pltfile format for Tecplot Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/AmrDeriveTecplot/GNUmakefile commit e2040f95ff47dcf621d2358ed98c417bc6c6aaae Author: Matthew Emmett Date: Wed Sep 24 11:26:11 2014 -0700 PyBoxLib: Add --disable-mpi build option. Src/Python/README Src/Python/setup.py commit f41494b9f7bea8fcc9494cc3c0fd924148c2966f Author: Weiqun Zhang Date: Tue Sep 23 15:23:37 2014 -0700 fixed a bug in index of stencil array Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit 362630e1c8f2b15323b24dc25ba49676bf95fe57 Author: Matthew Emmett Date: Tue Sep 23 13:14:37 2014 -0700 PyBoxLib: Honor USE_MPI environment variable. Src/Python/setup.py commit 8409f066203c2e265f63fdcfc7212fcb0d07337c Author: Matthew Emmett Date: Tue Sep 23 12:50:37 2014 -0700 PyBoxLib: Add a more informative error message when mpicc can't be found. Src/Python/setup.py commit 2b34a94066120697c7bea02472dea04e2595969d Author: Weiqun Zhang Date: Mon Sep 22 16:51:52 2014 -0700 cleanup Src/F_BaseLib/ml_layout.f90 commit 72ced02cfce8d0ef560056fdf0d2563a9b96bd6c Author: Weiqun Zhang Date: Mon Sep 22 15:25:25 2014 -0700 more cleanup Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 69d0d6bd64b64878f0a0a7c2d8014df89d528b1d Author: Weiqun Zhang Date: Mon Sep 22 15:16:46 2014 -0700 clean up Src/F_BaseLib/multifab_f.f90 commit 57e5f79b9f5fd04c7b4ad007f68c0ced29580b6e Author: Weiqun Zhang Date: Mon Sep 22 14:49:39 2014 -0700 removed pingpong.f90 from CMake Src/F_BaseLib/CMakeLists.txt commit d456083e44a168640f3307828f5dde8c89c7b88d Author: Weiqun Zhang Date: Mon Sep 22 14:08:51 2014 -0700 F90 BoxLib: moved boxarray_intersection_bx into ml_boxarray and made it private because (1) it is only used by ml_boxarray; (2) the naive implementation works perfectly because bx intersects with every boxes in ba. Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_boxarray.f90 commit 97a0c055757d18538eeeb57f9987fae80b640012 Author: Weiqun Zhang Date: Mon Sep 22 13:43:25 2014 -0700 F90 BoxLib: reimplemented boxarray-box intersection routines using the hash Src/F_BaseLib/layout.f90 commit a4960165f769e7625ee2225c2585c6887386bc26 Author: Weiqun Zhang Date: Mon Sep 22 11:17:34 2014 -0700 removed subroutines that do naive boxarray-box intersectin from boxarray module to layout module so that they can be reimplemented. Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_boxarray.f90 commit 0de8c31b99e817e19c288847f0779031f6c11269 Author: Michael Zingale Date: Sun Sep 21 19:51:16 2014 -0400 we were using the wrong variable in the indxmap for the bndryreg j = indxmap(j) --> j = indxmap(i) Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit f28bee18c3db8e6e81f8a1dff007fe1de10c6416 Author: vince Date: Fri Sep 19 13:59:10 2014 -0700 added nooutput option. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 3f5652791f439782ec599577dd4de353c4b79665 Author: vince Date: Thu Sep 18 11:56:21 2014 -0700 more region profiling. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 9da1a05b7596c3ff1b039b19dd15f98435cb257f Author: Marc Day Date: Tue Sep 16 14:36:12 2014 -0700 Uptick version number Tools/CMake/BoxLib_Version.cmake commit 47547ded742b348d9b32145a5860528e0c60fc71 Author: Weiqun Zhang Date: Tue Sep 16 11:26:04 2014 -0700 minor cleanup Src/F_BaseLib/layout.f90 commit c6d36bd20581d6229ff46eb39b9d87d766202231 Author: Matthew Emmett Date: Mon Sep 15 22:13:16 2014 -0700 PyBoxLib: Fix inclusion of libgfortran and libquadmath. Src/Python/GNUmakefile_CXX.mak commit 7721947b4d7f89dc11d7c838ff712a0e4cb495a4 Author: Matthew Emmett Date: Mon Sep 15 10:52:54 2014 -0700 PyBoxLib: Add library path for quadmath. Src/Python/GNUmakefile_CXX.mak commit 0cef41d13567367c6d78719e35c78c047247417b Author: Matthew Emmett Date: Mon Sep 15 10:52:32 2014 -0700 Make.defs: Increase template depth to support clang (LLVM). Tools/C_mk/Make.defs commit 7e3c0f1de5863575fd8a2db287212cf76842b559 Author: Matthew Emmett Date: Fri Sep 12 16:13:08 2014 -0700 PyBoxLib: Set MPI_HOME according to location of mpicc by default. Src/Python/setup.py Tools/C_mk/Make.mpi commit 400c9806ea9e9505fb9aa963b3efd45c6a51d777 Author: Matthew Emmett Date: Fri Sep 12 15:30:06 2014 -0700 PyBoxLib: Simplify PYLIBS. Src/Python/GNUmakefile_CXX.mak commit cafef0788cccc2bea527ac22efd3c2f7a2cfd2bb Author: Matthew Emmett Date: Fri Sep 12 13:15:33 2014 -0700 PyBoxLib: More trickery for Darwin. Src/Python/GNUmakefile_CXX.mak Src/Python/setup.py commit b9967948f0a0a872b4790c923179da593d5450f4 Author: Matthew Emmett Date: Fri Sep 12 13:15:10 2014 -0700 Make.mpi: Don't change FC, F90 etc on Darwin. Tools/C_mk/Make.mpi commit bc09acde57335390279611ceeb8ddc994d338f91 Merge: 56ddf44bb a85b2a66d Author: Matthew Emmett Date: Fri Sep 12 12:15:48 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 56ddf44bb2e903ce09eec0c2ec42bc06d72fd5af Author: Matthew Emmett Date: Fri Sep 12 12:15:37 2014 -0700 PyBoxLib: Move compiler defs to GNUmakefile and honor env CXX and CC. Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak commit d78dfed39e58e2f6d931aebea58efb2ee5cd6c78 Author: Matthew Emmett Date: Fri Sep 12 12:14:44 2014 -0700 Make.defs: Set defaults after checking USE_GCC, honor env CXX and CC if USE_GCC is true. Tools/C_mk/Make.defs commit a85b2a66d7dc511f57cb25149fa6b5970c07599f Merge: f0c82ad3c 4cddcc905 Author: Chris Malone Date: Fri Sep 12 12:39:07 2014 -0600 merge Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f0c82ad3c819a1712f9b236a98959d3dcb64ec93 Author: Chris Malone Date: Fri Sep 12 12:39:02 2014 -0600 dont use libmpi_f77 on my Mac! Tools/C_mk/Make.mpi commit ff275283384f58e8b831669b277a9b6eefcd0442 Author: Michael Zingale Date: Fri Sep 12 14:34:15 2014 -0400 change option name fcompare.f90 commit 3a6cdf6e87e3f02c2cf783d5aaa8e96bcc3ea300 Author: Michael Zingale Date: Fri Sep 12 14:20:19 2014 -0400 start of support for outputting a plotfile of diffs fcompare.f90 commit 490739f030b90f2d7f6757d64614223a4ae6285b Author: Michael Zingale Date: Fri Sep 12 14:17:37 2014 -0400 layout_build_ba now requires the pd argument tutorial/fwrite2d.f90 commit 4cddcc90526076fdb4cdebaba213b80aa120de9b Author: Weiqun Zhang Date: Sat Sep 6 13:41:44 2014 -0700 F90 BoxLib: use stable sort in building the list of least used cpus. There is no reason for not doing this, and this makes it consistent with C++ BoxLib. Src/F_BaseLib/fab.f90 commit f42eaa67bc1f9d3bd3993f72ddeea660b36c32f6 Author: Weiqun Zhang Date: Fri Sep 5 22:09:13 2014 -0700 minor update in F90 flux register Src/F_BaseLib/bndry_reg.f90 commit f1d5f8891e89732418116ffb33430d2cbc6cbde6 Author: Weiqun Zhang Date: Tue Sep 9 21:21:58 2014 -0700 Only if there are no periodic boundaries, we can return immediately from multifab_copy when ng=0 Src/F_BaseLib/multifab_f.f90 commit fb5db3b03ad7b259bdd05afdebc043ad2aca6709 Author: Weiqun Zhang Date: Tue Sep 9 10:59:33 2014 -0700 remove some outdated comments Src/F_BaseLib/multifab_f.f90 commit c25366d52ff53b71ae573e8a0c4b50e2c2ade5e2 Author: ajnonaka Date: Tue Sep 9 08:59:53 2014 -0700 multifab_fill_boundary and multifab_physbc return if ng==0 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/multifab_physbc.f90 commit 5a1c4fa295fcde2f0e0f42cb2dcc497093f2f84e Author: Weiqun Zhang Date: Mon Sep 8 16:09:28 2014 -0700 added one moer argument to ml_restrict_and_fill so that n components can share one type of boundaries Src/F_BaseLib/ml_restrict_fill.f90 commit 265d0fa585a41b90878510bf7755920722a07537 Author: Weiqun Zhang Date: Mon Sep 8 14:00:53 2014 -0700 should not include ml_restric_fill_module in FParalleMG.mk Src/F_BaseLib/FParallelMG.mak commit 8eac360e1c5287d630079bf11c5ae6e80c7340d1 Author: Weiqun Zhang Date: Mon Sep 8 13:44:17 2014 -0700 update to the new flux register MiniApps/AMR_Adv_Diff_F90/GPackage.mak MiniApps/AMR_Adv_Diff_F90/advance.f90 MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/reflux.f90 MiniApps/AMR_Adv_Diff_F90/regrid.f90 MiniApps/AMR_Adv_Diff_F90/update_phi.f90 commit 1e6886811f1dd2fa6a189dc8543a988d335de3d6 Author: Weiqun Zhang Date: Mon Sep 8 13:41:23 2014 -0700 forgot to add in last commit Src/F_BaseLib/ml_restrict_fill.f90 commit bfd4b589f3463a179f0691f898505f2b0fcd8ee2 Author: Weiqun Zhang Date: Mon Sep 8 13:16:31 2014 -0700 Added a new module for doing multi-level restriction and then fill all the boundaries because this needs to be done in so many places, and the new module saves half of fill_boundary calls for levels from 2 to nlevs-1. Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Tutorials/AMR_Adv_Diff_F/init_phi.f90 Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/AMR_Adv_Diff_F/update_phi.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/regrid.f90 Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 commit bf3d3a11e30f40584d349a04bcba5bb673979d02 Author: Weiqun Zhang Date: Sat Sep 6 21:44:06 2014 -0700 changed multifab_fill_ghost_cells to intentionally break (i.e., won't compile) codes that rely on the old behavior of ml_cc_restriction Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 9a608f43769aa5abeda45b33343b36498ea43bda Author: Weiqun Zhang Date: Fri Sep 5 17:40:39 2014 -0700 remove bl_error module from sort_i_module because bl_error_module uses sort_i_module Src/F_BaseLib/sort_i.f90 commit f149db8023def5de71fec66f464bc9b3dec35f01 Author: Weiqun Zhang Date: Fri Sep 5 17:32:34 2014 -0700 added a stable merge sort method Src/F_BaseLib/sort_i.f90 commit e0330fd6bf7ca3f3c46df469bfdf79844651e369 Author: Weiqun Zhang Date: Fri Sep 5 15:55:10 2014 -0700 removed multifab_fill_boundary from ml_cc_restriction Src/F_BaseLib/ml_cc_restriction.f90 commit 4d1323850145433910ac9788cda92da8d316a3e0 Author: Weiqun Zhang Date: Fri Sep 5 14:10:23 2014 -0700 update due to new way of including mt19937ar.f90 Tutorials/MultiGrid_F/GNUmakefile Tutorials/MultiGrid_F/mt19937ar.f90 commit 5728d31e809791a0d1b45c80f617c9f7430094a4 Author: Weiqun Zhang Date: Fri Sep 5 13:46:15 2014 -0700 comments Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 55abc796bca076bb73baadab8968adb641cbfa85 Author: vince Date: Fri Sep 5 11:18:22 2014 -0700 made prof dir names user settable. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 36d3ae4b28937f2eae1f21190adf89c467e6a213 Author: Weiqun Zhang Date: Fri Sep 5 08:36:59 2014 -0700 added 'is up to date.' as an indication of successful compilation to regression test script Tools/RegressionTesting/testnew.py commit 77104f10bb8756df54066b33d5ea95d8bd258cf7 Author: Weiqun Zhang Date: Fri Sep 5 08:26:54 2014 -0700 updated Tutorial/AMR_Adv_Diff_F due to flux register Tutorials/AMR_Adv_Diff_F/GPackage.mak Tutorials/AMR_Adv_Diff_F/advance.f90 Tutorials/AMR_Adv_Diff_F/compute_flux.f90 Tutorials/AMR_Adv_Diff_F/main.f90 Tutorials/AMR_Adv_Diff_F/reflux.f90 Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/AMR_Adv_Diff_F/update_phi.f90 commit b6465507084ae0cf2e3e90639aeaecc04ecdd8b1 Author: Weiqun Zhang Date: Fri Sep 5 08:24:55 2014 -0700 added flux register for subcycling to F90 BoxLib Src/F_BaseLib/bndry_reg.f90 commit 66f6ebe3212d8a8f027db8ac279fc8e922595c45 Author: Weiqun Zhang Date: Fri Sep 5 08:22:25 2014 -0700 F90 BoxLib: fixed a memory leak in multifab_fill_ghost_cells_t for subcycling Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 54bba805f8c185203f017f5d7c9b3a9727b4f860 Author: vince Date: Thu Sep 4 17:53:46 2014 -0700 added region profiling and parser support. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 5c2afed18377f0f92a986bdf4e26b3fca6baf5bb Merge: c4f11a21b e7d1eff4b Author: Ann Almgren Date: Thu Sep 4 13:23:25 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c4f11a21b2d49e996d3ee71525182e40147d4a03 Author: Ann Almgren Date: Thu Sep 4 13:21:42 2014 -0700 Have one test for implicit method and one for explicit method in the regression testing. Tutorials/HeatEquation_EX5_F/inputs-rt-expl Tutorials/HeatEquation_EX5_F/inputs-rt-impl commit e7d1eff4b3df77333c3d977978fc025a14681689 Merge: 5cfc1a1c8 c35a30cdb Author: Chris Malone Date: Thu Sep 4 13:51:06 2014 -0600 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5cfc1a1c87573544240974ce588c96bcc39f6b92 Author: Chris Malone Date: Thu Sep 4 13:50:48 2014 -0600 updates for my machine Tools/C_mk/Make.Darwin Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit c35a30cdb18998e8143ddecf68ea3cd218d655fe Author: Michael Zingale Date: Thu Sep 4 14:05:46 2014 -0400 if RANDOM is defined, then add mt19937.f90 to the f90sources Src/F_BaseLib/GPackage.mak commit 9947a3924a14b701fad37f679290dd6c0c5bdadb Author: Weiqun Zhang Date: Wed Sep 3 20:40:00 2014 -0700 commented on why OMP is removed in previous commit Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 20dde7730698d6592c8619ec65d662f1c4d041a3 Author: Weiqun Zhang Date: Wed Sep 3 17:55:48 2014 -0700 removed another OMP PARALLEL DO becuase it is no longer safe in the new bndry_reg Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 8469ca6184460cd22e11f75e3491e54baeca39a1 Author: Weiqun Zhang Date: Wed Sep 3 17:54:34 2014 -0700 intent(inout) --> intent(in) Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit b42b6d7269aeb996ccaf10ab00f7fae757f83c61 Author: Weiqun Zhang Date: Wed Sep 3 17:02:27 2014 -0700 removed an OMP PARALLEL DO becuase it is no longer safe in the new bndry_reg Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 21291febd604b2616845dab3b4cfe49d512e11e4 Author: Weiqun Zhang Date: Wed Sep 3 14:45:01 2014 -0700 F90 BoxLib bndry reg for cc linear solver: merged NDIM mulitfabs into one Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 34ab9897cc704e6d705817b8063a6f0b5f5dbe54 Author: Weiqun Zhang Date: Wed Sep 3 12:29:58 2014 -0700 F90 BoxLib bndry reg for cc linear solver: merged the two faces into one so that it now contains NDIM multifabs instead of 2*NDIM multifabs. This amortizes a lot of works such as building copy assoc. Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit a2bfbb528e8d6f442374b551b1c6e6167d52e722 Author: Weiqun Zhang Date: Tue Sep 2 20:18:04 2014 -0700 F90 BoxLib: use boxhash in the subroutine for removing overlaps in a boxarray Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/mt19937ar.f90 commit 48e3b8bed4925c22ba967fb8abef764f50e5f91c Author: Weiqun Zhang Date: Fri Aug 29 15:45:04 2014 -0700 F90 BoxLib: (1) Added optional argument "all" to saxpy. (2) Added optional argument "ngsrc" to multifab copy. Parallel copy used to only copy from valid region to valid region, whereas now it copies from valid region + ngsrc ghost cells to valid region. The caller is responsible for having good data in ghost cells of the source multifab if ngsrc is not zero. Note that the destination is still valid region only for reasons I will not go into details. (4) fillpatch: If coarse multifab does not have ghost cells while fine grids touch physical domain, a temporary multifab with enough ghost cells will be built. This relieves the burden from the caller. (3) Refactored fillpatch_t and multifab_fill_ghost_cells_t. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit ecf7f30e1784c00022c7a3abc3e87183bf96f116 Merge: d01ac2858 90ba4be80 Author: vince Date: Fri Aug 29 10:42:17 2014 -0700 conflict fix. commit d01ac285856ff424ddee302ee089237083c7ce75 Author: vince Date: Fri Aug 29 10:36:52 2014 -0700 added profiling. Tutorials/MultiGrid_C/main.cpp commit 02f149bd734ba3f1ac3d41abbf28f13cd539b6a6 Author: vince Date: Fri Aug 29 10:35:44 2014 -0700 more f90 profiling. Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_prof_stubs.f90 Src/F_BaseLib/layout.f90 Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 commit 90ba4be80dde46b35bd32294df9cbea45f59ea05 Author: Weiqun Zhang Date: Thu Aug 28 20:30:13 2014 -0700 updated fillpatch_t too Src/F_BaseLib/fillpatch.f90 commit 358ec873133f713f453b58819876779e2c7bb108 Author: Weiqun Zhang Date: Thu Aug 28 20:03:27 2014 -0700 added assertion and cycle when cbx is empty in fillpatch Src/F_BaseLib/fillpatch.f90 commit e947b5e760aa2aa748a7040f528ef33290d2adc1 Author: Weiqun Zhang Date: Thu Aug 28 20:01:47 2014 -0700 fixed a bug; did not set stencil_width when stencilwith_in is present Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 78b198c1080594e7d492ee70ccbe0e74f86f7f5b Merge: 6dde29d7c 898757b89 Author: vince Date: Thu Aug 28 18:12:10 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 6dde29d7cccc971f12f37f88d9c6ce06c0d1d1b7 Author: vince Date: Thu Aug 28 18:11:43 2014 -0700 fixed array dim, k instead of 1. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 898757b89d4e47b220fb755ef32670fcd913b09f Author: Chris Malone Date: Thu Aug 28 14:12:05 2014 -0600 this avoids an OSError if a repo doesnt exist Tools/C_scripts/makebuildinfo_C.py commit 13b8d23b2f1ce069f15d8dc885c6e1c1d1755029 Author: Chris Malone Date: Thu Aug 28 10:55:43 2014 -0600 remove vestigial loop Src/C_AMRLib/Amr.cpp commit 229c28e06cdd12a7740db638b0e5ac5295357799 Merge: 430c13f9b e89066db7 Author: Chris Malone Date: Thu Aug 28 10:53:53 2014 -0600 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 430c13f9b661807c8a85cef245c3e868fb372b24 Author: Chris Malone Date: Thu Aug 28 10:53:38 2014 -0600 updates for LANL machines Tools/C_mk/Make.mpi commit e89066db739a720757ab49350658f69ff93aff04 Author: Ann Almgren Date: Thu Aug 28 06:27:56 2014 -0700 Forgot to move define_bc_tower.f90 from the LinearSolvers/F_MG/FParallel.mak into the F_BaseLib/FParallel.mak Src/F_BaseLib/FParallelMG.mak Src/LinearSolvers/F_MG/FParallelMG.mak commit e9cc859c37ef00893d3dc91ada139d6be87751cf Author: Ann Almgren Date: Wed Aug 27 20:33:35 2014 -0700 Remove LinearSolvers/F_MG from the GNUMakefile ... this was kinda the point! Tutorials/AMR_Adv_Diff_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GNUmakefile Tutorials/HeatEquation_EX7_F/GNUmakefile commit 4f9245ea7bb4fe9029736de8012003bf973dbff3 Author: Ann Almgren Date: Wed Aug 27 20:29:53 2014 -0700 This is replaced by README_F Tutorials/README_HeatEquation_F commit 2b09b4f7dc24576438296f2da980771e1414c550 Author: Ann Almgren Date: Wed Aug 27 20:29:11 2014 -0700 Fix up the Tutorials... Tutorials/AMR_Adv_Diff_F/advance.f90 Tutorials/AMR_Adv_Diff_F/compute_flux.f90 Tutorials/AMR_Adv_Diff_F/init_phi.f90 Tutorials/AMR_Adv_Diff_F/inputs_2d Tutorials/AMR_Adv_Diff_F/inputs_3d Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/AMR_Adv_Diff_F/update_phi.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/regrid.f90 Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 commit e710eeae739b118b422ca4bf635dd8e428783de2 Author: Ann Almgren Date: Wed Aug 27 18:56:55 2014 -0700 More fixes due to the recent changes ... with this version VARDEN now builds. Src/F_BaseLib/ml_nd_restriction.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit c5f731746f8e2c9cf0d03c867b1a30fc5e3cd640 Author: Ann Almgren Date: Wed Aug 27 18:43:30 2014 -0700 Oops ... missed two changes ... Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit 8f086d2b69b9ab117d25206fa06477e74f4ea97a Author: Ann Almgren Date: Wed Aug 27 18:36:49 2014 -0700 Move a bunch of files from LinearSolvers/F_MG to F_BaseLib because they are needed for multilevel operations (mostly restriction), in particular in subcycling codes, and not just in the linear solvers. We don't want to have to include everything in LinearSolvers/F_MG when we're not doing a linear solve. MiniApps/AMR_Adv_Diff_F90/GNUmakefile MiniApps/AMR_Adv_Diff_F90/advance.f90 MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 MiniApps/AMR_Adv_Diff_F90/inputs_2d MiniApps/AMR_Adv_Diff_F90/inputs_3d MiniApps/AMR_Adv_Diff_F90/regrid.f90 MiniApps/AMR_Adv_Diff_F90/update_phi.f90 Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bc_functions.f90 Src/F_BaseLib/cc_restriction.f90 Src/F_BaseLib/edge_restriction.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/F_BaseLib/ml_nd_restriction.f90 Src/F_BaseLib/nodal_neumann_bcs.f90 Src/F_BaseLib/nodal_restriction.f90 Src/F_BaseLib/nodal_stencil_bc.f90 Src/LinearSolvers/F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit e419e44f868b941ced5e7d423268a590455161e3 Author: Ann Almgren Date: Wed Aug 27 18:00:47 2014 -0700 Dont have regression test in the miniap. MiniApps/AMR_Adv_Diff_F90/inputs-rt commit 20b1535bd1aa303c40695e0b64a01a8dc10c1fcd Author: Ann Almgren Date: Wed Aug 27 18:00:29 2014 -0700 Fixed in 3d. MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 commit 6ef4dc792a5e97b986f06bdb60dbcfb54b621c43 Author: Weiqun Zhang Date: Wed Aug 27 16:42:26 2014 -0700 F90 BoxLib: Assume grids are properly nested in fillpatch. So we no longer need to do the expensive O(N^2) check of whether one box array contains another box array. Src/F_BaseLib/fillpatch.f90 commit 56bc524e750104d7a5e41d52ce8d56b2fce50030 Author: Weiqun Zhang Date: Wed Aug 27 15:49:18 2014 -0700 added timer to boxarray_boxarray_contains function Src/F_BaseLib/boxarray_f.f90 commit 6e389fb2721f71ad65cdfa415c1c8e935b3c54a0 Author: vince Date: Wed Aug 27 15:33:48 2014 -0700 output cleanup. Src/C_AMRLib/StateData.cpp commit 21867f6cb180243db49b8a8ff841ebbb2a803b37 Author: vince Date: Wed Aug 27 14:58:29 2014 -0700 remove redudnant resizes. Src/C_BaseLib/DistributionMapping.cpp commit fecc1c7c9e7a865143d4592a94ba97cc113ae2da Author: vince Date: Wed Aug 27 14:33:33 2014 -0700 redid defaults for pfc topology. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/DistributionMapping.cpp commit 21dcde773ad4e803a7dca235a44d67d7faf54486 Merge: b90b06501 14736185e Author: Weiqun Zhang Date: Wed Aug 27 10:26:41 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit b90b065016a4a0b5efd56ae4c30df999b2b67642 Author: Weiqun Zhang Date: Wed Aug 27 10:26:34 2014 -0700 destroy bl_prof_timer before returning Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/ml_boxarray.f90 commit 14736185eace9e8ad67f0de61c6d052c685a5044 Author: Ann Almgren Date: Tue Aug 26 16:41:51 2014 -0700 Fix name of MultiFabTests to be consistent with others... Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/Make.package Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit 886709e7404110e1a75bffcdc9cfe96c80d65b29 Author: Ann Almgren Date: Tue Aug 26 16:36:27 2014 -0700 Fixed comment re particles leaving the domain. Src/C_AMRLib/Particles.H commit 7d8b1239000364ce5c01a27c98c27140a28d4f9e Author: Ann Almgren Date: Tue Aug 26 16:17:09 2014 -0700 Remove unused variable "ns_in" Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 48ee37c5e585571289daade1bd2a9777fad33ac5 Author: vince Date: Mon Aug 25 17:24:53 2014 -0700 more diagnostics. Src/C_BaseLib/DistributionMapping.cpp commit c4aa9d91c1bf344d4b0a9a802d3f071029d9bd71 Author: Ann Almgren Date: Fri Aug 22 12:42:53 2014 -0700 This directory was renamed AMR_Adv_Diff_F Tutorials/HeatEquation_EX6_F/GNUmakefile Tutorials/HeatEquation_EX6_F/GPackage.mak Tutorials/HeatEquation_EX6_F/advance.f90 Tutorials/HeatEquation_EX6_F/compute_flux.f90 Tutorials/HeatEquation_EX6_F/init_phi.f90 Tutorials/HeatEquation_EX6_F/inputs-rt Tutorials/HeatEquation_EX6_F/inputs_2d Tutorials/HeatEquation_EX6_F/inputs_3d Tutorials/HeatEquation_EX6_F/main.f90 Tutorials/HeatEquation_EX6_F/prob.f90 Tutorials/HeatEquation_EX6_F/reflux.f90 Tutorials/HeatEquation_EX6_F/regrid.f90 Tutorials/HeatEquation_EX6_F/tag_boxes.f90 Tutorials/HeatEquation_EX6_F/update_phi.f90 Tutorials/HeatEquation_EX6_F/write_plotfile.f90 commit 8f8686aab515614b48f7f3028beaa4ad9a97dbdf Author: Ann Almgren Date: Fri Aug 22 12:42:28 2014 -0700 Renamed some stuff, moved some stuff ... Tutorials/AMR_Adv_Diff_F/GNUmakefile Tutorials/AMR_Adv_Diff_F/GPackage.mak Tutorials/AMR_Adv_Diff_F/advance.f90 Tutorials/AMR_Adv_Diff_F/compute_flux.f90 Tutorials/AMR_Adv_Diff_F/init_phi.f90 Tutorials/AMR_Adv_Diff_F/inputs-rt Tutorials/AMR_Adv_Diff_F/inputs_2d Tutorials/AMR_Adv_Diff_F/inputs_3d Tutorials/AMR_Adv_Diff_F/main.f90 Tutorials/AMR_Adv_Diff_F/prob.f90 Tutorials/AMR_Adv_Diff_F/reflux.f90 Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/AMR_Adv_Diff_F/update_phi.f90 Tutorials/AMR_Adv_Diff_F/write_plotfile.f90 Tutorials/Exp_CNS_NoSpec_F/CNSEquations.tex Tutorials/Exp_CNS_NoSpec_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/GPackage.mak Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.h Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.x86.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/Make.package Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/Make.package Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/README Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/main.f90 Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/README Tutorials/Exp_CNS_NoSpec_F/README Tutorials/Exp_CNS_NoSpec_F/advance.f90 Tutorials/Exp_CNS_NoSpec_F/init_data.f90 Tutorials/Exp_CNS_NoSpec_F/inputs.jbb Tutorials/Exp_CNS_NoSpec_F/inputs_3d Tutorials/Exp_CNS_NoSpec_F/main.f90 Tutorials/Exp_CNS_NoSpec_F/write_plotfile.f90 Tutorials/README_F commit 9fb0089c3d72ce2334a13f902ceaa052a67273e0 Author: Ann Almgren Date: Fri Aug 22 12:34:17 2014 -0700 Add a MiniApps/AMR_Adv_Diff_F90 directory as a MiniApp to be used for profiling, and rename the Tutorials/HeatEquation_EX6_F directory to be Tutorials/AMR_Adv_Diff_F to reflect the fact that it is an AMR code with subcycling in time that handles advective and explicit diffusive fluxes. MiniApps/AMR_Adv_Diff_F90/GNUmakefile MiniApps/AMR_Adv_Diff_F90/GPackage.mak MiniApps/AMR_Adv_Diff_F90/advance.f90 MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 MiniApps/AMR_Adv_Diff_F90/inputs-rt MiniApps/AMR_Adv_Diff_F90/inputs_2d MiniApps/AMR_Adv_Diff_F90/inputs_3d MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/prob.f90 MiniApps/AMR_Adv_Diff_F90/reflux.f90 MiniApps/AMR_Adv_Diff_F90/regrid.f90 MiniApps/AMR_Adv_Diff_F90/update_phi.f90 MiniApps/AMR_Adv_Diff_F90/write_plotfile.f90 Tutorials/HeatEquation_EX6_F/advance.f90 commit f855924756e7026db348efe3c2000ddc300cf272 Author: vince Date: Fri Aug 22 12:26:23 2014 -0700 nstates. Src/C_BaseLib/DistributionMapping.cpp commit 5f10859663e00a840ae994b42666ab24d1758d5d Author: Ann Almgren Date: Fri Aug 22 12:25:52 2014 -0700 These are updated to include advective fluxes and fixed previous bugs in the refluxing. Tutorials/HeatEquation_EX6_F/GPackage.mak Tutorials/HeatEquation_EX6_F/advance.f90 Tutorials/HeatEquation_EX6_F/compute_flux.f90 Tutorials/HeatEquation_EX6_F/main.f90 Tutorials/HeatEquation_EX6_F/prob.f90 Tutorials/HeatEquation_EX6_F/reflux.f90 Tutorials/HeatEquation_EX6_F/regrid.f90 Tutorials/HeatEquation_EX6_F/update_phi.f90 commit 3e0531457a231e65b22f001b99bddade0610e692 Author: vince Date: Thu Aug 21 17:02:48 2014 -0700 multilevel distribution map. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 8bfdecd0100e845f71fe5c3e3d446a384f9879cc Author: Weiqun Zhang Date: Thu Aug 21 16:06:04 2014 -0700 Here, "rt" actually stands for regression test. Revert "Remove inputs.rt -- it didn't really do the RT problem" This reverts commit 16200b37f9b4f9b974003b2777ec03b033d905d6. Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt commit 16200b37f9b4f9b974003b2777ec03b033d905d6 Author: Ann Almgren Date: Thu Aug 21 15:02:36 2014 -0700 Remove inputs.rt -- it didn't really do the RT problem Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt commit 1dc300b9fac6a9bfcfc768dd43f0cd0466f095ce Author: Weiqun Zhang Date: Tue Aug 19 17:24:41 2014 -0700 removed parallel_reduce in sanity check in fillpatch Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_f.f90 commit a32c3141cfa99f2a5802672d82efe0018fe8c7c1 Author: Weiqun Zhang Date: Tue Aug 19 17:10:50 2014 -0700 double precision --> dp_t for consistence Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/cutcells.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/particles_f.f90 Src/F_BaseLib/tag_boxes.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_restriction.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/edge_restriction.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_applyop.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_restriction.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 commit 2e7367572e7bb989098589c2542578a7fbc4d766 Merge: b32248c40 c7b63bbc6 Author: Weiqun Zhang Date: Thu Aug 14 22:12:58 2014 -0700 Merge branch 'master' into dev commit b32248c4091d34041bff91ebc212f3c4b01670bf Author: Weiqun Zhang Date: Thu Aug 14 22:09:46 2014 -0700 added operator+= to BndryRegister class Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit c7b63bbc66ae6b24fe3d58c9acaa162facf50759 Merge: 0d414258c 8e6a22889 Author: ajnonaka Date: Thu Aug 14 12:34:08 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0d414258c97ddec677e1b977b2e4a15bf49129cc Author: ajnonaka Date: Thu Aug 14 12:33:45 2014 -0700 CIMS machines Tools/C_mk/Make.defs commit 8e6a2288957c8510f48a7bba4ae4576b52023f50 Author: Ann Almgren Date: Thu Aug 14 11:24:02 2014 -0700 Fix the stupid typos from the last commit. Src/C_AMRLib/Amr.cpp commit 65d098b78b961a3b3f97de6912f0c602ebb9e5af Author: Ann Almgren Date: Thu Aug 14 11:12:12 2014 -0700 Allow the user to set regrid_int = -1 as a signal not to regrid (at all or at that level) Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 89db152b047b8e87b94ec722fb86944e970ba969 Author: vince Date: Wed Aug 13 16:24:22 2014 -0700 added function to read checkpoint headers. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit da2e03ce297db1c50a57187dec192ea8c64d55c2 Author: Matthew Emmett Date: Wed Aug 13 15:29:51 2014 -0700 PyBoxLib: Tidy up make files, pull in isinf and isnan from std on Darwin. Src/C_BaseLib/FArrayBox.cpp Src/Python/GNUmakefile_CXX.mak commit e9312f5b880ae186a2e7325e881189467949093e Author: Ann Almgren Date: Wed Aug 13 12:49:11 2014 -0700 Add the option to use relativistic weighting of the mass (i.e. multiply by gamma) if the relativistic flag is set, which currently is only allowed if the NEUTRINO_PARTICLES flag is defined. Src/C_AMRLib/Particles.H commit 3eea21ac061f46448a548eba081c13089515a26f Author: Ann Almgren Date: Tue Aug 12 13:56:34 2014 -0700 Add a README so we can keep track of the different F90 HeatEquation* examples in BoxLib/Tutorials. Tutorials/README_HeatEquation_F commit 611ba4746d182ba0a7b6a4f9f0a2bda662bfa89d Author: Ann Almgren Date: Tue Aug 12 13:41:41 2014 -0700 Update subcycling description. Docs/F_AdvancedTopics/F_AdvancedTopics.tex commit f257c735d50c3bdde7d84a9e8119e56790c26d69 Author: Ann Almgren Date: Tue Aug 12 09:45:47 2014 -0700 Remove flags for ROSE compiler. Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GNUmakefile commit 1146ba3d3645b15aeb1332a4af6cd0eb8b3ff992 Author: Ann Almgren Date: Tue Aug 12 09:10:20 2014 -0700 Set NDEBUG = t Tutorials/HeatEquation_EX6_F/GNUmakefile commit 5747eafcd5970fecdc959954ffc22a88e86da809 Author: Ann Almgren Date: Tue Aug 12 09:08:01 2014 -0700 Get 3d working ... Tutorials/HeatEquation_EX6_F/inputs_3d Tutorials/HeatEquation_EX6_F/reflux.f90 Tutorials/HeatEquation_EX6_F/tag_boxes.f90 commit 03d32123a15640c021975c0044007661ecf58bf7 Author: Ann Almgren Date: Tue Aug 12 09:02:44 2014 -0700 set n_cell = 64 and max_levs = 3 in inputs file. Tutorials/HeatEquation_EX6_F/inputs_2d commit 3fbac6ba77f6bb475642d987f9ea6808279f8e3c Author: Ann Almgren Date: Tue Aug 12 09:01:36 2014 -0700 Fix bndry_reg copy when n > 1. Tutorials/HeatEquation_EX6_F/advance.f90 commit 5f540dd915f38f9e30702821b0f9aa257bc799e6 Author: Ann Almgren Date: Mon Aug 11 20:40:35 2014 -0700 Modify the Tutorials/HeatEquation_EX6_F code for explicit subcycling so that it uses new bndry_reg functions and new modified fillpatch and multifab_fill_ghost_cell routines. This works for max_levs = 2 but not yet for max_levs = 3. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Tutorials/HeatEquation_EX6_F/GNUmakefile Tutorials/HeatEquation_EX6_F/GPackage.mak Tutorials/HeatEquation_EX6_F/advance.f90 Tutorials/HeatEquation_EX6_F/cc_restriction.f90 Tutorials/HeatEquation_EX6_F/compute_flux.f90 Tutorials/HeatEquation_EX6_F/inputs_2d Tutorials/HeatEquation_EX6_F/main.f90 Tutorials/HeatEquation_EX6_F/ml_restriction.f90 Tutorials/HeatEquation_EX6_F/reflux.f90 Tutorials/HeatEquation_EX6_F/regrid.f90 Tutorials/HeatEquation_EX6_F/subcycling.f90 Tutorials/HeatEquation_EX6_F/tag_boxes.f90 Tutorials/HeatEquation_EX6_F/update_phi.f90 commit aa076f5aeb4a958e5e7f40b61e8dd7ff1b939901 Author: Matthew Emmett Date: Mon Aug 11 15:57:03 2014 -0700 PyBoxLib: Add python libs to linking stage. Src/Python/GNUmakefile_CXX.mak commit 1c4da796cfb8e492c270fec297548da863d53c73 Author: Weiqun Zhang Date: Fri Aug 8 12:25:53 2014 -0700 reduce the number of parallel reduce in Linear Solver Src/LinearSolvers/F_MG/ml_nd.f90 commit f0a7bd0d5ab6983f43bc692dfad70bca80a61900 Author: Weiqun Zhang Date: Fri Aug 8 12:16:48 2014 -0700 fixed typo Src/LinearSolvers/F_MG/itsol.f90 commit 66960bc198163617e8ca5eafa808dbd0bff700e8 Author: Weiqun Zhang Date: Fri Aug 8 12:13:31 2014 -0700 removed more unsafe saxpy; clean up Src/LinearSolvers/F_MG/itsol.f90 commit 28866df9e61db22fac3cea49c6ca0af0d4529fea Author: Weiqun Zhang Date: Fri Aug 8 11:58:01 2014 -0700 Changed a potentially unsafe call to saxpy because Fortan arrays are not supposed to aliased. Src/LinearSolvers/F_MG/compute_defect.f90 commit e10775c954d68e05ddaa0ec110e5799c80731451 Author: Weiqun Zhang Date: Fri Aug 8 11:45:38 2014 -0700 reduced number of parallel reduce in multi-level nodal convergence check Src/LinearSolvers/F_MG/ml_nd.f90 commit 108cdd95d07bdd8c20b10310402c364e3264414c Author: Weiqun Zhang Date: Fri Aug 8 11:19:05 2014 -0700 fixed a new bug Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit 96b94eccc99081471ad2f1558033e939aef4a06b Author: Weiqun Zhang Date: Fri Aug 8 10:37:13 2014 -0700 remove a multifab_fill_boundary in nodal solver Src/LinearSolvers/F_MG/ml_nd.f90 commit c076f376ed0564178e8a8688b45313f184227fa1 Author: Weiqun Zhang Date: Fri Aug 8 09:50:30 2014 -0700 removing more multifab_fill_boundary's in Linear Solver Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 4df53eb9ca353aa2214f6f03189d7aee0e6975c7 Author: Weiqun Zhang Date: Fri Aug 8 09:18:52 2014 -0700 cleanup Src/LinearSolvers/F_MG/ml_cc.f90 commit 8adca6d9c7fa77bed222c26c18076d373cc3e5d4 Author: Weiqun Zhang Date: Fri Aug 8 09:07:43 2014 -0700 removed more multifab_fill_boundary's in Linear Solver Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 8d412a2f311738e218e4ef61860ba7c683c40eeb Author: Weiqun Zhang Date: Fri Aug 8 07:27:33 2014 -0700 renaming for consistence; removed more multifab_fill_boundary's Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 2e135d14c613664a0e0d1fc3ec7d05492a7b36bb Author: Weiqun Zhang Date: Thu Aug 7 21:50:31 2014 -0700 cleanup Src/LinearSolvers/F_MG/ml_cc.f90 commit 8d55d8cbde81ab651a3ca5a5424d33f91cbdcbcc Author: Weiqun Zhang Date: Thu Aug 7 21:38:38 2014 -0700 remove a number of redundant mf_fill_boundary calls Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 3b50a4badea5357558102ea231b4e66c3eef12f1 Author: Weiqun Zhang Date: Thu Aug 7 18:03:22 2014 -0700 reduce the number of parallel reduce in checking multi-level convergence Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 4dda5d672c9626733cae2010b5ea445b1f5fece8 Author: Ann Almgren Date: Thu Aug 7 14:58:17 2014 -0700 Modify loops ... still some more to be done ... Src/F_BaseLib/bndry_reg.f90 commit 4ca7b457b4a7ea66e159bb44fa9f22f14271e5ba Author: Weiqun Zhang Date: Thu Aug 7 13:56:24 2014 -0700 fixed a bug in new bndry_reg when fine box touches physical boundaries Src/F_BaseLib/bndry_reg.f90 commit c863ba245bc618628160be7d5947c993fddec66d Merge: 863672981 668e9f0a8 Author: Weiqun Zhang Date: Thu Aug 7 12:48:50 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 8636729815e03a35aa8a5d9c5d8126f7ecac64b2 Author: Weiqun Zhang Date: Thu Aug 7 12:48:03 2014 -0700 Get around an Intel compiler bug by removing a name clash in the size interface so that maestro can compile with intel again. Note that Fortran standard permits name clash for generic interfaces by requiring a compiler to merge interface blocks. Src/F_BaseLib/particles_f.f90 commit 668e9f0a8b24968a7271c0cc85570fada1b4de7b Author: Ann Almgren Date: Thu Aug 7 11:41:42 2014 -0700 Fix the section on the bndryreg Docs/GettingStarted/GettingStarted.tex commit 2d8c671b1fd9e0e776608099c725341c4d97c3fe Author: Weiqun Zhang Date: Thu Aug 7 09:30:04 2014 -0700 get around Intel compiler issue Src/F_BaseLib/bndry_reg.f90 commit 8379ff5f7e6a26a1b0168e6f1802c97c31b17c15 Author: Michael Zingale Date: Wed Aug 6 21:21:41 2014 -0400 add the linear solver text I wrote for Maestro Docs/F_AdvancedTopics/F_AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/UsersGuide.tex commit 2bc35796cffb36e8ec1137181fb8e0d6428c7f15 Author: Weiqun Zhang Date: Wed Aug 6 14:18:34 2014 -0700 Added a new option to bndry_reg_module: Some fabs in bndry reg are entirely covered by the fine grids. The new option controls whether or not to keep these useless fabs. The default is to keep them (even though this increases the amount of data for communication and the amount of work for filling these fabs) because removing these boxes from the layout requires some expensive box calculus. Src/F_BaseLib/bndry_reg.f90 commit 49578d6d31427970e874e5e798cc0e0a7ec0a590 Author: Weiqun Zhang Date: Wed Aug 6 12:05:54 2014 -0700 special parallel copy for multi-level bndry_reg Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit c1bfc445408fb38b18258ecfe86d083c7e8969b7 Author: Weiqun Zhang Date: Tue Aug 5 15:51:43 2014 -0700 clean up Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit 82aa3463eb0fecbc42e7986f7ced534c71c3ea57 Author: Weiqun Zhang Date: Tue Aug 5 13:31:04 2014 -0700 bndry_reg: reduce the number of parallel copy from 6 to 3 Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit aeb2b143b9e89810a523f03f8e1bb531ce204a9f Author: Weiqun Zhang Date: Tue Aug 5 13:26:57 2014 -0700 removed useless fabs (i.e., covered by fine grids) from bndry reg Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit a9c553f195481816f17a3b15bd4f4c96a4c287fe Author: Weiqun Zhang Date: Tue Aug 5 13:22:30 2014 -0700 fixed a memory leak in the linear solver comparison test Tests/LinearSolvers/ComparisonTest/main.cpp commit 9acd7dba5dc35b7829779f9e59aa0aa20b1c6e84 Author: Ann Almgren Date: Fri Aug 1 08:34:48 2014 -0700 Add this subcycling figure. Docs/F_AdvancedTopics/subcycling_algorithm.eps commit 4d0a88cc2aee4b13a5121ef238fc91239e1326df Author: Ann Almgren Date: Thu Jul 31 18:34:03 2014 -0700 Add commentary about how subcycling is done in the F90 Tutorials example in HeatEquation_EX6_F. Docs/F_AdvancedTopics/F_AdvancedTopics.tex commit cf53b834919a8a7db4d563f52e03d2a23842ada2 Author: Ann Almgren Date: Thu Jul 31 18:33:25 2014 -0700 Modify these advance routines to look more like the one in the subcycling example, just so what changes is clearer. Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX5_F/advance.f90 commit ccd5d63fd8a596c33af92f613a014e2aa83962ae Author: Ann Almgren Date: Thu Jul 31 18:32:25 2014 -0700 Add a new Tutorials example which does subcycling in time for the explicit solution of the heat equation (an extension of HeatEquation_EX4_F). Tutorials/HeatEquation_EX6_F/GNUmakefile Tutorials/HeatEquation_EX6_F/GPackage.mak Tutorials/HeatEquation_EX6_F/advance.f90 Tutorials/HeatEquation_EX6_F/cc_restriction.f90 Tutorials/HeatEquation_EX6_F/init_phi.f90 Tutorials/HeatEquation_EX6_F/inputs-rt Tutorials/HeatEquation_EX6_F/inputs_2d Tutorials/HeatEquation_EX6_F/inputs_3d Tutorials/HeatEquation_EX6_F/main.f90 Tutorials/HeatEquation_EX6_F/ml_restriction.f90 Tutorials/HeatEquation_EX6_F/regrid.f90 Tutorials/HeatEquation_EX6_F/subcycling.f90 Tutorials/HeatEquation_EX6_F/write_plotfile.f90 commit 84f4419d706b247732887b2ec4e9df58b03d606f Author: Ann Almgren Date: Thu Jul 31 18:14:54 2014 -0700 Modify the comment that subcycling is only in C++ since we have an F90 Tutorial example with subcycling. Docs/Introduction/Introduction.tex commit b67227211e3635616111dbeb945e6ded65693d3f Merge: b1d8a242a ed2ec590b Author: Ann Almgren Date: Thu Jul 31 17:40:38 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ed2ec590b154168d891316e5aa72724f9f5af025 Author: Weiqun Zhang Date: Thu Jul 31 16:10:16 2014 -0700 more code consolidation in multilevel cell-centered solver Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 21d5f347ca3e76fab9e8c52aa866db9053dd7095 Author: Weiqun Zhang Date: Thu Jul 31 15:55:53 2014 -0700 fixed a bug in bndry reg; minor cleanup Src/F_BaseLib/bc.f90 Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 3f4cbe4c2830ce6b81098014bc8b9c0824b20210 Author: Ann Almgren Date: Thu Jul 31 15:38:18 2014 -0700 We have changed the way we use bndry_reg in the multilevel cell-centered solves to make them much more efficient. Eliminated an extra parallel copy and consolidated code. Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit b1d8a242a9c62668dffcb8851d1f26b47c1c0ff8 Author: Ann Almgren Date: Thu Jul 31 15:03:30 2014 -0700 Fix spelling error in comment. Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit db6ea0862096f9440375d3eb57e73653f0e77bb2 Author: Ann Almgren Date: Tue Jul 29 16:34:39 2014 -0700 Get this test code to work for cell-centered solve at multiple levels. Tests/LinearSolvers/F_MG/cc_multi.f90 commit a3be88a1a2fce4d512725aab74c66b3fd6ac53e2 Author: Weiqun Zhang Date: Fri Jul 25 15:32:52 2014 -0700 added USE_ACC to the make system Tools/C_mk/Make.Linux commit d12203f27bab5880eefa247561ee1ccf3af80a46 Author: Ann Almgren Date: Fri Jul 25 12:01:58 2014 -0700 Turns out the Cray compilers do not like the "isnan" function after all. Src/C_BaseLib/FArrayBox.cpp commit 0afb3fa96182c0b4c846ab9bc45873ae61ca8408 Author: Ann Almgren Date: Fri Jul 25 11:55:14 2014 -0700 Restore this file to the previous version -- turns out this wasn't really the problem with the cray compiler. Src/C_BaseLib/BLassert.H commit d0c5be6d206f3ff5dbe6ab52b82bedb84a003792 Author: Weiqun Zhang Date: Thu Jul 24 22:34:31 2014 -0700 For cray compilers, always run the opertion in BL_ASSERT to get around a possible Cray compiler bug. Hopefully this will fix the crash of Castro compiled by cray. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/BLassert.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp commit 0af26b79ff3a187a5f13fe51cea3beceb62d1d4e Merge: 90d9b43ad af8f7a4ed Author: Marc Day Date: Thu Jul 24 17:53:58 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 90d9b43ad9385b5b62ac93b7cb39129e27ec9bfd Author: Marc Day Date: Thu Jul 24 17:52:52 2014 -0700 Make the DiffFab.cpp function usable in a specialized regression test framework Tools/C_util/Convergence/DiffFab.cpp commit af8f7a4edb772588220e9531af6e6cc4887829ad Merge: c2baf150f 222751b81 Author: Michael Zingale Date: Thu Jul 24 18:26:05 2014 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c2baf150ff9e404a111e4ad9dfb3dd6d5c34f3db Author: Michael Zingale Date: Thu Jul 24 18:24:23 2014 -0400 sync this up to file movements Tools/RegressionTesting/Maestro-tests.ini commit 222751b818c0d2237aff9731443726731e1d6a06 Author: Michael Zingale Date: Thu Jul 24 12:43:49 2014 -0700 switch back to the old-style python formating in a print, since edison's default python (2.6.9) doesn't like the new style Tools/C_scripts/makebuildinfo_C.py commit 2690ab3dc9d70489d23e037afb29591db9d0069d Author: Weiqun Zhang Date: Wed Jul 23 22:55:09 2014 -0700 removed #if defined's around isnan and isinf because they have been in the standard since C99 and C++11; all compilers on Edison and Hopper support them. Src/C_BaseLib/FArrayBox.cpp Src/F_BaseLib/fabio_c.c Tools/C_mk/Make.Linux Tools/F_mk/comps/Darwin_intel.mak commit 9d74e0a1404d264834dc5897b186644de36aa2a6 Merge: ce24c80a5 b63add45e Author: vince Date: Tue Jul 22 16:19:19 2014 -0700 Merge branch 'master' into commprof commit b63add45e093bf7bcf8d8d73bd4ab2089eed1c3f Merge: 9738b88d6 f0ad6d651 Author: ajnonaka Date: Tue Jul 22 16:11:35 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9738b88d659119dfa2c88641842f6f0413f99153 Author: ajnonaka Date: Tue Jul 22 16:11:17 2014 -0700 comment out a broken timer until we figure out what's wrong Src/F_BaseLib/list_box.f90 commit f0ad6d651ef34592145cb844faa0363312e9a0f7 Author: Ann Almgren Date: Tue Jul 22 15:39:54 2014 -0700 Change default to DEBUG = FALSE and add a pure-F90 inputs file. Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.f90.3d commit f2a66eeb7f1588aafa6384d447163ec65abcb3d6 Author: ajnonaka Date: Tue Jul 22 11:23:55 2014 -0700 fixed a bpt_build error Src/LinearSolvers/F_MG/ml_prolongation.f90 commit a6d4709c574cdff87baa416144740b75581f574e Author: ajnonaka Date: Tue Jul 22 10:39:54 2014 -0700 enable bl_prof timers with PROF=t (broken at the moment) Tutorials/HeatEquation_EX5_F/main.f90 commit 334c4549cc08a283df589530b6fc136067002081 Merge: 5567bba5e 67b8c8470 Author: Adam Jacobs Date: Mon Jul 21 18:42:28 2014 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 5567bba5e502659977f99bc7d9755b7464575709 Author: Adam Jacobs Date: Mon Jul 21 18:40:54 2014 -0400 Change nesting enforcement so that the number of times it tries to fix nesting is relative to nlevs, not just the constant 3. Src/F_BaseLib/make_new_grids.f90 commit 67b8c847089a208eb6a71751de8a689dd4b800b2 Author: ajnonaka Date: Mon Jul 21 14:50:04 2014 -0700 renname f90 timers to avoid duplicate names Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit ce24c80a54c109965de31845b2ff7c759d68741a Author: vince Date: Fri Jul 18 10:37:21 2014 -0700 added text for fortran90 interface. Docs/Readme.profiling commit 2b06371e1044f3d0486f1a2b11901a07c1517fa3 Merge: c92e972e8 a4dc0aace Author: vince Date: Fri Jul 18 10:27:45 2014 -0700 Merge branch 'master' into commprof commit c92e972e8e65421eb2e7fe45cd0f08a3df2ae1c0 Author: vince Date: Fri Jul 18 10:26:41 2014 -0700 formatting. Src/C_BaseLib/Profiler.cpp commit 00bca4c7fa59565f69074817f410fc87af321285 Author: vince Date: Thu Jul 17 16:55:16 2014 -0700 more call stack tracing. inclusive and exclusive times in the html tree output. collapse html call tree at depth > 4 by default. added function name map to store ints in CallStats instead of strings. added report for inclusive function times, recursive times are subtracted. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit a4dc0aace2430234e07a6ab6fcb3d7a050429f64 Author: Michael Zingale Date: Wed Jul 16 19:57:55 2014 -0400 some cleanups Tools/F_scripts/makebuildinfo.py commit e6142e8e9a5b15b0ad631d4b538f13630cfa99e6 Author: Michael Zingale Date: Wed Jul 16 19:57:28 2014 -0400 argparse -> getopt -- argparse requires the latext python 2.7 which is not available everywhere. Tools/C_scripts/makebuildinfo_C.py commit dcae6d6ddf9315eefbdbf2a2c897d0407d4fa8a8 Merge: b1cba6ea0 929e73d4c Author: Ann Almgren Date: Tue Jul 15 11:23:03 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b1cba6ea0d6815484dc2efaf91429ced7232e2bc Author: Ann Almgren Date: Tue Jul 15 11:22:20 2014 -0700 Fix the use of Amr::UseFixedCoarseGrids -- the call to constructAreaNotToTag was missing in the AmrLevel constructor. Src/C_AMRLib/AmrLevel.cpp commit 929e73d4c655fa9e0a737932712835747dbeccc5 Author: Weiqun Zhang Date: Mon Jul 14 13:48:45 2014 -0700 fixed makebuilinfo_C.py in case not all 3 git directories are set Tools/C_scripts/makebuildinfo_C.py commit 2f9e06f3c73482502fa07b1bbfee6c1cc35f6d77 Merge: ad89384b4 0d5116d4b Author: Ann Almgren Date: Mon Jul 14 11:02:24 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ad89384b479bb2d15da16d755244e5e81f72ca14 Author: Ann Almgren Date: Mon Jul 14 11:02:06 2014 -0700 Add "Vater" 9-pt nodal stencil in 2d only. Src/C_AMRLib/Particles.H Src/LinearSolvers/C_to_F_MG/stencil_types.H Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/stencil_types.f90 commit 0d5116d4b77df19010ef072bd4ec7b7046d49c1e Merge: 7b1888dac 9ecead84a Author: Matthew Emmett Date: Mon Jul 14 10:54:20 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 7b1888dacf65242687368cc6bbafc987fa319cb9 Author: Matthew Emmett Date: Mon Jul 14 10:54:03 2014 -0700 PyBoxLib: Use F90 for linking and include -lstdc++. Src/Python/GNUmakefile_CXX.mak commit 9ecead84a061ffabe8e316618908aa1c41c6a7d6 Author: Weiqun Zhang Date: Mon Jul 14 10:47:34 2014 -0700 replaced -1e200 with -Huge() Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit c4f41857ed5645d8589c7cc86cf0ec7770deee6b Author: Michael Zingale Date: Sat Jul 12 19:24:14 2014 -0400 add a new python routine to handle the buildInfo.cpp file -- this is far easier to extend and much more readable than the shell script version. This mirrors the F90 one written for Maestro, and allows us to get the Castro buildInfo.cpp working again after the most recent commits broke it. Tools/C_scripts/makebuildinfo_C.py commit e689426115f63694d22411abcf86b3b046f8294e Author: Ann Almgren Date: Thu Jul 10 14:38:55 2014 -0700 Add functionality (UseFixedCoarseGrids) to define fixed grids up to a certain level and use adaptive refinement at all finer levels. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 8e4b07739d9c9a808775302c4d668445bae27f90 Author: Ann Almgren Date: Thu Jul 10 14:01:23 2014 -0700 Add additional functionality into the "buildInfo" capability -- this came from Jan and Wolfram. Tools/C_scripts/buildInfo.H Tools/C_scripts/make_build_info_cpp commit 61146c6ec1e179aae609aced4405c22be2ddb467 Author: Ann Almgren Date: Wed Jul 9 15:36:15 2014 -0700 Allow a stencil_type_in into the nodal_applyop routine. Src/LinearSolvers/F_MG/nodal_applyop.f90 commit d8b8ca38aa21a9022df695abdb9f80b8c7b859fa Author: Michael Zingale Date: Tue Jul 8 11:29:21 2014 -0400 kraken is no more. Long live darter. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 2976f60b2a2c2f97d93e3723fe9e6222b8c170cb Author: Matthew Emmett Date: Thu Jul 3 16:46:50 2014 -0700 PyBoxLib: Add ReduceRealMax and Geometry. Src/Python/boxlib/__init__.py Src/Python/boxlib/bl1.py Src/Python/boxlib/bl2.py Src/Python/boxlib/bl3.py Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id Src/Python/swig/boxlib.i commit aba8762074b3a6e2c659809140232ccd6356a309 Author: Matthew Emmett Date: Thu Jul 3 16:46:04 2014 -0700 PyBoxLib: Minor tweaks to Makefiles. Update README. Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak Src/Python/README commit 595a5a72f72bbae43361a848a9988203e70fa645 Merge: df5c72466 a09eecfa5 Author: vince Date: Tue Jul 1 16:44:06 2014 -0700 Merge branch 'master' into commprof commit df5c7246601b552a442301f2348c6b01693988a8 Merge: da9222a7d 49ac32483 Author: vince Date: Tue Jul 1 16:42:14 2014 -0700 Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof commit da9222a7d649dfd253d92df8960f0d9a465e152c Author: vince Date: Tue Jul 1 16:42:02 2014 -0700 added inclusive and exclusive times to the call trace tree. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit a09eecfa5aec7c18605ce351e1ce66ad842ee005 Merge: 7e77e449e 59ac03d2c Author: Ann Almgren Date: Mon Jun 30 17:37:30 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7e77e449ebb49782b70dd45ab337d342f28b5bcb Author: Ann Almgren Date: Mon Jun 30 17:37:02 2014 -0700 Fix the add_rh_nodal stuff that is used in the initVortProj stuff in Projection.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 59ac03d2cfbe0856a4c8aa7f8f3926c36628f943 Merge: 23eade895 c98c9c04e Author: Chris Malone Date: Mon Jun 30 16:14:01 2014 -0600 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 23eade8951fd772c1229dd3ae55c9d90e005790b Author: Chris Malone Date: Mon Jun 30 16:13:54 2014 -0600 some LANL machine stuff Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit c98c9c04e2f7615c4523f1e7c190a087947a14ca Author: Marc Day Date: Mon Jun 30 15:11:51 2014 -0700 Change interface to nodal_project solver to use PArrays Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 49ac3248305c3c1b554419148f51e046bd7e241e Author: Ann Almgren Date: Mon Jun 30 14:32:00 2014 -0700 Sync this up with the master version. Src/LinearSolvers/F_MG/ml_cc.f90 commit 1105852be729b4d2c814ae9826f0d032be99cdf3 Author: Ann Almgren Date: Mon Jun 30 14:30:34 2014 -0700 Fix the print statements ... hopefully. Src/LinearSolvers/F_MG/ml_cc.f90 commit b1c256797a20b3fcdfa0db2e8b5d7daab8ba3878 Author: Ann Almgren Date: Mon Jun 30 14:19:34 2014 -0700 Trying to fix print statements (only print statements, not convergence tests) so it is clearer what is going on. Src/LinearSolvers/F_MG/ml_cc.f90 commit 46b787dd1d7fc6fe17e10439134bc41b41a09070 Author: Ann Almgren Date: Mon Jun 30 13:40:07 2014 -0700 Correct spelling in comment. Tutorials/HeatEquation_EX1_F/main.f90 commit d9a2bf7842bf94ac25e46144d411447cedb3580f Author: Michael Zingale Date: Mon Jun 30 12:50:00 2014 -0400 change the definition of the relative norm. Before we were doing ||(A-B)/A||, now we do ||A-B||/||A|| -- this is more correct. fcompare.f90 commit 7c81fd86a11470760368d4466746085def199d49 Author: Weiqun Zhang Date: Fri Jun 27 10:56:06 2014 -0700 made an essentially identity transformation to accommodate Cray compiler Src/LinearSolvers/F_MG/coarsen_coeffs.f90 commit 080530e942b32a0b9272ffe8d5533a323608cfb1 Author: ajnonaka Date: Wed Jun 25 08:45:57 2014 -0700 bugfix: in the nodal restriction, we assumed the mask multifabs had the same number of components as the thing you are restricting. the mask should only have 1 component Src/LinearSolvers/F_MG/ml_restriction.f90 commit a4f99bf68c3aab34c51c702b9eff6a6fca5744cd Merge: 769228ca4 271f23d43 Author: ajnonaka Date: Wed Jun 25 06:25:38 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 769228ca4da257bf3f9eed76b47c95c231be4aa7 Author: ajnonaka Date: Wed Jun 25 06:25:08 2014 -0700 get this compiling again, won't affect results as fixed code wasn't being called by anything Src/LinearSolvers/F_MG/ml_restriction.f90 commit 271f23d43ee44fd9253e1c508afe32a8be48efb6 Author: Weiqun Zhang Date: Wed Jun 25 06:22:02 2014 -0700 modified the interface of the new ml restriction wrapper so that the code can compile Src/LinearSolvers/F_MG/ml_restriction.f90 commit d8d49e7aed990575abd0a27c2e8fe71f34e25416 Merge: 22bc1151d 07808fda8 Author: ajnonaka Date: Tue Jun 24 17:01:58 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 22bc1151d6fccb89192c18da21633a137045a441 Author: ajnonaka Date: Tue Jun 24 17:00:42 2014 -0700 added a simplified interface to do direct injection nodal restriction that only requires an ml_layout, bc_tower, and bc_comp passed in. testing underway. Src/LinearSolvers/F_MG/ml_restriction.f90 commit 07808fda8144607e3cec558b7abf1b087dd7c1c7 Author: Michael Zingale Date: Mon Jun 23 14:15:09 2014 -0400 remove a parallel_reduce by doing the rh norm_inf (bnorm) locally and then packing it into the parallel reduce already in this code. Src/LinearSolvers/F_MG/ml_cc.f90 commit 6338fc40bbba6b61045839d740d3bcb9ed8504e1 Author: vince Date: Thu Jun 19 14:22:19 2014 -0700 added more mpi types. Src/C_AMRLib/Particles.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/VisMF.cpp Src/C_TowerLib/Layout.cpp commit 644f094cbda847bfc05edbc4260f384b881aa79f Author: ajnonaka Date: Thu Jun 19 08:45:54 2014 -0700 greatly simplified this cell-centered heat equation implicit example by hooking into the simple ml_cc_solve interface. no more building mg_towers, coefficients, etc., in the advance routine. comes up clean in my regression Tutorials/HeatEquation_EX5_F/advance.f90 commit a451968fa19e9ada250685903aff4ece2dd9d963 Merge: 33183ff38 bbe1c9af2 Author: vince Date: Wed Jun 18 14:19:27 2014 -0700 merge fix. commit 33183ff38a62a1e1e3262b6b636115bbfb558d79 Author: vince Date: Wed Jun 18 14:13:39 2014 -0700 bl loc. MiniApps/FillBoundary/GNUmakefile commit 479b5aa79df4813df480ab6389f1fbab7083b410 Author: vince Date: Wed Jun 18 14:05:00 2014 -0700 more pfc. Src/C_BaseLib/DistributionMapping.cpp commit da0e46e1a6d3966130801dbfdbada7fe173b304f Author: vince Date: Wed Jun 18 14:01:15 2014 -0700 added function tracing. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit ac671cfe6274c9a1e1c4f3f573e6633f797203e1 Author: vince Date: Mon Jun 2 16:22:44 2014 -0700 create default if no topological map is found. Src/C_BaseLib/DistributionMapping.cpp commit bbe1c9af2cc72f83426d840ec5d3505035fcf253 Author: Weiqun Zhang Date: Fri May 30 17:46:30 2014 -0700 fixed a number of memory leaks Src/C_AMRLib/Particles.H commit c188580368cbec5b3065217c585d33ab50d8dfb6 Merge: 4aebcaba0 435eca6c9 Author: Weiqun Zhang Date: Fri May 30 16:59:14 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4aebcaba048f21d129ee71c4351342fab710441d Author: Weiqun Zhang Date: Fri May 30 16:59:11 2014 -0700 Fixed invalid conversion from const MultiFab * to MultiFab * that is not tolerated by some compilers. Src/C_AMRLib/Particles.H commit 435eca6c9e86dccba4e76b9ac7d891cf1cee1bfc Author: Ann Almgren Date: Fri May 30 12:22:45 2014 -0700 nodal_enforce.f90 --> nodal_enforce_dirichlet_rhs.f90 Src/LinearSolvers/F_MG/CMakeLists.txt commit cc7e537a7828ceb82842e3e8c288887e7105060a Merge: a40811067 350752c6b Author: Ann Almgren Date: Thu May 29 12:00:09 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a408110678667cb4fd537b599a0e817341b58d2c Author: Ann Almgren Date: Thu May 29 11:59:17 2014 -0700 Add new variable in Amr -- which_level_being_advanced -- with an access function level_being_advanced() so that the AmrLevel routines can know if post_regrid is being called within the advance for a level (which_level_being_advanced) which is different from lbase. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 350752c6ba5ef9c0f34cb4909108c1548bb6dfc3 Author: Ann Almgren Date: Wed May 28 16:36:22 2014 -0700 Need to allocate mgt%bottom_mgt inside a later test so that if we are unsuccessful in get_bottom_box_size we don't allocate it at all. Src/LinearSolvers/F_MG/mg.f90 commit f355cd832b48dabfbf32d3c18e75bff5d5101f27 Author: Ann Almgren Date: Wed May 28 16:31:00 2014 -0700 Remove un-needed print statements. Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 commit 020fa77a701657d732c276f0e2e70f0932eec04f Author: Ann Almgren Date: Wed May 28 14:54:04 2014 -0700 Version_One_Dot_Zero should default to reading *double* precision, not single. Src/C_AMRLib/Particles.H commit b1a92fdba898b8fe5132b6e99da965ec3adc1783 Author: vince Date: Wed May 28 11:39:48 2014 -0700 reindex. Src/C_BaseLib/DistributionMapping.cpp commit 131e8de0822a0d44f7d8ac2cb7d7578cf3f0a824 Author: Weiqun Zhang Date: Fri May 23 15:41:59 2014 -0700 moved the code for regridding single-level run on restart to a function so that it can be called by derivative of Amr Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 97a713512070520bbb201bed8c458a70b11f529b Author: Weiqun Zhang Date: Fri May 23 10:54:15 2014 -0700 use omp_lib --> include 'omp_lib.h' to make Cray compiler work Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_3D.F commit 57fa06190f307f2db4cce50d13160942dca154b0 Author: vince Date: Thu May 22 13:38:19 2014 -0700 removed cout. Src/C_BaseLib/DistributionMapping.cpp commit 4a7c38b4c3ed5bd8132560fe25256622abed889b Author: vince Date: Thu May 22 13:36:12 2014 -0700 added prof and commprof flags. Tests/C_BaseLib/GNUmakefile commit 727bf5c487eab3bb48ff5bea673c4b11dec52565 Author: vince Date: Thu May 22 13:33:10 2014 -0700 added tests. Tests/C_BaseLib/tFB.cpp commit 8b3a341560efb1ac01481af482e7048c8ecfc6fc Author: vince Date: Thu May 22 13:02:08 2014 -0700 added some profiling. MiniApps/MultiGrid_C/main.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 363dec5b56b02abebdb9af51744f1b8d3f1982fc Author: beckner2 Date: Wed May 21 10:08:37 2014 -0700 changes for intel compiler on cab. Tools/C_mk/Make.Linux commit bc6a7ac3db79554a27261aecdebf0f5232490195 Author: Ann Almgren Date: Wed May 21 09:33:04 2014 -0700 The 1d stencil didn't have enough space allocated. Src/LinearSolvers/F_MG/mg.f90 commit 92b5d6338320a02af02d1b405d192e3158ed7bb9 Author: Marc Day Date: Tue May 20 16:49:12 2014 -0700 Copy fsnapshot stuff here from AmrPostProcessing to simplify distribution to external collaborators Tools/Py_util/GNUmakefile Tools/Py_util/README Tools/Py_util/fsnapshot.f90 Tools/Py_util/plotsinglevar.py commit 0553c66c0a7ad159b554d3ecb329722292c20d49 Merge: 99a6d6380 6cb2cfe78 Author: Marc Day Date: Tue May 13 20:36:31 2014 -0700 Resolve conflict in plotfile.f90 commit 99a6d6380778264ca795dbf7daa3ddc62df7b872 Author: Marc Day Date: Tue May 13 20:34:22 2014 -0700 Add parameter to MultiGrid_C tutorial to avoid build f90 solvers Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/main.cpp commit 15951c0a0fe8ee5161284088d59214d50ccd81d4 Author: Marc Day Date: Tue May 13 20:33:32 2014 -0700 Allow longer variable names in plotfiles Src/F_BaseLib/plotfile.f90 commit 6cb2cfe780adad9483aeaf9c5978d074f2c6d7b5 Author: Michael Zingale Date: Tue May 13 14:57:06 2014 -0400 more work on the analysis bits Tools/RegressionTesting/Castro-SBU-tests.ini Tools/RegressionTesting/testnew.py commit 627ba324a1844dab64354a92eaea1ab63ac26b51 Author: Michael Zingale Date: Tue May 13 11:17:07 2014 -0400 update to add analysys plots to more tests Tools/RegressionTesting/Castro-SBU-tests.ini commit 699805b00aebd341a3df786fddea22c826195081 Author: Michael Zingale Date: Tue May 13 10:37:48 2014 -0400 add the ability to do post-test analysis Tools/RegressionTesting/Castro-SBU-tests.ini Tools/RegressionTesting/testnew.py commit d2f9a86738b018fb24f3aef4e282d5ac7634a6c8 Merge: 3ec2fafec 10086696b Author: Michael Zingale Date: Tue May 13 09:16:09 2014 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 3ec2fafecd39174d7dde5e4f5ded40067eacfcb5 Author: Michael Zingale Date: Tue May 13 09:15:51 2014 -0400 add analysis Tools/RegressionTesting/Castro-SBU-tests.ini commit 10086696b13a6c2accf546306502927f1996be47 Merge: ed38fcd58 af6972b70 Author: Weiqun Zhang Date: Mon May 12 21:11:06 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit ed38fcd584f5baae7f59f6d872cf5f0afcd2f5ad Author: Weiqun Zhang Date: Mon May 12 21:10:41 2014 -0700 PGI compiler requires explicit casting of int for std::sqrt Src/C_BaseLib/IArrayBox.cpp Src/C_BaseLib/iMultiFab.cpp commit af6972b7008a418938ef43194e934ee03d25672e Author: ajnonaka Date: Mon May 12 17:08:22 2014 -0700 fix the # of stencil points for higher-order stencils Src/LinearSolvers/F_MG/mg.f90 commit 63a291291bbe406f7c28a26cc9263bf2a0187afb Author: Michael Zingale Date: Mon May 12 19:00:11 2014 -0400 when not using --infile1 OR --infile2, we were not incrementing the farg counter. When using atleast one of --infile1 or --infile2, we were ok. fcompare.f90 commit 8d4a193fafd2a197084a1f844bad1dc78503b662 Author: Michael Zingale Date: Thu May 8 13:59:25 2014 -0400 add a -d switch that has the suite only run tests of a given dimensionality Tools/RegressionTesting/testnew.py commit e427815a5ee38e7f9c3420c7b918c0cc69568a73 Author: vince Date: Tue May 6 16:18:04 2014 -0700 more pfc, diagnostics still in the code. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit cfcfa36352df74641422953c460636176c1bfc8a Author: Michael Zingale Date: Tue May 6 19:01:32 2014 -0400 the Castro tests we run at Stony Brook Tools/RegressionTesting/Castro-SBU-tests.ini commit 4ac304b9716eb5eaf70e0cea6da31f289efa458c Author: Weiqun Zhang Date: Tue May 6 14:28:07 2014 -0700 fixed a minor thing that some compiler complains about Src/F_BaseLib/boxarray_f.f90 commit 5877a41596edecf57080ecf1b22a999e141a7df7 Author: Ann Almgren Date: Tue May 6 13:34:19 2014 -0700 Re-insert two lines which were accidentally removed. Src/LinearSolvers/F_MG/ml_solve.f90 commit 17d111c3855af852e20df6e491a38462ad37d4c5 Author: Ann Almgren Date: Tue May 6 13:34:01 2014 -0700 Remove some unneeded dependencies. Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90 commit e204203d00a6be7ad81a54bcc9e0862efdbae48a Merge: 53679a154 773ee0948 Author: ajnonaka Date: Tue May 6 09:40:45 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 53679a154ccb222e0d5e907b41445c9e2206ad7b Author: ajnonaka Date: Tue May 6 09:40:12 2014 -0700 generalize make.defs to handle aliased gfortran versions Tools/C_mk/Make.defs commit 773ee0948e395892236b8ec6ac37acbd114f12d0 Merge: 48f4b96d4 416771560 Author: Ann Almgren Date: Mon May 5 16:07:11 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 48f4b96d44666f3832e9426f54f5e11dde9febb0 Author: Ann Almgren Date: Mon May 5 16:05:44 2014 -0700 Modify enforce_outflow_on_divu_rhs to be enforce_dirichlet_rhs so that it sets the nodal rhs to zero anywhere the mask is dirichlet, not just at ouflow values. This takes care of setting the nodal rhs to zero at fine nodes at the coarse-fine interface. This routine is called inside of ml_nd_solve, so should not be called in codes which call ml_nd_solve. Moved the enforce... code out fo nodal_divu.f90 and into a new file: nodal_enforce_dirichlet_rhs.f90 Src/LinearSolvers/F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90 commit adf21957a4496c5d3dd22dcc496e46744947fca8 Author: Ann Almgren Date: Mon May 5 16:05:31 2014 -0700 Remove extra printing of tres in ml_cc.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 416771560dde5592569a3de706bb8e432667dbde Author: Weiqun Zhang Date: Mon May 5 14:39:55 2014 -0700 added a new function that returns whether a BoxArray intersects with a Box Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 51049d7b97d8627e31aa678a286f03bdaaf04698 Author: Marc Day Date: Wed Apr 30 12:21:12 2014 -0700 Increase max name length to 50 (from 20) for plotvars...probably should code this more robustly someday Src/F_BaseLib/plotfile.f90 commit 960b7b0531585baefa42481d7254e9f897c79287 Merge: be6543a4a e53999e85 Author: Ann Almgren Date: Tue Apr 29 13:46:08 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit be6543a4a6fe172aa2e82eb04e1114255d057a09 Author: Ann Almgren Date: Tue Apr 29 13:45:18 2014 -0700 1) Compute tres0 based on res, not rh 2) Use max_norm instead of bnorm in the first convergence test. Src/LinearSolvers/F_MG/ml_cc.f90 commit e53999e858634fcdb9f274211829f39981b780a6 Author: Weiqun Zhang Date: Sat Apr 26 20:27:34 2014 -0700 updated make system for Edison Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_intel.mak commit 00705295adfb9d0158b9f5e3ee096677ec19389c Author: ajnonaka Date: Tue Apr 22 16:14:33 2014 -0700 update to new solver interface Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit b8bebd8496e37a5301b1a697411875256ac6795a Author: Weiqun Zhang Date: Tue Apr 22 14:34:57 2014 -0700 added norm functions that can do multiple components so that MPI reduce calls can be aggregated Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 1bc9ff6009afaa476930688636124c235b9ba0ae Author: Ann Almgren Date: Fri Apr 18 12:29:22 2014 -0700 In mg_tower_cycle, use the cycle type "cyc" that is passed in, rather than using mgt%cycle_type. This allows us to use different cycle types for different iterations to test whether a combination of F- and V-cycles works better than pure F- or pure V-cycles. Src/LinearSolvers/F_MG/mg.f90 commit 748222b03f037d84398dda782447756e0135127d Author: Michael Zingale Date: Thu Apr 17 14:20:34 2014 -0400 only print the intepolation warning message from the IOProcessor Src/LinearSolvers/F_MG/ml_cc.f90 commit 43b16b8c2c961c096d6d4b3ea44b4314e6724e4f Author: vince Date: Thu Apr 3 16:46:55 2014 -0700 reworked reduction tracking. Src/C_BaseLib/ParallelDescriptor.cpp commit 7462dc41e66d680651e637d56d816881b12afb10 Author: ajnonaka Date: Thu Apr 3 15:46:03 2014 -0700 stencil_apply_nodal_xd works now matter how many ghost cells the "dd" multifab has, where dd is the nodal result "L(phi)". Before it required 1 ghost cell, which doesn't make sense since it only returns dd on the valid region and the boundary nodes Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 commit 438c087fb2e8dacf99a0d11b5048b63463892713 Author: vince Date: Thu Apr 3 12:31:23 2014 -0700 added error checking and reporting for the fortran interface. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit c1a80ecc8a9d0ac1bfba5fb74a91f9468ae96681 Merge: e9b6be546 5ad92e91c Author: vince Date: Fri Mar 28 12:20:06 2014 -0700 Merge branch 'master' into commprof commit e9b6be5467abc7fe6d3bab8e7cab065ba1f6c368 Author: vince Date: Fri Mar 28 12:18:25 2014 -0700 unconst Src/C_BaseLib/Profiler.H commit 5ad92e91c48626f90520aeaba3c31c7bd13f828c Merge: 8cd3ee0e6 a96717834 Author: vince Date: Fri Mar 28 12:14:58 2014 -0700 streamretry tweaks. commit 8cd3ee0e644adcb71b396e9218434ae885feda9b Author: vince Date: Fri Mar 28 12:10:31 2014 -0700 streamretry tweaks. Src/C_BaseLib/Utility.cpp commit a967178346ea3a4ed260117e786da911de10a193 Author: Weiqun Zhang Date: Thu Mar 27 16:04:22 2014 -0700 update make files for edison Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_intel.mak commit 0fcbb902dc70035cd2b0ebf85ec409a1ec606967 Author: ajnonaka Date: Tue Mar 25 16:13:49 2014 -0700 need to scale residual by -1 so nodal_applyop returns +del dot beta grad phi. appears to be working now Src/LinearSolvers/F_MG/nodal_applyop.f90 commit a90e5cbcdb821f734b26301ee8f9d0fcba62f8cf Author: ajnonaka Date: Tue Mar 25 15:48:51 2014 -0700 cleaning out cc_applyop Src/LinearSolvers/F_MG/cc_applyop.f90 commit 350ec5db82da61ead21f2c91ec5845e56a7e7463 Author: ajnonaka Date: Tue Mar 25 15:48:46 2014 -0700 add nodal_applyop.f90 Src/LinearSolvers/F_MG/GPackage.mak commit 6220b7cbbffe722de45634bc6b633a323213bf6c Author: ajnonaka Date: Tue Mar 25 15:48:30 2014 -0700 writing a nodal_applyop... wip Src/LinearSolvers/F_MG/nodal_applyop.f90 commit ebfa59870e6980340c7c603f1e1191ed62ca9171 Merge: ad13e2134 ca6da43db Author: ajnonaka Date: Tue Mar 25 09:57:17 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ad13e2134b5a2fb1fc8e19bd904fddd100dcac81 Author: ajnonaka Date: Tue Mar 25 09:57:03 2014 -0700 make ml_cc_applyop public Src/LinearSolvers/F_MG/cc_applyop.f90 commit ca6da43dbf3e1d595d9bf71f58eeee6186994451 Merge: efc9aaca5 0a629adbe Author: Michael Zingale Date: Tue Mar 25 12:16:10 2014 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit efc9aaca55f93d7935b69d3c548ed4c149e4272e Author: Michael Zingale Date: Tue Mar 25 12:15:56 2014 -0400 spelling Src/F_BaseLib/bl_constants.f90 commit 678f0d390623a22edc97e0d889f95d9806bda380 Author: Michael Zingale Date: Tue Mar 25 12:15:08 2014 -0400 add TWELVTH and SEVEN12TH Src/F_BaseLib/bl_constants.f90 commit 0a629adbe4db28e3816942ad5ef4d5a306d71df4 Author: ajnonaka Date: Tue Mar 25 08:36:52 2014 -0700 remove a comment Src/LinearSolvers/F_MG/ml_solve.f90 commit 27ce734dbc95beb831895682e9a3caf965e18743 Author: ajnonaka Date: Tue Mar 25 08:04:17 2014 -0700 update comments Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/mg.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90 commit fe06ba663db57dae1b6df80c2733e71369ce55af Author: ajnonaka Date: Tue Mar 25 08:02:16 2014 -0700 move mac_applyop into cc_applyop (delete mac_applyop.f90) and renname the function cc_applyop to be consistent with the rest of the mg naming convention. Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/mac_applyop.f90 commit b29eaafa072e6e474e1fe98fd9eb9fd61fc486ce Author: ajnonaka Date: Mon Mar 24 16:31:30 2014 -0700 eliminate scale_residual subroutines and just use a mult_mult_s_c. bonuts points is that 3d is now openmp'd Src/LinearSolvers/F_MG/cc_applyop.f90 commit bcd4d065b486c62ea840389b029a2dfddf12e45e Merge: 3085caade b4d57c5dd Author: ajnonaka Date: Thu Mar 20 15:44:35 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3085caadef5ea6b5d776a28cd99132eb4d6939c6 Author: ajnonaka Date: Thu Mar 20 15:44:14 2014 -0700 nodal_divu now works regardless of the number of ghost cells u or rh have Src/LinearSolvers/F_MG/nodal_divu.f90 commit b4d57c5dd9beae760eea2c70c8519274c4c7b418 Author: lijewski Date: Thu Mar 20 13:13:48 2014 -0700 norm_cor is no longer used. Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 1ae85820f4ab5e663aa29f8c187f802e89eff591 Author: Michael Zingale Date: Wed Mar 19 22:24:06 2014 -0400 add --complete_report_from_crash -- this allows you to generate the reports for a test suite run where the main test program crashed (or was disconnected from when run remotely). Tools/RegressionTesting/testnew.py commit 1e5991f1506b313f0b58d718bd5b9a27880f9dde Author: ajnonaka Date: Mon Mar 17 17:51:30 2014 -0700 fix error in max_level logic for ml_nd_solve_1 and ml_cc_solve_1 Src/LinearSolvers/F_MG/ml_solve.f90 commit 762411c90ebed6c33b74bfaae15ab03cf90071c3 Author: ajnonaka Date: Mon Mar 17 16:19:27 2014 -0700 moved the bottom solver (for type 4) logic test into ml_nd_solve_1 and ml_cc_solve_1 Src/LinearSolvers/F_MG/ml_solve.f90 commit 3dbd530f7ca603d7f00207a5529d205737a664fd Author: ajnonaka Date: Mon Mar 17 16:02:41 2014 -0700 more elaborate testing to determine mgt(n)%max_nlevel in both ml_cc_solve_1 and ml_nd_solve_1 Src/LinearSolvers/F_MG/ml_solve.f90 commit 117cd8f777464579102d6a850cec68c83092acb2 Merge: 5a8657fba 0a114070f Author: ajnonaka Date: Mon Mar 17 11:00:27 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5a8657fba2bdf90072b7795018293e673725b5c3 Author: ajnonaka Date: Mon Mar 17 11:00:00 2014 -0700 stencil_order is now an optional argument with a default value of 2 if not passed in Src/LinearSolvers/F_MG/mac_applyop.f90 commit 0a114070fc08700ba106bf5ffa4dc6911e80591b Author: Marc Day Date: Mon Mar 17 10:56:54 2014 -0700 Uptick tag version number Tools/CMake/BoxLib_Version.cmake commit f3024f2c96fc277c569023b68a5b9015cc37e876 Author: Marc Day Date: Mon Mar 17 10:54:08 2014 -0700 Explicitly cast the args in the pow function to quiet older compilers Src/C_BaseLib/IArrayBox.cpp commit fd256e44bb68699b368be11d60acfd504652a823 Author: ajnonaka Date: Fri Mar 14 15:32:55 2014 -0700 mgt_nodal_solve() now takes in eps and abs_eps as arguments (as it used to earlier in the week) and copies these values into the mg_tower object Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit be75e0292149c453a308e31ce057e5a1e6af4f0d Author: Ann Almgren Date: Thu Mar 13 21:31:55 2014 -0700 Modified BSD license stuff. README.txt license.txt commit eed5bf54f479e29f80d5201e2c84dec4b65eb2a8 Author: Ann Almgren Date: Thu Mar 13 21:30:25 2014 -0700 These are the new versions for our official modified BSD release of BoxLib version 02-28-2014. README.txt license.txt commit c81c8513ddad6fc2f59ceef1770e75173e3fb329 Author: ajnonaka Date: Thu Mar 13 16:35:47 2014 -0700 added the flexibility to pass in optional "S" and subtract this from the RHS for nodal solves Src/LinearSolvers/F_MG/ml_solve.f90 commit 8a5db38c3e2d2c03b14d09cc0d51fbeed3b2b3a3 Author: ajnonaka Date: Thu Mar 13 16:01:20 2014 -0700 cleanup only Src/LinearSolvers/F_MG/ml_solve.f90 commit fc9f71ad6cff07a2aa80f3d8c58e6231f5706eef Author: ajnonaka Date: Thu Mar 13 15:56:13 2014 -0700 use new add_divu_to_rhs feature, fix comments Src/LinearSolvers/F_MG/ml_solve.f90 commit 7d10d2fda8bd329b49a628af38453cf337cece97 Author: ajnonaka Date: Thu Mar 13 15:46:33 2014 -0700 add optional logical argument to subtract_divu_from_rh to *add* rather than *subtract* Src/LinearSolvers/F_MG/nodal_divu.f90 commit d8078bf91cc718768ad7dced9f10c6bc97e53351 Merge: 477ed7211 3f146ad73 Author: Ann Almgren Date: Thu Mar 13 15:20:12 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 477ed7211fb596d5f364dc10368d25a5165b72e1 Author: Ann Almgren Date: Thu Mar 13 15:19:12 2014 -0700 Make sure we use the tol and abs_tol that are passed in through the C++ interface -- they come in through the call from C++ in "mgt_solve" then are used to define mgts%mgt_eps and mgts%mgt_abs_eps which are actually used by the solver. Note that the C++ solvers always have to pass in the tolerance, they are not currently wired to use the default. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 3f146ad732a05275e150dfc04cc8fe4f6fd6c9aa Author: ajnonaka Date: Thu Mar 13 14:28:40 2014 -0700 plug memory leak. also fix sign convention in rhs for nodal solve. still wip. varden works, need to check MAESTRO for nonzero S to see if the sign convention holds Src/LinearSolvers/F_MG/ml_solve.f90 commit 6b6c79fd9b4115d0c9e7753676a563dfe2ad58b2 Author: ajnonaka Date: Thu Mar 13 13:12:18 2014 -0700 remove unnecessary optional arguments Src/LinearSolvers/F_MG/ml_solve.f90 commit de2c45d387b79dc984204e5bf68109d82843faf6 Merge: 104e43214 a87d89357 Author: ajnonaka Date: Thu Mar 13 13:02:59 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 104e432149e8d06bf04ca989c704a923f114fe58 Author: ajnonaka Date: Thu Mar 13 13:02:33 2014 -0700 need to pass in a boundary register to cc solver interface. projections need the boundary flux of phi to update at CF interfaces Src/LinearSolvers/F_MG/ml_solve.f90 commit a87d893575b381547c954ef9bfb63721beb79aaa Author: Matthew Emmett Date: Thu Mar 13 11:45:50 2014 -0700 PyBoxLib: Add setup.py. Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak Src/Python/setup.py commit 5343466a47339071e932f90c7ec5ad875d0cd056 Author: Matthew Emmett Date: Thu Mar 13 11:12:53 2014 -0700 PyBoxLib: Update basic multifab test, tidy up a bit. Src/Python/read.py Src/Python/tests/test-multifab.py Src/Python/write.py commit 376211419d7e9f65a98b714eabd8c49e0ca05f0a Merge: 5849550a1 74eb364c5 Author: Matthew Emmett Date: Thu Mar 13 11:09:41 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5849550a132882ca5d822f76452135cfb7a2d209 Author: Matthew Emmett Date: Thu Mar 13 11:09:28 2014 -0700 PyBoxLib: Remove old Fortran wrappers, update C++ wrappers (very basic for now). Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak Src/Python/GNUmakefile_F.mak Src/Python/GPackage.mak Src/Python/README Src/Python/boxlib/__init__.py Src/Python/boxlib/bl1.py Src/Python/boxlib/bl2.py Src/Python/boxlib/bl3.py Src/Python/boxlib/fbl/__init__.py Src/Python/boxlib/fbl/base.py Src/Python/boxlib/fbl/boxarray.py Src/Python/boxlib/fbl/fab.py Src/Python/boxlib/fbl/fabutils.py Src/Python/boxlib/fbl/layout.py Src/Python/boxlib/fbl/multifab.py Src/Python/boxlib/fbl/plotfile.py Src/Python/boxlib/fbl/pybl.py Src/Python/boxlib/fbl/utils.py Src/Python/contrib/chemSupport.H Src/Python/contrib/chemSupport.cpp Src/Python/contrib/support.H Src/Python/contrib/support.cpp Src/Python/fsrc/blobjects.f90 Src/Python/fsrc/blobjects.py Src/Python/fsrc/boxlib_numpy_c.c Src/Python/fsrc/boxlib_numpy_f.f90 Src/Python/fsrc/fboxlib.f90 Src/Python/src/boxlib_wrap_1.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_2.cpp.REMOVED.git-id Src/Python/src/boxlib_wrap_3.cpp.REMOVED.git-id Src/Python/swig/boxlib.i commit 74eb364c59db31f640b1c335180cca4eabb45614 Author: Andy Nonaka Date: Wed Mar 12 16:55:16 2014 -0700 index bug fix in new cc solver Src/LinearSolvers/F_MG/ml_solve.f90 commit 6c5e86d52ed7db8bf3c2fdd75cef66107ccac099 Author: Andy Nonaka Date: Wed Mar 12 15:49:12 2014 -0700 new interface for ml_nd_solve complete. now for testing Src/LinearSolvers/F_MG/ml_solve.f90 commit 844b241d9d4b470e596b35b49b685511475c3068 Author: Andy Nonaka Date: Wed Mar 12 14:51:15 2014 -0700 more progress on nodal solver interface. still not sure if sign convention on rhs is correct Src/LinearSolvers/F_MG/ml_solve.f90 commit d881574c1a2830f556048ad19064339cfffa0fba Author: Andy Nonaka Date: Wed Mar 12 12:12:48 2014 -0700 move enforce_outflow_on_divu_rhs to nodal_divu.f90 since each nodal projection code had its own local copy Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/nodal_divu.f90 commit 53d9a1bf92aa1f2d0bf5f13b8f425f605708f1c3 Author: Andy Nonaka Date: Wed Mar 12 10:46:03 2014 -0700 fixed a bug in the new cc multigrid interface... passing in wrong bc comp to mg_tower_build. some work on the new nd multigrid interface... WIP Src/LinearSolvers/F_MG/ml_solve.f90 commit 17c036ee3ffc4dae9b4120a87448744018abcb81 Author: Andy Nonaka Date: Wed Mar 12 10:32:51 2014 -0700 ml_cc_solve_1 internally figures out of the problem is parabolic now and sets is_singular to false in the call to mg_tower_build. for elliptic problems, no optional is_singular argument is passed in and mg_tower_build still checks the boundary conditions internally to see of the problem is singular Src/LinearSolvers/F_MG/ml_solve.f90 commit f7641dd3abf55b2d798eeeafe405fa2924362bd7 Author: ajnonaka Date: Tue Mar 11 13:38:24 2014 -0700 clean up the interface to the cc solve, and add a new simple interface to call the cc f90 solver Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mac_applyop.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 9589b356ad68006a27cbe4b547d5c3134bb13a79 Author: ajnonaka Date: Tue Mar 11 11:22:19 2014 -0700 cleanup only Src/LinearSolvers/F_MG/mg.f90 commit 11ee3291f552f9cc101d9fc8f831bd9a4cb9b57a Author: ajnonaka Date: Tue Mar 11 10:38:13 2014 -0700 interface changes to keep up with f90 solvers Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 86cdf8c960af4b9c9595e6efc237c1123b275930 Merge: 51a18aaa6 17b093ec8 Author: ajnonaka Date: Tue Mar 11 10:30:06 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 51a18aaa6e67751960a851982a6f11b92455437a Author: ajnonaka Date: Tue Mar 11 10:27:11 2014 -0700 don't pass in optional abs_eps and rel_eps arguments to ml_cc_solve and ml_nd_solve anymore and use the versions in the mg_tower object don't pass in ref_ratio anymore since it's available in the ml_layout Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Tutorials/HeatEquation_EX5_F/advance.f90 commit 17b093ec8febe0370bc0670d5cdcc8694c6e55f8 Merge: 78ab9eb96 8cad46286 Author: Matthew Emmett Date: Tue Mar 11 10:15:06 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 78ab9eb96cc1bbc7850a4de7491a49f8551d187f Author: Matthew Emmett Date: Tue Mar 11 10:14:51 2014 -0700 PyBoxLib: F90 version: Fold C routines into libpyfboxlib. Src/Python/GMakerules.mak Src/Python/GNUmakefile_F.mak Src/Python/GPackage.mak Src/Python/boxlib/fbl/fab.py Src/Python/fsrc/boxlib_numpy_c.c commit 12d90a963b416da47efa110d5a0c86eb715848c3 Author: vince Date: Thu Mar 6 11:58:24 2014 -0800 merge with master. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 9002dad422be09eb31f7a8687782a70df1e224be Merge: b3c209cfb 8cad46286 Author: vince Date: Thu Mar 6 11:51:32 2014 -0800 Merge branch 'master' into commprof commit 8cad46286a071739ae070f374031140d5746ba13 Author: vince Date: Thu Mar 6 11:33:14 2014 -0800 removed dumpi vars, they are now in Tools/C_mk. MiniApps/FillBoundary/GNUmakefile commit ff05b9aba11b1105a7d00713ebf17187ddb83745 Author: vince Date: Thu Mar 6 11:31:55 2014 -0800 added dumpi support to make system. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit c174932e63fe95df77318a8d185b1f0949b80bab Author: vince Date: Thu Mar 6 10:30:29 2014 -0800 new ncube code. MiniApps/MultiGrid_C/main.cpp commit bcef866b78625a96fcb93ebedbd8d2431ab514aa Author: vince Date: Thu Mar 6 10:29:54 2014 -0800 added ipm, dumpi, prof flags. made more consistent with fillboundary. MiniApps/MultiGrid_C/GNUmakefile commit b3c209cfbbfc7d38f2bca879a2666ebe3f402895 Merge: 5c10f2b9b 9f14e3455 Author: vince Date: Thu Mar 6 10:13:41 2014 -0800 merge with master. commit 9f14e34550fbafac4bed2e2afe221b4ce8390d0d Author: vince Date: Thu Mar 6 09:07:04 2014 -0800 iop around error output. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 466eed7a9e88d13766fc241413e959adc43575d0 Author: vince Date: Thu Mar 6 09:05:47 2014 -0800 we dont need the map since we are not going to reuse it. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 5c10f2b9b3ce6abaf6d54e6e9d5564293841e2a2 Merge: c864be4e7 e30e31f25 Author: vince Date: Wed Mar 5 17:33:59 2014 -0800 merged with master. commit c864be4e7e2dae8c5859889331547339e3cd6b51 Merge: bf0a35879 f5f0cbe58 Author: vince Date: Wed Mar 5 17:29:37 2014 -0800 about to merge the latest versions. commit e30e31f250f7f973d2183c1b9e86004b2b67d00f Author: vince Date: Wed Mar 5 17:02:02 2014 -0800 added vector initialization for older compilers. rewrote the N cubed check with a simple map lookup for small values. exp(log...) breaks sometimes because of roundoff (nprocs = 1000 for example). yes, it is always something. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 38d7b7a8db2774c5f98f6aa979fd293414cd5dd8 Author: vince Date: Wed Mar 5 17:01:34 2014 -0800 added new/old compiler flags and temporary dumpi support. MiniApps/FillBoundary/GNUmakefile commit e48a7d49b5d7f8020fa6fcd2a69f4caed9dcea0d Merge: c3f29f15c e9d6dcb9e Author: Adam Jacobs Date: Wed Mar 5 17:59:39 2014 -0500 Merge in sub-Chandra analysis routines in branch 'fsub_dev' commit e9d6dcb9e18fee233472cd9090aa7ef5829c3768 Author: Adam Jacobs Date: Wed Mar 5 17:56:15 2014 -0500 Committing the latest version of the sub-Chandra analysis routines. MAESTRO_sub_chandra/GNUmakefile MAESTRO_sub_chandra/fsubchandra.f90 MAESTRO_sub_chandra/fsubchandra_mod.f90 commit f5f0cbe5877f15a41a0e544984247d922bc5ad02 Author: vince Date: Wed Mar 5 12:24:26 2014 -0800 added run time. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit bf0a35879c7d218872592ac1ff2a5d2959e01972 Merge: d0c993252 afbb1e2da Author: vince Date: Wed Mar 5 11:44:16 2014 -0800 made these similar to the master branch versions. commit afbb1e2da6d15cf78185c64acfc6c861faed3ea4 Author: vince Date: Wed Mar 5 11:27:13 2014 -0800 added other run sizes. MiniApps/FillBoundary/qsub.ipm.bat commit efec85076e488c159334984332be4dc1c396dbdc Author: vince Date: Wed Mar 5 11:23:11 2014 -0800 changed filename. MiniApps/MultiGrid_C/README commit af59c68e6e39fd7ec07ea2dead7b90a699bb1bed Merge: 9b981521b 5f60ddd01 Author: Matthew Emmett Date: Wed Mar 5 10:37:43 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9b981521bdae666ac551633fe38338714e08b226 Author: Matthew Emmett Date: Wed Mar 5 10:37:35 2014 -0800 PyBoxLib: Move Fortran based version to its own directory. Begin importing C++ based version from Marc. Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak Src/Python/GNUmakefile_F.mak Src/Python/GPackage.mak Src/Python/boxlib/__init__.py Src/Python/boxlib/fbl/__init__.py Src/Python/boxlib/fbl/base.py Src/Python/boxlib/fbl/boxarray.py Src/Python/boxlib/fbl/fab.py Src/Python/boxlib/fbl/fabutils.py Src/Python/boxlib/fbl/layout.py Src/Python/boxlib/fbl/multifab.py Src/Python/boxlib/fbl/plotfile.py Src/Python/boxlib/fbl/pybl.py Src/Python/boxlib/fbl/utils.py Src/Python/fsrc/blobjects.f90 Src/Python/fsrc/blobjects.py Src/Python/fsrc/boxlib_numpy_c.c Src/Python/fsrc/boxlib_numpy_f.f90 Src/Python/fsrc/fboxlib.f90 Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/pybl.py Src/Python/swig/boxlib.i Src/Python/swig/numpy.i Src/Python/tests/test-multifab.py commit 5f60ddd012bb693b23dc75447413048975a81559 Author: Ann Almgren Date: Wed Mar 5 10:16:09 2014 -0800 1) Modify MultiGrid.H / MultiGrid.cpp so we can set a new flag (do_fixed_number_of_iters) in the MultiGrid class -- can only be set using SetFixedIter -- if this is set to 1 then the MultiGrid class will do exactly maxiter iterations without checking for convergence. The default value is 0, so if this is not set to 1 then the code will behave as before. 2) Modify the MiniApps/MultiGrid_C main.cpp so that it calls setFixedIter(1) to do just one iteration and stop without crashing. We also no longer need inputs.3d MiniApps/MultiGrid_C/inputs.3d MiniApps/MultiGrid_C/main.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 5e21da8590f3c1bedb34bebeb15d321477a0a317 Author: Ann Almgren Date: Mon Mar 3 12:43:51 2014 -0800 Create a multigrid MiniApp that doesn't require any inputs file. It creates a single 64^3 grid on each MPI process, and requires that the number of processes be a perfect cube so that the domain is N*N*N grids where N = cube root of NProcs. MiniApps/MultiGrid_C/COEF_3D.F MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/GNUmakefile MiniApps/MultiGrid_C/Make.package MiniApps/MultiGrid_C/README MiniApps/MultiGrid_C/RHS_3D.F MiniApps/MultiGrid_C/RHS_F.H MiniApps/MultiGrid_C/inputs.3d MiniApps/MultiGrid_C/main.cpp MiniApps/MultiGrid_C/qsub.ipm.bat commit 1a702ffb43633be10a208ce6fc6c43969cc1b607 Author: Ann Almgren Date: Mon Mar 3 10:33:53 2014 -0800 Add suggested numbers of processors. MiniApps/FillBoundary/README commit d0c9932523ca9707ab6d4427e0ab22796b9b582e Author: Ann Almgren Date: Mon Mar 3 10:32:11 2014 -0800 Add suggested runs. MiniApps/FillBoundary/README commit 114650dd70c12aeb8849170bf2c9180ebf8bcf4a Author: vince Date: Fri Feb 28 14:29:49 2014 -0800 added ipm support for hopper. MiniApps/FillBoundary/GNUmakefile MiniApps/FillBoundary/README MiniApps/FillBoundary/qsub.ipm.bat commit b8d154f56b59812272a2c1f4491ccd4bf83807cf Author: vince Date: Fri Feb 28 13:21:31 2014 -0800 sanitized version for ipm/dumpi tracing. MiniApps/FillBoundary/GNUmakefile MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/FillBoundary/README commit 294b9467de71dba19cb4c405a8e595d779c42521 Author: vince Date: Fri Feb 28 12:23:57 2014 -0800 files from commprof. MiniApps/FillBoundary/GNUmakefile MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/FillBoundary/README commit 964e8b13fd9057dc317ef0c1ebe00eebce66dcac Author: Ann Almgren Date: Fri Feb 21 00:12:33 2014 -0800 test3d --> fbtest3d MiniApps/FillBoundary/README commit c212b268b3e93fdd58e7d127e37af209897ee78c Author: vince Date: Thu Feb 20 18:03:51 2014 -0800 squished into nested loops, added commprof tags. MiniApps/FillBoundary/GNUmakefile MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit c7043bbec4f6379d6d2f1c48e8c02e1f86af3281 Author: vince Date: Thu Feb 20 17:59:54 2014 -0800 removed some diagnostic output. Src/C_BaseLib/DistributionMapping.cpp commit 14c5981beeb74e9f7383b0b7337b5b65b5dc20b8 Author: Ann Almgren Date: Thu Feb 20 16:07:36 2014 -0800 Fixed domain_hi. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit e42f6e9f9a3309ebdb098d40d2d6ad38a424537e Author: Ann Almgren Date: Thu Feb 20 16:03:28 2014 -0800 Fixed. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit a38c90d1bfd52d5439efd60fe79bd469da42e811 Author: Ann Almgren Date: Thu Feb 20 15:50:30 2014 -0800 Added info on how to build and run the code. MiniApps/FillBoundary/README commit d59a7f52515d95c04d4570dde57f7d5e25194d2e Merge: 975ae4a11 09aff0e1f Author: Ann Almgren Date: Thu Feb 20 15:40:41 2014 -0800 Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof commit 975ae4a11b3596adc6907e762a042dda1d7ab305 Author: Ann Almgren Date: Thu Feb 20 15:40:30 2014 -0800 This code is a very simple code designed to profile communication patterns associated with the MultiFabFillBoundary operation, which exchanges ghost cells between the FABs in a single multifab. All this code does, for a certain set of parameters, is to * create a MultiFab which has "nGhost" ghost cells and "nComp" components * fill the data with the value 1.0 everywhere * exchange "nGhost" ghost cells of "nComp" components of the data in the FABs in this MultiFab * exchange either the faces only ("cross" = true) or all 26 nearest neighbor exchanges ("cross" = false") We have a separate call for each combination: * nComp = 1, 4, 20 * nGhost = 1, 2, 3, 4 * cross = true or false MiniApps/FillBoundary/GNUmakefile MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/FillBoundary/README commit 09aff0e1f93668afd1245633d0d33404e5938604 Author: vince Date: Thu Feb 20 14:56:26 2014 -0800 added information to header, rename bl_comm_prof dir if it exists. Src/C_BaseLib/Profiler.cpp commit ceb2f6742692de8453a82c30d2adf391eebc3670 Author: Michael Zingale Date: Thu Feb 20 17:48:32 2014 -0500 allow for 2 extra build directories Tools/RegressionTesting/testnew.py commit c67e088d1a333948d42c0ecd47712667d16c5377 Merge: 8b080ad78 6451e7bc3 Author: vince Date: Wed Feb 19 10:23:28 2014 -0800 Merge branch 'master' into commprof commit 6451e7bc31e41088198a01acda162af559ced768 Author: Michael Zingale Date: Wed Feb 19 13:14:02 2014 -0500 update of mostly comments + 1 parameter (time) in the wrong object Tools/RegressionTesting/testnew.py commit a7539a654804ea68f6233c5d3dfa22aec0f7a564 Author: Michael Zingale Date: Wed Feb 19 11:59:42 2014 -0500 take care of the rarely encountered situation of having no active tests defined, in which case, we do not want to print a row in the main webpage Tools/RegressionTesting/testnew.py commit 8b080ad784111057c62598f849c0bbc55da324b2 Author: vince Date: Tue Feb 18 17:33:39 2014 -0800 added enum num. Src/C_BaseLib/Profiler.H commit 5acb5f9e309162aca4b05f3a2ccc26fb1ec07fbb Author: lijewski Date: Thu Feb 13 13:56:00 2014 -0800 I've been doing some experimentation regarding the order sends() in MPI Irecv/Send pairs. This code randomly shuffles the order of the sends. The idea is better spread the MPI traffic across the network. I'm checking the code in with the controlling variable defaulted to false. Got to gather more data to decide when/where it's really useful. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit 2c951c1c1478bc3a268f834b71bc6e19e910dc5c Author: Marc Day Date: Wed Feb 12 15:59:32 2014 -0800 Uptick version Tools/CMake/BoxLib_Version.cmake commit e6110f8e9284b692387c8a3a61b4827c125ee3e4 Author: Marc Day Date: Wed Feb 12 15:58:13 2014 -0800 Test mulitcomp Tests/C_BaseLib/tMF.cpp commit 320df5ee1cdaf968bd0a6914ca0b2ff4bf59c247 Author: vince Date: Wed Feb 12 12:59:48 2014 -0800 added timer for commstats flushing. Src/C_BaseLib/Profiler.cpp commit e0475f7c64e75d16db7424717633a046a2c55848 Author: vince Date: Wed Feb 12 12:03:17 2014 -0800 removed some nametag tracing. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit ecc779fd71a8c63750695aa6dea71f9c16955852 Merge: 63497f348 613599605 Author: vince Date: Wed Feb 12 11:43:05 2014 -0800 fix merge conflict. commit 63497f3483dcfc2eab03a85b495a5e0ab0bbb607 Author: vince Date: Wed Feb 12 11:28:57 2014 -0800 added -DDEBUG flag Tools/C_mk/Make.defs commit e1fe5ac69c796f1066396982d7e5aa8b5efc0dfc Author: vince Date: Wed Feb 12 11:26:47 2014 -0800 temporary diagnostics for new mappings. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp commit 2c450bcebc1e70b55e155f744cfcb4286544439f Author: vince Date: Wed Feb 12 11:24:51 2014 -0800 more work on proximity mapping, diagnostics are still in the code. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Profiler.H commit 613599605e5552ac7143795782bf24f4a67a5275 Author: cmalone Date: Wed Feb 5 21:23:29 2014 -0800 shouldn't need libg2c anymore, if using GCC4.x+ Tools/C_mk/Make.CYGWIN_NT commit 48ede641c7198eb0462abfe8b3affe2463ec2282 Author: Weiqun Zhang Date: Wed Feb 5 14:16:21 2014 -0800 regression test script: added diff to restart test Tools/RegressionTesting/testnew.py commit dc164ba7be6c4d470021ea7c5d4cb4ff1d30c7f0 Author: Weiqun Zhang Date: Wed Feb 5 11:11:04 2014 -0800 get around an Intel compiler 14.0.1 bug Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit d7d84e5789b53ced6411f863840466efe794467c Author: vince Date: Tue Feb 4 14:01:37 2014 -0800 mpi lib fix for mothra. Tools/C_mk/Make.mpi commit 165d70d40f5edcc1276e0dfcaf26c994483e12f4 Author: lijewski Date: Mon Feb 3 09:03:07 2014 -0800 Reverted out my latest mods; they were unnecessary given how we checkpoint. Src/C_AMRLib/Particles.H commit 88061881bd1aa6063a2f24d059b1cb4c6322150d Author: lijewski Date: Fri Jan 31 10:06:42 2014 -0800 Comment out some debugging output. The Intel compiler doesn't like one of my format statements. Src/F_BaseLib/layout.f90 commit ac91571ce6d9b1db9602f04aa1da0dda901597f9 Author: lijewski Date: Thu Jan 30 14:13:34 2014 -0800 Merged Vince's stream retry idea into Checkpoint(). Src/C_AMRLib/Particles.H commit 247bf8893f0490711e5e362cb9bb7f8204f11e88 Author: lijewski Date: Thu Jan 30 14:12:44 2014 -0800 Added const std::string Unnamed to be used as default argument in ParallelDescriptor::Barrier() instead of creating a string on the fly. Src/C_BaseLib/ParallelDescriptor.H commit 9793a45fea52546971b1251916ce51efaf5d44cb Merge: 382f14ad0 8defec763 Author: Marc Day Date: Wed Jan 29 10:02:23 2014 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 382f14ad0f7e658d6b82f33e38d5d60bad3332ef Author: Marc Day Date: Wed Jan 29 10:02:09 2014 -0800 Add Mattis machine to list of known machines Src/C_BaseLib/ParmParse.cpp Tools/C_mk/Make.Darwin Tools/C_mk/Make.defs commit 8defec7633af93039de1a3143983ba547af56194 Author: lijewski Date: Mon Jan 27 14:14:19 2014 -0800 More aggressize free()ing of memory in RedistributeMPI(). Src/C_AMRLib/Particles.H commit d64de77f6fa118c38b03169f7ae9b087e7659a83 Author: lijewski Date: Mon Jan 27 14:13:49 2014 -0800 Increased fabarray.maxcomp to 25. Src/C_BaseLib/FabArray.cpp commit 571e50dd7743a4e90318b69071ac89760dbd1a98 Author: vince Date: Fri Jan 24 16:12:23 2014 -0800 removed output. Src/C_AMRLib/Amr.cpp commit 3c58105910aff179b7bfc49945221a5920427574 Author: Adam M. Jacobs Date: Fri Jan 24 15:50:42 2014 -0500 Modified fillpatch.f90 to safely handle empty boxes. Problems were noticed when attempting to refine the sub-Chandra MAESTRO problem to 4 levels. Src/F_BaseLib/fillpatch.f90 commit ca3c6cf22c829ba05321a779796130d21b4b0df7 Author: vince Date: Fri Jan 24 11:52:44 2014 -0800 comment. Src/C_AMRLib/Amr.cpp commit 4e347c6bf27f3b7f9e137d33d0674538f01e92bb Merge: 786ed5a27 61d55284f Author: vince Date: Thu Jan 23 15:26:38 2014 -0800 Merge branch 'master' into streamretry commit 61d55284fafc9793244951b90fcc1db3d72eeca6 Merge: 0839880f7 efae9210c Author: vince Date: Thu Jan 23 15:26:18 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 786ed5a27da9759f909bd411bb1fdfacc264a34f Author: vince Date: Thu Jan 23 15:25:33 2014 -0800 less verbosity. Src/C_AMRLib/Amr.cpp commit 39e1329c469e2a2eab11cb89552e658dcc35f3e1 Author: vince Date: Thu Jan 23 14:30:29 2014 -0800 changed temp file verbose output. Src/C_AMRLib/Amr.cpp commit 981b912a76b4f3e1b30321e7d1176bf78e316868 Author: vince Date: Thu Jan 23 13:55:44 2014 -0800 more stream information on retry. Src/C_BaseLib/Utility.cpp commit efae9210cf2a609caa703122fd2231d67e4dbe59 Merge: 696c31845 f9e1facca Author: Adam M. Jacobs Date: Thu Jan 23 14:32:28 2014 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 696c31845faebabf122de8065d9c543347959c1f Author: Adam M. Jacobs Date: Thu Jan 23 14:31:20 2014 -0500 add some optional arguments to allow for potentially empty boxes. These changes should not affect any output, but will be used for a safer fillpatch to come... Src/F_BaseLib/box_f.f90 Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/multifab_f.f90 commit 6e5efc72983682ccd0ce9304210174b2e62b7767 Author: vince Date: Wed Jan 22 15:36:26 2014 -0800 checkpoint and plotfiles now have temporary names until they are complete. then stream retry will rename them if there were stream errors. if the checkpoint or plotfile names exist, those directories are renamed with a random suffix. this includes the temporary file names. more output from stream errors. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit f9e1faccad9e6a9a0d8ad0d9038d893ad3165c76 Author: lijewski Date: Wed Jan 22 11:22:28 2014 -0800 Modest reduction in memory use for TagBoxArray::collate(). This function collects all the tagged cells to the I/O processor, who then removes duplicates and broadcasts'm back, as part of the grid generation procedure. The tagged cells are passed around as arrays of IntVects. Duplicates are removed by first sorting the vector of IntVects. On the 9000 core LMC run I'm currently nursing on edison, I've got roughly 13000 grids at level 2. This leads to about 360000 tagged cells out of which about half turn out to be duplicates. This is a pretty large array to be sorting. Luckily the sort algorithm is NlogN. Src/C_AMRLib/TagBox.cpp commit 0839880f777d51edef85c98e3e73b7e8fd3de11d Author: vince Date: Thu Jan 16 16:22:25 2014 -0800 make temporary filenames for plotfiles and checkpoints, then rename them only if they are complete. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 914755561f18ee8831d963f4b4e985e10473ca2d Author: vince Date: Thu Jan 16 14:10:50 2014 -0800 delay reset of fab format. Src/C_AMRLib/Amr.cpp commit 0e5a543239d0e67bf3a33e37e345b2cc0b9d6a8b Author: Ann Almgren Date: Thu Jan 16 11:15:28 2014 -0800 Define the pd in line 200 of fillpatch rather than using the not-yet-defined "cdomain". Src/F_BaseLib/fillpatch.f90 commit e41f84fca7f18e63528b0090d40ddf0e3859f930 Author: lijewski Date: Thu Jan 9 14:56:52 2014 -0800 Some simplification. Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BoundaryLib/FabSet.cpp commit 5a175be3101502223ab36572e401ad809181f1dd Merge: a42a5afab ae21e5185 Author: vince Date: Thu Jan 9 11:25:00 2014 -0800 Merge branch 'master' into commprof commit ae21e5185848ddb942cd6021d6eb4e74d1625a03 Author: lijewski Date: Tue Jan 7 09:48:07 2014 -0800 A little simplification. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 2035bcddae7fe2cc06e59296c0c88fe3bda57ba4 Author: lijewski Date: Mon Jan 6 15:27:29 2014 -0800 Now print out particle byte spread in Redistribute if m_verbose > 0 instead of m_verbose > 1. Src/C_AMRLib/Particles.H commit 9d69f548db80dd6a451162a0e8b985eb75b8cd07 Author: lijewski Date: Mon Jan 6 13:42:34 2014 -0800 Some more cleanup to quite the compiler. Src/C_BaseLib/FabArray.H Tests/LinearSolvers/C_CellMG/GNUmakefile commit 0c9bf88da00a459c86a91531ccf5801d39379d45 Author: lijewski Date: Mon Jan 6 12:34:00 2014 -0800 Always use F90 solvers. Tests/LinearSolvers/C_CellMG/MacOperator.cpp commit 6b1eb18b93766487956742f23c7e73e931a8d05f Author: lijewski Date: Mon Jan 6 12:13:53 2014 -0800 Shut up compiler about "possible" uninitilized data. Src/F_BaseLib/bc.f90 commit 2024c2f802317418ff022b738b11ede8d222fb98 Merge: c3a32c84d a9df0246d Author: ajnonaka Date: Thu Jan 2 15:22:18 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c3a32c84d3a9fa6a083ab1cfa8212481081472d3 Author: ajnonaka Date: Thu Jan 2 15:22:02 2014 -0800 add USE_WBAR option Tools/C_mk/Make.defs commit a9df0246d2419d83096fbf80d331124c51070cc0 Merge: 9e97f4777 26bd28d04 Author: Adam Jacobs Date: Thu Jan 2 17:03:26 2014 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 9e97f47779c185b9dc72f7cece090f13c8210f97 Author: Adam Jacobs Date: Thu Jan 2 17:02:19 2014 -0500 Updated GMakeMPI.mak from jaguar to titan. Tools/F_mk/GMakeMPI.mak commit 26bd28d049c6ee1a4d2fd0aa86910339e233c3eb Author: Weiqun Zhang Date: Thu Jan 2 10:52:02 2014 -0800 fixed a bug in 1D fifth-order interpolation Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/Interpolater.cpp commit a6aeedc1e9e73e243a649d4616b7698359f64c9d Author: lijewski Date: Thu Jan 2 10:17:19 2014 -0800 Removing the high water counters for boxarray. They really uglified the code. Now that I "think" I've got the metadata heap issues resolved they're not really needed anyway. We do use lots of boxarray; the more levels the merrier. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 4ba9c16e1cf5377f676d1467dc5d9a4b397bbf80 Author: lijewski Date: Thu Jan 2 07:55:08 2014 -0800 I think I finally figure out why I'm having memory issues on very large runs where I'm trying to squeeze as much FAB data onto a processor as possible. Basically it comes down to a quirk of how std::deque are implemented. The really short, cryptic, problem with std::deque, when you have potentially tens, or hundreds of thousands of'm lying around, is that they can waste memory. They allocate memory in large "chunks", much of which can go to waste, depending on how many entries you end up pushing into the deque. Weiqun suggested I try "massif" which is a heap-profiling tool in valgrind. It was playing around with massif that I noticed the "unused space" in the heap. Switching to using std::vector in the data caches, I can use a trick (once I've build all the vectors for a given operation) to force the vector to use the minimal amount of memory needed to contain all the elements I've add to it. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 48e6c8d6d702421e54cc75a1589114eefbf6b814 Author: lijewski Date: Mon Dec 30 15:57:03 2013 -0800 We now flush the meta-data caches on every regrid, not just on a level 0 regrid. Most of the hard work is going on the finest level anyway. There's still something weird going on with my 21k runs on hopper which I can't duplicate on smaller runs. Basically all the meta-data caches, as well as the high water marks for the number of BoxArrays are all nicely bounded, but the amount of bytes contained in BoxArrays is growing more or less monotonically. Not sure what's going on. There are no memory leaks as far as valgrind is concerned. I'm starting to wonder if it's a feature of the newer g++ on hopper. Src/C_AMRLib/Amr.cpp commit be639c644027432608ee5997dba02ec124eaab8f Author: lijewski Date: Fri Dec 27 16:06:50 2013 -0800 Some more compressing of meta data. Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 29f6cd355082f7e254afde5c504478a946c0c44e Author: lijewski Date: Sat Dec 21 08:35:20 2013 -0800 More massaging of meta data statistics. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.cpp commit cd3623d77d1593863d9049032627dfff3c95da79 Author: ajnonaka Date: Thu Dec 19 16:49:02 2013 -0800 in the tensor solve, when looking at the inf_norm of the rhs or residual, look at all the components instead of just the first. Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 7aaa49b1af63e5270d7f6552adbd68f0400758d1 Merge: b9f636646 8a9a55123 Author: Marc Day Date: Thu Dec 19 15:36:20 2013 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 8a9a55123472a9a58653fe7ae043d895c96e3128 Author: lijewski Date: Thu Dec 19 14:08:01 2013 -0800 Forgot to remove a debug statement. Src/C_BaseLib/FabArray.cpp commit a6a8671bcedd90746efe7cf526ce1502f6ec718f Merge: 14eb3879f c7a21f31f Author: lijewski Date: Thu Dec 19 14:03:34 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 14eb3879f19277fab2592173455083d2e5804244 Author: lijewski Date: Thu Dec 19 14:02:02 2013 -0800 Decreased the default sizes of the Fill_Boundary() and copy() caches to 25. This seems to get a majority of the reuse cases without leading to excessive metadata size. Src/C_AMRLib/AuxBoundaryData.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit c7a21f31f4aa92a24492082a576bd436e06e1392 Author: Weiqun Zhang Date: Thu Dec 19 13:11:39 2013 -0800 fixed comment Src/C_BaseLib/FabArray.H commit 55e484a35abc2fa27641f5831e4ebcbf67d8ae50 Author: lijewski Date: Wed Dec 18 14:19:43 2013 -0800 Some cleanup. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/BndryData.cpp commit 0a0b0845b0e181f7656e07b126ecc2e71cd87e6e Author: lijewski Date: Wed Dec 18 11:20:55 2013 -0800 Exclude the AuxBoundaryData parallel copy()s from being cached. Src/C_AMRLib/AuxBoundaryData.cpp Src/C_BaseLib/FabArray.cpp commit e934e3b82d3c9db6ec2c8c4c7635eb03a81913c6 Author: lijewski Date: Wed Dec 18 10:35:41 2013 -0800 Added ability to specify not to cache the data patterns for parallel copy. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit fdb518aa6d27c8c564ac9164f74ec019cf9b61c6 Author: lijewski Date: Wed Dec 18 09:03:51 2013 -0800 Removed a redundant line. Reduced the default max size of the copy cache from 200 -> 100. Might have to go even smaller unless I can squeeze out more memory from the BoxArrays. Or another route would be to not add the chemistry parallel copy()s to the cache. Src/C_BaseLib/FabArray.cpp commit 37870b6f3e13537e15a429142e8df68f347d854b Author: lijewski Date: Tue Dec 17 14:11:18 2013 -0800 Removed BoxArray::reserve(). As best I can tell this is not used anywhere. If someone is using it, you should be able to just delete the call to it and all should be well. It's really just a hint to the underlying containing to "reserve" memory for future operations on the BoxArray. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 3823c4ff1ca3cfd13e14e2760e645308b9b4a91b Author: lijewski Date: Tue Dec 17 14:05:29 2013 -0800 Some cleanup. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit fc37e7e5f84e970d4b8e7f448b40fa057dee011a Author: lijewski Date: Tue Dec 17 11:12:34 2013 -0800 I'm now also keeping track of the total number of bytes stored in BoxArrays. This turns out to be surprising difficult to do given the various ways BoxArrays can built and destroyed. Hopefully I'm at least close to having in correct. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit b9f63664670d3b10e0901b5020ae07b71c74977a Author: Marc Day Date: Tue Dec 17 10:19:35 2013 -0800 Double colon rule so we can extend if necessary Tools/C_mk/Make.rules commit 3dc63f6e64cebe358dcc6bd11582dd64e8f9e657 Author: lijewski Date: Mon Dec 16 16:51:39 2013 -0800 One more try to get the I/O I want. Src/C_AMRLib/Amr.cpp commit 666f88f11111620093fa54ff21a406c8b4b6f431 Author: lijewski Date: Mon Dec 16 16:41:53 2013 -0800 Cleaned up some verbose output. Src/C_AMRLib/Amr.cpp commit 6b796779c89086de14a0fa66d9644081a835319b Author: lijewski Date: Mon Dec 16 15:34:45 2013 -0800 Added counters for the high water mark of distinct BoxArrays and build hash tables. It looks like I've been overestimating the amount of data in hash tables. I missed a place in the code (hidden in the .H file not the .cpp file) where hash tables can go away. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit a42a5afabc468d764c5fc443b72badf28bcbbb76 Merge: 80f93b01c 5158d5741 Author: vince Date: Mon Dec 16 15:12:44 2013 -0800 Merge branch 'master' into commprof commit 5158d57411912b76fee25001ae5d371d30e18321 Author: lijewski Date: Mon Dec 16 13:58:19 2013 -0800 Squeezed out some more memory from the hash tables. Src/C_BaseLib/BoxArray.cpp commit f09c2c015f2a26dec7e9353f539d72e7aad3f8e5 Author: lijewski Date: Mon Dec 16 12:28:08 2013 -0800 Added code to print out the high-water mark of bytes held in BoxArray hash tables at the end of each coarse time step (similar to FAB bytes spread). As best I can tell these hash tables are the only thing in the C++ code that grows as the total number of Boxes, not the total number of Boxes that a CPU owns. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 0886ef64524fea4d74e225e049661ee35f4e2731 Author: Ann Almgren Date: Sun Dec 15 20:00:54 2013 -0800 Add an option to moveKick in Particles.H that allows one to store the acceleration at the particle location in the data of the particle. This option is only exercised if the component passed in is relevant, aka > the components of the data used to store the velocity. Src/C_AMRLib/Particles.H commit 0094bb4772a147d968ec5a5a314699a4bc585c4b Author: lijewski Date: Fri Dec 13 11:00:22 2013 -0800 More BoxHash statistics. Src/C_BaseLib/BoxArray.cpp commit d10568f6f6cdb48f72df5d9aa95ecf3a8998bdf9 Author: lijewski Date: Fri Dec 13 10:40:59 2013 -0800 Added a clear_hash_bin(). AddBox() calls intersections() ... Src/C_AMRLib/FluxRegister.cpp commit 0d275e200155e13cd66cde4ff2f1b610bb7ddf74 Author: lijewski Date: Fri Dec 13 10:40:40 2013 -0800 Added a clear_hash_bin(). Src/C_AMRLib/TagBox.cpp commit c3f29f15c9ca9a3da46ca7395819fab463b86eac Merge: 6b6173ad7 2301d2fe1 Author: Michael Zingale Date: Fri Dec 13 12:08:09 2013 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit 6b6173ad7f6c8f89d55860f77755dc123df79d0f Author: Michael Zingale Date: Fri Dec 13 12:07:45 2013 -0500 don't require --infile1 --infile2 fcompare.f90 commit 99c5a38e4cdf8da4480e0218c82497dab25fce06 Merge: 54455d099 b0f52489b Author: Ann Almgren Date: Thu Dec 12 21:06:01 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 54455d099333385481f04cce1f1ef7d96c2e43a9 Author: Ann Almgren Date: Thu Dec 12 21:05:31 2013 -0800 Set default value of regrid_int = 1; you will now get a warning instead of an error if you don't set it in the inputs file. Src/C_AMRLib/Amr.cpp commit b0f52489bd4ecd9dba8c8e2a935558aeef575370 Author: lijewski Date: Thu Dec 12 15:30:07 2013 -0800 Some debugging stats for init_box_hash_bin(). I'd like to turn this into a "map" but it Fortran ... Src/F_BaseLib/layout.f90 commit 87fcf0a786506ff613978ef8056056c0cb093219 Author: Ann Almgren Date: Thu Dec 12 14:42:03 2013 -0800 Remove left over print statement. Src/C_AMRLib/Particles.H commit 073e517498db8a364599af46401490b35595c0e9 Merge: 5ae0aa654 e61253f14 Author: Ann Almgren Date: Thu Dec 12 14:37:29 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5ae0aa65408f100c5e9adb9da9adf040762cc8e5 Author: Ann Almgren Date: Thu Dec 12 14:31:09 2013 -0800 Add the access function GetParticleCPU. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/Particles.H commit e61253f1426d731075d2b56f61ca8ed34d596a20 Merge: aecad7327 9501c07f0 Author: lijewski Date: Thu Dec 12 13:39:00 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit aecad7327fc9cfcfdf8ca5c75075ce7448d443d7 Author: lijewski Date: Thu Dec 12 13:38:24 2013 -0800 Added more debugging statistics to box hash bin code. Src/C_BaseLib/BoxArray.cpp commit 9501c07f0891dbb8686cdcec84125097e3e357e5 Author: Ann Almgren Date: Thu Dec 12 13:37:09 2013 -0800 Modify the "GetParticle.." routines to change how we access the particle data, and pass it through the Amr object to the outside. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/Particles.H commit 24ed8b623b65f9183936949f7a4fdb6283ab8a5c Author: lijewski Date: Wed Dec 11 12:23:51 2013 -0800 On edison use -target=compute_node instead of -target=linux on compiles. Tools/C_mk/Make.Linux commit 0cb5cf9f2a952563cb513f0e00675381b353db8e Author: lijewski Date: Wed Dec 11 10:55:03 2013 -0800 Much more memory efficient implementation of the Box Hash stuff. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 4d19780fbaa4ee32409b556b5f488c2689428a1d Merge: 945be8a4b 1b1022d08 Author: lijewski Date: Tue Dec 10 17:56:23 2013 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 945be8a4b387d2fcbfadcc6425616b367468920b Author: lijewski Date: Tue Dec 10 17:55:00 2013 -0800 I'm adding back in the critical region that builds the hash bins. I seem to recall that the particle code needs this. Something along the lines of particles using BoxArray::contains() in OMPd loops, where contains() calls the intersect code under the covers. Src/C_BaseLib/BoxArray.cpp Src/F_BaseLib/layout.f90 commit 1b1022d081e70f75b7eb60f9ed4d054394b495b7 Author: Ann Almgren Date: Tue Dec 10 17:21:40 2013 -0800 Removed commented line. Src/C_AMRLib/Particles.H commit 7f4dbd2ecd773919e7df8ffc1a772d30e224fd5b Author: Ann Almgren Date: Tue Dec 10 17:18:08 2013 -0800 Add the virtual routine particle_redistribute so that we can call it from Amr::ParticleRedistribute. Src/C_AMRLib/AmrLevel.H commit 86711b56231a9f9263e2d8ef8c5eea153aaa66ed Author: Ann Almgren Date: Tue Dec 10 17:14:46 2013 -0800 1) Make the default ref_ratio be 2 for all directions and levels, instead of setting it to zero and having an error if not set in the inputs file. 2) Clean up the geometry stuff: we now define an external geometry by setting the intersection points of grid lines with the boundary in each coordinate direction (both hi and lo). This is a crude representation -- just one location for the face in each cell where it intersects. 3) Add Real coarseTimeStepDt which is the same as coarseTimeStep except it returns the dt that it used. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit eab5cd44d834e31f0d10212eb9b353334fa6136f Author: lijewski Date: Tue Dec 10 15:25:06 2013 -0800 Be a little more aggressive clearing box_hash_bin. Src/F_BaseLib/layout.f90 commit 8b3d74ccb0a3499fbafc63182d8a36478de1080d Author: lijewski Date: Tue Dec 10 12:53:32 2013 -0800 Don't OMP loops containing layout_get_box_intersector calls. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 0e2a5c4a257a146cd8ed8e0f07008c7aca26a9bf Author: lijewski Date: Tue Dec 10 12:53:04 2013 -0800 Some cleanup. Src/C_BaseLib/BoxArray.cpp commit 854f9b632dc0ec1a1871a9a1529c42ec05d10ac6 Author: lijewski Date: Tue Dec 10 12:24:34 2013 -0800 Some simplification. Also removed the critical section around the innards of intersections(). It's now no longer thread-safe. Hope I've found all places where I was trying to do intersections in threads and remomved'm. Src/C_BaseLib/BoxArray.cpp commit 5a96be8830ce893841aa6652104484c452d042ac Author: lijewski Date: Mon Dec 9 21:51:31 2013 -0800 Increased verbosity level at which some debug output appears. Src/F_BaseLib/layout.f90 commit db809ba217350f29cf12ab62aca235bb3aa3863c Author: lijewski Date: Mon Dec 9 21:27:05 2013 -0800 Yet one more clear_hash_bin() call for the evening. Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit a3fc87a222a7c5d3fbe51ae08ef75112203a09f2 Author: lijewski Date: Mon Dec 9 21:24:14 2013 -0800 Inserted more clear_hash_bin() calls. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 46aa58e636678c640900ce51cddd2389dcf494e6 Author: lijewski Date: Mon Dec 9 21:15:12 2013 -0800 Merged in some calls to BoxArray::clear_hash_bin(). Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/FabSet.cpp commit aeecb9d0b30c3db7b15680044f95c5598b78b0ae Author: lijewski Date: Mon Dec 9 21:08:09 2013 -0800 Clear out the hash bin in a BoxArray after using intersections() to put a cached object into the FillBoundary() and parallel copy() caches. Src/C_BaseLib/FabArray.cpp commit 6641c63dc865d3e0227c41667be4ddfc4fa7997c Author: lijewski Date: Mon Dec 9 21:04:11 2013 -0800 Merged in call to clear_hash_bin(). Src/LinearSolvers/C_CellMG/LinOp.cpp commit 34c53faa1d30158202324572cad9e73697f02089 Author: lijewski Date: Mon Dec 9 21:03:01 2013 -0800 Added BoxArray::clear_hash_bin(). Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 17cf353a3aff597b990250c4604d5c692f0bd49f Author: lijewski Date: Mon Dec 9 21:02:39 2013 -0800 Removed some debugging output. Src/F_BaseLib/layout.f90 commit ae5f02d46ab013a2b7655d54a16fdb9c0dc2e0d2 Author: lijewski Date: Mon Dec 9 20:40:35 2013 -0800 Compressed out some of the memory in the fast box intersection hash routine. This routine (and the one in F90) are looking like the metadata memory hogs that I've been searching for. I think there's more that can be done to cut down memory use here. Src/C_BaseLib/BoxArray.cpp commit 3a8c25e72a0966e48956b2d9226558a68a2d3e31 Author: lijewski Date: Mon Dec 9 15:08:34 2013 -0800 Added clear_box_hash_bin(). There may be some strategic places where we can call this routine to cut down on memory usage. Src/F_BaseLib/layout.f90 commit 8058550e7eac2d0aef64ac70490452126f991bb8 Author: lijewski Date: Mon Dec 9 14:37:31 2013 -0800 Squeezed out some memory from the boxarray hash. Src/F_BaseLib/layout.f90 commit 937f7dd31d9096c08e62530e95fad181eeaaa430 Author: lijewski Date: Mon Dec 9 12:48:21 2013 -0800 Added some code to calculate the maximum # of bytes in a boxassoc -- the structure that is used by layout for managing FillBoundary()s. Src/F_BaseLib/layout.f90 commit 33c76f15356bc1af23bdaccc8e08a74f9a18acc9 Author: lijewski Date: Mon Dec 9 12:09:01 2013 -0800 Pulled something from the stack and put it on the heap. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 70c17746bcd664ec0c276fd866ded1091ba45519 Author: lijewski Date: Mon Dec 9 10:44:37 2013 -0800 Some cleanup. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 60bcd5cea1aab117e68857b8b44bb69cbbed6a50 Merge: b0598e875 ae59f33d8 Author: lijewski Date: Mon Dec 9 10:22:22 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b0598e8758e9a52bacc3edd4984c3ba9beebb014 Author: lijewski Date: Mon Dec 9 10:21:47 2013 -0800 Don't build the mask() lmultifabs in the ml_layout. They appear to only be used by the cell-centered code. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 15125246349905723d05ebf2d7c4d9e5b0b34247 Author: lijewski Date: Mon Dec 9 10:20:53 2013 -0800 Only try to delete the mask() lmultifabs if they've actually been built. Src/F_BaseLib/ml_layout.f90 commit ae59f33d8eaf2024366be1d0da3472016fc5c33d Author: Ann Almgren Date: Sat Dec 7 12:12:18 2013 -0800 Add sanity checks and comments in ParticleContainer::addOneParticle() Src/C_AMRLib/Particles.H commit 49043a8ff794b176dfa6845fc399100bf3140f22 Author: lijewski Date: Fri Dec 6 14:14:47 2013 -0800 Fix typo. Src/C_BaseLib/FabArray.cpp commit c4c328e5dda9ed6d9626d2d5d01d56b9cf2be509 Merge: 45923b1e7 f51c278f0 Author: lijewski Date: Fri Dec 6 13:54:51 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 45923b1e783926e2c6a5559262d354d03e24ca32 Author: lijewski Date: Fri Dec 6 13:51:05 2013 -0800 Parallel copy() is now set up to do fabarray.maxcomp components at once. That is to say, we agglomerate MPI messages as always, but we only do fabarray.maxcomp (instead of ncomp) at one time. I'm occasionally getting killed by the Out-Of-Memory process of hopper. I'm wondering if it's because the internal MPI buffers are getting too big. So I want to do somewhat smaller MPI transfer. Large transfer happen, in particular, when we're rearranging state data for chemistry solves, amongst other times. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit f51c278f0dd449c6380b5813d48ba70f37b44c14 Author: Ann Almgren Date: Wed Dec 4 14:01:25 2013 -0800 Fix coefficients in tridiag. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit a45f1b2de98a205fea872fe2bd69b9f271194de3 Merge: 8dea6f284 6cd84b159 Author: Ann Almgren Date: Tue Dec 3 16:20:23 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8dea6f284219934d582b5903f12fa41a6aa31642 Author: Ann Almgren Date: Tue Dec 3 16:20:11 2013 -0800 Add new files to Make.package Src/C_BaseLib/Make.package commit f4cd0a5c3ae833ef72e932cc83cb6463dd0e0940 Author: Ann Almgren Date: Tue Dec 3 16:19:29 2013 -0800 Add iMultiFab.{H,cpp} and IArrayBox.{H,cpp} to the repo. Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/IArrayBox.H Src/C_BaseLib/IArrayBox.cpp Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit 6cd84b15942581f59c790b8a41ea28a53eb19c68 Merge: 464efc4bc f5ded3935 Author: Weiqun Zhang Date: Mon Dec 2 21:27:22 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 464efc4bca8669ffae14cb69df3018fcad5b979d Author: Weiqun Zhang Date: Mon Dec 2 21:27:15 2013 -0800 use OMP ATOMIC instead of OMP CRITICAL in a few places Src/C_AMRLib/Particles.cpp Src/C_BaseLib/BaseFab.H Src/F_BaseLib/bl_mem_stat.f90 commit f5ded39350c5173978c8c3cc54d8cfd4cd52fd1b Author: Ann Almgren Date: Mon Dec 2 13:44:47 2013 -0800 DatasetClient.H no longer lives in this directory. Src/C_AMRLib/CMakeLists.txt commit daf3dfbf38d78b6d2b7475f3694128b9616d9dd5 Author: Ann Almgren Date: Mon Dec 2 13:22:35 2013 -0800 Add nodal_stencil_apply.f90 to CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit b7497068128a17c9d99b03d37bc59c92278dedb4 Author: Ann Almgren Date: Mon Dec 2 13:19:02 2013 -0800 Add compute_defet.f90 to CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit 24977ac52d148b2ff552974976d3132a50389bef Merge: db7734e2f ee50cde90 Author: Ann Almgren Date: Mon Dec 2 13:01:23 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit db7734e2fd87bb2962a9f24ad90c752bf84988a1 Author: Ann Almgren Date: Mon Dec 2 13:01:02 2013 -0800 Update mg_tower_smoother.f90 --> nodal_mg_tower_smoother.f90 and cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/CMakeLists.txt commit ee50cde9044c0655d8007ad17bf063c2bb8ccf2c Author: Weiqun Zhang Date: Mon Dec 2 11:27:16 2013 -0800 Avoid using result, a Fortran keyword, as variable name although it is legal. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 134fd58f06f37ae4c7714b6811a2979132893818 Author: Weiqun Zhang Date: Mon Dec 2 10:40:09 2013 -0800 fixed OMP bugs Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit 72d2d83153979a3b0a498f6511d1588a73292b55 Author: Weiqun Zhang Date: Mon Dec 2 10:06:46 2013 -0800 fixed an OMP bug Src/F_BaseLib/create_umac_grown.f90 commit 9a1bb1e7171afd9e7952b2eea42f98ba3706c949 Author: Weiqun Zhang Date: Mon Dec 2 09:46:33 2013 -0800 removed unsafe OMP. The OMP do was on fine index, whereas the loop body wrote to an array on coarse grid. Thus it was possible that two threads with different fine index might write to the same coarse index. Src/C_AMRLib/INTERP_3D.F commit 6f2757fdbce61e8089e82ba5f6d8949ee02fab5b Author: lijewski Date: Sat Nov 30 19:32:22 2013 -0800 Set some defaults for mg.maxiter and mg.maxiter_b for F90 calls from C++. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 3ddddebc8292184cfa1dde80d3531377b7c7b2ab Author: Weiqun Zhang Date: Wed Nov 27 12:39:03 2013 -0800 Removed OMP from TagBoxArray::mapPeriodic because it is unsafe. Note that the valid boxes in TagBoxArray are actually grown boxes. So cells in a TagBox can have multiple sources during the merge with periodically shifted TagBoxes. Src/C_AMRLib/TagBox.cpp commit 15273708fa30982edea975e8e5058596df34c0cb Author: Weiqun Zhang Date: Wed Nov 27 10:54:50 2013 -0800 Removed OMP from reflux because it's not safe. Suppose there is a coarse cell next to the joint of the two fine boxes. Then the reflux onto the corase cell comes from two fine boxes. Thus it is unsafe to OMP over intersection boxes of the flux registers based on the fine grid and the coarse grid. Src/C_AMRLib/FluxRegister.cpp commit a8e6f4f676151ebac7024e821b24e83909039044 Author: Weiqun Zhang Date: Tue Nov 26 14:34:33 2013 -0800 fixed a minor OMP problem Src/C_BaseLib/BaseFab.H commit 27bd3fcba68060e82ec6ab998809f15d22816848 Author: Weiqun Zhang Date: Mon Nov 25 20:11:39 2013 -0800 fixed OMP bugs in my recent commit that will lead to race condition if the number of threads is large Src/C_AMRLib/FLUXREG_3D.F commit 6ff0478d4b6b07dd102f3407a11e54acb125241e Author: lijewski Date: Mon Nov 25 20:00:51 2013 -0800 Some OMP fixes. Src/LinearSolvers/F_MG/ml_nd.f90 commit dbf5c7b51521767125d9afd4930abd98ddbcee70 Merge: c12be2ac9 4731d7142 Author: Ann Almgren Date: Mon Nov 25 19:34:35 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Src/LinearSolvers/F_MG/ml_nd.f90 commit c12be2ac917e1ccb40116b6c3f5553f51e0f83f5 Author: Ann Almgren Date: Mon Nov 25 19:33:00 2013 -0800 Fix indices in nodal_stencil_norm. Src/LinearSolvers/F_MG/ml_nd.f90 commit 4731d7142973e7396985dc1b194a2a14b8cb58e0 Author: lijewski Date: Mon Nov 25 19:24:16 2013 -0800 Some OMP bug fixes. Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 commit 76c9d75e490b256ad53bc76b6098b592f91f1dd6 Author: Ann Almgren Date: Mon Nov 25 17:42:41 2013 -0800 1) remove unused variable in nodal_smoothers. 2) fix nodal_stencil_norm. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 4d632064aa7556d37b29aaa75841ce5ff4d29e4a Author: Ann Almgren Date: Mon Nov 25 16:58:06 2013 -0800 We need to use a different function for the stencil norm for the nodal solver. Src/LinearSolvers/F_MG/ml_nd.f90 commit 34b1a5eb396ccc4758d8f3f3632548a70727ef4a Author: Ann Almgren Date: Mon Nov 25 16:46:11 2013 -0800 Remove lp from OMP declaration where it isn't used Src/LinearSolvers/F_MG/cc_stencil.f90 commit 80f93b01ca69eda2040a3f409afb5689ebf2a76a Author: vince Date: Mon Nov 25 14:34:15 2013 -0800 reset strategy fix. Src/C_BaseLib/DistributionMapping.cpp commit 23ad74d5cd219963e6e86d7b2a2b2f31c4165725 Author: Weiqun Zhang Date: Mon Nov 25 13:32:00 2013 -0800 fixed a bug in nodal stencil Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 318dc85f0868960a852096f24e4fb6cfb3c69fa3 Author: Weiqun Zhang Date: Mon Nov 25 10:16:27 2013 -0800 Fixed new OMP bugs. Also added "collapse". If compilers have trouble with "collapse", we can take it out, and move "omp do" two loops down. Src/C_AMRLib/FLUXREG_3D.F commit afba92b0f6d67530abe98c5a6da8ff66929ff1e7 Author: lijewski Date: Mon Nov 25 08:53:00 2013 -0800 Make the C-F MG translation code understand CABiCG solver. Set it up so that it CG, BiCG and CABiCG get properly translated between C++ and Fortran. While in the C++ code we set cg_solver as cg.cg_solver we allow cg.cg_solver and mg.cg_solver. Default to CABiCG if nothing is set. If you want different bottom solvers in C++ and Fortran use mg.bottom_solver, set to the correct F90 value. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 48cb1ff9b69b6ec7bc2367e5347a7f57609d9f59 Author: lijewski Date: Fri Nov 22 15:42:22 2013 -0800 Fixed typo. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 771ad0ca781794ac139fdef97eed673d8ad187bf Merge: 3534844d6 1208cf040 Author: Ann Almgren Date: Fri Nov 22 15:35:42 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3534844d6e732cfbe3c008e5a15539b9966b9729 Author: Ann Almgren Date: Fri Nov 22 15:35:22 2013 -0800 Fix the way we impose Neumann bc's on sg in nodal stencil fill. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 1208cf0404abbcc3082e20057bde4eb5a67d2de7 Merge: 70514976e 286446875 Author: lijewski Date: Fri Nov 22 12:40:04 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 70514976e9aff8bb8ffbf63422be9f59d8759c22 Author: lijewski Date: Fri Nov 22 12:37:21 2013 -0800 Added code so that we thread a couple of these routines if they're NOT called from within a parallel region. In general, the most common place to call these routines from is within FillPatch, where they're called by threading over boxes in C++. Src/C_AMRLib/INTERP_3D.F commit 286446875950a0b91c551879cc21796a333ad8e5 Author: Ann Almgren Date: Fri Nov 22 11:16:25 2013 -0800 Only have diagonalize=true for nodal solve. Src/LinearSolvers/F_MG/itsol.f90 commit 364ed421238af14b0ae505c6c3023e65cbb30c97 Author: Ann Almgren Date: Fri Nov 22 11:09:09 2013 -0800 No longer pass ns into mg_tower_build. Tutorials/HeatEquation_EX5_F/advance.f90 commit a2c8773e23c85823b89160aca5017170a3d52701 Author: Ann Almgren Date: Fri Nov 22 11:03:08 2013 -0800 More changes to be compatibale with the new nodal stencil (and the fact that we no longer pass ns into mg_tower_build). Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 7411f531a53c5c1dc46a382a726b03042a7cbb80 Author: lijewski Date: Fri Nov 22 10:50:08 2013 -0800 Turns out there's an easy way to figure out whethe or not we're currently in an OMP parallel region. The FineAdd Fortran routines are now written to only thread if they're not in an OMP region. When the MultiFab version of FineAdd() is used we thread in C++ over the boxes and hence don't thread within the Fortran. When the FAB version of FineAdd() is called we thread the Fortran. More of this to come ... Src/C_AMRLib/FLUXREG_3D.F commit 67e497c75796015a271cae2add3573fbe33e7761 Author: Ann Almgren Date: Fri Nov 22 10:43:41 2013 -0800 ns --> mgt%ns Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90 commit 001c73e24828f250114594b120c6e752a797d592 Author: Ann Almgren Date: Fri Nov 22 10:43:07 2013 -0800 These are the new versions of the nodal solver which carries the cell-centered coefficient rather than filling the nodal-based stencil. Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 20aa80c46b6c3db22acf052357639c44b55c800a Author: Ann Almgren Date: Fri Nov 22 10:16:35 2013 -0800 Use mgt%ns, not ns. Src/LinearSolvers/F_MG/mg.f90 commit b476c15405745e1fe6b3c9db02e93c8b0f1a1378 Author: Ann Almgren Date: Thu Nov 21 16:41:46 2013 -0800 These are the nodal files that used the stencil-based as opposed to the new sg-based nodal stencil. Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/compute_defect.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/itsol.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_nd.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_solve.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_interface_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_cpp.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_tower_smoother.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_smoothers.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_apply.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_fill.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_sync_resid.f90 commit 2ca4e87d5759eea0cc36f6109a387c3aee73b390 Merge: f13c4100f f451ddb07 Author: Ann Almgren Date: Thu Nov 21 16:40:12 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f13c4100fb1797663e105e779e2adab5fb2e4df9 Author: Ann Almgren Date: Thu Nov 21 16:39:38 2013 -0800 Create a new directory: BoxLib/Tests/LinearSolvers/F_MG_Old_Nodal_Stencil to hold the source code and test code for the stencil-based nodal solver. Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/bc_interp.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_multi.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_rhs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_1lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_2lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_1lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_2lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/init_cell_coeffs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.cross Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.dense Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.cross Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.dense Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/main.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/makefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_multi.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_rhs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/regression Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_smoother.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/wrapper.f90 commit eea8556a0e4b9bf1176d1beedfa959728ee10c70 Author: Ann Almgren Date: Thu Nov 21 16:38:06 2013 -0800 No longer keep these scripts. Tests/LinearSolvers/F_MG/test_dir Tests/LinearSolvers/F_MG/test_script commit 33107689e7fe654bf6ab6bd8393b1aa68d44f75f Author: Ann Almgren Date: Thu Nov 21 16:37:43 2013 -0800 These are the new test routines for the new sg-based nodal solver. Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/init_cell_coeffs.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_rhs.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit b8219db9e952ba63b7e4b55c876392d5bfd0ddc6 Author: Ann Almgren Date: Thu Nov 21 16:32:35 2013 -0800 More cleanup -- no functional change. Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/mac_applyop.f90 commit f451ddb0783d6b5631273cdc026ae8f4b8fcdc19 Author: Weiqun Zhang Date: Thu Nov 21 13:06:38 2013 -0800 fixed makefile in F_MG for C++ codes Src/LinearSolvers/F_MG/FParallelMG.mak commit 37d373f2a46d991073fbc8f515998633748762ec Author: Ann Almgren Date: Thu Nov 21 12:30:12 2013 -0800 These changes should not make any difference in the answers, they are just rearrangement and some renaming of subroutines. Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit be6420325dddf7a4caf565a11baeded10004c323 Author: Ann Almgren Date: Wed Nov 20 14:20:13 2013 -0800 Update the testing routines with new inputs*nodal* files and new grids files. Clean up the printouts as well. Tests/LinearSolvers/F_MG/grids_2d_1lev Tests/LinearSolvers/F_MG/grids_2d_2lev Tests/LinearSolvers/F_MG/grids_3d_1lev Tests/LinearSolvers/F_MG/grids_3d_2lev Tests/LinearSolvers/F_MG/init_cell_coeffs.f90 Tests/LinearSolvers/F_MG/inputs.2d.nodal.cross Tests/LinearSolvers/F_MG/inputs.2d.nodal.dense Tests/LinearSolvers/F_MG/inputs.3d.nodal.cross Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit c153ac9ace79f0f5e89f3e3a2204f6e469fd4329 Merge: 338ba0351 ab8cfa3bd Author: Ann Almgren Date: Wed Nov 20 12:37:05 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 338ba03513f88beb2b9e1cefddfc5ace108e1916 Author: Ann Almgren Date: Wed Nov 20 12:36:45 2013 -0800 Clean up of nodal multigird and the testing program in Tests/LinearSolvers/F_MG. Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 23813471edb80c674dc6af7a7fa4dbd1fef74350 Author: Ann Almgren Date: Wed Nov 20 12:36:08 2013 -0800 The filest are listed in GNUmakefile instead. Tests/LinearSolvers/F_MG/GPackage.mak commit 803a729eaadb86df36645a8c6be4f23099ba4f31 Author: Ann Almgren Date: Wed Nov 20 12:33:32 2013 -0800 Get rid of Jacobi options within smoothers. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 1dfc4a42a2cb1d866a443b71cb466036ecdac43c Author: Ann Almgren Date: Wed Nov 20 12:33:12 2013 -0800 Better formatting. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 9c155a3910dfe8d9669d502abbc133dda99cbd4a Author: Ann Almgren Date: Wed Nov 20 12:32:37 2013 -0800 Make sure rh has exactly one ghost cell. Src/LinearSolvers/F_MG/ml_nd.f90 commit a9a546922ba28eded57cba98b9268f78667fbedc Author: Ann Almgren Date: Wed Nov 20 11:28:47 2013 -0800 Get rid of Jacobi smoother. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit ab8cfa3bde5154d0e5bb6b6f6553322c1aafaaab Author: lijewski Date: Tue Nov 19 12:03:37 2013 -0800 Verbose flags should be integer. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 956acec5f3d84ac93d162b236a5686ff4b88bbab Author: lijewski Date: Tue Nov 19 09:50:47 2013 -0800 Added a verbose option, defaulted to false, to MGT_Solver. This way we can set the default on a case by case basis, instead of just using the ParmParsed valued of mg.v. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 8c3e78c724b3176be0e25934328cd9c2f7fe5066 Author: lijewski Date: Mon Nov 18 15:08:48 2013 -0800 Example now shows how to reduce a map where the key is a structure. I use and IntVect since BoxLib knows how to sort IntVects. Tests/C_BaseLib/tMF.cpp commit a45ed369c9c37f831536454f57477e5e4cef8c09 Author: lijewski Date: Mon Nov 18 14:13:54 2013 -0800 A little cleanup. Tests/C_BaseLib/tMF.cpp commit ff06d0d671caa944bb0d8fc5db33328f37047020 Author: lijewski Date: Mon Nov 18 14:10:38 2013 -0800 This test is now a simple example of how to reduce a std::map across CPUs. Tests/C_BaseLib/tMF.cpp commit b1f7ed0caf83d88be872a42c8197f8ed716bedec Author: Ann Almgren Date: Fri Nov 15 12:18:53 2013 -0800 Add check on whether mf is nodal in build_nodal_dot_mask. Src/F_BaseLib/multifab_f.f90 commit 825538d256944b942b864d89d3bac091668b062b Author: vince Date: Wed Nov 13 15:42:37 2013 -0800 added proximity order diagnostic. added simulation of hopper distributions for testing locally. pfc order looks correct. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 7af7e68ae4de13f3d7af8c05b6ee2d1fde6e26d4 Author: Weiqun Zhang Date: Wed Nov 13 11:19:41 2013 -0800 sum_integrated_quantities does not need to be virtual Tutorials/AMR_Advection_C/Source/ADR.H commit 2301d2fe1c14e2d3d2542c667918cccdb3d88e8c Author: Chris Malone Date: Tue Nov 12 18:23:52 2013 -0800 remove debug print statements MAESTRO_xrb/fbuoyancy.f90 commit 777cbfaf5f66c756c05d7b547e52eee6bbc471b5 Author: Ann Almgren Date: Tue Nov 12 16:18:17 2013 -0800 We no longer use mgt%st Src/LinearSolvers/F_MG/mg_tower.f90 commit 2d1ea50456d1699f34095c24feb1a0a761cd1c32 Author: Chris Malone Date: Tue Nov 12 15:21:44 2013 -0800 get this compiling again MAESTRO_xrb/fbuoyancy.f90 commit 9809e560cd149f6a74446789c3bfcc9c66400172 Author: Marc Day Date: Mon Nov 11 18:13:16 2013 -0800 Redo solve_ function to look more like scalar solve, add access function to AmrData, uptick ccse lib version Src/Extern/amrdata/AmrData.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Tools/CMake/BoxLib_Version.cmake commit f7a4a80846c9b83845da8cd6de85ce8252ff379b Author: vince Date: Mon Nov 11 12:00:18 2013 -0800 removed print. Tests/IOBenchmark/IOTest.cpp commit 706bfea493e83150f168dd1a8eea0de842008ae9 Author: Weiqun Zhang Date: Mon Nov 11 11:53:16 2013 -0800 removed DatasetClient.H and .cpp from a couple of makefiles because DatasetClient has been moved to ArrayView Tools/C_util/Convergence/Make.package Tools/C_util/Statistics/Make.package Tools/C_util/ViewMF/Make.package commit 0cc049ebad52c5f93fa0bc03b1264d89be48ca7c Author: lijewski Date: Mon Nov 11 10:07:40 2013 -0800 Fix to quiet PGI compiler. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit dbb2a1ddbbf09cfa705e6c642c1d7f1fb0fde9c3 Author: Weiqun Zhang Date: Tue Nov 5 16:45:35 2013 -0800 update regression test files Tools/RegressionTesting/BoxLib-tests.ini Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/Nyx-tests.ini Tools/RegressionTesting/RNS-tests.ini Tools/RegressionTesting/SMC-tests.ini Tools/RegressionTesting/VARDEN-tests.ini commit a803c9de2ac77526cd852e6f15b25e5115a929a3 Author: Weiqun Zhang Date: Tue Nov 5 16:23:50 2013 -0800 removed middle data stuff; these were intended for SDC, but now SDC is done in a different way Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 19664675dd48a00cb0e0ac958c11f48fcff8a785 Merge: bd94fa89d 22f02da2f Author: vince Date: Mon Nov 4 12:09:31 2013 -0800 Merge branch 'master' into commprof commit 6b72b245761faf034ae249709594b61f2a48f89b Author: Chris Malone Date: Fri Nov 1 09:42:41 2013 -0700 new routine to calculate the total mass on the grid for all species MAESTRO_xrb/fspec_total_mass.f90 commit bd94fa89df0a6944a7b16f53733fa41a50fb1406 Merge: ba3a3524e 29128de49 Author: vince Date: Thu Oct 31 11:23:55 2013 -0700 Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof commit 22f02da2fe74a665fc7c29d11d3468af1a19be41 Merge: 78f8f87e7 71ecc2a85 Author: vince Date: Tue Oct 29 16:30:21 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 78f8f87e78ed8056b7ed911edd6fe0301256de3a Author: vince Date: Tue Oct 29 16:30:00 2013 -0700 fixed parallel bug for fabs and multifabs. Src/Extern/amrdata/AmrData.cpp commit f0e54bd4e413b2b0c4611f61ed0025b141df991f Author: Chris Malone Date: Mon Oct 28 17:02:11 2013 -0400 actually add a usage statement MAESTRO_xrb/frates.f90 commit 71ecc2a852651cb8ddea9d466f6e792cab2e0c0c Merge: 029b6b67d 6643af2eb Author: lijewski Date: Mon Oct 28 09:23:19 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6643af2eb356230f3f0ddcb7553486d4063d8580 Author: lijewski Date: Sun Oct 27 10:32:53 2013 -0700 Examine NERSC_HOST as well as uname for the hostname. Currently edison doesn't appear in 'uname -a'. Tools/C_mk/Make.defs commit 029b6b67d3f7cb7ec30758bf3a5096ea63b2cbb6 Author: lijewski Date: Fri Oct 25 14:58:08 2013 -0700 Added version of bCoefficients() that takes a FArrayBox and grid # instead of a MultiFab. Also ZeroACoefficients(); it's equivalent to a call of aCoefficients() where the passed MultiFab was setVal()d to zero, without having to build the MultiFab. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp commit ba3a3524ed066ac599442f8c9aab61fc95fe6be9 Author: vince Date: Fri Oct 25 11:42:22 2013 -0700 close file. Src/C_BaseLib/VisMF.cpp commit 956cc01b4db574823977fe8f99486bf44a0e5f1d Author: vince Date: Fri Oct 25 11:42:05 2013 -0700 close file. Src/C_BaseLib/DistributionMapping.cpp commit 29128de49448912b20d8c91d25f8bc51322c2bad Author: vince Date: Thu Oct 24 15:28:35 2013 -0700 hopper test. Src/C_BaseLib/DistributionMapping.cpp commit a2515efec704a241d39140980e7b2f1c2b4dd96a Author: Marc Day Date: Thu Oct 24 12:37:40 2013 -0700 Add code to fill corner cells at phys corners...if0 it out, but leave it around for later use Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 07783e0be527d2d6a1ea7b28ed23b77a62652791 Author: vince Date: Wed Oct 23 15:54:22 2013 -0700 hopper test. Src/C_BaseLib/DistributionMapping.cpp commit fa09f5521c25e10557918b817ed669d806e88e80 Author: vince Date: Wed Oct 23 15:14:29 2013 -0700 procname. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 9bf88b2cc0d9a37cd0751e9fb2279dcf1396c3e8 Author: vince Date: Wed Oct 23 14:51:30 2013 -0700 no report for zero perfmon procs. Src/C_BaseLib/ParallelDescriptor.cpp commit 5b0a555cd93cb3ac157205a2f42d7916adb4957b Author: vince Date: Wed Oct 23 14:30:38 2013 -0700 hopper fix. Src/C_BaseLib/Profiler.cpp commit e7b2f60f1a9e28dfdd512a90e64fa0afb3d1de95 Author: vince Date: Wed Oct 23 14:19:58 2013 -0700 more proximity mapping. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Profiler.cpp commit 18a24a56abfee0fc923610d04a0f9f3dd371864d Author: Ann Almgren Date: Mon Oct 21 09:58:46 2013 -0700 No more DatasetClient.cpp in CMakeList... Src/C_AMRLib/CMakeLists.txt commit 370ea59a519cd4c2ca7bc78d5e82fff8f43b8fbe Merge: abdf551b9 5c0b00718 Author: vince Date: Fri Oct 18 15:16:25 2013 -0700 Merge branch 'master' into commprof commit 5c0b00718828a38aaf59190b76a3c298e403fc2f Author: vince Date: Fri Oct 18 15:12:47 2013 -0700 added arrayview support. Tools/C_mk/Make.defs commit 8eb35d155df6e5e4bd72a4a27ad5d5bf9537d53f Author: vince Date: Fri Oct 18 15:10:50 2013 -0700 added arrayview support. Src/C_AMRLib/DatasetClient.H Src/C_AMRLib/DatasetClient.cpp commit abdf551b9b96a6c9e6f3e920c0fe0fcaefbec19f Author: vince Date: Tue Oct 15 14:22:50 2013 -0700 more proximity mapping. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 49ff570e8fb97afc196985cc6e108ab56f0132e1 Merge: 75941244d 479a9faf4 Author: vince Date: Fri Oct 11 15:12:08 2013 -0700 Merge branch 'master' into commprof commit 75941244da19951d74bb45f32522251ace3ba7b2 Author: vince Date: Thu Oct 10 16:10:41 2013 -0700 helper functions for proximity ranking. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 479a9faf4fda6c1d7ad6a0a490f6856a4044d1ca Merge: 1b456f267 007af70f3 Author: lijewski Date: Wed Oct 9 13:28:05 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1b456f26795ec273a68f7c644dc5f914e66483f3 Author: lijewski Date: Wed Oct 9 11:02:23 2013 -0700 Added version of contains_nan() and contains_inf() that take an IntVect that gets set to a relevant cell when the routines return true. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit 007af70f39e2d17b438c050e3039ce0cc28d77b3 Merge: 92fb28b7c 3aac624ec Author: Matthew Emmett Date: Wed Oct 9 10:33:45 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 92fb28b7c81b844be0ca5b4b51238ede879dbd64 Author: Matthew Emmett Date: Wed Oct 9 10:33:34 2013 -0700 AmrLevel: Add fineRatio. StateData: Remove unused setMidData. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 3aac624ec4259a70ee438130504630d5a4ecc82d Author: Ann Almgren Date: Tue Oct 8 21:48:18 2013 -0700 Only print the warning (about not using linear interp if ref_ratio = 4 instead of 2) once per solve rather than once per v-cycle. Src/LinearSolvers/F_MG/ml_cc.f90 commit 6ef670b353eefd989a99c2cf456c56637b61f7f5 Author: Ann Almgren Date: Tue Oct 8 12:29:27 2013 -0700 Remove the Tests/LinearSolvers/C_NodalMG directory since we no longer support the code that this tests. Tests/LinearSolvers/C_NodalMG/files.2d Tests/LinearSolvers/C_NodalMG/files.3d Tests/LinearSolvers/C_NodalMG/gt_breaks_27pt Tests/LinearSolvers/C_NodalMG/inputs Tests/LinearSolvers/C_NodalMG/proj.cpp Tests/LinearSolvers/C_NodalMG/test_grids/3d_4_level.grids Tests/LinearSolvers/C_NodalMG/test_grids/gr.11 Tests/LinearSolvers/C_NodalMG/test_grids/gr.15 Tests/LinearSolvers/C_NodalMG/test_grids/gr.16 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19l3 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2.4 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.11 Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.25 Tests/LinearSolvers/C_NodalMG/test_grids/gr.7 Tests/LinearSolvers/C_NodalMG/test_grids/gr.8 Tests/LinearSolvers/C_NodalMG/test_grids/gr.8a Tests/LinearSolvers/C_NodalMG/test_grids/gr.ann.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.sstanley.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr0 Tests/LinearSolvers/C_NodalMG/test_grids/gr0a Tests/LinearSolvers/C_NodalMG/test_grids/gr0b Tests/LinearSolvers/C_NodalMG/test_grids/gr1 Tests/LinearSolvers/C_NodalMG/test_grids/gr1mike.thin Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.0 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.inf Tests/LinearSolvers/C_NodalMG/test_grids/gr2a2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2a4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l0 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p3 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p5 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p6 Tests/LinearSolvers/C_NodalMG/test_grids/gr2b Tests/LinearSolvers/C_NodalMG/test_grids/gr2c Tests/LinearSolvers/C_NodalMG/test_grids/gr2cross Tests/LinearSolvers/C_NodalMG/test_grids/gr2d Tests/LinearSolvers/C_NodalMG/test_grids/gr2d2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2d4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2dave Tests/LinearSolvers/C_NodalMG/test_grids/gr2e Tests/LinearSolvers/C_NodalMG/test_grids/gr2f Tests/LinearSolvers/C_NodalMG/test_grids/gr2g Tests/LinearSolvers/C_NodalMG/test_grids/gr2h Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike3 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r3 Tests/LinearSolvers/C_NodalMG/test_grids/gr3.rz Tests/LinearSolvers/C_NodalMG/test_grids/gr3a Tests/LinearSolvers/C_NodalMG/test_grids/gr3ann Tests/LinearSolvers/C_NodalMG/test_grids/gr3ann2 Tests/LinearSolvers/C_NodalMG/test_grids/gr3b Tests/LinearSolvers/C_NodalMG/test_grids/gr3c Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike.3 Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gr4 Tests/LinearSolvers/C_NodalMG/test_grids/gr4level Tests/LinearSolvers/C_NodalMG/test_grids/gt.32 Tests/LinearSolvers/C_NodalMG/test_grids/gt.bill1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.inputs.3d.spin.grids Tests/LinearSolvers/C_NodalMG/test_grids/gt.jbb.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sas Tests/LinearSolvers/C_NodalMG/test_grids/gt.scott.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.32 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.64 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3 Tests/LinearSolvers/C_NodalMG/test_grids/gt0 Tests/LinearSolvers/C_NodalMG/test_grids/gt010 Tests/LinearSolvers/C_NodalMG/test_grids/gt012 Tests/LinearSolvers/C_NodalMG/test_grids/gt016 Tests/LinearSolvers/C_NodalMG/test_grids/gt05 Tests/LinearSolvers/C_NodalMG/test_grids/gt1 Tests/LinearSolvers/C_NodalMG/test_grids/gt12 Tests/LinearSolvers/C_NodalMG/test_grids/gt12.2 Tests/LinearSolvers/C_NodalMG/test_grids/gt12.3 Tests/LinearSolvers/C_NodalMG/test_grids/gt2 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t1 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t3 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t4 Tests/LinearSolvers/C_NodalMG/test_grids/gt3 Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann2 Tests/LinearSolvers/C_NodalMG/test_grids/gt4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2.4.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2a Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.2.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.4.2 Tests/LinearSolvers/C_NodalMG/test_grids/gt5 Tests/LinearSolvers/C_NodalMG/test_grids/gt5s2 Tests/LinearSolvers/C_NodalMG/test_grids/gt5s4 Tests/LinearSolvers/C_NodalMG/test_grids/gt6 Tests/LinearSolvers/C_NodalMG/test_grids/gt6s Tests/LinearSolvers/C_NodalMG/test_grids/gt6s2 Tests/LinearSolvers/C_NodalMG/test_grids/gt6s4 Tests/LinearSolvers/C_NodalMG/test_grids/gt7a Tests/LinearSolvers/C_NodalMG/test_grids/gt7aa Tests/LinearSolvers/C_NodalMG/test_grids/gt8 Tests/LinearSolvers/C_NodalMG/test_grids/gt8a Tests/LinearSolvers/C_NodalMG/test_grids/gt8b Tests/LinearSolvers/C_NodalMG/test_grids/gt8c Tests/LinearSolvers/C_NodalMG/test_grids/gt8ms2 Tests/LinearSolvers/C_NodalMG/test_grids/gtbig Tests/LinearSolvers/C_NodalMG/test_grids/gtbig2 Tests/LinearSolvers/C_NodalMG/test_grids/gtbig3 Tests/LinearSolvers/C_NodalMG/test_grids/gtbig4 Tests/LinearSolvers/C_NodalMG/test_grids/gtbig5 Tests/LinearSolvers/C_NodalMG/test_grids/gtclearlarge Tests/LinearSolvers/C_NodalMG/test_grids/gtclearsmall Tests/LinearSolvers/C_NodalMG/test_grids/gtgrav2 Tests/LinearSolvers/C_NodalMG/test_grids/gtgrav4 Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb2 Tests/LinearSolvers/C_NodalMG/test_grids/gtpfail Tests/LinearSolvers/C_NodalMG/test_grids/gtrick commit aeef800a7bcd6838d589cf08566bca5f71b38678 Author: Ann Almgren Date: Tue Oct 8 12:28:47 2013 -0700 Removing the Src/LinearSolvers/C_NodalMG directory since this code is no longer used by any of the applications. Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/OpenSource.txt Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.2.f Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.2.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.f Src/LinearSolvers/C_NodalMG/hg_avg3d.f Src/LinearSolvers/C_NodalMG/hg_cg.cpp Src/LinearSolvers/C_NodalMG/hg_cg2d.f Src/LinearSolvers/C_NodalMG/hg_cg3d.f Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f Src/LinearSolvers/C_NodalMG/hg_proj2d.f Src/LinearSolvers/C_NodalMG/hg_proj3d.f Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit d3cba7d875424223c059c4246fd4bbefb10c8dde Merge: 014247c3a 724ae0ace Author: Michael Zingale Date: Mon Oct 7 19:23:39 2013 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 014247c3a1646a3dcaef5a62e09754ec1e545e98 Author: Michael Zingale Date: Mon Oct 7 19:22:22 2013 -0400 move the warning of dropping to piecewise constant prolongation if ir /= 2 up higher in the call stack so it is not output as much -- note: this does not affect MG. No output differences should occur except for a lot fewer warnings. Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 724ae0ace551bb74aa2c3b43bffa602b33f60224 Merge: e29e7b769 c802343b5 Author: lijewski Date: Mon Oct 7 16:21:42 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e29e7b769423b64472d6a9b8d91f04e742a40045 Author: lijewski Date: Mon Oct 7 16:20:47 2013 -0700 Don't thread over calls to setPhysBoundaryValues(). It doesn't play well with the Inflow code. Src/C_AMRLib/AmrLevel.cpp commit c802343b5dcb9b122f39da1ce8ddc402dddcb4bb Author: Ann Almgren Date: Mon Oct 7 14:13:23 2013 -0700 Put comments in the inputs.3d.nodal.dense and set ba_maxsize = 128 so at first this will have only one grid. Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense commit 5c3948c452e12571a4e58fe0276d397f37fbcfa2 Author: Ann Almgren Date: Mon Oct 7 14:08:11 2013 -0700 Create a new 3d nodal dense smoother -- subroutine nodal_smoother_3d_opt -- that can be used to experiment with optimizations having to do with not storing the stencils. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 30e0a236d267f01256acc8d2a4649da403ad8727 Author: lijewski Date: Mon Oct 7 13:28:06 2013 -0700 Inputs for nodal dense stencil test. Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense commit ac79074fa1fcd842cb13c3c6b474a1e196b7988d Author: Michael Zingale Date: Sun Oct 6 20:38:36 2013 -0400 change the way the defaults are indicated -- now we do a logical and output "[*]" via a merge instead of printing the default value alongside the current value. This is a lot easier to read. Tools/F_scripts/write_probin.py commit 447ba9f1ce3c1f9b7c8d928ccec8eff725eb2591 Author: Ann Almgren Date: Fri Oct 4 17:04:45 2013 -0700 We can now restart from a plotfile if the appropriate data has been stored in the plotfile. This works for both grid data and particles, but the application must be in charge of making sure it can find the data that it needs. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit ac193cebce3c01e474daaae51fa415c9a5c52c8c Author: lijewski Date: Thu Oct 3 14:53:18 2013 -0700 Uses can now choose single -vs- double precision at compile time. The C preprocessor symbol BL_SINGLE_PRECISION_PARTICLES, when defined at compile time causes floating point particle data to be stored as floats instead of the default, which is doubles. Src/C_AMRLib/Particles.H commit 8ec807a24fcefcd78ea10500247936c59b909b20 Author: lijewski Date: Thu Oct 3 14:27:59 2013 -0700 I'm now appended "single" or "double" to the version string in checkpoint files for particles. This allows me to know how they were written so that I can properly read them in. It thus gives us the ability to decide at compile time whether to use single or double precision for storing floating point data in particles. As of this commit all you have to do is edit Particles.H and change one typedef. To come will be a way to do this when compiling. The default floating-point precision as of this commit is back to double precision. Src/C_AMRLib/Particles.H commit b46a3dad7312bbf3ca64fbcde16c4cbb9dfe2711 Merge: cd670f134 c6972484f Author: Michael Zingale Date: Wed Oct 2 20:41:06 2013 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit cd670f1345a386dcdc758a8142fdede3cb74614f Author: Michael Zingale Date: Wed Oct 2 20:40:42 2013 -0400 add default values in [] in the print routine Tools/F_scripts/write_probin.py commit c6972484f7a6ee228933276deeb08f99e20f94b4 Author: lijewski Date: Wed Oct 2 14:37:26 2013 -0700 PeriodicShift() now returns bool indicating whether or not it shifted the particle. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 3cc2fe303c6dd031af290ed10f66b06c537c5030 Author: lijewski Date: Wed Oct 2 14:07:31 2013 -0700 When a particle is out of or on the boundary we now shift a fixed .125*CellSize() to try and get it back it. Got some strange precision issues with mixed float and double arithmetic. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 74e4904f85045743297cd5c387b7b4ccaf012ea6 Author: lijewski Date: Wed Oct 2 12:52:44 2013 -0700 Particles positions and data are now stored as floats instead of doubles. The code should be able to read old and new checkpoint files. Likewise it should be able to read binary double as well as binary float particle input files. Src/C_AMRLib/Particles.H commit 0cba9469c8d837babdbbd290f5230dbf99619399 Author: lijewski Date: Wed Oct 2 12:51:16 2013 -0700 Incremented version string for particles using float not double data. Src/C_AMRLib/Particles.cpp commit a5f6100fe7d0fb7ff56505d15c149e3956b1ea93 Author: lijewski Date: Wed Oct 2 10:22:55 2013 -0700 InitFromBinaryFile() can now automagically read either float or double data. Src/C_AMRLib/Particles.H commit c764f82846264e236c997a1ae02b79335430a54a Author: lijewski Date: Tue Oct 1 16:27:45 2013 -0700 More work on double -> float conversion. Src/C_AMRLib/Particles.H commit f07d166aa9efc65247c5fd370e5c42b8bc3f44f6 Author: lijewski Date: Tue Oct 1 16:18:27 2013 -0700 Some work storing/using real data in particles as float instead of double. Src/C_AMRLib/Particles.H commit 32cc164b27b16be39d3bb3180c7f461fd17a6001 Author: Ann Almgren Date: Tue Oct 1 15:18:38 2013 -0700 This change defines USE_PARTICLES instead of BL_USE_PARTICLES -- this is the flag that is seen in the rest of the code. Tools/CMake/CCSEOptions.cmake commit 59f6503c44f6d7441796fe0de6bac4e9c5be811c Author: Ann Almgren Date: Tue Oct 1 11:12:40 2013 -0700 Add ParticleBoxArray option for AdvectWithUmac. Src/C_AMRLib/Particles.H commit 76fac8eff863dfd68a09dfe71ba10be71d5ad296 Author: Ann Almgren Date: Mon Sep 30 21:36:53 2013 -0700 Must remember to make the particle DistributionMap on restart as well as on initialization -- put that section of code into a new routine, make_particle_dmap, which is called from init and from restart. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit d10713c754250d8f8ea7ad978b2a722cff0b228b Author: Ann Almgren Date: Mon Sep 30 16:54:56 2013 -0700 Decided we don't need to worry about copy on ghost cells as long as we copy after the temporary mf has completed SumBoundary. Src/C_AMRLib/Particles.H commit c77d74c0bc7985d5a12387e81dfec9e6ae04a495 Author: Ann Almgren Date: Mon Sep 30 16:38:42 2013 -0700 This version has the working multilevel AssignDensity which allows for particle_grids != grids. Still not sure what to do about ghost cell copies though. Src/C_AMRLib/Particles.H commit 6df6e56c7329afd8062f4618aa7f584b4d96520c Merge: 8e14b6cc2 586687569 Author: Ann Almgren Date: Mon Sep 30 12:44:53 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8e14b6cc2778b919427a96a3cb43b5393fcdccd7 Author: Ann Almgren Date: Mon Sep 30 12:43:14 2013 -0700 Inside addOneParticle, if a particle seems to be on the domain boundary we move it slightly inside. Src/C_AMRLib/Particles.H commit 586687569325d599cb008a3c1f1e1c2be2108878 Author: Matthew Emmett Date: Mon Sep 30 09:57:36 2013 -0700 Remove MLSDC from BoxLib (moved to RNS). Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/MLSDCAmr.cpp Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_AMRLib/Make.package commit b4fbbd08f50f50639644d3bc1016f15e2dd24ae6 Author: Matthew Emmett Date: Mon Sep 30 09:54:45 2013 -0700 Add setMidData. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 16e90f7768365682a2a1f13c2f152960a540ef0a Author: Ann Almgren Date: Mon Sep 30 08:59:27 2013 -0700 Back out latest changes to get this to work again. Src/C_AMRLib/Particles.H commit 5bf99a3dbd122e58c8f5f0bfee1416a11fc81f74 Author: Ann Almgren Date: Mon Sep 30 08:50:39 2013 -0700 Allow the particles to live on a different boxarray than the grid data lives -- this is particle_grids as opposed to grids. The default for now is that the boxarrays are identical. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 17114cc2c1b0337803256bad8baaa8b45e9f5ad4 Author: Weiqun Zhang Date: Fri Sep 27 13:22:47 2013 -0700 optimization of the 5th-order interpolator Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 5bb660c3d5f6e52a687448f0ac50a8bdc0c1a278 Author: Weiqun Zhang Date: Fri Sep 27 11:07:09 2013 -0700 5th-order interpolation in 3D Src/C_AMRLib/INTERP_3D.F commit 15c00d42c832de9d40374cecfd43223eb4a9dfb8 Merge: 539a89ce9 244bc86a0 Author: Ann Almgren Date: Fri Sep 27 08:23:27 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 539a89ce96227093d98368d976090ce144baf25a Author: Ann Almgren Date: Fri Sep 27 08:22:29 2013 -0700 Modify the test at the end of moveKickDrift so that particles at level 0 flying along at cfl > 1 can leave a grid and not have their velocities and positions correctly updated, but still not get lost entirely. Src/C_AMRLib/Particles.H commit 244bc86a03625969fde27730872b1ba1908b92a2 Merge: 6661744a4 393583d8f Author: Weiqun Zhang Date: Thu Sep 26 22:17:42 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6661744a4fbd6d55eb653678c3c24ba8dd024acd Author: Weiqun Zhang Date: Thu Sep 26 22:12:29 2013 -0700 added 5th-order interpolation based on quartic polynomial dimension by dimension; so far 1D and 2D are implemented; Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit 393583d8f549e9f130527e03fb30688e4b8e4341 Author: lijewski Date: Thu Sep 26 15:54:03 2013 -0700 Little more tweaking of output in InitFromBinaryMetaFile() Src/C_AMRLib/Particles.H commit 7ae21fa76ceb71fd726cc0651f1b94bd2a7f1f1c Author: lijewski Date: Thu Sep 26 15:41:53 2013 -0700 Added some verbosity. Src/C_AMRLib/Particles.H commit f2f8b536a3fde6079f9df8e06cb613e84e949174 Author: lijewski Date: Thu Sep 26 15:38:42 2013 -0700 Added InitFromBinaryMetaFile(). Src/C_AMRLib/Particles.H commit 18b17f750aa4ea68c5f933bcd75f9169b4341878 Author: Ann Almgren Date: Thu Sep 26 12:52:02 2013 -0700 Restore DistributionMapping.{H,cpp} to be the same as before the previous commit -- we don't need that extra define after all. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit ec4f9d656b5dce42fc7aa8f03bb0bb9a80b09520 Author: vince Date: Thu Sep 26 11:16:14 2013 -0700 proximity mapping tests. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.cpp Tools/C_mk/Make.Linux commit 3d887e647f456471b287436ecbadc497a72656f0 Author: Ann Almgren Date: Thu Sep 26 10:07:47 2013 -0700 Remove left-over print statement when particles left the domain before being periodically shifted back in. Src/C_AMRLib/Particles.cpp commit 163228ee5fe388df0556af3db58229dbf18bced2 Author: Ann Almgren Date: Thu Sep 26 09:17:24 2013 -0700 Add a new version of DistributionMapping::define which takes an already-made pmap as an argument. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit f80372f3a0a23f5e8dacadc542190e66b8810f65 Merge: 6804de4fc 21410eb94 Author: vince Date: Tue Sep 24 12:44:58 2013 -0700 Merge branch 'master' into commprof commit 21410eb944523da5067a73183a3b253ccc88db87 Author: Michael Zingale Date: Tue Sep 24 10:07:54 2013 -0400 update Maestro tests Tools/RegressionTesting/Maestro-tests.ini commit ffecfd932b198cac595bf154d07e920f60279722 Author: Michael Zingale Date: Fri Sep 20 13:50:00 2013 -0400 fix globalAddToExecString Tools/RegressionTesting/testnew.py commit d0785d1d4d10ff7b2287d2011c70e35d72aa3b48 Author: lijewski Date: Fri Sep 20 09:29:40 2013 -0700 Remove GETPLANE. Src/F_BaseLib/fabio_c.c commit b530dfae3a7c8602d86df14f02b0f62718d77b04 Merge: 12bea5320 9046677e1 Author: jbb Date: Thu Sep 19 20:06:27 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 12bea5320767975c64846187f57975eb71bf1272 Author: jbb Date: Thu Sep 19 20:05:46 2013 -0700 fixed bug in check of uniform mesh Src/LinearSolvers/F_MG/mg.f90 commit 9046677e16948a78535e83168700cf2b3f07d09f Author: Weiqun Zhang Date: Thu Sep 19 17:12:46 2013 -0700 made the regression testing script write out correct html page in the case variables names contain special characters "<" and ">". Tools/RegressionTesting/testnew.py commit 1c7ebd8804f1f3912b3a1fcd588845f542ad034f Merge: 79deeb35a b4d9c0c53 Author: jbb Date: Thu Sep 19 10:47:34 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b4d9c0c53d961a9184a6b43257c57a5b45211dfd Merge: f7d3e1cef 4854c02d4 Author: Marc Day Date: Wed Sep 18 17:30:09 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit f7d3e1cef8bac451914be36494219570cb4b5fd2 Author: Marc Day Date: Wed Sep 18 17:30:00 2013 -0700 Fix up declaration/define strings with D_DECLs, fix CMakeLists.txt to properly remove Particle stuff is BL_USE_PARTICLES is set to 0 Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/Particles.H commit 4854c02d467951365a7d2bf3599c8c6577242db4 Merge: e29c9eaec 000e0fac9 Author: Ann Almgren Date: Wed Sep 18 15:58:36 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e29c9eaec00b556bfb93231639cb1b448ab9c711 Author: Ann Almgren Date: Wed Sep 18 15:57:35 2013 -0700 Fixed up the case when the domain is not periodic and particles live in the cell next to the domain boundary. Before this wasn't allowed; now if we set the flag "allow_particles_near_boundary" to true then the particles can live in those cells, but the part of their contribution to AssignDensity that falls outside the domain will be ignored. Src/C_AMRLib/Particles.H commit 000e0fac95241cceb7e6b7da0dc0294491beb907 Merge: 99926f67c 6069e79b9 Author: lijewski Date: Wed Sep 18 15:20:30 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 99926f67cca9001c9bfcde4f279cb8c0ec504dc4 Author: lijewski Date: Wed Sep 18 15:18:10 2013 -0700 Some work on FORT_GETPLANE(). This is needed to implement INFLOW on the F90 side of the house. It's a translation of IAMR/Source/INFLOW/inflow.cpp. It's not done yet as there's an issue with "long" int values. We don't currently use such things, but the offsets into turbulence files in 3D get bigger than can be held in a standard Fortran integer. Src/F_BaseLib/fabio_c.c commit 6069e79b9a3ef1a7e0abe46a8a27d8553a55fc58 Author: Marc Day Date: Wed Sep 18 12:49:45 2013 -0700 up the tagged version num Tools/CMake/BoxLib_Version.cmake commit 99faad02f872880bf99928502433f2b37097aca8 Author: lijewski Date: Wed Sep 18 12:46:52 2013 -0700 Changed mpi module name to fboxlib_mpi so not to conflict with system-supplied names. Src/F_BaseLib/parallel.f90 Src/F_BaseLib/pingpong.f90 commit 42ba19b714c7d9684ae2e782a686c0abf9ba390a Author: Marc Day Date: Mon Sep 16 16:58:13 2013 -0700 Redo CMake stuff to more properly use command-line options to the cmake command for setting/overriding defaults CMakeLists.txt Tools/CMake/CCSEOptions.cmake Tutorials/MultiGrid_C/CMakeLists.txt commit 971e67c3192f6249a7b10b7295021f56fffc4b60 Author: Weiqun Zhang Date: Mon Sep 16 09:29:39 2013 -0700 Made AmrLevel::addOneParticle not pure so that classes derived from AmrLevel can be instantiated without implementing addOneParticle. Src/C_AMRLib/AmrLevel.H commit 59ca02bdafc0f2314d8c9d87ae66d1e624cd5815 Merge: df4e3075c fa60838f8 Author: Ann Almgren Date: Fri Sep 13 11:43:29 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit df4e3075c0e7545ab037a9bf9ca816be861fc3f8 Author: Ann Almgren Date: Fri Sep 13 11:42:43 2013 -0700 Modify Amr and Particle classes to allow Amr to be defined from an outside class and not to read from inputs file. Also allow particles to be copied in one by one. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit fa60838f809f20f7015c6835eae3b1e1863ce49a Author: lijewski Date: Fri Sep 13 10:04:14 2013 -0700 Added constructors to FabArray and MultiFab that take a DistributionMap. This way folks don't have to do the usual two-step process of creating a MultiFab and then calling define() if they want to specify their own DistributionMap. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 3ed20f94aa677b8de47e3432d1ef0a69bd41b72d Merge: 912dc6043 7f63035e2 Author: Ann Almgren Date: Thu Sep 12 16:00:13 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 912dc60434e76884b0a879dd91b47c428911cdf8 Author: Ann Almgren Date: Thu Sep 12 15:59:54 2013 -0700 Make the minimum physical box size 1.e-8 instead of 1.e-6. Src/C_BaseLib/RealBox.cpp commit 6804de4fcf02664e7cde12ed3452b064292582e5 Author: vince Date: Thu Sep 12 15:44:17 2013 -0700 procnums and names. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 7f63035e210582dc5ad6ebc086a27ac4087e331c Author: Marc Day Date: Thu Sep 12 12:29:08 2013 -0700 Add usage comment, remove debugging note CMakeLists.txt Tools/CMake/InstallManager.cmake Tutorials/MultiGrid_C/CMakeLists.txt commit 685922dc94d363e966060ada160d501112d1eb02 Merge: 53099d016 9d40f4f61 Author: Marc Day Date: Thu Sep 12 12:16:53 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 53099d0169e9065af09e99a7f030dba02405e6c8 Author: Marc Day Date: Thu Sep 12 12:16:43 2013 -0700 never-ending mods to cmake files... CMakeLists.txt Src/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Tools/CMake/CCSEOptions.cmake Tools/CMake/FindCCSE.cmake Tools/CMake/InstallManager.cmake Tutorials/MultiGrid_C/CMakeLists.txt commit 9d40f4f6127abaa3639172b6b1fc008283995497 Author: Ann Almgren Date: Thu Sep 12 11:32:47 2013 -0700 Allow us to initialize an AMR object with RealBox and coord already set so we don't have to parmparse those in Geometry. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 3e0fedeabce3e0657a4b97732ab752e8643cd3f1 Author: Ann Almgren Date: Thu Sep 12 10:02:25 2013 -0700 Add domain vs lev0_grids check in defBaseLevel. Src/C_AMRLib/Amr.cpp commit 722ca85420f7ab5057ff7cdeb7bf024d4705ccaf Author: lijewski Date: Thu Sep 12 08:38:33 2013 -0700 Consolidated the two versions of initialInit() and defBaseLevel() into single routines. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 92c8956cc619d1602a867f027fcea8cb2d7b9f67 Merge: 094ba4536 3b9d54b21 Author: Ann Almgren Date: Wed Sep 11 17:19:32 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 094ba4536c44dd775b3d6f44d729f7094cb0d049 Author: Ann Almgren Date: Wed Sep 11 17:18:45 2013 -0700 Add versions of init, initialInit and defBaseLevel that take both a BoxArray and a pmap. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 3b9d54b21fb3be0d2a8caa92e260829d03ee8c74 Author: Marc Day Date: Wed Sep 11 16:48:49 2013 -0700 Update version file Tools/CMake/BoxLib_Version.cmake commit d084ab5733b7761d4b91aa57280d7679a0735f18 Author: Marc Day Date: Wed Sep 11 16:42:55 2013 -0700 ick...more hacking on cmake CMakeLists.txt Tools/CMake/BoxLib_Version.cmake Tools/CMake/InstallManager.cmake commit cd6569d33774b6c31544ceb804938746b7e95242 Merge: b05593c08 7de30444d Author: Marc Day Date: Wed Sep 11 15:52:21 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit b05593c08b7f9c81d311c8da9a6b97805010a5fb Author: Marc Day Date: Wed Sep 11 15:52:13 2013 -0700 Final twiddling of CMake files for now (I hope) CMakeLists.txt Tools/CMake/BoxLib_Version.cmake Tools/CMake/CCSEOptions.cmake Tools/CMake/InstallManager.cmake Tools/C_scripts/gen_release_tarball commit 7de30444dcf652e1ae199c867abb5ec9c97b0127 Merge: 11437bdc4 779f0784d Author: lijewski Date: Wed Sep 11 15:18:35 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 11437bdc4b9c7a866c1a9c42ecb22a56d2c948ad Author: lijewski Date: Wed Sep 11 15:17:23 2013 -0700 Added ability to pre-load the distribution mapping cache by simply building a DistributionMapping with a pmap and asking for it to be added to the cache. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 779f0784df4ea975a5000acd1ab831a8414305e0 Author: Ann Almgren Date: Wed Sep 11 14:16:02 2013 -0700 Make the first lines of DM/Header in a plotfile be the same as the first lines of DM/Header in a checkpoint file. Src/C_AMRLib/Particles.H commit de5e5f03aa14fe55768a7eb46bd2a500d6b18c99 Author: Ann Almgren Date: Wed Sep 11 13:07:29 2013 -0700 Clean up Solver.cpp and add contact info for Tulin. Tutorials/AMR_Trilinos_C/README Tutorials/AMR_Trilinos_C/Solver.cpp commit 78e363325dfa75a7c9dbca1b5a1944845df98da1 Author: Marc Day Date: Wed Sep 11 10:31:46 2013 -0700 More tweaks to CMake files Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 0acb7e688d872c0a14e5aae92539156ddadccea6 Author: Marc Day Date: Wed Sep 11 10:16:38 2013 -0700 Add a couple tests to the CCSEOptions to be sure stuff is defined Tools/CMake/CCSEOptions.cmake commit eda0e9008ede8320960cbcc89435c0121c355938 Author: Marc Day Date: Wed Sep 11 09:45:30 2013 -0700 Small mods working with Andreas Src/C_AMRLib/Particles.H Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/FabSet.H commit b68eaef35be3fd26f28ce8ff1f2d0bd11578b3e5 Author: Marc Day Date: Wed Sep 11 01:18:03 2013 -0700 CMake install the mod files Src/CMakeLists.txt commit 7ad9bdc6d0e47daf332682d5024ab8f0d2d82e54 Author: Marc Day Date: Wed Sep 11 00:41:49 2013 -0700 Start to collect BL_DEFINEs throughout, and set some defaults CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit b2d4666d54ea6b8e18ed5e49cd36173ee3142d24 Author: Marc Day Date: Tue Sep 10 23:56:02 2013 -0700 Add buildInfo.H to install CMakeLists.txt commit 169b7d29eeff62e30a5d7529bf58040562199673 Author: Marc Day Date: Tue Sep 10 18:47:50 2013 -0700 Add Particles.cpp and Particles.H to CMakeLists Src/C_AMRLib/CMakeLists.txt commit 17e469a78c3b5891ab08e565b330485137ca98f6 Author: Marc Day Date: Tue Sep 10 18:12:24 2013 -0700 Consolidate all the CMake-built C++ libs into one using the OBJECT library feature post 2.8.8 CMakeLists.txt Src/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Src/C_BoundaryLib/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit c2acf0b9f51d940b35901163babfaa4330a9aadb Merge: e4c6ecb43 2aefba4c0 Author: Marc Day Date: Tue Sep 10 15:31:01 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2aefba4c0b120e98b7d08000eb03c3b474b7dec9 Merge: b6bbaecf4 8c0c8dcf0 Author: lijewski Date: Tue Sep 10 14:57:12 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit b6bbaecf4fd6d3209d76a53aa4ce1c4dd721c57b Author: lijewski Date: Tue Sep 10 14:56:26 2013 -0700 Some cleanup using latest gnu compiler on edison. Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/cluster_f.f90 commit e4c6ecb43aaededd1b7afbeb679181de36668aba Author: Marc Day Date: Tue Sep 10 14:26:45 2013 -0700 Working cmake a bit...in progress CMakeLists.txt Src/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 8c0c8dcf062b7d15baa8c34b59ee81b0233d391b Author: Ann Almgren Date: Tue Sep 10 13:23:33 2013 -0700 Add comment about RHS and SOLN and visualizing these. Tutorials/AMR_Trilinos_C/README commit bd8c6d2d0dbc9c36db55caa808d2dd9f71c7082c Merge: ddaf6d709 9c35e04c8 Author: Ann Almgren Date: Tue Sep 10 13:21:11 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ddaf6d70991b2faeba3be20737eaf448f1fb8cf2 Author: Ann Almgren Date: Tue Sep 10 13:20:48 2013 -0700 Tutorial example of how to call a Trilinos solver (Epetra) from a BoxLib C++ code. Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/AMR_Trilinos_C/Make.package Tutorials/AMR_Trilinos_C/README Tutorials/AMR_Trilinos_C/Solver.H Tutorials/AMR_Trilinos_C/Solver.cpp Tutorials/AMR_Trilinos_C/SolverBoundary.cpp Tutorials/AMR_Trilinos_C/driver.cpp Tutorials/AMR_Trilinos_C/inputs Tutorials/AMR_Trilinos_C/writePlotFile.H Tutorials/AMR_Trilinos_C/writePlotFile.cpp commit 9c35e04c849400cf08c77f9729511087988cc260 Author: Weiqun Zhang Date: Tue Sep 10 12:23:01 2013 -0700 merged 2 MPI_Bcast into 1 Src/C_AMRLib/Amr.cpp commit 0acfc7802d48f8c23b7740bfa9f353579f09e8fc Author: Marc Day Date: Fri Sep 6 20:12:37 2013 -0700 Small changes...one for portability to CGSolver.cpp (works on the machines I tested...let me know if it fails on yours), and few virtuals added to MCLinOp.H to ease extensions to other cases, and a slight redef of a CMake oddity...anyone love CMake as much as I do? Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Tools/CMake/PreprocessBoxLibFortran.cmake commit f0d0efd1d4febb92f08a718701791fb0733b6a42 Author: Marc Day Date: Fri Sep 6 19:04:55 2013 -0700 Revert "Small changes...one for portability to CGSolver.cpp (works on the machines I tested...let me know if it fails on yours), and few virtuals added to MCLinOp.H to ease extensions to other cases, and a slight redef of a CMake oddity...anyone love CMake as much as I do?" This reverts commit fd5ca5be470f61cc3ee8696734886ee72d4423aa. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Tools/CMake/PreprocessBoxLibFortran.cmake commit fd5ca5be470f61cc3ee8696734886ee72d4423aa Author: Marc Day Date: Fri Sep 6 18:12:08 2013 -0700 Small changes...one for portability to CGSolver.cpp (works on the machines I tested...let me know if it fails on yours), and few virtuals added to MCLinOp.H to ease extensions to other cases, and a slight redef of a CMake oddity...anyone love CMake as much as I do? Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Tools/CMake/PreprocessBoxLibFortran.cmake commit 7346d93bbd394e91b68845e7993a28286b853e14 Author: Michael Zingale Date: Fri Sep 6 13:01:41 2013 -0400 find the / detection fextract.f90 commit 145ac8ffa1451e426c7028a99d557450e843e8dc Author: lijewski Date: Wed Sep 4 15:15:02 2013 -0700 Reduced the amount of data transferred via MPI in the Reflux() routines to the bare minimum. Previously Cy noticed that we "ship" more data than needed. We were sending a full FluxRegister boundary data set whenever some coarse FAB needed any of its data. This was due to the difficulty of figuring out intersections of cell-centered entities with face-centered ones. I've checked it with HyperCLaw and LMC. We'll see if the regression tests turn up anything. Src/C_AMRLib/FluxRegister.cpp commit b13670cdebeba00d2e166bad651493936e17fbba Author: vince Date: Tue Sep 3 14:04:07 2013 -0700 added interface callable from f90. Src/C_BaseLib/BLProfiler_F.f Src/C_BaseLib/Make.package Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 3919d17f0f5a327d154082492651aab65daecf39 Author: Ann Almgren Date: Fri Aug 30 12:26:30 2013 -0700 Add interface to estTimeStep in Particles.H that doesn't take "a" Src/C_AMRLib/Particles.H commit 6baa30aae5f62f6a2f2965ee2f83013d65d92da1 Author: lijewski Date: Fri Aug 30 08:23:29 2013 -0700 Minor bug fix. Wasn't properly indicating "good" failure of CABiCGStab back to the MG solver when we want to do additional smooths. I noticed this when a case I was running was doing additional bottom smooths in the BiCG case but was not in the CABiCG case. Curiously, in that case, both the CiCG and the CABiCG MG solves converged in the same number of iterations. The additional smooths done when the BiCG didn't solve the bottom problem to the requested precision, didn't do much of anything, except waste time. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 611715b869b3d890a752a5702ab726b3e9ecf1c2 Merge: 87d070e0c 90d485a37 Author: Marc Day Date: Thu Aug 29 00:45:08 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 87d070e0c297486d5cb2abf91bbb9297e6688b47 Author: Marc Day Date: Wed Aug 28 20:02:16 2013 -0700 more minor mucking with cmake Src/LinearSolvers/C_TensorMG/CMakeLists.txt commit ddda8fdfb6a431ebd0ec658b4f91b05de52d8ed7 Author: Marc Day Date: Wed Aug 28 19:45:37 2013 -0700 minor mucking with cmake Src/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt commit 90d485a37b4cfa428453507d52ed65871bdb098d Author: lijewski Date: Wed Aug 28 13:31:33 2013 -0700 Now use trilinear interp instead of piecewise constant. Src/LinearSolvers/C_CellMG/MG_3D.F commit 6967154f5b363a672fd4ded4750aa4cabb076c23 Author: lijewski Date: Wed Aug 28 11:58:52 2013 -0700 Now use bilinear interp instead of piecewise constant. Src/LinearSolvers/C_CellMG/MG_2D.F commit 4c31c5ad8916bcc9498ddad172966f0ee3678532 Author: Marc Day Date: Mon Aug 26 20:58:48 2013 -0700 Moved function into MCLO_3D.F Src/LinearSolvers/C_TensorMG/DV_3D4.F commit b47cf54cbae2190c6969877393f8434c20a5d5ef Author: Marc Day Date: Mon Aug 26 20:42:55 2013 -0700 Small changes to tensor solver code to enable generalization to similar, but different, systems Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLO_3D.F Src/LinearSolvers/C_TensorMG/MCLO_F.H Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Make.package commit f1e40111713d5416c35bfcd960893fe463ae7f1f Author: vince Date: Mon Aug 26 16:17:27 2013 -0700 additions so compiles work with mpi/prof/commprof on/off. Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/ccse-mpi.H commit d034bc900a705d9da38c81b5d83ec209dda59813 Author: Michael Zingale Date: Sat Aug 24 14:21:21 2013 -0400 if a job_info file exists, store its contents (commented out) at the end of the slice file -- this gives us context fextract.f90 commit fe330e16b9ccb5bd6e9e415a0f05db8e7b21df1e Author: Michael Zingale Date: Sat Aug 24 13:56:44 2013 -0400 depreciate the "-p" option and allow a plotfile to be specified at the end of the commandline -- this is more in line with the other routines fextract.f90 commit ad2dd6ad271f27e15f9459bdc789bf19414fe582 Author: vince Date: Fri Aug 23 12:34:57 2013 -0700 added amr init information. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 37d1de0f9268f7fa9ddfba5e49e6b3237638ea7c Author: vince Date: Thu Aug 22 16:00:00 2013 -0700 version support, global header file, procnames. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 98eae4aa343800220f6c7708a67e649c4ca0023f Merge: 01ff1a202 91b2704e2 Author: vince Date: Thu Aug 22 12:41:25 2013 -0700 Merge branch 'master' into commprof commit 91b2704e2b6a4bedc8dfc7b56505d586157c0846 Author: Matthew Emmett Date: Tue Aug 20 14:59:28 2013 -0700 Make regrid virtual, add InitAmr routine to avoid repetition. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 01ff1a20231d06db693f7e4bbccdb1d7cb1475c8 Author: vince Date: Fri Aug 16 15:51:16 2013 -0700 more in-situ, on/off, noprof, prof, commprof. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit bdae32d5a003f7070916a93d8e30aa91b20af331 Author: Jonathan Wang Date: Fri Aug 16 10:38:43 2013 -0700 Changed REaDME Tutorials/MultiGrid_F/README commit d46257269787ebdf253b8658d2acbefe38cb7d4a Author: Jonathan Wang Date: Fri Aug 16 10:37:50 2013 -0700 Added 3d inputs files Tutorials/MultiGrid_F/inputs_fmg_lin_3d Tutorials/MultiGrid_F/inputs_fmg_pc_3d Tutorials/MultiGrid_F/inputs_v_lin_3d Tutorials/MultiGrid_F/inputs_v_pc_3d commit da1e5c2817ae9881f5fdd78e9f34b9ef0504256c Author: vince Date: Thu Aug 15 14:55:11 2013 -0700 more in-situ support. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/ccse-mpi.H commit f4e7deb456ea7ac259827c41b34a858b91288303 Merge: d7bbc61dc 31f91ddac Author: Jonathan Wang Date: Thu Aug 15 13:16:58 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d7bbc61dc199d75719ed335a82b5ba96db935005 Author: Jonathan Wang Date: Thu Aug 15 13:16:05 2013 -0700 Remove executables; added parallel_IOProcessor to fmg_cycle.f90 Tutorials/MultiGrid_F/fmg_cycle.f90 Tutorials/MultiGrid_F/main.Linux.gfortran.exe.REMOVED.git-id Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe.REMOVED.git-id commit 31f91ddac88ec3df444c72faf71f94ebc6053c0e Author: Ann Almgren Date: Thu Aug 15 11:13:34 2013 -0700 Only print memory stats if we set memory_verbose = .true. Tutorials/MultiGrid_F/main.f90 commit 378dbf43194a6a70b27cb3aa8dd80730f6928b04 Author: Ann Almgren Date: Thu Aug 15 11:08:41 2013 -0700 1) Don't want to have executables in the repo. 2) Don't need GPackage.mak since the files are listed in the GNUmakefile. Tutorials/MultiGrid_F/GNUmakefile Tutorials/MultiGrid_F/GPackage.mak Tutorials/MultiGrid_F/main.Linux.gfortran.exe.REMOVED.git-id Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe.REMOVED.git-id commit aae84d6b788db5ea4ceb3f79010f13b1d8644f6a Merge: 5f7660940 71a9d0321 Author: Jonathan Wang Date: Thu Aug 15 11:03:39 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5f76609409d47849671f34744e8426caf41b12b3 Author: Ann Almgren Date: Thu Aug 15 11:01:32 2013 -0700 New Tutorial for fortran 90, multigrid, Jonathan Tutorials/MultiGrid_F/GNUmakefile Tutorials/MultiGrid_F/GPackage.mak Tutorials/MultiGrid_F/README Tutorials/MultiGrid_F/constants.f90 Tutorials/MultiGrid_F/cycle_tower.f90 Tutorials/MultiGrid_F/fmg_cycle.f90 Tutorials/MultiGrid_F/init_coeffs.f90 Tutorials/MultiGrid_F/init_rhs.f90 Tutorials/MultiGrid_F/inputs_fmg_lin_2d Tutorials/MultiGrid_F/inputs_fmg_pc_2d Tutorials/MultiGrid_F/inputs_v_lin_2d Tutorials/MultiGrid_F/inputs_v_pc_2d Tutorials/MultiGrid_F/main.Linux.gfortran.exe.REMOVED.git-id Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe.REMOVED.git-id Tutorials/MultiGrid_F/main.f90 Tutorials/MultiGrid_F/mt19937ar.f90 Tutorials/MultiGrid_F/solve.f90 Tutorials/MultiGrid_F/traverse.f90 Tutorials/MultiGrid_F/v_cycle.f90 commit 71a9d0321e1d9a8c86c006980f9645e22a25abae Author: vince Date: Wed Aug 14 09:52:40 2013 -0700 and an mpilib.... Tools/F_mk/GMakeMPI.mak commit ba17a1e94e9ebc72eb05a31316d44df30e52e131 Author: vince Date: Wed Aug 14 09:48:54 2013 -0700 and for fortran. Tools/F_mk/GMakeMPI.mak commit 4bc1ce87f6120ff57bb1424314a25ae726f56998 Author: vince Date: Wed Aug 14 09:45:00 2013 -0700 fix for gigan. Tools/C_mk/Make.mpi commit e9098e07a1cc2be447849e10cfb581f2c6721910 Merge: 68a80a8e3 395bf788c Author: vince Date: Thu Aug 8 15:06:42 2013 -0700 Merge branch 'master' into commprof commit 68a80a8e31674984c35fb713415c07741adbf805 Author: vince Date: Thu Aug 8 12:48:40 2013 -0700 working version of in-situ mpi process for dynamic optimization. the process doesn't do much yet, just rides along. not yet tested with the finalize function stack not empty. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 395bf788cab9e5da6d3c9e9b42a8e7677c9c2a85 Author: lijewski Date: Wed Aug 7 10:41:02 2013 -0700 Removed the qaxpy() stuff. It didn't appear to work properly. Not a big deal anyway. The dots() and sums() are the important stuff. Now to see if it makes any difference on real problems in parallel. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit fa135ceeb24e5fbe2f1bf16bb318132e84857119 Author: lijewski Date: Tue Aug 6 14:33:05 2013 -0700 In qsotxy() do the parallel reduction in quad precision by sending all the partial sums to the IO processor and having it do the sum in quad precision and then broadcast it back to the other processors. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 49350f1697459d2135f38d901d8cac8106d59fcb Author: lijewski Date: Tue Aug 6 13:57:33 2013 -0700 Some code rearrangement to get XBLAS & non-XBLAS code to coexist. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit a11ce8acec5e90e08b3c72d82e61a783e632b964 Author: lijewski Date: Tue Aug 6 13:42:48 2013 -0700 Added qdotxy(). Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 3ff7b93a56b893fb428406d264048605d893e691 Author: lijewski Date: Tue Aug 6 12:31:13 2013 -0700 Some work on adding a version of CABiCGStab that uses the quad precision routines from XBLAS. It's disabled at the moment so it shouldn't affect anyone. My plan is to see if a more accurate bottom solver can solve some problems with fewer iterations. It may also be the case that with a more accurate bottom solver we can up the max "S" in the CABiCGStab from 4 -> 8 or somesuch. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit ad85ec68b8a8b3f490024195883d0c6972d9ac9a Author: lijewski Date: Mon Aug 5 15:02:10 2013 -0700 Some code rearrangement to make some multi-level testing I'm doing easier. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 9e76c8827fe196b542db290247c9377fc0d97d47 Author: lijewski Date: Mon Aug 5 14:59:49 2013 -0700 Checked in some code that builds cfine in the cfine -> fine multilevel prolongation routines with one grow cell so that the interpolation doesn't have to do piecewise-constant interp on the grid boundaries. It's disable for now until I do more testing. Also added similar code for the nodal multi-level prolongate. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit c30ce2fefc2bbd6e1dedde50c07b2f7d590de2b3 Author: lijewski Date: Mon Aug 5 12:46:50 2013 -0700 Make lininerp the default for cell-centered interpolators. Src/LinearSolvers/F_MG/mg_tower.f90 commit d1b147f53a23ac80cf004d1889046c23e0857f0e Author: lijewski Date: Mon Aug 5 11:41:15 2013 -0700 Just a little code rearrangement. Src/LinearSolvers/F_MG/mg.f90 commit 9a666662bcc41fc199a626133867001f653c6f42 Author: lijewski Date: Mon Aug 5 11:22:06 2013 -0700 Changed how I impose BCs for #D CC interpolators. Src/LinearSolvers/F_MG/mg.f90 commit 90f9944b6079be910633a3b89adbbe50813444fd Author: lijewski Date: Mon Aug 5 09:50:38 2013 -0700 Changed how I impose 2D BCs for CC interpolators. Src/LinearSolvers/F_MG/mg.f90 commit 2f1f68c99cffad6fa17f0dca88e293f4e69c2b1c Author: lijewski Date: Thu Aug 1 15:22:05 2013 -0700 Some code rearrangement. Put the lininterp pys BC stuff into their own routines. Src/LinearSolvers/F_MG/mg.f90 commit 02c6c3c214c23559a5c2a9832cf57f05cd080f2c Author: lijewski Date: Thu Aug 1 14:08:32 2013 -0700 Some work on edges & corners for 3D lininterp. Src/LinearSolvers/F_MG/mg.f90 commit 48ad430e1ecdec46744f56de51893ecbf278e49e Author: lijewski Date: Thu Aug 1 10:26:51 2013 -0700 Work on getting corners right for 2D interp. Still got to do corners & edges for 3D. I'm checking this stuff in with the lininterp defaulting to FALSE. I want to get it pushed to the repo before I get too ahead of myself. Soon we'll want to default to lininterp but I'm not yet ready. Src/LinearSolvers/F_MG/mg.f90 commit 5b4e5d6c3a62cb4a91ca28d169005e5363f14198 Author: lijewski Date: Thu Aug 1 09:20:42 2013 -0700 Can now set linear or piecewise constant on command line or inputs file. Tests/LinearSolvers/F_MG/wrapper.f90 commit 3578598173ee359f1dd60fd434dca0efb7e13e70 Author: lijewski Date: Thu Aug 1 08:59:51 2013 -0700 mg tower now takes a "ptype" and we can set it on the command line or inputs file. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 96a8943fb685464794bd90b69d7646add26adb3e Author: lijewski Date: Thu Aug 1 08:06:49 2013 -0700 Added phys BCs to mg tower. Need'm to get BCs for lininterp. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 commit d7775fd47da02d8faebb56dd3d2baf1b340ad908 Author: lijewski Date: Wed Jul 31 13:30:25 2013 -0700 Added use_lininterp to mg_tower, defaulting to false. In mg_tower_build, if not passed as an argument, set it to true for 3D. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 55cdbe597962731acba6cbbb73203da7602ef413 Author: lijewski Date: Wed Jul 31 13:29:46 2013 -0700 Removed a reference to ml_cc_prolongation which isn't called from here. Src/LinearSolvers/F_MG/cc_applyop.f90 commit 75b67cd77fa153ed5d7f81f3285cff84f872100a Author: lijewski Date: Wed Jul 31 10:35:50 2013 -0700 Consolidated where all the various parameters for prolongaton are set. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 522b2b05cfdbbc5ee454ec5f2e5c830842f29ecf Author: lijewski Date: Tue Jul 30 17:04:31 2013 -0700 Fixed a calling sequence bug I recently introduced. Made the calling sequences for PC on linterp look like the stuff in mg.f90. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 873ff05c3527ee0b28cd967e967c239c3b69a61b Author: lijewski Date: Tue Jul 30 16:56:16 2013 -0700 A little cleanup. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit d20ff565f837cf0927160776205ee72b1e81fbd4 Author: lijewski Date: Tue Jul 30 16:09:51 2013 -0700 Some code rearrangement in mg_tower_prolongation. We should think about making linear interp the default for cell-centered. Src/LinearSolvers/F_MG/mg.f90 commit fa822fbbfc58e9636431db262840651a7376ca6e Author: lijewski Date: Tue Jul 30 15:55:21 2013 -0700 Changed the cell-centered lininterp routines to use ghost cells or not depending on how they're called. If the coarse fab has one grow cell it will use it, otherwise it'll use PC interp on the face cells and linear interp on the interior. Moved the setting of cc_ptype and nodal_cubic into mg_tower_prolongation. My testing showed that lininterp is a benefit, but only if you do it in both the F and V-cycles. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit d3ba32081b9d79f7081a5929c5a4b68c6357852e Author: lijewski Date: Tue Jul 30 14:55:45 2013 -0700 Bug fix. Src/LinearSolvers/F_MG/mg.f90 commit cfa44d21f4cbdc43b31f1790032e49756ffb99cd Author: lijewski Date: Tue Jul 30 13:45:54 2013 -0700 Added some commented out debugging code. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit ff7364983078205204c03ad916dc5c3dd7ca67c9 Author: lijewski Date: Tue Jul 30 13:36:14 2013 -0700 Tricubic interpolation also doesn't assume it has ghost cells. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit e60c74b4ca2e43b53635f399d1744e99316b8345 Author: lijewski Date: Tue Jul 30 13:30:06 2013 -0700 The bicubic will now call linear interp if it doesn't have enough grow cells, and then call itself on the interior. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 80b3646501882adcdb5fe8d363b2c3b8fb03162a Author: lijewski Date: Tue Jul 30 11:12:13 2013 -0700 Separated out the [bi,tri] cubic nodal prolongation stuff into own functions. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 6a995cc0a47f6275b5c62e2791943c56b3b61ffd Author: lijewski Date: Mon Jul 29 15:34:38 2013 -0700 Added some debugging code. Src/LinearSolvers/F_MG/ml_nd.f90 commit 49a62af5794bfeee3783b0899fe18212534a8820 Author: lijewski Date: Mon Jul 29 15:33:44 2013 -0700 mg.cycle_type is now ParmParse'd so we can pass it to F90 MG. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 8edf03a4957382de62c0aa3f51e4a1422dc6a755 Author: lijewski Date: Mon Jul 29 15:33:12 2013 -0700 Print out cycle_type when outputting settngs. Src/LinearSolvers/F_MG/mg.f90 commit 14150e1e08fe0c3a520dc74d564cfcf182f2cc5f Author: lijewski Date: Mon Jul 29 12:29:39 2013 -0700 Some cleanup. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit cb76b6ebea9c5613041e7d722d3861c55a8bbcc4 Author: lijewski Date: Fri Jul 26 17:38:49 2013 -0700 I "think" the tricubic interpolators are working. Still got more testing to do though. Checking'm in so I don't lose'm over the weekend. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit f99bdb81a9c2f095a6c88a9d3c3d1ac2d8d050f7 Author: lijewski Date: Fri Jul 26 17:14:26 2013 -0700 bicubic wasn't quite right on high nodes. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 6df575963b75af3a6fb0452e9f897f51286f15e9 Author: lijewski Date: Fri Jul 26 16:56:51 2013 -0700 More work on tricubic. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 7941eeee7db12f3030a70e8db48d670cbe943cf6 Author: lijewski Date: Fri Jul 26 16:10:30 2013 -0700 More prep work for tricubic. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit a07ae518d486d6d2186a4135db7b619b07e780b6 Author: lijewski Date: Fri Jul 26 15:31:46 2013 -0700 Some preparation for trying to implement tricubic nodal prolongators. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit ef46d899f58901927519aa7f321d66565ad32a5e Author: lijewski Date: Fri Jul 26 15:25:39 2013 -0700 Removed some divides. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit ff0f38e7adfcfed7a743e1c52759337bde9f2d6f Author: lijewski Date: Fri Jul 26 14:44:56 2013 -0700 Merged back in specialized unrolled PC interpolators for ir=2. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit d0969812e442f507373f5dc0be59d1a92e09bc7a Merge: 4c9b082ad 1ecae5aa9 Author: lijewski Date: Fri Jul 26 14:22:54 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4c9b082adbb4572d89a5223f36f669a66831e6de Author: lijewski Date: Fri Jul 26 14:15:27 2013 -0700 The multi-level solves now have the ability to call either the piecewise constant or linear prolongators, just like in the multigrid code proper. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit c1209ce40c52c7888668075cd43de26e4f879d20 Author: lijewski Date: Fri Jul 26 14:01:46 2013 -0700 Made the multigrid and multi-level solves both call the same piecewise constant cell-centered prolongators. Used the interface of the multi-level solves and integrated those into the multigrid ones. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 1ecae5aa9f3879416f436964a23b27b2ad3b9de0 Author: vince Date: Fri Jul 26 10:32:03 2013 -0700 fix for intel on gimantis. Tools/C_mk/Make.defs commit 09d9bc46de58ae6575d1fa76fe6194f5451d72b2 Merge: 862fbe01f 4f0e3edcf Author: lijewski Date: Thu Jul 25 15:28:11 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 862fbe01f7c0fa0fc29628faa512158cb3d7cff7 Author: lijewski Date: Thu Jul 25 15:25:56 2013 -0700 Checked in specialized nodal_prolongation_2d(). This mirrors the 3D one in that it minimized the number of arithmetic operations. It was my starting point for developing the bicubic. Might as well use it when ir=2. It'll be faster, but both it and the 3D version may produce slightly different numbers due to floating point roundoff compared to the more general versions. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 8e55aae4003e55033d3dd158ebd1f7583aa6f81c Author: lijewski Date: Thu Jul 25 15:11:47 2013 -0700 Specialized version of nodal_prolongation_3d that assumes ir=2. It minimizes the number of arithmetic operations and doesn't need a temporary allocatable array. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 29171c2ed000fcf3a21598a46d248bafdc8511b2 Author: lijewski Date: Thu Jul 25 14:45:40 2013 -0700 Got bicubic working again (but checked in disabled). Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 86925e0188bff401d5a8bfc3772d8d6e0029e422 Author: lijewski Date: Thu Jul 25 12:30:19 2013 -0700 We now use the nodal prolongators in mg_prolongate. Got to do the same for cell-centered. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 15da49f0de12ecb04f2749917de3d1ab73b4d177 Author: lijewski Date: Thu Jul 25 11:18:25 2013 -0700 Rewrote interfaces to nodal prolongation routines. I want to call the routines in mg_prolongation in ml_prolongation. No need to have duplicated routines lying around. I like to see if bicubic has any effect in 2D multi-level solves too. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 4f0e3edcf1d5b3da9610d72480efa29ca12bb554 Author: Matthew Emmett Date: Thu Jul 25 10:40:16 2013 -0700 MLSDC: Add multi-level SDC files (work in progress). Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/MLSDCAmr.cpp Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_AMRLib/Make.package Tutorials/.gitignore Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Advection_C/Source/main.cpp commit ae7906899c364713dd365cab6a9acb96a01e6190 Author: lijewski Date: Wed Jul 24 17:08:40 2013 -0700 Had a bug in how cc() was dimensioned in nodal progate 3D. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit e89d0bf8ddadcc3da9ce53012e19ad76043b93d4 Author: lijewski Date: Wed Jul 24 16:47:26 2013 -0700 Implemented classic #D full-weighting restriction. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit cd810d276767c93340e3027f03da7092bbdc1e12 Author: lijewski Date: Wed Jul 24 16:47:04 2013 -0700 Removed those HACK multiplies after restrictions. Src/LinearSolvers/F_MG/mg.f90 commit 1e0c733a72ea292c81b2c717594df3517629d5ef Author: lijewski Date: Wed Jul 24 15:29:43 2013 -0700 Implemented full weighting 2D nodal restrictor. The previous restrictor took FABs of constant one and restricted them to constant four. That's why mg.f90 had that weird multiplicative factor in it. The previous restrictor didn't weight the fine cells quite right either. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 6abfb421409b7fd742ae2887ff24cbbaf7bfa4b3 Author: lijewski Date: Wed Jul 24 13:37:50 2013 -0700 Finished mucking with bicubic for now. Doesn't look like a win generally :-( Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 376097d2985679a6b9e2f13df10a3944b9f4b8b0 Author: lijewski Date: Wed Jul 24 11:07:16 2013 -0700 Added an assertion that we have enought ghost cells. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 3da73826a3e44c2f8b132398789254e541d7e893 Author: lijewski Date: Wed Jul 24 10:49:30 2013 -0700 Some cleanup. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit e0db65c889e1378071935667b333ba648daa739a Author: lijewski Date: Wed Jul 24 09:01:14 2013 -0700 Checked in so we don't use the 2D bicubic nodal prolongation stuff. Src/LinearSolvers/F_MG/mg.f90 commit f39d1dccff2e2ee310e10305eb17ba5c76afe4d8 Author: lijewski Date: Wed Jul 24 08:30:42 2013 -0700 More work on bicubic. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit d847ae283cf05cbadf8bd40cfdec7aa96ffae146 Author: lijewski Date: Tue Jul 23 16:56:12 2013 -0700 More work on bicubic. Still not sure I like how BC_DIR are done. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 950d86536798c0b4cfc0d074798ebbaa9dfeacb4 Author: lijewski Date: Tue Jul 23 16:27:59 2013 -0700 Some work getting bicubic prolongation to work for 2D nodal. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit f2a97605a646b4398e8b4d2ca37a13a69d02af65 Author: vince Date: Tue Jul 23 15:07:54 2013 -0700 added support for wrapped sequence numbers for partial queries and io bracketing. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit faab0d9926d91e14f5367fe964060e766649b66c Merge: 8b5ea0d7f 85624973a Author: lijewski Date: Tue Jul 23 10:05:46 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 85624973a6f8a664469c342ccbca7f60e29e3efa Author: Ann Almgren Date: Mon Jul 22 12:37:15 2013 -0700 Add new file cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG/GNUmakefile commit a7cf3d1927274a294cd256ba8c78bf9e4f8c0ed1 Author: Ann Almgren Date: Mon Jul 22 11:48:38 2013 -0700 We now have coeffs_type = 0: constant coefficients ( = 1) coeffs_type = 1: variable coefficients in [1,11] coeffs_type = 2: variable coefficients in [1,101] Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90 commit 6eb1e729825ac029b5eebb3a97549b2b35c82294 Author: Michael Zingale Date: Mon Jul 22 14:19:57 2013 -0400 squash some compiler warnings: lwb(), upb(), and get_dx() all return arrays of the actual dimensionality rather than MAX_SPACEDIM. This was picked up by the debug flags, but there is no real memory issue here. fextract.f90 commit e28596c8a118ee1e26be4368094dc0473101a6b2 Author: Ann Almgren Date: Mon Jul 22 10:36:54 2013 -0700 Change the default value of nub from 10 to 0. This is the number of smooths that are automatically done after a CG or BiCG bottom solve has reduced the residual by the requested orders of magnitude. In theory we shouldn't need to do any relaxations here, but one can always set it in the inputs file to 10 or higher if needed. Src/LinearSolvers/F_MG/mg_tower.f90 commit 04db2a8f993daaa718ca15cf3ae7408ecbdd61a5 Author: Ann Almgren Date: Sun Jul 21 07:09:22 2013 -0700 If you set coeffs_type = 1 now you get variable coefficients for the solve -- currently they vary by about 1:100. Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/test_script Tests/LinearSolvers/F_MG/wrapper.f90 commit 8b5ea0d7f6ca897f698ded6348a1b538ee8da1f9 Author: lijewski Date: Sat Jul 20 21:35:21 2013 -0700 Added specialized versions of pc interp & restrict operators in 2D & 3D for ir==2. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 995db26d3b643865eb086d9488a72685a319b4a6 Author: lijewski Date: Sat Jul 20 21:34:08 2013 -0700 Added specialized versions of pc interp operators in 2D & 3D for ir==2. Src/LinearSolvers/F_MG/cc_restriction.f90 commit 6b9dce38403ede60d7a6533c0813326517931f83 Author: lijewski Date: Fri Jul 19 17:07:08 2013 -0700 Removed the need for a fill_boundary on prolongation. The linear interpolators do PC interp on faces & linear on interior. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 4439960d5d98047262ccf1fbbb0b65b09ad048f2 Author: lijewski Date: Fri Jul 19 14:52:44 2013 -0700 Little more cleanup. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 77dc95ed85f950d094f84bd153f5e37e456e8cae Author: lijewski Date: Fri Jul 19 13:45:05 2013 -0700 Some cleanup of new linear prolongation operators. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 5e84f4d881577186f7b10442554288bd553fc4e0 Author: lijewski Date: Fri Jul 19 12:04:18 2013 -0700 Removed unnecessary fill_bounary() in special bottom solver. Src/LinearSolvers/F_MG/mg.f90 commit e0d2d50cd6745ef0bfb89aa758bb49159f20f4b4 Author: lijewski Date: Fri Jul 19 11:14:05 2013 -0700 Removed some unnecessary neumann stuff from 1D nodal restriction. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 4a51703c92eda9905f9f95c3dc45657a3e1bd648 Merge: 25c31dfab dfba1990f Author: Ann Almgren Date: Fri Jul 19 10:45:51 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 25c31dfabd851cf63c5afb6c3521790c87d8f1fd Author: jmwang214 Date: Fri Jul 19 10:44:28 2013 -0700 Add random nmber RHS for Tests/LinearSolvers/F_MG. Tests/LinearSolvers/F_MG/cc_rhs.f90 commit dfba1990f604c67ded1bb5fe8f549edf8b47bbfe Author: lijewski Date: Fri Jul 19 10:28:53 2013 -0700 Added optional argument "eps" to mg_tower_bottom_solver(). I want to test the effect of bottom solver tolerances on the F cycle. Src/LinearSolvers/F_MG/mg.f90 commit 16158b3fc199cc657f4db7bc1257d9ff4539ed77 Author: lijewski Date: Fri Jul 19 10:21:44 2013 -0700 Some cleanup. Removed unnecessary mg_defect() calls from fmg_cycle. Removed bl_timer routines from mg_tower. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 commit ea2547ec0fbf07070706ad81b5809f154cd5967b Author: Ann Almgren Date: Thu Jul 18 15:59:39 2013 -0700 Add inputs for the new problem with Dirichlet bc's Tests/LinearSolvers/F_MG/inputs.2d.fcycle.dir Tests/LinearSolvers/F_MG/inputs.2d.vcycle.dir Tests/LinearSolvers/F_MG/inputs.3d.fcycle.dir Tests/LinearSolvers/F_MG/inputs.3d.vcycle.dir commit bec4e3096f592ba85e3483542800083a44080a49 Author: Ann Almgren Date: Thu Jul 18 15:58:34 2013 -0700 Add test problem where we start with exact phi, compute the Laplacian, then use that as the RHS. This works with Dirichlet bc's. Tests/LinearSolvers/F_MG/cc_rhs.f90 Tests/LinearSolvers/F_MG/test_dir commit 16cc6dc1703d9ebeff01efb3c40a2fe4291383ef Author: Ann Almgren Date: Thu Jul 18 15:56:48 2013 -0700 Add options for linear interpolation in 2d and 3d. Currently the linear only works for ref_ratio = 2. Default is still to use piecewise constant so this shouldn't change anything. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 6d5b98107bd406fbd6d8f2c086c1151070ae7b4c Author: Ann Almgren Date: Thu Jul 18 14:06:25 2013 -0700 Fix up this code so it is easier to run different test problems, with different rhs or using F- vs V-cycle Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_rhs.f90 Tests/LinearSolvers/F_MG/inputs Tests/LinearSolvers/F_MG/inputs.2d.fcycle Tests/LinearSolvers/F_MG/inputs.2d.vcycle Tests/LinearSolvers/F_MG/inputs.3d.fcycle Tests/LinearSolvers/F_MG/inputs.3d.vcycle Tests/LinearSolvers/F_MG/test_script Tests/LinearSolvers/F_MG/wrapper.f90 commit 3b08cc4bd1258cd9642b8e2683fb74b616f5edfa Author: Ann Almgren Date: Thu Jul 18 13:10:32 2013 -0700 Separate out the rhs routines from nodal_multi.f90 and cc_multi.f90 Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_rhs.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_rhs.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 5950edb119c3f3f7e80eeb3158a0de2e65ff8b51 Merge: 1aeb6c00c 553372ea8 Author: Michael Zingale Date: Wed Jul 17 08:59:10 2013 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 1aeb6c00c1794663717e04aa7c401820b4d0e291 Author: Michael Zingale Date: Wed Jul 17 08:54:11 2013 -0400 add FIVE3RD Src/F_BaseLib/bl_constants.f90 commit 553372ea81d1fd85e6fd60b56ee04d2d2d0ec158 Author: lijewski Date: Tue Jul 16 15:08:15 2013 -0700 Nodal FMG cycle now seems to be working. At least it takes no more cycles than does V-cycle. Src/LinearSolvers/F_MG/mg.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 8406279233f0226b42e2f03235854adf27e38228 Author: Weiqun Zhang Date: Tue Jul 16 10:06:28 2013 -0700 omega is no longer part of mg_tower Tutorials/HeatEquation_EX5_F/advance.f90 commit b3f9b1151ee5d268de1272d868c2dc761fa6f29f Author: Ann Almgren Date: Mon Jul 15 15:32:49 2013 -0700 Add timer stuff to f_cycle. Src/LinearSolvers/F_MG/mg.f90 commit af9fb0a8e460347dc2dc52bee0e66c3030bb6e5a Author: Ann Almgren Date: Mon Jul 15 15:30:57 2013 -0700 Remove unused nodal_flag in fmg_cycle. Src/LinearSolvers/F_MG/mg.f90 commit 4668443b165517bcd500b10cff4bd2171499abcb Author: lijewski Date: Mon Jul 15 14:54:23 2013 -0700 Removed the GS_LEX smoother stuff. Never used. Just use GSRB. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit 7afdd9d31a7d74fdac89c940048112a964662fe2 Author: lijewski Date: Mon Jul 15 14:37:43 2013 -0700 Omega is no longer a part of the mg_tower. Nor is omega passed to the smoother routines. The smoother routines now use their own omega. Also removed the unused lgs_* smoother routines added by Chuck long ago. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 11335bd16ce17a5ae85719e5000d63d6b2f99e7e Author: lijewski Date: Mon Jul 15 13:43:20 2013 -0700 Only set mgt%face_type if nodal. Src/LinearSolvers/F_MG/mg.f90 commit 9d8f16f60a65210d3d5804b119fb66fa6b6e4933 Author: lijewski Date: Mon Jul 15 13:22:28 2013 -0700 Skewed stuff. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit 3ef8e6cf4f2be5221c2dd64daae532ced2694b3c Author: lijewski Date: Mon Jul 15 13:21:43 2013 -0700 Only build mgt%skewed and mgt%skewed_not_set if cell-centered. Src/LinearSolvers/F_MG/mg.f90 commit e133afa37d06c4c30d622d278f727a14c2f42fc9 Author: lijewski Date: Mon Jul 15 12:11:56 2013 -0700 Do error check for cycle_type. Src/LinearSolvers/F_MG/mg.f90 commit d844836f97b46b40c93eb2ad8a958471d8ca7c8e Author: lijewski Date: Mon Jul 15 12:11:37 2013 -0700 Added --cycle_type. Tests/LinearSolvers/F_MG/wrapper.f90 commit 6a91c1e7330981d85f9d07d13d92f7165cada24e Author: vince Date: Mon Jul 15 11:41:51 2013 -0700 spacing. Src/C_BaseLib/Profiler.cpp commit 29cef88b1555cdd48b4a22973359c1a513904fa6 Author: vince Date: Mon Jul 15 10:46:01 2013 -0700 optimized nametags. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 2e89dd7603df0af7d214a5dc9de378679f486a61 Author: Weiqun Zhang Date: Thu Jul 11 07:42:26 2013 -0700 updated some tests due to the removal of gamma from mg_tower_build interface Tests/LinearSolvers/F_MG/wrapper.f90 Tutorials/HeatEquation_EX5_F/advance.f90 commit cf8ee73e5f3fbd0cbdbf210cf2f949abca2f3074 Author: ajnonaka Date: Wed Jul 10 13:36:43 2013 -0700 comments for mg_max_levels function Src/LinearSolvers/F_MG/mg.f90 commit 6c1e221000dc930298ab8e951ddd36005ba1d9af Author: Ann Almgren Date: Wed Jul 10 12:43:33 2013 -0700 Add default value of 1.33 for omega for 1d nodal only. Src/LinearSolvers/F_MG/mg.f90 commit 39ea8ff10067a3922aa83144132c2db37d08a6b5 Author: jmwang214 Date: Wed Jul 10 12:41:21 2013 -0700 1) Fix the F-MG cycle -- it can be used by setting cycle_type.. 2) remove gamma and omega from the inputs of mg_tower_build Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit f301b64e2e36e773d79a94e58cc747df54a914e8 Author: vince Date: Wed Jul 10 11:49:38 2013 -0700 more profiling, timer time. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit b98dd34a8637e9c8ab462bf7ff7e56dc17fa8b7e Author: Ann Almgren Date: Wed Jul 10 11:19:07 2013 -0700 Remove gamma and omega as inputs from the mg_tower_build call. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit aa2117997b708ff500fd8022bfc89883e03c5f2f Author: Ann Almgren Date: Wed Jul 10 11:18:27 2013 -0700 Remove gamma and omega from the calling sequence when calling from C++. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 8ec0ba34da7d0af6558d481d0df1c0f55998b263 Author: Ann Almgren Date: Mon Jul 8 15:52:40 2013 -0700 Declare mgt%visited. Src/LinearSolvers/F_MG/mg_tower.f90 commit c7e2338491380253d7f53c7e82eea4b296d542eb Author: Ann Almgren Date: Mon Jul 8 15:52:27 2013 -0700 Try to fix the logic for the F-cycle. Src/LinearSolvers/F_MG/mg.f90 commit 0f42bcae4c817f6c8281d92cda9cc5cfbce39451 Merge: 006f51d58 ed5334763 Author: Ann Almgren Date: Mon Jul 8 13:34:06 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ed53347632d752367ed5120a47f9ef27c5902e72 Author: lijewski Date: Mon Jul 8 10:13:21 2013 -0700 More work speeding up nodal_restriction; hadn't done all cases. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 353d818955d750a8e396e7c974d6300bd2c33b66 Author: lijewski Date: Mon Jul 8 09:33:49 2013 -0700 Rearranged the nodal_restriction code to be faster & more memory efficient. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 006f51d58d4217fee746a3bd586450651cff90e3 Author: Ann Almgren Date: Sat Jul 6 10:01:34 2013 -0700 We were printing the wrong final number of iterations. Src/LinearSolvers/F_MG/ml_cc.f90 commit e5bbcc8a0f7a2470ff580ffea087efdbf99fbb11 Merge: 147ee88b5 7a337048a Author: lijewski Date: Sat Jul 6 09:27:49 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7a337048a66dcdaf54a5cca09d842ca6e14ceae9 Author: Michael Zingale Date: Fri Jul 5 09:19:20 2013 -0400 remove duplicate tests (if any) when using the --tests "..." argument. Otherwise we crash Tools/RegressionTesting/testnew.py commit 147ee88b5e2557aa1187eea59f9ccace275d5787 Merge: c59454aab 1be5d09bf Author: lijewski Date: Tue Jul 2 14:54:21 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1be5d09bff9ef9a9c7a6a732ae23fa7bd30099e0 Author: Ann Almgren Date: Tue Jul 2 13:45:57 2013 -0700 Add WritePlotFile in Particles.H Src/C_AMRLib/Particles.H commit c59454aab6b93f3e73e0b3172275789518fbdc70 Merge: 2093cf3a4 e519b89e7 Author: lijewski Date: Tue Jul 2 11:05:40 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e519b89e70f5ddfc8f3581aaecef7a54bb12007e Author: ajnonaka Date: Tue Jul 2 10:59:43 2013 -0700 don't prevent nodal solves from reducing to a global 2x2 bottom solve. certain bc's means this becomes a problem with 1 unknown which we've seen can stall multigrid Src/LinearSolvers/F_MG/mg.f90 commit 2093cf3a479dce8cc62109b031cf9022a32a4d9b Author: lijewski Date: Mon Jul 1 15:21:55 2013 -0700 Moved the memory stats stuff till after we've flushed the copyassoc cache. Checked it in commented out. Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 35d949d2645a2b4dfdd984173000c2b8551aec3c Author: lijewski Date: Mon Jul 1 13:05:37 2013 -0700 Reverting right back out the four-color dense 2D GS smoother. Sometimes better smoothers aren't necessarily a win; especially when they're so much more communication intensive. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 403a7e55ecf3b57a0c7c48d84a1fd7b5a304e1fb Author: lijewski Date: Mon Jul 1 13:02:15 2013 -0700 I've implemented four-color GS scheme for the dense nodal 2D stencil. I'm checking it in here to document it. I'm going to immediately revert out these files to their previous contents. Turns out doing four FillBoundary()s per smooth is a serious lose in 2D. On my test case my nodal solves were about 20% slower on 64 cores on hopper, and about 50% slower on 512 cores. This despite the four-color scheme being a "better" smoother, sometimes leading to fewer V-cycles in the MG. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit b04b99b31bbe350fec3748e277e4bb49341fa6d4 Author: lijewski Date: Mon Jul 1 12:41:48 2013 -0700 Made the bottom solve timer work for bottom_solver=4. Src/LinearSolvers/F_MG/mg.f90 commit 65957dae4dbe7e9a9b0008bb2a6e749a9f0f0bc1 Merge: 1edd6bc6e e737a9cd7 Author: ajnonaka Date: Mon Jul 1 10:36:23 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1edd6bc6e4c33eb146c7140ab9549326f9a84cfb Author: ajnonaka Date: Mon Jul 1 10:35:57 2013 -0700 fixed some mg level calculation weirdness that prevented cc fancy bottom solver from converging Src/LinearSolvers/F_MG/mg.f90 commit e737a9cd723528b3edc75f078bdc0020e6c5b85d Author: Weiqun Zhang Date: Mon Jul 1 08:30:55 2013 -0700 get around a PGI compiler bug Src/F_BaseLib/multifab_f.f90 commit e74ff2acd38d73f3ca8ad3fb11c8f4608c6333e7 Author: ajnonaka Date: Mon Jul 1 08:16:52 2013 -0700 fixed logic to handle the case when you try to invoke the fancy bottom solver and you have between 1 and (2**dm)-1 grids... in this case you can't use it so revert to bottom_solver_type=1 Src/LinearSolvers/F_MG/mg.f90 commit 603149054b97a896a9272103a3246740f690a729 Author: ajnonaka Date: Fri Jun 28 16:01:22 2013 -0700 change default value of max_bottom_nlevel to 3 so fancy bottom solver coarsens two levels (i.e., reducing # grids by factor of 8) Src/LinearSolvers/F_MG/mg_tower.f90 commit 8d7029f7ff732e987937d722c8c1b79da9ef7e40 Author: ajnonaka Date: Fri Jun 28 15:59:36 2013 -0700 eliminated some fancy bottom solver logic that was a) preventing the fancy bottom solver from ever being used if there are exactly 8 grids in the original bottom solve b) always forcing the max number of new levels to be 3. this should be controlled by max_bottom_nlevel, which will be default 3 Src/LinearSolvers/F_MG/mg.f90 commit e538c479f4f4e7e2d797f55996351ee006e12fc0 Author: ajnonaka Date: Fri Jun 28 15:07:11 2013 -0700 when calling_tower_build, you can pass in an optional argument "fancy_bottom_type_in" that controls the bottom solver for bottom_solver type 4. This is useful if you would rather do smooths than the default BiCGStab Src/LinearSolvers/F_MG/mg.f90 commit 1619a2162dd955a32ca379ad5b2e8ce18d73f785 Author: lijewski Date: Wed Jun 26 11:12:26 2013 -0700 Rearranged lin_cc_interp_3d to do fewer allocate()s and be more cache efficient. Src/F_BaseLib/interp.f90 commit cdc3ae04c80f104913c97bd0552cfac440cc932f Author: lijewski Date: Wed Jun 26 11:08:28 2013 -0700 Removed some trim() calls on string comparisons. Tutorials/AMR_Advection_C/Source/network.f90 commit 331e03d24cf35842fa4d94c5477077bd8ffe9db3 Author: lijewski Date: Wed Jun 26 08:11:33 2013 -0700 Got another 20% out of fourth_order_interp_2d(). Src/F_BaseLib/interp.f90 commit 8132e4cddbfc09d436105186db54149aa077e2f1 Merge: cb7dc7c63 129e41478 Author: lijewski Date: Tue Jun 25 15:38:10 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 129e4147873a04e33bfb7fd36e5fac8fd7314ae0 Author: vince Date: Tue Jun 25 14:52:15 2013 -0700 added nametags. Src/C_BoundaryLib/FabSet.cpp commit 46f9b03be5414476ba1bd8741822bfef3d7d7e20 Author: vince Date: Tue Jun 25 14:51:20 2013 -0700 added nametags. Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 5bbda07491084de7ac93b5c60510c6ad4b23095a Author: vince Date: Tue Jun 25 14:48:15 2013 -0700 added nametags. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp commit 58e31d8c93a60969a698f7851258e3935bf062d3 Author: vince Date: Tue Jun 25 14:41:41 2013 -0700 added to docs for comm profiling. Docs/Readme.profiling commit cb7dc7c632d1c5be1a6a55d12b4992d81dbca8f8 Author: lijewski Date: Tue Jun 25 10:40:52 2013 -0700 Build and use a local copy of the transpose of A2 in the fourth order interpolator. Src/F_BaseLib/interp.f90 commit feb179c601aed2283e3c3f02c860665acfc63961 Merge: c0751132a 95572b8f3 Author: lijewski Date: Mon Jun 24 16:21:27 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c0751132a0d5843bacbb7871f60909d8892c2703 Author: lijewski Date: Mon Jun 24 16:17:38 2013 -0700 Made fourth_order_interp_2d() more cache efficient by declaring the tmp variable c(:,:,:,:) such that the first dimension holds the values at each cell, not the last dimension. It could be made more efficient if A2 in fourth_order_interp_coef_module were defined as A2(15,0:3) instead of the other way around. But that could only be done all routines using it were changed as well. Src/F_BaseLib/interp.f90 commit 95572b8f38725f63d63f462496c71465fbbc2ddd Author: cmalone Date: Mon Jun 24 18:06:45 2013 -0500 cray compiler requires IO unit on flush Src/F_BaseLib/parallel.f90 commit 7220636412b95efbabe18f3027e3f94227af1462 Author: lijewski Date: Mon Jun 24 15:55:15 2013 -0700 kind=8 -> kind=dp_t Src/F_BaseLib/fourth_order_interp_coeffs.f90 commit ca332897acbbc6ff1c0a65bab3fa58dc5ad0ef75 Author: Michael Zingale Date: Mon Jun 24 16:34:00 2013 -0400 fix the _1d stuff -- the ss(0) was defined incorrectly (all ss's should sum to 0) Src/LinearSolvers/F_MG/nodal_stencil.f90 commit ff1d1e88cc4a959f2737daea1e271f7b44626140 Author: Weiqun Zhang Date: Mon Jun 24 09:53:32 2013 -0700 No ghost cells are needed; having no ghost cells can also eliminate a lot of Valgrind warnings Tutorials/AMR_Advection_C/Source/ADR_setup.cpp commit e5a4f3b73689a251a5e22931e4cf27a871420ccf Merge: 6b5a0ec16 b66983729 Author: Weiqun Zhang Date: Sun Jun 23 21:45:48 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6b5a0ec16694db6d12ec33200b82292660922092 Author: Weiqun Zhang Date: Sun Jun 23 15:17:48 2013 -0700 fixed a minor memory issue Tutorials/AMR_Advection_C/Source/ADR_setup.cpp commit b669837294274d86b118ae4d6b452a6cade563f9 Merge: b1b6204ae 83736f590 Author: lijewski Date: Sun Jun 23 07:57:50 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b1b6204ae1066ba4ad1ad0fd8248a9a8137c09fb Author: lijewski Date: Sun Jun 23 07:57:30 2013 -0700 Mod to parallel_create_communicator(). Src/F_BaseLib/parallel.f90 commit 83736f590f998e513330b4183e0d3caff9c9a76d Author: Ann Almgren Date: Fri Jun 21 15:56:23 2013 -0700 Update the Tutorials/AMR_Advection_C/Exec/UniformVelocity test problem. Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Advection_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Advection_C/Source/ADR_setup.cpp commit e06519fc697f6e20d994a2b2d56bd9d6a4249d59 Author: lijewski Date: Fri Jun 21 14:20:36 2013 -0700 Added back in Ann's tweak to get_bottom_box_size(). Src/LinearSolvers/F_MG/mg.f90 commit 5f5ceddb868a9b289f0811a0a7e7165a8b90575e Author: lijewski Date: Fri Jun 21 14:18:54 2013 -0700 Can't use bl_error_module; just print & abort by hand. Src/F_BaseLib/parallel.f90 commit c452e410448f2b06026a576c5a395145cb1a13dc Author: lijewski Date: Wed Jun 19 15:26:06 2013 -0700 Some cleanup. Src/LinearSolvers/F_MG/mg.f90 commit 81fa3d9d9cfe520d37c62c90c7c810076023eeff Author: lijewski Date: Wed Jun 19 15:25:38 2013 -0700 Added signatures for functions I recently added to parallel.f90. Src/F_BaseLib/parallel_stubs.f90 commit ef1c126bb38b907d9e28b3d89edde7dfc9f770b2 Author: lijewski Date: Wed Jun 19 14:56:50 2013 -0700 Added parallel_null_communicator(). Added optional comm argument to parallel_ioprocessor(). Src/F_BaseLib/parallel.f90 Src/LinearSolvers/F_MG/itsol.f90 commit 56cc55cba61f1cb57ba288fa611ff08651762185 Author: lijewski Date: Wed Jun 19 14:37:46 2013 -0700 Used parallel_communicator() instead of MPI_COMM_WORLD. Src/LinearSolvers/F_MG/mg.f90 commit d719549ebe1a3bc10f522d6c74b4cf1fe865d155 Author: Matthew Emmett Date: Wed Jun 19 14:33:06 2013 -0700 BaseFab: Tidy SAXPY signature, fix SAXPY domain bug. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 297838f8ad9a1bd6410261a6fa814257a9b299be Author: lijewski Date: Wed Jun 19 14:30:28 2013 -0700 Added parallel_create_communicator() and parallel_free_communicator(). Src/F_BaseLib/parallel.f90 Src/LinearSolvers/F_MG/mg.f90 commit 5ed901c14a609e70c872aad5545fb47bc376a04f Author: Matthew Emmett Date: Wed Jun 19 14:18:02 2013 -0700 BaseFab: Add SAXPY. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit c1f7a09ae5a48b1c52ee330b28eab7f5448b2c2b Author: lijewski Date: Wed Jun 19 13:57:28 2013 -0700 Some initial work getting bottom_solver=4 to use its own communicator. Src/LinearSolvers/F_MG/mg.f90 commit b7a15c7a50e1087494793915192aefa214147362 Author: lijewski Date: Wed Jun 19 13:55:12 2013 -0700 First cut at making BICGStab and CABiCGStab work with a given MPI communicator instead of the default one: MPI_COMM_WORLD. Src/LinearSolvers/F_MG/itsol.f90 commit 8f45746d891c28cc30d0d92e718507027427e877 Author: lijewski Date: Wed Jun 19 13:52:35 2013 -0700 Changed the default of max_bottom_nlevels from 10 -> 4. Added an MPI communicator data member that will be set in the mg_tower that does the bottom solve for the bottom_solve=4 case. The idea is that we pick a communicator that includes only those MPI procs involved in the bottom solve and pass it to routines that do global reductions to make those reductions go faster. Src/LinearSolvers/F_MG/mg_tower.f90 commit 7d5a2c317429048ef5b2c8c9136d3273be837479 Author: lijewski Date: Wed Jun 19 13:51:34 2013 -0700 multifab_dot() and multifab_norm_inf() now take optional MPI communicators. Src/F_BaseLib/multifab_f.f90 commit 83293019744ebb9da18470239003795674867b88 Merge: fbe99e5bb 850b16801 Author: Matthew Emmett Date: Wed Jun 19 12:17:43 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit fbe99e5bb36f97eddabcb857aa9d8f24b45eb7db Author: Matthew Emmett Date: Wed Jun 19 12:17:35 2013 -0700 Amr.H: Mark timeStep as virtual, sync parameter names with Amr.cpp. Src/C_AMRLib/Amr.H commit 850b16801b01ad699dd081706a9408a393587328 Author: Chris Malone Date: Wed Jun 19 11:52:50 2013 -0700 updates for hyades.ucsc.edu Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 0ebbbd284e46abcb824b1695dc3fd44dbe57ce7a Author: lijewski Date: Wed Jun 19 08:00:34 2013 -0700 3d nodal dense test case on 256^3 base grid with 64^3 grids for Legion folks. Tests/LinearSolvers/F_MG/inputs.simple.3d commit 63adb8585a1a54c8c03908594bdbe053ab6037e2 Author: lijewski Date: Wed Jun 19 08:00:02 2013 -0700 Set up for non-MPI non-OpenMP for Legion folks. Tests/LinearSolvers/F_MG/GNUmakefile commit 2e2f196538c3ce0fa36f2eae5cbd23c30ca82d0b Merge: d7480296e 4bbd22d11 Author: Ann Almgren Date: Tue Jun 18 14:17:50 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d7480296e462381bf80309acafc62d3d35a65e8c Author: Ann Almgren Date: Tue Jun 18 14:17:26 2013 -0700 Remove unneded "use" statements. Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit e91bdf0255b993942a1354b3e977f7fd119ddee9 Author: Ann Almgren Date: Tue Jun 18 14:06:44 2013 -0700 Updated which modules are included. Tutorials/WaveEquation_F/main.f90 commit 4bbd22d1144011f20933b591d90433b46505e3ba Author: lijewski Date: Mon Jun 17 16:26:03 2013 -0700 Some mods to get it to compile again. Tests/LinearSolvers/C_CellMG/main.cpp commit 5e05ab50da21b4ba9aee04b8e5b3462ec867db43 Author: lijewski Date: Mon Jun 17 16:24:32 2013 -0700 Thread sxay() over FABs in the MultiFab. The FABs themselves are too small to make threading over their Fortran boxes cost effective. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit ffd8c4b967c513cadecdec0f7a3a677d027f6580 Author: lijewski Date: Mon Jun 17 16:08:38 2013 -0700 Removed the multiply by alpha in axpy() since it's always one. Likewise optimized gemv() knowing alpha==1.0 and beta==0.0. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 681c2d4a549c75f5e31270be6fa526970ae581c8 Merge: 2e343961e d4465b78b Author: lijewski Date: Mon Jun 17 14:40:54 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2e343961ed9d17d16e2f1cd67052982a1afe2788 Author: lijewski Date: Mon Jun 17 14:40:26 2013 -0700 Removed grow cells on MultiFabs in BiCGStab that weren't needed. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 1ad7c53e51fe5059adafd424434406610945909a Author: lijewski Date: Mon Jun 17 14:22:51 2013 -0700 Beefed up error checking in CABiCGStab. Also removed ghost cells from MultiFabs where not needed. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 6b6ecabbc778a65025015977c6af0aa5b3c5644c Author: lijewski Date: Mon Jun 17 14:11:17 2013 -0700 FApply() didn't correctly use src_comp, dst_comp and num_comp. Src/LinearSolvers/C_CellMG/Laplacian.cpp commit d4465b78b3af378410e2da61e9e48d86d6f1702d Author: Ann Almgren Date: Mon Jun 17 11:50:14 2013 -0700 Fix some comments only. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 commit ef53d634cec9f40e251094ae008b96730c72bbe5 Author: lijewski Date: Fri Jun 14 18:48:08 2013 -0700 Little more OMP tweaking of my previous mod. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 commit 406a64270fda32ef7b615f27aaeed463793dd0e8 Merge: c922a5637 4132beb88 Author: lijewski Date: Fri Jun 14 15:19:32 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c922a563785d4893e2f4d1af32ea348c8dc40c3c Author: lijewski Date: Fri Jun 14 15:17:57 2013 -0700 Make itsol_defect() aware when it's being called from the bottom solver. Src/LinearSolvers/F_MG/itsol.f90 commit dfa068f3c1036b9bd2f895d7dfcc852ac0c8b4ea Author: lijewski Date: Fri Jun 14 15:11:28 2013 -0700 We now pass a flag to itsol_stencil_apply() indicating whether or not we're doing a bottom solve. It passes that flag to the relevant 3d apply routine, which then threads its loops if it's NOT in a bottom solve. This threads better for fewer boxes than threading over the calls to the apply op itself. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 29bc9ed5fa6ee96da23b5512e776fd98e24d3765 Author: lijewski Date: Fri Jun 14 14:18:55 2013 -0700 Changed the name of a constant. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 3806e12bcd569d79a43f6d66219bf6c18d27c75b Author: lijewski Date: Fri Jun 14 11:58:44 2013 -0700 Attempted to make some of the minion stencils more memory efficient by doing as much work as possible on them in one pass instead of multiple passes. Also, OMP over the bit twiddling in mask. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 05594729a22b3dce60a1b4f155243a7d16312a8e Author: lijewski Date: Fri Jun 14 10:52:40 2013 -0700 Some OMP tweaking. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 4132beb88232b6d81850bbfffa282d4d8c684101 Author: Weiqun Zhang Date: Thu Jun 13 21:33:10 2013 -0700 fixed a bug in my new code; now fillpatch seems to be working in cases that don't need interpolation in time (which is the case for multi-level SDC) Src/C_AMRLib/StateData.cpp commit ae39dafa13d0b2103ce99db7667a759b6eb535c0 Author: Weiqun Zhang Date: Thu Jun 13 17:56:30 2013 -0700 added multi-level SDC nodes Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/BaseFab.cpp commit c4e35a45c13bc5e415957e20d70e925005df6404 Author: lijewski Date: Thu Jun 13 17:16:22 2013 -0700 Added some barriers. Tests/C_BaseLib/tFB.cpp commit 965b5600eefeb67d02d69d2e2dc122673649e812 Merge: 224b9f55e 4af1dd8ca Author: lijewski Date: Thu Jun 13 12:58:22 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 224b9f55e1bb1da9e37b548071d639c3d0c1f9d5 Author: lijewski Date: Thu Jun 13 12:51:53 2013 -0700 New FillBoundary() test I want to run. Tests/C_BaseLib/tFB.cpp commit 4af1dd8ca891ce7e9d839b2ee68094b104dba179 Author: Weiqun Zhang Date: Thu Jun 13 10:11:31 2013 -0700 added some functions for getting, allocating and removing middle data in AmrLevel Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit e71ad749db2a7bd14c0da1554994205a70b0f40e Author: Weiqun Zhang Date: Wed Jun 12 17:52:46 2013 -0700 added quadratic interpolation in BaseFab, but the Fortran code is not implemented yet Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 5568ef7e7921b312d98c7e38bcf53b7d70f04ae8 Author: Weiqun Zhang Date: Wed Jun 12 12:44:47 2013 -0700 rename linInterp Interp because it will no longer only do linear interpolation Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 8c6cd115e071255d5f4f3d51b68edfba607e7c57 Author: Weiqun Zhang Date: Wed Jun 12 11:21:19 2013 -0700 pass MultiFabId and time of middle SDC nodes into time interpolator Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit aa404ca98561633fa8d7c7352ae8e902b3113354 Author: vince Date: Wed Jun 12 16:07:10 2013 -0700 quick fix for omp prof, need to track individual thread times, scoping issue. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit f7150e91aaacfe4b6bc49fb8f027dd562cbfb8fb Author: lijewski Date: Wed Jun 12 14:35:07 2013 -0700 PR in itsol_CABiCGStab doesn't need any ghost cells. Src/LinearSolvers/F_MG/itsol.f90 commit b6e011c881e8ef29d77a765ff57f04ea52392ada Merge: baa8cb13d f0a3abfae Author: lijewski Date: Wed Jun 12 14:08:37 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit baa8cb13d16723a71d30f87b1ebd05d6c9539724 Author: lijewski Date: Wed Jun 12 14:08:15 2013 -0700 Mods due to formal argument changes. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit c2ae04f8f7add7a4e625e0cb8c5b3d1e880be031 Author: lijewski Date: Wed Jun 12 13:46:04 2013 -0700 Destroy a boxarray. Tests/LinearSolvers/F_MG/wrapper.f90 commit dd4b40150f68841602f454a8bf6b69d421f6f95c Author: lijewski Date: Wed Jun 12 12:54:13 2013 -0700 Removed a bunch of unused variables and formal arguments. Really trying to get the code to compile clean in debug mode. Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 1c21e3c7940efa62406fc551eb746e5e6f1a2eba Author: lijewski Date: Wed Jun 12 11:01:27 2013 -0700 Fix bug in s_simple_1d_nodal(). Src/LinearSolvers/F_MG/nodal_stencil.f90 commit b00526a9dd7ec5af56e80fefe9be129f753a4dd8 Author: lijewski Date: Wed Jun 12 10:54:30 2013 -0700 Fixed bug in stencil_set_bc_nodal(). Added set_faces_edges_corners_2d(). Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 74e0ecbdef14b1cdd97236418f50b7cc8254190a Author: lijewski Date: Wed Jun 12 10:30:08 2013 -0700 Some OMP tweaking. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 commit f0a3abfaecd5cc7c2bab6a33320c9bef52f9ecce Author: Weiqun Zhang Date: Tue Jun 11 21:41:58 2013 -0700 pass SDC node times into StateData Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit fbafe0c5268eeb4e6c2ca7458660371b42f9ae8c Author: Weiqun Zhang Date: Tue Jun 11 17:45:46 2013 -0700 added SDC nodes information to Amr Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit d6533e1430cdd964280d40e0b54978483e80ca68 Author: Weiqun Zhang Date: Tue Jun 11 15:28:56 2013 -0700 added mid_data to StateData class for the storge of SDC middle nodes Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/PArray.H commit 9350fb7040ffe371b57b1d71c76bf030418dd274 Author: lijewski Date: Mon Jun 10 10:37:41 2013 -0700 A little memory cleanup. Src/C_AMRLib/StateData.cpp commit 30f00044614dcb731264100bd7a75847c4dc9391 Author: lijewski Date: Mon Jun 10 10:29:06 2013 -0700 Fixed OMP bug. Src/C_AMRLib/AmrLevel.cpp commit 7571772210af9a063b51e9d640a3c7442460f55a Author: lijewski Date: Sun Jun 9 19:29:07 2013 -0700 Added version of linInterp() in which the two src boxes & the dest box are all the same. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/MultiFab.cpp commit fabe75e25750d40aa8cc78a682aee7e8de91462f Author: lijewski Date: Sun Jun 9 18:56:18 2013 -0700 Added specialized version of BaseFab::sum() for Reals. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 272cdb01701269ff36b4920f31400aa183ad5868 Author: lijewski Date: Sun Jun 9 17:38:28 2013 -0700 Added some profilers. Src/C_AMRLib/AmrLevel.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp commit c4cabc4d70e0c420caded84a24df06f03b45df23 Author: lijewski Date: Thu Jun 6 13:46:24 2013 -0700 Reverting out the eight-color nodal dense smoother. With the number of fill_boundary()s required it's a lose. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit a755746070af26c8923eeb2b221d38686b58756c Author: lijewski Date: Thu Jun 6 13:13:21 2013 -0700 Removed the OMP from multifab_dot_cc(). Do the calculaton as a sum of partial sums. Src/F_BaseLib/multifab_f.f90 commit 63284f8b7110a405d8b0f12ccc37a3a1561160dd Author: lijewski Date: Thu Jun 6 13:13:02 2013 -0700 Named the critical section. Src/C_BaseLib/BaseFab.H commit cf728d42d5de1ef0adee26e2207e4ec01876da0d Author: lijewski Date: Thu Jun 6 12:56:20 2013 -0700 Had to add a critical region around the code in BaseFab::define() in which we maintain global track of the amount of data allocated in FABs. Multiple threads can hit this code at the same time. Src/C_BaseLib/BaseFab.H commit e4a460da5a074319594442c30e75f7f44dfcc48f Author: lijewski Date: Thu Jun 6 07:30:35 2013 -0700 Fixed OMP bug. Src/F_BaseLib/multifab_f.f90 commit d05f0e9db2d374827dde544ccf56b9f3d06fe8ae Merge: 3292f936c 9aa35369e Author: lijewski Date: Wed Jun 5 14:14:55 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3292f936c24a6a796e83c3eb7e4fb43a53a0b97a Author: lijewski Date: Wed Jun 5 14:08:50 2013 -0700 OMP over operations on boxes in boxarray. Src/F_BaseLib/boxarray_f.f90 commit 9f08aca704fdd5053fb9a26b82e3dda3ae041997 Author: lijewski Date: Wed Jun 5 13:51:20 2013 -0700 OMP over the various loops in BoxArray that operate on all the boxes. This appears to be a win a modest # of boxes. Should be a big win with very large box counts. Src/C_BaseLib/BoxArray.cpp commit 9aa35369e7cbe56c43057d2190c7d5d163a144ed Author: Ann Almgren Date: Wed Jun 5 12:06:29 2013 -0700 Need different template depth if USE_IN_SITU is true. Tools/C_mk/Make.defs commit c971eda7c658726f224df5b2d5f1b49f497c30e1 Author: lijewski Date: Wed Jun 5 11:00:09 2013 -0700 Explicitly write out the sum() operation in multifab_dot_cc(). Src/F_BaseLib/multifab_f.f90 commit 87d76c9c70fd9193cefe16946d11e63dc1dea8b8 Author: lijewski Date: Wed Jun 5 10:26:27 2013 -0700 A little cleanup. Src/C_AMRLib/AmrLevel.cpp commit d77a259d5058233ea8720bac4af6bbf5cc347950 Author: lijewski Date: Wed Jun 5 10:05:19 2013 -0700 OMP over number of boxes when building proper grid for FabSets. Src/C_BoundaryLib/BndryRegister.cpp commit e7fa42bce9a26e20f47be06871168904105262d4 Author: lijewski Date: Wed Jun 5 09:21:53 2013 -0700 OMP over faces when interpolating bndry data. Src/C_BoundaryLib/InterpBndryData.cpp commit 6d7ab2f0defc6b2cece6479a4fe3f043eafe0e26 Author: lijewski Date: Wed Jun 5 09:21:15 2013 -0700 Promote MultiFab::IndexMap() to be a public member. Src/C_BoundaryLib/FabSet.H commit f8937b3463e53ed98bf608038d82a42e922849e1 Author: lijewski Date: Wed Jun 5 08:37:03 2013 -0700 OMP over the tagboxes in a tagboxarray. Src/C_AMRLib/TagBox.cpp commit 1cad8026b610ef7a533cd289d6d6366ace79e849 Author: lijewski Date: Wed Jun 5 08:36:15 2013 -0700 OMP over the various faces in fluxregisters not in the individual Fortran routines themselves. Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FluxRegister.cpp commit fe5acbf00dafd836939a5df85b07cb7567053e03 Author: lijewski Date: Wed Jun 5 08:35:11 2013 -0700 OMP fillpatch. We want to be able to OMP over all the small boxes. Especially for the interpolations. This means we don't OMP in the interpolator routines themselves. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/INTERP_3D.F commit ffc8d3ab182dc53fb27f5ad9eb5557ef62aa169b Author: lijewski Date: Tue Jun 4 19:30:32 2013 -0700 Fixed OMP bug. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit d4af672f8b05c23de1d64ebf1d8df12ab37cd8e5 Author: lijewski Date: Tue Jun 4 17:09:46 2013 -0700 Fixed OMP bug. Src/F_BaseLib/multifab_f.f90 commit f80c0c85b421ba58e179a640d352906a666ff7d4 Author: lijewski Date: Mon Jun 3 17:45:29 2013 -0700 The stencil apply functions are only called by the bottom solver. The boxes are too small to profitably OMP. Instead OMP over FABs. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 48be938ac8bb41b95fd4031dd40d6a59cd01e3ec Author: lijewski Date: Mon Jun 3 17:18:47 2013 -0700 Use cpy_d() instead of generic pointer copy assignment. Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit b3120a5e9002abe83b6a9d842ec2a9a51d8a5158 Author: lijewski Date: Mon Jun 3 16:33:52 2013 -0700 Some OMPing. Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit c1e74e55c8d3b9d7d86c5e6cd6bf4e6d1ac38440 Author: lijewski Date: Mon Jun 3 14:59:39 2013 -0700 Now print out solve time and accumulated time in the bottom solver. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 36bb633db039df48a6aac5301a6366f389f4d773 Author: lijewski Date: Mon Jun 3 10:59:04 2013 -0700 Some cleanup. Src/F_BaseLib/multifab_f.f90 commit 1e55ddb531b1071147cd23322f907ac220b838c1 Author: lijewski Date: Mon Jun 3 10:36:07 2013 -0700 Added multifab_norm_l2_doit(). Src/F_BaseLib/multifab_f.f90 commit c9f030559ffe33b9ae89ac6229bb4dad13329223 Author: lijewski Date: Mon Jun 3 10:24:40 2013 -0700 Thead over FABs in multifab_dot(). They're almost always called with tiny boxes that can't be threaded over individually. Src/F_BaseLib/multifab_f.f90 commit f4a1a2e11dcebe304fb631ad56d24806e2f69b8c Author: lijewski Date: Mon Jun 3 09:18:09 2013 -0700 Tweaking the OMP IF constaints on some loops. Src/F_BaseLib/multifab_f.f90 commit 76132aed7cd1fd0e93d44bd092118790faae44f1 Author: lijewski Date: Wed May 29 16:17:37 2013 -0700 Can now call gs_lex_dense_smoothers in mg_tower_smoother. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit a2613a6cd80ddaf0634ecf1941bc0438333fbf66 Author: lijewski Date: Wed May 29 16:00:43 2013 -0700 Some cleanup. Also, make sure mg_tower_smoother calls the fourth order smoothers the proper number of times. Only the 2-D HO cross stencil does red-black; the others do a full sweep. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit af798e7726cf6947e49b18798f887c4a99c6041b Author: lijewski Date: Wed May 29 15:14:15 2013 -0700 Only use the 8-color dense nodal smoother if OMP=t and don't have enough FABs. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit dd91b45e2ba6c07e9ee6455ad88b26e846efa63f Author: lijewski Date: Wed May 29 15:13:31 2013 -0700 Can now use the F90 omp_module from the C++/Fortran side of things. Src/F_BaseLib/FParallelMG.mak commit 6bd4e0602e0d70a3c4e862195982aee78f18b833 Author: lijewski Date: Wed May 29 13:51:03 2013 -0700 Added an 8-color GS nodal dense smoother for 3D that's OMP'd. It's only called when the number of FABs in the multifab is fewer than the maximum number of threads available. Otherwise we thread over the FABs in the multifab when calling the nodal dense smoothers. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 9a42bcd0b03dbfee237f95c641658476b7297980 Author: lijewski Date: Wed May 29 12:26:36 2013 -0700 I'm partially backing out some of my recent OMP changes. I want to use the old threading model over FAB boxes, and the new way of threading over multifabs only when the FAB box can't be threaded. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 0593d8b5f0ea755f41b8c0c536f65850821b9856 Author: Weiqun Zhang Date: Tue May 28 21:21:32 2013 -0700 Fixed an assertion bug in initializing random number generator. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 2bfcd50ab3adce68bc409a43240ecb95d2989b1d Author: lijewski Date: Tue May 28 18:24:22 2013 -0700 Back to old way of doing some OMP. Nesting has too much overhead. Src/F_BaseLib/multifab_f.f90 commit d0bc11c3e86d2a266f353cfeb46834cb864f5ca8 Author: lijewski Date: Tue May 28 16:50:47 2013 -0700 Had a tmp array in BuildGramMatrix() dimmensioned too small. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 7aaac044187a802a0b96846300a86c0bebf610c5 Author: lijewski Date: Tue May 28 16:23:17 2013 -0700 More uses of only_small_boxes(). Src/F_BaseLib/multifab_f.f90 commit 739dd1eeb9489ae06c16ee5a31c4d08c36840eb7 Author: Weiqun Zhang Date: Tue May 28 15:40:12 2013 -0700 disable nested OMP parallel regions by default Src/F_BaseLib/boxlib_f.f90 commit aee52bc703dca26cc3cabdfb9cb40eef44e4ec8e Author: lijewski Date: Tue May 28 15:22:12 2013 -0700 Added only_small_boxes() which returns whether or not a multifab only has "small" boxes. We use it to decide whether or not to OMP some loops. Src/F_BaseLib/multifab_f.f90 commit 9b96165cca37586b4a8f647af14fa3c6334578d7 Merge: 7f3356929 fab13473f Author: Weiqun Zhang Date: Tue May 28 14:21:36 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7f3356929b184c2da25742fdf38801580f546bc4 Author: Weiqun Zhang Date: Tue May 28 14:18:35 2013 -0700 In mf_fb_fancy_*, turn off some unsafe OMP parallel regions for nodal multifabs. In principle, the unsafe scenario could also happen for cell-centered multifabs that have overlapped valid cells. Src/F_BaseLib/multifab_f.f90 commit fab13473f19041a3ba72c635f978fd47bd8c399e Author: lijewski Date: Tue May 28 13:55:52 2013 -0700 Only reduce the upper triangle of the Gram matrix. After reduction fill in the rest via symmetry. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 13859d215a3cbf5c92853c1712fb9eb17fbc7658 Author: lijewski Date: Tue May 28 13:06:23 2013 -0700 Only reduce the upper triangular part of the Gram matrix in the CABiCGStab instead of the whole matrix. Use symmetry to fill it in after the allreduce(). Src/LinearSolvers/F_MG/itsol.f90 commit 2bfd7365f10d239af0f5cabb7c940713e1c1ec41 Author: lijewski Date: Tue May 28 11:25:04 2013 -0700 Some OMPing. Src/LinearSolvers/F_MG/ml_solve.f90 commit ceed66499769a741a9853bb552d95834590700fb Author: lijewski Date: Tue May 28 10:22:34 2013 -0700 Remove boxarray_boxarray_diff() and its synonym boxarray_complementIn(). Force people to use layout_boxarray_diff(). Src/F_BaseLib/boxarray_f.f90 commit 8b3347f5d6570bdb66d902c5e20808e4aa33e666 Author: lijewski Date: Tue May 28 10:22:16 2013 -0700 Use layout_boxarray_diff() instead of boxarray_boxarray_diff(). Src/F_BaseLib/make_new_grids.f90 commit c938d060a945607363bfaae49fb2cdb22a4d13e2 Author: lijewski Date: Tue May 28 09:11:48 2013 -0700 OMP over call to ml_interface_[123]_crse() that include calls to layout_get_box_intersector(). Not sure what I tweak exactly to make this work but I'm going with it. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 9b002d3c92d26ad5f038ca6a501f965b476912a8 Author: lijewski Date: Tue May 28 09:11:13 2013 -0700 Further refinement of critical region placement for layout_get_box_intersector(). Src/F_BaseLib/layout.f90 commit 103884c33d528173d2486b92959f04477b0bdbf2 Author: lijewski Date: Mon May 27 18:40:25 2013 -0700 Refined the critical area in layout_boxarray_diff(). I'd really like to understand why I can't call layout_get_box_intersector() directly in an OMP loop. Src/F_BaseLib/layout.f90 commit ab16587a4f3fdee823249e2a68c6110320bb077b Merge: b60bd36a2 0ee9eb1a3 Author: lijewski Date: Mon May 27 17:52:53 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b60bd36a258302346e4763633bfeb17679be60ac Author: lijewski Date: Mon May 27 17:52:13 2013 -0700 Removed some OMP loops in the multifab_sync routines. Src/F_BaseLib/multifab_f.f90 commit 0ee9eb1a3e9ddab2faaa790026ee07b5c79794ec Author: lijewski Date: Mon May 27 16:56:41 2013 -0700 Fixed bug I recently introduced. Src/F_BaseLib/multifab_f.f90 commit 14e6d30a23f1f5c992f7484c44b95267434fe387 Author: lijewski Date: Mon May 27 13:40:40 2013 -0700 Moved critical section to inside of layout_boxarray_diff() instead of around it. I still don't understand why layout_get_box_intersector() isn't thread-safe. Src/F_BaseLib/layout.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit a2edf6c3cb62bb37cb74a4998d3019896fc392f2 Author: lijewski Date: Mon May 27 11:11:18 2013 -0700 Made some internal layout routines much more efficient for large boxarrays. Src/F_BaseLib/layout.f90 commit 0ceee12536c7d2b9f1154d1949d5d6c390267c77 Author: lijewski Date: Mon May 27 10:34:01 2013 -0700 Added layout_boxarray_diff(). This is a much more efficient version of boxarray_boxarray_diff(). Use this in place of the latter, which I'll be removing soon. Src/F_BaseLib/layout.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 8eccbdb32ad09dd76729df699c6ea2eaf82e1c27 Merge: f09a25794 957d48a62 Author: lijewski Date: Sun May 26 18:26:17 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 957d48a6244f0ca42d89f05df26e0c19a6b86eb2 Author: lijewski Date: Sun May 26 18:06:07 2013 -0700 Fix typo. Src/LinearSolvers/F_MG/itsol.f90 commit f09a2579485f329273714a1f0ed27a761cb81008 Author: lijewski Date: Sun May 26 10:39:01 2013 -0700 Moved most of the OMP for MG over the FAB in a multifab. This turns out to be a big win. We do a lot more calls of the smooth() and apply() on very small boxes. And as problems get bigger this will only increase. It doesn't help the extreme case (much) where you only have one grid per MPI process, but for multilevel problems where you almost certainly have multiple grids per MPI process it's a clear win. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/edge_restriction.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 3eaa6724124c4d4c587290146aa70c875e1e6de1 Author: lijewski Date: Sun May 26 10:22:54 2013 -0700 Fixed typo. Src/F_BaseLib/multifab_physbc.f90 commit 7b69628394474045c9f7b0d0583c930da0281d07 Author: lijewski Date: Sat May 25 22:09:53 2013 -0700 Some more OMPing. I'm lifting OMP loops out of simple routines and writing loops around nfabs() or nboxes() instead in cases where the amount of work to do in the original OMP loops is small. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 commit 50933c9e21a82808e78d3a8ab0a14d686476693d Author: lijewski Date: Sat May 25 20:19:39 2013 -0700 More OMP polishing. Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/itsol.f90 commit cd1ac4699d34169866260bfc724a1bf6e31af884 Author: lijewski Date: Sat May 25 20:18:59 2013 -0700 Make the memory statistics stuff thread safe using critical regions. Src/F_BaseLib/bl_mem_stat.f90 commit a55b857e3c1497de08f590d3fbf25e22315a1d7a Author: lijewski Date: Sat May 25 19:09:20 2013 -0700 Don't OMP the interp routines. Instead OMP over all the typically small grids in routines like fillpatch, make_umac_grown and fill_ghost_cells. Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/multifab_physbc.f90 commit dddb059e8f619649ede8c7b59e82ac4a0904ccb8 Author: lijewski Date: Sat May 25 11:29:05 2013 -0700 Don't thread dot() or saxpy(); they're mostly used on really small boxes. Src/F_BaseLib/multifab_f.f90 commit b5f7f9270751d943346d2eb0fedbe4ec20364de0 Author: lijewski Date: Sat May 25 10:23:45 2013 -0700 Tweak to CABiCGStab. Needed to fill both components of "ph" with "uu" at start. Src/LinearSolvers/F_MG/itsol.f90 commit e7015baec104ec762ac455c9c378a2c53262d42b Author: lijewski Date: Fri May 24 15:06:57 2013 -0700 Removed some OMP loops that were effectively nested. Src/LinearSolvers/F_MG/itsol.f90 commit 1dc821139326d539ee61e48a87ce9124c300284f Author: lijewski Date: Fri May 24 14:46:25 2013 -0700 OMPing across FABs instead of within FABs on MG routines that often use small boxes. Src/LinearSolvers/F_MG/cc_restriction.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/nodal_restriction.f90 commit f051c8d570c434a77e340f1fdd34e9a3597ffe08 Author: lijewski Date: Fri May 24 14:45:20 2013 -0700 OMP'd a loop. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit 5a7bb4a22b2acff96d69727e6b54fa2de14ddbba Author: lijewski Date: Fri May 24 14:33:34 2013 -0700 Added an IF directive to an OMP loop. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 commit fd476bc9e1a701c1fd1dc6eac0d11121e664136c Author: lijewski Date: Fri May 24 14:04:50 2013 -0700 For things used in the bottom solver I'm now OMPing over FABs not within the very small FABs. Src/LinearSolvers/F_MG/itsol.f90 commit fa273ae45560affce1098e077f9d15d48b0257cd Author: lijewski Date: Fri May 24 14:03:27 2013 -0700 Did some more OMPing in things like the copy()s in FillBoundary() and such places. Also, for things like saxpy() that are primarily used in the bottom solver, I'm OMPing over the FABs in the MultiFab, not across the FAB, which could be very small. Src/F_BaseLib/multifab_f.f90 commit d0f13c679e502b4d1051c4db573a7cbb1e72a9de Author: lijewski Date: Fri May 24 09:14:52 2013 -0700 Added a critical section around the call to init_box_hash_bin(). Src/F_BaseLib/layout.f90 commit 415fc462245427d81c39858d8197120b71127712 Author: lijewski Date: Wed May 22 17:03:28 2013 -0700 OMP's part of BuildGramMatrix(). Src/LinearSolvers/F_MG/itsol.f90 commit 0a529046c43bd807ae82177ed7428245d61a20ab Author: lijewski Date: Wed May 22 16:19:14 2013 -0700 Call itsol_apply_stencil() on pp & rr together in the CA algorithm. Cuts out half the fill_boundary() calls. Src/LinearSolvers/F_MG/itsol.f90 commit 116ad24495325c69a7dcddebbf98c72d84c866ce Author: lijewski Date: Wed May 22 15:44:46 2013 -0700 Some OMP loop polishing. Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 65d4dd0ab4b1f6a93073c70452f97be8fdfca000 Author: lijewski Date: Wed May 22 15:15:39 2013 -0700 Put some small arrays on the stack instead of the heap. Polished up some of the OMP loops. Src/LinearSolvers/F_MG/cc_smoothers.f90 commit 51a7d8b9c27dbaa7c69ea10eb88d3871b5655353 Author: lijewski Date: Wed May 22 14:24:43 2013 -0700 Removed some unnecessary setval()s. Src/LinearSolvers/F_MG/itsol.f90 commit ab4ff4202538713305acb34ba1f7aa74809d2890 Author: lijewski Date: Wed May 22 14:05:53 2013 -0700 More cleanup. Src/LinearSolvers/F_MG/itsol.f90 commit 50d342aa1e81201c36593659988453d3aa1ff30a Author: lijewski Date: Wed May 22 13:28:10 2013 -0700 Some cleanup. Src/LinearSolvers/F_MG/itsol.f90 commit d79268b2f9d984bc740ba43d1af170ce40c66117 Author: lijewski Date: Wed May 22 13:01:11 2013 -0700 Added is_an_inf() and is_a_nan() routines for checking single double values. Src/F_BaseLib/fab.f90 Src/LinearSolvers/F_MG/itsol.f90 commit 558b1e9d780c919d99764e7b7b741e1c447eca4a Author: lijewski Date: Wed May 22 12:51:38 2013 -0700 Made BuildGramMatrix() a contain'd routine. Src/LinearSolvers/F_MG/itsol.f90 commit b66969e46133573e41882386bbd27c5f0d4395ae Author: lijewski Date: Wed May 22 12:21:37 2013 -0700 Integrated in isinf() stuff. Src/LinearSolvers/F_MG/itsol.f90 commit a46f509259096b66400ec384828bb8f3a0df0451 Author: lijewski Date: Wed May 22 12:09:32 2013 -0700 Added val_is_nan() and val_is_inf() routines. Src/F_BaseLib/fabio_c.c commit b0519ceeaa9cd6006bef959bd932b90349c669e9 Author: lijewski Date: Wed May 22 10:54:29 2013 -0700 Elided some multiplies via strategic use of parentheses. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit e0e21c182c7b5dfcea422e9ee6206492ea7e3378 Merge: bf8310278 4982ee7de Author: lijewski Date: Tue May 21 16:13:09 2013 -0700 Merge branch 'CA' commit 4982ee7de76efa624fe329606918cfceabcaa1d3 Author: lijewski Date: Tue May 21 16:08:17 2013 -0700 Fixed bug I recently introduced. Src/F_BaseLib/multifab_f.f90 commit e31da1fab01be2a02f5be93b1a3840266e681707 Author: lijewski Date: Tue May 21 16:02:53 2013 -0700 More cleanup of unused formal subroutine parameters. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit bf8310278e26a5319ec924d04c53071aa45e75bd Author: Ann Almgren Date: Tue May 21 15:42:21 2013 -0700 Fixed the cc wrapper and removed the memory print statements. Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit cb4ff4b2affe1b8bfd0e6e51e221927b8b260f8c Author: lijewski Date: Tue May 21 15:30:37 2013 -0700 Cleaned up some unused formal subroutine arguments. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit dab91a7cf951486c21bdfeebee73e4f5b8e7c8e8 Author: lijewski Date: Tue May 21 15:21:09 2013 -0700 Removed the unused "uu" argument to itsol_converged(). Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 commit f7dba8978fe382f4679b5f8fb2483a08e32e81ef Author: lijewski Date: Tue May 21 15:16:13 2013 -0700 Some more cleanup. Src/LinearSolvers/F_MG/itsol.f90 commit 189860aa227467a258b7b5f72fd4ee4253fcb239 Author: lijewski Date: Tue May 21 15:01:05 2013 -0700 Seems to work; at least for a simple nodal solve. Src/LinearSolvers/F_MG/itsol.f90 commit 0034acec085a13e3ad118016e73f0d23e072ea17 Author: lijewski Date: Tue May 21 14:46:24 2013 -0700 Still working on CABiCGStab. Src/LinearSolvers/F_MG/itsol.f90 commit 744b602aa312c748e1961279b6129d87dc656fff Author: lijewski Date: Tue May 21 13:56:33 2013 -0700 Yet more progress on CABiCGStab. Src/LinearSolvers/F_MG/itsol.f90 commit 0c49cfeb6313b7d2007383794dfc6763a8638e1e Author: lijewski Date: Tue May 21 13:01:36 2013 -0700 Added a optional args nodal_mask and local to multifab_dot_cc. Now multifab_dot_c() and multifab_dot() both call that routine. Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/itsol.f90 commit 98088be68b1678264f1c3cb1ec5125358be021d9 Author: lijewski Date: Tue May 21 11:21:39 2013 -0700 Some work on building Gram matrix. Src/LinearSolvers/F_MG/itsol.f90 commit 7b741b03a9d9f67ffd6b35f917ca193bec609dde Author: lijewski Date: Tue May 21 10:19:25 2013 -0700 Got "PR" filled. No way to know whether it's right or not yet. Src/LinearSolvers/F_MG/itsol.f90 commit 432433d65a3235f32cf58e42abff85ea2ffebee1 Author: lijewski Date: Tue May 21 09:27:14 2013 -0700 Elided some more reductions. Src/LinearSolvers/F_MG/itsol.f90 commit 10a082decd6fd58b85aa9c2a0cdb07669d79a0cf Author: lijewski Date: Tue May 21 08:58:14 2013 -0700 Some cleanup on the way ... Src/LinearSolvers/F_MG/itsol.f90 commit f3fb9d8269858dd27d532658228f90f27d9beb3b Author: lijewski Date: Mon May 20 13:34:33 2013 -0700 Some cleanup of DGEMV(). Src/LinearSolvers/F_MG/itsol.f90 commit d2eecbdb801945d7b2f73d1d228c9548f4a35020 Author: lijewski Date: Mon May 20 13:28:48 2013 -0700 Merged in slightly simlified version of the BLAS DGEMV() matrix-vector multiply routine. Src/LinearSolvers/F_MG/itsol.f90 commit ff3571c6512ee121ba7e8f2c82f67b594a330bce Author: lijewski Date: Mon May 20 11:28:19 2013 -0700 Added SetMonomialBasis(). Src/LinearSolvers/F_MG/itsol.f90 commit b594672c0d91f22e39871049ec3ebd68a6e2530b Author: lijewski Date: Mon May 20 11:06:35 2013 -0700 Still plugging away at CA algorithm. Src/LinearSolvers/F_MG/itsol.f90 commit 47cf7f234dc452cfbd3956b8b84d9c2b7d2bc0fb Author: lijewski Date: Mon May 20 10:50:14 2013 -0700 Yet more work on CA bottom solver. Src/LinearSolvers/F_MG/itsol.f90 commit 8e0acc7d076a19e0d850d1999c75cf53ad58f6c9 Author: lijewski Date: Mon May 20 09:48:29 2013 -0700 Just getting started with CA BiCGStab algorithm. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit aff94e0367cdee4d4fdf896c4f62c6eb004e5f54 Author: lijewski Date: Fri May 17 16:19:12 2013 -0700 Added BL_PROFILE() calls around MPI_Alltoall and MPI_Alltoallv in CollectData(). Src/C_BaseLib/FabArray.H commit 45be522aeb1d82f3e21766a39706cf28780b7d84 Author: lijewski Date: Fri May 17 10:34:19 2013 -0700 Used an OMP region instead of sequence of parallel do loops. Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 commit 3ab12cab946f3e0d6df32b2e05f79e0d9a7fbbfc Author: lijewski Date: Fri May 17 10:22:50 2013 -0700 Removed some divisions. Src/LinearSolvers/F_MG/nodal_divu.f90 commit f126c77f7e052a52e7efb51167006cc93d318ebf Author: lijewski Date: Fri May 17 09:59:39 2013 -0700 Some OMPing and code simplification. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit f2d59f01ed42b574d5236734cb39d12ff85e3468 Author: lijewski Date: Thu May 16 22:12:49 2013 -0700 More OMPing. Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 commit 88eda120b51b19da6d05cec6f699ceb793a5c738 Author: lijewski Date: Thu May 16 21:09:31 2013 -0700 Some OMPing. Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 commit 081e2f273f0049e756543272c9af25887bfee00e Merge: 2d6785e76 a90167a62 Author: lijewski Date: Thu May 16 20:19:56 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a90167a62f76f7f568ad83e836513f49ebb8940f Author: Ann Almgren Date: Thu May 16 19:15:57 2013 -0700 This is a cleaned up version that appears to work, for the nodal dense stencil in 2d anyway (using inputs.simple) Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/cc_single.f90 Tests/LinearSolvers/F_MG/inputs.simple Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_single.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 2d6785e76234d850a19b85955e387497cdb79574 Author: lijewski Date: Thu May 16 15:44:51 2013 -0700 Regularized some constants in the code. Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 commit 6b603fde54703ad38c5882d09b29c2dae846b413 Author: lijewski Date: Thu May 16 14:30:31 2013 -0700 Removed some divides. Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 282f1b267bbf99b53a6c58bb3896cf1b3ae245b6 Author: Weiqun Zhang Date: Thu May 16 12:25:40 2013 -0700 added functions to reset random number seed Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 01121c8ac4c4c90a99b7fc33e20c4a2fb06255cc Author: lijewski Date: Wed May 15 14:11:31 2013 -0700 Some code cleanup. Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit d3493605bff62e346e25643ee82b38d70b9f4a18 Author: lijewski Date: Wed May 15 13:34:33 2013 -0700 Now can print out solve time for tensor solve. Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 1f04c3098c011e28a57c7de71cdc40d7220a3d26 Author: lijewski Date: Wed May 15 13:34:21 2013 -0700 Tweak to output. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit c68cc3c711f24a9f75c6fe4464f94b62f24d0926 Author: Matthew Emmett Date: Wed May 15 09:50:28 2013 -0700 Add zmq_suffix and hdf_suffix. Tools/F_mk/GMakedefs.mak commit 46c4cab4ff7f33c12244435ce468a6c602e0946d Author: Weiqun Zhang Date: Tue May 14 14:14:10 2013 -0700 PGI does not like to have threadprivate as the last line in a class definition Src/C_BaseLib/Utility.H commit 75cc3f48c5986f5f11804c92e2be573236d18a9a Author: Weiqun Zhang Date: Tue May 14 12:09:57 2013 -0700 made changes because PGI is picky about where threadprivate directive is put. Src/C_BaseLib/Utility.H commit 22b9e1e1a9c680d0723dbfd8f6eb88e35d9a8129 Author: Weiqun Zhang Date: Mon May 13 17:53:10 2013 -0700 added functions to return the size of the random number generator state Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 56364e863f848c0448064512ca4ea79f35e8369f Author: lijewski Date: Mon May 13 12:28:50 2013 -0700 Unpacked some "array" assignments so I could OMP the loops. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 082e05b561ca9f53bcb7203b40a70c389ac7d1a7 Author: lijewski Date: Mon May 13 12:27:20 2013 -0700 Removed unused variable. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 000b4e454960b6f6161f58cab9a292bc248c1c81 Merge: 967f2f329 d0fc0f62e Author: lijewski Date: Mon May 13 11:26:36 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d0fc0f62e2708bf1d028bf5b8f9e0912b7485fe4 Author: Weiqun Zhang Date: Mon May 13 11:12:58 2013 -0700 minor changes to the initialization of random number seeds Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Utility.cpp commit 967f2f329eec4d0272a0017c49868d3c9e82b26b Author: lijewski Date: Mon May 13 10:58:48 2013 -0700 More MPI_Allreduce() elimination/reduction. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 63971e4b334f6d10b66212694f67f17cdd1779ad Merge: 29df26d59 d1fa3ab08 Author: lijewski Date: Mon May 13 10:58:29 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d1fa3ab0838beb4e459fe6cf44910fe4cb4f96b8 Author: Weiqun Zhang Date: Mon May 13 10:55:09 2013 -0700 made random number generator thread safe Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 29df26d597d0bf12edef02d49455ab12eaad6499 Author: lijewski Date: Mon May 13 10:11:02 2013 -0700 Little more OMPing. Src/LinearSolvers/F_MG/cc_stencil.f90 commit affac169ecf00ce5d01649d40a4b0c2b63e7b4e6 Author: lijewski Date: Mon May 13 10:02:10 2013 -0700 For stencil_norm and max_of_stencil_sum we thread on fab boxes not within fab boxes. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 0501a99d7c790f1f0a7479235f6c09b410533b2a Author: lijewski Date: Fri May 10 20:35:59 2013 -0700 Simiplification. Src/F_BaseLib/fab.f90 commit 380fa6291f9d7554ad3a0c0a232ecd8191aadb40 Author: lijewski Date: Fri May 10 20:35:26 2013 -0700 Fixed a bug I introduced earlier. Src/LinearSolvers/F_MG/cc_stencil.f90 commit d476ec557fbc326cebe5db2eb6b1a0159846b950 Author: lijewski Date: Fri May 10 20:10:03 2013 -0700 OMP'd max_of_stencil_sum(). Src/LinearSolvers/F_MG/cc_stencil.f90 commit 7d805b06a4617a9b51d4769b5d038cfe8a0f480c Author: lijewski Date: Fri May 10 19:49:09 2013 -0700 Threaded BuildGramMatrix() except for the reduction. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 91390572b51d0de91d0a72ecc65cba8959a2c381 Author: lijewski Date: Fri May 10 15:30:24 2013 -0700 Tad bit of refinement. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_norm.f90 commit ddad0537023c264e921db784f021529397fc58d3 Author: lijewski Date: Fri May 10 14:19:44 2013 -0700 Elided more reductions. Src/LinearSolvers/F_MG/ml_cc.f90 commit 5726458df6f87089297c191f34990fa47c5d1511 Author: lijewski Date: Fri May 10 14:19:17 2013 -0700 Added optional "local" flag to max_of_stencil_sum(). Src/LinearSolvers/F_MG/cc_stencil.f90 commit 9a106d613dc0b22b6f2c63dad070cb82c50af237 Author: lijewski Date: Fri May 10 13:39:29 2013 -0700 Yet more parallel reduction elision. Src/LinearSolvers/F_MG/ml_cc.f90 commit 65f57a7a32e253436740541255b64c0e20ee4582 Author: lijewski Date: Fri May 10 13:31:14 2013 -0700 Some parallel reduction elimination. Src/LinearSolvers/F_MG/mg.f90 commit 8d70c47a39a70746bb3da284da9349d6f1986e8d Author: lijewski Date: Fri May 10 13:30:11 2013 -0700 Added optional "local" flag to ml_norm_inf(). Src/LinearSolvers/F_MG/ml_norm.f90 commit 3a84d385e331ba9c2d181140e37566c54f57d662 Author: lijewski Date: Fri May 10 10:47:57 2013 -0700 More debugging & performance analysis output. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 585e1f3b938fb9c6107441865ce43d76ac148395 Author: lijewski Date: Thu May 9 22:40:59 2013 -0700 Elided some global reductions. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit fa27ae34a772e459f5dcde95c20d52a5be27572c Author: lijewski Date: Thu May 9 21:50:46 2013 -0700 Now can print out the multigrid time and accummulated bottom solver times. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 683d7656cb817b63af59a4d4e20d6ee53ccf8833 Author: lijewski Date: Thu May 9 17:21:51 2013 -0700 Removed multifab "sh" from BiCGStab; reuse "ph" instead. Src/LinearSolvers/F_MG/itsol.f90 commit 152df4fc1186e8039f29f737ac69088529dc813f Author: lijewski Date: Thu May 9 14:50:03 2013 -0700 Some cleanup and code simplification. Src/LinearSolvers/F_MG/itsol.f90 commit c0e4a8ee21694b75c2d4a9b3b6d889b12c662b64 Author: lijewski Date: Thu May 9 14:20:43 2013 -0700 Elided a few more reductions. Src/LinearSolvers/F_MG/itsol.f90 commit 9ae2a658a3701902c5efc8f8b74b6f695ef02bb6 Author: Weiqun Zhang Date: Wed May 8 17:31:38 2013 -0700 added reducelonglongsum to non-MPi build Src/C_BaseLib/ParallelDescriptor.cpp commit deb55b69b26a3c21e14ee27cd5d32059cff185bb Author: Weiqun Zhang Date: Wed May 8 17:22:51 2013 -0700 added -lmpich back Tools/C_mk/Make.mpi commit 972f4cc5bc4fbb76c8819565f73331d68eb90949 Merge: 4369b5b01 a4d54e6c4 Author: Weiqun Zhang Date: Wed May 8 16:24:22 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4369b5b0122ddd2dc02f45cf50df0c88906ad1f3 Author: Weiqun Zhang Date: Wed May 8 16:21:05 2013 -0700 Added long long to Mpi_typemap. Use long long for total number of particles in some functions. Some were not updated because it would require more significant changes. Src/C_AMRLib/Particles.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit a4d54e6c46c8f09f0841cce4114542965252654d Author: Michael Zingale Date: Wed May 8 19:20:25 2013 -0400 force double precision plotfiles + other changes Tools/RegressionTesting/Maestro-tests.ini commit 9bbb335719e1486f9ed67e5483ebccdd42fbae4d Author: Michael Zingale Date: Wed May 8 19:19:57 2013 -0400 ok -- for real now... Tools/RegressionTesting/testnew.py commit ead14f52c53ec177f4609267e49ee714623bdb4b Author: Michael Zingale Date: Wed May 8 19:03:57 2013 -0400 self -> suite in the enw parameter Tools/RegressionTesting/testnew.py commit d11fbbcbdef25583dabb895573062fbe066c8ee1 Author: Michael Zingale Date: Wed May 8 18:56:36 2013 -0400 add globalAddToExecString argument to allow a runtime option to be appended to all jobs. For Maestro, e.g., this is useful for forcing all plotfiles to be double precision via: globalAddToExecString = "--single_prec_plotfiles F" also fix a bug in the recent git updates that didn't work with the external build directories. Tools/RegressionTesting/testnew.py commit 3568310fe0f8c03ac73a465393938984137bff8d Author: lijewski Date: Wed May 8 14:57:09 2013 -0700 Increased SSS_MAX from 4 -> 6. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 0e08aa885ca39150a9f6e0257ca3a9a56d85127b Author: lijewski Date: Wed May 8 13:51:32 2013 -0700 Added some more verbose output. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 45b6e025945915d083e1baf8a51333a67e38e179 Author: lijewski Date: Wed May 8 11:19:29 2013 -0700 Added option variable_SSS which implies we "telegraph" the outer CABiCGStab loop from 1 -> SSS_MAX. This is on by default. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit bfce34457565d76321f3c51d2d348b3b823282a6 Merge: 55c0e55e8 ac1b3a666 Author: vince Date: Wed May 8 10:01:24 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ac1b3a666c086b3818de02d55458747fd0cf240a Author: lijewski Date: Tue May 7 15:31:42 2013 -0700 Some cleanup and improved comments. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 86ac79cda1698b5fe2e2d4d5ead32fab1aa3aabb Author: lijewski Date: Tue May 7 14:58:34 2013 -0700 Changed some of my verbose output. No longer try and calculate the norm_inf(r). Just go with the L2_resid as calculated by the algorithm. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 854dc7022069fdf61f1db0c380f2fb468a36b33d Author: lijewski Date: Tue May 7 14:37:49 2013 -0700 Merged in Sam's latest changes. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 55c0e55e84ca0fda2a07284f4eed760ec5043f21 Author: vince Date: Tue May 7 14:35:42 2013 -0700 prof def. Tools/C_mk/Make.defs commit e95bea145a9d7854375ba3d767701e09109b79c6 Merge: cf424f41d d2852871a Author: vince Date: Mon May 6 12:25:06 2013 -0700 Merge branch 'master' into commprof commit 2a8c6bce89e00d09efb79c952257f115d8561ea5 Merge: f98256641 a29472d8d Author: Chris Malone Date: Mon May 6 11:43:36 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit f982566413d1b24ba90c61f5a0742ce3bd622e59 Author: Chris Malone Date: Mon May 6 11:41:14 2013 -0700 simple program that calls the make_rates routine for a network, and builds a plotfile of the local rates based on the thermodynamic state this assumes the network is structured similar to that done in AstroDev/networks/rprox MAESTRO_xrb/GNUmakefile MAESTRO_xrb/frates.f90 commit cf424f41df7cc0a5b90492debabf2fc55dcb4581 Merge: be86c1c86 68e4f73de Author: vince Date: Mon May 6 11:28:04 2013 -0700 Merge branch 'master' into commprof commit d2852871af7aecd88d8f504a3dbb591c1cae49a0 Author: lijewski Date: Mon May 6 11:25:38 2013 -0700 Still more include "file" -> include Thought I had all of'm earlier. Src/LinearSolvers/C_CellMG/CG_1D.F Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F commit be86c1c8686d09c383817db97d56e0961ef67144 Author: vince Date: Mon May 6 11:24:07 2013 -0700 profiling doc. Docs/Readme.profiling commit 6d4c5dd163c4a60ccf6229c45cdf396a97d15277 Author: lijewski Date: Mon May 6 10:40:46 2013 -0700 A little code rearrangment. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 68e4f73ded6ed4f777c069814d030dfbba1e9746 Author: lijewski Date: Mon May 6 10:07:34 2013 -0700 The "S" in the CABiCGStab is now an input variable. It's currently limited to be in the range: [1,4]. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit b7d4bafcccf525cfce05d0aff8c2fadab76059fd Author: lijewski Date: Fri May 3 16:05:17 2013 -0700 Cut the number of apply() calls in CABiCG by two by doing each of the powers of p and r together in a single call instead of one call for each of the powers of p and r separately. Mostly this cuts down on FillBoundary() calls and should be a win in parallel. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit a0b8266219cde444f7fb8d9cdd2d7cf95ee56901 Author: lijewski Date: Fri May 3 16:03:46 2013 -0700 Removed a number of num_comp==1 assertions. I wanted to be able to call apply() with more than one component. Appears to work. Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit efeaf0671913329354714201d781dda83a092977 Author: lijewski Date: Fri May 3 14:17:53 2013 -0700 Changed some ifndef clauses to the more natural ifdef. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit bcb36eb3df770f3d8a9d70dd46bf01374f7d1dc6 Author: lijewski Date: Fri May 3 13:58:58 2013 -0700 Some more work on convergence criteria for CABiCG. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 2d4630b331ac3426e1df07771d47e1e5b502aa2c Author: lijewski Date: Fri May 3 09:56:17 2013 -0700 Be a little more careful about convergence tests. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit feda545f762b5f95d730ebb40d0266ba25956ba8 Author: lijewski Date: Fri May 3 09:05:18 2013 -0700 Removed some unneeded code. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit ebb69b5c6d6594d50f974a14a4b0460b5d01d710 Author: lijewski Date: Thu May 2 19:57:04 2013 -0700 Some refinrements and bug fixes. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit a38faca3c9020a1803203d10a92347ae91525090 Author: lijewski Date: Thu May 2 16:06:04 2013 -0700 A little code rearrangement. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit a52da0ecd005f09dfeba4e86830b3e6dd557956a Author: lijewski Date: Thu May 2 15:39:28 2013 -0700 Some work on making CABiCGStab output like BiCGStab output. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit d5dc20de4928011bd0a9030455e05aedc1be2101 Author: vince Date: Thu May 2 14:19:33 2013 -0700 fix for serial. Src/C_BaseLib/Profiler.cpp commit 22ab0d2edbfd4f3b9988e772ec4fbf2266a551d0 Author: vince Date: Thu May 2 14:09:20 2013 -0700 added mf test code. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit f4c41047ad8d6b77c56cda2ef4c9b901b15b4d21 Merge: 2f5baa126 1631f8df5 Author: vince Date: Thu May 2 14:08:17 2013 -0700 merge issue. commit ea2602cccb8a26594aec0e2ea590d0a913cb2b3a Author: lijewski Date: Thu May 2 14:06:15 2013 -0700 Added some profiler calls. Seems to work in parallel. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 2297a7a2583949b82dabb48093de94917158dd94 Author: lijewski Date: Thu May 2 12:49:54 2013 -0700 Looks to be more-or-less working! Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 7c03932be11cc40600b5174d1b155b240d50dc8d Author: lijewski Date: Wed May 1 17:20:46 2013 -0700 Getting closer ... Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 979c34ea079a9da14e1c6ff05ef061d4b6067b97 Author: lijewski Date: Wed May 1 16:40:44 2013 -0700 Getting close to having something testable. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 9788e6d4bc7b6acd1e6f9178f7b38b9aac8ca053 Author: lijewski Date: Wed May 1 16:12:05 2013 -0700 Don't think I had BuildGramMatrix quite right. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit b537a44e3f2f95a28c58939b359c8c0ed25eece9 Author: lijewski Date: Wed May 1 15:39:59 2013 -0700 Added BuildGramMatrix() code. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 69802194d69acaa4022f4e888f07bcd040129450 Merge: 3c8400801 8525cefd5 Author: lijewski Date: Wed May 1 14:51:55 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3c84008012765703453826cc600122f72796a4e3 Author: lijewski Date: Wed May 1 14:51:41 2013 -0700 More work ... Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 84e6ed32e1fbddec6a7af1450aeffd0c505ac467 Author: lijewski Date: Wed May 1 14:42:24 2013 -0700 A little more progress. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 8406d0bf3529a3dc266f4baf40033e1c3c1c6a59 Author: lijewski Date: Wed May 1 13:52:41 2013 -0700 More work on CA BiCGStab. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 8525cefd53e37b161a48de4a975ef3fed810b96f Author: Weiqun Zhang Date: Wed May 1 13:37:16 2013 -0700 added ReduceLongLongSum so that we can safely sum up big integers Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 674a50f2a4f67e5eccbac890acc6136a1ac331f5 Author: Ann Almgren Date: Wed May 1 13:07:51 2013 -0700 Changes for Blue Waters Cray compiler. Tools/C_mk/Make.Linux commit 00f35e832c7bc0fa8a226be9e5a6859e0db92936 Author: lijewski Date: Wed May 1 12:58:24 2013 -0700 Some work on CA BiCGStab. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 2010de83d487184f470cd5c80155558886f77c4d Author: lijewski Date: Wed May 1 12:24:53 2013 -0700 A little cleanup. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit b1b0de8e2f75c14eef18e34b98d837a4a54824dc Author: lijewski Date: Wed May 1 11:13:21 2013 -0700 Some setup to try & implement a communication avoiding BiCGStab solver. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 9380a35c3116f7eadf28faf69d359d5e019ca456 Author: lijewski Date: Wed May 1 11:12:48 2013 -0700 Removed stuff for setting default CG solver. It's now only in one place: in the CG code itself. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit afa293fcaa781aa0313c69c465bfa1964eb8d245 Author: Weiqun Zhang Date: Tue Apr 30 14:40:46 2013 -0700 Added optional argument verbose to ParticleBase::Reset so that we can turn off a print statement. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 7a6c5573acc3f504e6874210748cc855055733e3 Author: Weiqun Zhang Date: Tue Apr 30 14:19:03 2013 -0700 Added latex file describing equations solved by Exp_CNS_NoSpec. Tutorials/Exp_CNS_NoSpec/CNSEquations.tex commit 1631f8df5816625e223e34adb9c7e00e6230db3c Author: beckner2 Date: Fri Apr 26 13:42:11 2013 -0700 new machines. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 2f5baa1269d51e3dfc9bfa2e78e832744d5aaeec Author: vince Date: Wed Apr 24 16:05:07 2013 -0700 fixed ivLevel, ivLoc. Src/Extern/amrdata/AmrData.cpp commit aa937d5f640f707b6da5fdbcc8e4e179294c0a32 Author: Weiqun Zhang Date: Wed Apr 24 13:02:03 2013 -0700 Added more functions for random numbers. In addition to the old Real BoxLib::Random() that returns a number belonging to [0,1], Real BoxLib::Random1() returns a real number that belongs to [0,1); Real BoxLib::Random2() returns a real number that belongs to [0,1); unsigned long BoxLib::Random_int(unsigned long n) returns an integer belonging to [0,n). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 22a273535577c9f6989071031a7b11c7dd6bc852 Merge: 1c2b8ba58 f9ed13314 Author: lijewski Date: Fri Apr 19 16:31:55 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1c2b8ba582abd5ee4a45662b12abcc1d62870572 Author: lijewski Date: Fri Apr 19 16:24:05 2013 -0700 Removed an unnecessary setVal(). Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 5cc42a554764bc0cb08bf5f2f3b7d5bddc3de096 Author: vince Date: Thu Apr 18 15:03:02 2013 -0700 before/after call changes. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.cpp commit f9ed133141970d6307b9e19e7c9b9e1827dde1de Author: Matthew Emmett Date: Wed Apr 17 15:49:08 2013 -0700 Add parallel_set_comm. Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit f1508ce08bde62993d0a22ad954f058a64d40aaa Author: vince Date: Wed Apr 17 14:21:37 2013 -0500 garnet. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit cd446ccd68e322fc454994018025351d9e372178 Author: Weiqun Zhang Date: Tue Apr 16 11:02:31 2013 -0700 Using subprocess for git-checkout to avoid warning being sent to stderr of shell. Tools/RegressionTesting/testnew.py commit f475723f000ffa59ea8076bf172299fbb33fcebb Author: lijewski Date: Mon Apr 15 10:18:29 2013 -0700 OMP'd some more loops. Src/LinearSolvers/F_MG/ml_nd.f90 commit 46f70385c6ca272b68fbb9c3e96ef64c76986f34 Author: lijewski Date: Mon Apr 15 10:07:15 2013 -0700 OMP some more loops. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 commit cd16624f2d84bb156d959d00938741f46b405585 Author: lijewski Date: Mon Apr 15 09:48:37 2013 -0700 Some rearrangement to enhance vectorization. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit b2d4ad552a90d70271b0935b64790bf139f92092 Author: lijewski Date: Fri Apr 12 15:39:34 2013 -0700 Added some "IF" clauses to OMP loops so that we ignore threading when the Z dimension is too small to yield useful work. Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/itsol.f90 commit a7355407c639ab45555c6d702c8bbd8057193aba Author: vince Date: Fri Apr 5 13:33:09 2013 -0700 beforecall. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit e905bb0c385b4e107d7d4ce5758997ebe09c393b Author: lijewski Date: Thu Apr 4 15:13:35 2013 -0700 Yet more replacements of divisions by multiplications. Src/LinearSolvers/C_TensorMG/DV_3D1.F Src/LinearSolvers/C_TensorMG/DV_3D4.F commit d4f97207a4df35a9eaad4b21d391ddb0ef6211cc Author: lijewski Date: Thu Apr 4 14:49:21 2013 -0700 Replaced more divisions with multiplies. Src/LinearSolvers/C_TensorMG/DV_3D3.F commit 3b0bc2926e2f70756e82d740019364922630e2f4 Author: lijewski Date: Thu Apr 4 13:20:27 2013 -0700 Elide another reduction in the "singular" portion of BiCGStab. Src/LinearSolvers/F_MG/itsol.f90 commit 0bce69fd1e977ae24168490566c541684847d7a4 Author: lijewski Date: Thu Apr 4 11:25:16 2013 -0700 Elided another reduction in BiCGStab by combining the reductions for two dot-products into the same call. Src/LinearSolvers/F_MG/itsol.f90 commit c350825d8c62e18d91aef59952767348a39ae071 Author: lijewski Date: Thu Apr 4 11:23:44 2013 -0700 Added optional "local" argument to multifab_dot() to calculate only the "local" value of the dot_product. Src/F_BaseLib/multifab_f.f90 commit 008b7618973e15e0bcafd9de6e42b4b425413383 Author: lijewski Date: Thu Apr 4 10:51:21 2013 -0700 Elide some reductions in BiCGStab. Src/LinearSolvers/F_MG/itsol.f90 commit 14f1e672df6320eea860b338faea30d98988a1db Author: lijewski Date: Thu Apr 4 10:51:00 2013 -0700 stencil_norm() now takes an optional "local" flag. Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 commit e6c0469433b77b1a05940ce7337dbde748d6aa2d Author: lijewski Date: Thu Apr 4 10:05:43 2013 -0700 Added optional argument "local" to norm_inf() so we can calculate the local value of the norm without doing the parallel reduce. Src/F_BaseLib/multifab_f.f90 commit 4616685846173995e45e8f4117fe0805279aeba7 Author: lijewski Date: Wed Apr 3 16:16:50 2013 -0700 Elided another reduction in BiCGstab by calculating the local values of two norms() and then reducing them together. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 735105b9b533d8319f38c450aca343290daf3723 Author: lijewski Date: Wed Apr 3 15:28:27 2013 -0700 More eliding of divides. Src/LinearSolvers/C_TensorMG/DV_3D1.F Src/LinearSolvers/C_TensorMG/DV_3D2.F commit d920c3b85c029fea9cfe6c8fd43e771007db4eae Author: lijewski Date: Wed Apr 3 15:00:39 2013 -0700 Replaced most divides by multiplies in apply(). Src/LinearSolvers/C_TensorMG/DV_3D1.F commit ac33c28c5665ad3c37336ef5d8de6fb2e25b2b46 Author: vince Date: Wed Apr 3 13:30:26 2013 -0700 nfiles for headers. smaller header files. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Profiler.cpp commit 44daec6c9f47d3caf4cdfa2c37ff2c3e7558dd90 Merge: bab312e30 d9baef115 Author: Chris Malone Date: Tue Apr 2 15:08:27 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit bab312e308b18b047056b0beeb2e3033cd91c450 Author: Chris Malone Date: Tue Apr 2 15:07:41 2013 -0700 UCSC pleiades --> hyades changes Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit d9baef115645e1626128a5c223ccf34832f74651 Author: lijewski Date: Tue Apr 2 13:46:04 2013 -0700 Yet more cleanup of unused variables. Src/F_BaseLib/parallel_stubs.f90 Src/LinearSolvers/C_TensorMG/DV_3D2.F Src/LinearSolvers/C_TensorMG/DV_3D3.F Src/LinearSolvers/C_TensorMG/DV_3D4.F commit bc330180d5ee531641ce6716efe63a68f6bf16cd Author: lijewski Date: Tue Apr 2 12:11:26 2013 -0700 Cleaned out some unused variables. Src/LinearSolvers/C_TensorMG/DV_2D.F commit 59128b2e6ced09433758bf7962958cc5829c5ee9 Author: lijewski Date: Tue Apr 2 12:10:47 2013 -0700 Added -Wno-maybe-unitialized flag to [f,F]DEBF. Tools/C_mk/Make.defs commit c1a80caf85f3f4a1bcf7d7b54891495004db895a Author: lijewski Date: Tue Apr 2 09:10:22 2013 -0700 Now gcc, g++ & gnu are equivalent when used as COMP. Tools/C_mk/Make.defs commit 5558da5748520ef743cc892c42db9a7b6169b7c1 Author: beckner2 Date: Mon Apr 1 16:40:33 2013 -0700 fixed nfiles init. Src/C_BaseLib/VisMF.cpp commit d01971f54d6dc38d034608be941a0f6465801e2f Author: beckner2 Date: Mon Apr 1 16:39:12 2013 -0700 fixed init nfiles. Src/C_AMRLib/Amr.cpp commit 79deeb35afc617853928787601e8c167bfe9a197 Merge: 98d822a4e 36d111f2e Author: jbb Date: Mon Apr 1 15:07:19 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 98d822a4e2f996e1acfe882b3f6798d833b031c3 Author: jbb Date: Mon Apr 1 15:06:56 2013 -0700 fixed mpi path on mothra Tools/F_mk/GMakeMPI.mak commit c7c986a9c6704f25a6e3d63c6fc3714c30873e13 Merge: 7b60415aa bea384748 Author: beckner2 Date: Mon Apr 1 14:55:23 2013 -0700 hera. commit bea3847480c3284d9f5ea5c7948ad23afd6e63b8 Merge: fde2c3f61 36d111f2e Author: vince Date: Mon Apr 1 14:48:55 2013 -0700 Merge branch 'master' into commprof commit fde2c3f61fdf2bf2490d687c8b969f2a089171ce Author: vince Date: Mon Apr 1 14:47:45 2013 -0700 tweak for waitsome. Src/C_BaseLib/Profiler.cpp commit 36d111f2e2d499fb4e5c86aaad533c7dc840816d Author: lijewski Date: Mon Apr 1 14:08:39 2013 -0700 A little cleanup. Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit fe306cf69eba3be4d1660a696460fd2938b4d555 Author: lijewski Date: Mon Apr 1 13:42:54 2013 -0700 Elided one of the global reduction operations in the BiCGStab by doing the "local" part of two dot products and then calling one global reduction on the "pair" of values. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 7b60415aa1a88fb4cc9ffdfcb3d2faabdf15647b Author: Vincent Eric Beckner Date: Mon Apr 1 11:51:53 2013 -0700 hera. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 1a563d14da6f8644638397fa9e34d47a4fda98bf Author: lijewski Date: Mon Apr 1 11:11:31 2013 -0700 Removed OpenMP stuff. Not enough work in bottom solver to be worth it. Src/LinearSolvers/C_CellMG/CG_3D.F commit ccd7082165d17e5452b05dd2eefe4b92d6cc19cb Author: vince Date: Fri Mar 29 17:20:45 2013 -0700 more support for send recv and nametags. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 8c92d23f96eb500c4074a3d42b7a517c45680623 Author: lijewski Date: Fri Mar 29 09:20:22 2013 -0700 Changed many of the divides to multiplies for a modest speedup. Src/LinearSolvers/C_TensorMG/DV_3D3.F commit ad4ac342e975b83d1fb70203b2f3b233d7c0e24b Author: vince Date: Wed Mar 20 16:18:04 2013 -0700 improved flushing. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 8791cb85c8a26c2d7ab1f7cb213ec560ad59160e Author: lijewski Date: Wed Mar 20 15:59:49 2013 -0700 Don't need -ftree-vectorize for gnu. It's implied with -O3. Tools/C_mk/Make.defs commit 37eeb30dc74d19688efa5d72c15dbc13b43ef686 Author: vince Date: Wed Mar 20 10:42:56 2013 -0700 added more profiling. Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp commit 6665c67d5d0868813df9eb0bacdbeb57b020e46a Merge: 4ef6bf774 c88f2cd49 Author: lijewski Date: Mon Mar 18 14:18:23 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c88f2cd49459208e27100e9835808f52d10a1972 Author: Weiqun Zhang Date: Mon Mar 18 14:17:22 2013 -0700 added -std=c99 to CFLAGS for gcc and icc ib F_mk Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/gfortran.mak commit 4ef6bf77493dab05f3e79bf5dd51c324669b05d1 Author: lijewski Date: Mon Mar 18 14:16:29 2013 -0700 Turned on -std=c99 for both gnu & intel C compilers. This allows the "restrict" keyword in C files; we want to add this in select places in our chemistry mechanism files as it leads to better optimization. Also, only for gnu, added the -ftree-vectorize option to the C optimization flags. Tools/C_mk/Make.defs commit bc3f5f901deb7409c0e7ea909d150bc2c31302b7 Author: vince Date: Mon Mar 18 12:50:41 2013 -0700 more flushing. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 76b74d0293793d2388a4503417ea05603dc9ad0e Author: Weiqun Zhang Date: Fri Mar 15 17:30:51 2013 -0700 added vectorization to gcc in F_mk; if nothing breaks, we can add that to C++ part too. Tools/F_mk/comps/gfortran.mak commit d874380851c3f0109c4d2f0a58e1f1ba5e8efa37 Author: lijewski Date: Fri Mar 15 14:37:39 2013 -0700 Changed the default optimization flags for Intel12 and Intel13 from "-O3 -ip -mp1" to "-O2 -ip -fp-model source -xHost". This can be a big win for some codes. On a MAESTRO test (wdconvect) my run went from 153 seconds -> 96 seconds with this change on edison.nersc.gov. Tools/F_mk/comps/Linux_intel.mak commit dd712ece83e9dc5b525f6221d99b81b811dbd356 Author: lijewski Date: Fri Mar 15 14:32:55 2013 -0700 For Intel changed -fp-model precise -> -fp-model source Also added -xHost to optimization flags. Tools/C_mk/Make.defs commit 9cfd84c1f7379ee7ef90fca40d3fb3c97f0683b4 Author: Weiqun Zhang Date: Fri Mar 15 13:35:53 2013 -0700 ifdef STDC99, add c99 support option to gcc and intel. Note that pgi and cray now support c99 by default. Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/gfortran.mak commit dcb4972adff853edacd09679eb2a6eac9d28ece3 Author: lijewski Date: Thu Mar 14 13:38:47 2013 -0700 A little cleanup. Tools/C_mk/Make.defs commit 80bdc38e2c4f584ac7abf9a742e63c712516e922 Author: lijewski Date: Thu Mar 14 12:56:37 2013 -0700 Make sure C flags are same as C++ flags for gnu. Tools/C_mk/Make.defs commit 0bb9c429f4a21572d0cfe52746f3501c0a7bbb2b Author: vince Date: Tue Mar 12 16:19:57 2013 -0700 verified flushing, allow profiling without comm, named more barriers, cached times to header. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp Tools/C_mk/Make.defs commit b990d85c9adf2d3723690882eec1e008afc8563e Author: vince Date: Mon Mar 11 16:21:37 2013 -0700 made call orders consistent. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit f3e6570c7ee4b5810d70941ac63a6c6ce8ce72cb Author: vince Date: Fri Mar 8 13:22:21 2013 -0800 merged interfaces, added calls. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit a29472d8dfd7906fb74f85fdc2d00eab8e11f00a Author: Weiqun Zhang Date: Mon Mar 4 13:00:08 2013 -0800 Option to dump a plotfile for errors in finite-difference fcompare ffdcompare.f90 commit 4eb59f5a1dee502d0d1b836e6bb1f1234ce5159c Author: vince Date: Fri Mar 1 14:51:53 2013 -0800 added tracking of reduction wait times. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 5381c7f30e54a84a334385f88a4763b951c9dbad Merge: 566a141c9 52974d185 Author: Matthew Emmett Date: Thu Feb 28 13:31:30 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 566a141c963bd835c7f9737693069eff301b37ea Author: Matthew Emmett Date: Thu Feb 28 13:31:24 2013 -0800 Add profiling to multifab_saxpy_3. Src/F_BaseLib/multifab_f.f90 commit 18779b057e7dbfc3cd0b5a0aafa713460cdebee9 Author: vince Date: Thu Feb 28 12:01:51 2013 -0800 barrier changes. Src/C_BaseLib/Profiler.cpp commit 62a83c3b9d8ccb91ab34d2960df240852ea7cd7c Author: vince Date: Thu Feb 28 11:24:38 2013 -0800 more tags, reduced function parameters. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 52974d185c6279a21d2dd61b1d9edf687250059d Author: ajnonaka Date: Thu Feb 28 10:22:01 2013 -0800 cleanup of max_mg_nlevels. also fixed the single-grid case, which was not allowing for a 2x2 bottom solve due to some messed up logic that was protecting us in the (unused to my knowledge) minwidth=1 case Src/LinearSolvers/F_MG/mg.f90 commit 8bbe7e30f32f7941d7f35991b728b3b42705b366 Author: lijewski Date: Tue Feb 26 09:08:23 2013 -0800 Added "-fp-model precise" to the optimization options for both the C++ and Fortran flags for Intel. This fixes an optimization bug in the DME_jet problem on edison. Weirdly, the default for Intel is to allow extensive floating point rearrangement during optimization. The above option disables enough of that such that the problem appears to run correctly. Tools/C_mk/Make.defs commit b4d423c88a9768d239421439928725c24b577ec2 Author: lijewski Date: Tue Feb 26 07:21:39 2013 -0800 A workaround to the tellp() bug we found on edison.nersc.gov. Hopefully it doesn't break anything else :-) Src/C_BaseLib/VisMF.cpp commit 51c883df928cd7216b777b5841b96ddb792e9532 Author: Weiqun Zhang Date: Mon Feb 25 13:37:14 2013 -0800 fcompare for finite-difference results ffdcompare.f90 commit 731b22279d0fb0f917a307f72d23854135161894 Author: Ann Almgren Date: Sat Feb 23 17:19:02 2013 -0800 Add GetParticleData access routine. Src/C_AMRLib/Particles.H commit 9deb2847018ed1e32df0576020644fd5a0ae9fcc Author: Michael Zingale Date: Fri Feb 22 19:18:58 2013 -0500 add -h fp0 to all the Cray optimized flags. Experimentation on Titan has shown that this prevents strange compilation errors resulting in crashes in BoxLib. This forces the compiler not to do any crazy optmizations that violate the floating point standard. Tools/C_mk/Make.Linux commit 3de72abfa656b5bfb23e5924ddd643443b25684f Author: lijewski Date: Thu Feb 21 16:49:10 2013 -0800 A little cleanup. Tools/C_mk/Make.defs commit 09d454ea62292669fbddb59547ed947fd88a250b Author: lijewski Date: Thu Feb 21 14:58:35 2013 -0800 Merged in GhostParticleID and VirtualParticleID and cleaned up CreateVirtualParticles() and CreateGhostParticles() a bit. Src/C_AMRLib/Particles.H commit 1c068b937e94ac3c94bb9026810586ffa3d4cc42 Merge: a9f35c7c6 75a5406c9 Author: lijewski Date: Wed Feb 20 12:54:05 2013 -0800 Merge branch 'redistribute' commit a9f35c7c6e7d09dfd37dc6ddf3036a2818cb8d92 Author: lijewski Date: Wed Feb 20 08:38:53 2013 -0800 Removed IF() qualifiers on OMP PARALLEL DO loops. I recently found an example on edison where the presence of one of these qualifiers caused a compile to take 100x longer than when it's not present. I just don't think the compiler can be doing anything good/useful in that time. Src/LinearSolvers/F_MG/cc_restriction.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/edge_restriction.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_restriction.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit d51e8c22051ee32646ca429b1bf8cc5ae3b627d2 Author: vince Date: Tue Feb 19 17:36:57 2013 -0800 added user filtering and name tags to separate parts of the code for easier communication analysis. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 4c75c8659529cf2c4394eea31d394d520d7f2a01 Author: lijewski Date: Tue Feb 19 15:11:23 2013 -0800 Got this stuff to compile again; it's been a while. Not sure whether it works or not. Some of the stuff with the new way to specify stencils may require some modification. Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_single.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_single.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 6c33a16bafa01391f4e87a60d9edde4f09dc3fb0 Author: lijewski Date: Tue Feb 19 15:10:31 2013 -0800 Added edison stuff to mirror hopper. Tools/F_mk/GMakeMPI.mak commit 052d256725fdd7a826d8788c4dbae8f7cc3a6e51 Author: vince Date: Tue Feb 19 14:59:47 2013 -0800 implemented flushing of the commstats. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit bc0e193844cef5aabe510bb79b76c2a178d70fb3 Author: lijewski Date: Tue Feb 19 13:58:14 2013 -0800 Remove some COLLAPSE() stuff I recently added. The Intel compiler on edison generates bad code. Src/C_BaseLib/SPECIALIZE_3D.F commit 7fe3ef6fde23bb2cc94e7a3b5715817dd1b0c74f Author: lijewski Date: Tue Feb 19 12:35:13 2013 -0800 Revert out all the recent OMP COLLAPSE stuff. The lastest Intel compiler on edison (13.0.1) produces bad code. Hopefully I can find a simple example that illustrates the bug to pass on to Intel. Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab_f.f90 commit dfa81aac6c16efef3d3eacd63da1cd92619deea3 Author: lijewski Date: Tue Feb 19 09:08:15 2013 -0800 Add -openmp flag for Intel C compiler when USE_OMP=TRUE. Tools/C_mk/Make.defs commit caef7a901564d19019494c8b805337250e8306e4 Author: lijewski Date: Tue Feb 19 09:04:41 2013 -0800 Wrapped omp pragmas with ifdef _OPEN to shut up warnings when OpenMP is not enabled. Src/F_BaseLib/fabio_c.c commit bb57c9b81cc3b50112025696e30c9304664a326f Author: lijewski Date: Tue Feb 19 08:18:11 2013 -0800 Duplicated hopper stuff for edison. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 75a5406c9e2e453ad7e58677de0c28fea786c45c Author: lijewski Date: Sat Feb 16 21:19:27 2013 -0800 Fixed bug in commit for case where boundaries aren't all periodic. Src/C_AMRLib/Particles.H commit 4178ef03779bc3946b49bb431b352d2acf2f1783 Author: lijewski Date: Sat Feb 16 19:08:13 2013 -0800 Some cleanup. Src/C_AMRLib/Particles.H commit 2fbe6f14ee98b62c75f75dcd1854e0e0d2b7c25b Author: vince Date: Thu Feb 14 15:25:14 2013 -0800 named barriers, local message filtering, all/none filtering. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/VisMF.cpp commit 51a920c36e22a5468c7270f0f569906a45b2f2f2 Author: lijewski Date: Thu Feb 14 11:22:43 2013 -0800 A little cleanup. Src/C_AMRLib/Particles.H commit c6d7f78568c39c7cc25370dd763f9c791a331c6b Merge: e0268fede 766c05a90 Author: Chris Malone Date: Thu Feb 14 13:44:55 2013 -0500 Merge branch 'master' of https://ccse.lbl.gov/pub/Downloads/BoxLib commit e0268fede151c9333cae64e1c397e4659f678f09 Author: Chris Malone Date: Thu Feb 14 13:44:28 2013 -0500 some cleanup and get this working with cce/8.1.3 Tools/C_mk/Make.mpi commit 766c05a9008d6315d6f45eb20fd80ec325befb88 Merge: 2184e5753 4099ee3c6 Author: lijewski Date: Wed Feb 13 16:02:13 2013 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2184e5753d927ec4210c89314ad810a1a673c15e Author: lijewski Date: Wed Feb 13 16:01:55 2013 -0800 Made the destructor for ErrorRec virtual. Src/C_AMRLib/ErrorList.H commit 61d1bbe0b7e07d3ff6b9e4b8214d9ed6ca6b9168 Author: lijewski Date: Wed Feb 13 15:53:24 2013 -0800 Little more work on AssignDensityDoit(). Still needs testing. Src/C_AMRLib/Particles.H commit 3462886374a83200f2de381abfab22054da729f8 Author: lijewski Date: Wed Feb 13 15:14:08 2013 -0800 More work on AssignDensityDoit(). Src/C_AMRLib/Particles.H commit 4099ee3c6d16dc8709073da7d5fe7495c39abd18 Author: Chris Malone Date: Wed Feb 13 17:33:08 2013 -0500 generalize the fix for PGAS error for Cray versions >= 8.1.2 Tools/C_mk/Make.mpi commit a1c576431d77856a43d5c51944d769c21ea9640b Author: lijewski Date: Wed Feb 13 14:32:47 2013 -0800 Some work on AssignDensityDoit() to use send/recv pairs instead of Alltoallv(). Src/C_AMRLib/Particles.H commit 2b9bb0dfa4f3170151c51b8c940e922e92ab104e Merge: 138819038 9c0a79140 Author: lijewski Date: Wed Feb 13 13:07:35 2013 -0800 Merge branch 'redistribute' commit 9c0a79140c0a4749f4ace67d95c69d5891af6542 Author: lijewski Date: Wed Feb 13 13:04:15 2013 -0800 Merged RedistributeMPI() into AddParticlesAtLevel(). Src/C_AMRLib/Particles.H commit 138819038ac8957e990591de3f6f6244977951e6 Author: Weiqun Zhang Date: Wed Feb 13 12:47:58 2013 -0800 got around Cray compiler bug Src/F_BaseLib/multifab_f.f90 commit bc29013aff6cd118760e197afeb44c1681de15d2 Author: lijewski Date: Wed Feb 13 12:25:52 2013 -0800 Merged in RedistributeMPI(). Src/C_AMRLib/Particles.H commit 07dc4c92ec454e69eec44b17eff9fb4fee3d15d8 Author: lijewski Date: Wed Feb 13 10:45:49 2013 -0800 Finished Redistribute(). Now uses Send/IRecv instead of Alltoallv(). AddParticlesAtLevel() needs to be redone as well. Src/C_AMRLib/Particles.H commit 83e71c3421988fbbfb34276300597b3db5148309 Merge: bf75c369d 9a5758554 Author: vince Date: Tue Feb 12 16:52:13 2013 -0800 Merge branch 'master' into commprof commit bf75c369d40e2a165fd40444cb105a195d1774b2 Author: vince Date: Tue Feb 12 16:51:10 2013 -0800 some changes to the output format. Src/C_BaseLib/Profiler.cpp commit 4972f2a8b45a5521ffc9d7977672008e66618e91 Merge: d744b9519 a80712e76 Author: vince Date: Tue Feb 12 11:03:52 2013 -0800 Merge branch 'master' into commprof commit d744b95195dd156e08ebc3686fd4492c8fde3286 Author: vince Date: Tue Feb 12 11:03:35 2013 -0800 more support for the output parser. Src/C_BaseLib/Profiler.cpp commit baf877ad6e7ff4d590663965c5a2c142b5f01343 Author: lijewski Date: Mon Feb 11 21:14:25 2013 -0800 Looking good. Redistribute() now uses Send/IRecv pairs instead of Alltoallv. Src/C_AMRLib/Particles.H commit aa49f8c36763f910a0ec21b183e65bb27debda6b Author: lijewski Date: Mon Feb 11 20:50:33 2013 -0800 Closer still. Appears to work. A little more refining to go. Src/C_AMRLib/Particles.H commit a0f0285e2ae53aaa3b037f3ba23467f1951fc8f7 Author: lijewski Date: Mon Feb 11 19:55:41 2013 -0800 More work on Redistribute(). Getting close. Src/C_AMRLib/Particles.H commit 30e1f57b67df23321213f8f9c95dde472d066945 Author: lijewski Date: Mon Feb 11 19:24:06 2013 -0800 Yet more work on Redistribute(). Src/C_AMRLib/Particles.H commit c191aac43a4bb8b9a6506c9f6e7046a132757742 Author: lijewski Date: Mon Feb 11 18:59:35 2013 -0800 More work on Redistribute(). Src/C_AMRLib/Particles.H commit bde99fbf1bda15798cdfc741903095c2c651d340 Author: lijewski Date: Mon Feb 11 18:21:59 2013 -0800 Some work on Redistribute(). Src/C_AMRLib/Particles.H commit 70d3222cf3d3585e5df7ea77beb4fee683a76e70 Author: vince Date: Fri Feb 8 14:58:46 2013 -0800 binary nfile output with header. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 9a57585542e9d0eb887bdaf790d6191aa44db318 Author: lijewski Date: Fri Feb 8 14:56:25 2013 -0800 Reverting out previous mod. Src/C_AMRLib/FLUXREG_3D.F commit 489e912400499bd9712b4028f5d813683e1a40ec Author: lijewski Date: Fri Feb 8 14:03:51 2013 -0800 Some OMP tweaking. Src/C_AMRLib/FLUXREG_3D.F commit 46d08c353342b570378b590b640786935cd9dd37 Author: lijewski Date: Fri Feb 8 13:45:58 2013 -0800 Some OMP tweaking. Src/C_BaseLib/SPECIALIZE_3D.F commit 808b7576faf5b9c6de0dadbd87e739f8e80b1b99 Merge: d3cc0d47b cfe1e71c7 Author: ajnonaka Date: Fri Feb 8 10:31:24 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d3cc0d47bf47451caa1278e3f194cd9625fe7fdb Author: ajnonaka Date: Fri Feb 8 10:31:06 2013 -0800 more bc types for stokes_preconditioner code Src/F_BaseLib/bc.f90 commit cfe1e71c7920651526915388b56f447b3dd69f52 Author: Weiqun Zhang Date: Thu Feb 7 21:59:07 2013 -0800 It appears that Intel compiler has a bug in debug mode. It got some internal compiler errors with some new OpenMP stuff. So some changes were made to get around that. Src/F_BaseLib/multifab_f.f90 commit b6d4cbf66bab53778381dd2f4c9d44b42fd325bf Author: Weiqun Zhang Date: Thu Feb 7 17:12:34 2013 -0800 added OMP to reshape_d_? in data packing/unpacking for MPI Src/F_BaseLib/multifab_f.f90 commit b86d54cdd8d3f34c2dd8c0970080a7c3f3c24a7b Author: Matthew Emmett Date: Thu Feb 7 10:46:33 2013 -0800 Python: Minor tweaks. Src/Python/pyboxlib/fab.py Src/Python/src/fboxlib.f90 commit 0365100bc54b9cd861af0fcdaf93460a370bb71a Author: Matthew Emmett Date: Thu Feb 7 10:45:19 2013 -0800 Remove volume from finite-difference convergence tool. Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp commit fc961e42ed7d301581fb9181515102be4d2631c9 Author: Adam Jacobs Date: Thu Feb 7 11:41:20 2013 -0500 More faverage edits/fixes to the RMS calculations faverage.f90 commit ddcc2c52b6d51300c3edff26834c0a5cfa847eb0 Author: vince Date: Wed Feb 6 17:22:53 2013 -0800 added more message tagging support. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 2eccebf90229f5b2fcfa7868152c5222c720536c Author: vince Date: Wed Feb 6 16:19:02 2013 -0800 implemented nfiles for bl_prof output from all procs. Src/C_BaseLib/Profiler.cpp commit 4117e35b2076300d26c0db1f18573656279d7ff3 Author: Weiqun Zhang Date: Wed Feb 6 16:14:52 2013 -0800 added OMP to setval in F_BaseLib Src/F_BaseLib/fab.f90 commit bc4853f44d629cc457fa697cb98bf7a24da116fd Author: Weiqun Zhang Date: Wed Feb 6 16:14:00 2013 -0800 added OMP to sum_d in F_BaseLib Src/F_BaseLib/multifab_f.f90 commit 95704452d929b4c924a4278e313687b81321cf41 Author: vince Date: Wed Feb 6 15:30:50 2013 -0800 added more counters. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 9add098c56d691e49207692819090ece3f34c3e7 Author: Adam Jacobs Date: Wed Feb 6 17:38:56 2013 -0500 Fixed AmrPostprocessing/F_Src/faverage.f90 so that it properly weighs data from coarse cells. faverage.f90 commit ba22852db7d2bdfa340396ccf34f5d77251aaf05 Author: Weiqun Zhang Date: Wed Feb 6 14:23:54 2013 -0800 OMP multifab copy in F_BaseLib Src/F_BaseLib/multifab_f.f90 commit 62bc03e72db963a742655752ab1a02619f9e43d9 Merge: 0f141093b 0826b85cb Author: Weiqun Zhang Date: Wed Feb 6 13:08:26 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0f141093b5f624cad89064203d21f8b64283f483 Author: Weiqun Zhang Date: Wed Feb 6 13:07:25 2013 -0800 Collapsed some OMP DO's. Src/F_BaseLib/multifab_f.f90 commit 0826b85cbed41614dd58b663e87e26c40f2b9299 Author: cmalone Date: Wed Feb 6 12:00:30 2013 -0600 updates for BW Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 4db455c576be9e1977339d859c2bc8751e87c534 Author: vince Date: Tue Feb 5 16:32:46 2013 -0800 more handling profiled names that are not on the ioproc. Src/C_BaseLib/Profiler.cpp commit 92cca5ae86d3febe8dbbbbd58d78494237bea528 Author: vince Date: Tue Feb 5 15:58:15 2013 -0800 handle profiled names that are not on the ioproc. Src/C_BaseLib/Profiler.cpp commit 57bd6f117fbc00c053adaea7c5bfae01eb90851d Author: vince Date: Mon Feb 4 15:05:19 2013 -0800 synced profiled names list across procs. Src/C_BaseLib/Profiler.cpp commit da755fe74e8317503539df577d7147903384c4c7 Author: vince Date: Fri Feb 1 14:11:32 2013 -0800 nfiles for commstats, cleaner init. Docs/Readme.profiling Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit f392d2cb8c015b3006ab0884348c04d461c5977b Merge: d74183b13 66f8d7cd1 Author: Ann Almgren Date: Fri Feb 1 13:51:28 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d74183b13aa7bfae8e26d263a4bb8d884b4601d4 Author: Ann Almgren Date: Fri Feb 1 13:51:16 2013 -0800 Add more functions to ParticleContainerBase. Src/C_AMRLib/Particles.H commit 66f8d7cd1efc85d46c95ab952f71b38f389ec940 Author: Michael Zingale Date: Fri Feb 1 15:02:11 2013 -0500 one more clean-up -- there were two separate blocks for the GNU compilers, one invoked if we did COMP=gcc and the other for COMP=g++ -- they both did the same thing. Now we define a variable USE_GCC if we come in with either of these COMPs, and have a single block for the GNU compilers. Tools/C_mk/Make.defs commit 082302ee47cf1e2170125d77f5cf1ecf7dd8a45e Merge: 03eedb10c a6eea6ddd Author: Michael Zingale Date: Thu Jan 31 18:50:36 2013 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 03eedb10ceece8b2850c3def6287bb5c797cd279 Author: Michael Zingale Date: Thu Jan 31 18:48:37 2013 -0500 remove atlas and yana -- they've been retired also remove the special stuff for sn.astro here -- it can use the MPI wrappers. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 2ec510a7a3c19316493b3dd6021bea93fb7ea748 Author: vince Date: Thu Jan 31 15:47:20 2013 -0800 implemented message filtering. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit a6eea6ddd673d53ccc23029600b959c949c0e8cb Author: Ann Almgren Date: Thu Jan 31 15:37:34 2013 -0800 Add new functions to the ParticleContainerBase. Src/C_AMRLib/Particles.H commit dce29a5ac70f94e7c62ff0f8d1db4497c6e0581b Author: Michael Zingale Date: Thu Jan 31 14:18:53 2013 -0500 remove support for the Cray Y-MP, J90, and C90 Tools/C_mk/Make.CRAY Tools/C_mk/Make.defs commit 0b6a49edb0686a2a7f04d0e21fd4725da08e7187 Author: Michael Zingale Date: Thu Jan 31 13:58:51 2013 -0500 some cleaning. Remove old machines and architectures. Cray X-1, IRIX, OSF1 (a DEC O/S), SUPERUX (NEC SX6), and the T3E. Also Make.frank seems to have been orphaned. Finally, also remove the Franklin machine, since that no longer exists Tools/C_mk/Make.CRAYX1 Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.Linux Tools/C_mk/Make.OSF1 Tools/C_mk/Make.SUPERUX Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.frank Tools/C_mk/Make.mpi commit 7cd59e1dae472d05333425cca6781554c749255e Author: lijewski Date: Thu Jan 31 10:13:11 2013 -0800 Tweaks to InitFromBinary(). Src/C_AMRLib/Particles.H commit b58385f27eaf6a7c22e66fca537c872e0389181f Author: lijewski Date: Thu Jan 31 09:54:30 2013 -0800 Added non-template abstract base class ParticleContainerBase from which the templatized ParticleContainer class now publicly inherits. This is so we can maintain a list (or vector) of pointers to ParticleContaiers as ParticleContainerBases. Any functions we wish to call using those pointers need to be declared as pure virtual functions in the base class, exactly matching the signature in the ParticleContainer class itself. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit e276c3ddc2dfa3fe116f55fe6b2dd8ed30b09838 Author: vince Date: Wed Jan 30 17:19:50 2013 -0800 barrier tagging, named comm types. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 8535168382cfbd454b4d34b61ebe413b9d2e8901 Author: Ann Almgren Date: Wed Jan 30 13:43:39 2013 -0800 Correction to new impose_refine_grid_layout call (must pass in lbase as new_finest) Src/C_AMRLib/Amr.cpp commit d6cf73142b82ec9f6b00c3221725dfbad7a6b3d9 Author: Ann Almgren Date: Wed Jan 30 13:42:22 2013 -0800 Impose refine_grid_layout at level 0 earlier in the grid_places routine so that it is still imposed even if we return with fixed_grids. Src/C_AMRLib/Amr.cpp commit edc453753571e00bc475d2380c74198636c8912f Author: lijewski Date: Tue Jan 29 16:47:45 2013 -0800 An attempt to better distribute the NReader processes in IntFromBinaryFile() by building a set of NReaders processes from the full range [0,NProcs) using a random number generator. The idea is to minimize the number of reader processes per Node, so that each reader can use more of the available memory on the Node. Src/C_AMRLib/Particles.H commit a0a0d20165ca686a5c18eb6116d0e33d5c409567 Author: vince Date: Tue Jan 29 15:48:06 2013 -0800 more communications profiling. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit a80712e76c2821e0cfeb9820edb385054dd2de99 Author: Ann Almgren Date: Tue Jan 29 15:03:37 2013 -0800 If we can't use mg.bottom_solver = 4 then just set it to one instead of aborting with an error. Src/LinearSolvers/F_MG/mg.f90 commit 571b3193aac8750b598eddd336a9724a26c16017 Author: Ann Almgren Date: Tue Jan 29 10:29:42 2013 -0800 Fix comment about Nprocs > ngrids. Src/C_AMRLib/Amr.cpp commit e569788d3a8a511f2143371ad6c57c8e539b16aa Author: Ann Almgren Date: Tue Jan 29 10:21:49 2013 -0800 We now impose the refine_grid_layout criterion (breaking up grids into smaller chunks if nprocs > ngrids) in a call from defBaseLevel as well as in a call from regrid so we fix the grids at level 0 at the initial time (unlike before) and if max_level = 0 (unlike before). Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 92a320fdda62a6dda9154ae7461e7a3bd7b62131 Author: vince Date: Mon Jan 28 11:31:09 2013 -0800 start of comm profiling. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 844566b5f89002f56fc1519a77402c537015822b Author: vince Date: Fri Jan 25 14:20:34 2013 -0800 eliminated warnings. Tests/RoseTests/CPP/NullTransTest/PROB_3D.F commit e74e4f8fe46373c179e07807d09e636ec92030bf Merge: e1a8550f0 0ea7403d0 Author: Marc Day Date: Fri Jan 25 14:15:49 2013 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 0ea7403d0fb6dd638ee0adf0b8bbb0b3b9865aae Author: vince Date: Fri Jan 25 14:13:49 2013 -0800 added code to gracefully exit on user stop request, so the profiling will still print. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit e1a8550f05625ede943d838912ee388b681b2c88 Author: Marc Day Date: Fri Jan 25 13:42:21 2013 -0800 Fixed other remnants of multi-component operator data Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 252cb95afe4040542f3e27858197d6d6f899217a Merge: e79624957 760742952 Author: Marc Day Date: Thu Jan 24 09:50:16 2013 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e79624957b678d52df3c5f6485a975c833f19933 Author: Marc Day Date: Thu Jan 24 09:49:53 2013 -0800 Bad default value for bndry_comp Src/LinearSolvers/C_CellMG/LinOp.H commit 76074295241683314fb063222478c0268cc0d41c Author: Weiqun Zhang Date: Thu Jan 24 09:46:11 2013 -0800 Fixed Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_intel.mak commit 82638b52edb67b6c4f760b22db4b2c5f5f2fbbf7 Author: Weiqun Zhang Date: Thu Jan 24 09:21:11 2013 -0800 Update makefile for Intel 13 Tools/F_mk/comps/Linux_intel.mak commit e9ebb1d9178f586892c9f148e6f3ff18a51acf2b Merge: e30ac42b9 2fcbad44d Author: Marc Day Date: Wed Jan 23 18:37:46 2013 -0800 Merge commit 'd573eaa' commit 2fcbad44df8db7597517e54bb6ae60194c22f33e Author: Marc Day Date: Wed Jan 23 18:36:29 2013 -0800 Modify interface to a number of linear solver support structures to generalize access/usage Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit e30ac42b96688169140ddffa66a2444f12638666 Author: Weiqun Zhang Date: Wed Jan 23 11:01:39 2013 -0800 More OMP to the nonblocking multifab_fill_boundary Src/F_BaseLib/multifab_f.f90 commit 00883ce89cd151f421929e0e7501cffe268f5838 Author: Chris Malone Date: Wed Jan 23 12:54:14 2013 -0500 fix how we capture version number for Cray; this is a hack Tools/C_mk/Make.mpi commit 73b4a949d1aaca18aa7b3576ca8483fd9c11ff55 Author: Christopher Malone Date: Wed Jan 23 12:40:15 2013 -0500 titan updates Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 09ff8675f9da9e217a7c8da3f82432516a544ce4 Author: Weiqun Zhang Date: Tue Jan 22 13:41:01 2013 -0800 OpenMP part of nonblocking fill_boundary Src/F_BaseLib/multifab_f.f90 commit d716954356863a76b035e9a5e335cd107dae6b95 Author: Weiqun Zhang Date: Tue Jan 22 13:13:13 2013 -0800 OpenMP FAB_CONTAINS_NAN and INF Src/F_BaseLib/fabio_c.c commit f4a3135d0c9e5a3162e24645b4b56335c5226f5f Author: Michael Zingale Date: Sun Jan 20 18:53:04 2013 -0500 remove python_plotfile python_plotfile/vis.in commit 2c0da77fac31d76e5552cac6e739b51d165448d6 Merge: 33bbe98e0 e0dd78252 Author: Michael Zingale Date: Sun Jan 20 18:52:39 2013 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit 33bbe98e0021218408001f80e012d836ebf6b7b3 Author: Michael Zingale Date: Sun Jan 20 18:52:09 2013 -0500 moved python_plotfile python_plotfile/GNUmakefile python_plotfile/contourcompare.py python_plotfile/fsnapshot.f90 python_plotfile/plot1dflame.py python_plotfile/plotparticles.py python_plotfile/plotsinglevar.py python_plotfile/plotsinglevar_parts.py python_plotfile/runtimevis.py commit e0dd782521138019546ccc2ce6df42c517db76c1 Author: Michael Zingale Date: Sun Jan 20 16:10:02 2013 -0500 fix a comment python_plotfile/plotsinglevar.py commit 6cff139de9d11ff38d7e40b65be3a047aee2de85 Author: Michael Zingale Date: Sun Jan 20 16:08:55 2013 -0500 greatly simplify the GNUmakefile -- we only really need the BoxLib F_Src python_plotfile/GNUmakefile commit d865661320552a45b4ddd26c238ac10b2b1c093a Author: Michael Zingale Date: Sun Jan 20 13:32:16 2013 -0500 sample runtimevis.py inputs file python_plotfile/vis.in commit a06844cbc0f830dfb8eaf7251759b3f605742b39 Author: Michael Zingale Date: Sun Jan 20 13:31:44 2013 -0500 add tight_layout -- this really makes things look better. Also fix the problem if the plt file ends in / python_plotfile/runtimevis.py commit 620c542ed9c1c9a2a05b52139ebaf789a3baa365 Author: Ann Almgren Date: Wed Jan 16 13:31:59 2013 -0800 Remove XGRAPH stuff for BoxLib version of this. Tutorials/AMR_Advection_C/Source/main.cpp commit aebe3add3e7948700e69f4a571104f28658ec987 Author: Regression Tester account Date: Wed Jan 16 09:58:58 2013 -0800 Regression Testing script: added capability of switching to non-master branches Tools/RegressionTesting/testnew.py commit a65a93f79a9e51e36b54ee3acd80a8015d4edeb5 Author: vince Date: Tue Jan 15 16:05:14 2013 -0800 changed flags for fortran. Tests/RoseTests/CPP/NullTransTest/GNUmakefile commit b6ac683b89a8ce6160007bc029a6603b2afbd1ef Author: vince Date: Mon Jan 14 15:21:46 2013 -0800 added some simple rose translation tests. see weiqun for the f90 parts. Tests/RoseTests/CPP/NullTransTest/GNUmakefile Tests/RoseTests/CPP/NullTransTest/PROB_3D.F Tests/RoseTests/CPP/NullTransTest/PROB_F.H Tests/RoseTests/CPP/NullTransTest/README Tests/RoseTests/CPP/NullTransTest/RoseNullTest.cpp Tests/RoseTests/F90/Readme Tests/RoseTests/F90/test1/GNUmakefile Tests/RoseTests/F90/test1/main.f90 Tests/RoseTests/F90/test2/GNUmakefile Tests/RoseTests/F90/test2/main.f90 Tests/RoseTests/F90/test3/GNUmakefile Tests/RoseTests/F90/test3/bc.f90 Tests/RoseTests/F90/test4/GNUmakefile Tests/RoseTests/F90/test4/main.f90 Tests/RoseTests/F90/test5/GNUmakefile Tests/RoseTests/F90/test5/main.f90 Tests/RoseTests/F90/test6/GNUmakefile Tests/RoseTests/F90/test6/main.f90 Tests/RoseTests/F90/test6/omp.f90 Tests/RoseTests/F90/test7/GNUmakefile Tests/RoseTests/F90/test7/main.f90 Tests/RoseTests/F90/test7/probin.f90 Tests/RoseTests/F90/test7/runtime.f90 Tests/RoseTests/F90/test8/GNUmakefile Tests/RoseTests/F90/test8/init_data.f90 Tests/RoseTests/F90/test8/main.f90 commit 8a548f8b1c6a4f7486d4af6bb95c98993e9d1316 Author: lijewski Date: Mon Jan 14 10:00:33 2013 -0800 Compile fillfab.f into tFillFab. Tests/C_BaseLib/GNUmakefile commit e91336235e135e80e5fab3c9c410bb3459bff1cf Author: Michael Zingale Date: Sun Jan 13 21:16:34 2013 -0500 add time python_plotfile/runtimevis.py commit 4b14eac704902614284f3b3fbcdc3d3d814838d9 Author: Michael Zingale Date: Sun Jan 13 20:44:15 2013 -0500 looking prettier now python_plotfile/runtimevis.py commit ab6f981fbf73df69f57850172d8e717c102448b8 Author: Michael Zingale Date: Sun Jan 13 20:29:57 2013 -0500 basic functionality working python_plotfile/runtimevis.py commit 493d7b0bdec21c703c9c303d0d955268124f7cbb Author: Michael Zingale Date: Sun Jan 13 18:21:10 2013 -0500 more progress python_plotfile/runtimevis.py commit f3762790be4353659a0786196fe786658aad2bf9 Merge: 554da93a6 b979a3d74 Author: Michael Zingale Date: Sun Jan 13 18:09:28 2013 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit 554da93a6449e61df63fafc38bdfd652286f3f30 Author: Michael Zingale Date: Sun Jan 13 18:00:08 2013 -0500 start of a runtime vis script python_plotfile/runtimevis.py commit 6072455b4e7121dc815cecbec81f1cee0ee9936e Merge: 056caf570 85f2b65a5 Author: ajnonaka Date: Thu Jan 10 16:52:27 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 056caf5702b1b918cdf382b3103102553478ff98 Author: ajnonaka Date: Thu Jan 10 16:51:06 2013 -0800 introducing HOM_DIR bc type. certain problems need to distinguish between EXT_DIR (e.g., for inflow) and HOM_DIR (e.g., for velocity at a wall) Src/F_BaseLib/bc.f90 commit 85f2b65a55886bc992c50c81750caafbf3285b06 Merge: 5f246de87 092128efd Author: Ann Almgren Date: Wed Jan 9 15:21:54 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5f246de877722cc0465f5458fbf4b3b346bdd3ae Author: Ann Almgren Date: Wed Jan 9 15:21:39 2013 -0800 local_only --> only_local so declarations match. Src/C_AMRLib/Particles.H commit 092128efdc14a70ab0c947a3c50486f6480a635d Merge: 7ca3c6e49 4741de849 Author: vince Date: Wed Jan 9 14:49:16 2013 -0800 Merge branch 'streamretry' commit 4741de8491a9cce849441861758ffbdc31d109cc Author: vince Date: Tue Jan 8 16:15:19 2013 -0800 stream retry for checkpoint and plotfiles. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 7ca3c6e4966a60e39ce6ce84ed5da2d178c3ae53 Author: lijewski Date: Tue Jan 8 09:23:45 2013 -0800 Check in with tMF enabled not tFillFab. Tests/C_BaseLib/GNUmakefile commit 542470e133c78bcaf05a29d18ac4d38c02bc23bd Merge: e3a64d6c7 e3fab0d33 Author: lijewski Date: Tue Jan 8 09:05:16 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e3a64d6c74b51b563e85f7d41aaa87977c8ef0a7 Author: lijewski Date: Tue Jan 8 09:04:49 2013 -0800 Added FillFab stuff to add values from a file into a fab. Only works for 2D at the moment. Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/fillfab.f Tests/C_BaseLib/tFillFab.cpp commit e3fab0d33eefcd3c796ac93b6f822e8936d00f9b Author: ajnonaka Date: Mon Jan 7 06:50:39 2013 -0800 bugfix; referencing wrong optional argument Src/LinearSolvers/F_MG/mg.f90 commit 90734ced36e6fdedae9a6adeafebdc84bdfba0fb Author: Weiqun Zhang Date: Fri Jan 4 16:54:09 2013 -0800 Added -rose:openmp Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/gfortran.mak commit 0ddf2f7ea201091b1c6d5a5b84a2a0f14fd476e7 Merge: 622139901 a459a6c9e Author: ajnonaka Date: Fri Jan 4 15:38:32 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 622139901102d0fc2fc687f526b99acae49458e6 Author: ajnonaka Date: Fri Jan 4 15:37:33 2013 -0800 added the option for the code to *not* abort if you have reached the maximum number of v-cycles, as controlled by abort_on_max_iter in mg_tower.f90. Fixed a bug in the ml_cc solver where on the *last* v-cycle, the solver didn't actually do any smooths Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit a459a6c9e4b71503c547fd950b6c510c75954c23 Author: Weiqun Zhang Date: Thu Jan 3 16:40:08 2013 -0800 Made make for ROSE again. Tools/F_mk/GMakedefs.mak commit a2e1a037a06af842c056193ba8eb2163815268c3 Author: Weiqun Zhang Date: Thu Jan 3 16:26:45 2013 -0800 Fixed a bug in the make system introduced by me today. The perl scripts require a space after "-I". Tools/F_mk/GMakedefs.mak commit 74b021f6cac585005db8be163a0c83a1b0dc34c3 Author: Weiqun Zhang Date: Thu Jan 3 16:13:28 2013 -0800 Minor changes to make the code more readable and ROSE happy, because ROSE cannot handle d%d. Src/F_BaseLib/cutcells.f90 Src/F_BaseLib/vector_i.f90 commit 25f4668f016d53c7faf06a23d8ac38a395524813 Author: lijewski Date: Thu Jan 3 12:11:44 2013 -0800 Fixed OMP bug. Src/F_BaseLib/create_umac_grown.f90 commit c43ad437d67a91aa08d03ce604338b772bf0c388 Merge: 9225faa1f e6efe3dcf Author: Weiqun Zhang Date: Thu Jan 3 10:45:58 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9225faa1ff930416149a07e9ec1905c7191e08d8 Author: Weiqun Zhang Date: Thu Jan 3 10:44:51 2013 -0800 Rose support for F_mk Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/gfortran.mak Tools/F_mk/comps/rose.mak Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GNUmakefile commit e6efe3dcfa3ed9aabedd2e3433c01b8d9848fd68 Author: ajnonaka Date: Thu Jan 3 08:42:36 2013 -0800 interface changes to simplify mac_applyop Src/LinearSolvers/F_MG/mac_applyop.f90 commit eb84a5045d5ea24055fc3b66958504fc779e84dd Merge: a067b5fc1 f118e4256 Author: ajnonaka Date: Thu Jan 3 08:26:29 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a067b5fc19147d889c45aee6c63488196a2ae5bb Author: ajnonaka Date: Thu Jan 3 08:24:53 2013 -0800 move mac_applyop from VARDEN and MAESTRO into BoxLib/Src/LinearSolvers/F_MG... more applications will be needing this Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mac_applyop.f90 commit f118e425653a9af7313afed70641973f6b955e93 Author: Michael Zingale Date: Wed Jan 2 19:05:39 2013 -0500 explain Real in C++ and dp_t in F90 Docs/GettingStarted/GettingStarted.tex commit a8f07c4897d9b23b364c305ce65b91bf89dec252 Author: Weiqun Zhang Date: Wed Jan 2 14:31:48 2013 -0800 Get around an Intel compiler bug that makes unnecessary copy when a_pointer(a_type%a_integer:) is passed to the first argument of parallel_isend and parallel_irecv. Src/F_BaseLib/multifab_f.f90 commit b992f8202c6203b3322cf3426ab07348c0e4d818 Author: Weiqun Zhang Date: Thu Dec 20 21:31:28 2012 -0800 Use -h noomp rather than -h thread0 to disable OMP for craycc Tools/F_mk/comps/Linux_cray.mak commit c0a1a3822d679e6f46e518c0183fa3870d056534 Author: Weiqun Zhang Date: Thu Dec 20 17:34:04 2012 -0800 Explicitly disable OMP for Cray C compiler when OMP is not defined. Tools/F_mk/comps/Linux_cray.mak commit f42381a2b7916efc91b38f48187cd89503901123 Author: Weiqun Zhang Date: Thu Dec 20 17:25:10 2012 -0800 CFLAGS must also have -openmp when OMP is defined, otherwise SMC will fail when built with OMP using Intel. Tools/F_mk/comps/Linux_intel.mak commit 286a7607343ea723a0d3e4a873c870bbf73e3208 Merge: 959c92bd5 7db6b2c15 Author: vince Date: Wed Dec 19 16:12:26 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 959c92bd5fa639a6e4984f0e51c5402aa84555af Author: vince Date: Wed Dec 19 16:12:12 2012 -0800 added rose support for mk. Tools/C_mk/Make.defs Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/rose.mak commit b979a3d7440617c6648d071cfa7aec86386b5137 Author: Michael Zingale Date: Wed Dec 19 09:26:59 2012 -0800 use tight_layout() if it exists. Also reduce the number of tick labels for very narrow domains python_plotfile/plotsinglevar.py commit 7db6b2c153760915c0298dea868436accb1fe52a Author: Ann Almgren Date: Tue Dec 18 08:14:12 2012 -0800 Modify how we deal with initial_grids_file and regrid_grids_file -- we now read in the boxarrays soon after we parmparse the names of the files, and store these as static BoxArrays. Then later when they are needed in grid_places() we have them stored and do not read them in again. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit a3c14989e94ad24dbcad01fec586676bf1e9452e Author: ajnonaka Date: Mon Dec 17 13:02:57 2012 -0800 a note about space/time-dependent boundary conditions in multifab_physbc Docs/F_AdvancedTopics/F_AdvancedTopics.tex Docs/Introduction/Introduction.tex commit b4ae593c3e64a018cfd9348da02010d339db570e Author: ajnonaka Date: Mon Dec 17 12:31:00 2012 -0800 added optional arguments: time, dx(:), prob_lo(:), prob_hi(:) for space/time-dependent boundary conditions Src/F_BaseLib/multifab_physbc.f90 commit 6cf9bad98784b2c11794e14e312228062bf6fec0 Author: Ann Almgren Date: Fri Dec 14 15:33:10 2012 -0800 Add the option to set amr.initial_grid_file = as well as amr.regrid_file = This is similar to the regrid_file option, except that: 1) it is only used to set the initial grids file; there is no file specified for later regrids. 2) the max_grid_size criterion is not enforced on the initial grids generated this way, rather it is imposed after the grids are read. The point is to allow us to initially read in grids specified by an external routine which did not know about max_grid_size. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit cfb8dfe9c8f319f955128d715ddee8ef62d3f1cf Merge: 84589d673 d3d670015 Author: Weiqun Zhang Date: Thu Dec 13 17:23:37 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 84589d673b0bd38583e2babf7d3dd2a429be258f Author: Weiqun Zhang Date: Thu Dec 13 17:21:31 2012 -0800 Fixed some minor probelms such as 0_dp_t should read 0.0_dp_t otherwise Cray compiler might be unhappy. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/knapsack.f90 commit d3d670015f267148291c783b4745980b1d2bc0b8 Merge: a02be70f4 2ed05a07c Author: lijewski Date: Thu Dec 13 11:00:06 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a02be70f40e2f864dce0895bdd3487180a129374 Author: lijewski Date: Thu Dec 13 10:58:08 2012 -0800 Added ParticleBase::MaxParticlesPerRead() for use in InitFromBinaryFile(). It's the number of particles that each reader should try to read before everyone does a Redistribute(). Currently it's defaulted to 100000. It's ParmParse-able as particles.nparts_per_read. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 2ed05a07cb5f7e17da64f7aa867cf4f35f9792e4 Merge: 77cbb2a6c 4c2503a99 Author: Michael Zingale Date: Wed Dec 12 19:51:21 2012 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 77cbb2a6c9435477aa658ec8d0337efb8d235f96 Author: Michael Zingale Date: Wed Dec 12 19:50:36 2012 -0500 add a new printing clause that can be used to write a pretty printing method for the runtime parameters Tools/F_scripts/write_probin.py commit 4c2503a99663cde2faba78b35d8ee8297c447697 Author: lijewski Date: Wed Dec 12 16:16:06 2012 -0800 More work on InitFromBinaryFile(). Src/C_AMRLib/Particles.H commit c2d70c646ac8dc2f851dea86e811f0709c7984d9 Author: lijewski Date: Wed Dec 12 15:57:52 2012 -0800 A little more tweaking on InitFromBinaryFile(). Src/C_AMRLib/Particles.H commit bcb80ee518a8975e68601fbf7523cd5088e6b071 Author: lijewski Date: Wed Dec 12 15:52:27 2012 -0800 More work on InitFromBinaryFile(). Src/C_AMRLib/Particles.H commit c2c320eec8b04364f36491584400d5c946191eb0 Author: lijewski Date: Wed Dec 12 14:44:01 2012 -0800 Some work making InitFromBinaryFile() faster in parallel with large numbers of particles. Src/C_AMRLib/Particles.H commit 8326ad3b4e4dba5bd6ca440c3068882c8a14ebd1 Author: Ann Almgren Date: Tue Dec 11 11:32:02 2012 -0800 Added writePlotNow routine to Amr.cpp and to AmrLevel. In Amr this routine now contains the various tests on whether to write a plotfile at this timestep. In AmrLevel it allows the application at level 0 to tell Amr to write a plotfile now. There should be no changes in the default behavior. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 65bff3680c2b0f6c651d8f76ce550712a9ec2ef9 Author: Marc Day Date: Mon Dec 10 14:26:05 2012 -0800 Virtualize a couple of functions to allow easier extensions into derived classes. Src/C_AMRLib/Amr.H Src/C_AMRLib/ErrorList.H commit 961947240f9b33a3411b3eefd8dd1ad26b34e19c Author: vince Date: Fri Dec 7 16:19:52 2012 -0800 writeavg pct fix. Src/C_BaseLib/Profiler.cpp commit d403b60f6279434ac37d94bef158d452ef8fb1b5 Merge: c867f627d 05e4606c1 Author: vince Date: Fri Dec 7 15:07:00 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c867f627dedca677a24b786e0076aead7a4f0121 Author: vince Date: Fri Dec 7 15:06:28 2012 -0800 fixed writeavg percent. Src/C_BaseLib/Profiler.cpp commit 05e4606c1f14c43d132aaabba1284189e4ff89f0 Author: lijewski Date: Fri Dec 7 14:53:38 2012 -0800 some profiling tweaks Src/C_AMRLib/Amr.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit c62e5c678b3be0fa8b47a9f6f5862e56e2ae3853 Author: lijewski Date: Fri Dec 7 13:19:38 2012 -0800 Added profilers to SFC & KNAPSACK. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 20645ded8f015e44c3a5502af6b254f68fdc3658 Author: lijewski Date: Fri Dec 7 12:41:29 2012 -0800 added some Profilers Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BoundaryLib/FabSet.cpp commit a5296f8e3b9056a06e02ecd0e50434b886fb42c3 Author: lijewski Date: Thu Dec 6 15:11:28 2012 -0800 Comment out the "-warn all" stuff for Intel Fortran compiler. The EGLib stuff is just to old & crufty to pass this test. Tools/C_mk/Make.defs commit e3aad1c4d7c9b1a852539232263de8b027242d4f Author: lijewski Date: Thu Dec 6 10:40:04 2012 -0800 Add more compile time checking when using Intel fortran compiler. Tools/C_mk/Make.defs commit c8403e62f6595852333b3c6655186a5a15732272 Author: Weiqun Zhang Date: Wed Dec 5 11:45:06 2012 -0800 Made the nonblocking multifab_fill_boundary safer in case it is not used properly. Src/F_BaseLib/multifab_f.f90 commit 1b1cab8354d1555caf43b204a2fac5a91d9e5fe7 Author: Weiqun Zhang Date: Tue Dec 4 16:02:43 2012 -0800 Switch the order of isend and irecv in the nonblocking multifab_fill_boundary. In principle, posting irecvs before isends is the right thing to do. Src/F_BaseLib/multifab_f.f90 commit 651ff06c16b25de2e590ebcc6499b14c3fd6c278 Author: Weiqun Zhang Date: Tue Dec 4 10:12:21 2012 -0800 Fix typo Tools/Release/release.py commit 4e5d76c8f0ae23754fb0fc58feea7199828a4489 Author: vince Date: Mon Dec 3 12:07:31 2012 -0800 added stream retry for some output. Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 317bef6bef5dcc3e76b12f5e255e37ae451e2625 Merge: 5b39c0d96 1d0cfaea4 Author: Matthew Emmett Date: Sat Dec 1 08:47:21 2012 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 5b39c0d96e5e7e9b05425725d51c15780d0f06ac Author: Matthew Emmett Date: Sat Dec 1 08:47:09 2012 -0500 Add DiffSameDomainRefinedFD utility. Does the same as DiffSameDomainRefined, but for finite difference schemes. Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp commit 1d0cfaea4d2729c84398060651fd95b36ada4eff Author: vince Date: Tue Nov 27 17:36:11 2012 -0800 update to the i/o benchmark. Tests/IOBenchmark/IOTestDriver.cpp commit 0effe73143dd34320aee12e332d6fdc6ab50c4ab Author: vince Date: Tue Nov 27 17:31:54 2012 -0800 tweaked the profiling output. Src/C_BaseLib/Profiler.cpp commit 04c8054abf9b7e0aa134fb4b5f65fee4c2b5df95 Author: Weiqun Zhang Date: Tue Nov 27 14:48:12 2012 -0800 Special treatment for the case of no MPI jobs in the nonblocking multifab fill boundary. Src/F_BaseLib/multifab_f.f90 commit 9c0f7bf2ff194729ee28a8da6e126b74cea61a7f Merge: 709e5f823 a0b2f1d39 Author: Weiqun Zhang Date: Tue Nov 27 12:20:42 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 709e5f8233314b6e0a5eda637caa159ac56bd4de Author: Weiqun Zhang Date: Tue Nov 27 12:17:56 2012 -0800 Changed the default sfc_threshold from 4 to 0 for F_BaseLib. This is a win for many tests. Also, F_BaseLib is now consistent with C_BaseLib. Src/F_BaseLib/layout.f90 commit a0b2f1d39fe0b55bd434201b7c7074654f6a1640 Author: lijewski Date: Tue Nov 27 10:54:47 2012 -0800 Changed the default for sfc_threshold from 4 to 0. This way, even if we have fewer grids than cores we'll get the Space Filling Curve distribution. Tests on hopper indicate this is a win. Src/C_BaseLib/DistributionMapping.cpp commit 5fe9a115f54f2c80cbc7055386673fc981a48bbd Author: Weiqun Zhang Date: Mon Nov 26 17:06:32 2012 -0800 Fix a bug in parallel_test_one. I don't think anyone ever used this function. Src/F_BaseLib/parallel.f90 commit 0a3ae51666a8031d18a5f80afa164bffec2f52ea Author: Ann Almgren Date: Sun Nov 25 10:01:03 2012 -0800 Cleaned up version. Src/C_AMRLib/Particles.H commit d3f0b736df362ef15978c75ff59c8b0e037b39cc Author: Weiqun Zhang Date: Wed Nov 21 10:41:19 2012 -0800 Fix a bug in my last commit. Src/F_BaseLib/multifab_f.f90 commit d7555c1b90994c0686a7f3b3952f0f7a9a1fb684 Merge: 2811edbd0 daf2cb95f Author: Weiqun Zhang Date: Wed Nov 21 10:32:12 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2811edbd088e2dd3f3cbaa25a045e09111d688fe Author: Weiqun Zhang Date: Wed Nov 21 10:29:51 2012 -0800 Add multifab_fill_boundary_waitrecv that will return when messages are received regardless the status of sending messages. Src/F_BaseLib/multifab_f.f90 commit daf2cb95f381845c236c26475bfa32a05709285a Merge: 47e81b0be 7f8b03a7e Author: Ann Almgren Date: Tue Nov 20 17:27:51 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 47e81b0be60066173920af86798179e8bf08eebe Author: Ann Almgren Date: Tue Nov 20 17:27:37 2012 -0800 Add new access functions in Particles.H Src/C_AMRLib/Particles.H commit 7f8b03a7ee5a9c1a21d4cf8e674ec631d7987fc7 Author: vince Date: Tue Nov 20 15:43:59 2012 -0800 moved readme to docs. Docs/Readme.profiling commit a02eb25e4fed2cfb3132feb841a8719ec1886746 Author: vince Date: Tue Nov 20 15:35:43 2012 -0800 rewrote the c++ boxlib profiler. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/Readme.profiling commit 5d69def97432f227bde8b372a84b47716b2330e9 Author: Ann Almgren Date: Fri Nov 16 15:16:45 2012 -0800 Add GetParticleVelocities routine. Src/C_AMRLib/Particles.H commit 64c404cae3c30a2b39d055268644a643e82a551a Author: Ann Almgren Date: Tue Nov 13 14:29:50 2012 -0800 If bottom_solver type is not defined by the calling routine, then set default to BiCGStab (type 1) rather than type 3 which no longer exists. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit dd6d5f2a44706ed06ff5103190bbd698c05761ec Author: Weiqun Zhang Date: Tue Nov 13 13:35:35 2012 -0800 For nonblocking multifab_fill_boundary_nowait, MPI tag is passed in as argument. Src/F_BaseLib/multifab_f.f90 commit e1e9ef6e606fe3d563024e34a95a6623ea5a0d34 Author: Weiqun Zhang Date: Tue Nov 13 08:14:19 2012 -0800 Option to initialize MPI with thread support Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit c4680d99d6e0b4686f1181b818569acaffa1c88e Author: Weiqun Zhang Date: Mon Nov 12 17:24:11 2012 -0800 real "add mpi_test to the nonblocking multifab_fill_boundary" Src/F_BaseLib/multifab_f.f90 commit 236f68cc5357d9cd0d4696880e3ca7e9674d80bc Author: Weiqun Zhang Date: Mon Nov 12 17:21:52 2012 -0800 Revert "add mpi_test to the nonblocking multifab_fill_boundary" because I accidently committed some files. This reverts commit c26377021d3906bafbcfef68a42cb66f6d5c2cbc. Src/F_BaseLib/multifab_f.f90 Tests/LinearSolvers/ComparisonTest/main.cpp Tools/C_mk/Make.Linux Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_pgi.mak Tutorials/Exp_CNS_NoSpec/GNUmakefile commit c26377021d3906bafbcfef68a42cb66f6d5c2cbc Author: Weiqun Zhang Date: Mon Nov 12 16:24:07 2012 -0800 add mpi_test to the nonblocking multifab_fill_boundary Src/F_BaseLib/multifab_f.f90 Tests/LinearSolvers/ComparisonTest/main.cpp Tools/C_mk/Make.Linux Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_pgi.mak Tutorials/Exp_CNS_NoSpec/GNUmakefile commit 0f3b0e9dd6508916a31e9d35a214eb66046c5a88 Merge: f0e1468a7 9b748a687 Author: vince Date: Thu Nov 8 17:25:26 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f0e1468a7d1bf8bf5c8efebe5995df147aadac15 Author: vince Date: Thu Nov 8 17:25:15 2012 -0800 added random initialization, mb2, and more compact boxarray. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/README commit 9b748a6877016c06d048602f887af38fa1293872 Merge: 88ac51588 b5208013c Author: Weiqun Zhang Date: Thu Nov 8 17:12:06 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 88ac51588040b769d355eda7b17484098fdeefb7 Author: Weiqun Zhang Date: Thu Nov 8 17:11:31 2012 -0800 Revert my previous change because it does not make any difference in performance Src/F_BaseLib/multifab_f.f90 commit b5208013c7542e11edcbfca6a84c965ae6b417f0 Merge: ad0bda7be 788d8cb75 Author: Michael Zingale Date: Thu Nov 8 17:55:56 2012 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit ad0bda7bebd06a5c37741a3026446cbe79df991a Author: Michael Zingale Date: Thu Nov 8 17:55:05 2012 -0500 when indexing a multifab with the particles grid, we need to use local_index when getting the dataptr() Src/F_BaseLib/particles_f.f90 commit 788d8cb7535685855a32cab0a83c9263f325abf3 Author: vince Date: Thu Nov 8 14:24:34 2012 -0800 added some profiling. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Profiler.H commit b3291378a9d7af14a50292965780e2423f5147c4 Author: Weiqun Zhang Date: Thu Nov 8 14:11:31 2012 -0800 nonblocking fill boundary: do mpi_test Src/F_BaseLib/multifab_f.f90 commit 99aeb2b7a0b924021f5e68cb5701204805c798cf Author: lijewski Date: Wed Nov 7 13:11:37 2012 -0800 Explicitly disallow copy assignment operator for ParmParse. Src/C_BaseLib/ParmParse.H commit 34bf15893f8a6e1b7aa85ce806466be280a4f28a Author: Weiqun Zhang Date: Wed Nov 7 11:29:12 2012 -0800 Fix call to isend to make Cray happy Src/F_BaseLib/multifab_f.f90 commit e1ef33546e4fae4e7fdf549bad2b18b722999b02 Author: Weiqun Zhang Date: Wed Nov 7 10:54:48 2012 -0800 fine tune nonblocking fill_boundary Src/F_BaseLib/multifab_f.f90 commit d1f89a610be59548c992f917bde126bcd388bbd6 Author: Weiqun Zhang Date: Tue Nov 6 16:59:01 2012 -0800 Add nonblocking multifab_fill_boundary Src/F_BaseLib/multifab_f.f90 commit 8394f1f97d7840e9711a70261ecdfd2e319650f9 Author: Weiqun Zhang Date: Mon Nov 5 13:41:09 2012 -0800 CC linear solver: The convergence test and the way to compute residues have changed. In the old way, at the beginning of ml_cc, a new RHS was computed using the initial guess, and then what the solver really solved was the redefined problem: Lap(\delta \phi) = RHS_new, where RHS_new = RHS_0 - Lap(\phi_0). After the solver converged on the new problem, the full solution is updated as \phi += \delta \phi. In the new way, the convergence test uses the original RHS and the latest full solution. Src/LinearSolvers/F_MG/ml_cc.f90 commit d982f6cecce31e1144c6a56b195e9502132849f3 Author: Weiqun Zhang Date: Fri Nov 2 22:41:23 2012 -0700 minor improvement of the new fill_boundary Src/F_BaseLib/layout.f90 commit 924d115f89e2fb5d057c671498c7625143d9eb3f Merge: be7877559 f9ede3298 Author: Weiqun Zhang Date: Fri Nov 2 22:31:01 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit be7877559cb0cb6c90b29874005be896db64302c Author: Weiqun Zhang Date: Fri Nov 2 22:30:52 2012 -0700 force cross to be true when idim .ne. 0 in the new multifab_fill_boundary Src/F_BaseLib/multifab_f.f90 commit f9ede329880643442e6368087a568de053f02d63 Author: ajnonaka Date: Fri Nov 2 22:08:06 2012 -0700 added author list so we can officially be referenced Docs/UsersGuide.tex commit 87a953feedf014c6f09fffad020d4d61a820f93b Author: Weiqun Zhang Date: Fri Nov 2 17:54:41 2012 -0700 multifab_fill_boundary can now fill boundaries in only one direction Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 3fb1de2a02424d2fe46c8269cb01f89b8b1c968f Author: Weiqun Zhang Date: Fri Nov 2 16:48:46 2012 -0700 Add optional argument dim to multifab_fillboundary; not doing anything yet Src/F_BaseLib/multifab_f.f90 commit 0d0c0d5a0f74e871eb583406812a3f8eb94e7f44 Author: Michael Zingale Date: Fri Nov 2 14:47:53 2012 -0400 enforce string length limits by truncation Tools/F_scripts/makebuildinfo.py commit 1c7b23b1a47c0a4c54fb60ac165786b108aa47e9 Author: Marc Day Date: Wed Oct 31 13:44:09 2012 -0700 Add several minor features to speed converge Src/C_TowerLib/MFTower.cpp Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp commit 873b9372634aa0247508dc878a516d296429bffd Author: Marc Day Date: Wed Oct 31 10:27:33 2012 -0700 Chase down a few memory leak issues, and add a 3-level example file Src/C_TowerLib/Layout.H Src/C_TowerLib/Layout.cpp Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_3lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/AMR_PETSc_C/Source/MLBoundary.H Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp commit 42614975d330834389ac6db954bbee4f142f3d73 Author: Marc Day Date: Tue Oct 30 18:04:48 2012 -0700 Add a README file Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_PETSc_C/README commit 17af2caa9b721fa0321492b57552e16728b69355 Author: Marc Day Date: Mon Oct 29 19:31:04 2012 -0700 slightly better PETSc run parameters Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file commit b5bfff1ea3cf5e5bbb5aa0d735dc8ca17df7dc04 Merge: 54ec788f9 b121df32d Author: Marc Day Date: Mon Oct 29 19:02:24 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 54ec788f9c353188413f1bf8f05d04264e80cd5c Author: Marc Day Date: Mon Oct 29 19:02:03 2012 -0700 Fix up PETSc tutorial to work multilevel with a fixed-grid file Src/C_AMRLib/Amr.H Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_2lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file Tutorials/AMR_PETSc_C/Source/Darcy.H Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F Tutorials/AMR_PETSc_C/Source/MLBoundary.H Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp commit b121df32d47515aacc93198b28222014054a8418 Author: Ann Almgren Date: Fri Oct 26 09:21:48 2012 -0700 Remove OMP stuff from GetParticleLocationsAndMass since the "cnt" stuff won't work right with omp there. This should only be used for low numbers of particles anyway. Src/C_AMRLib/Particles.H commit 304e67389f1e6107086440ce9966c9489471cbbb Author: Ann Almgren Date: Fri Oct 26 06:38:35 2012 -0700 Only call MPI_Gather if BL_MPI is defined. Src/C_AMRLib/Particles.H commit 05616bafdd3a5843254d646b32fcee20a0038ead Merge: f635b19dd 6ddd1f884 Author: Ann Almgren Date: Thu Oct 25 15:23:30 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f635b19dd7a8fd6eeba152567fd33f8a3b4d7299 Author: Ann Almgren Date: Thu Oct 25 15:23:13 2012 -0700 Make the GetParticleLocationsAndMass new routine work in parallel. Src/C_AMRLib/Particles.H commit 6ddd1f8846b2115657fc92cd9949beafab312bba Merge: 220d22244 50867f315 Author: Marc Day Date: Thu Oct 25 13:58:44 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 220d222446f661a0e6b31c5d66b46179b208ab84 Author: Marc Day Date: Thu Oct 25 13:58:20 2012 -0700 Rearrange the boundary conditions code, and fix a bug in periodic Src/C_TowerLib/Layout.cpp Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file Tutorials/AMR_PETSc_C/Source/Darcy.H Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/AMR_PETSc_C/Source/MLBoundary.H Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp Tutorials/AMR_PETSc_C/Source/Make.package commit 50867f315e741322ec875789a54487e9669e8dde Author: Michael Zingale Date: Thu Oct 25 12:48:28 2012 -0400 fix the quotes when compile lines wrap to 2 strings Tools/F_scripts/makebuildinfo.py commit fffc5f319ae82405464801e8bb76dc3bf2bcea6a Merge: 13d77c1d6 267de8e57 Author: Michael Zingale Date: Wed Oct 24 19:54:05 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit 13d77c1d64f4eee0402e04daabd33909be2fa10f Author: Michael Zingale Date: Wed Oct 24 19:53:44 2012 -0400 add ability to specify min/max for second plot python_plotfile/plotsinglevar.py commit 70ab68fe0f7e9ea97bb8a13aca1543b6f7a64524 Merge: 6dd8847c5 8a9e08e6a Author: Ann Almgren Date: Wed Oct 24 15:39:08 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6dd8847c55fc0070f76ca1dca6e1aa216681a38a Author: Ann Almgren Date: Wed Oct 24 15:35:47 2012 -0700 1) Added TotalNumberOfParticles to return total number of particles. 2) Add GetParticleLocationsAndMass to return this data to an outside routine. 3) Fix abs --> std::abs in estTimeStep so that we use the real, not integer, version of abs. Src/C_AMRLib/Particles.H commit 8a9e08e6a8ce51a60a96adc9fcde29646e5d8ebf Author: Michael Zingale Date: Wed Oct 24 16:36:43 2012 -0400 build_hash -> build_git_hash Tools/F_scripts/makebuildinfo.py commit a260612b80529d0ca4baca24739d6c2c081cfd33 Author: Michael Zingale Date: Wed Oct 24 16:31:45 2012 -0400 python version of make_build_info -- the shell version was getting hard to maintain. This one adds yet another git hash if it detects that we are compiling in a directory that is not part of the source tree, i.e. MAESTRO_Exec/ instead of MAESTRO/Exec/ Tools/F_scripts/makebuildinfo.py commit 25a7cc05c3eda114403d49b6c2c18be3b7075e96 Author: Weiqun Zhang Date: Mon Oct 22 17:09:19 2012 -0700 print more information Tools/RegressionTesting/reg_test_blame.py commit d98aaae50713f9abf8a9a58864cc460d74f04a7c Author: Marc Day Date: Mon Oct 22 10:22:17 2012 -0700 Minor tweaks to solver interface Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp commit d66dd8b8b3427b7a7077d9667943f6179e0fd813 Merge: f4cad54bf 19c294817 Author: Marc Day Date: Fri Oct 19 14:13:10 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 19c294817273c4e0549b336f89af7b0b740a7d01 Author: Marc Day Date: Fri Oct 19 10:57:00 2012 -0700 Fix up PETSc tutorial problem to run to completion. Still lots to cleanup though. Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp commit e842bbbffacaf874e2068c7e2d45f15981ead559 Author: Marc Day Date: Thu Oct 18 17:45:54 2012 -0700 Insert first cut of PETSc interface and MFTower/Layout structures needed to support it, along with a tutorial app to work out the kinks. Note that the demo tutorial (Tutorials/AMR_PETSc_C) does not yet work and is still taking shape. It does represent a considerable departure from the traditional BoxLib apps, in that it implements a fully-implicit time-discretization using Newton iterations (using the PETSc SNES and KSP solvers). The tutorial app builds, but currently fails. Not only is it being debugged, it is still be designed, adn it is being used to evaluate the MFTower implementation as well - many of the old-styles associated with the BoxLib C++/Fortran linkage are being cleaned out in this example, partly because the form of the solver used seems to dictate a more general approach to things like multi-level advance routines, as well as boundary conditions, etc. Finally, note that I have put the MFTower/Layout classes in their own area (parallel to C_AMRLib for example) to keep my updates/reorgs from impacting the base BoxLib libraries - the plan will be to merge these structures into the C_BaseLib area when they become sufficiently stable. Similarly, the tutorial will be documented properly when it reaches stability. If you have any questions about this part of the CCSE codes, contact MSDay@lbl.gov Src/C_TowerLib/Layout.H Src/C_TowerLib/Layout.cpp Src/C_TowerLib/MFTower.H Src/C_TowerLib/MFTower.cpp Src/C_TowerLib/MFTower_2D.F Src/C_TowerLib/MFTower_3D.F Src/C_TowerLib/MFTower_F.H Src/C_TowerLib/Make.package Tutorials/AMR_PETSc_C/Exec/Make.PETSc Tutorials/AMR_PETSc_C/Exec/UniformVelocity/.gdbinit Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Make.package Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_PETSc_C/Source/Darcy.H Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F Tutorials/AMR_PETSc_C/Source/DarcySNES_F.H Tutorials/AMR_PETSc_C/Source/Darcy_2D.f90 Tutorials/AMR_PETSc_C/Source/Darcy_F.H Tutorials/AMR_PETSc_C/Source/Make.package Tutorials/AMR_PETSc_C/Source/extern_probin.template Tutorials/AMR_PETSc_C/Source/interpolate.f90 Tutorials/AMR_PETSc_C/Source/main.cpp commit 267de8e578fddb6f9ab9c08b91e282c38a94d3e3 Author: Michael Zingale Date: Wed Oct 17 17:58:58 2012 -0400 get this compiling again tutorial/GNUmakefile commit f4cad54bfe0395ce749c8cd1de18aa6f75ebaa0c Merge: cdf5481ba bf3871343 Author: Marc Day Date: Mon Oct 15 13:49:59 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit bf387134385084c5cfee61c741d0f430fe64861f Author: Michael Zingale Date: Sun Oct 14 17:46:21 2012 -0400 some formatting, add builddir if useExtraBuildDir is 1 Tools/RegressionTesting/testnew.py commit 0d08c695863c45fc3eaf45ebd042e1994f799d04 Author: Michael Zingale Date: Sat Oct 13 17:13:10 2012 -0400 update to reflect changing directory structure and presence of MAESTRO_Exec Tools/RegressionTesting/Maestro-tests.ini commit e09b5332f274ac2caddeba071eb2ca75585c6076 Author: Michael Zingale Date: Sat Oct 13 10:49:12 2012 -0400 add extraBuildDir -- this can be selected on a problem-by-problem basis to enable compiling the problem in an alternate source tree (and git repo) from the SourceDir Tools/RegressionTesting/testnew.py commit 27bfdab84a43bd2c3aaa315da219321bc4244058 Merge: 18b27a285 c64a1fe95 Author: Weiqun Zhang Date: Thu Oct 11 14:53:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 18b27a2859d7506e1f651d9e378440bf3be63cb7 Author: Weiqun Zhang Date: Thu Oct 11 14:48:47 2012 -0700 Commented out some debug print statements that are not thread safe. Src/C_AMRLib/INTERP_3D.F commit c64a1fe95c865d7047dad5f95ac8646b7b900f86 Author: ajnonaka Date: Thu Oct 11 14:11:23 2012 -0700 comment out the C++ stuff until we have something more substantial to say Docs/UsersGuide.tex commit e36aa6059c1d88f4548c4b2c32532ac8f2b7933e Author: lijewski Date: Wed Oct 10 15:48:04 2012 -0700 Fix long-standing bug in GSRB found as race-condition by helgrind. Src/LinearSolvers/C_TensorMG/DV_3D3.F commit 0715bbdf4a4cdf089b33eae496eb4905dce5d796 Author: lijewski Date: Wed Oct 10 15:47:42 2012 -0700 Tweak to OpenMP to quiet helgrind. Src/C_BaseLib/SPECIALIZE_3D.F commit eeea78047ad5bfc43b4e031897f5a2547bd679b7 Author: Weiqun Zhang Date: Wed Oct 10 11:22:31 2012 -0700 Quit and print error message if COMP is not set properly. Tools/F_mk/GMakedefs.mak commit 5f37cf2f80e3ad5c296b01e56abcfabd83eaaa3a Author: Weiqun Zhang Date: Wed Oct 10 11:21:20 2012 -0700 Fix typos. errorrr -> error Tools/F_mk/comps/Darwin_intel.mak Tools/F_mk/comps/Linux_intel.mak commit 16d41e1680a3a7e3114d5c6fdabefaae25da069f Author: Weiqun Zhang Date: Tue Oct 9 13:50:05 2012 -0700 Add a script for cleaning up old regression testing runs. Tools/RegressionTesting/reg_test_gc.py commit b3fbde45effb0c4c0f6981abb1b3271634eb260d Author: Weiqun Zhang Date: Tue Oct 9 12:38:30 2012 -0700 Fix a bug in make_build_info2 Tools/F_scripts/make_build_info2 commit 23ad4cd938bef5e35a94b6388d8bcb4ffe801f5b Author: Weiqun Zhang Date: Tue Oct 9 11:12:04 2012 -0700 Add make_build_info2. It is similar to make_build_info with an extra feature of allowing things like chemistry model being passed into the job info module. Tools/F_scripts/make_build_info2 commit 662a9b2206bb6385f8faef76b11efbee4f21927d Author: Weiqun Zhang Date: Tue Oct 9 11:11:27 2012 -0700 clean up reg_test_blame.py Tools/RegressionTesting/reg_test_blame.py commit 8efd3424ea3f56c33eb75f7b5a3726bb3ff6e020 Author: Marc Day Date: Mon Oct 8 12:07:58 2012 -0700 Add pp option for vismf verbosity Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 079ef6df190602c9f0d0cacca84f9ae0b1d02da1 Author: Michael Zingale Date: Fri Oct 5 13:08:05 2012 -0400 automatically take the abs() of the data if you are logging and any of it is < 0 python_plotfile/plotsinglevar.py commit bfde31a6a70430727b795a4b406593eadd09b832 Merge: 9e6648ed8 0a97cdb05 Author: Michael Zingale Date: Fri Oct 5 12:35:29 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit 9e6648ed8b7c7bcd95424a82de65740183727e48 Author: Michael Zingale Date: Fri Oct 5 12:34:58 2012 -0400 fix limits for 3-d slices -- there should be a global limit used for all 3 slices python_plotfile/plotsinglevar.py commit f68b7499fe54fcdbd77a5ee06b05008fd5bdb90e Author: Weiqun Zhang Date: Wed Oct 3 21:38:42 2012 -0700 Releasing tool: Fix the taget repo. Tools/Release/release.py commit 2bc854e443fa2f8457dd2c463a2919442ad7ffae Author: Weiqun Zhang Date: Wed Oct 3 17:43:05 2012 -0700 Public releasing tool. Tools/Release/ppCleanup.py Tools/Release/release.py commit ff0c18bd709d9bb50be29ff67fbe16bc96108f68 Author: Ann Almgren Date: Wed Oct 3 13:05:33 2012 -0700 Fix MultiFab::norm0 so it now works correctly when the MF is all zero. Src/C_BaseLib/MultiFab.cpp commit b9d063d6b1c1842592be8cd35c2647a21fe948d6 Merge: 496d46906 6b1dbc3ef Author: Ann Almgren Date: Wed Oct 3 12:31:34 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 496d469069fbffeb24c624ad4cf6345cd34990af Author: Ann Almgren Date: Wed Oct 3 12:31:25 2012 -0700 Get this compiling again. Tests/F_BaseLib/t_main.f90 commit 6b1dbc3ef1a408ba18423ec9a145d035b28cf2a7 Author: Weiqun Zhang Date: Wed Oct 3 11:55:11 2012 -0700 Regression testing script: add reportActiveTestsOnly option Tools/RegressionTesting/BoxLib-tests.ini Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/Nyx-tests.ini Tools/RegressionTesting/testnew.py commit 44ddd4a10d177c7f8ca05e46fe75e3aeaeafe2f2 Author: lijewski Date: Mon Oct 1 12:23:05 2012 -0700 Fixed typos. Src/F_BaseLib/multifab_f.f90 commit 0a97cdb05300fd15958f3716c799dc67f120a04b Author: Weiqun Zhang Date: Mon Oct 1 10:35:04 2012 -0700 fcompare: Fix 2D case fcompare.f90 commit 1f8bcf95d411e1acfd1795a8ee3edcb11014a41b Author: lijewski Date: Mon Oct 1 09:42:23 2012 -0700 Added contains_inf() and contains_nan() for multifabs to match calls for fab routines. Src/F_BaseLib/multifab_f.f90 commit 69a4d4cdfd1ebd5e61f624504a79f4926c94ed33 Merge: b7ace7cd5 4ea093187 Author: Weiqun Zhang Date: Sun Sep 30 21:25:22 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing commit 4ea093187ac1f779475734319209951ac7836ac8 Author: Michael Zingale Date: Sat Sep 29 12:53:49 2012 -0400 not supported fIDLdump.f90 fIDLdump3d.f90 commit d62704353e0e19881196f11e1fa674d8ae2776d7 Author: Michael Zingale Date: Sat Sep 29 11:34:40 2012 -0400 add NaN detection fcompare.f90 commit 200fcf9aef3ce21fe1f3e3e8a42e41ae35b0faea Author: lijewski Date: Fri Sep 28 15:49:48 2012 -0700 Substituted a select case statement for a long if/elseif string. Src/LinearSolvers/C_TensorMG/DV_3D3.F commit e3c7e4efee32f41e9ce5729810f6222724797df3 Author: ajnonaka Date: Thu Sep 27 14:48:15 2012 -0700 only providing OMP support for 3D in the base infrastructure now Docs/GettingStarted/GettingStarted.tex Docs/UsersGuide.tex Tutorials/HeatEquation_EX1_C/advance_2d.f90 Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 commit 49d88e1dad9c30f6bfc80733d45ab1a5757f2e72 Author: ajnonaka Date: Thu Sep 27 10:43:11 2012 -0700 Fix regrid so that we delete the old multifabs before we delete the layouts on which they are based. Tutorials/HeatEquation_EX5_F/regrid.f90 commit 7e2ceb0bbb45bc98be60fbe346b01d1da0e3c640 Author: Ann Almgren Date: Thu Sep 27 08:36:25 2012 -0700 Move CASTRO_hydro routines into Castro/Diagnostics/Sedov. CASTRO_hydro/GNUmakefile CASTRO_hydro/fsedov1d.f90 CASTRO_hydro/fsedov2d_cart.f90 CASTRO_hydro/fsedov2d_cyl_in_cartcoords.f90 CASTRO_hydro/fsedov2d_cyl_in_cylcoords.f90 CASTRO_hydro/fsedov2d_sph_in_cylcoords.f90 CASTRO_hydro/fsedov3d_cyl.f90 CASTRO_hydro/fsedov3d_sph.f90 commit 65998a5d96d0bfe15683cac2d3abfad73e4ec40a Author: Ann Almgren Date: Wed Sep 26 13:35:34 2012 -0700 Add protections against divide by 0, and clean up 1d/2d/3d a little. fcompare.f90 commit 9026e709276e5f0c125a8bb5a0d1d680aca9948b Author: Ann Almgren Date: Mon Sep 24 12:16:34 2012 -0700 Updated Nyx regression testing. Tools/RegressionTesting/Nyx-tests.ini commit c38897bc8b80955a9457204c8dca8eeab6082e7d Author: Ann Almgren Date: Mon Sep 24 12:15:36 2012 -0700 Fix regrid so that we delete the old multifabs before we delete the layouts on which they are based. Tutorials/HeatEquation_EX4_F/regrid.f90 commit 981b2dc056f82e9bb065d46b7da2c51139b7f76a Author: Ann Almgren Date: Mon Sep 24 12:10:52 2012 -0700 When we take only 1/8 of the particles in WriteCoarsenedAsciiFile we want the mass in the domain to be unchanged (more or less) so we multiply each remaining particle's mass by 8. Src/C_AMRLib/Particles.H commit bd5af5fd29bdee43acd8feb5198bcdef536c5f67 Author: Ann Almgren Date: Mon Sep 24 11:27:26 2012 -0700 Moved these files into Castro/Diagnostics. CASTRO_gravity/GNUmakefile CASTRO_gravity/fdustcollapse1d.f90 CASTRO_gravity/fdustcollapse2d.f90 CASTRO_gravity/fdustcollapse3d.f90 commit 0cc899e3768ed7a02170accaaaf91091183974c3 Author: Matthew Emmett Date: Mon Sep 24 12:41:59 2012 -0400 PyBoxLib: Simplify utils. Src/Python/pyboxlib/utils.py commit 786e78271c3787f38f0465b7777a1adc47628246 Author: Ann Almgren Date: Mon Sep 24 08:33:01 2012 -0700 Need to include PArray.H -- now compiles again. Src/LinearSolvers/C_NodalMG/amr_multi.H commit 15427b9cef270f57fd9dbc98d89ff9df4135799f Author: Ann Almgren Date: Fri Sep 21 17:56:14 2012 -0700 Replace CoarsenAndPrint by WriteCoarsenedAsciiFile which writes nparticles then only the particles from even cells into a new ascii file. Src/C_AMRLib/Particles.H commit 0f18ae598baafd80f7b155fab892c4ef27a43dac Merge: 1625c4478 74be6e07d Author: Ann Almgren Date: Fri Sep 21 17:41:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1625c44784f419caf7b549b02aba645ec2622f0c Author: Ann Almgren Date: Fri Sep 21 17:41:05 2012 -0700 Add a routine which writes out particles from every other cell -- this is useful when creating coarser versions of existing particle files. Src/C_AMRLib/Particles.H commit 74be6e07d68d6ef8cd3a0ce9c9b72809827e714a Merge: fcba448e3 d921c0ee4 Author: Weiqun Zhang Date: Fri Sep 21 16:35:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d921c0ee421951167d3c0ec771c24b14383dc8d0 Merge: 938039071 21c8aa7dc Author: cmalone Date: Fri Sep 21 16:32:36 2012 -0700 Merge branch 'master' of https://ccse.lbl.gov/pub/Downloads/BoxLib commit 9380390718df4f16e26a4eeb3fa747e4df30f686 Author: cmalone Date: Fri Sep 21 16:32:22 2012 -0700 hanlde ifndef blocks properly Tools/ppCleanup/ppCleanup.py commit fcba448e3ca372577107547aed6da6712ff27efb Author: Weiqun Zhang Date: Fri Sep 21 16:31:30 2012 -0700 a new ppCleanup python script for cleaning up IFDEF regions Tools/Release/cleanWords.txt Tools/Release/ppCleanup.py Tools/ppCleanup/ppCleanup.py commit 21c8aa7dc326e3d42bd5dd302e4aec11a364509c Author: Mike Lijewski Date: Fri Sep 21 18:00:33 2012 -0400 Cleaned up some warning messages from g++. Src/C_AMRLib/ErrorList.H Src/C_BaseLib/FabArray.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/F_MG/itsol.f90 commit ca23fe981876c9ddefde2c70cbd6b46d0691bd77 Author: cmalone Date: Fri Sep 21 11:48:21 2012 -0700 I *think* this is working for the pathological nested cases Tools/ppCleanup/ppCleanup.py commit 5931433badc48498f373a5b9b2f3f7b9b21872e7 Author: cmalone Date: Fri Sep 21 11:17:16 2012 -0700 fix character eating with -o option Tools/ppCleanup/ppCleanup.py commit 36f1546b0f7e22c01f6cb235f8d3407563b05a7f Author: Chris Malone Date: Thu Sep 20 19:49:44 2012 -0700 no longer need to have version 2.7.X Tools/ppCleanup/README commit e66a765c947ff4d488a38d5f94b428e610fb4101 Author: Chris Malone Date: Thu Sep 20 19:44:27 2012 -0700 workaround for versions less than 2.7 arg parsing Tools/ppCleanup/ppCleanup.py commit 5f5ea57cd87eb914f912c53698a90355fa699028 Author: Ann Almgren Date: Thu Sep 20 15:02:18 2012 -0700 These are the ifdef sections we want to eliminate for the first public release of CASTRO. Tools/ppCleanup/cleanWords.txt commit 3e9c8ff3b09e22617c664d83edacde6a16e77d7a Author: Marc Day Date: Wed Sep 19 13:45:42 2012 -0700 Fix up CMake files Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit b42acf5fcbd2668fca46a808cf2ca87a8768d6f4 Author: Michael Zingale Date: Tue Sep 18 18:12:08 2012 -0400 forgot to commit this originally Src/F_BaseLib/bl_prof_backtrace.f90 commit 6f887163f53dcaf045c97217f431756fd0d271c6 Author: Michael Zingale Date: Tue Sep 18 13:03:58 2012 -0400 bl_error cannot include the bl_prof stuff needed for a stacktrace, because when we run with PROF=t, we get circular dependencies. Now create a separate bl_error just for the backtracing stuff. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_error_backtrace.f90 commit a48cf41f4d3ed704ce5814a78d646ab5df70517b Author: Matthew Emmett Date: Mon Sep 17 20:58:15 2012 -0400 PyBoxLib: Various updates to run utilities and fabric utilities. Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/fabutils.py Src/Python/pyboxlib/plotfile.py Src/Python/pyboxlib/utils.py commit b7ace7cd5fe71a2222da9c67869fb01b716dd8bb Merge: a144d1f28 a94ea2736 Author: Weiqun Zhang Date: Mon Sep 17 13:50:34 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing commit ae7ba37ef461b1db042643611863fa959afea64f Author: lijewski Date: Mon Sep 17 13:49:06 2012 -0700 Include Tutorials/AMR_Advection_C/Source/ADR.cpp commit f07230fd82b77d7ec3f1a603b9a519f4505b2c7d Author: Ann Almgren Date: Mon Sep 17 13:39:33 2012 -0700 Fix GNUmakefile in AMR_Advection_C Tutorial. Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile commit bb6450eb3c5eb722fbd54a2be201491b69f21f53 Author: Ann Almgren Date: Mon Sep 17 09:58:57 2012 -0700 Modify 1d and 3d versions of diagonalization as well as 3d. Src/LinearSolvers/F_MG/itsol.f90 commit 948716153d99d4afc509ca8641c3738717a5a16d Author: Ann Almgren Date: Mon Sep 17 09:57:21 2012 -0700 Protect against divide by zero in diagonalization. Src/LinearSolvers/F_MG/itsol.f90 commit a400f59e1bb8830b25be1b926631628dba30f05f Author: Weiqun Zhang Date: Fri Sep 14 18:03:57 2012 -0700 Fix C_Src part of regression testing script Tools/RegressionTesting/testnew.py commit 871fc241787672377715443ac484d2ebd3b32565 Author: vince Date: Fri Sep 14 16:31:16 2012 -0700 instrumented the unoptimized hypterm. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 commit 975a50ad69ca1e269e2b45376f8cb231ede3a229 Merge: 9fa4f4590 04faea34e Author: lijewski Date: Fri Sep 14 09:37:05 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 04faea34e228f5cb7be2ad79d0d2718bd1d13e5d Author: Michael Zingale Date: Fri Sep 14 11:06:35 2012 -0400 latest Maestro tests Tools/RegressionTesting/Maestro-tests.ini commit ca33abf1fbde952da7af4d24f5aa33696941a2f8 Author: Michael Zingale Date: Fri Sep 14 10:54:20 2012 -0400 add support for debug tests Tools/RegressionTesting/testnew.py commit 9fa4f45902516d33126bd87a87b61bc997dd8d97 Merge: 2ce4e17ba eef78283e Author: lijewski Date: Thu Sep 13 20:44:51 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2ce4e17bacac69fb15f7cfc820a6e89102b06478 Author: lijewski Date: Thu Sep 13 20:44:31 2012 -0700 Specialized copyToMem() and copyFromMem() for Real. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit feddf5e12083b9c9b066ef6bcfc5136492edefcb Author: lijewski Date: Thu Sep 13 19:48:01 2012 -0700 Merged in copyFromMem(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 8a11e48ffd5f7e94a730851865fea74d7d546f04 Author: lijewski Date: Thu Sep 13 19:47:25 2012 -0700 Added copyFromMem() to complement copyToMem(). Src/C_BaseLib/BaseFab.H commit 40fba1d7b6794ed8db200d7a24ba3408e83358c6 Author: lijewski Date: Thu Sep 13 19:13:16 2012 -0700 Merged in new copyToMem() calls in place of doing a copy to a temporary fab and then a memcpy(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 5e29327afe832c6c2eaa8398f7f01427889606de Author: lijewski Date: Thu Sep 13 19:12:07 2012 -0700 Renamed MemCopy() -> copyToMem() and made it a member function not a static member function. Src/C_BaseLib/BaseFab.H commit 6e83bf0f16b06d9bcbafdbbae799a54b55986b3d Author: lijewski Date: Thu Sep 13 17:31:53 2012 -0700 Added static BaseFab::MemCopy(). Specialized version of copy() that goes from a FAB to a raw T* memory location. Src/C_BaseLib/BaseFab.H commit eef78283ea9aa467f5df3c7d45ec162b2f82734c Merge: 150537920 fd828b1e3 Author: ajnonaka Date: Thu Sep 13 15:00:16 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 150537920391432bdbbf9b43f8cf700a6a4b56d8 Author: ajnonaka Date: Thu Sep 13 14:59:32 2012 -0700 changed the_bc_tower class to use local indices for boundary conditions instead of global indices. Changed the rest of the source code to refer to the local indices. Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 commit fd828b1e30d28b9f93285b488f75bfea93ddb12d Author: Matthew Emmett Date: Thu Sep 13 16:41:09 2012 -0400 PyBoxLib: Remove (empty) utils. Src/Python/pyboxlib/fabutils.py commit 3b1db25f07d20d083660dab52354a5547af6a179 Author: Matthew Emmett Date: Thu Sep 13 16:40:22 2012 -0400 PyBoxLib: Print warning if libpycboxlib.so can't be loaded. Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/pybl.py commit 3fc1074826d443547885d031cbc966a62faedc59 Author: Matthew Emmett Date: Thu Sep 13 16:35:39 2012 -0400 PyBoxLib: Try again... Src/Python/pyboxlib/pybl.py commit 7b232aa72ed33c7bb8b0ca90c716864d275df3cf Author: Matthew Emmett Date: Thu Sep 13 16:33:50 2012 -0400 PyBoxLib: Print warning of libpyboxlib.so can't be loaded. Src/Python/pyboxlib/pybl.py commit 346f882eee0fccf8de31b322748c671055b78bc7 Author: Matthew Emmett Date: Thu Sep 13 13:57:54 2012 -0400 PyBoxLib: Add fabutils.py. Src/Python/pyboxlib/fabutils.py commit 12b2dd736fd20a3355901fab038167ca6828d89d Author: ajnonaka Date: Thu Sep 13 10:27:03 2012 -0700 bugfix: during regrid, after building the level 1 layout, you need to call bc_tower_level_build on level 1 so that the bc arrays are consistent with a possibly new layout Tutorials/HeatEquation_EX4_F/regrid.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 commit 34e7c60bd42b72c41e776a73a97df4b3fee37d54 Author: vince Date: Thu Sep 13 10:16:34 2012 -0700 updates for new boxlib changes. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90 commit ec61940b62f5553fe04d3b04a7e64162481a1cd4 Author: Matthew Emmett Date: Thu Sep 13 11:22:54 2012 -0400 PyBoxLib: Finish plotfile support and add "compare" routines. Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/multifab.py Src/Python/pyboxlib/plotfile.py Src/Python/src/boxlib_numpy_c.c Src/Python/src/boxlib_numpy_f.f90 Src/Python/src/fboxlib.f90 commit e340783674accbf4e7c37d9f63ece98007d8efe2 Merge: ebaa6061e 0406d4261 Author: Matthew Emmett Date: Thu Sep 13 11:23:15 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 0406d4261d04ed09cb904d374c124c30acd9058a Merge: 35c74ffe5 e259e4f9e Author: ajnonaka Date: Wed Sep 12 14:23:13 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 35c74ffe50f1f3f4f24b697730b09eb0dc25e4b0 Author: ajnonaka Date: Wed Sep 12 14:22:39 2012 -0700 fix multilevel bug. after ml_restricted_build, la_array is not consistent with mla%la. Therefore we must redefine/build the_bc_tower stuff Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX5_F/main.f90 commit e259e4f9e20d540d7331ac30cee1bd03405ccaec Author: Marc Day Date: Wed Sep 12 13:14:19 2012 -0700 Fix templatization issues in FillBoundary calls and add inline funcs in Amr Src/C_AMRLib/Amr.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 15605c7d0203b996d6f438f523f51b22ff2384b7 Author: Marc Day Date: Wed Sep 12 11:55:07 2012 -0700 Try again to fix cmake Src/F_BaseLib/CMakeLists.txt commit e85cb9e525d3bda3e1dcfdbfdad43d6e135c275a Author: Marc Day Date: Wed Sep 12 11:42:36 2012 -0700 Fixup CMakeLists.txt files in fort folders Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit 7cdee3ef2723ac89b9b63f6c3a45d22f6c1a01a7 Author: Marc Day Date: Wed Sep 12 11:19:20 2012 -0700 update CMakeLists file in F_Baselib Src/F_BaseLib/CMakeLists.txt commit 6bcf94b1d73b430e64c3dc818ac05f56d20375ca Merge: 9d22582c9 4adea6416 Author: Marc Day Date: Wed Sep 12 10:48:42 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 9d22582c9229396352c261d6604aef6c9dbf1902 Author: Marc Day Date: Wed Sep 12 10:48:14 2012 -0700 Remove check/plot writes in Amr destructor, move last writes to main Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 4adea64168bf775263daa9dac23726c06c5658d6 Author: ajnonaka Date: Wed Sep 12 10:29:57 2012 -0700 more cleanup in preparation for EXASCALE Src/F_BaseLib/define_bc_tower.f90 commit 27defe976dddeea5ac979a74fc6712ee026074c3 Merge: 48f18a47d af7dbd5da Author: Marc Day Date: Wed Sep 12 10:07:37 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit af7dbd5da8180eb8294c59a9b03c3354b1558ba6 Author: ajnonaka Date: Wed Sep 12 09:35:20 2012 -0700 some cleanup of define_bc_tower allocation/deallocation. ngrids is also no longer part of the_bc_level. prep work for upcoming switch to use local indices for bc stuff Src/F_BaseLib/define_bc_tower.f90 commit 48f18a47d26ebe3328cf902d7be3f712888a47ff Merge: 0f43f1356 bc0c5e46d Author: Marc Day Date: Wed Sep 12 08:35:55 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit bc0c5e46d3e76233a5574713b2f332b003db46a1 Author: ajnonaka Date: Wed Sep 12 08:01:29 2012 -0700 bugfix... changed do i = 1, nboxes(fine%la) call push_back(pbl, box_nodalize(get_box(fine,i),fine%nodal)) end do to do i = 1, nboxes(fine%la) call push_back(pbl, box_nodalize(get_box(fine%la,i),fine%nodal)) end do Src/F_BaseLib/fillpatch.f90 commit 2651849894c684c6023cf2c937dcbe7db0a9f1eb Author: Michael Zingale Date: Wed Sep 12 09:47:11 2012 -0400 add the backtrace stuff if we call bl_error. For this to work, we need to set BACKTRACE := t in the GNUmakefile. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_prof_stubs.f90 commit 8463f1626f639e239630e26af81602e9cbde8b5f Author: ajnonaka Date: Tue Sep 11 14:48:06 2012 -0700 local/global indexing bugfix Src/LinearSolvers/F_MG/cc_stencil.f90 commit 294a143efc336e72ed87ee2559b9db52b94848d6 Author: lijewski Date: Tue Sep 11 12:39:30 2012 -0700 A little cleanup. Src/LinearSolvers/F_MG/nodal_divu.f90 commit ebaa6061e1ee4a9c42868b134e3f1911fd67afd9 Merge: c01714669 62d0ea971 Author: Matthew Emmett Date: Tue Sep 11 15:30:53 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c017146691782318d3bc89013589cea67321f433 Author: Matthew Emmett Date: Tue Sep 11 15:30:39 2012 -0400 MODDEP: Ignore iso_c_binding module. Tools/F_scripts/moddep.pl commit 62d0ea971dfde79fc10e21c15b42527c29c949c4 Merge: aa742b54d 2c4744e8e Author: lijewski Date: Tue Sep 11 12:09:37 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit aa742b54dc460903177e24de5643eaa972d933aa Author: lijewski Date: Tue Sep 11 12:07:42 2012 -0700 Forgot to pass the multifab nodal flags to a couple box_nodalize() calls. For some weird reason the nodal flag argument to box_nodalize() is optional :-( Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 2c4744e8e6ffd635fda9809e1515c57f604524cd Author: Ann Almgren Date: Tue Sep 11 11:00:51 2012 -0700 Add README file for new Tutorial example. Tutorials/AMR_Advection_C/README commit f2fa3e5d8c6252e35e97604b1428d21e01d963df Merge: d7a8b15ff d5b6a72f4 Author: Ann Almgren Date: Tue Sep 11 10:57:55 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d7a8b15ff4e8b4240846aa86f73844aa446f6cf5 Author: Ann Almgren Date: Tue Sep 11 10:57:03 2012 -0700 Add new example to BoxLib/Tutorials -- this is a multilevel ADR problem in the C++ framework. About as simple as you can make an AmrLevel-type application. Tutorials/AMR_Advection_C/Exec/Make.ADR Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Advection_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Advection_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Advection_C/Source/ADR.H Tutorials/AMR_Advection_C/Source/ADR.cpp Tutorials/AMR_Advection_C/Source/ADRBld.cpp Tutorials/AMR_Advection_C/Source/ADR_F.H Tutorials/AMR_Advection_C/Source/ADR_advance.cpp Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp Tutorials/AMR_Advection_C/Source/ADR_error.cpp Tutorials/AMR_Advection_C/Source/ADR_nd.f90 Tutorials/AMR_Advection_C/Source/ADR_react.cpp Tutorials/AMR_Advection_C/Source/ADR_setup.cpp Tutorials/AMR_Advection_C/Source/Derive_F.H Tutorials/AMR_Advection_C/Source/Diffusion.H Tutorials/AMR_Advection_C/Source/Diffusion.cpp Tutorials/AMR_Advection_C/Source/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/ACT_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ACT_sums_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/React_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/fill_diff_coeff_2d.f90 Tutorials/AMR_Advection_C/Source/burner.f90 Tutorials/AMR_Advection_C/Source/extern_probin.template Tutorials/AMR_Advection_C/Source/interpolate.f90 Tutorials/AMR_Advection_C/Source/main.cpp Tutorials/AMR_Advection_C/Source/meth_params.f90 Tutorials/AMR_Advection_C/Source/network.f90 Tutorials/AMR_Advection_C/Source/prob_params.f90 Tutorials/AMR_Advection_C/Source/sum_integrated_quantities.cpp commit d5b6a72f48540644aca9d104dc028d0b42c37ae0 Author: ajnonaka Date: Tue Sep 11 09:59:44 2012 -0700 fix the boundary conditions so we refer to the global index. seems to run fine now in parallel Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 commit 24cc32c154870c8202dfd8f6c4d54533e0827ef6 Author: lijewski Date: Mon Sep 10 18:00:57 2012 -0700 Moved some of the new multifab code into layout. Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit a52600368050df6b5a62262ff13717ac77ff620c Merge: 09c296588 92518cb25 Author: lijewski Date: Mon Sep 10 17:54:42 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 92518cb258c4a94d3f15fa5480080d7319a8b51f Author: ajnonaka Date: Mon Sep 10 17:06:16 2012 -0700 fix lall option of multifab_volume Src/F_BaseLib/multifab_f.f90 commit 09c2965885bf355ba271fa0d557fd11954a04573 Merge: c0ddd8999 731f5da6f Author: lijewski Date: Mon Sep 10 16:16:05 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 731f5da6f1eaca2c129d6ec7ef7e96c24d99759a Author: Weiqun Zhang Date: Mon Sep 10 15:25:16 2012 -0700 Fixed a very old bug that was exposed by the recent changes. Src/F_BaseLib/bndry_reg.f90 commit 551fa4c86104fb1f6ccf37f01111b4d28fe1773e Author: Weiqun Zhang Date: Mon Sep 10 14:59:58 2012 -0700 Update MG CC solver for the latest nfabs changes. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit c0ddd899961f2b224ec8c1a54b3eca2b507d218d Author: lijewski Date: Mon Sep 10 14:53:13 2012 -0700 Now using the same gfortran options as they use in the F90 side of the code. Tools/C_mk/Make.defs commit e6f12a8f650985005b6a75ecef58db3658c87358 Author: ajnonaka Date: Mon Sep 10 14:49:21 2012 -0700 update all fortran tutorials and documentation to update latest way to loop over grids Docs/F_AdvancedTopics/F_AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 commit e53b1ae8e73c0d3e8b0fb951903d0b1142de8041 Merge: 1e243e2ff 9ebd1c555 Author: ajnonaka Date: Mon Sep 10 14:42:21 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1e243e2ff2c9de107964c96fd4dffa14aa381ffe Author: ajnonaka Date: Mon Sep 10 14:41:36 2012 -0700 fixed buggy paralle logic in ml_interface_c Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 9ebd1c5552e8ffa3052c6addea22831e95c43ff2 Author: lijewski Date: Mon Sep 10 13:26:29 2012 -0700 Shut up a couple warnings about unused variables. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 1d32b3ffc1e167e8be56c7065198402518c70851 Author: Weiqun Zhang Date: Mon Sep 10 13:16:12 2012 -0700 nboxes => nfabs Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/tag_boxes.f90 commit eead96b0f6a32b47eba35996484d65a1053b297e Author: lijewski Date: Mon Sep 10 12:59:12 2012 -0700 MAESTRO appears to work with new multifab stuff. Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 8b68fb35649012232e85bc991104e13a7a28d097 Author: lijewski Date: Sun Sep 9 11:38:30 2012 -0700 Use binary search in local_index(). Src/F_BaseLib/multifab_f.f90 commit e133615341a8e1b6aefe1440073a2d4a2d3ee745 Author: lijewski Date: Sun Sep 9 09:46:44 2012 -0700 Merged in [ilz]multifab_global_index(). Src/F_BaseLib/fabio.f90 Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit af773773e0ff7278490ffea2d40db68a341d3dc5 Author: lijewski Date: Sat Sep 8 17:09:04 2012 -0700 mf%nboxes ==> mf%nfabs [ilz]multifab_nboxes() => [ilz]multifab_nfabs() Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit b1a7830c828558d42d0b284c5da0c9afe5e37c03 Author: lijewski Date: Sat Sep 8 10:51:41 2012 -0700 %nboxes -> nboxes() in a few places. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 commit 1989d2b4086a1ab20e7b469954bdb9bd27d81fcd Author: lijewski Date: Sat Sep 8 10:40:22 2012 -0700 More local_index() stuf. Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit df3a0dcd8cae8640b54d0cabc0b8fc4bfc642207 Author: lijewski Date: Sat Sep 8 10:10:52 2012 -0700 Space for face_type & skewed is allocated & defined only for FABs we own. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit bf61c2049c96f4ac0b83abc40270f1ea835c0cdf Author: lijewski Date: Sat Sep 8 09:42:48 2012 -0700 Merged in local_index(). Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 commit ace4119fc279d5fa27204f1515fb1077d7fe18a3 Author: lijewski Date: Sat Sep 8 08:24:45 2012 -0700 Had to nodalize mask before growing it to get effective pbox. Src/LinearSolvers/F_MG/nodal_divu.f90 commit fd4c280901bd150ad594dc617fba80097b8c7ae0 Author: lijewski Date: Fri Sep 7 20:40:52 2012 -0700 Closer to working code. mgt%face_type(:,:,:) and mgt%skewed(:) must be indexed by global indices not local ones. Src/F_BaseLib/ml_multifab.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 8900fde0e9735579e598b5f70df821ba503493c2 Author: lijewski Date: Fri Sep 7 16:35:26 2012 -0700 Tweak to local_index(). Src/F_BaseLib/multifab_f.f90 commit e61124bc1ecea777e1fa63e683239eb71077c60a Author: lijewski Date: Fri Sep 7 16:23:03 2012 -0700 Merged in local_index() calls. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 175e50ee12cdd66b9b7134860f94c343483e6749 Author: lijewski Date: Fri Sep 7 16:04:31 2012 -0700 Got things to compile & run in serial. Almost surely there's parallel issues to be found. Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_multifab.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 18f66e595dc26a68dbd65f47034d9b1e58f40bcf Author: lijewski Date: Fri Sep 7 13:02:09 2012 -0700 get_[ip]*box() work on local indices. Src/F_BaseLib/multifab_f.f90 commit 194fc5da1988beea9067298fe34a8bc20cbaf8b6 Author: lijewski Date: Fri Sep 7 10:41:33 2012 -0700 Merged in local_index(). Src/F_BaseLib/multifab_f.f90 commit 4baa51710862cb407a06e663f2ebfaaa8834429e Author: lijewski Date: Fri Sep 7 10:07:26 2012 -0700 Added local_index(). Still need to merge into all the right places. Src/F_BaseLib/multifab_f.f90 commit d1300884c8b8276f9e6ff08574cbeb960fca47dc Author: lijewski Date: Fri Sep 7 09:27:54 2012 -0700 Removed "most" remote() calls. Got a couple that are more tricky to do. Src/F_BaseLib/multifab_f.f90 commit a3b3dc3b6facfe53c63f32887de833c35a1583c4 Author: lijewski Date: Fri Sep 7 09:07:10 2012 -0700 fbs(:) is now sized to be just the local fabs. idx(:) are the global boxarray indices for the local fabs. Removed remote() and local() functions. Src/F_BaseLib/multifab_f.f90 commit 280aa5acbc8385b5cef4c3936db0b65c96e8ecce Author: lijewski Date: Thu Sep 6 15:23:23 2012 -0700 Removed the Do_AllToAllV code. This is unlikely to be useful as we move to exascale. I left the multifab_set_alltoallv() function since I "think" that may be callable by some input parsing code -- it does nothing now. Src/F_BaseLib/multifab_f.f90 commit a9d9e4db45f12450732f5efd195eb2a0f379014f Author: lijewski Date: Thu Sep 6 12:52:27 2012 -0700 Reverted out an ill-advised numcomp -> ncomp substitution. Src/C_AMRLib/FluxRegister.cpp commit 5302bf795b94eb435990a1ee0f4a36b1fd96bf86 Author: Weiqun Zhang Date: Wed Sep 5 20:45:44 2012 -0700 Fix a minor bug in make system I just introduced. Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 3343bf21e1733dd8d76aaac02e5044f07480a5e1 Author: Weiqun Zhang Date: Wed Sep 5 14:52:35 2012 -0700 The make system can handle dependence of "include" lines in f90 files now. Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/C_scripts/moddep.pl Tools/F_mk/GMakerules.mak Tools/F_scripts/moddep.pl commit a1bdeceb40b3f12377aa05a2a25961e322c1f503 Author: lijewski Date: Wed Sep 5 14:31:26 2012 -0700 Made the CrseInit() that takes FABs a bit more memory efficient. Src/C_AMRLib/FluxRegister.cpp commit 3ababc4fe91cdbde7dcb7f01ce4ac2987ee7c124 Author: lijewski Date: Wed Sep 5 09:02:51 2012 -0700 Pulled some computation out of an inner loop. Src/C_AMRLib/FluxRegister.cpp commit cac9e4134241314716527c25b14919a818558944 Merge: 8665bbbcf e8d8cddf0 Author: lijewski Date: Tue Sep 4 15:01:01 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8665bbbcfcce714934d71368460a39ba54817f56 Author: lijewski Date: Tue Sep 4 15:00:48 2012 -0700 Simplified mapPeriodic() a bit. Src/C_AMRLib/TagBox.cpp commit e8d8cddf0c256b743818d4dfbb0d9870f8b1ff8b Author: Ann Almgren Date: Tue Sep 4 14:11:48 2012 -0700 Fix test on ref_ratio -- we were just doing the wrong test on whether all the components were the same ... (was previously testing across levels, just meant to test across 1:dm) Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit d9a50c8a531611e8b0c8f670ff2bc0b9773601b2 Author: lijewski Date: Tue Sep 4 12:25:19 2012 -0700 Replaced the specialized CrseInit() parallel implementation with one that uses parallel copy()s. I'd like to do the same for the parallel implementation of Reflux() but that's more complicated ... Src/C_AMRLib/FluxRegister.cpp commit d8c967d0cfd70ede90262a51de867f9a823b51cc Author: Mike Lijewski Date: Sat Sep 1 14:47:53 2012 -0400 Yet more early exits from nested loops. This about finishes (hopefully) my rewrite of our MPI communication and caching infrastructure. We should be ready for exascale. Metadata has been minimized & should not be an issue. The new code is also significantly faster than the new, with the difference increasing as the number of MPI processors increases. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 23db1acc901207629aa734b9cf695566c3a320f7 Merge: 0f88845c5 bec05050d Author: lijewski Date: Fri Aug 31 13:39:43 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bec05050d939a403a5117e88287f4ec13be94517 Author: vince Date: Fri Aug 31 13:37:55 2012 -0700 more make and output tweaks. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 commit 0f88845c51dba752ccb1c3b209ae93c2925c2070 Author: lijewski Date: Fri Aug 31 12:28:15 2012 -0700 More short-circuiting out of loops. Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit c165dfd4dd9e3afd3f1a05427599c154560e0c83 Merge: 8c2c9a795 0d6949495 Author: lijewski Date: Fri Aug 31 10:56:28 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8c2c9a7950f95febf4177d3f789af2e02ef5601e Author: lijewski Date: Fri Aug 31 10:53:45 2012 -0700 Have Finalize() flush cache. Src/C_BaseLib/DistributionMapping.cpp commit 0d69494953238ea2f373d97436e469f325fe0236 Author: vince Date: Thu Aug 30 17:34:09 2012 -0700 set up the makefiles to allow local setting of optimization flags. there is something wrong with the f90 flux minmax output for rho. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile commit 45046d20a22b1c3aaf30aecd0101142fb76903ea Author: lijewski Date: Thu Aug 30 15:44:20 2012 -0700 Refinement of the count of bytes held by the caches. I was overcounting. Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 04383c384aaf4b8893b427714b82e58adfa58f40 Author: lijewski Date: Thu Aug 30 15:22:09 2012 -0700 Some speedups. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit e323638ac689b34eb637e995e085e5b6a8ffe93f Author: vince Date: Thu Aug 30 13:23:58 2012 -0700 added openmp flag for c. Tools/C_mk/Make.defs commit b8943740e35fb97964e2991605ea3ab0b98e347a Author: vince Date: Wed Aug 29 16:13:28 2012 -0700 undid some changes from hopper. Tools/C_mk/Make.defs commit 97035a229992903265f8a4cbf55d7cb7cd593a1e Author: vince Date: Wed Aug 29 16:07:07 2012 -0700 set omp flag for regular c. Tools/C_mk/Make.defs commit ac7eef4e9066cf2604d9915d9bd729bfbf3f0088 Author: vince Date: Wed Aug 29 15:54:22 2012 -0700 omp fix. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F commit 6afb27459948ddd1e2fd57134dbd5ac3b7ca595a Author: vince Date: Wed Aug 29 15:24:03 2012 -0700 made the output more consistent between cases. cleaned up some code. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90 commit 7245a35688b070e045a486751fbce0fa7499ed1d Author: vince Date: Wed Aug 29 12:59:21 2012 -0700 reused files. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer_c.c commit 0e8432cffbedc705ad11d315cec5c36e87797189 Author: lijewski Date: Wed Aug 29 11:06:36 2012 -0700 Some cleanup. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H commit 85bad3b9159086d648a65250b1279d72c463124f Author: lijewski Date: Wed Aug 29 10:36:03 2012 -0700 For now always print out the DistributionMapping cache stats; i.e. ignore whether or not verbose is set. I want to get a good handle on the total amount of metadata being used. Src/C_BaseLib/DistributionMapping.cpp commit eae90f2b59655b3d37a8cb1da695af5ab741c589 Author: lijewski Date: Wed Aug 29 10:28:29 2012 -0700 Little code cleanup. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryRegister.H commit c01f75d096ccbd8dc59e0dc8b6a5dee294744b23 Author: lijewski Date: Wed Aug 29 10:13:03 2012 -0700 Simpler (but equally good) key calculation for copy cache. Src/C_BaseLib/FabArray.cpp commit b05487efa7fb80461172bb42deac39858b7f125f Author: lijewski Date: Wed Aug 29 10:10:31 2012 -0700 Moving short inlines directly into class declaration. This seems to make the code a little easier to read and cut down total amount of code. Src/C_AMRLib/Amr.H Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/BCRec.H Src/C_AMRLib/Cluster.H Src/C_AMRLib/StateData.H commit dcffdef7bafbd99ffdd5a77d6a071381e429775e Author: lijewski Date: Wed Aug 29 08:52:08 2012 -0700 Wrapped some long lines. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/Pointers.H commit 6763e6d11e5673ff41a20ad8ee13b81a7ec7ec2d Merge: d423475a5 2b028d606 Author: lijewski Date: Tue Aug 28 16:49:25 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d423475a53cbedcd82881dc92677701a3eef3b5a Author: lijewski Date: Tue Aug 28 16:46:21 2012 -0700 Some simplification. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H commit 2b028d60638e39a73fac7975ca16520d65ca804b Author: vince Date: Tue Aug 28 13:16:41 2012 -0700 some cleanup. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/README commit 6f6eee43fe6e96fa1aaa5c8f37058ebbdea0d733 Author: vince Date: Tue Aug 28 13:05:13 2012 -0700 they should all be working now. stil need to sync timings and consolidate duplicate files. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/Make.package Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90 commit 6838e79f981c9b512597225ce2851a47a9375a6a Author: lijewski Date: Tue Aug 28 11:17:54 2012 -0700 A little cleanup of some output I had left in. I'd Key used in the copy cache is better than previously, but SyncRegister::FineAdd() can generate a number of distinct calls to plusFrom() that all yield the same Key :-(. Src/C_BaseLib/FabArray.cpp commit afc71d45b80603fe51516e3f4adf378c146178f7 Author: lijewski Date: Tue Aug 28 11:03:57 2012 -0700 Came up with better Key into the multimap for the caches in an attempt to minimize the search time. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 96bd04bd24089eaa357c9ff99467c18febeac56a Author: lijewski Date: Mon Aug 27 17:16:21 2012 -0700 Shortcut out of a nested loop a little earlier than before. Src/C_BaseLib/Geometry.cpp commit fb8bddb6474343f988cc79d767ac014fcdf2ebac Author: lijewski Date: Mon Aug 27 16:56:02 2012 -0700 Increase max size of FillPeriodicBoundary() cache. Src/C_BaseLib/Geometry.cpp commit ea2f3f76dc03dccc517aa878b0b4499262ad123f Merge: 5b2a8391c b76b4c5c2 Author: lijewski Date: Mon Aug 27 16:44:14 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5b2a8391c0c03ccadf6ae281f5bcf2bebc93329e Author: lijewski Date: Mon Aug 27 16:43:41 2012 -0700 Implemented SunBoundary() using intersection & communcation info from the FillBoudary() cache. Src/C_BaseLib/MultiFab.cpp commit b76b4c5c2c808bd561b870e9e319fed786a75f95 Author: vince Date: Mon Aug 27 16:15:04 2012 -0700 added u and q initialization, fixed loop and pencil ranges. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c commit 5c7dcdb84042922a3df9b88362e87fedf865baca Author: lijewski Date: Mon Aug 27 15:29:24 2012 -0700 Some code consolidation. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit ad1c4ab357e5b1c62ce4bc521e3af77c38e6d569 Author: lijewski Date: Mon Aug 27 15:07:24 2012 -0700 Increased the size of the caches to 100 entries. Refined the count of number of bytes contained by the caches. Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit d2dcccba023e98e9141cd0485d8ac4fc1fcab21b Author: lijewski Date: Mon Aug 27 14:18:01 2012 -0700 New implementationof copyFrom()/plusFrom() that uses FabArray::copy(). This means that it'll be able to use the copy cache & all that entails. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit bca2d41fe46f3a5bfa1855701cbe99ca4ea4f6c2 Merge: 663e36aec 31af8dfae Author: lijewski Date: Mon Aug 27 12:18:06 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 31af8dfae9f67b28db0894252a16af9850094166 Author: Weiqun Zhang Date: Mon Aug 27 10:59:42 2012 -0700 Fix a bug in getRecentFileName in regression testing python script Tools/RegressionTesting/testnew.py commit 663e36aeca2d812e9a1d890c6d44d22a5d00ce98 Author: lijewski Date: Sun Aug 26 13:52:48 2012 -0700 Call FabSet::Cache() on regrid of level 0. Src/C_AMRLib/Amr.cpp commit f22cb9829d0be64c06395da77374d6bd4c5b275e Author: lijewski Date: Sun Aug 26 13:51:40 2012 -0700 Added a cache for the grid intersection & communication info for copyFrom() and plusFrom(). Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit ac37878b28f20190ad6e42150ca1e30f6a676943 Author: lijewski Date: Sun Aug 26 12:47:31 2012 -0700 Generalized the copy cache stuff so I can maintain separate copy caches for different purposes. I want to have a copy cache for FabSet::copyFrom() and FabSet::plusFrom(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 46c35981395d99a8820bb21c4527e66c650252c4 Author: lijewski Date: Sun Aug 26 09:55:55 2012 -0700 Simplified Reflux(). Src/C_AMRLib/FluxRegister.cpp commit cf770382a9b5b3ede1b4ef6caa873814dc582484 Author: lijewski Date: Sun Aug 26 09:21:48 2012 -0700 Simplified CrseInit(). Removed CrseInitDoit(). Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit f6c359eaf033fab1599eb9c578761e55569195df Author: lijewski Date: Sat Aug 25 19:43:54 2012 -0700 Attempt to get a little communication/computation overlap. Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 1187ddad5dddcfb554e4258fd90510ac6b16160b Author: lijewski Date: Sat Aug 25 19:11:41 2012 -0700 Yet more code consolidation. Src/C_BaseLib/FabArray.H commit a623cc6f3a69de17de0e72bfcd5778484c34034e Author: lijewski Date: Sat Aug 25 15:06:31 2012 -0700 Found my bug. Back to the hand-optimized version of Reflux(). Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 19f371bb5268727fa1cd56e68321ef0b8eea8ec6 Author: lijewski Date: Fri Aug 24 22:42:14 2012 -0700 I'm reverting back to a slightly older version. Something's weird. Running a single timestep multiple times on 256 cores on hopper, the FAB byte spread varies from run to run. Unfortunately it should be the same for identical runs. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit d1ab1d65d3570ab509f48205917a91487b7ebcab Author: lijewski Date: Fri Aug 24 22:14:40 2012 -0700 Didn't have some logic quite right. Src/C_BoundaryLib/BndryData.cpp commit 39691ce6485c0382d1df298bf5ccb4f4de4c9ac6 Author: lijewski Date: Fri Aug 24 19:08:29 2012 -0700 Uses iterators when running over pshifts. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Geometry.cpp commit 5a91e5f65c12b157b118e7a6b3cd0b8d1a9b3755 Author: lijewski Date: Fri Aug 24 18:20:49 2012 -0700 Elide a periodicShift() call. We call it twice in the same routine on the same Box. Just reuse the pshifts result from the first call. Src/C_BoundaryLib/BndryData.cpp commit e6bfff18547e3f0362d0d2b8d5fbbd8de545282b Author: lijewski Date: Fri Aug 24 16:53:39 2012 -0700 Removed some #if 0 code. Src/C_BaseLib/FabArray.cpp commit ebf427193d14da2dff43d97532d2abd43c1b4738 Author: lijewski Date: Fri Aug 24 16:46:45 2012 -0700 Minor performance mod to periodicShift(). Src/C_BaseLib/Geometry.cpp commit a066f85ee2b6dc60af6c372fe79e6260f01a0212 Author: lijewski Date: Fri Aug 24 16:11:12 2012 -0700 Changed some static member functions of FabArrayBase to member template functions and was able to consolidate more of the recent communication code I wrote. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit b47e005c519a81d44499d529ff13988d55d31b8d Author: lijewski Date: Fri Aug 24 14:09:50 2012 -0700 A little more refinement. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit c5cc93e5e8545ebebcbe1e68719e90d9a6b1f8bc Author: lijewski Date: Fri Aug 24 13:30:35 2012 -0700 A little more refinement. Src/C_AMRLib/FluxRegister.cpp commit 8c1f7c6d7583f1e28effcd20fabd0211b5a04a2a Author: lijewski Date: Fri Aug 24 13:13:09 2012 -0700 Handcoded optimized parallel Reflux routine. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit c2901a659f0b7ecfb2095e339890912e817ac5e4 Author: lijewski Date: Thu Aug 23 17:35:59 2012 -0700 Further simplification. Src/C_AMRLib/FluxRegister.cpp commit da4623e60be0eb7eeb30f93a9b0871fedac28428 Author: lijewski Date: Thu Aug 23 15:58:04 2012 -0700 Some more cleanup of Reflux(). I added another argument to FORT_FRREFLUX() -- an IntVect shift. It's (0,0,0) if it's being called when the two boxes concerned overlap, but it's how much the dest fab must be shifted when being updated due to periodic shifts. Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 44250bb178303274a28eeaede71ad595d0af55fc Author: lijewski Date: Thu Aug 23 13:21:04 2012 -0700 Very modest simplification of Reflux(). Src/C_AMRLib/FluxRegister.cpp commit 44b9aaff981ebefb78ecb5748d5fe468614cc982 Author: lijewski Date: Wed Aug 22 15:47:34 2012 -0700 More typedef regularization. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 716827337c477a9aef15f439cf85b63007a3444d Author: lijewski Date: Wed Aug 22 15:35:51 2012 -0700 Regularized some typedefs. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 5657538a5e16e6a5b553f0f248065fa04596c8db Author: lijewski Date: Wed Aug 22 15:19:15 2012 -0700 Some simplification. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 0c955f5f0372a26755c963aae5e32d71f9f11975 Author: vince Date: Wed Aug 22 12:49:59 2012 -0700 our cpp calling sam's c hypterm. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/Make.package Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/hyptermbench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer_c.c commit 5e88ef995df840298645a23df0865ee3d25543b7 Author: vince Date: Wed Aug 22 12:37:42 2012 -0700 sam's c_c version. need to check the answers. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/timer.x86.c commit e4854af457a4a86bc5b39ecb3fefa21bfc100206 Author: lijewski Date: Wed Aug 22 12:27:28 2012 -0700 Inlined some stuff that seems to matter at high CPU counts. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 842e8e35e8121b0addf582f3131eac73be4722b1 Author: lijewski Date: Wed Aug 22 11:11:31 2012 -0700 OMP'd couple routines over ncomp. At least for LMC ncomp is sometimes NSPECIES or BL_SPACEDIM so OMP "might" give us a nudge. Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FluxRegister.cpp commit bcded6f7907a2f309a91a4ae7a9ff0d252088238 Author: lijewski Date: Wed Aug 22 10:54:38 2012 -0700 Made the constant volume Reflux() call the more general one. Was able to get rid of a lot of code. I'd like to simplify the more general Reflux() routine enough that I can provide a hand-optimized parallel version. Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.cpp commit 3caf944bed102cba11e58a770b62db2c9a58433b Author: lijewski Date: Wed Aug 22 09:44:26 2012 -0700 Removed PIRec and PIRMVector stuff -- no longer used. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit a8b17a43bc35029d150c51cb2537517875067071 Author: lijewski Date: Wed Aug 22 09:37:16 2012 -0700 Handcoded optimized parallel routine for SumPeriodicBoundary(). Src/C_BaseLib/Geometry.cpp commit 6c7aba8980486e419fe889678f8e5fbb957afb1a Author: lijewski Date: Wed Aug 22 08:28:49 2012 -0700 Fixed compilation bug when !BL_USE_MPI. Src/C_BaseLib/FabArray.cpp commit 765ab7378b8a724faa877a326bdbd5e51b2ea022 Author: lijewski Date: Tue Aug 21 20:13:59 2012 -0700 Yet more code cleanup & consolidation of new parallel routines. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit 7bad31b4f6f84a247adc67891bc1a3ca8c067e9a Author: lijewski Date: Tue Aug 21 19:30:31 2012 -0700 Removed SIRec structure -- no longer used. Src/C_BaseLib/FabArray.H commit 4dfdc99956c48d763b332f7bef2af1ce28d5d3fc Author: lijewski Date: Tue Aug 21 19:27:24 2012 -0700 More code consolidation. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit fce07e7dbf0e85eb6f5d14eff0e59b79e5d7df55 Author: lijewski Date: Tue Aug 21 17:45:26 2012 -0700 Some code consolidation. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit 1a615c75ec352eaf45fefc390d6c77e674833a72 Author: lijewski Date: Tue Aug 21 16:38:05 2012 -0700 Handcoded parallel routine for SumBoundary(). Src/C_BaseLib/MultiFab.cpp commit d745bff987c70c7f812bf6bf765aa6b9cf2e1624 Merge: fa47894d3 f2608c9c6 Author: lijewski Date: Tue Aug 21 16:37:45 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f2608c9c67ca62e25e64407e14f51a927cbb4e7d Author: vince Date: Tue Aug 21 16:05:29 2012 -0700 the cpp_F version. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/Make.package Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/timer_c.c commit 6cfe6f37adcfe46b771b6dac3c066715857e7b4d Author: vince Date: Tue Aug 21 15:53:41 2012 -0700 the f90_f90 version. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/README Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90 commit fa47894d38ae6d7b0c49ccf6c894bc854f43ffc1 Author: lijewski Date: Tue Aug 21 15:02:17 2012 -0700 Removed a data structure no longer used by CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 2b0f795b17eeae9b9df9d940c63e9ff22471af99 Author: Ann Almgren Date: Tue Aug 21 13:41:17 2012 -0700 Fix order of tests on bottom solver type when setting up mg_tower because in some cases the bottom solver type is set to 4 but we override that and set it to 1. We need to make sure we make the nodal_mask after that change. Src/LinearSolvers/F_MG/mg.f90 commit b6647ae740e37adf7882ecd8e324c87dcb9a5b90 Merge: 051ef928d 2135af5c8 Author: lijewski Date: Tue Aug 21 10:48:26 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 051ef928d61bb223dc79f02f141f19c684520621 Author: lijewski Date: Tue Aug 21 09:22:08 2012 -0700 Consolidated two CrseInit() functions into single CrseInitDoit() that they both call. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit b5bf478ee8a1faee147dcffe934f5b042813e7b4 Author: lijewski Date: Mon Aug 20 21:59:18 2012 -0700 Handcoded parallel routine for copyFrom(). Added an assertion that wasn't in the old code: I now check that ngrow <= src.nGrow(). I found one place in MacProj.cpp where it was calling copyFrom() on a src MultiFab and asking to fill more ghost cells than the MultiFab had. I could have silently done the right thing in my code, but it just didn't seem right to allow people to ask for filling with more ghost cells than the MultiFab contains. Hopefully MacProj.cpp is the only code that did that :-) Src/C_BoundaryLib/FabSet.cpp commit 2135af5c88c729763624f4d9ae3e1e1452b9db5c Author: ajnonaka Date: Mon Aug 20 19:59:32 2012 -0700 add support for USE_LMC_SDC. Will compile in #ifdef LMC_SDC items Tools/C_mk/Make.defs commit 10e139c62c28af518954c9a26867bf6d5c60ff10 Author: lijewski Date: Mon Aug 20 19:26:12 2012 -0700 Some cleanup. Two Reflux() functions still call CollectData(). I'll eventually get to them but they're a tad more complicated than the CrseInit()s. I'll work my way up to'm. Src/C_AMRLib/FluxRegister.cpp commit 95163b082d55e0216f227a90904ca113040d01b8 Author: lijewski Date: Mon Aug 20 17:19:39 2012 -0700 Handcoded special parallel routine for other CrseInit() -- the one that takes an area MultiFab. Src/C_AMRLib/FluxRegister.cpp commit 077f3b628e6357aabb719cba5ac28b7e6d0edcf7 Author: lijewski Date: Mon Aug 20 15:55:07 2012 -0700 Handcoded parallel routine for FluxRegister::CrseInit(). This avoids the MPI_alltoall and MPI_alltoallv routines in CollectData(). Src/C_AMRLib/FluxRegister.cpp commit 62802abf084ad649619c34e0c3bf61feadf3b8b4 Author: lijewski Date: Mon Aug 20 13:26:08 2012 -0700 Deleted some no-longer-used static variables. Increased the maximum size of the caches. We could "probably" go without limiting their size in any way, as they're cleared every level zero regrid. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 75d8bf8f72ca6bd2c71f50260d4f17b4f2e9a247 Author: lijewski Date: Mon Aug 20 13:08:27 2012 -0700 Final Final. Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit ea162ad6fe7239ce01c08bbd48ce039d510c3906 Author: lijewski Date: Mon Aug 20 11:20:52 2012 -0700 The caching stuff is looking good in tests on hopper & jaguar. Hopefully this'll be the last update to this stuff for a while. We're now running with bigger caches and each MPI process maintains the bare minimum amount of data it needs to do its job. It's time to rewrite a few more of the routines that call CollectData() that can be rewritten to avoid MPI_alltoall and MPI_alltoallv calls. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 9b40dab41fa3030d243affe34bd37352df8c6b6f Author: lijewski Date: Sun Aug 19 12:17:27 2012 -0700 Fix bug in FlushCache() code. Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 15b5817f8be6375b8636532b019ae1c75a743188 Author: lijewski Date: Sun Aug 19 11:53:45 2012 -0700 Fixed a bug I just introduced and did some cleanup. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit f5cfff6a1dc9f54a045370dc63bdfb1d7cfac4d5 Author: lijewski Date: Sun Aug 19 11:08:11 2012 -0700 Don't insert FB objects into FillBoundary() cache if that particular MPI process doesn't have any work to do on it. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 9eade3566ba824c9bd320bc28e1df97a4b96ecd2 Author: lijewski Date: Sun Aug 19 10:40:54 2012 -0700 Don't insert CPCs into the copy cache if that MPI proc has no work to do in the copy(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 2d23fc744c7a4aa7def872997c1f498a223bb02a Author: lijewski Date: Sun Aug 19 10:01:43 2012 -0700 Don't add an entry to the FPB cache if that paarticular MPI procroc has no work to do. This is a little tricky ... Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 6a92b3d3dc68f5f21f4130ffdff6a6c34f5e92dc Author: lijewski Date: Sun Aug 19 09:02:47 2012 -0700 Print out the max amount of space used by the caches when they're being flushed. This happens on regrid of level 0 and on program exit. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 60415b22109aa5acc61d0cbfdb8bd8d7258a8758 Author: lijewski Date: Sun Aug 19 07:40:03 2012 -0700 Increase the default size of caches. I'm doing some experiements to see how big I can let these get. For the FillPeriodicBoundary and FillBoundary ones we may be able to let these be unlimited in size, and then clear'm at a level 0 regrid. For copy() not so much, at least for LMC, where we're doing a lot a rather unique copy()s for redistributing chemistry. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 1e06be05a0e8b3d9ee23794b71ca7e65c2ddab3c Author: lijewski Date: Sat Aug 18 18:40:11 2012 -0700 Inlined FabComTag constructor. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit c5e8f266bbecadec6aa9df152cc1c5879c03a356 Author: lijewski Date: Sat Aug 18 18:24:43 2012 -0700 Remove all the do_alltoallv stuff. Never used. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b751a89be663712f67c1959f0583cd3edd7ac75f Author: lijewski Date: Sat Aug 18 18:06:04 2012 -0700 Minimized memory allocation & object construction in the cache stuff. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit e2f70000068212b5fdc0ccf1245a25006b235b5f Author: lijewski Date: Sat Aug 18 17:16:32 2012 -0700 Inlined a couple heavily used member functions. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit b5b8fdd56b71d1df48cf10896b99e2dfe8d09a3c Author: lijewski Date: Sat Aug 18 10:54:58 2012 -0700 Rewrote FillPeriodicBoundary() so it no longer calls CollectData(). This eliminates an MPI_Alltoall() and MPI_Alltoalv() call on initial build. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 2694e849df03640780ed8cec1d934bf0e8031388 Author: lijewski Date: Sat Aug 18 09:13:33 2012 -0700 Untemplatized TheFPB(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 5c7bb152c51e95da9bcfea9dae281196546b4cc7 Author: lijewski Date: Fri Aug 17 16:26:05 2012 -0700 A little more error checking of input cache sizes. Src/C_BaseLib/FabArray.cpp commit ba43d34a796b1f7b39bdb8bf11d8380408356c91 Author: lijewski Date: Fri Aug 17 16:23:13 2012 -0700 Rewrote FillBoundary() to not use CollectData(). Should be faster since it avoids a MPI_alltoall() and MPI_alltoallv() on initial construction. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 4191b8f22d8f1bbffd30c3979d347baa2af26442 Author: lijewski Date: Fri Aug 17 14:34:28 2012 -0700 Moved some copy() code that doesn't depend on the templace type out of the .H file into the .cpp file. Simplified code a bit. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit c69660c1b19941ae147c1577bb39be348941288d Merge: eb8c2d0af e55252c53 Author: lijewski Date: Fri Aug 17 13:56:51 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit eb8c2d0af30d87fde3b305d398afe82ac4df7fc9 Author: lijewski Date: Fri Aug 17 13:55:19 2012 -0700 Moved the do_alltoallv stuff in copy() into its own function. I'm thinking of removing the do_alltoallv stuff entirely. It's hard for me to imagine as we run on larger & larger machines & communication patterns get sparser that MPI_Alltoallv can beat MPI_Irecv/MPI_Send pairs. Src/C_BaseLib/FabArray.H commit b770f5bd47b1e22565c5611e39b3bf3db76db054 Author: lijewski Date: Fri Aug 17 13:33:00 2012 -0700 Moved the portion of CollectData() that uses do_alltoallv into its own helper function. Src/C_BaseLib/FabArray.H commit e55252c53e76b0bac666c1f78e76e2e28efb6b5e Merge: 0332420ca 7aec5ef27 Author: vince Date: Fri Aug 17 13:22:53 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 0332420cae3af3dcad8e07bcd2d5a142c413a507 Author: vince Date: Fri Aug 17 13:22:23 2012 -0700 gnu. Tutorials/Exp_CNS_NoSpec/GNUmakefile commit 7aec5ef278ac9a2460555e34cd88f4611aa97060 Author: Mike Lijewski Date: Fri Aug 17 13:37:32 2012 -0400 Use SameRefs() in copy & fillboundary() cache code. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d24047ab8c04734be8b8b0414b74d556c279a7da Author: Mike Lijewski Date: Fri Aug 17 13:35:26 2012 -0400 Added static functon SameRefs() to test if the underlying reference counted pointers are the same. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit ade2714f21ffedd20abe79a5b88188931020245e Author: Mike Lijewski Date: Fri Aug 17 13:32:08 2012 -0400 Inline operator==() in reference counted pointer class for testing if underlying pointers are the same. Src/C_BaseLib/Pointers.H commit dfbe31fc635f8e57e562fb01aa89e2000054c62c Author: lijewski Date: Thu Aug 16 19:48:35 2012 -0700 Built a map of iterators into FabComTagContainer to avoid a modest N^2 loop when receiving FAB data in CollectData(). Src/C_BaseLib/FabArray.H commit ba73e896d1e5bd72c30f4f94e56f2287bb49df03 Author: lijewski Date: Thu Aug 16 19:18:26 2012 -0700 More performance tweaking in CollectData(). Got one more thing I wnat to try before pushing this stuff. Src/C_BaseLib/FabArray.H commit ed900fb80387527348c521abb725b7cea4a8e9d0 Author: lijewski Date: Thu Aug 16 18:03:10 2012 -0700 More tweaks to CollectData(). Src/C_BaseLib/FabArray.H commit 16c71389229504dba58d900f1ef191469fef794b Merge: c3a6c4716 9775f5f32 Author: lijewski Date: Thu Aug 16 14:47:02 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c3a6c4716ab5a064ad147484fabf35ff0a07a27a Author: lijewski Date: Thu Aug 16 14:46:49 2012 -0700 Squished out more memory from CollectData(). Src/C_BaseLib/FabArray.H commit 3ae6b1ace430ad47fb0c8175e53e9aba564e5681 Author: lijewski Date: Thu Aug 16 13:03:21 2012 -0700 Removed unused variable. Src/C_BaseLib/FabArray.cpp commit 9775f5f32bfa7b484d7f82ef7ac20b27cc8e6801 Author: Ann Almgren Date: Thu Aug 16 11:50:53 2012 -0700 Add extra assertions and comments to make sure we understand the deletion of ghost particles at the end of moveKickDrift in Particles.H Src/C_AMRLib/Particles.H commit b11fc3984e846c2f470f64edbc217cdda179bf8c Author: lijewski Date: Thu Aug 16 10:44:45 2012 -0700 Changed how caches are passed to CollectData() to cut down on memory allocations. Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit ecc35050513d896914a8132004087b846f6b39d9 Author: lijewski Date: Thu Aug 16 10:04:00 2012 -0700 Changed the send count cache used by FillBoundary & FillPeriodicBoundary() from an Array to std::map. This'll keep the size of the cache entries from growing as the number of cores grows. Hence we can increase the size of the cache a bit w/o much problem. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit bf277d92910413d04955c915bce038e518175ed5 Merge: 6ee84d5ec 110bf78ef Author: Weiqun Zhang Date: Tue Aug 14 16:23:58 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 110bf78ef9165c447bf5e556980cc8773b08d2c1 Author: lijewski Date: Tue Aug 14 16:02:43 2012 -0700 Added an optional third argument to KnapSackProcessorMap(). It's a pointer to a double into which the efficiecy will be placed if it's not NULL. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 6ee84d5ec665720ec9e346996a2f9e45219d4fd1 Merge: 018c29e28 bbc9cffe5 Author: Weiqun Zhang Date: Tue Aug 14 10:37:31 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 018c29e282efcf307b3ff89ec97c0287b5ea4c16 Author: Weiqun Zhang Date: Tue Aug 14 10:37:18 2012 -0700 Fix a comment Tools/RegressionTesting/testnew.py commit bbc9cffe55afb28bd00e096de0b981504c168783 Merge: ac01b7ec7 a008f1027 Author: lijewski Date: Tue Aug 14 09:35:59 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ac01b7ec7c46cb865cf2d67114dd7f9342f51758 Author: lijewski Date: Tue Aug 14 09:11:08 2012 -0700 Set verbose to false. Src/C_AMRLib/AuxBoundaryData.cpp commit a008f1027c25dfa429d2be5e262d508a8e778e09 Author: Matthew Emmett Date: Tue Aug 14 11:57:56 2012 -0400 Add 'build' and 'destroy' interfaces to BC tower. Src/F_BaseLib/define_bc_tower.f90 commit dbdf4a0696113835e08348201fe19d0336376206 Author: Weiqun Zhang Date: Mon Aug 13 22:18:33 2012 -0700 Fix a bug in regression testing script for the case when extSrcGitHash is used Tools/RegressionTesting/testnew.py commit abbad860eea943db21b674e2515ad6911d2c403b Author: Matthew Emmett Date: Mon Aug 13 19:03:14 2012 -0400 PyBoxLib: Begin adding plotfile support. Src/Python/pyboxlib/base.py Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/multifab.py Src/Python/pyboxlib/plotfile.py Src/Python/src/blobjects.f90 Src/Python/src/blobjects.py Src/Python/src/fboxlib.f90 Src/Python/tests/test-multifab.py commit 6f6f256efd85cd3ddf81b7b11aad834cc9c0cb0e Author: Matthew Emmett Date: Mon Aug 13 19:09:11 2012 -0400 HeatEqaution: Tweak regrid. Tutorials/HeatEquation_EX4_F/regrid.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 commit a94ea27364cfce5850cd5bad778598a60ad1cf63 Author: Michael Zingale Date: Wed Aug 8 21:10:40 2012 -0400 some minor fixes (deallocates, comments) python_plotfile/fsnapshot.f90 commit 0ee73c673eb746f877b7833c6dff8913e345b95b Author: Matthew Emmett Date: Wed Aug 8 19:35:28 2012 -0400 CHEMOTAXIS: Tidy, use first-order stencils. Tutorials/Chemotaxis_F/README Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/chemotaxis.py Tutorials/Chemotaxis_F/chemotaxis.tex Tutorials/Chemotaxis_F/codegen/README Tutorials/Chemotaxis_F/codegen/__init__.py Tutorials/Chemotaxis_F/codegen/compile.py Tutorials/Chemotaxis_F/codegen/polyquad.py Tutorials/Chemotaxis_F/codegen/symbolic.py Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/kernels.f90 Tutorials/Chemotaxis_F/kernels.py Tutorials/Chemotaxis_F/kernels.tmpl.f90 commit c40565b9a98b3d07dfad4c1fe498b6550af9db43 Author: Michael Zingale Date: Wed Aug 8 16:14:05 2012 -0400 add new routine to make a plot of several variables from a flame_1d plotfile python_plotfile/plot1dflame.py commit 3264938566768737a17c3eb74d39364100f5e6b1 Author: Michael Zingale Date: Wed Aug 8 14:37:34 2012 -0400 add methods to get at the variable names python_plotfile/fsnapshot.f90 commit 7f7b316e19f2914c01e0884b8029b3c6c9fcefa2 Author: Michael Zingale Date: Wed Aug 8 12:48:08 2012 -0400 add support for 1d data, for flame plotting python_plotfile/fsnapshot.f90 commit ee711ba36a7859e663cb50675ff03f3a00aa7a0c Author: lijewski Date: Tue Aug 7 20:28:35 2012 -0700 Added extra constructor that takes a pointer to BndryData. We want to be able to reuse BndryData types in linear solves. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit f3ac2bdbf03d40e534fc9fb4fd2f3f08c39c095f Author: lijewski Date: Tue Aug 7 18:53:03 2012 -0700 A little cleanup of the BndryData hierarchy. Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/MacBndry.H Src/C_BoundaryLib/MacBndry.cpp commit 1974d30aa18aab83ca4cd099f35d12e91abd6327 Merge: 7fb673949 fb97ef858 Author: lijewski Date: Tue Aug 7 18:50:39 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit fb97ef8580070405c0b67045c2eb8d58d706fc4d Merge: c1f369bfb b35a4773d Author: Weiqun Zhang Date: Tue Aug 7 17:28:04 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c1f369bfb3e1793f5f70337ef389a5e5f4c24b4b Author: Weiqun Zhang Date: Tue Aug 7 17:27:53 2012 -0700 Increase the precision of numbers written to Header Src/F_BaseLib/fabio.f90 commit 7fb673949b15adceccbf8f6a688803c0f8a2a730 Author: lijewski Date: Tue Aug 7 10:31:53 2012 -0700 Attempt to allow so reuse of BndryData objects. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit b35a4773dd72731686153619b675819af4dc6e73 Merge: 0b21947c6 135cb6358 Author: Matthew Emmett Date: Tue Aug 7 10:13:10 2012 -0400 Merge branch 'chemotaxis' commit 135cb635815e08130a62356c41d1ed9b5ba39848 Author: Matthew Emmett Date: Tue Aug 7 10:11:46 2012 -0400 CHEMOTAXIS: Add codegen, tweak some parameters. Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/codegen/README Tutorials/Chemotaxis_F/codegen/__init__.py Tutorials/Chemotaxis_F/codegen/compile.py Tutorials/Chemotaxis_F/codegen/polyquad.py Tutorials/Chemotaxis_F/codegen/symbolic.py Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/kernels.f90 Tutorials/Chemotaxis_F/kernels.py Tutorials/Chemotaxis_F/kernels.tmpl.f90 commit 0b21947c6387d3443ede8a2d5eaecacb46cf2cae Author: Matthew Emmett Date: Tue Aug 7 10:12:21 2012 -0400 PyBoxLib: Bug fix. Src/Python/pyboxlib/fab.py commit 6b666b227420c8733e8b9bb9942c8d1734a8dfc4 Author: cmalone Date: Mon Aug 6 14:06:29 2012 -0700 ppCleanup is a C PreProcessor macro cleanup script that removes unwanted code associated with specified macros. This is useful for stripping out bits of code before releasing it to the masses. Currently this requires python 2.7.X to run; let me know if this is a problem... Tools/ppCleanup/README Tools/ppCleanup/cleanWords.txt Tools/ppCleanup/ppCleanup.py commit 61e93d8ec279b59b3f22ddbb4502f0e7c2c9c7d3 Merge: 8a1560001 87c538892 Author: Weiqun Zhang Date: Sat Aug 4 20:52:32 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 87c5388925b28b8c33a1f930b2017e8c9404db36 Author: lijewski Date: Sat Aug 4 13:56:24 2012 -0700 Changed define() so that we can reuse BndryData and derived types. This way in LMC (and other codes) where we diffuse a raft of species, we can reuse these objects instead of building a new one for each component we diffuse. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 8a1560001c61a9c645d8be5eaede731f49f89524 Merge: f02a39ca5 1c690de70 Author: Weiqun Zhang Date: Fri Aug 3 10:49:19 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1c690de7035138be10ade0f182c14fffe538cceb Author: ajnonaka Date: Fri Aug 3 10:41:58 2012 -0700 revert Src/F_BaseLib/define_bc_tower.f90 commit 526298a88956076011b93a908cc7bd5d33d58b57 Author: ajnonaka Date: Fri Aug 3 10:41:15 2012 -0700 revert Src/F_BaseLib/fabio.f90 commit f02a39ca518a03da35fcf10781c8d6ab562acdd8 Merge: 89b461758 4f146bfd9 Author: Weiqun Zhang Date: Thu Aug 2 21:16:10 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 89b4617584a32e2a398dc010cefe8199e8b1a634 Author: Weiqun Zhang Date: Thu Aug 2 18:18:20 2012 -0700 Update stencil_types.H according to stencil_types.f90. Src/LinearSolvers/C_to_F_MG/stencil_types.H commit ba700fdd2cc0f4abc8a4a02122ec7d76db9f44a9 Author: Weiqun Zhang Date: Thu Aug 2 18:13:55 2012 -0700 Due to a bug in either etags or Emacs (on my Ubuntu 10.04?), absolute path has to be used in tagging. Tools/F_mk/GMakerules.mak commit 4f146bfd9d94788d57bfee9a8488fbf1454412a4 Merge: a1af24886 1867561d1 Author: Sandra May Date: Thu Aug 2 16:51:12 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a1af248865060d5c27ba51e9e6bbe71b53f2a7a6 Author: Sandra May Date: Thu Aug 2 16:48:50 2012 -0700 typos Docs/F_AdvancedTopics/F_AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex commit 1867561d19dda0f1a57d2d6d98abf2fdb85587ee Author: ajnonaka Date: Thu Aug 2 16:37:51 2012 -0700 test commit Tutorials/HeatEquation_EX5_F/main.f90 commit a45761f0f4c200d513ae34998a7e2574780dd353 Author: Weiqun Zhang Date: Thu Aug 2 14:03:10 2012 -0700 Fix a bug. "if (stencil_type .eq. 1)" is no longer good. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 98fdb2daa9565a951f42db33d6a30326cf7bf47a Author: lijewski Date: Wed Aug 1 21:19:08 2012 -0700 Fixed the assignment of the "nodal" data member in [ilz]multifab_build() in the presence of an optional argument. Interestingly, it was correct for multifab_build(). Src/F_BaseLib/multifab_f.f90 commit 0249714dad0c781ae31924f1d87e1cb0c568378a Author: Michael Zingale Date: Wed Aug 1 19:57:57 2012 -0400 add a diffOpts attribute to tests -- this is the flags we want to invoke diff with when comparing plain text files (through diffDir). This is useful for instance to ignore comment lines in the output Tools/RegressionTesting/testnew.py commit 393c1e561c4b28a676d6a1dbc03b69d54a1ccb27 Merge: 8aecacdb7 c320b4137 Author: lijewski Date: Wed Aug 1 14:45:31 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8aecacdb75941503ad804cdbbd6f7f18f80535e0 Author: lijewski Date: Wed Aug 1 14:45:07 2012 -0700 Didn't have src_comp & dst_comp quite right in new compFlux(). Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit c320b4137356dfb2e9025a3da0797c5a4085a9bf Merge: 9da9a14a3 076caf03f Author: Ann Almgren Date: Wed Aug 1 14:36:08 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9da9a14a395c550b794ea8bb21d2d70be238d23d Author: Ann Almgren Date: Wed Aug 1 14:35:48 2012 -0700 More transition from size(ss) to using stencil_type. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/stencil_types.f90 commit 076caf03f7a71c448b259c8319a0a7a3a79f00e2 Merge: 0ad9be847 c4f956598 Author: lijewski Date: Wed Aug 1 13:38:10 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0ad9be84716ed13bd280aa98a24d7b4dc4c236d9 Author: lijewski Date: Wed Aug 1 13:34:16 2012 -0700 More general compFlux(). Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit ef86d1002f6199dc9f086c0108561297c781cec0 Author: lijewski Date: Wed Aug 1 13:33:55 2012 -0700 Fixed typo in my previous fix. Src/C_BoundaryLib/BndryData.cpp commit 588a501a41d79895cea90b464586cbe3a7db1f95 Author: lijewski Date: Wed Aug 1 12:51:54 2012 -0700 Added scomp, dcomp & ncomp to compFlux() with obvious defaults. Src/LinearSolvers/C_CellMG/LinOp.H commit 59448172921f5b7d50433b6348deda934ace7216 Author: lijewski Date: Wed Aug 1 12:49:57 2012 -0700 ngrd -> grd in a couple find() functions. Src/C_BoundaryLib/BndryData.cpp commit c4f956598607497e57fcc7053886e752779af2ee Author: Michael Zingale Date: Wed Aug 1 14:47:59 2012 -0400 add the execution time for each test on the test's web page Tools/RegressionTesting/testnew.py commit ab6bd1ae8655183d4ae8e3421cdaa82831ce3ef1 Merge: 9510c17cb a44bec09e Author: Sandra May Date: Wed Aug 1 11:13:14 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a44bec09eef1ff597bec18bc0b287a34896cf924 Author: ajnonaka Date: Wed Aug 1 11:12:07 2012 -0700 added an lmultifab_build_edge subroutine Src/F_BaseLib/multifab_f.f90 commit 1d5487133b9873b39217316c6b9c4d4af442fb1e Author: Michael Zingale Date: Wed Aug 1 12:55:37 2012 -0400 add a --tests option to allow one to specify multiple individual tests to run, instead of just a single test via --single_test. Note, tests must be together in a single string with "" Tools/RegressionTesting/testnew.py commit 2659498080db20648cd687f61c00c8e1b589e502 Author: lijewski Date: Tue Jul 31 19:32:02 2012 -0700 Had argument order switch. Src/C_BaseLib/MultiFab.cpp commit 89d8fdeb1d5dd083906e12ab24132ccfba888750 Author: lijewski Date: Tue Jul 31 18:40:15 2012 -0700 Enable cross=true for FillBoundary() in LinOp::applyBC(). My test indicate it isn't needed. We'll see what the regression tests say ... Src/LinearSolvers/C_CellMG/LinOp.cpp commit ddb91c8c6ea2120e0d1de0a4a279ddf78edb8a87 Author: lijewski Date: Tue Jul 31 17:33:03 2012 -0700 Work on adding the "cross" idea to the C++ FillBoundary from FORTRAN. Then will have to add the add the calls to use it when appropriate. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit b54b0dbdf98f37c0c9f055858aa735f8b57606ae Author: Matthew Emmett Date: Tue Jul 31 16:34:49 2012 -0400 Chemotaxis: Implement SDC time-stepping. Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/main.f90 commit 9510c17cbfdd48945c55dd39945e874cf95970ee Merge: 048e70adf 10ace5fa4 Author: Sandra May Date: Tue Jul 31 12:32:30 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 10ace5fa49cc0e36449355ddd6da3ddb2480f0e4 Author: Matthew Emmett Date: Tue Jul 31 15:16:09 2012 -0400 Chemotaxis: Minimal model working. Tutorials/Chemotaxis_F/GNUmakefile Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/kernels.f90 Tutorials/Chemotaxis_F/main.f90 commit 7789eaa7dce86817fa31cb76e21d21012c07d894 Author: Matthew Emmett Date: Tue Jul 24 10:27:17 2012 -0400 CHEMOTAXIS: WIP. Tutorials/Chemotaxis_F/chemotaxis.py commit 00a1184d4d52cbd1b1241f0e4fd1d48bba633aee Author: Matthew Emmett Date: Tue Jul 24 09:59:00 2012 -0400 CHEMOTAXIS: WIP. Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/chemotaxis.py Tutorials/Chemotaxis_F/chemotaxis.tex Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/main.f90 Tutorials/Chemotaxis_F/sdcquad.f90 commit ffff709e03e916bd98750219ba5612acc1688b73 Author: Matthew Emmett Date: Fri Jul 20 21:02:21 2012 -0400 CHEMOTAXIS: Create skeleton chemotaxis example. Tutorials/Chemotaxis_F/GNUmakefile Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/main.f90 Tutorials/Chemotaxis_F/write_plotfile.f90 commit e851724b8a3907d9a921272215df5b3cba285c20 Author: Matthew Emmett Date: Tue Jul 31 15:24:33 2012 -0400 PyBoxLib: Update make structure, fix indexing with multiple components. Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GPackage.mak Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/pybl.py commit d753a35052bb32ddb2a0feda96321cd54fe821aa Author: Ann Almgren Date: Tue Jul 31 11:11:19 2012 -0700 Add definitions of FLOW, IRRFLOW, etc, Src/F_BaseLib/cutcells.f90 commit e45399e4ebfe2582a5036145c7925d919da80553 Author: Weiqun Zhang Date: Mon Jul 30 16:27:57 2012 -0700 Make these tests work with current MGT_Solver. Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tutorials/MultiGrid_C/main.cpp commit 09d40221c732766595f709c3dcbf0c0a6d6ec681 Author: Weiqun Zhang Date: Mon Jul 30 16:02:48 2012 -0700 Delete one of the MGT_Solver constructor. Make stencil_type a non-optional argument of the MGT_Solver constructor, so that it will not compile without stencil_type. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit e53f151825e9815f36834806e837742ac0238bdb Author: Weiqun Zhang Date: Mon Jul 30 16:02:31 2012 -0700 Add #ifndef _STENCIL_TYPES_H_ in stencil_types.H, and some comments Src/LinearSolvers/C_to_F_MG/stencil_types.H Src/LinearSolvers/F_MG/stencil_types.f90 commit 048e70adfc61d44641549f2b9a645e5ddd21f820 Merge: 0928570c9 feebc5b40 Author: Sandra May Date: Mon Jul 30 10:11:04 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit feebc5b403936ffc45edb7ccaea78fe70f890aae Author: ajnonaka Date: Sun Jul 29 22:00:16 2012 -0700 get this compiling and running again with latest interfaces changes to mg_tower_build Tutorials/HeatEquation_EX5_F/advance.f90 commit 472d4487fa295db2cca7c6b579833a7006cb2180 Merge: 408298a50 a5450a02f Author: Michael Zingale Date: Sat Jul 28 21:12:32 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 408298a5023c414b8960ba06984d0205fd9566a9 Author: Michael Zingale Date: Sat Jul 28 21:11:38 2012 -0400 add a check on whether a restart test produced any output before going forward to the restart run. Otherwise, abort the test and move onto the next. This fixes a crash. Tools/RegressionTesting/testnew.py commit a5450a02f2143ce258d689f7e8430c99caa2aa34 Author: Ann Almgren Date: Sat Jul 28 17:48:25 2012 -0700 Fix stupid logic mistake in defining mgt%lcross given mgt%stencil_type. Also fix more uses of lcross in ml_cc.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 6136ceb72f1c0318fd865a8041fa07d2036f42d3 Merge: c49274312 1f350be1a Author: Weiqun Zhang Date: Sat Jul 28 07:28:39 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c492743125ffe4233ef8245efc5ab3e0b8ad0bf1 Author: Weiqun Zhang Date: Fri Jul 27 22:29:30 2012 -0700 Simplify the make_build_info script and add more comments Tools/C_scripts/make_build_info_cpp commit 1f350be1a19635fcaaef94fe5e7c472a2fde6a70 Author: Ann Almgren Date: Fri Jul 27 21:59:46 2012 -0700 Start to use stencil_type rather than ncomp of the stencil to know which stencil we're actually using. Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 08c07daf45bd3050e79901b13616c7b7582c5419 Author: Ann Almgren Date: Fri Jul 27 21:43:28 2012 -0700 We now define a stencil_type and lcross as part of the mg_tower. We will use stencil_type rather than testing on ncomp of the stencil to decide which stencil we're actually using. Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 54b82b28c27ed21a3d6ce842b5ee502634db77d9 Author: Weiqun Zhang Date: Fri Jul 27 17:04:22 2012 -0700 minor update of usage string Tools/RegressionTesting/testnew.py commit fa275bbda0fa29f6ef1e8df4e52ddd1cfcac9419 Author: Weiqun Zhang Date: Fri Jul 27 16:31:08 2012 -0700 Add git hash to job_info file in plotfiles Tools/C_scripts/buildInfo.H Tools/C_scripts/make_build_info_cpp commit 0c375332c4ed8a3ed35b01af678fcf0e895aa3c1 Author: Ann Almgren Date: Fri Jul 27 14:31:32 2012 -0700 Add stencil_types.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/stencil_types.f90 commit 9334c387520501debefc559b4567682d486be3ca Author: Ann Almgren Date: Fri Jul 27 14:29:05 2012 -0700 We now pass the stencil_type explicitly through from the calling routine to the F90 multigrid -- this requires a change in the calling sequence from each application. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/C_to_F_MG/Make.package Src/LinearSolvers/C_to_F_MG/stencil_types.H commit 7563c83dddf14d140aac91151a2a7af8743a0e74 Author: vince Date: Fri Jul 27 11:48:16 2012 -0700 added debug checks for varnames. Src/Extern/amrdata/AmrData.cpp commit 440322bb4e3e8315572ac0ab600de0e1a9abae9a Merge: d4fd568d6 76ef58d1e Author: lijewski Date: Fri Jul 27 08:42:49 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d4fd568d67151bccdc89eb7a456f607539192d4d Author: lijewski Date: Fri Jul 27 08:42:29 2012 -0700 Some simplification. Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 76ef58d1ea9a448aeea9127b3773d6bb4da71e9f Author: Michael Zingale Date: Thu Jul 26 22:38:47 2012 -0400 really fix it now... Tools/F_scripts/make_build_info commit 4cedbff6b4fbee5db42b2adfba7b304907678036 Author: Michael Zingale Date: Thu Jul 26 22:37:49 2012 -0400 fix compilation Tools/F_scripts/make_build_info commit a9e9e65e00c1223ed3787a58cf7068950cc8f293 Author: Michael Zingale Date: Thu Jul 26 22:31:17 2012 -0400 add git hashes for boxlib, source (e.g. Maestro). and extra (e.g. AstroDev) Tools/F_scripts/make_build_info commit ec9e708036df7e360012093d21cbe924a24200af Author: Regression Tester account Date: Thu Jul 26 16:35:50 2012 -0700 Add restart tests Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/Nyx-tests.ini commit ac5c879feb0c1d3ba38b4ffbaa283216d7cfd743 Author: Regression Tester account Date: Thu Jul 26 14:39:58 2012 -0700 Add some regression restart tests Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/Nyx-tests.ini Tools/RegressionTesting/radiation-tests.ini Tools/RegressionTesting/testnew.py commit 42f716e170299bdf82dd4e2690eea21cb6a034e9 Author: Weiqun Zhang Date: Thu Jul 26 13:09:21 2012 -0700 The precision of Checkpoint Header is changed to 17 from 15. According to IEEE 754, if a double precision number is saved in clear text and is then convected back to double precision number, the clear text number must have at least 17 significant decimal for the new number to exactly match the original. Src/C_AMRLib/Amr.cpp commit fe4d6b5b1dce798d8c656859ac2b9600979e59c4 Author: lijewski Date: Tue Jul 24 13:56:09 2012 -0700 More cleanup & simplification. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 7ee801e6c994442954c9053f81cbd84fb861f08f Author: Regression Tester account Date: Tue Jul 24 12:11:15 2012 -0700 inputs files for regression tests Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir Tests/LinearSolvers/ComparisonTest/inputs-rt-Neu Tutorials/HeatEquation_EX5_F/inputs-rt commit 608ce6980766b6d26dfc81985c436165d0d01321 Author: Weiqun Zhang Date: Tue Jul 24 12:03:39 2012 -0700 Update README for regression testing scripts. helmeosDir is no longer required for a test suite that does not have any tests using helmeos. Tools/RegressionTesting/BoxLib-tests.ini Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/Nyx-tests.ini Tools/RegressionTesting/README Tools/RegressionTesting/radiation-tests.ini Tools/RegressionTesting/test-Ubuntu.py Tools/RegressionTesting/testnew.py commit 17d23f1a299114e80672ee4c0eacbcfb52f8be4e Author: Ann Almgren Date: Tue Jul 24 10:29:02 2012 -0700 These have a more general interface to s_dense_2d_nodal. Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 7deb6bebce809b2b644d8104f9a5cb1bea638f3e Author: Michael Zingale Date: Tue Jul 24 12:32:18 2012 -0400 revamp the NEEDS_EOS_NETWORK stuff -- now it will work with stuff in AstroDev/ and also pull in the proper dependencies GNUmakefile commit 59acb76441c75fc0f8e1f6263a730f50445db0dd Author: Matthew Emmett Date: Tue Jul 24 10:28:12 2012 -0400 PyBoxLib: Add is_periodic argument to layout creation routines. Src/Python/pyboxlib/layout.py Src/Python/pyboxlib/pybl.py Src/Python/src/fboxlib.f90 commit f37ce477372080bb6f138b7c43bde805460a1f77 Author: Matthew Emmett Date: Tue Jul 24 10:00:55 2012 -0400 PyBoxLib: Added bxrange to fab and switched to global indexing. Src/Python/pyboxlib/fab.py commit dce757058418762cd7d183730e8def320aeec9e4 Merge: 71df56a47 32dfbe9a0 Author: Michael Zingale Date: Mon Jul 23 21:35:27 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 71df56a47a374fc5104a8d8ed2d4f0ca62b3cfc7 Author: Michael Zingale Date: Mon Jul 23 21:35:01 2012 -0400 fix a comment in the mg_tower options Tutorials/HeatEquation_EX5_F/advance.f90 commit 32dfbe9a0756dc64434d51ec34c05dde7516c5a9 Merge: e3c90a2f4 0dffc7858 Author: Weiqun Zhang Date: Mon Jul 23 18:23:03 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0dffc7858780777041eeb36c485352362849c3af Author: lijewski Date: Fri Jul 20 16:33:15 2012 -0700 Using the new BoxArray::const_iterator. Src/C_BoundaryLib/FabSet.cpp commit b87d5058bff6d728608230d5618b40a5468f2ba2 Author: lijewski Date: Fri Jul 20 16:32:18 2012 -0700 Using the new BoxArray::const_iterator. Src/C_BaseLib/DistributionMapping.cpp commit 7b86fa175ba2ddf2569dd572bdb375cdc42d7a4f Author: lijewski Date: Fri Jul 20 15:56:27 2012 -0700 Added const_iterators to BoxArray. They can now be used like a const STL container. We don't allow non-const iterators because BoxArrays are reference counted and we don't want folks to modify them without using the regular BoxArray interface. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit e3c90a2f4bd5dc1529163dd55ec7e1dcaabda9c6 Merge: 0964322ed 2b199421a Author: Weiqun Zhang Date: Fri Jul 20 14:51:01 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2b199421a4010e926c62bf781b42029f3d3049d6 Author: lijewski Date: Fri Jul 20 14:45:51 2012 -0700 Used iterators more extensively. Src/C_AMRLib/AmrLevel.cpp commit 0964322edd13c989b26bd6cd0b234afcb332a12d Merge: 9805b0577 effbad3ed Author: Weiqun Zhang Date: Thu Jul 19 07:05:01 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9805b05770ae5422f3ea8dbc8298c30bf14ccc8f Author: Weiqun Zhang Date: Thu Jul 19 07:04:54 2012 -0700 Add baragon to F_mk Tools/F_mk/GMakeMPI.mak commit effbad3ed2ae0964034f8481e789febdc3bcf463 Author: Michael Zingale Date: Wed Jul 18 23:54:59 2012 -0400 add aux1 and aux2 to hold additional build information Tools/C_scripts/buildInfo.H Tools/C_scripts/make_build_info_cpp commit ec59b73498f8ba9a2e1d683021498fe9991550d6 Author: Michael Zingale Date: Wed Jul 18 23:34:19 2012 -0400 add COMP and FCOMP Tools/C_scripts/buildInfo.H Tools/C_scripts/make_build_info_cpp commit b975364b94ac585716bd5c5f38a71d2855c6f7d2 Merge: e62cbd39b b541a461f Author: Michael Zingale Date: Wed Jul 18 19:41:17 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e62cbd39bf397df1e05fb41be792868d7161897e Author: Michael Zingale Date: Wed Jul 18 19:39:47 2012 -0400 add support for build information for job_info files for C++ codes Tools/C_scripts/buildInfo.H Tools/C_scripts/make_build_info_cpp commit b541a461f0befef8424bb99f99ba81488bdd74d9 Author: lijewski Date: Wed Jul 18 16:13:53 2012 -0700 Just a minor tweak. Src/C_BaseLib/FabArray.H commit 0fce2ee6c2dcebccfaf48e659d15244dfd37cca1 Author: lijewski Date: Wed Jul 18 15:04:54 2012 -0700 Be more sophisticated when inserting elements into std::map<>s in those cases when we "know" the index is increasing, say when the index corresponds to the index into a BoxArray. Src/C_AMRLib/AmrLevel.cpp Src/C_BoundaryLib/BndryData.cpp commit 7333f3da52d31a32775374fc7031fb6710cd6a48 Merge: 589b2528f 641f32a0e Author: lijewski Date: Wed Jul 18 12:14:10 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 589b2528f3eb9915bd6f1b640b8c4adc393ba90d Author: lijewski Date: Wed Jul 18 12:12:14 2012 -0700 Fixed bug I introduced yesterday. I was using the std::vector::back() function to refer to the last element in a vector. That's fine as it goes but the reference returned can be invalidated if the vector is resize()d with the addition of new elements. Also shorted the names of some data members of FillPatchIteratorHelper. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit cdf5481ba2a73528cdceae38ef72747824f66de0 Merge: 2e3ed22b6 641f32a0e Author: Marc Day Date: Wed Jul 18 12:02:43 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2e3ed22b6ebef1bde1871b21df1ff463b204add1 Author: Marc Day Date: Wed Jul 18 12:02:33 2012 -0700 need quadmath on Marcs laptop Tools/C_mk/Make.Darwin commit 641f32a0ec95efa254aa88b66acb99844ea776f6 Author: Michael Zingale Date: Wed Jul 18 09:27:48 2012 -0400 writes had an extra ',' in them -- Cray doesn't like this. Get this compiling again. Src/F_BaseLib/cutcells.f90 commit 0f43f1356872a4cbe7f6dca9ff7a9ba7dc2b002d Merge: e061dc5e1 cb0de77f3 Author: Marc Day Date: Tue Jul 17 22:57:27 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit cb0de77f36d71c5205ec23868f56ff088ca2f1d1 Author: lijewski Date: Tue Jul 17 14:21:50 2012 -0700 Added defineDoit() to consolidate two define() functions. Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 5dd8e159a23b9cf0cd3f105922c134f041c8c7a8 Author: lijewski Date: Tue Jul 17 14:21:07 2012 -0700 Simplifed class declaration a bit. Since we really only wrap an integer let the compiler generate copy constructor & assignment operator. Src/C_BoundaryLib/BoundCond.H commit e3c1166bc9010f779c8e0c6de0561393041b4559 Merge: d6db06214 4abd3e522 Author: lijewski Date: Tue Jul 17 13:26:24 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d6db06214d597b8d719d9a2867ff4130e92e917b Author: lijewski Date: Tue Jul 17 13:26:08 2012 -0700 Squeezed out a little more memory. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit e061dc5e147c9527d7a0318ba0ff1021bd7553ea Merge: e2927da3b 4abd3e522 Author: Marc Day Date: Tue Jul 17 11:24:24 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e2927da3b36a98d5375482558d7140804627516b Author: Marc Day Date: Tue Jul 17 11:23:39 2012 -0700 add TagBox include file Tools/C_util/ViewMF/viewMF.cpp commit 1ec96f93c0d7d68866b8e2c6be9076fe83a04a0e Author: Marc Day Date: Tue Jul 17 11:23:07 2012 -0700 Add special rules for hedorah Tools/F_mk/GMakeMPI.mak commit 4abd3e52284cca92adc6fe7b505ab526cf682779 Author: Weiqun Zhang Date: Tue Jul 17 10:52:22 2012 -0700 Fixed a bug due to underestimating the complexity of git history. Tools/RegressionTesting/reg_test_blame.py commit 047d5cbec8e63832f4078bdf331125796324aaa2 Merge: 96e53fb94 94a2fd279 Author: ajnonaka Date: Tue Jul 17 08:34:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 96e53fb946cf438edaebd54249bb6f06a5d18841 Author: ajnonaka Date: Tue Jul 17 08:34:21 2012 -0700 alpha and beta going into cc solve do not need ghost cells Tutorials/HeatEquation_EX5_F/advance.f90 commit 94a2fd279135ef6b250e9353d12f14e5d7426ca1 Author: Michael Zingale Date: Mon Jul 16 16:43:44 2012 -0400 get this working with the latest version of the test suite -- in particular, the extSrc replacing AstroDev stuff Tools/RegressionTesting/Maestro-tests.ini commit c538288b718fef40c59e2af527d235e753f71d83 Author: lijewski Date: Mon Jul 16 10:36:47 2012 -0700 Provide a specialization of invert() for Real. The implementation is an OpenMP'd Fortran function. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit f83f80a181b7e28917e2dda3446c3d3000d7c8bf Author: lijewski Date: Fri Jul 13 16:52:37 2012 -0700 Pass MultiFabIDs by value not const reference. They're just integers. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 50322def0aa532c9e9795bde2686886801c2a4b8 Author: lijewski Date: Fri Jul 13 16:51:42 2012 -0700 Inline the default constructor. Contrary to the previous documentation it does nothing. Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp commit 79492d67e04c724fd427738d6f9b284d37df858a Author: lijewski Date: Fri Jul 13 16:51:05 2012 -0700 Inline the FluxRegister::Rec constructors. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 677cca87a3a4d900185160d03f028b8c488a68ee Author: lijewski Date: Fri Jul 13 16:05:48 2012 -0700 Got rid of the "len" member data in RealBox. Had to throw out the length() member function. Calculate the len(dir) on the fly. Also had to throw out the length() member function in Geometry. This latter doesn't appear to have been used anywhere I could find. Src/C_BaseLib/Geometry.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp commit 15827247ec7bd688faef2d7e866f27a09ec9ba53 Author: lijewski Date: Fri Jul 13 15:50:00 2012 -0700 Pass Orientations and IndexTypes by value not const reference. They're just fancy integers. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit a6311943e99069c168a2fc2088bca07093c16c5b Author: lijewski Date: Fri Jul 13 13:56:39 2012 -0700 Minor cleanup. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 5fbcd2ff0fe37a3248c0fac0d4f173e9b20e383d Merge: b24215abd 0d5dc2540 Author: Weiqun Zhang Date: Fri Jul 13 13:26:44 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b24215abde15dc836ee49ef1af8f8a3ce862d4dd Author: Weiqun Zhang Date: Fri Jul 13 13:25:11 2012 -0700 minor updated Tools/RegressionTesting/testnew.py commit 0d5dc25405b457c04ce4e5e798508adfc6b74c23 Merge: afa695a23 62564cf96 Author: lijewski Date: Fri Jul 13 13:01:08 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit afa695a23b5da8d43e7a5874deaebf6a46ecafd8 Author: lijewski Date: Fri Jul 13 13:00:00 2012 -0700 In BndryData changed the following member data: PArray masks[2*BL_SPACEDIM]; to std::map masks; Also, changed the following member function: const PArray& bndryMasks (const Orientation& face) const; to const MaskTuple& bndryMasks (int igrid) const; using to the following typedef: typedef Tuple MaskTuple; In MCLinOp.H, changed the following member data: Array< Array< Array< Mask*> > > maskvals; to Array< std::map > maskvals; Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 62564cf968d3151ff3981509208e8ecc58a63a5d Author: Weiqun Zhang Date: Fri Jul 13 12:59:05 2012 -0700 another bug Tools/RegressionTesting/testnew.py commit 70e7ff4451459b3f35b34547254a2277370cc0d2 Author: Weiqun Zhang Date: Fri Jul 13 12:43:22 2012 -0700 fix bug Tools/RegressionTesting/testnew.py commit 1729079a3167a4b1ffd9f1e7c03ba5fd21685f7e Author: Weiqun Zhang Date: Fri Jul 13 12:21:42 2012 -0700 testnew.py now takes --no_update=value, where the case-insensitive "value" can "all" or "none" or a list of names separated by ",", such as "Castro,AstroDev". reg_test_blame.py now supports an extra git source other than the main source code and BoxLib. Tools/RegressionTesting/reg_test_blame.py Tools/RegressionTesting/testnew.py commit 18b66a7ec9a05a998ace9f60baceaec2ad4b64f9 Author: Weiqun Zhang Date: Thu Jul 12 16:33:38 2012 -0700 Fix outputFile. Add a new script called reg_test_blame.py that will find out which commit of either the main source code or BoxLib to blame. Tools/RegressionTesting/reg_test_blame.py Tools/RegressionTesting/testnew.py commit 0928570c926ac809be55c8efbf27ad1074d87a9d Author: Sandra May Date: Thu Jul 12 15:38:08 2012 -0700 changes to enable inflow and outflow b.c. Src/F_BaseLib/define_bc_tower.f90 commit 77b95da20064f35cf3c13d1a167a5f255d758236 Merge: 1a731bfb9 58d1996a2 Author: lijewski Date: Thu Jul 12 14:29:58 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1a731bfb999d1ac9ba748f0f160b082d91f9a4f4 Author: lijewski Date: Thu Jul 12 14:27:57 2012 -0700 Prototype of BndryData::bndryConds() changed from const Array& bndryConds (const Orientation& face, int igrid) const; to const Array< Array >& bndryConds (int igrid) const; The "new" outer dimension is over Orientation. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 2d4c37bfb9dc24750af6dc51743a03acded258e9 Author: lijewski Date: Thu Jul 12 14:08:15 2012 -0700 Changed the prototype of BndryData::bndryLocs() from Real bndryLocs (Orientation face, int igrid) const; to const RealTuple& bndryLocs (int igrid) const; where RealTuple is defined: typedef Tuple RealTuple; Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit caf98a6bd57fe939b2205fae5d553ef57951489b Author: lijewski Date: Thu Jul 12 13:45:18 2012 -0700 bcond is now a single map instead of an array of'm. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MacBndry.cpp commit 58d1996a276e608220d1427bfd13445eb39404a6 Author: vince Date: Thu Jul 12 12:43:00 2012 -0700 changed default. this is not used anymore. Src/C_BaseLib/VisMF.H commit 54c8541cee166b3e2151e4ae128e5971b386b9e0 Author: lijewski Date: Thu Jul 12 12:37:41 2012 -0700 Used std::map for bcloc instead of Array> to cut down on memory overhead. If we write the inner loops on Orientation this also puts data used per grid together. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MacBndry.cpp commit b1b6bb509d2c24323b8a3ac466acaa74715c8b37 Merge: 373f29185 3a9c9cae6 Author: lijewski Date: Thu Jul 12 11:00:07 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 373f29185750b5d6c97e673a41715b0cc8e71438 Author: lijewski Date: Thu Jul 12 10:59:01 2012 -0700 To further cut memory overhead, maskvals & lmaskvals use a Tuple instead of Array for each grid they own. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit da4aa23458939d4de9ad63878907d050d59966ba Author: lijewski Date: Thu Jul 12 10:38:48 2012 -0700 Squeezed out more memory by using std::map<>s for maskvals and lmaskvals. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit b745ad3eb1c5f88e60fdd594266bc2d4766159ed Author: Sandra May Date: Thu Jul 12 09:59:22 2012 -0700 added integer parameter to define FLOW, SOLID, IRRFLOW Src/F_BaseLib/cutcells.f90 commit 6ee2c12757e889f9e8ef0ccad5faef14e84e7d6f Author: lijewski Date: Thu Jul 12 09:22:27 2012 -0700 Replaced some uses of std::vector with Array. The former is great if you're trying to save storage, but it does bit twiddling which is more expensive than just accessing an integer. Src/C_AMRLib/StateDescriptor.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_TensorMG/DivVis.H commit 3a9c9cae6a9786aaa6bd6f0329b16772535bb8a1 Author: Matthew Emmett Date: Thu Jul 12 11:35:10 2012 -0400 PyBoxLib: Add read/write. Tidy Makefiles. Src/Python/.gitignore Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GPackage.mak Src/Python/Makefile Src/Python/README Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/layout.py Src/Python/pyboxlib/multifab.py Src/Python/pyboxlib/pybl.py Src/Python/read.py Src/Python/src/boxlib_numpy_c.c Src/Python/src/boxlib_numpy_f.f90 Src/Python/src/fboxlib.f90 Src/Python/write.py commit b0cac50fd9ec3895c2afaf9ea2549e7b5eb81fdf Merge: 9a5f30a6b 28a75ccd0 Author: Matthew Emmett Date: Wed Jul 11 21:33:46 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 9a5f30a6b01f978bae601ed7f02531255d807807 Author: Matthew Emmett Date: Wed Jul 11 21:33:27 2012 -0400 PyBoxLib: Use boxlib_initialize instead of parallel_initialize. Src/Python/src/fboxlib.f90 commit 28a75ccd0c83f5d1f75c00a578f2376c4eea933f Merge: 24fa0cf1b 2f34a0611 Author: Ethan Van Andel Date: Wed Jul 11 18:18:55 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2f34a061166e3d356af448ccafc65be4ee4ba9ba Author: lijewski Date: Wed Jul 11 16:46:21 2012 -0700 In BndryData, change the following member data: Array bcloc[2*BL_SPACEDIM]; to std::map bcloc[2*BL_SPACEDIM]; Changed the following member function: const Array& BndryData::bndryLocs (const Orientation& _face) const to const Array& BndryData::bndryLocs (const Orientation& _face, int igrid) const Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MacBndry.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit d6a2b29609301581300f8a46c4519b143138c32b Author: lijewski Date: Wed Jul 11 15:56:42 2012 -0700 In BndryData, change the following member data: Array< Array > bcond[2*BL_SPACEDIM]; to std::map< Array > bcond[2*BL_SPACEDIM]; Changed the following member function: const Array< Array >& bndryConds (const Orientation& face) const; to const Array& bndryConds (const Orientation& face, int igrid) const; Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MacBndry.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 24fa0cf1b1ef21e81737313f8774c731c40c8b5a Author: Ethan Van Andel Date: Wed Jul 11 14:57:07 2012 -0700 Fixed PList pop. Src/C_BaseLib/PList.H commit 50d45cf218eecde231a1ec01c8ed5f084683bd82 Author: lijewski Date: Wed Jul 11 14:16:22 2012 -0700 Got rid of the following data member in StateData.cpp: Array< Array > bc; Got rid of the member function: Array& StateData::getBCs(); Changed the member function StateData::getBC() from const BCRec& getBC (int comp, int i) const; to const BCRec getBC (int comp, int i) const; This latter changes means that instead of writing: const int* b_rec = state[State_Type].getBC(strt_comp+n,gridno).vect(); you'll have to write: BCRec bcr = state[State_Type].getBC(strt_comp+n,gridno); const int* b_rec = bcr.vect(); I "think" I've made all necessary changes to stuff I have access to in the GIT repository. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit da94587ab956068fae97076c33d0cd04e4fb990e Author: Ethan Van Andel Date: Wed Jul 11 13:28:17 2012 -0700 Added PList class for memory-managed lists of pointers. Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/PList.H commit 28628134a2ab20a5d4f2b7c2ae76ac55ba59bd68 Author: lijewski Date: Wed Jul 11 12:25:13 2012 -0700 Squeezed out some memory when running in parallel by using std::map<>s instead of Array<>s based on the length of the BoxArray. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 44134951f00854ffba7d407365b39d27773b39b5 Author: lijewski Date: Wed Jul 11 09:13:34 2012 -0700 A little simplification. Src/C_AMRLib/AmrLevel.cpp commit e4959279c88e68633d631c10473b08722ad6dcee Author: Sandra May Date: Tue Jul 10 18:28:23 2012 -0700 changed 2 things to be able to use the CartGrid option of amrvis Src/F_BaseLib/fabio.f90 commit 2ab261c27eacaf26c1fe01c400d0c8c59e9a1f0d Author: lijewski Date: Tue Jul 10 16:25:15 2012 -0700 Cached a little more stuff for multifab copy(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 68fa6b4a12e995be72ad003ab57ea7d2e45e4f4a Author: Sandra May Date: Tue Jul 10 13:06:54 2012 -0700 added 2d option Src/F_BaseLib/cutcells.f90 commit 5ccff3043226f4f7ed827507ee422acbb332fbbf Author: lijewski Date: Mon Jul 9 20:11:26 2012 -0700 Removed unused variable. Src/C_BaseLib/FabArray.H commit 87e5f5532ec24794252d9953adf67d5c8730607e Merge: d08613c94 2dbe9053f Author: Mike Lijewski Date: Mon Jul 9 23:07:24 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d08613c94c51897d6a4d798b38794f37d3183219 Author: Mike Lijewski Date: Mon Jul 9 23:06:46 2012 -0400 A little more overlap of computation & communication. Src/C_BaseLib/FabArray.H commit 2dbe9053f66a85afe436500a5e7f6849981378bd Author: vince Date: Mon Jul 9 16:37:43 2012 -0700 changed comp to gfortran Tutorials/Exp_CNS_NoSpec/GNUmakefile commit 16b57f02002a6f26bb2c9d1fc8a1333880fa7ec9 Author: Ethan Van Andel Date: Mon Jul 9 12:17:54 2012 -0700 Removed debug messages Src/C_AMRLib/Particles.H commit 1f00c0b9078bb70f3f03e8612a6bf780c2dead11 Merge: a3ba992af 45514f14b Author: Ethan Van Andel Date: Mon Jul 9 11:10:00 2012 -0700 Merge branch 'master' into hybrid_sub commit a3ba992afdd02adf13fe49a299836c2c630f1425 Author: Ethan Van Andel Date: Mon Jul 9 11:09:11 2012 -0700 Added finest_level option to AssignDensity Src/C_AMRLib/Particles.H commit 45514f14b1118e9594e175108e55ec8544a91e9d Author: ajnonaka Date: Mon Jul 9 10:02:47 2012 -0700 a call to FillPeriodicBoundary with do_corner=true now fills all corners, including those at periodic boundaries. previously the corners were only filled if they were behind physical boundaries Src/C_BaseLib/Geometry.H commit 32a0267ff42a56170cace19c153ab10d454aad42 Author: lijewski Date: Fri Jul 6 20:25:38 2012 -0700 Sped up Checkpoint() by eliding work when no particles at a level. Src/C_AMRLib/Particles.H commit 62e6f30e59a42145872900b47451e994d8fe392a Author: smay Date: Fri Jul 6 10:26:37 2012 -0700 added many arguments to the cutcell module, modified the build and print command Src/F_BaseLib/cutcells.f90 commit 868ea9ca4a6c7a744fda8c0ca88a738b722a5bd3 Author: lijewski Date: Fri Jul 6 09:41:14 2012 -0700 Turn off some uninformative Cray C++ compiler warning messages. Tools/C_mk/Make.Linux commit 3d2b1314c762dc177b56376e61e34aa5ec57ee36 Author: lijewski Date: Fri Jul 6 09:21:02 2012 -0700 Going with the NERSC-recommended Cray optimization flags: no explicit flags. Tools/C_mk/Make.Linux commit d85e82ad86e12c1ea6009f0ca44a864e5cc4e197 Author: cmalone Date: Thu Jul 5 12:41:52 2012 -0700 file not used in docs Docs/Preface/preface.tex commit efddf49666b45e24907c8f2e08a445cbe6a1aaad Merge: 3348ba0b6 f821fcfe9 Author: Michael Zingale Date: Thu Jul 5 16:20:41 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 3348ba0b680e87341db0053fce8171ed75c6eef7 Author: Michael Zingale Date: Thu Jul 5 16:20:01 2012 -0400 if we are doing a diffDir and making benchmarks, print a note about the diff file that was archived Tools/RegressionTesting/testnew.py commit f821fcfe95e58c891604bd97ede6da31b867d2c2 Author: vince Date: Tue Jul 3 16:15:04 2012 -0700 added enum back. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 88a3dbaaadad1e6d0287aa5ad1ed66638d2d0631 Author: lijewski Date: Tue Jul 3 15:53:08 2012 -0700 Sped up Timestamp a bit as well as added a ASSERT(). Src/C_AMRLib/Particles.H commit 331d70899fba1acf23208da0aaae50eab7720cf2 Author: vince Date: Tue Jul 3 15:40:43 2012 -0700 added mf read benchmark. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit bbceb25c8088f3844428c40f44710268f0274fd6 Merge: 3f008b642 fb3d7f306 Author: vince Date: Tue Jul 3 14:09:11 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3f008b642f113e529ea5495f706646804c38169b Author: vince Date: Tue Jul 3 14:08:44 2012 -0700 changed VisMF::How and updated io benchmark. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit fb3d7f30604d91c17a7189f4c9ea14c20535ea97 Merge: 3cce76c18 19a30dd34 Author: lijewski Date: Tue Jul 3 13:59:03 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3cce76c184a23776c9acf0e43e55ee65b71421ef Author: lijewski Date: Tue Jul 3 13:58:28 2012 -0700 Added some more stuff to cutcells. Src/F_BaseLib/cutcells.f90 commit 19a30dd342c62ace49af1f7eb29b61fe6b55f667 Author: Michael Zingale Date: Tue Jul 3 16:17:23 2012 -0400 sync Maestro-tests.ini up with the latest directory structure + script. Merge in Weiqun's diffdir changes Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/testnew.py commit a510c67f5a206122a79a345b9bb4ad0bd0c259b7 Merge: 906d2a5c4 95d012814 Author: Michael Zingale Date: Tue Jul 3 15:16:24 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 95d01281443c432140c6216a04f8248d2927e416 Author: lijewski Date: Tue Jul 3 09:52:44 2012 -0700 Added ParticleContainer::NumberOfParticlesAtLevel(). Src/C_AMRLib/Particles.H commit 7940aa9fb640364a176265914718d1fc5c9a4545 Author: lijewski Date: Tue Jul 3 09:52:20 2012 -0700 Change the default value for verbosity from true to false. Src/C_BaseLib/DistributionMapping.cpp commit 611100c97630cd4fcf4a21c97d6bd8235ec80e3c Merge: 5c94ddc5f 372fc2ca7 Author: lijewski Date: Mon Jul 2 12:53:42 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5c94ddc5f8c72acb27c9168cbd385ee8f4b85101 Author: lijewski Date: Mon Jul 2 12:51:27 2012 -0700 Some better memory management. Now KNAPSACK time also includes time spent in LeastUsedCPUs() which does an MPI_Allgather(). SFC time already included that time. I'd been wondering why SFC time was so much greated that KNAPSACK time when running large parallel jobs. They should now be more comparable. Src/C_BaseLib/DistributionMapping.cpp commit 33848e8a2fee9e8779a48658fef52c5cc8e797b4 Author: lijewski Date: Mon Jul 2 10:52:18 2012 -0700 Added a couple more typedefs to facilitate possible future tweaks. Removed some debugging code I left in. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 372fc2ca7150435e204a7fd65af20f1b151ab81e Author: Ethan Van Andel Date: Mon Jul 2 10:45:41 2012 -0700 Added setDtLevel for specific level. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 85b3f9ca1db9a402c6debdf8934220ad5c280244 Author: lijewski Date: Mon Jul 2 09:59:07 2012 -0700 Check that at most one of do_alltoall & do_async_send can be true. Src/C_BaseLib/FabArray.H commit 1e41472c683f0ba1ace9f9d524fa000ef34476f1 Author: Ann Almgren Date: Sat Jun 30 09:08:39 2012 -0700 Fix the bottom_solver = 4 option, hopefully for real this time! Src/LinearSolvers/F_MG/mg.f90 commit 906d2a5c40385cc0b31519260f85cb93925c7941 Merge: e562ac7ea b13415c11 Author: Michael Zingale Date: Fri Jun 29 20:20:24 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e562ac7eaac0720f08f4e7d22984f8f1f16f6db4 Author: Michael Zingale Date: Fri Jun 29 20:20:00 2012 -0400 start merging in some of Weiqun's changes Tools/RegressionTesting/testnew.py commit b13415c11f0dbd1613561508e68b53a311e415da Author: vince Date: Fri Jun 29 14:37:01 2012 -0700 addition for ipm gnu Tools/C_mk/Make.Linux commit 2275750facb3904a2783d0cfcd44ad379dbbb9e2 Author: vince Date: Fri Jun 29 14:20:02 2012 -0700 instrumented the code with bl_prof. Src/F_BaseLib/bl_prof.f90 Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/main.f90 commit 257e58eadce324720b309db658163712d9b872dd Merge: 99f241cca 4817c7a22 Author: vince Date: Fri Jun 29 13:57:27 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 4817c7a2260e9803c533d3bb12facf4328be9829 Author: lijewski Date: Fri Jun 29 13:26:06 2012 -0700 Fixed something I just broke; forgot to test non-MPI. Src/C_BaseLib/ParallelDescriptor.cpp commit c6472d2a517617673bbbab0358836606ee799024 Author: lijewski Date: Fri Jun 29 13:25:40 2012 -0700 Defined MPI_DATATYPE_NULL for non-MPI builds. Src/C_BaseLib/ccse-mpi.H commit bce6f8721ea7abe0c437beac79730ee62e83c34c Author: lijewski Date: Fri Jun 29 13:08:42 2012 -0700 Moved "struct RF" from an unnamed namespace in the .cpp file into the class definition of FluxRegister. Also renamed it to "Rec". This way we can reuse this struct in other code. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 3098356851ce630fdd2a9e7ad3ed0e67601206a2 Author: lijewski Date: Fri Jun 29 12:51:21 2012 -0700 Fixed typo. Src/C_BoundaryLib/FabSet.cpp commit 4f1e9eb1521eb7d5d1677ad4db8a625848b060d3 Author: lijewski Date: Fri Jun 29 12:37:01 2012 -0700 Removed some redundant code. Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 8dd6ad5b0981f62c25a3bcb7f2b3edd6a7d68f54 Merge: 005d55975 e45f5cb0c Author: lijewski Date: Fri Jun 29 11:26:46 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 005d55975db65c07b8f2b7c11dddf08f3b81ca50 Author: lijewski Date: Fri Jun 29 11:26:35 2012 -0700 Removed some redundant code. Src/C_BaseLib/BoxArray.cpp commit e45f5cb0c8e4ff3e849349d904839859f335a4a1 Merge: a5e45e08b 11dd21187 Author: Ethan Van Andel Date: Fri Jun 29 11:19:38 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a5e45e08be28efd3e863782756c84c336c102899 Author: Ethan Van Andel Date: Fri Jun 29 11:18:28 2012 -0700 Fix to initial timestep fix. It now pays attention to regridding -and- checks input flags Src/C_AMRLib/Amr.cpp commit 11dd2118721b6bf5794b1f8b4aaf4e4c42d61977 Author: lijewski Date: Fri Jun 29 10:20:49 2012 -0700 Added skeleton for cut cells stuff. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/cutcells.f90 commit 0800b32a1f8c4e8e3f496078f32c39293680b80b Author: lijewski Date: Fri Jun 29 10:17:08 2012 -0700 Removed the isects.reserve() calls. They're now embedded in the BoxArray intersections() calls. Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/FabSet.cpp commit 0145f3d54ac9a1bcf03cf5c2be5385159668bf2c Merge: 397b601d0 37216f4ce Author: lijewski Date: Fri Jun 29 09:59:09 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 37216f4ce163dfba81f5c1d4c7bef24a186533d6 Merge: 8c07a3ea7 bee5cacae Author: Ethan Van Andel Date: Fri Jun 29 09:56:19 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8c07a3ea771b8cb71191b130e014fa0d422be87a Author: Ethan Van Andel Date: Fri Jun 29 09:54:46 2012 -0700 Fixed bug where Level 0 initData could be called multiple times. Src/C_AMRLib/Amr.cpp commit 397b601d0081689f2c8527e11368cbcfbb7b92fa Author: lijewski Date: Fri Jun 29 09:40:47 2012 -0700 A final bit of polishing. Src/C_BaseLib/FabArray.H commit d19c44581df24021c67fbc12ffa52faaec06981d Author: lijewski Date: Fri Jun 29 09:14:45 2012 -0700 Inlined & simplified some stuff. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit bee5cacae28aa50fafb849335792064136d4ed5c Author: lijewski Date: Thu Jun 28 17:37:28 2012 -0700 Inlined a few things. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 02a1ca287e7bb970bedc814489dc5c59f28dd081 Author: lijewski Date: Thu Jun 28 17:08:43 2012 -0700 Use std::deque<> for fabComTagList and fabCopyDescList instead of std::vector<>. Src/C_BaseLib/FabArray.H commit f9d45e422ed633f806377de1350df96ea325d698 Author: lijewski Date: Thu Jun 28 15:47:26 2012 -0700 Squished out some more memory. Also added some new typedefs. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 09c5eecdcc0c523d7cc251e080ce835bc06024d4 Merge: 017989dd9 8a8ab5ee1 Author: lijewski Date: Thu Jun 28 15:45:07 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 017989dd937bd8ccef18d4d0e2f5f89b59c44259 Author: lijewski Date: Thu Jun 28 15:24:03 2012 -0700 Squished out a little more memory. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 8a8ab5ee148bb1900523c47176444264e504db80 Merge: 9283e75f6 e7742482a Author: Ethan Van Andel Date: Thu Jun 28 15:18:54 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9283e75f6420a07c32a0c0ea8de57263c8b8a5bd Author: Ethan Van Andel Date: Thu Jun 28 11:17:55 2012 -0700 Subcycling bugfixes and a change to initial dt computation. This change may slightly change the size of the first timestep and break regression tests. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit e7742482ae4032088b3d1c3b3e7b15444d4ac44e Author: Michael Zingale Date: Thu Jun 28 15:48:55 2012 -0400 all repos are now git. Make the changelogs work for all the git and finish the AstroDev inputs Tools/RegressionTesting/testnew.py commit f4e8f625afd98d1ac63878aaf429af6f2aa89b85 Author: Ethan Van Andel Date: Wed Jun 27 15:17:20 2012 -0700 Optimal Subcycling added. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit f1d0d9b85e371114dfb969bce5f6e7ab3258a8b2 Author: lijewski Date: Wed Jun 27 13:59:23 2012 -0700 A little more cleanup. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/MultiFab.cpp commit e731e53fa7c9d0cb0c0fb0054c5597a856c0446d Author: lijewski Date: Wed Jun 27 12:45:11 2012 -0700 Minor efficiency improvements. Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp commit c92de450af90489d49cfd2b1740416af9a4fe9eb Author: lijewski Date: Wed Jun 27 12:26:46 2012 -0700 Some memory efficiency improvements. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 8e202b0907ca929f2288659e355f2fc5c70e9b45 Merge: d01315c17 841d86e5c Author: Ethan Van Andel Date: Wed Jun 27 12:26:06 2012 -0700 Merge branch 'master' into opt_sub commit 841d86e5c803cb7799e913c71aa24d787013aff6 Author: Ethan Van Andel Date: Wed Jun 27 11:28:53 2012 -0700 One more ADDI fix. Src/C_AMRLib/Particles.H commit e481fe2c23511735ae8ee7c884deddc077ea2d1c Author: Ethan Van Andel Date: Wed Jun 27 11:19:01 2012 -0700 Level indexing fix for AssignDensityDoIt Src/C_AMRLib/Particles.H commit d981c716e0e49ea8f5aadd8c36ac477534839546 Author: Ethan Van Andel Date: Wed Jun 27 10:35:41 2012 -0700 One more small virtual numbering change. Src/C_AMRLib/Particles.H commit 123dbd6ab42030ad909526fc6a25811b43ae1dc0 Merge: 1d48be39d a609992ec Author: Ethan Van Andel Date: Wed Jun 27 10:30:56 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1d48be39dd4a5072db751484f32749f9e55fe211 Author: Ethan Van Andel Date: Wed Jun 27 10:30:02 2012 -0700 Fix to AddParticlesAtLevel and virtual/ghost particle numbering. Src/C_AMRLib/Particles.H commit d01315c17ff37733f40262f346e90b1206c1bcc4 Author: Ethan Van Andel Date: Wed Jun 27 10:29:24 2012 -0700 Work on optimal subcycling Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit a609992eca400d0c0c8c1493d7893ce450798cce Author: lijewski Date: Tue Jun 26 17:35:57 2012 -0700 Minor simplification to collate(). Src/C_AMRLib/TagBox.cpp commit b8d3ef752753cbb2451e4b7cadc1e460f3ce6f21 Author: lijewski Date: Tue Jun 26 17:11:06 2012 -0700 Some cleanup of minIndex() and maxIndex(). Src/C_BaseLib/MultiFab.cpp commit 1c69d52df91600273c560f02cec9c8d8f746b6f5 Author: lijewski Date: Tue Jun 26 16:34:47 2012 -0700 Cut down on number of heap allocations. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 53018677062b4ae7d5d29f125dabe8485b0c3efb Author: lijewski Date: Tue Jun 26 14:42:50 2012 -0700 Improved the memory efficiency of copy() and CollectData(). Trying to miniminze the number of NProc size arrays needed. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 53105d4311974ed8cd3674e8b009daebec0e27d3 Author: lijewski Date: Tue Jun 26 14:14:32 2012 -0700 Replaced as many uses of std::list<> with std::deque<> as possible for efficiency reasons. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.cpp commit 1627a19717ec9f1cc514c8351a9b7e8a7c8cbaa8 Author: Michael Zingale Date: Tue Jun 26 13:07:31 2012 -0400 better way to do the labels python_plotfile/contourcompare.py commit 339b17ea5be87542ee170c078b8ba27cd656fad6 Author: lijewski Date: Fri Jun 22 14:12:56 2012 -0700 We now have the capability to switch between using synchronous MPI sends and asynchronous MPI sends in CollectData() and copy(), controlled by ParmParse'd variables. The default is to use synchronous sends as we've been using for years. I had a vague hope that the asynchronous sends might be faster on hopper, but that doesn't appear to be the case. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d5df165440d1f790e64f473aef90651735fd0eba Author: lijewski Date: Fri Jun 22 09:07:26 2012 -0700 Cleaned up some warnings. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit b89b72deef3f6765e30ce5a31174ce9aa67e8231 Author: Weiqun Zhang Date: Thu Jun 21 17:00:42 2012 -0700 add @echo SUCCESS for regression testing Tutorials/HeatEquation_EX5_F/GNUmakefile commit cfe97295371ca3f8e5116c686ed6fd348e93d74f Author: Weiqun Zhang Date: Thu Jun 21 15:27:25 2012 -0700 Fix makefile for this tutorial Tutorials/MultiGrid_C/GNUmakefile commit cd83f7c1b607d963cbba2327ee8bd6be6d1b50cf Author: Weiqun Zhang Date: Thu Jun 21 15:16:11 2012 -0700 Add @echo SUCCESS so that regression testing would know whether or not the compilation is successful. Tests/LinearSolvers/ComparisonTest/GNUmakefile Tutorials/MultiGrid_C/GNUmakefile commit 49f3f88a3648f180ff0f5c92e6fc431a82fe9c74 Merge: c93fb0515 cd12415df Author: Michael Zingale Date: Thu Jun 21 13:28:27 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit c93fb051597f313f340b274e035fff60305a5a2e Author: Michael Zingale Date: Thu Jun 21 13:27:58 2012 -0400 new analysis routines for sub_Chandra MAESTRO_sub_chandra/GNUmakefile MAESTRO_sub_chandra/fsubchandra.f90 commit e3e80424bb045518c5c30040f312174226327e68 Author: Vince Beckner Date: Wed Jun 20 16:46:19 2012 -0700 fix for battra. Tools/C_mk/Make.mpi commit 487fa6d6c73876bb31422d236d228312f0a4193a Author: ajnonaka Date: Wed Jun 20 15:13:10 2012 -0700 fixed error in makefile documentation Docs/GettingStarted/GettingStarted.tex commit d318519c0e7b111b05e0e357c33ace02e4d92a4d Author: ajnonaka Date: Wed Jun 20 14:41:52 2012 -0700 note about makefiles Docs/GettingStarted/GettingStarted.tex commit d93f86db6ebe40a84d4824e118aedeb40a7285e1 Author: Ethan Van Andel Date: Wed Jun 20 10:49:21 2012 -0700 Added method for computing optimal subcycling. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit a45f8d984c63a6c918f2a1c24a347f23ef29a2fd Author: Ann Almgren Date: Wed Jun 20 09:35:59 2012 -0700 Fix logic for whether we can use bottom_solver = 4 in the F90 mg -- it should only be used when the grids completely fill their bounding box. Src/LinearSolvers/F_MG/mg.f90 commit 8efc98b729d48b2c8e281bf1dd8751c6bc328637 Author: Ann Almgren Date: Tue Jun 19 17:33:24 2012 -0700 Somehow the bottom_solver = 4 option can create more rather than fewer grids at the bottom level. If this happens, ignore the new grids and use bottom_solver = 1 instead. Src/LinearSolvers/F_MG/mg.f90 commit baa6426c132a22207c8c47d402ca82029cdc83c7 Author: Ann Almgren Date: Tue Jun 19 16:23:49 2012 -0700 Force a full regrid if we change n_cycle on restart (this is a prelude to optimal subcycling) Src/C_AMRLib/Amr.cpp commit 24905a0e20e293a2e8bf47564a406d2cf111f503 Author: lijewski Date: Tue Jun 19 14:35:07 2012 -0700 Merged in new BoxArray::intersections(). Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit e3b3c18e3e8ff52e03571c9c61ed6ce95e5cf0c3 Merge: 0edb5813d cc96b7696 Author: lijewski Date: Tue Jun 19 14:30:52 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0edb5813dd0f9ff578129ff22da94adfca6eb753 Author: lijewski Date: Tue Jun 19 14:13:13 2012 -0700 Added new version of intersections() that takes the std::vector<...> as an argument, instead of returning it. For codes that use intersections() a lot (like Particle codes) this'll make things run faster. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit cc96b7696bf49bd92b3384e2efbb7b1b196fdae5 Author: Ann Almgren Date: Tue Jun 19 13:28:59 2012 -0700 Fix typo: "ghost" --> "ghosts" Src/C_AMRLib/Particles.H commit a503482941253cafcc6098c14a1aab8233743b21 Merge: 4259202de e88a49e69 Author: Ann Almgren Date: Tue Jun 19 13:26:27 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 4259202de49259ead068278d7c1e0526436ce508 Author: Ann Almgren Date: Tue Jun 19 13:25:47 2012 -0700 Fix the logic when regrid_on_restart is true -- we should only do special case when max_level == 0, not when finest_level == 0. Also replace "and" by "&&" in two places. Src/C_AMRLib/Amr.cpp commit e88a49e69d84b38fb1d530f9852ebf3f08ebed20 Merge: 3f77f5111 2c98c9488 Author: Michael Zingale Date: Tue Jun 19 15:55:43 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2c98c948871f371bc35a929b1de22d71d39402d1 Author: lijewski Date: Tue Jun 19 12:48:17 2012 -0700 Pass PBoxes by reference in a few routines where they were being passed by copy. Fixed some bugs in AddParticlesAtLevel(). Src/C_AMRLib/Particles.H commit 3f77f511111a6f04c0e22d21fab00860b87c631b Merge: baf683c18 821c51768 Author: Michael Zingale Date: Tue Jun 19 15:37:59 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit baf683c186f21ddb22cdfb5e523960be6ead6d8f Author: Michael Zingale Date: Tue Jun 19 15:37:32 2012 -0400 specify defaults on the declaration line Tools/F_scripts/write_probin.py commit 821c51768b5486d1023aaefc9e938cf70a132a40 Author: Ethan Van Andel Date: Tue Jun 19 12:13:16 2012 -0700 Optimized ghost/virt creation and assignment and removed a stray print. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit fab1f9eb3a97b7943d51cdc7fcb479d7a50b4c88 Author: lijewski Date: Tue Jun 19 10:36:44 2012 -0700 Simplified RemoveParticlesNotAtFinestLevel() & RemoveParticlesAtLevel() among other minor tweaks. Src/C_AMRLib/Particles.H commit cd12415df4fc64c029df1d2e25176ee17371a75a Merge: 293eb66c1 6d9a5558e Author: Michael Zingale Date: Tue Jun 19 13:09:16 2012 -0400 tweaking of the makefile commit 293eb66c1c4b4467fc087fda7dff26b7cbbe38f4 Author: Michael Zingale Date: Tue Jun 19 13:04:27 2012 -0400 get this compiling again GNUmakefile commit 7b983114b54e8b92cca32f0d0178d0bfc45352b3 Author: lijewski Date: Tue Jun 19 09:27:37 2012 -0700 Try to be a little more const correct. In FineCellsToUpdateFromCrse() use resize(0) instead of clear() to cut down on memory allocation. Src/C_AMRLib/Particles.cpp commit df4bbb550c0b9718f9f62045faf11974ccfa3048 Author: lijewski Date: Mon Jun 18 15:20:01 2012 -0700 Call CIC_Cells_Fracs_Basic() from CIC_Cells_Fracs() when dx_geom == dx_part. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 356ada175bb4fcf9519646ca622b14b1545011e0 Author: lijewski Date: Mon Jun 18 14:42:47 2012 -0700 Un-inlined ParticleBase::CIC_Cells_Fracs(). Other minor cleanup. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 5a9bd264c68abf0619be2931814222486a18c08f Author: Ethan Van Andel Date: Mon Jun 18 10:17:26 2012 -0700 More cleanup Src/C_AMRLib/Particles.H commit 49eda20f13cc42ed837dd8e64e3783a6c480470b Author: Ethan Van Andel Date: Mon Jun 18 10:16:21 2012 -0700 Pre-push cleanup Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit 5cd6ad2a1b109e43472b1e30f990571a12596aa9 Merge: e90391e76 8d0832877 Author: Ethan Van Andel Date: Mon Jun 18 09:40:35 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8d08328777ed2c18ead0ad6ef3e0e14c3ce20503 Author: Chris Malone Date: Fri Jun 15 19:51:48 2012 -0700 add libquadmath for all gfortran's in Darwin Tools/C_mk/Make.Darwin commit 00acc1625e31ede1f37d2ca085e53ba0d94484d4 Author: Chris Malone Date: Fri Jun 15 19:19:51 2012 -0700 add the optional do_finalize_MPI input to parallel_finalize calling sequence to sync up with parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit e90391e763def85956d52c2cf1b848422a25b446 Author: Ethan Van Andel Date: Fri Jun 15 17:59:58 2012 -0700 Minor refactoring and debugs to variableSetup Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit e8cb9279124418f82cb839f63c3573e9e4660ec6 Author: Ethan Van Andel Date: Fri Jun 15 16:56:15 2012 -0700 Minor additions to subcycling parse logic. Src/C_AMRLib/Amr.cpp commit 0c85cc97cbb2bc826fb322aadef83cc064de00b8 Author: Ethan Van Andel Date: Fri Jun 15 16:20:23 2012 -0700 Big Commit. Added new subcycling controls/logic. Documentation to follow. Fixed a sneaky bug in nosubcycling AssignDensity. Added Particle Aggregation for virtual particles. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit fe33277b1cbc0a0c50a28ddedb6b2baed6624d90 Author: Marc Day Date: Fri Jun 15 15:56:06 2012 -0700 The MPI_Comm_Free call seems to cause a core dump...so for now, we will live with a small mem leak Src/F_BaseLib/parallel.f90 commit b724bfff6c7f0f9b2d387e172ab1ab9d00953885 Merge: 0afdbf3e1 59fc94004 Author: Marc Day Date: Fri Jun 15 14:26:50 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 0afdbf3e1348bcb9549447d25556ab1cb30a19bc Author: Marc Day Date: Fri Jun 15 14:26:38 2012 -0700 Add omega to f_mg args, clean up some loose memory, virtualize more of Amr, etc... Src/C_AMRLib/Amr.H Src/C_BaseLib/Utility.cpp Src/F_BaseLib/parallel.f90 Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 59fc94004ee42152d651b4564a728018f497bb06 Merge: 382eaf9d4 7d923f2c7 Author: Michael Zingale Date: Fri Jun 15 15:57:08 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 382eaf9d4cc4b17c9710042b5239b6b65e9ec121 Author: Michael Zingale Date: Fri Jun 15 15:56:30 2012 -0400 remove references to Atlas and Franklin -- those machines no longer exist Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Darwin_intel.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_pathscale.mak commit 7d923f2c70703e2470818111058f3825a119ffe5 Author: lijewski Date: Fri Jun 15 10:01:35 2012 -0700 Explicitely state that operators <, <=, > and >= are NOT strict weak orderings usable by STL sorting algorithms. Src/C_BaseLib/IntVect.H commit 6ba57f8f5658eccf5c472bcfefa22f7e07df21a7 Author: Michael Zingale Date: Wed Jun 13 18:01:14 2012 -0400 if we are storing velocities along with the particle info, we need to increase the number of fields in the format statement Src/F_BaseLib/particles_f.f90 commit de8c957945550cf40763f2fca4658f480efc5ed8 Author: Ethan Van Andel Date: Tue Jun 12 15:17:28 2012 -0700 Fixed fix to nosub, removed sum debug in subcycling AssignDensity. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit 99f241ccab9c11e6988b4fc9f4d5832076ce44fc Author: vince Date: Tue Jun 12 12:53:13 2012 -0700 added IPM suffix. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tutorials/Exp_CNS_NoSpec/GNUmakefile commit 18385fc339043b4e7323cbf4bae6084fa47f0d7d Merge: e2391576f 57b98e234 Author: Michael Zingale Date: Tue Jun 12 13:14:55 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e2391576ff8f3b9d709a10425b6d41ed88e0c522 Author: Michael Zingale Date: Tue Jun 12 13:08:34 2012 -0400 remove bender-specific stuff. With update to F17, we can use BOXLIB_USE_MPI_WRAPPERS Tools/F_mk/GMakeMPI.mak commit 8fce1fd20a9bd9d4ccbf6cbf7618b42565f5fe13 Merge: 8d5217cfd 57b98e234 Author: Ethan Van Andel Date: Mon Jun 11 09:30:05 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 57b98e234444c43ac4f9450daefaf82184c046be Author: Ann Almgren Date: Sat Jun 9 17:35:34 2012 -0700 Enforce that MGTSolver always sends a status flag to mgt_solve; note that ml_cc still has to take on if present(status) because the F90 codes may call ml_cc directly. But mgt_solve is only called from MGTSolver so we can safely modify that interface. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit d0ad1081a647c295a9d66cb3c0eb95d75dffa166 Merge: c3d17f3ce b7e55de61 Author: Ann Almgren Date: Sat Jun 9 15:09:40 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c3d17f3ce853d6930638edde794a2263bb48fb48 Author: Ann Almgren Date: Sat Jun 9 15:09:09 2012 -0700 Now the mgt_solve version does *not* take a status flag and mgt_solve_stat does. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 8b245b591daecf71d4aeb2016bbf0eac40043189 Author: Ann Almgren Date: Sat Jun 9 15:07:47 2012 -0700 Need to differentiate between the ones that take a status flag and the ones that don't. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 8d5217cfd2366cb277a6d7f3c849a066f67d9c6b Author: Ethan Van Andel Date: Fri Jun 8 16:38:32 2012 -0700 DERP fix. Src/C_AMRLib/Amr.cpp commit 0e96ce047dd309fc1aee8e799ccfc3c9c76354d0 Author: Ethan Van Andel Date: Fri Jun 8 15:35:16 2012 -0700 Fixed nosub setting in Amr.cpp, particle tweaks. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit bf335c15e4fe916d6b937d9d62ea37ff134a6e9d Author: Ethan Van Andel Date: Fri Jun 8 14:33:04 2012 -0700 Fixes to subcycling assign density. Src/C_AMRLib/Particles.H commit b7e55de616083f37c2937843b3a7e9fa1ec82f40 Author: Michael Zingale Date: Fri Jun 8 10:23:54 2012 -0400 remove references to nan -- we can use BOXLIB_USE_MPI_WRAPPERS now Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit fa36c37db90ba540d7e28861ea6bae2d724c52a5 Author: Ethan Van Andel Date: Thu Jun 7 16:23:19 2012 -0700 Minor fix to periodic ghost cell densities. Src/C_AMRLib/Particles.H commit e7bacf1f0198d908c38e20295d8daa545266a62d Author: Ethan Van Andel Date: Thu Jun 7 11:04:36 2012 -0700 Debug to nonsybcycling redistribute. Src/C_AMRLib/Particles.H commit 395b1e7704f799ada8d2cc80e3e862b632ddbfa7 Author: Ethan Van Andel Date: Thu Jun 7 10:44:24 2012 -0700 Modifications for working DM particle subcycling. - Ghosts, Virtuals - CIC for particles with arbitrary radii (at the CIC level, not the assign density level) Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 6d9a5558e8742fa9af0e74bee5ae39dbdeb695c1 Author: Christopher Malone Date: Thu Jun 7 11:28:44 2012 -0400 get this working with updated make system GNUmakefile commit ae05305c64f09e58a6731f20fc02824ffe8831f4 Merge: 8626cc4ab 860efc01f Author: Marc Day Date: Wed Jun 6 13:20:52 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 8626cc4abb73eafdeab5e6d772e3641059db68d1 Author: Marc Day Date: Wed Jun 6 13:20:44 2012 -0700 Fix uniinitialized status flag, and pull omega through the options Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 860efc01f2a19a8f784555af822a36901aac14b1 Author: vince Date: Wed Jun 6 13:08:58 2012 -0700 init for max and div optimizations. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 06229c90b767152e8b4baecfd8ad17ad9e68581d Author: Ethan Van Andel Date: Tue Jun 5 13:01:05 2012 -0700 One more merge fix. Src/C_AMRLib/Particles.H commit 5a06978bcdd57e81c81872e051b9309d9ff77819 Merge: 3d53bf94e cb1cb9b45 Author: Ethan Van Andel Date: Tue Jun 5 12:56:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit cb1cb9b45293fcffefee1e6db2e97c3c9b7eec8d Author: Ann Almgren Date: Tue Jun 5 11:47:30 2012 -0700 Modify NReaders and NRedist in Particles.H in order to be able to read large particle files when N_processor >= 4K Src/C_AMRLib/Particles.H commit 6eb6014702570642b558174e13cf3b9b8666c2bd Author: lijewski Date: Tue Jun 5 10:39:28 2012 -0700 Added finest_level argument to Where() and PeriodicWhere() that defaults to -1. The -1 implies to use m_amr->finestLevel(). Changed Redistribute() and AssignDensity() to the effective finest level, not to blindly use m_amr->finestLevel(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 92532dd5f2e881f71a0f95707f0328a36dc02821 Author: ajnonaka Date: Tue Jun 5 08:13:42 2012 -0700 give multifab_build_edge and multifab_build_nodal the optional "stencil" argument Src/F_BaseLib/multifab_f.f90 commit 0e8a8587dd6db43372fc33101ff143a161e9016c Author: ajnonaka Date: Tue Jun 5 07:53:29 2012 -0700 added subroutine multifab_build_nodal Src/F_BaseLib/multifab_f.f90 commit a1e902e82e9940572e905ff71221c79274c0a2b8 Merge: a9038645e 7e20188a6 Author: Michael Zingale Date: Mon Jun 4 20:17:25 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing commit 3d53bf94ece34d492b7a0c265c141963bec41486 Author: Ethan Van Andel Date: Mon Jun 4 17:17:03 2012 -0700 Working Ghost particles, debugs. Src/C_AMRLib/Particles.H commit a9038645e7836db646463f12ac82c6ba708ad2af Author: Michael Zingale Date: Mon Jun 4 20:16:14 2012 -0400 remove constants and random as packages needed for the build GNUmakefile commit c7a1b0cc2d322ddd13152a5a53c4d6fc55f64ead Author: Michael Zingale Date: Mon Jun 4 15:27:04 2012 -0400 add more flexibility to detecting the appropriate gfortran library. First look for libgfortran.a (as we were doing). If gfortran just returns the name w/o a path, then it did not find it. In that case, look for libgfortran.so. Some linux boxes don't have the static libraries installed by default. Tools/C_mk/Make.defs commit 4e361e933e4e961013637a1e0685e1e0c25f7f80 Author: cmalone Date: Mon Jun 4 11:12:10 2012 -0700 removed extra -J definition; already handled in Make.defs for gfortran Tools/C_mk/Make.Darwin commit f1f446529747c8929402ddc9ad9097e5883550d0 Author: cmalone Date: Mon Jun 4 10:11:59 2012 -0700 swap and elifdef for an else ifdef as Macs don't like former syntax Tools/C_mk/Make.mpi commit 3d4befc7cdbe902275dd7903eb7bb112ab54c5fa Merge: d2a50439b dc71f6060 Author: Michael Zingale Date: Mon Jun 4 12:30:03 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d2a50439b69ebe0811a56f3babbfe0a51d5e9cbb Author: Michael Zingale Date: Mon Jun 4 10:28:11 2012 -0400 make the list of modules an array so we can print them one per line. Tools/F_scripts/make_build_info commit dc71f6060107e8d13ab9ba60dabdff21b02f92fd Author: Michael Zingale Date: Sun Jun 3 20:56:49 2012 -0400 add support for AstroDev Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/testnew.py commit 4ca67a0b1c3b9bfeb0d57f7e6f383c2285f49ab2 Author: Ethan Van Andel Date: Fri Jun 1 16:24:52 2012 -0700 Modified Nyx move/density routines, added creation routines to support subcycling and virtual particles. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit cd0cf60dc35389d3e2539484072069f3e01baf1e Merge: eee9a54d4 dc788ecf1 Author: vince Date: Fri Jun 1 14:29:40 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit eee9a54d4220853efa6bab438e75422b906f0f0b Author: vince Date: Fri Jun 1 14:29:19 2012 -0700 changes for battra and naphta. Tools/F_mk/GMakeMPI.mak commit a144d1f28c24041462feacc0f95c5c2615a26ddf Merge: aded7cab5 7e20188a6 Author: Weiqun Zhang Date: Fri Jun 1 13:04:34 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing commit aded7cab50e6ef1416700b05955b2e1ff08a91dc Author: Weiqun Zhang Date: Fri Jun 1 13:04:11 2012 -0700 chmod a+x plotsinglevar.py python_plotfile/plotsinglevar.py commit dc788ecf188d47fcea0be6b11679e0820dbd32bb Merge: 5372c2b16 700a16a7c Author: Michael Zingale Date: Thu May 31 21:45:19 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 5372c2b16bc495fe508b1d6d17a651d273edae93 Author: Michael Zingale Date: Thu May 31 21:44:41 2012 -0400 for a generic Linux machine, is BOXLIB_USE_MPI_WRAPPERS is set, then we compile with mpic++ and mpif90 Tools/C_mk/Make.mpi commit f4feb176c6525332c050990b559dde3c378587c8 Author: Ethan Van Andel Date: Thu May 31 12:47:16 2012 -0700 Started work on Nyx subcycling, change to assign density, bugfix to MGT_Solver Src/C_AMRLib/Particles.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 700a16a7cbaad7551c719f67a62fc9967856120a Author: Ann Almgren Date: Thu May 31 10:43:24 2012 -0700 For some reason, BL_ASSERT using (a == b == c) dies a horrible death, but BL_ASSERT (a == b) is fine. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit f5ea75d37fd05e58df9e63fe39d296d53b0f38c9 Author: Ann Almgren Date: Thu May 31 09:54:56 2012 -0700 No longer need cvs scripts. Tools/F_scripts/cvs2cl.pl commit 7183836c63238d70787b967e3ebcad9b5f9562d9 Author: Ann Almgren Date: Thu May 31 09:54:13 2012 -0700 Remove Tools/F_scripts/idlbl directory completely -- we don't want to support IDL stuff. Tools/F_scripts/idlbl/README Tools/F_scripts/idlbl/batch.pro Tools/F_scripts/idlbl/color.pro Tools/F_scripts/idlbl/color_index.pro Tools/F_scripts/idlbl/colorbar2.pro Tools/F_scripts/idlbl/dump_surface.pro Tools/F_scripts/idlbl/flamelength.pro Tools/F_scripts/idlbl/flash_colors.tbl Tools/F_scripts/idlbl/get_idlbl_path.pro Tools/F_scripts/idlbl/nolabel.pro Tools/F_scripts/idlbl/partvelvec.pro Tools/F_scripts/idlbl/plotflash.pro Tools/F_scripts/idlbl/plotraw.pro Tools/F_scripts/idlbl/rawread.pro Tools/F_scripts/idlbl/rawread3d.pro Tools/F_scripts/idlbl/scale_color.pro Tools/F_scripts/idlbl/start_linux.pro Tools/F_scripts/idlbl/tvimage.pro Tools/F_scripts/idlbl/vcolorbar.pro Tools/F_scripts/idlbl/xaverage.pro commit 91979f901e48ecee7109faec985d0676585a7a84 Author: Ann Almgren Date: Thu May 31 09:53:13 2012 -0700 Move Tools/C_util/regtests to Tools/RegressionTesting Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/README Tools/RegressionTesting/gen_compile_test.sh Tools/RegressionTesting/radiation-tests.ini Tools/RegressionTesting/test-Ubuntu.py Tools/RegressionTesting/test.py Tools/RegressionTesting/testnew.py commit 24c55539d182f715b82255d54a2c74efd98dcf9e Merge: 28b508671 19a030126 Author: Ethan Van Andel Date: Tue May 29 10:46:54 2012 -0700 Merge branch 'subcycling' commit 19a030126448b8cea051f09baf014a645ffbb077 Author: Ethan Van Andel Date: Tue May 29 10:43:52 2012 -0700 Minor fix to Where Src/C_AMRLib/Particles.cpp commit 4584324c9b2136c1ed9efbede0e2b77ba5d64e46 Author: Ethan Van Andel Date: Tue May 29 09:55:15 2012 -0700 Removed redundant method declarations, changed to default param. Src/C_AMRLib/Particles.H commit 28b50867151a744d2c2591e195990e434a32f549 Author: lijewski Date: Thu May 24 13:02:16 2012 -0700 Changes for Aleks. Tools/F_mk/GMakeMPI.mak commit f736038b400f822ee57aa4b75d3d95f4a7e394c5 Author: ajnonaka Date: Wed May 23 21:16:36 2012 -0700 builds correctly now after Ethan's re-org to add C_AdvancedTopics Docs/GNUmakefile commit 483a2d429945bf6c3fe0a6c3d77f055444a0a7c5 Author: Ethan Van Andel Date: Wed May 23 15:07:58 2012 -0700 Added support for particles leaving the domain across a non-periodic boundary (they are invalidated and removed at the coarse timestep). Src/C_AMRLib/Particles.H commit 1010c3a7da4f792dabdfe7b565593b46c4168201 Author: Ethan Van Andel Date: Wed May 23 15:05:00 2012 -0700 Important bugfix to 2d hoextraptocc (seldom used) Src/C_AMRLib/FILCC_2D.F commit d91e0014b0f7be34f7cc6f0cace5972d566e03c8 Author: Ethan Van Andel Date: Tue May 22 14:30:34 2012 -0700 Debug fixes to particle subcycling Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit c4a3856d2ec2c266c7233a2eb44ab202bd4efcca Merge: 09e8489f8 33894bd58 Author: vince Date: Tue May 22 13:20:35 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 09e8489f8a2cfe7c6cf294032216aa52efab07c5 Author: vince Date: Tue May 22 13:19:20 2012 -0700 changed default PLOTPER test. Src/C_AMRLib/Amr.cpp commit 33894bd58e2b8d9fdb5c1fe1515ca587a99119b3 Merge: 3843d29b5 c92321544 Author: Ann Almgren Date: Tue May 22 11:08:16 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3843d29b54a015b59c91230ae5c6be6dd60737b9 Author: Ann Almgren Date: Tue May 22 11:07:49 2012 -0700 1) Formatting in mg.f90 2) We no longer allow the dense stencil in 2D since the multilevel divergence operator is known to be wrong. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/F_MG/mg.f90 commit c92321544510b012ae628a038bb64995657af492 Merge: 1190e8adc 52e8219ef Author: ajnonaka Date: Tue May 22 10:25:14 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1190e8adcb4967673631e757b7d7328cf6edd331 Author: ajnonaka Date: Tue May 22 10:25:02 2012 -0700 fixed a comment Tutorials/HeatEquation_EX5_F/advance.f90 commit 52e8219ef4475b933139f4dc852702314afcf6f2 Author: Michael Zingale Date: Tue May 22 09:59:24 2012 -0400 add OpenMP support for fParallel jobs Tools/C_util/regtests/Maestro-tests.ini Tools/C_util/regtests/testnew.py commit 4347b47a968bfa1c14d1ffeb713429be13b20075 Author: Ethan Van Andel Date: Mon May 21 17:02:28 2012 -0700 Seemingly working particle subcycling; more tests needed. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 1ea94681a8f3005dbeffed9303240f46784323df Author: Marc Day Date: Mon May 21 16:37:03 2012 -0700 Some small (hopefully ineffectual) changes to minimize redundant code Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 6842dcbbc15be94090df7569255064d0ba724458 Merge: 9c567a897 88afdb7c5 Author: Ethan Van Andel Date: Mon May 21 12:03:21 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 88afdb7c5eb7b0635ddf7376d12b86dad3423811 Author: Michael Zingale Date: Mon May 21 11:27:56 2012 -0400 remove explicit inf section Tools/F_mk/GMakeMPI.mak commit 18957b6f115ab57205353c84ad2b45cb95eed770 Merge: 80d806ae7 22fb3ecc0 Author: Michael Zingale Date: Mon May 21 11:20:27 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 22fb3ecc0efc0476dbc30d2e9e62a6c1a6fe5418 Author: Michael Zingale Date: Mon May 21 11:19:08 2012 -0400 remove xrb specific section Tools/F_mk/GMakeMPI.mak commit 80d806ae76e49167539c0c5e6de0fa4c3335cc6a Author: Michael Zingale Date: Mon May 21 11:06:42 2012 -0400 remove sn specific make -- use the generic BOXLIB_USE_MPI_WRAPPERS now Tools/F_mk/GMakeMPI.mak commit fd0afaadff22146c865e9bf804af2c61c031bbab Author: Michael Zingale Date: Mon May 21 10:56:37 2012 -0400 MAESTRO -> BOXLIB :) Tools/F_mk/GMakeMPI.mak commit 12c41a764b82d33f8431fa8b88cf70ed7dd10060 Author: Michael Zingale Date: Mon May 21 10:55:19 2012 -0400 remove the nan-specific entry. Add a generic Linux MPI that is more general than the old one -- now look for the environment MAESTRO_USE_MPI_WRAPPERS Tools/F_mk/GMakeMPI.mak commit 296cf9b78db925302b3d14a5b8027124302bb3d1 Merge: 84d8481b7 9a7e15047 Author: Michael Zingale Date: Mon May 21 10:33:25 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 84d8481b7abcd047e0d547d94d69fbbbf77505f7 Author: Michael Zingale Date: Mon May 21 10:33:04 2012 -0400 some pretty printing stuff Tools/F_mk/GMakedefs.mak commit 9c567a8972179477e98df6d4f26923ca223efc14 Author: Ethan Van Andel Date: Fri May 18 14:31:02 2012 -0700 More doc additions. Docs/C_AdvancedTopics/C_AdvancedTopics.tex commit 99ff76f41c3ee9c12efc175b564421568741cdc7 Merge: 557f3e7cd 9a7e15047 Author: Ethan Van Andel Date: Thu May 17 15:38:12 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9a7e15047bc14f42ef7ebbf2c2efcdd31cffbb5a Author: ajnonaka Date: Thu May 17 13:47:58 2012 -0700 linear solver note Docs/AdvancedTopics/AdvancedTopics.tex commit 557f3e7cd30acb05c9b1e9c9b056b0b47bb708b0 Merge: 7d0c13778 56f6938c6 Author: Ethan Van Andel Date: Thu May 17 13:46:26 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7d0c137785536ac46c9ac469521fc043192438f0 Author: Ethan Van Andel Date: Thu May 17 13:45:57 2012 -0700 Added Assertions to check vcomp validity. Src/C_AMRLib/Particles.H commit 98d10cd3a567c0bcf43beb156905809b30fdf4a9 Author: Ethan Van Andel Date: Thu May 17 13:42:51 2012 -0700 Added empty Users Guide section for "State Data" Docs/C_AdvancedTopics/C_AdvancedTopics.tex commit 88e2909e29df8fb3f51a34f093f2b4388fabe204 Author: Ethan Van Andel Date: Wed May 16 16:45:36 2012 -0700 Typo correction to main page, additions to particle documentation. Docs/C_AdvancedTopics/C_AdvancedTopics.tex Docs/UsersGuide.tex commit 34ac08edbde155f4c6a006ce329db49e29cb6266 Author: Ethan Van Andel Date: Wed May 16 16:13:29 2012 -0700 Added a UsersGuide Stub chapter for Advanced Topics with C++ that will cover particles. Docs/C_AdvancedTopics/C_AdvancedTopics.tex Docs/F_AdvancedTopics/F_AdvancedTopics.tex Docs/F_AdvancedTopics/bc_example1.eps Docs/F_AdvancedTopics/bc_example1.fig Docs/F_AdvancedTopics/bc_example2.eps Docs/F_AdvancedTopics/bc_example2.fig Docs/F_AdvancedTopics/bc_example3.eps Docs/F_AdvancedTopics/bc_example3.fig Docs/F_AdvancedTopics/hopper_omp.run Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit 26ee365a0e75fe54f4787d1b6f475185138bd33c Author: Ethan Van Andel Date: Wed May 16 14:19:35 2012 -0700 Added vcomp parameter to allow offset velocity storage in mdata. Minor documentation additions. Src/C_AMRLib/Particles.H commit 7e482f4b5b9f9a562d76df7435b11b28779f5840 Author: Ethan Van Andel Date: Wed May 16 11:21:40 2012 -0700 Added Periodic particle motion to AdvectWithUMAC. Minor Documentation additions. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 56f6938c6b8ba7bff5b3c58d0f506a83f2d72ea5 Author: Marc Day Date: Wed May 16 09:19:45 2012 -0700 Rearrange so that solver fails give slightly more info Src/LinearSolvers/F_MG/ml_cc.f90 commit f5124bd91aab713c95e49b2b7352c2b210ccc92d Author: lijewski Date: Sat May 12 19:14:49 2012 -0700 InitFromBinaryFile() appears to be working. Note that I didn't carry over the "Nrep" argument from InitFromAsciiFile(). If that's really needed it should just be a simple cut & paste. Src/C_AMRLib/Particles.H commit 2707402ea9c357882e4a9d2e212eb50964068234 Author: lijewski Date: Sat May 12 17:23:15 2012 -0700 A first cut at InitFromBinaryFile(). Src/C_AMRLib/Particles.H commit ade7da1d666d87c3faea4a156943fb2a4f9409c0 Merge: c2934e505 6ed6ef97f Author: Ann Almgren Date: Thu May 10 13:30:26 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c2934e505e33669604c07a3662ab7ce9226c6f36 Author: Ann Almgren Date: Thu May 10 13:29:31 2012 -0700 Shift the cell as well as the grid of a fine particle talking to a coarse grid across a periodic boundary. Src/C_AMRLib/Particles.cpp commit 6ed6ef97f9e6a52bf31efcbea307b7b21025cda4 Merge: af57493c1 77debfccd Author: Mike Lijewski Date: Thu May 10 12:40:39 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit af57493c1cfebc25fda6dc2e5f49d55ec1161b8b Author: Mike Lijewski Date: Thu May 10 12:39:02 2012 -0400 Don't set more than the compiler when setting FC or fC. Any flags will be lost on machines like jaguar or hopper where the machine overrides FC and fC with ftn. Put generic compiler flags into FFLAGS and fFLAGS. This fixes the problem with .mod files not getting into the proper directory. Tools/C_mk/Make.defs commit ebda2e9d02053f13670474bcb61a15b139f1d068 Author: Mike Lijewski Date: Thu May 10 12:37:57 2012 -0400 Removed some stuff that g++ doesn't like when run in strict mode. Src/C_BaseLib/winstd.H commit 77debfccd605b31cd12d396194506c5dd6c23c28 Author: Marc Day Date: Wed May 9 19:26:23 2012 -0700 Not sure what happened, but the last version ended up broken....put it back Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 63b1e076cbbcb6ce90b071bd3940765573ce7fc9 Author: Marc Day Date: Wed May 9 19:14:35 2012 -0700 Remove since it requires that I remember to manually update it BoxLib_Version.txt commit 22dd3c2ce8aef1f606777451285fad43ed430bfd Merge: e72aeada4 61d414fba Author: Marc Day Date: Wed May 9 19:10:54 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e72aeada4fd336d3a02bb3134836ba41f0365ac8 Author: Marc Day Date: Wed May 9 19:10:45 2012 -0700 Forgot to pass the growth flag down into the levels. flag was uninitialized without these lines.... Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 61d414fba2affe50d4c8988dec3d696edb7e67c9 Author: lijewski Date: Tue May 8 13:13:11 2012 -0700 Merged in protected_divide() to AssignDensity(). Src/C_AMRLib/Particles.H commit 2f522ada671530363dab3e401a74be5018e9c987 Author: lijewski Date: Tue May 8 13:11:33 2012 -0700 Added protected_divide(). This is similar to divide() except it only does the division if the denominator is "true" or non-zero. In does nothing in the case where the denominator is not "true" or non-zero. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit cd26936e78257c3ccabd33b2a353e3bd9b696a2a Author: Ann Almgren Date: Tue May 8 10:35:05 2012 -0700 Fix the placement of velocities onto the grid in AssignDensityAndVels -- we need to sum up momenta then divide by total mass in the cell rather than summing up velocities Src/C_AMRLib/Particles.H commit 0b391ee96a34d50d6f62d1f6ef41563c60ea250c Author: lijewski Date: Tue May 8 08:59:14 2012 -0700 Also constrain mult() in single-level AssignDensity() as previous commit. Src/C_AMRLib/Particles.H commit 6418f07b31721eb4eb29fc7812fdbf07d85c2797 Author: Ann Almgren Date: Tue May 8 08:52:31 2012 -0700 In AssignDensityAndVels in Particles.H, we divide the mass by volume to get density, but don't divide the velocities by volume. Src/C_AMRLib/Particles.H commit 5b6b0981928fb44b1c44995a2940af6085c2f78c Author: lijewski Date: Mon May 7 15:10:02 2012 -0700 Inlined some ParticleBase routines. Now go about 10% faster on my SantaBarbara test case on my machine with g++/gfortran. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit a62d2ca81df57dda4b5e77cadba8bd99270e548c Author: lijewski Date: Mon May 7 10:31:08 2012 -0700 Some more BL_ASSERT()s. Src/C_AMRLib/Particles.H commit 1b8bf767bd5663c1018882248248174e563f9f28 Author: lijewski Date: Sun May 6 08:10:35 2012 -0700 Got AssignDensity() working in parallel for > 1 components. Had to move it from ParticleBase to ParticleContainer. Now use ncomp components of m_data instead of m_pos. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit d5c10d4bc407b3c3a28ebc6cb492b4f9eb003397 Author: Ann Almgren Date: Sat May 5 08:38:06 2012 -0700 Add the option in Particles.H to initialize the gas velocities as well as density from the particle file. Src/C_AMRLib/Particles.H commit 1d0b7f4ed49ae52b0aaabcb34502054a83abdc3e Merge: 7b4f3f5d7 06e862baf Author: Ann Almgren Date: Fri May 4 17:42:22 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7b4f3f5d7ba147e7e63276973ea4911e01372da6 Author: Ann Almgren Date: Fri May 4 17:41:50 2012 -0700 One more place to add max_L0_growth so that it is passed through from inputs file to ml_cc.f90 Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 06e862bafe283f2a156a938023b21f36faab1809 Author: Marc Day Date: Fri May 4 17:20:09 2012 -0700 manual update of version textfile BoxLib_Version.txt commit 2a50c46010c64fb02f7d412cd568364be288042a Merge: 08cf50817 ca8220a40 Author: Ann Almgren Date: Fri May 4 16:50:11 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 08cf508178f57dc4b4c5ceed761f5125409ae474 Author: Ann Almgren Date: Fri May 4 16:49:11 2012 -0700 Modify the mg stuff so that the max_L0_growth defaults to -1 and isn't used, but should be able to be set from the C++ inputs file. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit ca8220a40ec6e039ee3bd6cfcafeec4a4f0a4fd1 Author: lijewski Date: Fri May 4 14:53:11 2012 -0700 Changed some large 2-D stack allocated arrays to be allocatable. Some OpenMP. Src/F_BaseLib/create_umac_grown.f90 commit 4b7d1ae1937edf8a41e870177d35ae9e082ab18c Author: Marc Day Date: Fri May 4 13:26:57 2012 -0700 addition solved case Src/LinearSolvers/F_MG/ml_cc.f90 commit ed9fcf27cb49cdae1967c0ad3b97104f899e96b1 Author: lijewski Date: Fri May 4 10:23:38 2012 -0700 I've checked in an OpenMP'd Jacobi solver for the dense stencil into nodal_smoother_3d(). It's in the "else" part of a "if (.true.) then else endif" chunk of code so that the usual Gauss-Seidel solver is still used at the moment. We'd like to give folks the option of using either Jacobi or Gauss-Seidel, with the code defaulting to Jacobi if OMP=t. Got to think about how to do that. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 266cf05a1c8136a4bf3f696d035266e00976cb91 Author: ajnonaka Date: Thu May 3 13:45:03 2012 -0700 some VisIt documentation Docs/GettingStarted/GettingStarted.tex Docs/GettingStarted/VisIt_2D.eps Docs/GettingStarted/VisIt_3D.eps commit f9351fa710fbf0865f334cc088814c0bfc3cc128 Author: ajnonaka Date: Thu May 3 13:10:29 2012 -0700 fix variable name Tutorials/HeatEquation_EX1_C/writePlotFile.cpp commit edbbd94e6e6e816be729a6bf8442f61c4141f30d Merge: e6ce6f548 562de9149 Author: Marc Day Date: Thu May 3 12:32:55 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e6ce6f5489e08ad08bb4e1d86768f313d8cd671c Author: Marc Day Date: Thu May 3 12:32:45 2012 -0700 Begin process of adding status flag to fortran solvers so that they kick out if things are going south (rather than core-dumping after they have cratered). Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 Tools/CMake/CCSEOptions.cmake commit 562de914976ca593e22d7a8a1c4822abda7b0185 Author: Weiqun Zhang Date: Thu May 3 10:12:51 2012 -0700 Add Sanchez-Pomraning boundary for radiation Src/C_BoundaryLib/LO_BCTYPES.H commit 7e20188a670d8be0d2667c31433042433126d49f Author: Michael Zingale Date: Wed May 2 12:06:24 2012 -0400 add the ability to zoom in by specify xmax, ymax, or zmax python_plotfile/plotsinglevar.py commit 1dba1f3d192289f3546dfee40ca5e3381f025f65 Author: lijewski Date: Wed May 2 08:42:43 2012 -0700 Didn't have my shortcut out of FillPeriodicBoundary() quite right for the case when the MultiFab is not cell-centered. Curiously I did write it correctly for the SumPeriodicBoundary() routines. Early Onset Alzheimer's? Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 2ab75e0ce5e1ac10c80cb9830d436e5001c12c0c Author: lijewski Date: Tue May 1 13:32:50 2012 -0700 Came up with a another way to shortcut SumPeriodic & FillPeriodic Boundary. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit ae44e053c2a80eb1eb97c594e89d6048c4c2226e Author: lijewski Date: Tue May 1 11:20:12 2012 -0700 Consolidated the innards of the two SumPeriodicBoundary() routines into one routine. Src/C_BaseLib/Geometry.cpp commit a3367e01cd152cca0b8412335bbddeca7c38d78d Author: lijewski Date: Tue May 1 11:19:22 2012 -0700 A little cleanup. Src/C_BaseLib/FabArray.cpp commit cfc4a3e94bc213e5bdc07f866e0172e98eedc6fa Author: lijewski Date: Tue May 1 10:37:52 2012 -0700 Shortcut out of TagBoxArray::mapPeriodic() if there's no parallel work. Src/C_AMRLib/TagBox.cpp commit 4814e3bf4392599437834f3b2abb4746f31ac8d7 Author: lijewski Date: Tue May 1 10:02:32 2012 -0700 Shortcut out of FillPeriodicBoundary() and SumPeriodicBoundary() if there's no work to do. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 658aacb01976a6d1833a1dde796fa0d26b6232ab Merge: 33cc30e39 c69ccd566 Author: lijewski Date: Mon Apr 30 17:07:12 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 33cc30e39b1e6b4d93eab0f4bb5a787d198b386a Author: lijewski Date: Mon Apr 30 17:06:55 2012 -0700 Some simplification & cleanup after merging in new sum_boundary() stuff. Src/F_BaseLib/multifab_f.f90 commit a3e2b637256a80fd6ed403955c99667b6a8bbc87 Author: lijewski Date: Mon Apr 30 17:06:21 2012 -0700 New sumassoc stuff appears to be working. Src/F_BaseLib/layout.f90 commit c69ccd566d907ad45ae8ab50563aee616a30cc72 Author: Marc Day Date: Mon Apr 30 16:32:45 2012 -0700 Dang, wrong text, wrong place....might be better now. Tools/CMake/CCSEOptions.cmake commit 5a8660fbf8290aa326f515c06d05c9b70ccfdd96 Author: lijewski Date: Mon Apr 30 13:35:53 2012 -0700 Cleaned up some unused variable warnings. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit b45ddf2a6e2565dc73d31d0759143323373cd88c Merge: e2e7940e2 f1cadcf60 Author: lijewski Date: Mon Apr 30 13:23:06 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f1cadcf606a00218be2fc5f5e4b8c5645028f6ed Author: Marc Day Date: Mon Apr 30 13:20:25 2012 -0700 Fixup CMake files to deal with DEBUG=TRUE/FALSE via standard CMake variables BoxLib_Version.txt Tools/CMake/CCSEOptions.cmake commit e2e7940e2e6d27d6685eb964d20508464f40f01c Author: lijewski Date: Mon Apr 30 13:19:52 2012 -0700 Merged new boxassoc_build() call that also can build optimized sumassoc structures into [l]multifab_sum_boundary(). Src/F_BaseLib/multifab_f.f90 commit 35d93808257f7f14a77f590bc4c640d22823b31f Author: lijewski Date: Mon Apr 30 13:17:47 2012 -0700 Added sumassoc_build_innards(). This routine does all the calculations needed to minimize the number of MPI communication needed for a sum_boundary() call. It's called from boxassoc_build() when passed the appropriate flag. I haven't (yet) made a cache of these. Src/F_BaseLib/layout.f90 commit e3226a4eadeeafb861ff30c9ab203e6a52907b39 Author: lijewski Date: Mon Apr 30 12:07:07 2012 -0700 Split out the box intersection stuff in boxassoc_build() into boxassoc_build_innards() in anticipation of adding an option to boxassoc_build() to build the appropriate optimized MPI structure for sum_boundary(). Src/F_BaseLib/layout.f90 commit 24613584704add65e4c6b56fb099bdf5d3166f5f Author: ajnonaka Date: Fri Apr 27 16:18:34 2012 -0700 cover fig Docs/Introduction/varden1.eps.REMOVED.git-id Docs/Introduction/varden2.eps.REMOVED.git-id Docs/Introduction/varden3.eps.REMOVED.git-id Docs/Introduction/varden4.eps.REMOVED.git-id Docs/UsersGuide.tex commit 714888d5f2dec4f0f844e1eb77731e9ea0e7d71f Author: lijewski Date: Fri Apr 27 15:04:51 2012 -0700 Added lml_internal_sync_fancy to match mf_internal_sync_fancy. Not sure anyone currently used this, but ... Src/F_BaseLib/multifab_f.f90 commit a67d32cb59384022d64cb9b5711b2d64d2ea2dc5 Author: lijewski Date: Fri Apr 27 14:36:17 2012 -0700 Merged sum_d and logical_or into the sum_boudnary() routines. Made some internal routines private. Src/F_BaseLib/multifab_f.f90 commit 1193e457d384fa84e3da78d8a9bcc89d3c597fe2 Merge: df9fb35da 3d9015f3d Author: Marc Day Date: Fri Apr 27 09:53:40 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 3d9015f3d15b55278c1c1946ab34a88b2fb34c02 Merge: e7108b7f4 c0e9eaa48 Author: ajnonaka Date: Thu Apr 26 17:11:50 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e7108b7f4812a77788f124b0e9a2a39ef01094ed Author: ajnonaka Date: Thu Apr 26 16:59:24 2012 -0700 some User's Guide updates Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit c0e9eaa48be02edfb02d30dd73008ca7b8dce909 Merge: 37856ddd3 a8f367102 Author: lijewski Date: Thu Apr 26 15:53:09 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 37856ddd32b085181b33314a69545c50d576a709 Author: lijewski Date: Thu Apr 26 15:52:36 2012 -0700 Consolidated all the info for calculating CIC stuff into minimum number of required routines. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 70c16ebe6219bb84be38fde92827fb258d2680bf Author: lijewski Date: Thu Apr 26 14:18:33 2012 -0700 Some cleanup. Src/C_AMRLib/Particles.H commit b1cd50e703d77db569374ee0a22ca53081e4f70b Author: ajnonaka Date: Thu Apr 26 14:15:21 2012 -0700 comments Tutorials/HeatEquation_EX5_F/advance.f90 commit a8f367102aceeca41a2471fb3ab6196f6f695bd3 Author: ajnonaka Date: Thu Apr 26 13:40:35 2012 -0700 remove print statement Src/F_BaseLib/cluster_f.f90 commit a864f460260f560ea0c5fd6fb4f480aa1944bebf Author: lijewski Date: Thu Apr 26 13:21:03 2012 -0700 Use sum_boundary() and fill_boundary() to enforce a logical .or. on overlapping ghost & valid cells. Src/F_BaseLib/cluster_f.f90 commit 95a3a95385c57f41ace7671b4abf87dc28820832 Author: lijewski Date: Thu Apr 26 08:06:32 2012 -0700 Added lmultifab_sum_boundary(). It does a logical "or" of all ghost cells that overlay valid cells with those valid cells. Should be useful in error tagging. Src/F_BaseLib/multifab_f.f90 commit 7b3cb2e10196880cd3003c96268e389c7877e283 Author: lijewski Date: Thu Apr 26 07:55:32 2012 -0700 Mods to get to compile again. Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_main.f90 commit 011a73848e98f3dd3e46978c3e57eb69f81e6633 Author: ajnonaka Date: Thu Apr 26 06:02:31 2012 -0700 put WaveEquation examples back until I make a multivariable tutorial based on HeatEquation with all the bells and whistlesZ Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/Make.package Tutorials/WaveEquation_C/advance_2d.f90 Tutorials/WaveEquation_C/advance_3d.f90 Tutorials/WaveEquation_C/init_data_2d.f90 Tutorials/WaveEquation_C/init_data_3d.f90 Tutorials/WaveEquation_C/inputs_2d Tutorials/WaveEquation_C/inputs_3d Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp Tutorials/WaveEquation_F/GNUmakefile Tutorials/WaveEquation_F/GPackage.mak Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/inputs_2d Tutorials/WaveEquation_F/inputs_3d Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit b78bf8e84bbe376e93be3d6ae56e5d439821fd75 Merge: f6953a4ec a911c31ef Author: ajnonaka Date: Wed Apr 25 15:44:06 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f6953a4ec1de58ebb27dc7f6a90f143135f5f1a7 Author: ajnonaka Date: Wed Apr 25 15:42:56 2012 -0700 temporary band-aid to get proper nesting to work properly. You will lose information about buffered tagged cells that should have been passed to the valid regions of neighboring grids. fix for that coming tomorrow. Src/F_BaseLib/cluster_f.f90 commit a911c31ef75219c0d691273a25a71945e68636d2 Merge: 9796c0a84 d94f83a11 Author: lijewski Date: Wed Apr 25 13:51:27 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9796c0a84068b86d28dc66449cb2c90ea70888af Author: lijewski Date: Wed Apr 25 13:50:01 2012 -0700 Inlined Box::operator&=(Box), Box::operator&(Box) and Box::intersects(Box). This greatly speeds up some BoxArray operations. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit d94f83a110018f24ffe540d9b10f71e08863c6a8 Merge: 15e6cc618 71d767dcf Author: ajnonaka Date: Wed Apr 25 13:43:51 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 71d767dcffe8b00bdbce6e1bf53687685b1a8f9a Merge: e0c6ce933 950e03054 Author: lijewski Date: Wed Apr 25 13:38:51 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e0c6ce933f5cc7c6c60274d022924f1aa45e4aed Author: lijewski Date: Wed Apr 25 13:38:38 2012 -0700 Inlined some Box stuff. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 950e03054fe76d305e3ef1193c4752e1942ac520 Author: vince Date: Wed Apr 25 11:59:25 2012 -0700 added comments clarifying creating a distmap with an array. Src/C_BaseLib/DistributionMapping.H Tutorials/MultiFabTests/MultiFabReadWrite.cpp commit 3fbd7f0a429906ebe5077495772deb107fa0f397 Author: lijewski Date: Wed Apr 25 11:56:25 2012 -0700 Final fix to FineToCrse() and hence AssignDensity(). Problem was yet one more place where coarsening & refining don't quite work right when indices go negative. This looks to be the last bug in this code :-) Src/C_AMRLib/Particles.cpp commit 15e6cc618d9b2304a832b73a1bc62a15efba647e Author: ajnonaka Date: Wed Apr 25 11:06:09 2012 -0700 min_eff to 0.7 Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX5_F/inputs_3d commit 83eb0e866fae0087555b2313a2af357877f71d93 Author: ajnonaka Date: Wed Apr 25 10:54:46 2012 -0700 update docs Docs/AdvancedTopics/AdvancedTopics.tex commit 10b49ded0e906d91979b39d8edd71d839f7277f8 Author: ajnonaka Date: Wed Apr 25 10:27:15 2012 -0700 shake out some bugs in implicit example Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/inputs_2d Tutorials/HeatEquation_EX5_F/inputs_3d commit 501db84e6ee295c8ed2755331c305be3b3d45092 Author: ajnonaka Date: Wed Apr 25 09:43:27 2012 -0700 linear solver progres Tutorials/HeatEquation_EX5_F/advance.f90 commit df9fb35dab8497985c7e038e299a57bef967e948 Author: Marc Day Date: Wed Apr 25 09:21:29 2012 -0700 Add some robustness stuff in AmrData::FlushGrids, handling the case when it is called before any data is actually read Src/Extern/amrdata/AmrData.cpp commit eb6c9031e994c357fbe7faee2e0ec0ccaf6a6493 Author: ajnonaka Date: Wed Apr 25 09:20:23 2012 -0700 include ml_solve.f90 in F_MG/GPackage.mak Src/LinearSolvers/F_MG/GPackage.mak commit 012d3e6f3eccc6d1636fb3acae254ecf9e982a5a Author: Michael Zingale Date: Wed Apr 25 10:20:15 2012 -0400 add compiler version Tools/F_mk/comps/Linux_cray.mak commit b5fc2eb2a73ea94d820ba246d18a8a8fca4d942d Merge: 9e1e6ab3b c0b4292c3 Author: Michael Zingale Date: Wed Apr 25 10:13:09 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 9e1e6ab3bda9f099e86428cfff3f6318390b3536 Author: Michael Zingale Date: Wed Apr 25 10:12:54 2012 -0400 add support for compiler version # in output Tools/F_scripts/make_build_info commit e5d9222672dee201424745d1b7f04367315190c4 Author: Michael Zingale Date: Wed Apr 25 10:12:30 2012 -0400 add support for compiler version # in output Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/gfortran.mak commit c0b4292c3a2c7f1f7cdd2b99aefdbdde1cf32864 Merge: 445781fb5 4bae23b75 Author: ajnonaka Date: Tue Apr 24 16:58:58 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 445781fb5bd8068335a80db88989af442376f3f8 Author: ajnonaka Date: Tue Apr 24 16:58:39 2012 -0700 implicit example, just starting Tutorials/HeatEquation_EX5_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GPackage.mak Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/inputs_2d Tutorials/HeatEquation_EX5_F/inputs_3d Tutorials/HeatEquation_EX5_F/main.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 Tutorials/HeatEquation_EX5_F/write_plotfile.f90 commit 4bae23b75f98a641ee3bec5a053de0820a2b60bc Merge: c761f25d7 b2f84b6af Author: lijewski Date: Tue Apr 24 16:55:30 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b2f84b6af31f5ed60be4fdec94f9babcf33fd266 Merge: 5342efbee 608f1717f Author: vince Date: Tue Apr 24 16:08:52 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5342efbeebe098fa9ed370be7a6a8da19f29ccc7 Author: vince Date: Tue Apr 24 16:08:29 2012 -0700 fix for FlushGrids. Src/Extern/amrdata/AmrData.cpp commit c761f25d791e5bd6259bf21d1a9468a920f0aaac Author: lijewski Date: Tue Apr 24 15:33:36 2012 -0700 Make sure the most common case can be accessed quickly. Src/C_AMRLib/Particles.H commit 86ec6465d01bc9e43eb8af7c6057d140c2d009d7 Author: lijewski Date: Tue Apr 24 15:01:27 2012 -0700 Yet more cleanup. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 9f61cf3d6ad66a9203438b1b0fee5a11d926a924 Author: ajnonaka Date: Tue Apr 24 14:41:50 2012 -0700 remove local tag_boxes.f90 Tutorials/HeatEquation_EX4_F/tag_boxes.f90 commit 26dc4062e6a8c1c610feb39d412bd117dfa12816 Author: ajnonaka Date: Tue Apr 24 14:41:10 2012 -0700 modify initial condition so we can use the F_BaseLib version of tag_boxes.f90 Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Src/F_BaseLib/tag_boxes.f90 Tutorials/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 commit 64d94b9b9b1509709649aaa78f77204d681879fb Author: lijewski Date: Tue Apr 24 13:14:35 2012 -0700 Some cleanup. Src/C_AMRLib/Particles.H commit 608f1717f55942e45ec1844835ca35620810a477 Author: lijewski Date: Tue Apr 24 09:38:40 2012 -0700 An attempt to minimize excessive memory allocation/deallocation in AssignDensity. I'm allocating arrays in outer routines & passing'm into inner routines. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit b022e533994c64a2e30845629ebeab77d55c1ead Author: lijewski Date: Tue Apr 24 09:15:44 2012 -0700 When shifting periodically into the fine level, I was using the coarsened version of the fine shift. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit aafeef073d82b13abd749135a0e840263aeb454b Author: lijewski Date: Mon Apr 23 20:48:04 2012 -0700 Call the single level version of AssignDensity from the multi-level version if there's only one level. It's likely much faster. Src/C_AMRLib/Particles.H commit fbefac88376417722cf1225c4d7885f1dbf2b951 Author: lijewski Date: Mon Apr 23 15:29:46 2012 -0700 I'm going to push this stuff. I'm getting really close to having the various period special cases finished. I don't want to lose what I've got to date. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit f492708fc4b9be4fd1f7b98233b703dd7a03597e Author: lijewski Date: Mon Apr 23 14:55:43 2012 -0700 Dealt with the special case where the fine grids totally covers the coarse. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 3770a5621271f9fb06c53ea18ac441c75bb82350 Author: lijewski Date: Mon Apr 23 13:41:24 2012 -0700 More work on C-F periodic overlap. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 49a0da3ee63d10679574b47a280d5c0c489f2fb8 Merge: 03b9ce680 e8bb70380 Author: lijewski Date: Mon Apr 23 08:51:32 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e8bb70380afeae1ccb360d23af8d0146ac4786fa Author: lijewski Date: Mon Apr 23 08:50:15 2012 -0700 Simplify Make.mpi a tad to help someone's old version of make. Tools/C_mk/Make.mpi commit 03b9ce68097c5f73bea5f6af61e2efa351f13ecd Author: lijewski Date: Sun Apr 22 19:37:09 2012 -0700 Some changes I want to save; still not soup yet! Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit efc253283db70d480efce299387701e614d74608 Merge: a1ace350c bb8566fd4 Author: lijewski Date: Sun Apr 22 16:45:08 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a1ace350c3dfe765c6d62e5192b7f89b58d813a3 Author: lijewski Date: Fri Apr 20 16:26:32 2012 -0700 More progress on Fine->Crse periodic. The case when level 1 is fully refined works. Other cases not so much. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit bb8566fd42cf92265a0d683382fa1c4c8802cc78 Author: ajnonaka Date: Fri Apr 20 14:04:34 2012 -0700 update to point to new HeatEquation tutorials in Fortran and C++ Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/GettingStarted/hopper.run Docs/UsersGuide.tex commit d5c8ac9a8f8f0ee156ed1129a1a603d1a9b6711f Author: ajnonaka Date: Fri Apr 20 14:03:56 2012 -0700 WaveEquation tutorials are now replaced by HeatEquation Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/Make.package Tutorials/WaveEquation_C/advance_2d.f90 Tutorials/WaveEquation_C/advance_3d.f90 Tutorials/WaveEquation_C/init_data_2d.f90 Tutorials/WaveEquation_C/init_data_3d.f90 Tutorials/WaveEquation_C/inputs_2d Tutorials/WaveEquation_C/inputs_3d Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp Tutorials/WaveEquation_F/GNUmakefile Tutorials/WaveEquation_F/GPackage.mak Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/inputs_2d Tutorials/WaveEquation_F/inputs_3d Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit 7234f939976537172dfe2aab8875dab4d26c6d56 Author: lijewski Date: Fri Apr 20 13:58:02 2012 -0700 More work on periodic in AssignDensity(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 7454321eb3fd4364ccebb95b5d14393e24ba9fbd Author: ajnonaka Date: Fri Apr 20 13:35:54 2012 -0700 added geom.FillPeriodicBoundary. Now gives exactly same answer in 2D and 3D as fortran tutorial Tutorials/HeatEquation_EX1_C/main.cpp commit 14a1967e6b38417344582e40a9f12e12f45f0e68 Author: ajnonaka Date: Fri Apr 20 13:24:39 2012 -0700 index bug Tutorials/HeatEquation_EX1_C/advance_2d.f90 Tutorials/HeatEquation_EX1_C/advance_3d.f90 commit ee16e1cfeeb28f1b0d26618d3ec23d85c7e27d82 Author: ajnonaka Date: Fri Apr 20 12:45:52 2012 -0700 C version compiles and runs, but doesn't give correct answer yet Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_C/Make.package Tutorials/HeatEquation_EX1_C/advance_2d.f90 Tutorials/HeatEquation_EX1_C/advance_3d.f90 Tutorials/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/HeatEquation_EX1_C/inputs_2d Tutorials/HeatEquation_EX1_C/inputs_3d Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp commit 0a8df097fc0122aa48c286f7b440711ded0471f3 Merge: 09ab8ee9d 6d700f95a Author: ajnonaka Date: Thu Apr 19 20:51:31 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 09ab8ee9d5f68bb2f4819e1d3af12016b459632a Author: ajnonaka Date: Thu Apr 19 20:51:02 2012 -0700 note about new example Docs/AdvancedTopics/AdvancedTopics.tex commit 6d700f95a0e8d003ec7b0573b88be17523f9b335 Author: Ann Almgren Date: Thu Apr 19 15:22:25 2012 -0700 Set ng = nghost(uu) rather that using mgt%ng in calls to smoothers. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit 1dd52c89385d44074166d7bb00c26a96c3b44e11 Merge: 3b0279e41 677103d04 Author: lijewski Date: Thu Apr 19 13:29:23 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3b0279e41bb6b3822698735149db2d7c845cb68b Author: lijewski Date: Thu Apr 19 13:24:16 2012 -0700 Contains Ann's latest changes to finetocrse. This is possibly as best as we can do. Also moved the SumBoundary() and SumPeriodicBoundary() into own loop after ParticleBase::AssignDensityDoit(mf,data) call. Src/C_AMRLib/Particles.H commit 677103d04b9396b64f0945036b39bec17d181468 Author: ajnonaka Date: Thu Apr 19 13:12:46 2012 -0700 turn off OMP and MPI by default Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX2_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GNUmakefile commit 38b503b650fd8b7f3c27b6f398e71402a5530961 Merge: b94d7b8fc 9f9742792 Author: ajnonaka Date: Thu Apr 19 12:37:45 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit b94d7b8fcec472b7f59f7b5c4cdceb255a797e56 Author: ajnonaka Date: Thu Apr 19 12:37:11 2012 -0700 adaptive gridding works Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/regrid.f90 commit c8685984dbe249e2adabf81e6141ea71adfb4d49 Author: ajnonaka Date: Thu Apr 19 11:31:30 2012 -0700 regridding seems to work - still needs cleanup. other various multilevel cleanups Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/GPackage.mak Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/tag_boxes.f90 commit 9f97427925e1c0629886241b7f427a8b3f8196cd Merge: bcf9d2eb9 030fa6e89 Author: lijewski Date: Thu Apr 19 10:41:00 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bcf9d2eb9f3213a19ecfbbe9d8e7701b9eada7e6 Author: lijewski Date: Thu Apr 19 10:40:19 2012 -0700 More refinement to finetocrse. May be the best we can do for now. Still have to deal with fine grid on periodic boundary ... Src/C_AMRLib/Particles.H commit 030fa6e8970406a104281fb56ec79bf46db71bd0 Author: ajnonaka Date: Thu Apr 19 10:12:37 2012 -0700 clean up some parallelization and memory issues Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/WaveEquation_F/main.f90 commit d1113131ea28e11ad49fcedf15ad01a440d1c7c7 Author: ajnonaka Date: Wed Apr 18 16:50:08 2012 -0700 more AMR progress, updating older examples Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/tag_boxes.f90 commit c99b20ab34555c7feef4e85db4c2d162ddefb3fe Author: ajnonaka Date: Wed Apr 18 16:12:55 2012 -0700 using the 'max_levs' convention that the AMR example will inherit Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/main.f90 commit ab1353abb01f2e083620f8d9231e88ce9cff705e Merge: 423064b72 56e0bb908 Author: Ann Almgren Date: Wed Apr 18 15:29:43 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 423064b72553d5b5a6c95c424f66c123ce3a90b8 Author: Ann Almgren Date: Wed Apr 18 15:29:02 2012 -0700 New improved version of how particles assign their density at coarse-fine interfaces. This one works better at faces but still is "off" at edges and corners. It does not currently work for multiple fine grids. Src/C_AMRLib/Particles.H commit 56e0bb90843553304af2b213ba3941d3f1489fa5 Merge: 2373e62c2 9569f7e35 Author: lijewski Date: Wed Apr 18 15:17:54 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2373e62c2c47f6ad440c6e2d32f427b41de16921 Author: lijewski Date: Wed Apr 18 15:16:03 2012 -0700 Integrated FineToCrsePeriodic() into FineToCrse(). FineToCrse() now considers fine cells that are outside the fine domain and only considers them a FineToCrse boundary if that fine cell won't be periodically shifted into a valid fine region. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit bf3c4bc94e232d4f2fa798ba38bfcdda00728383 Author: lijewski Date: Wed Apr 18 13:56:45 2012 -0700 A little cleanup. Src/C_AMRLib/Particles.cpp commit f32fec308d4d872eb4b2793e3b9630715fb9cf3f Author: lijewski Date: Wed Apr 18 13:33:56 2012 -0700 Added FineToCrsePeriodic(). Need to integrated into AssignDensity(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 9569f7e3533bfad2515d73c543810a84a4616c34 Author: ajnonaka Date: Wed Apr 18 13:24:02 2012 -0700 minwidth is now the minimum length on a side for any newly created fine regions. before minwidth was applied to the blocking_factor-coarsed tagboxes logical multifab, so the min length on a side was minwidth*blocking_factor Src/F_BaseLib/cluster_f.f90 commit adaa696011e1a3a19a1298163b15c2c6027c0623 Author: ajnonaka Date: Wed Apr 18 11:02:16 2012 -0700 saving progress - lots of AMR work Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/tag_boxes.f90 commit b925b34ddde194d1bea9bf4329e39708cb3718fa Author: ajnonaka Date: Wed Apr 18 09:19:25 2012 -0700 AMR example Tutorials/HeatEquation_EX4_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GPackage.mak Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/tag_boxes.f90 Tutorials/HeatEquation_EX4_F/write_plotfile.f90 commit 51a13bf6c4347b48f7db00ae227d4c0841033bb2 Author: ajnonaka Date: Wed Apr 18 09:17:57 2012 -0700 tidying up Tutorials/HeatEquation_EX3_F/main.f90 commit 2747e8f95a043705b620bf22eb57cf17b6ec383c Author: ajnonaka Date: Wed Apr 18 09:01:08 2012 -0700 clean up tag_boxes, add comments Src/F_BaseLib/tag_boxes.f90 commit a93bb9d55337ab33717ba882d284b0e80aa0c747 Author: ajnonaka Date: Wed Apr 18 08:51:25 2012 -0700 comment Src/F_BaseLib/tag_boxes.f90 commit 3b66642d76a7360ffb1873bbdffeb24f5c40d086 Author: ajnonaka Date: Wed Apr 18 07:10:39 2012 -0700 comments in ml_layout.f90 Src/F_BaseLib/ml_layout.f90 commit 157a1e79b1792f6e74aaf60b1bf629064ced7b08 Author: ajnonaka Date: Tue Apr 17 20:01:09 2012 -0700 some cleanup of tutorials Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit a67ff7e58281650aac2082e1e8d45a0c9d98b816 Author: lijewski Date: Tue Apr 17 13:48:26 2012 -0700 More work on parallelization of AssignDensity(). Seems to work but could use more testing. Still have to do the special Fine->Crse periodic case. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 4512bcf75f7066cca01bed1d181a728f704292c9 Author: lijewski Date: Tue Apr 17 13:16:32 2012 -0700 Some work making new AssignDensity() work in parallel. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit d405ad7a3b5bd3c2e64eae4b6eaf11bfa9403788 Author: lijewski Date: Mon Apr 16 13:03:45 2012 -0700 Some cleanup. Removed all OpenMP references in multi-level AssignDensity(). Just doens't seem worth it to try & OpenMP. Src/C_AMRLib/Particles.H commit aede0f2fbb7524826cd64c3126e3d61d3ed663c5 Author: ajnonaka Date: Sun Apr 15 20:40:33 2012 -0700 tweak the tutorial example by moving initial Gaussian profile slighly off-center (greatly helps with examining the effects of non-periodic boundary conditions) Docs/AdvancedTopics/AdvancedTopics.tex Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/main.f90 commit 2b941e5cf757293b2ea0d68832a486441b5d6087 Author: lijewski Date: Fri Apr 13 13:56:36 2012 -0700 Factored some stuff in ParticleBase routines. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit f2c29cf257aa1450d5e425a1a4a4a8b85c89a88e Author: lijewski Date: Fri Apr 13 13:12:27 2012 -0700 Simplified FineToCrse(). Removed "some" ref_ratio==2 assumptions. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit f2e1d4de4d4365b9773c8586f4013987c3e7b097 Author: lijewski Date: Fri Apr 13 12:41:52 2012 -0700 Damn! I've had this correct for some time. I forgot that I changed the offset in init.cpp from .5 -> .49 for some previous debugging. You can't have uniform distribution if the particles aren't uniformly distributed. Src/C_AMRLib/Particles.H commit 831e77462f142e611051665d5ccdeb720c72ebd6 Author: lijewski Date: Fri Apr 13 10:07:05 2012 -0700 Didn't have my CrseFine fractions -> Fine correct. Src/C_AMRLib/Particles.H commit f7ce7f99b64f91119b34f076f72685bd27e1fe74 Author: lijewski Date: Fri Apr 13 09:16:08 2012 -0700 Some more debugging tests. Src/C_AMRLib/Particles.H commit de6f8c51627cc7efefff59951bd43709bcaa09d3 Author: Michael Zingale Date: Thu Apr 12 20:21:16 2012 -0400 add support for 3 plotfiles python_plotfile/contourcompare.py commit b577f1cafc0364f42eb6ebac6436cd9e1c237d33 Author: lijewski Date: Wed Apr 11 16:12:04 2012 -0700 I "think" I've come up with a way to calculate the fine cells and their respective fractions in the case when moving some mass from a coarse cell to a fine cell. I'm still don't appear to be getting constant density. More to do ... Src/C_AMRLib/Particles.H commit fe1fff7ab56c4e2521461983edf358df588dd84b Author: lijewski Date: Wed Apr 11 08:30:22 2012 -0700 I'm going to commit and push the new AssignDensity(). It isn't correct but it's close. The fine->crse stuff is OK (with the possible exception when coarse & fine overlap at a periodic boundary). It also doesn't work in parallel if you try with more than one level. I'll get it working in parallel after it's totally done. The sticking point is when we're at a coarse level and have some mass that wants to be placed on the fine level: how to calculate the cell indices & fractions for the fine level? Src/C_AMRLib/Particles.H commit 64ab809f1f933c287a9c8bfd77d770abb2fdc685 Author: lijewski Date: Tue Apr 10 16:02:46 2012 -0700 Crse->Fine is looking better. Still not quite right. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit ccec48a6e7020f0db1b8ac1903156e6b1e1d0ee5 Author: lijewski Date: Tue Apr 10 14:10:35 2012 -0700 I'm feeling pretty good about the Fine->Crse code. It's still serial but that can be fixed. The Crse->Fine still needs work. Src/C_AMRLib/Particles.H commit 807c3ecef1e224299d7b4d6041dde9e16db9ca08 Author: lijewski Date: Tue Apr 10 10:13:09 2012 -0700 The Fine->Crse stuff "might" be working in serial. Little hard to tell till the Crse->Fine is also working the the RH array in TestAdiabatic comes out looking uniform. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit f82bc644944dbe59b742be5a686f27cfa910b1c3 Merge: e79845aaa 5aa58215b Author: lijewski Date: Mon Apr 9 17:33:56 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e79845aaa7e051b33e4f2fc6044fefa86f0493a5 Author: lijewski Date: Mon Apr 9 11:15:15 2012 -0700 A little cleanup. Still more to do on AssignDensity(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 5aa58215b931bfdf34716e3e8d3ccfb2b8365eef Author: ajnonaka Date: Mon Apr 9 11:09:59 2012 -0700 a few more additions Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/UsersGuide.tex commit 4a363fb27a0dce43f3afd44d0dfbf9b73b7f6d2a Author: lijewski Date: Mon Apr 9 10:50:23 2012 -0700 CrseToFine() and FineToCrse() now use AssignDensityCoeffs(). which is now a bool[]. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 5325b53d78d83642707a288f36233144a121e4eb Author: lijewski Date: Mon Apr 9 09:32:25 2012 -0700 Removed AssignDensityDoit(). Implemented the single level & multi-level AssignDensity() separately. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 564ae4b627a8d741c5e21f27b50e96ec923c7a6a Author: lijewski Date: Sun Apr 8 10:28:30 2012 -0700 Added some more comments to direct my future work on Crse->Fine. Src/C_AMRLib/Particles.H commit ebb4b4675e78099e111c352d38129cf1f69d2fb4 Author: lijewski Date: Sun Apr 8 10:21:28 2012 -0700 Some work on Crse->Fine issue in AssignDensity. More to do. I've disable threading in AssignDeisntyDoit() for now. Once it's working I'll make sure threading works. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 12c3169541570c7430b6b20e1147d2d7d8ab9645 Author: lijewski Date: Sat Apr 7 19:05:23 2012 -0700 Integrated in AssignDensityCoeffs(). The Fine->Crse stuff looks good. Crse->Fine to go. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit e4e67c6e5e99b146106c8dc2145e540b3e4f19a7 Author: lijewski Date: Sat Apr 7 10:18:37 2012 -0700 Some work on AssignDensity() Fine-Crse issue. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 1c3d58788abb5d1cc0d4e29c2a94831528216872 Author: lijewski Date: Sat Apr 7 08:29:22 2012 -0700 Final (hopefully) tweak to FineToCrse(). Src/C_AMRLib/Particles.cpp commit 0daba532258f31f7ce9056d1e6c6109034584dc0 Author: lijewski Date: Sat Apr 7 08:26:55 2012 -0700 Refined FineToAdd(). Src/C_AMRLib/Particles.cpp commit ee6b14de0dbd69d10fb6bb2b7cad51bb73bd8be3 Author: ajnonaka Date: Fri Apr 6 21:21:28 2012 -0700 more User's Guide and Tutorial progress. In pretty good shape now. Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/Preface/Preface.tex Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX3_F/advance.f90 commit 6c38a98176f704873310d14e1b7679c6c1bc9f1f Author: ajnonaka Date: Fri Apr 6 16:55:29 2012 -0700 tutorial Docs/AdvancedTopics/AdvancedTopics.tex commit 5c933173a2d9422b060893f9781bb3ab5003bbba Author: ajnonaka Date: Fri Apr 6 16:39:14 2012 -0700 fix comments, get the multilevel example working by hooking into the F_MG restriction calls Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/main.f90 commit db271ecbab07654cefe9c64366e935967aeda919 Merge: c47493349 31f0af443 Author: lijewski Date: Fri Apr 6 15:52:59 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c47493349f33d68311c68a4ded7a95a67885f4b3 Author: lijewski Date: Fri Apr 6 15:50:44 2012 -0700 Added ParticleBase::FineToCoarse(). Needed by AssignDensityDoit(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 31f0af443154403362fb3b949554b7806eea93b1 Author: ajnonaka Date: Fri Apr 6 15:50:29 2012 -0700 forgot to add init_phi.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 commit 06eb0f2580756910787cd40d7cf8f61be4d94a7e Author: ajnonaka Date: Fri Apr 6 15:50:06 2012 -0700 this is as far as I can go before I move the restriction stuff into F_BaseLib Tutorials/HeatEquation_EX3_F/advance.f90 commit 5ddf5155a64c20d8ae93c6b2050c2d13c69287af Author: ajnonaka Date: Fri Apr 6 15:39:15 2012 -0700 first cut at multilevel extension of HeatEquation_EX2. This one uses ml_layouts and ml_boxarrays instead of just arrays of layouts and boxarrays Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GPackage.mak Tutorials/HeatEquation_EX3_F/README Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_data.f90 Tutorials/HeatEquation_EX3_F/initialize.f90 Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX3_F/make_fluxes.f90 Tutorials/HeatEquation_EX3_F/write_plotfile.f90 commit f5ac0c0af21e5d04cd41e9e02c5e1e369a19c95c Author: ajnonaka Date: Fri Apr 6 15:00:13 2012 -0700 destory the_bc_tower Tutorials/HeatEquation_EX2_F/main.f90 commit eed1ac4425038faf3037e566a575dad6bc6c16ed Author: ajnonaka Date: Fri Apr 6 14:20:31 2012 -0700 more Tutorial updates Docs/AdvancedTopics/AdvancedTopics.tex commit 258a3410790e2f670e4bf4638255395830ed9ae3 Author: ajnonaka Date: Fri Apr 6 13:38:07 2012 -0700 bugfix; the ncomp feature wasn't implemented in multifab_physbc.f90 Src/F_BaseLib/multifab_physbc.f90 commit 1d591e378a7fe6e0429a1e1aad26e46894f91667 Author: ajnonaka Date: Fri Apr 6 13:32:59 2012 -0700 pass in hi to physbc_2d/3d instead of computing it with fortran size() tricks within Src/F_BaseLib/multifab_physbc.f90 commit 8bd1c9aa46e59175ae50ed9895061aaff29c14f1 Author: ajnonaka Date: Fri Apr 6 10:09:34 2012 -0700 updated test problem description Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex commit 571b77670c84f57edae7b39a89aa8cfdcf356b30 Author: ajnonaka Date: Fri Apr 6 09:37:09 2012 -0700 3d version of boundary conditions. Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX2_F/advance.f90 commit b197bd0339798acba279bbbe00a4a67e6613dcb1 Author: ajnonaka Date: Thu Apr 5 22:22:44 2012 -0700 bug in 2d bc's Tutorials/HeatEquation_EX2_F/advance.f90 commit 00c8dd76c1210a3029d831c75164e5f0b6ebd03b Author: ajnonaka Date: Thu Apr 5 22:06:38 2012 -0700 spruced up the first two heat equation examples. the boundary condition example is finished, with options for a 'source' dirichlet wall, outflow (phi_n=0) and periodic Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/multifab_physbc.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/main.f90 commit 562d5155cb577d6c78cc44f801218b6d7f83f02f Author: ajnonaka Date: Thu Apr 5 19:22:33 2012 -0700 more bc example progress Src/F_BaseLib/define_bc_tower.f90 Tutorials/HeatEquation_EX2_F/inputs_2d Tutorials/HeatEquation_EX2_F/inputs_3d Tutorials/HeatEquation_EX2_F/main.f90 commit 208fc1bc8aaa325e54bf9b0a5261af02bfd79135 Author: ajnonaka Date: Thu Apr 5 18:13:41 2012 -0700 some documentation updates Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex commit 3b68a969007a93e47630408fb76cbc5d5b989cba Author: ajnonaka Date: Thu Apr 5 18:12:47 2012 -0700 start the HeatEquation_EX2_F boundary condition example by copying the EX1 example. Tutorials/HeatEquation_EX2_F/GNUmakefile Tutorials/HeatEquation_EX2_F/GPackage.mak Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/inputs_2d Tutorials/HeatEquation_EX2_F/inputs_3d Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX2_F/write_plotfile.f90 commit 093046f19000eddfc0e896592c68c405c7edb865 Author: ajnonaka Date: Thu Apr 5 18:11:50 2012 -0700 renname example Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GPackage.mak Tutorials/HeatEquation_EX3_F/README Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_data.f90 Tutorials/HeatEquation_EX3_F/initialize.f90 Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX3_F/make_fluxes.f90 Tutorials/HeatEquation_EX3_F/write_plotfile.f90 commit 7f34f8aaca449e3ba7ba76ae9175c79b55f5c8f6 Author: ajnonaka Date: Thu Apr 5 17:07:42 2012 -0700 first attempt at a generic boundary condition type Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/multifab_physbc.f90 commit 485309f0ea1487c3cb0cb41545674b84be7dfff4 Author: ajnonaka Date: Thu Apr 5 17:07:13 2012 -0700 don't need to include files already in F_BaseLib/GPackage.mak Tutorials/HeatEquation_F/GPackage.mak commit 0f1917ceed3f2596c5ef2bdfc1689109addbdb78 Author: ajnonaka Date: Thu Apr 5 15:00:56 2012 -0700 HeatEquation_F will use F_BaseLib boundary condition stuff Tutorials/HeatEquation_F/define_bc_tower.f90 Tutorials/HeatEquation_F/multifab_physbc.f90 commit 5a2614b56bb85644246973fc0cfcce9aa0217f0c Author: ajnonaka Date: Thu Apr 5 15:00:17 2012 -0700 f90sources += create_umac_grown.f90 f90sources += define_bc_tower.f90 f90sources += fillpatch.f90 f90sources += multifab_fill_ghost_cells.f90 f90sources += multifab_physbc_edgevel.f90 f90sources += multifab_physbc.f90 Src/F_BaseLib/GPackage.mak commit a02e95cf7f7a3ffbfe9d632fadab896fccb53fe6 Author: ajnonaka Date: Thu Apr 5 14:59:07 2012 -0700 add define_bc_tower and multifab_physbc to F_BaseLib. Still need to clean these up to be the 'simplest' case for use in HeatEquation tutorials. Now, the F_BaseLib/GPackage.make contains f90sources += create_umac_grown.f90 f90sources += define_bc_tower.f90 f90sources += fillpatch.f90 f90sources += multifab_fill_ghost_cells.f90 f90sources += multifab_physbc_edgevel.f90 f90sources += multifab_physbc.f90 so local codes won't have to Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/multifab_physbc.f90 commit d1b68f81c3d4ed3671e96fc83a5ffaace0ea6cb2 Author: lijewski Date: Thu Apr 5 14:13:31 2012 -0700 Little cleanup. Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Tutorials/HeatEquation_F/main.f90 commit d404721615f29e83cbcd12e4a1ee7e84e1227455 Merge: 52cc86f2b bbdcd3121 Author: Ann Almgren Date: Thu Apr 5 13:45:22 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 52cc86f2bc3772732b8bfeae1803110cbd398574 Author: Ann Almgren Date: Thu Apr 5 13:45:13 2012 -0700 Fix call to layout_build_ba. Src/LinearSolvers/F_MG/ml_solve.f90 commit bbdcd3121fa21ba847e6eb92dd744421c3cf0367 Author: ajnonaka Date: Thu Apr 5 13:36:13 2012 -0700 completely eliminate the string "setbc" from all files and filenames in the fBoxLib source and HeatEquation tutorial Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 Tutorials/HeatEquation_F/GPackage.mak Tutorials/HeatEquation_F/multifab_physbc.f90 Tutorials/HeatEquation_F/setbc.f90 commit a3fc8ca05ad5f9ff72513e7fe4f12a79920b9829 Author: ajnonaka Date: Wed Apr 4 15:38:47 2012 -0700 latest Docs/AdvancedTopics/AdvancedTopics.tex commit c779afa50c7e8a57fc19954f1bd54a2d49a26488 Author: ajnonaka Date: Wed Apr 4 15:38:23 2012 -0700 forgot to commit this Docs/AdvancedTopics/hopper_omp.run commit dc1c8d646e7eeb47d7f958ccdb7c4556e9bb3485 Author: ajnonaka Date: Wed Apr 4 13:52:15 2012 -0700 finished section on OMP and accompanying example code Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/GettingStarted/hopper.run Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit 584fa2ce051c6c6f56a4fba1f7287c96abe16999 Author: ajnonaka Date: Wed Apr 4 13:28:08 2012 -0700 code comments Tutorials/HeatEquation_EX1_F/advance.f90 commit 849ead71bd97802b5ad14bbb9182a82ccf1359b7 Author: ajnonaka Date: Wed Apr 4 13:26:57 2012 -0700 comments Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/main.f90 commit a1fde75049dcfc729e4b6bec07df582a293755f1 Author: ajnonaka Date: Wed Apr 4 12:47:24 2012 -0700 more progress on User's Guide Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex commit fc4b02eee2b3fb58bfe55bd15be5df78791be392 Author: ajnonaka Date: Wed Apr 4 12:46:54 2012 -0700 some cleanup of WaveEquation_F Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 commit 6a580d3d8ab0aa42aa0c322195d19fa9ae2ad0b5 Author: ajnonaka Date: Wed Apr 4 12:45:13 2012 -0700 simple OMP-enabled heat equation example Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX1_F/GPackage.mak Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX1_F/inputs_2d Tutorials/HeatEquation_EX1_F/inputs_3d Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX1_F/write_plotfile.f90 commit ce868bc0ff4f692dc6103a19279b19916e6aad56 Merge: e5a32dc2a cb07ca5f2 Author: ajnonaka Date: Wed Apr 4 10:55:44 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e5a32dc2a0f8d67304a1ad4d0667fad2ef68bbec Author: ajnonaka Date: Wed Apr 4 10:55:19 2012 -0700 rewriting advanced topics chapter Docs/AdvancedTopics/AdvancedTopics.tex Docs/UsersGuide.tex commit f3f535bc8ce22980df04ffcce58f3f801dcbecb6 Author: ajnonaka Date: Wed Apr 4 10:31:17 2012 -0700 update to the new layout_build_ba interface Tutorials/WaveEquation_F/main.f90 commit cb07ca5f2dddcd916bbde0e13601b710dbcce5bf Author: Ann Almgren Date: Wed Apr 4 10:28:39 2012 -0700 Fix the call to layout_build_ba. Tutorials/Exp_CNS_NoSpec/main.f90 commit 22a641c508e58092afe336ef552d21c314873e71 Merge: aab4a4265 968af7334 Author: Ann Almgren Date: Wed Apr 4 10:26:03 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit aab4a4265d98c48e6da96fbc5e19c393f790d2be Author: Ann Almgren Date: Wed Apr 4 10:25:34 2012 -0700 Add boxarray_bbox(ba) to the layout build calls where needed since the problem domain argument is no longer optional. Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 968af7334bdeb61bdbc0188dcebececffa26aa6a Author: lijewski Date: Wed Apr 4 10:12:31 2012 -0700 Destroy the_bc_tower and call layout_flush_copyassoc_cache() to keep valgrind happy. Tutorials/HeatEquation_F/main.f90 commit 234aff90a7a859cb6e4c9231e5e8c7853611f310 Merge: fc4559dea ce5f59650 Author: lijewski Date: Wed Apr 4 10:12:16 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ce5f596502b3beb41b27894fedd060f7bf16e23e Author: Ann Almgren Date: Wed Apr 4 10:09:06 2012 -0700 The problem domain argument (pd) is no longer optional in the call to layout_build_ba in layout.f90 Src/F_BaseLib/layout.f90 commit fc4559deabfc2087b5e7a9d927ba7e672fa41f00 Author: lijewski Date: Wed Apr 4 09:59:35 2012 -0700 OMP'd. Tutorials/HeatEquation_F/advance.f90 Tutorials/HeatEquation_F/init_data.f90 Tutorials/HeatEquation_F/make_fluxes.f90 commit bb7671044b3da03fc259ed0d624667a9f7cbd8cd Author: Ann Almgren Date: Wed Apr 4 09:15:48 2012 -0700 Add 3d inputs file. Tutorials/HeatEquation_F/inputs_3d commit 9e31c43313715aa078884d452689fac12f288264 Author: Ann Almgren Date: Wed Apr 4 09:15:24 2012 -0700 Get 3d version working. Tutorials/HeatEquation_F/GNUmakefile Tutorials/HeatEquation_F/init_data.f90 Tutorials/HeatEquation_F/make_fluxes.f90 commit f64374acac27226787aa7e064418212c30c0f6de Author: Ann Almgren Date: Wed Apr 4 08:02:14 2012 -0700 Don't let nlevs > 3 for now just because we haven't defined grids at the higher levels. Tutorials/HeatEquation_F/main.f90 commit 98a6ccca5184ded7a4f3637a983aa100880efe3c Author: Ann Almgren Date: Wed Apr 4 08:01:15 2012 -0700 Added README. Tutorials/HeatEquation_F/README commit 4575480fa0e8f974c42f11de7222cf35f9793dc8 Author: Ann Almgren Date: Wed Apr 4 07:57:50 2012 -0700 More cleanup... Tutorials/HeatEquation_F/define_bc_tower.f90 Tutorials/HeatEquation_F/main.f90 commit 3cca78aab416373b51cc935efb9544912f4ea2ab Author: Ann Almgren Date: Wed Apr 4 07:55:23 2012 -0700 Add more comments. Tutorials/HeatEquation_F/main.f90 commit 417f3d7c25513ed5206df2fd2c8264aa106bbc19 Author: Ann Almgren Date: Wed Apr 4 07:45:49 2012 -0700 This is a multilevel explicit solver for the heat equation using forward Euler. The boxes are currently hardwired in the main.f90 routine. Tutorials/HeatEquation_F/GNUmakefile Tutorials/HeatEquation_F/GPackage.mak Tutorials/HeatEquation_F/advance.f90 Tutorials/HeatEquation_F/define_bc_tower.f90 Tutorials/HeatEquation_F/init_data.f90 Tutorials/HeatEquation_F/initialize.f90 Tutorials/HeatEquation_F/inputs_2d Tutorials/HeatEquation_F/main.f90 Tutorials/HeatEquation_F/make_fluxes.f90 Tutorials/HeatEquation_F/multifab_physbc.f90 Tutorials/HeatEquation_F/setbc.f90 Tutorials/HeatEquation_F/write_plotfile.f90 commit 402ebd7f92adffbc52aec2d8855944151b8128de Author: Marc Day Date: Tue Apr 3 12:41:31 2012 -0700 What the heck...declare v1.0.0 BoxLib_Version.txt commit 113e2345baf3c866c0fcb6799fc62547fc9cda38 Author: lijewski Date: Thu Mar 29 15:51:34 2012 -0700 Changed := -> : in a couple places. Tools/C_mk/Make.defs commit daa0c6fc8d929a8f679b3cacfc0451c7d47af540 Author: Marc Day Date: Thu Mar 29 13:55:28 2012 -0700 Generalize refinement and derive functionality to allow user to build at runtime BoxLib_Version.txt Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit e4cfd5ac0836e190cba712ef2d12a19efd4c7c1e Author: Marc Day Date: Thu Mar 29 13:24:48 2012 -0700 Modify where data pulled in simpleg stencils to avoid creating inconsistent edge data Src/LinearSolvers/F_MG/cc_stencil.f90 commit d8ad93fbb73f1ecc3459afff1266ad010fe69bd9 Merge: 914f6f45c 2553af5cf Author: lijewski Date: Thu Mar 29 07:17:21 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 914f6f45c448e078d5a1bf915e26c871f86133b9 Author: lijewski Date: Thu Mar 29 07:16:48 2012 -0700 Fix from Manuel Cotelo. Src/C_BaseLib/FabArray.H commit 2553af5cf15c25d67595d87ed1716910945731ef Merge: 231c3334e 1db0382cf Author: vince Date: Wed Mar 28 10:38:03 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 231c3334ea69aafb29dc175128b013899ae93b38 Author: vince Date: Wed Mar 28 10:37:43 2012 -0700 added FillBoundary. Tutorials/MultiFabTests/MultiFabReadWrite.cpp commit 1db0382cfaf8d2ee8f164199fd111d49297161af Merge: 1810b0a16 e4f87bf00 Author: lijewski Date: Wed Mar 28 10:33:21 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1810b0a168fe4fa2ef4de3432df906c661f5f85a Author: lijewski Date: Wed Mar 28 10:32:41 2012 -0700 Mods requested by Donev. Tools/C_mk/Make.defs Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/gfortran.mak commit e4f87bf00458dd4051451571198ebd59cf5ab64d Author: vince Date: Tue Mar 27 17:55:18 2012 -0700 example to do multifab functions. Tutorials/MultiFabTests/GNUmakefile Tutorials/MultiFabTests/Make.package Tutorials/MultiFabTests/MultiFabReadWrite.cpp commit 244c544f592610dac2871d911424f722cfbffee9 Author: ajnonaka Date: Thu Mar 22 12:35:26 2012 -0700 mothra no longer overrides GNUmakefile to force Intel compilers Tools/F_mk/GMakeMPI.mak commit 672fec9496ff8f71ebd65925ec1df369edf48135 Author: Matthew Emmett Date: Thu Mar 22 14:04:10 2012 -0400 PyBoxLib: Tweak imports, add multifab.get_info method. Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/base.py Src/Python/pyboxlib/multifab.py commit aa03a399e863f279c36ebf053fe1662acbf4fab3 Author: Ann Almgren Date: Fri Mar 16 12:32:24 2012 -0700 Fix bug where RelaxType was called instead of RAPType in the Hypre stuff. Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp commit bd4400c5a83843e574a5c3432257f7d8d5253349 Author: Marc Day Date: Thu Mar 15 18:22:29 2012 -0700 Shoops....forgot the box transform for the derive source data. Src/C_AMRLib/AmrLevel.cpp commit d146b8b27bda387fd25afcda9b4151046507fa63 Author: Marc Day Date: Thu Mar 15 17:56:37 2012 -0700 Fix the derive function that does not use a Fortran function, specifically for the case that the source data needs to be larger than the derived data. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit bc352b4529ef566f38703b63ef768a678642100d Author: Michael Zingale Date: Thu Mar 15 19:02:32 2012 -0400 add functions to convert between the integer bc names to strings and vice-versa Src/F_BaseLib/bc.f90 commit cf045fe724d85b14cd782f9059079983d45d9c12 Merge: 50c58a493 f5dbbd078 Author: lijewski Date: Thu Mar 15 14:13:05 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 50c58a49317ebf3af13732e219139c05aacd388e Author: lijewski Date: Thu Mar 15 14:12:24 2012 -0700 When splitting grids we split on Z then Y then X. Then tends to be more efficient cache-wise than X -> Y-> Z. Src/C_AMRLib/Amr.cpp commit f5dbbd0782b0777503c2497e3e92e7b19f0f3bc1 Author: Marc Day Date: Thu Mar 15 13:19:32 2012 -0700 Make particle replication stuff dimension independent Src/C_AMRLib/Particles.H commit 49f9128d7e650c575b4b630c23d9abee620ed201 Author: Marc Day Date: Thu Mar 15 13:17:58 2012 -0700 Add define for particles used in some app codes Src/C_AMRLib/Make.package commit 9bf9a46693f57051fb199d6de728a49cbdaa133b Author: Michael Zingale Date: Wed Mar 14 13:52:30 2012 -0400 switch etags to ctags -e for TAGS to allow for options that support Fortran interfaces. Works great in emacs now. Tools/F_mk/GMakerules.mak commit ee85c651ff22a06e2018b7b2a2672dcb8265651a Merge: f18d8d42b 1e1c5058e Author: Michael Zingale Date: Wed Mar 14 13:37:52 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit f18d8d42bbc5102fd2305450c7921ad609ba3e3b Author: Michael Zingale Date: Wed Mar 14 13:37:22 2012 -0400 add support for Fortran interface blocks to the tags target Tools/F_mk/GMakerules.mak commit 25d3fb903cdca4aa1224d3e6840b263c7df30fdc Author: Ryan Orvedahl Date: Wed Mar 14 11:29:42 2012 -0400 Ryan's routines for plotting particle data on top of plotfile variables. The driver, plotparticles.py, makes a bunch of plots and movies. python_plotfile/plotparticles.py python_plotfile/plotsinglevar_parts.py commit 1e1c5058ee1f42554a6f70f895c3fdf17c39e77e Author: lijewski Date: Tue Mar 13 14:06:27 2012 -0700 Wrapped some output in mgt%verbose > 0. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 71010464d91021dd970cdcfefa4adf754f1a0245 Author: lijewski Date: Tue Mar 13 12:44:01 2012 -0700 Removed -mp and added -ip for Intel. Tools/C_mk/Make.defs commit 5850e132d0b3ca86ae5a302a0044dca0a2c5c3f1 Author: lijewski Date: Tue Mar 13 12:43:34 2012 -0700 Commented out some really old Intel Version 5 stuff. Src/C_BaseLib/winstd.H commit f66324129a05cea069c0241fd2604965d51e3ff6 Author: lijewski Date: Mon Mar 12 13:19:47 2012 -0700 Revert out some of my previous changes. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.H commit 761868adb4e12af370b1d97b4f4e0f19dc09a493 Author: ajnonaka Date: Fri Mar 9 10:24:23 2012 -0800 remove some antiquated comments and redundant BL_ASSERT statement Src/LinearSolvers/C_CellMG/LinOp.cpp commit 1ce175892a0217529048d063e8eba08f11abeb74 Author: lijewski Date: Wed Mar 7 12:56:34 2012 -0800 Use _OPENMP instead of BL_USE_OMP for wrapping #pragma omp lines. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxLib.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit cc461eedab71b4301d9b132827aff30233dcaea2 Author: lijewski Date: Wed Mar 7 12:55:33 2012 -0800 Fixed to not need/use LinOp::bndryData(BndryData&). Tests/LinearSolvers/C_CellMG/main.cpp commit 93c6dd4c7ec97deb98d9dfb0277eb5c6c75a7398 Author: Matthew Emmett Date: Wed Mar 7 13:27:41 2012 -0500 PyBoxLib: Use ctypes. Src/Python/GMakerules.mak Src/Python/GPackage.mak Src/Python/Makefile Src/Python/README Src/Python/mkpyfboxlib Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/base.py Src/Python/pyboxlib/boxarray.py Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/layout.py Src/Python/pyboxlib/multifab.py Src/Python/pyboxlib/pybl.py Src/Python/src/blobjects.f90 Src/Python/src/blobjects.py Src/Python/src/boxlib_numpy.c Src/Python/src/boxlib_numpy.f90 Src/Python/src/fboxlib.f90 Src/Python/test.py commit 028c142d4b6a11bff1d8aa2b4bb184daa4669dd7 Author: Ann Almgren Date: Fri Mar 2 13:58:08 2012 -0800 Add subroutine simple_2d_const to fill 2d stencils when the coefficients beta are constant (already existed in 3d) Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 commit d8448582742fa28651721dbdc9977eb938228242 Author: Ann Almgren Date: Fri Mar 2 13:38:57 2012 -0800 1) Fix the computation of fluxes on high edges when using a higher-order cell-centered stencil (change to cc_stencil_apply.f90) 2) Fix the computation of ghost cells between AMR levels when at an interior corner -- we need to first average the fine solution onto the coarse grid before using the coarse cells to interpolate, because the coarse cells under the fine grid can be used in constructing the slope in the coarse cell not under the fine grid. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 2ffa11eda56cd52d463a29d7f41942678dc58226 Author: Weiqun Zhang Date: Thu Mar 1 14:22:07 2012 -0800 Add REAME for the multigrid tutorial. Tutorials/MultiGrid_C/README commit 3a8c8a561fa91fdf62afb6d6402022ae6db6f70e Merge: 46b6efc88 83d9ccd6a Author: Weiqun Zhang Date: Wed Feb 29 16:38:30 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 83d9ccd6a4ccf2045b176c00fcb3230bb8dd72bb Author: lijewski Date: Wed Feb 29 12:58:24 2012 -0800 Commented out a couple warning messages. Src/C_BaseLib/FArrayBox.cpp commit 2a0ae8b2494bbb238f53e6bcfe6cd5819f138853 Author: Michael Zingale Date: Wed Feb 29 11:17:16 2012 -0500 get this compiling again python_plotfile/GNUmakefile commit 86799afeb8f4c9007d30c5d6d32092c644c5957c Author: Michael Zingale Date: Mon Feb 27 19:20:00 2012 -0500 add projection, eos, and incompressible tests. Also update to the new data_processing location Tools/C_util/regtests/Maestro-tests.ini commit a7f53f34f3b3d2160ace117b8d15e46fecf50e74 Author: Michael Zingale Date: Mon Feb 27 19:06:31 2012 -0500 more sensible (optional) fParallel location to get this to compile if you have a MAESTRO checkout at the same level as AmrPostprocessing GNUmakefile commit 78554fce22b0e9a8441ac55ba0e6f59041066190 Author: Ann Almgren Date: Fri Feb 24 13:10:20 2012 -0800 Fix the quadratic terms in subroutine FORT_CQINTERP in INTERP_2D.F. They were missing the 1/2 in front of phi_xx * dx^2 term. Src/C_AMRLib/INTERP_2D.F commit 8e2153069231b0ad5cd5ed152605228d241b2d70 Author: lijewski Date: Thu Feb 23 15:07:11 2012 -0800 BOXLIB_HOME default should be ../../.. not ../.. Tutorials/MultiGrid_C/GNUmakefile commit 8281538311c41fe6b9dac74ff891bd0678c38e1d Author: lijewski Date: Thu Feb 23 15:04:54 2012 -0800 Make the BndryData member a const reference instead of a concrete data member. This means that the BndryData object passed to the constructor had better not be destroyed before we use it. The "right" way to do this would be to pass a reference-counted pointer to a BndryData. I'll put that on my list ... Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.H commit 011daf8e344a6398bce506b6b3efe5a978cbcdbb Author: lijewski Date: Thu Feb 23 15:02:59 2012 -0800 Disallow some copy constructors and assignment operators. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp commit 5d75cb3ed633854d1b03f82848a0ca8bde73a630 Author: lijewski Date: Thu Feb 23 13:45:58 2012 -0800 Make copy constructor & assignment operator private. Src/C_BoundaryLib/FabSet.H commit fef565de395cf6dbaee9653e5f098821e01604f4 Author: lijewski Date: Thu Feb 23 13:29:38 2012 -0800 Use PArrayNoManage instead of PArrayManage to cut down on copy()ing. Tutorials/MultiGrid_C/main.cpp commit aeccb241ceaee211d8a3f7975dc607e28d3d41aa Author: Michael Zingale Date: Tue Feb 21 21:29:19 2012 -0500 add the ability to add a string to the compilation command -- useful for forcing the code to use alternate microphysics. Tools/C_util/regtests/testnew.py commit 46b6efc886be881bb5fcf2e4fcca98e6b4240c05 Merge: 54d1b37dd 439f2bde4 Author: Weiqun Zhang Date: Tue Feb 21 15:40:31 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 439f2bde4642e8efeaca0c771c2513c9381b843c Author: John Bell Date: Sat Feb 18 16:16:28 2012 -0800 added note about how to build Tutorials/Exp_CNS_NoSpec/README commit a286a3544f6860b4a7a83f212edb70b9a6626c80 Author: John Bell Date: Sat Feb 18 16:14:25 2012 -0800 added a README to the compact app Tutorials/Exp_CNS_NoSpec/README commit 44a90d052d479b5bc0791de7fa0b6e670a2570b2 Author: Ann Almgren Date: Fri Feb 17 16:25:10 2012 -0800 Convert fParallel/data_processing to AmrPostprocessing/F_Src. CASTRO_gravity/GNUmakefile CASTRO_gravity/fdustcollapse1d.f90 CASTRO_gravity/fdustcollapse2d.f90 CASTRO_gravity/fdustcollapse3d.f90 CASTRO_hydro/GNUmakefile CASTRO_hydro/fsedov1d.f90 CASTRO_hydro/fsedov2d_cart.f90 CASTRO_hydro/fsedov2d_cyl_in_cartcoords.f90 CASTRO_hydro/fsedov2d_cyl_in_cylcoords.f90 CASTRO_hydro/fsedov2d_sph_in_cylcoords.f90 CASTRO_hydro/fsedov3d_cyl.f90 CASTRO_hydro/fsedov3d_sph.f90 CASTRO_radiation/GNUmakefile CASTRO_radiation/fgaussianpulse.f90 CASTRO_radiation/flgt_frnt1d.f90 CASTRO_radiation/fradshock.f90 CASTRO_radiation/fradsource.f90 CASTRO_radiation/fradsphere.f90 CASTRO_radiation/frhdshocktube.f90 GNUmakefile MAESTRO_tests/GNUmakefile MAESTRO_tests/fgaussianpulse.f90 MAESTRO_tests/fmlcompare.f90 MAESTRO_tests/fmlconverge.f90 MAESTRO_tests/fnorm.f90 MAESTRO_wdconvect/GNUmakefile MAESTRO_wdconvect/feint.f90 MAESTRO_wdconvect/fthermo.f90 MAESTRO_wdconvect/fthermo_driver.py MAESTRO_wdconvect/fwdconvect.f90 MAESTRO_xrb/GNUmakefile MAESTRO_xrb/fad_excess.f90 MAESTRO_xrb/fbuoyancy.f90 MAESTRO_xrb/fconv_slopes.f90 MAESTRO_xrb/fspeciesmass.f90 Palette fIDLdump.f90 fIDLdump3d.f90 faverage.f90 fboxinfo.f90 fcompare.f90 fextract.f90 fextrema.f90 fsnapshot2d.f90 fsnapshot3d.f90 ftime.f90 fvarnames.f90 old_flame/GNUmakefile old_flame/fbubble_position.f90 old_flame/fbubble_position_3d.f90 old_flame/fcusp.f90 old_flame/fcylflame.f90 old_flame/fflamelength.f90 old_flame/finteg.f90 old_flame/fturbkin.f90 old_flame/fwidth.f90 python/README python/column_depth.py python/conv_slopes.py python/dumpparthistory.py python/eos_data.txt python/helmeos.py python/parseparticles.py python/test_helmeos.py python/test_parseparticles.py python/timestamp_00.REMOVED.git-id python/timestamp_02.REMOVED.git-id python_plotfile/GNUmakefile python_plotfile/contourcompare.py python_plotfile/fsnapshot.f90 python_plotfile/plotsinglevar.py tutorial/GNUmakefile tutorial/fspeciesmass2d.f90 tutorial/fwrite2d.f90 commit 891b9d855b4f2921f3afda0fc32805ccea299977 Author: Ann Almgren Date: Fri Feb 17 14:56:04 2012 -0800 Add new MultiFab norm0 function which takes a BoxArray. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 20936ac991c4944cf4501967b8f74f5ae09ee21a Author: Michael Zingale Date: Fri Feb 17 16:45:11 2012 -0500 make individual tests links off the main results page Tools/C_util/regtests/testnew.py commit 8eb0e27af6be8fb83a86044ba8facbb40c3faf0b Author: Marc Day Date: Wed Feb 15 16:11:27 2012 -0800 Remove -fast-math on GNU stuff due to vode finickyness Tools/C_mk/Make.defs commit 27b2501411fcbab30700143481e5cabf96925a9b Author: lijewski Date: Wed Feb 15 14:28:38 2012 -0800 Removed flags turning off exceptions for GNU. Either way it doesn't make much difference in run times. Added -ffast-math to the GNU optimization flags. This can make a sizeable difference in run times. This "can" break codes though. In particular, we don't have it on in the F_mk stuff as it breaks MAESTRO somehow. Tools/C_mk/Make.defs commit 54d1b37dda958d18a1d06b44c3a0a6c18cfe056d Author: Weiqun Zhang Date: Wed Feb 15 14:11:00 2012 -0800 Fix 3D inflow boundary for F90 nodal solver. Src/LinearSolvers/F_MG/nodal_divu.f90 commit bd6d4550a8ee8e82e47420f2bcea8a3812c83ea5 Author: lijewski Date: Wed Feb 15 14:01:46 2012 -0800 Use -O2 instead of -O3 with gfortran. The latter can sometimes be slower. Tools/C_mk/Make.defs commit 1f88d7568d96f73f081f1161c5cf9b2171c8f90e Author: lijewski Date: Wed Feb 15 12:47:27 2012 -0800 Don't output any plotfiles if plot_int <= 0. Tutorials/Exp_CNS_NoSpec/main.f90 commit 5dc37e889b3e255bf461d556c98dd5fb68dd3a0b Author: lijewski Date: Wed Feb 15 10:37:46 2012 -0800 Make calculation of courno in ctoprim() optional. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 6da56df15584c29bc9a3668616cb67962c77da1f Author: Weiqun Zhang Date: Tue Feb 14 16:01:50 2012 -0800 Fix bugs for 2D inflow boundary. 3D still needs to be fixed. Src/LinearSolvers/F_MG/nodal_divu.f90 commit cc578d03ddecf28f594da4d8ad9cbc9fc7ceb18d Author: lijewski Date: Tue Feb 14 15:53:05 2012 -0800 Fixed typo. Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit 0b65cf3afa6e0d7b8415c5a4c9028c8e25d31ac6 Author: lijewski Date: Tue Feb 14 15:52:12 2012 -0800 Made write_plotfile() more generic. Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit 043143705ecf16b7480c4651e2cdb985eb8c9205 Author: lijewski Date: Tue Feb 14 15:35:59 2012 -0800 Moved final output statement before boxlib_finalize(). Tutorials/Exp_CNS_NoSpec/main.f90 commit d1a4846494b9bc8d286714892905fd5bc0e5c236 Author: lijewski Date: Tue Feb 14 14:26:42 2012 -0800 Some code rearrangement. Tutorials/Exp_CNS_NoSpec/advance.f90 commit bce89d965d34ff22074b37740af8d522e4ed3ef2 Author: lijewski Date: Tue Feb 14 13:44:12 2012 -0800 New inputs file. Tutorials/Exp_CNS_NoSpec/inputs.jbb commit da5a874b06c1a0b87481ac6d7a0f904307b5f557 Author: lijewski Date: Tue Feb 14 13:43:54 2012 -0800 More like what JBB wanted. Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/inputs_3d commit a423817f00686214b6491406d760a3923271eb0d Author: lijewski Date: Tue Feb 14 13:26:18 2012 -0800 Replaced some divides with multiplies. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 20c0b584d55854572956cc8ecb3e84159c64c979 Author: lijewski Date: Tue Feb 14 13:03:45 2012 -0800 Some memory and performance improvements. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 6b49dc83fe140adb61f217e1216fb6fd2b5715dd Author: lijewski Date: Tue Feb 14 12:34:50 2012 -0800 Some cleanup. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 commit a382242b2862d72fd079020c097a7e002b34c9dd Merge: 2444664aa 6ccd79989 Author: lijewski Date: Tue Feb 14 11:12:14 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2444664aab53e7b2aa0452aa53b157f1a0fa24a7 Author: lijewski Date: Tue Feb 14 11:12:04 2012 -0800 OMP init_data Tutorials/Exp_CNS_NoSpec/init_data.f90 commit 6ccd79989133470578a0bedb21af6ad35e7a94cb Author: Michael Zingale Date: Tue Feb 14 13:49:29 2012 -0500 new main page format -- makes it easier to view many tests Tools/C_util/regtests/testnew.py commit a8f150f9f3a9852d48f0d474972d526351439cd4 Author: lijewski Date: Tue Feb 14 10:48:54 2012 -0800 Some OMP tweaking. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 2d3e59d0e1047dace9743d3b2aa3cd75bf8b8e17 Author: lijewski Date: Tue Feb 14 10:23:10 2012 -0800 OMP'd diffterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 commit 6089cc7622f01d38dc0f48281f9d6cb0719a24a8 Author: lijewski Date: Tue Feb 14 10:01:44 2012 -0800 OMP'd hypterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 commit c9b8fb01a568e9e06d3684d7c6984f335c08ef73 Author: lijewski Date: Mon Feb 13 21:23:05 2012 -0800 Some renaming and added newer namelist stuff to example inputs file. Tutorials/Exp_CNS_NoSpec/inputs_3d Tutorials/Exp_CNS_NoSpec/main.f90 commit a13ef3ec3d291361304297f4f1cab4ac46603b8b Author: lijewski Date: Mon Feb 13 20:58:08 2012 -0800 Now write out when outputing a plotfile. Add more things to the namelist so they can be set in an input file. Some more cleanup. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit 696b2c7de74b5cb6e4be44ddd091aa28ba917e0a Merge: 543c12467 d40620b11 Author: lijewski Date: Mon Feb 13 20:28:22 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 543c12467f4c4dba05932cad3bf827d387d448bc Author: lijewski Date: Mon Feb 13 20:27:52 2012 -0800 Fixed bug; now appears to be working. Did some cleanup as well. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/inputs_3d Tutorials/Exp_CNS_NoSpec/main.f90 commit 630493c829a6b6b29dadbe3a71bc1d1f5efa0ab6 Author: lijewski Date: Mon Feb 13 17:49:49 2012 -0800 Fixed bug in difflux(). Now calculate dt based on CFL/courno. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/main.f90 commit d40620b113a2c2abb5f71b970319799158a82f69 Merge: a09b0aeb6 71ecefda5 Author: Michael Zingale Date: Mon Feb 13 20:39:01 2012 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit a09b0aeb6ea8a47171401eaf47a2c6147b2abda3 Author: Michael Zingale Date: Mon Feb 13 20:38:40 2012 -0500 add compareFile parameter to tests to allow us to explicitly specify the file to be used in the comparison make sure that the buildDir is infact valid if all are compileTests, then don't worry about if the benchmark directory exists Tools/C_util/regtests/testnew.py commit 71ecefda5efba025de5be5777d588247a4f1a97b Author: lijewski Date: Mon Feb 13 16:53:50 2012 -0800 Getting closer to working code. Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit 045c4c197e3e8142bb30919833c48cbe58896f97 Author: lijewski Date: Mon Feb 13 16:29:09 2012 -0800 Added a couple more named constants. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 088c2810ba3402d383b46c7e0d536a41ea17e401 Author: lijewski Date: Mon Feb 13 16:18:56 2012 -0800 Now calling diffterm(). Using dummy values for ETA and ALAM. Still got to init data correctly as well. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 2b107f23005d1f5e7b579ec285f4de346076f10f Author: lijewski Date: Mon Feb 13 15:48:12 2012 -0800 Some work getting diffterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 commit c008a32063db8ef89004fe6dd2965de093feb185 Author: lijewski Date: Mon Feb 13 15:20:48 2012 -0800 Actually call ctoprim() & hypterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 commit cf14e49b4ac6653cebe4d1f9f5050c758ef9d7c4 Author: lijewski Date: Mon Feb 13 14:47:28 2012 -0800 Brought in ctoprim() and hypterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit a248aa18a770980a150cc02491ea6152f1680df3 Author: lijewski Date: Mon Feb 13 12:11:40 2012 -0800 Removed various flags used to turn off C++ exceptions. The various compilers on jaguarpf really want exceptions enabled. Shouldn't really effect performance. Tools/C_mk/Make.Linux commit 3b1ec9fe16dec95f4121c2141956292182b51021 Author: Marc Day Date: Fri Feb 10 20:45:11 2012 -0800 Virtualize a couple functions to support more generic control of plotfile and checkpoint output BoxLib_Version.txt Src/C_AMRLib/Amr.H Tools/C_scripts/gen_release_tarball commit 26f0f72eb9e8fc885f4fa0fd1e2e12a40dd93c1d Merge: 3d51f048d 7a4a6867d Author: Marc Day Date: Fri Feb 10 20:44:45 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 7a4a6867d63ef6258d320b4a2153b6897b47868a Author: lijewski Date: Fri Feb 10 16:02:04 2012 -0800 Some cleanup. Tutorials/Exp_CNS_NoSpec/advance.f90 commit abdbeddd62cd55ad47784a501e2f6df88e729fcb Author: lijewski Date: Fri Feb 10 16:01:49 2012 -0800 Plug a couple memory leaks. Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/WaveEquation_F/main.f90 commit 6ce0c23d7cdd17ecf7a7f88b551473b2b37a11d8 Author: lijewski Date: Fri Feb 10 15:26:35 2012 -0800 Some work on RK3 algorithm. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/main.f90 commit fa0215b730e735333cb82017e2b61a229ea39c2f Author: lijewski Date: Fri Feb 10 14:12:38 2012 -0800 A little more cleanup. Still just WaveEquation. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 commit 62c79d63654a10f06591e66a4eb6a538dc996335 Author: lijewski Date: Fri Feb 10 14:06:26 2012 -0800 A little cleanup. Tutorials/Exp_CNS_NoSpec/inputs_2d Tutorials/Exp_CNS_NoSpec/inputs_3d Tutorials/Exp_CNS_NoSpec/main.f90 commit dd839d6adaa81d39a809fe311ce09dac030f65b7 Author: lijewski Date: Fri Feb 10 13:38:49 2012 -0800 Just copied files from WaveEquation_F. Tutorials/Exp_CNS_NoSpec/GNUmakefile Tutorials/Exp_CNS_NoSpec/GPackage.mak Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/inputs_2d Tutorials/Exp_CNS_NoSpec/inputs_3d Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit f0d87b4b692ac1cbe97b448b8b9a3bd9a120f219 Author: lijewski Date: Fri Feb 10 09:03:54 2012 -0800 Some patches from Chris for Macs. Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 4531f6e08cd51b0681e891b7ab3b365b53ce90c1 Author: Ann Almgren Date: Fri Feb 10 08:26:27 2012 -0800 Put Mike's fixes in for gcc/g++. Tools/C_mk/Make.defs commit 573f5bd5e08b0b1d9a300ee91f2676c3ab7597d7 Author: Michael Zingale Date: Thu Feb 9 16:31:03 2012 -0500 add a sort to the test problem Tools/C_util/regtests/testnew.py commit df39ebc07be178479ec7da207ca1080b6b861e90 Author: Ann Almgren Date: Thu Feb 9 12:58:19 2012 -0800 The alpha term was incorrectly included in s_minion_cross_fill_2d and s_minion_cross_fill_3d Src/LinearSolvers/F_MG/cc_stencil.f90 commit 1a7b77957efd1ee4c7f5767a4a06c77bf560a7b9 Author: Michael Zingale Date: Wed Feb 8 20:02:30 2012 -0500 fix some typos Tools/F_scripts/write_probin.py commit c275e7e0515eb79b23595186214cf569aa4d0cd3 Author: Michael Zingale Date: Wed Feb 8 20:00:43 2012 -0500 make the problem names more unique. Eliminate docs Tools/C_util/regtests/gen_compile_test.sh commit 5af08d4d17797825a858b0012e102cfd3d9f7327 Author: lijewski Date: Wed Feb 8 09:14:26 2012 -0800 A little more generalization in support of Aleks. Tools/C_mk/Make.defs commit a6e5bf356db06c4c7b330853e74f85c2a3176e0c Merge: c3ae40bf9 547359a14 Author: Michael Zingale Date: Tue Feb 7 19:33:55 2012 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c3ae40bf9a4037115c6d672313c5194a63e732f2 Author: Michael Zingale Date: Tue Feb 7 19:33:11 2012 -0500 add a tool to automatically generate the compile test parameters for all problems with a GNUmakefile Tools/C_util/regtests/gen_compile_test.sh commit 547359a149520539d50dc8afb14adf9033c9b17d Author: Michael Zingale Date: Tue Feb 7 19:17:17 2012 -0500 add support for compile-only suites (no other parameters other than build directory are needed) fix the webTopDir checks (now makes sure there is a "/" minor output tweaks don't print cvs/git info on webpage if we ran with --no_update Tools/C_util/regtests/testnew.py commit e40d39953668c8f29750876d0dab1d61467c33f9 Author: lijewski Date: Tue Feb 7 13:07:24 2012 -0800 Some mods to enable Aleks to use "gfortran46" instead of gfortran. Tools/C_mk/Make.defs Tools/F_mk/GMakedefs.mak commit d45c5acc0a38408fab94c80edfd79bc80c94cc26 Author: lijewski Date: Tue Feb 7 13:06:23 2012 -0800 Use -O1 instead of -O when debugging. It compiles faster and gives better debug info inside gdb. Tools/F_mk/comps/gfortran.mak commit d544493b7d1aebaab5e2ab9cc34e7d1580a68c1e Author: lijewski Date: Tue Feb 7 10:05:24 2012 -0800 BOXLIB_HOME macro wasn't quite right. Tests/LinearSolvers/ComparisonTest/GNUmakefile commit f99af059784002311fde1e5d318ae82260540291 Merge: 9281a575b 64bee3d37 Author: Weiqun Zhang Date: Mon Feb 6 14:10:14 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9281a575baa662e6772f2fab744d9d669b89ff0d Author: Weiqun Zhang Date: Mon Feb 6 14:09:21 2012 -0800 OpenMP the sync residue subroutines. Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 64bee3d379a8ef546bd147e5573efd67c07dccc2 Author: Michael Zingale Date: Mon Feb 6 14:09:53 2012 -0500 add RT, update build directories to reflect new directory structure Tools/C_util/regtests/Maestro-tests.ini commit 102a70764c55bfce90b276dbb987c9bbd3655797 Author: Michael Zingale Date: Mon Feb 6 14:09:35 2012 -0500 if we fail to compile during a normal test, show the make output Tools/C_util/regtests/testnew.py commit 8b5b4869b86a1a551a001fa638963870618ad6fe Author: Ann Almgren Date: Sun Feb 5 16:38:27 2012 -0800 Define lo_inflow(:) and hi_inflow(:) instead of lo_inflow(3) and hi_inflow(3) in nodal_divu.f90/subroutine divu. Src/LinearSolvers/F_MG/nodal_divu.f90 commit ef22f6063771c22c26f7586c8801dc2a10bb75f8 Author: Weiqun Zhang Date: Thu Feb 2 17:59:22 2012 -0800 Support the case when fine grids touch inflow boundaries. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit dc87d9c4472e4b0ce55f44ee63ad23f6e266a0cb Author: Weiqun Zhang Date: Thu Feb 2 15:42:52 2012 -0800 Call bl_error if nonuniform grids are used in the F90 nodal solver. Src/LinearSolvers/F_MG/mg.f90 commit 424bb6c5d67e95ec4b9ede645b18156b36ac7189 Author: Weiqun Zhang Date: Thu Feb 2 13:41:17 2012 -0800 Pass velocity in ghost cells into the F90 nodal solver in order to support inflow boundary. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit c71123bb376b949bb0bd56a901122619a4855c0f Author: Weiqun Zhang Date: Wed Feb 1 17:00:03 2012 -0800 put subtract_divu_from_rh back Src/LinearSolvers/F_MG/nodal_divu.f90 commit 3aa4a44dbb49afa46247dcc26b1e64accdb59098 Author: Weiqun Zhang Date: Wed Feb 1 14:09:03 2012 -0800 Fix a bug in computing the new u in 3D nodal projection. The bug was due to confusing rho and sigma (which is 1/rho). Src/LinearSolvers/F_MG/nodal_newu.f90 commit 1dad7f7162d8e0de304498d62df0297d6e75a334 Author: Weiqun Zhang Date: Wed Feb 1 13:31:59 2012 -0800 Fix a bug in 3D nodal projection with the dense stencil. MG towers were used before they were built. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 51ff44fadce0339c75df0470eed5c559450ef8f7 Author: Weiqun Zhang Date: Wed Feb 1 12:50:39 2012 -0800 Fix a bug in 3D nodal projection Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/nodal_divu.f90 commit a23edb764e04c5a7871e0d7cf07a247c36bdbdd5 Merge: e0a50f35c 3145a47ed Author: Weiqun Zhang Date: Tue Jan 31 17:27:36 2012 -0800 Merge branch 'dev' commit 3145a47ed9d739691804fa3f767602671959f195 Author: Weiqun Zhang Date: Tue Jan 31 16:11:21 2012 -0800 3D support for have_divu Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit e0a50f35cd47a286be1b4e6d9be834000f879b77 Merge: 0cfb40e34 549c15363 Author: Michael Zingale Date: Tue Jan 31 19:01:04 2012 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 0cfb40e34cdfdfcbd0509083fa9ef250c7fd89e3 Author: Michael Zingale Date: Tue Jan 31 19:00:17 2012 -0500 remove -J and -I for nan -- the default Make.defs handles this now, and gfortran doesn't like it specified twice. Tools/C_mk/Make.Linux commit 549c15363858c97139f71f2da208b8455b5160c5 Author: Weiqun Zhang Date: Mon Jan 30 14:01:17 2012 -0800 Fix bugs for the cases when both fine and coarse levels touch physical boundaries. Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 3ecbd58fe31419ade98c400850a061c4ea82dbae Author: Weiqun Zhang Date: Fri Jan 27 16:18:57 2012 -0800 Fix a bug. 2D version of mgt_set_vold was used in 3D. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 1bf2bb10a0c2a9877e3d7dd7572a003f8a15de60 Author: Weiqun Zhang Date: Fri Jan 27 13:21:32 2012 -0800 Delete "call flush()" that was checked in accidentally. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 13bf0f77edbc8bb50c10d9be825c15baaf4b627d Merge: 1ef07bdff 9642b15d9 Author: Weiqun Zhang Date: Fri Jan 27 13:15:47 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9642b15d99d25cd0eff7b4b285bdfd0950c6e02b Merge: 04a35fe6d 002ce0d7f Author: vince Date: Fri Jan 27 13:12:27 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 04a35fe6de09752e76f8b0a89a2ed2960a3c253a Author: vince Date: Fri Jan 27 13:12:09 2012 -0800 set version string for fabs and multifabs. Src/Extern/amrdata/AmrData.cpp commit 1ef07bdffc42fe23a5835e71e8b63694905a5128 Author: Weiqun Zhang Date: Fri Jan 27 13:11:19 2012 -0800 Fix a bug in computing source at the interface due to passed rhs. Make bnorm = max(bnorm, tres0), otherwide we may have trouble if tres0 is too big. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 002ce0d7f2aca6c86cdaf0a1067d5c634d9168ab Author: lijewski Date: Fri Jan 27 12:52:10 2012 -0800 Added the ability to flush fortran output (unit=6). This can be used to help sync up C++ and Fortran output when debugging. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 7b2b3cfaad35ea373166dbbc6185e7f8a9975d53 Author: Weiqun Zhang Date: Thu Jan 26 13:49:50 2012 -0800 Add some comments Src/LinearSolvers/F_MG/nodal_divu.f90 commit 45dc997da4dc466cbaedbfb5150ce72502263d4a Author: Weiqun Zhang Date: Thu Jan 26 13:43:26 2012 -0800 clean up Src/LinearSolvers/F_MG/nodal_divu.f90 commit 8ac9b0018ae57bcc6e8567646a167a95b2e2fbcb Author: Weiqun Zhang Date: Wed Jan 25 17:51:13 2012 -0800 support have_divu Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 3d51f048d2dff9cf0aee76f165dfc4f5e8900c4a Merge: 9c1a93bbb 67d9dc7c7 Author: Marc Day Date: Wed Jan 25 16:38:01 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 9c1a93bbbb138c715d3db9b2b584440735a7b6d9 Author: Marc Day Date: Wed Jan 25 16:35:24 2012 -0800 Remove CMake hack suggested by one of the Amanzi folks CMakeLists.txt commit 67d9dc7c77f19f90f57ef37312d087c72b7b86dd Merge: 647a910dd a1b94f35e Author: Weiqun Zhang Date: Fri Jan 20 13:24:31 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 647a910dd7aebde3b8fee59b4312abaa0bb33671 Author: Weiqun Zhang Date: Fri Jan 20 13:23:38 2012 -0800 Fix a parallel bug Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit a1b94f35edd59d41030435f0d36e107b3e09e4d0 Merge: beefe3db1 6eb27e917 Author: Michael Zingale Date: Fri Jan 20 12:08:12 2012 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit beefe3db1de22c97460d2bcca86c689817730293 Author: Michael Zingale Date: Fri Jan 20 12:07:28 2012 -0500 on bender, override the default compilers by mpif90 and mpicxx to be the versions that are in the current path. Tools/F_mk/GMakeMPI.mak commit 6eb27e91727e2aaa129c210bb5a51db40f126825 Merge: 4c9dfd40c 83076388c Author: Weiqun Zhang Date: Thu Jan 19 17:17:14 2012 -0800 Merge branch 'dev' commit 83076388cf880d435a37a2dcba22e7f9dbc2bd36 Author: Weiqun Zhang Date: Thu Jan 19 17:10:50 2012 -0800 3D implemented for nodal sync residue. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 4c9dfd40c927af81b1e6a3d60fd2e75f9f2ab939 Author: vince Date: Thu Jan 19 17:00:14 2012 -0800 rle update pubtest 4 Tests/IOBenchmark/README commit f10d5b42793783423e909015e9f3b7ad4c488ad2 Author: vince Date: Thu Jan 19 16:46:28 2012 -0800 rle update pubtest 3 Tests/IOBenchmark/README commit 0fe7449d45e5fd768d50f138344e33a35915c13b Author: vince Date: Thu Jan 19 16:43:18 2012 -0800 rle update pubtest 2 Tests/IOBenchmark/README commit 71ad807b68035a4357dd5c32fdf444c51ab03437 Author: vince Date: Thu Jan 19 16:38:05 2012 -0800 rle update pubtest Tests/IOBenchmark/README commit 6e31a391a7af478946547057f78fce12e046cb29 Merge: 85360cee8 1f4cd361a Author: vince Date: Wed Jan 18 15:49:48 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 85360cee8ceb790c42f2ddde726842511713d284 Author: vince Date: Wed Jan 18 15:49:28 2012 -0800 rme update 3 Tests/IOBenchmark/README commit 1f4cd361a7b4ac5ca0e0fb60767020d186af48fe Merge: 32e65e812 c428c2aa2 Author: Weiqun Zhang Date: Wed Jan 18 15:34:42 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 32e65e812f2f7f78774bc460cdf0641764d04813 Author: Weiqun Zhang Date: Wed Jan 18 15:33:55 2012 -0800 Fix a few memory leaks. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit c428c2aa2a40c588c14a6fbab0b5c8b2e79fe2ef Author: vince Date: Wed Jan 18 11:19:14 2012 -0800 rme update 2 Tests/IOBenchmark/README commit a101b1817ef1bc8eb0e661936a95baa6c098adff Author: vince Date: Wed Jan 18 11:08:17 2012 -0800 rme update Tests/IOBenchmark/README commit f361fff44e719d6262f7146b716e0995b5db7dce Author: Michael Zingale Date: Tue Jan 17 15:56:48 2012 -0500 update inf for new F16 install Tools/F_mk/GMakeMPI.mak commit 07ae0bad2d7883618bf602c3e4c15f4f1e985530 Author: Weiqun Zhang Date: Fri Jan 13 15:51:52 2012 -0800 Allow stencil type be passed to MGT_Solver. MGT_Solver still reads mg.stencil_type. But the optional _stencil_type argument in the MGT_Solver constructor, if provided, will have higher priority. The reason for the modification is to make sure the MG solver and the nodal projection class in IAMR are consistent. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 4ee48fca13b59ea25e371061f0f869daecb2cbf7 Merge: 7b965b4ac da8422a6f Author: Weiqun Zhang Date: Fri Jan 13 14:26:40 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7b965b4ac4559bbf33460ca66f9de633a8200fc3 Merge: c65f06351 5cb61cff1 Author: Weiqun Zhang Date: Fri Jan 13 14:26:23 2012 -0800 Merge branch 'dev' commit 5cb61cff151b921361e2656b890851a5905fc607 Author: Weiqun Zhang Date: Fri Jan 13 14:23:16 2012 -0800 change the size of zero_rh from (nlevs) to (2:nlevs) because rh(1) was never used. Src/LinearSolvers/F_MG/ml_nd.f90 commit da8422a6f6c89555611b96300da21ce175fc7d9c Author: lijewski Date: Fri Jan 13 08:25:43 2012 -0800 Some cleanup. Tools/C_mk/Make.defs commit 5ad761c7076a770079bcf9e5dbdec97b6fe79354 Merge: 766de365b aa6f683b2 Author: lijewski Date: Thu Jan 12 21:03:39 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit aa6f683b2d49b65b6e790326ec89db11fe34a0d8 Merge: e2015b91a 78fcd0be1 Author: lijewski Date: Thu Jan 12 20:27:37 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 766de365b48f0d9159800820618bf30a83a904d7 Author: lijewski Date: Thu Jan 12 20:24:27 2012 -0800 Minor tweak to get .mod files in the right place on hopper. Tools/C_mk/Make.defs commit 78fcd0be1ad9d822bdb9aa7d153b72ed30393561 Merge: 12fec316e c65f06351 Author: Marc Day Date: Thu Jan 12 17:18:45 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 12fec316ec3feedfed4e0625262307317662020a Author: Marc Day Date: Thu Jan 12 17:18:29 2012 -0800 more 2D Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/main.cpp commit 8064cbb629db4fc9a02874f20ffc82199fb2e00b Author: Marc Day Date: Thu Jan 12 17:17:18 2012 -0800 switch mpi on hedorah Tools/C_mk/Make.mpi commit da553035ba9de29ed1716cba30f9ed0a3eda8e27 Author: Marc Day Date: Thu Jan 12 17:15:11 2012 -0800 Allow 2D in solver tutorial Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/RHS_2D.F commit e2015b91adaec57d38f9d772a78978599a33d5a1 Author: lijewski Date: Thu Jan 12 16:48:12 2012 -0800 Fix to GNU FC stuff to get .mod files written to the appropriate place on hopper. The problem was that the "-J" flag was being set on the FC and fC lines, which are overwritten on Cray computers with ftn. Solution was to move all those flags set together with the compiler into [fF]FLAGS. Tools/C_mk/Make.defs commit c65f0635170d2ccdaa79e0e889f17023b3b18eee Merge: e7148bb2f 2055d9cd2 Author: Weiqun Zhang Date: Wed Jan 11 16:58:12 2012 -0800 Merge branch 'dev' commit 2055d9cd2efd465f1390c76d24cfcae82f83702b Author: Weiqun Zhang Date: Wed Jan 11 16:54:59 2012 -0800 Change the way of getting sync resid from the MG solver for safety. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit e7148bb2fbf1bbd58d0fae19f34cba078d0034a5 Merge: 43a07818b f06e3eaaf Author: Weiqun Zhang Date: Wed Jan 11 15:35:28 2012 -0800 Merge branch 'dev' commit f06e3eaaf29ed3660e73bcaccb071b56d99bc6db Author: Weiqun Zhang Date: Wed Jan 11 15:32:01 2012 -0800 Fix a bug. The ghost cells of sync_resid should be set to zero. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 43a07818bffd0b34331f28385a7cd2bb57a050cb Merge: 8fd653aa2 0c9c990f9 Author: Weiqun Zhang Date: Wed Jan 11 11:00:41 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8fd653aa2478818b19080976740bc12b1391484e Author: Weiqun Zhang Date: Wed Jan 11 10:52:53 2012 -0800 Remove the hack in nodal smoother that try to match the C++ nodal solver. The 2D hack had a bug. Moreover, the old way is also problematic because the color (i.e., red or black) depends upon the layout of grids. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 0c9c990f904d7fae8a02a3cd7affa50bda7d768a Author: ajnonaka Date: Tue Jan 10 17:41:17 2012 -0800 boundary condition figures Docs/AdvancedTopics/bc_example1.eps Docs/AdvancedTopics/bc_example1.fig Docs/AdvancedTopics/bc_example2.eps Docs/AdvancedTopics/bc_example2.fig Docs/AdvancedTopics/bc_example3.eps Docs/AdvancedTopics/bc_example3.fig commit cde14fc3f6746b3325c44c3abea22337a259a664 Author: ajnonaka Date: Tue Jan 10 17:40:37 2012 -0800 starting a daunting documentation Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex commit 15d4aad1b6fc7ff3d0583c3042c8bd8376a3ab62 Author: ajnonaka Date: Tue Jan 10 16:35:45 2012 -0800 moving this Docs/GettingStarted/hopper.run commit 0706f6a50deb519a2207fa4464f870f7c4b1e6b8 Author: ajnonaka Date: Tue Jan 10 16:35:33 2012 -0800 moving this Docs/AdvancedTopics/hopper.run commit 9da7729692bd300e7fb2346cbbb36a4bae23c2db Merge: ac9795142 9e45d9488 Author: Weiqun Zhang Date: Tue Jan 10 12:50:28 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ac9795142089aed3eb623ad47276a92938938fc7 Author: Weiqun Zhang Date: Tue Jan 10 12:48:54 2012 -0800 cleanup Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 9e45d9488a5c250ad4cc381e02c95ac2d73b1b9d Author: ajnonaka Date: Mon Jan 9 17:40:42 2012 -0800 minor updates Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit 99ebd701c0bca8465ae1a98cd4cf4a193c6193d6 Author: Weiqun Zhang Date: Mon Jan 9 17:35:14 2012 -0800 It works for the simple problem now. Cleanup is needed. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 8c1609efeb54e066e019834f3cb0e54a61ebe2ad Author: Weiqun Zhang Date: Mon Jan 9 14:30:52 2012 -0800 Turn on do_diagnostics when mg.v >= 4. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 47e65e8337086a8a7889fb293cf787a0a7b910bd Author: Weiqun Zhang Date: Mon Jan 9 14:26:40 2012 -0800 Allow MGT_Solver change smoother. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 87cb5aea00f0da2484f8df4b2bd7200902c67820 Author: Weiqun Zhang Date: Mon Jan 9 13:59:18 2012 -0800 There are cases that err = ml_residual is zero while err = ml_cycle is not. Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 6ae218541e731fac4d451b7850f2c3b91f8713a8 Author: Michael Zingale Date: Sat Jan 7 17:09:52 2012 -0500 add bender Tools/F_mk/GMakeMPI.mak commit b52861c17cac9da9ce4954d03fe407c78e93e5d1 Merge: df5956911 78827113d Author: Michael Zingale Date: Sat Jan 7 15:43:38 2012 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit df595691115874800870972f1b3c684700c8874f Author: Michael Zingale Date: Sat Jan 7 15:41:36 2012 -0500 update with separate web directory Tools/C_util/regtests/Maestro-tests.ini commit 78827113d0b5ebb97da817d3c86a12c718bff8ac Author: Ann Almgren Date: Fri Jan 6 14:46:15 2012 -0800 1) Fix the mini_cycle routine which is used only for factor 4 refinement between AMR levels. 2) Adjust the print statements which are used for verbosity > 3 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit b5586b6b66a9369d8c0b3ebcbe98c9f20f26e158 Author: Ann Almgren Date: Fri Jan 6 13:22:13 2012 -0800 Modify how we set do_diag so that it matches how it is set in the F_MG stuff; i.e. if verbosity >= 4 then do_diag = 1 (before it was hard-wired to 0) Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 52850887c98c011458afa12c2c9d5349b5d84e82 Merge: 8053a2fd7 ac3326c31 Author: Weiqun Zhang Date: Thu Jan 5 17:21:17 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8053a2fd79e7a16d6a3cd715b4ee1d59e92944f8 Author: Weiqun Zhang Date: Thu Jan 5 17:20:01 2012 -0800 Fixed a bug. one_sided_ss should be built with stencil=.true. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit ac3326c310457ea24fcc0f0455614db03d59e4c7 Author: vince Date: Thu Jan 5 16:10:10 2012 -0800 added rodan. Tools/C_mk/Make.mpi commit 48b8c80053cb4a2e18d68d430025373ea9c2a3d4 Merge: 7927830f1 98b28c80e Author: lijewski Date: Wed Jan 4 14:07:59 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 7927830f195c8e365749a621684859e99f17b95d Author: lijewski Date: Wed Jan 4 14:07:41 2012 -0800 GNUmakefile for use with DUMPI trace package on hopper. Tests/LinearSolvers/C_CellMG/GNUmakefile.dumpi commit 98b28c80e26c927517c7f57f79c3064121f77c1b Author: Marc Day Date: Wed Jan 4 13:52:42 2012 -0500 Add mpi stuff for LENS at ORNL Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 79daab5aa421244e930fd5f5c1daec5769d849fb Author: Ann Almgren Date: Tue Jan 3 14:42:36 2012 -0800 Change verbosity test in Amr.cpp to verbose>0 instead of verbose>1 when use_efficient_regrid=1. Src/C_AMRLib/Amr.cpp commit 744d0d069a9c577be423028d48136af860aceb4d Author: Ann Almgren Date: Tue Jan 3 13:13:16 2012 -0800 Add use_efficient_regrid flag which allows us to not recreate existing AmrLevels when the regridding process does not change the boxArray. Src/C_AMRLib/Amr.cpp commit b8bd868a12e2732cda1bee75aa750c5568493e1a Author: Matthew Emmett Date: Sat Dec 31 21:10:30 2011 -0500 PyBoxLib: Add "read" and "copy" methods to multifab class. Src/Python/pyboxlib/base.py Src/Python/pyboxlib/multifab.py Src/Python/src/fboxlib.f90 Src/Python/test.py commit 3b4caaa07e5a6b2abd92c1c33731a84fb0758ec1 Author: Matthew Emmett Date: Sat Dec 31 01:37:28 2011 -0500 PyBoxLib: Add "write" method to multifab class. Src/Python/pyboxlib/multifab.py Src/Python/src/fboxlib.f90 commit 6aa39f19ca4cd5ab0faa717b364691853d7796ff Author: Matthew Emmett Date: Fri Dec 30 23:44:29 2011 -0500 PyBoxLib: Add "nboxes" and "local_boxes" methods to layout class. Src/Python/GMakerules.mak Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/layout.py Src/Python/pyboxlib/multifab.py Src/Python/src/fboxlib.f90 commit f00a7a911c0c315f08a0c44b955d4e0a5b85bd9c Merge: c2f55abf4 1f50b4c57 Author: Ann Almgren Date: Thu Dec 29 12:26:40 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c2f55abf4674b3e150d43a8bf86d462924175996 Author: Ann Almgren Date: Thu Dec 29 12:26:04 2011 -0800 Fix the way we set dt_level in Amr.cpp when we restart with max_level > previous max_level and no subcycling. Src/C_AMRLib/Amr.cpp commit 1f50b4c57b25d64a401b0fedcd684ae38f7a9584 Author: lijewski Date: Mon Dec 26 09:51:18 2011 -0800 Added code for cims.nye.edu for Aleks. Tools/C_mk/Make.mpi commit 57596441009f9deb410800a05c988edfdbbb8c9b Author: Ann Almgren Date: Sun Dec 25 17:47:34 2011 -0800 Remove unused variable in Particles.H. Src/C_AMRLib/Particles.H commit cc966bb833dfb310f97e7609fc3d4671a4f7a7be Author: Weiqun Zhang Date: Thu Dec 22 11:10:12 2011 -0800 work in progress Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 978d1bc738472fe6775332bd8e157e243e1815dc Merge: e3529e7d8 a414c71a0 Author: Ann Almgren Date: Wed Dec 21 08:49:30 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e3529e7d8842f07509055bb3c14cc8f6f259f016 Author: Ann Almgren Date: Wed Dec 21 08:49:10 2011 -0800 Fix defaults for NReaders and NRedist. Src/C_AMRLib/Particles.H commit a414c71a075f6c1a6df77cf1b15a66dc4ce1e501 Author: ajnonaka Date: Tue Dec 20 17:41:45 2011 -0800 staggered grid convergence tester complete Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp commit 4874e94f8e2f92f2702755141b08a2d0d164e796 Author: ajnonaka Date: Tue Dec 20 16:16:17 2011 -0800 good progress on the staggered grid convergence utility. works now for x-direction, need to generalize to all directions and ref_ratios Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/GNUmakefile commit 538bb7c00898b211cfc10572009fe66ee407b97c Author: ajnonaka Date: Tue Dec 20 09:50:28 2011 -0800 fix comments, check in new template for staggered grid convergence testingZ Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp commit b64b15ee5443dc6e8be514f12bd17a7d3ab41bee Author: ajnonaka Date: Mon Dec 19 12:20:33 2011 -0800 clean this up Tools/C_util/Convergence/GNUmakefile commit 2f9eccc8cc25a9383d9d8f54f91de5a4fe39d3e6 Author: lijewski Date: Thu Dec 15 09:12:51 2011 -0800 Added a critical section around the std::cout call in Reset() just to be safe. Src/C_AMRLib/Particles.cpp commit 428168ca7f1fa4bef9e5449aa3b90a98c93c6b72 Author: lijewski Date: Wed Dec 14 22:14:26 2011 -0800 Added a critical section around that part of intersections() that builds the hash table. Src/C_BaseLib/BoxArray.cpp commit 27ac052933629a9996c41388a69000e7204a8bc7 Author: lijewski Date: Wed Dec 14 13:15:09 2011 -0800 More mods for Gunther. Src/C_BaseLib/GNUmakefile commit 314c7d96d17e102cb68721fce1257220bdafc97d Merge: 45f62aa0d edc86555f Author: Michael Zingale Date: Mon Dec 12 18:52:24 2011 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 45f62aa0db528f9cdf20cafb85e03c60e0954194 Author: Michael Zingale Date: Mon Dec 12 18:51:46 2011 -0500 fix cray path Tools/F_mk/GMakedefs.mak commit edc86555f7912c46cfe664cbd7dc56d69b6b2952 Author: Ann Almgren Date: Mon Dec 12 12:46:49 2011 -0800 Add domlo and domhi to interface for ErrorFunc2. Src/C_AMRLib/ErrorList.H commit 9345b7bf52ed19df7ec1ff0c87bc0f4d0d44d0bc Author: Matthew Emmett Date: Mon Dec 12 12:01:27 2011 -0500 PyBoxLib: Add "interleave" flag to multifab create method. This allows PyBoxLib to create interleaved FABs, which are indexed according to (c,i,j,k) instead of (i,j,k,c). Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/multifab.py Src/Python/src/boxlib_numpy.c Src/Python/src/boxlib_numpy.f90 Src/Python/src/fboxlib.f90 commit 2fc342ef2d7f4dfb30541e0ad7a91170b4d1a062 Author: Weiqun Zhang Date: Fri Dec 9 18:41:33 2011 -0800 Add a couple of functions to MGT_Solver. It now gets a cell center mask from Projection. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit f6d28f76507ae7c1eb35832f00d3fa059d32dd8e Author: lijewski Date: Fri Dec 9 16:36:59 2011 -0800 Inlined some one liners. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 195c52e5dd2b2946d9c76d6d521314ec63a74457 Merge: 56dd11c5a ed8901097 Author: lijewski Date: Fri Dec 9 15:37:54 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 56dd11c5ade2a36a629df28798c4f22b9002578e Author: lijewski Date: Fri Dec 9 15:37:37 2011 -0800 Mods requested by Gunther for VisIt. Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package commit ed8901097e1d705124bcc65ffaa817a7dc26078a Merge: 3a644c9ad d2b905afb Author: Weiqun Zhang Date: Thu Dec 8 17:25:36 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3a644c9ad10752f1385a624de3b4b3f2da3ab1f4 Author: Weiqun Zhang Date: Thu Dec 8 17:25:09 2011 -0800 undo change in .gitignore .gitignore commit 6e2da55db30729823d5180c33050b1ff09161185 Author: Weiqun Zhang Date: Thu Dec 8 17:22:06 2011 -0800 If both rhs and v are provided, the nodal solver will use rhs + div v as RHS. If only v is provided, it will use div v as RHS, as before. .gitignore Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit d2b905afbcd2460018d9687633d6da799e1e242c Author: Ann Almgren Date: Thu Dec 8 14:56:47 2011 -0800 Remove defined-but-unused "gridloc" Src/C_AMRLib/Particles.H commit d9197576fbaeecf8400e9ee6766fb4d2da8f1f68 Merge: e11cbc6fe af0876fa7 Author: Ann Almgren Date: Thu Dec 8 14:12:35 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e11cbc6fe63a18d1b502b3016e90595c851c6d2a Author: Ann Almgren Date: Thu Dec 8 14:12:07 2011 -0800 We do need to call post_regrid from level 0 up, not level "start", after all. Src/C_AMRLib/Amr.cpp commit af0876fa787b95a2d0eef1cdd8007b45171f498b Merge: 21074f94f c3dc0c3d2 Author: Weiqun Zhang Date: Thu Dec 8 13:32:58 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 21074f94ffcfd7cc2be5b33c974effda42c63940 Author: Weiqun Zhang Date: Thu Dec 8 13:32:53 2011 -0800 Fix a typo/bug when BL_FORT_USE_UPPERCASE Src/LinearSolvers/F_MG/mg_cpp_f.h commit c3dc0c3d2338f55aa939540d64d477db7fd7c6ae Merge: 446b54871 debfc4047 Author: Ann Almgren Date: Thu Dec 8 13:11:35 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 446b5487162292f4017feaf949bfb562ff415f4a Author: Ann Almgren Date: Thu Dec 8 13:10:55 2011 -0800 Only call post_regrid on the levels where the grids have actually changed; previously it was called from level 0 up, even though lbase may have been higher. Src/C_AMRLib/Amr.cpp commit 2c8c6c573b4fb32ddd33fa4849ed8a0cc0bd86b7 Author: Ann Almgren Date: Thu Dec 8 13:10:05 2011 -0800 Create new interface for F90 solvers from C++ that just sets the coefficients to be -1 off-diagonal and alpha = 0; this process now avoids making a bunch of extra arrays which just carried constant values. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit debfc40474e90de4bdbc8a45252078a9e2e69ae1 Author: Michael Zingale Date: Wed Dec 7 20:21:39 2011 -0500 pretty it up some more Tools/C_util/regtests/testnew.py commit adcf1302d5321b160cfe9fad829345475d1e1e7e Merge: c6853f05d 3fcf8a6ac Author: Michael Zingale Date: Wed Dec 7 15:41:41 2011 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c6853f05dbead68bdc9d8130d9c4f3dfeb1981a0 Author: Michael Zingale Date: Wed Dec 7 15:40:53 2011 -0500 allow for the web directory to be specified independently also update the CSS some Tools/C_util/regtests/testnew.py commit 3fcf8a6ac5aa0ee51d99a4e396685b44ce0009f7 Merge: 75a89a0f3 9d5b3e8fb Author: Marc Day Date: Wed Dec 7 00:34:40 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 75a89a0f3f5faef6e4f75f26dd15414a5f1c4655 Author: Marc Day Date: Wed Dec 7 00:34:03 2011 -0800 Combine all calls to setPhysBoundaryVals in FillPatch, allowing one to intercept the default behavior of calling a static to fill bcs Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Tools/C_scripts/gen_release_tarball commit 9d5b3e8fb19750d6e2686e94247f8c0acadccc2d Author: Ann Almgren Date: Tue Dec 6 10:12:44 2011 -0800 Change default verbosity of CGSolver.cpp from 1 to 0. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 8cdac197c875314c73fa18ba495e893c9bc42f0b Author: Ann Almgren Date: Tue Dec 6 10:11:31 2011 -0800 Need to fix NRedist default. Src/C_AMRLib/Particles.H commit 9d1641a1eca4af1f3f01e86a961dc7fa96a359a5 Merge: ff84d1fdb 2bedf7c5a Author: Weiqun Zhang Date: Mon Dec 5 14:42:31 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2bedf7c5a0874292c777e6959d6697e59a20e675 Merge: a9aaaa716 a8e0a3026 Author: ajnonaka Date: Mon Dec 5 14:41:57 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a9aaaa716f48e15809dcecaef3998f6067828536 Author: ajnonaka Date: Mon Dec 5 14:41:39 2011 -0800 back out of some of Ann's solvability changes Src/LinearSolvers/F_MG/ml_cc.f90 commit ff84d1fdb32972da7416e18033fbc1f925d5b1b6 Author: Weiqun Zhang Date: Mon Dec 5 14:32:48 2011 -0800 Fix a bug in deallocating multifabs for the nodal solver with the dense stencil. The one_sided_ss multifab is not allocated in that case. The communication between MGT_Solver and the underlying F90 solver is changed so that the multifabs in the MGT_Solver can have an arbitrary number of components. This saves memory because we do not have to copy the state data into the MGT solver. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit a8e0a3026809eda6b295f1672ffc9844fc6f2e34 Merge: 9b5b069d5 c26d20408 Author: Weiqun Zhang Date: Mon Dec 5 14:31:04 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9b5b069d5679c06800eae4581bafde2cb2c9d784 Author: Weiqun Zhang Date: Mon Dec 5 14:28:40 2011 -0800 Fine tune the setup of Hypre AMG solver according to the recommendation of Ulrike Meier. Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp commit c26d20408b87fdcb2514e751a62489861eb0fd86 Author: lijewski Date: Mon Dec 5 13:15:45 2011 -0800 Shut up a compiler warning about a possibly unset variable. Src/C_AMRLib/Particles.H commit 8bc2c0084d587feb0dab80d8a024c794cd8d2356 Merge: e0876e378 cc2709bb7 Author: Marc Day Date: Fri Dec 2 10:11:02 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e0876e378bbb934180e75271c072e30dea8805e3 Merge: 87fcbfc35 021dd8ad2 Author: Marc Day Date: Fri Dec 2 10:08:28 2011 -0800 Merge branch 'master' of /home/marc/src/CCSE/tmp/../BoxLib commit 021dd8ad2243818051e25e2a904abc82801f330d Author: Marc Day Date: Fri Dec 2 10:06:46 2011 -0800 Other part of rename Tools/C_scripts/gen_release_tarball.txt commit ca2926d21274fa994f1efe2959cdaff3ae8bd965 Author: Marc Day Date: Fri Dec 2 10:06:07 2011 -0800 Make tarball notes into a script Tools/C_scripts/gen_release_tarball commit 87fcbfc359d44d6090d339f916ac461238f7bab5 Author: Marc Day Date: Fri Dec 2 10:01:56 2011 -0800 cmake fixes due to Ben Andre CMakeLists.txt Tools/CMake/InstallManager.cmake commit cc2709bb79066fa8fcac737e9e206dc007b927e2 Author: Ann Almgren Date: Mon Nov 28 21:27:52 2011 -0800 Fix up InitFromAsciiFile. Src/C_AMRLib/Particles.H commit 9be027c61b6aa28a04db3d5a354ec890a93d5c48 Author: Ann Almgren Date: Mon Nov 28 19:27:59 2011 -0800 This version breaks up the Redistribute calls into chunks in InitFromAsciiFile in Particles.H Src/C_AMRLib/Particles.H commit 7f02504e1d9e3f0a4bbbf18968e6f10f376a4452 Author: lijewski Date: Mon Nov 28 17:08:05 2011 -0800 Revert m_id & NextID() back to int. Keep num_particles and num_particles_read as longs. NextID() now checks if we try to read/initialize more than INT_MAX particles per any MPI process. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 806c3b51197d9d319ee2b1430ef2ebd98f874f45 Author: Ann Almgren Date: Mon Nov 28 15:33:20 2011 -0800 One more int --> long in Particles.H Src/C_AMRLib/Particles.H commit a704ed8d86499604877e752de9b5623a5acd1ed5 Author: Ann Almgren Date: Mon Nov 28 15:32:12 2011 -0800 One more int --> long in Particles.H Src/C_AMRLib/Particles.H commit 80800af66cff83828df20312dd671c9a341102f4 Author: Ann Almgren Date: Mon Nov 28 15:27:54 2011 -0800 We need m_id and next_id to be long instead of int for the case when we have lots and lots of particles. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 19102747070b8af5f81ebefba8351e1f7b09741e Merge: 521ec25b6 ab4c2e116 Author: Ann Almgren Date: Mon Nov 28 15:17:22 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 521ec25b6867479f29a6155d30a3b9f3091d1c0b Author: Ann Almgren Date: Mon Nov 28 15:17:13 2011 -0800 Fix error print statement. Src/C_AMRLib/Particles.H commit ab4c2e1160ae1cf14607cb6d7a9930c3f33f5ebe Merge: be92f3ee5 ffc5d7793 Author: Michael Zingale Date: Mon Nov 28 13:59:53 2011 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit be92f3ee508bfcd3bafbd6076ec022e43293862f Author: Michael Zingale Date: Mon Nov 28 13:59:05 2011 -0500 if there are no parameters defined, create the namelist anyway, with a dummy parameter, just to make sure that things compile. Tools/F_scripts/write_probin.py commit ffc5d77934c331d4f536380f7e35a53e05295ab4 Author: Ann Almgren Date: Sat Nov 26 08:40:54 2011 -0800 We don't need to enforce solvability ahead of time when nlevs = 1 because we now enforce it each V-cycle when n = 1. Src/LinearSolvers/F_MG/ml_cc.f90 commit 50c9942a655f1f3f26433c5256c8310f975b7cf6 Author: Ann Almgren Date: Sat Nov 26 08:37:50 2011 -0800 We must pass the coeffs_sum_to_zero from mgt(1) to mgt(1)%bottom_mgt in order for the CG or BiCG solver to know the system is singular when using bottom_solver = 4. Change for cell-centered only. Src/LinearSolvers/F_MG/ml_cc.f90 commit fc7cc64d6a1a7e7398c55f204d271c3794178dcf Author: lijewski Date: Thu Nov 24 09:24:37 2011 -0800 Added ParticleBase::MaxReaders(). This is the maximum number of readers wanted for InitFromAscii(). It's settable via ParmParse as: particles.nreaders=N. It defaults to min(NProcs,64). Note that this number is always std::min()d with itself and NProcs since we can never have more readers than MPI processes. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 0fec7466e5edcf39583e3eb714948a1f24ed19ca Author: lijewski Date: Thu Nov 24 08:46:45 2011 -0800 New version of InitFromAscii() that tries to cut down on Redistribute() overhead. Src/C_AMRLib/Particles.H commit fc405dc6d7a6e8cee2141cf9d5d8db60c869dde1 Author: lijewski Date: Wed Nov 23 13:56:14 2011 -0800 Inlined index(). This is used in BaseFab::operator() for indexing into a FAB with an IntVect. Doing this greatly sped up Particle::InterpDoit() and things like GetGravity(), MoveKick(), MoveKickDrift() which call InterpDoit() ... Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 0b0f1ffa846556502923c629010480c2882bc748 Author: lijewski Date: Wed Nov 23 13:54:00 2011 -0800 Removed the "len" argument to GetGravity(). Added an intermediate ifrac[n] = (1-frac[n]) n InterpDoit() to force the calculation to be done only once. Results in a modest speedup with g++ at least. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit db4d91f3cac5d497bad151fa8c6d3273058f5ce4 Author: Ann Almgren Date: Wed Nov 23 10:49:15 2011 -0800 Fix shifting in domain replication in Particles.H Src/C_AMRLib/Particles.H commit 00c9f0e210eb1d6079adb6c7ba5eda9fa3459a04 Author: Ann Almgren Date: Wed Nov 23 10:39:14 2011 -0800 Remove random debug statement. Src/C_AMRLib/Particles.H commit 1949980a5bd7c01507ca45e0bb7318a48b41bd63 Author: Ann Almgren Date: Wed Nov 23 10:38:11 2011 -0800 Fix test for print statement. Src/C_AMRLib/Particles.H commit 9a9380d6476af50d700cf6f9ca4ca4cecbcdcb6d Author: Ann Almgren Date: Wed Nov 23 10:35:25 2011 -0800 Fix typo with lNrep... Src/C_AMRLib/Particles.H commit f0581865a9cd5f1c160a28b822e75c36d9f9e74f Author: lijewski Date: Wed Nov 23 10:23:31 2011 -0800 Changed the Nrep argument to InitFromAscii() to const IntVect* and defaulted it to zero. Src/C_AMRLib/Particles.H commit c6c446e5135ef415835e7d569851c400f0150d86 Merge: ea21a3a0c 10a53f6c0 Author: lijewski Date: Wed Nov 23 09:43:26 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ea21a3a0c7aa059362694b76a345c89d150c59e2 Author: lijewski Date: Wed Nov 23 09:42:33 2011 -0800 Use -O1 instead of -O0 for gcc/g++ when DEBUG=TRUE. This still gives good debugging info but yields much faster code. Tools/C_mk/Make.defs commit 10a53f6c0ce6e546c06f2931e20ffb86b0d84eeb Author: Ann Almgren Date: Wed Nov 23 09:39:43 2011 -0800 Pass Nrep through the calling sequence instead of hard-wiring it. Src/C_AMRLib/Particles.H commit 19ebaf8328b766e977d38aa077805961c66d7084 Author: ajnonaka Date: Wed Nov 23 08:03:37 2011 -0800 more progress - wrote parallel jobs section Docs/AdvancedTopics/AdvancedTopics.tex Docs/AdvancedTopics/hopper.run Docs/GettingStarted/GettingStarted.tex Docs/UsersGuide.tex commit c485955af611644870ba06a5902421a8f2807e32 Author: Michael Zingale Date: Tue Nov 22 20:41:20 2011 -0500 frontmatter page numbers should be roman, main page numbers normal Docs/UsersGuide.tex commit 6da04ac24e29622a71d7f68437d9f0d501f905e6 Author: Ann Almgren Date: Tue Nov 22 14:44:53 2011 -0800 Change defaults for how far the bottom solver can go -- we now limit by keeping the min in any direction to be 8 rather than by number of levels. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 commit 88310dfe7a412f5353a6b87f6c7909721236def6 Author: ajnonaka Date: Tue Nov 22 14:08:41 2011 -0800 new color scheme. fixed typo Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit ed81fd3ef96a523706fa9bb38079872d6fe26414 Author: Ann Almgren Date: Tue Nov 22 11:54:05 2011 -0800 Allow for the option of replicating the domain in InitFromAsciiFile. Src/C_AMRLib/Particles.H commit c3653475edaf7eff7af6dd1c8cdb9bafa551c108 Author: ajnonaka Date: Tue Nov 22 11:21:25 2011 -0800 getting started section complete Docs/GettingStarted/GettingStarted.tex commit 6ee747ea552b310b271bf8e6bd7fb73c755fdd23 Author: ajnonaka Date: Tue Nov 22 10:25:04 2011 -0800 more progress Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/UsersGuide.tex commit 30434223cdac0e8059c7700f87d875d7c5650d56 Author: ajnonaka Date: Tue Nov 22 08:38:11 2011 -0800 more progress and some re-org Docs/GNUmakefile Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit 44c9130df6087c17eff48cde0ea040630a84c418 Author: ajnonaka Date: Tue Nov 22 08:37:53 2011 -0800 new section Docs/AdvancedTopics/AdvancedTopics.tex commit a03dd508ac17e1368deb927eee7ff3dcef08e717 Author: ajnonaka Date: Tue Nov 22 08:06:44 2011 -0800 turn off MPI by default Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_F/GNUmakefile commit 7462cb066a4311c18e7072f38ea7de643804d8f5 Author: ajnonaka Date: Tue Nov 22 07:19:01 2011 -0800 clean these up a bit Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/Introduction/index_grid.odg Docs/Introduction/index_grid2.eps Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/Make.package Tutorials/WaveEquation_F/GNUmakefile Tutorials/WaveEquation_F/GPackage.mak commit d8b2248aeb9e71ff043836464ea0cdede0231ee0 Author: ajnonaka Date: Mon Nov 21 15:42:25 2011 -0800 starting to take shape Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/Introduction/index_grid.odg Docs/Introduction/index_grid2.eps Docs/UsersGuide.tex Tutorials/WaveEquation_F/main.f90 commit bb93ec51f3f9f4432c1309131bd688429d94ef6c Author: ajnonaka Date: Mon Nov 21 14:34:16 2011 -0800 new fig Docs/Introduction/AMR.eps Docs/Introduction/Introduction.tex commit 9fb9032fa6b22ff29fe1df90978f5010f355f121 Merge: 7a5dd89f2 cc8a90b9c Author: ajnonaka Date: Mon Nov 21 13:40:32 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7a5dd89f2866906d588eb187676552b8b0b1da57 Author: ajnonaka Date: Mon Nov 21 13:40:12 2011 -0800 fixed to use regular old layouts and boxarrays Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit cc8a90b9cb825a588960244fe1c38d85215a50e5 Merge: cfde33f44 a478d0399 Author: lijewski Date: Mon Nov 21 12:42:11 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit cfde33f44a07d3a4b4c61c4dcb11e9517ec05a5c Author: lijewski Date: Mon Nov 21 12:41:54 2011 -0800 Mod to compile with PGI on hopper. Src/C_BaseLib/CoordSys.cpp commit a478d039993463b7e514f654a092116a1e877817 Author: ajnonaka Date: Mon Nov 21 11:25:15 2011 -0800 saving progress Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit 5d0c8edaed40183b8b69223d505846e9741e3d98 Author: ajnonaka Date: Mon Nov 21 09:37:20 2011 -0800 now this builds again Docs/Introduction/Introduction.tex commit 77e494a5cf3e0225d23d42b655721509f0504431 Author: ajnonaka Date: Mon Nov 21 09:35:37 2011 -0800 more playing around with git - hope this works Docs/Overview/Overview.tex Docs/Overview/boxlib_directory_bw2.eps Docs/Overview/castro_scaling.eps Docs/Overview/data_loc.odg Docs/Overview/data_loc2.eps Docs/Overview/index_grid.odg Docs/Overview/index_grid2.eps Docs/Overview/lmc_scaling.eps Docs/Overview/maestro_scaling.eps commit 2539cea70b07ad162fe4f2c86db36d702ebecbc3 Author: ajnonaka Date: Mon Nov 21 09:35:07 2011 -0800 more playing with git. hope this works Docs/GNUmakefile Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/Introduction/boxlib_directory_bw2.eps Docs/Introduction/castro_scaling.eps Docs/Introduction/data_loc.odg Docs/Introduction/data_loc2.eps Docs/Introduction/index_grid.odg Docs/Introduction/index_grid2.eps Docs/Introduction/lmc_scaling.eps Docs/Introduction/maestro_scaling.eps Docs/UsersGuide.tex commit 80e66de4936530af228b896a580d015f4d641708 Author: ajnonaka Date: Fri Nov 18 17:33:20 2011 -0800 lots of comments in code, wrote small section in User's guide. This could actually be released now Docs/GettingStarted/GettingStarted.tex Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit c30d3baf3fe084028b5e5571b0c81575455982d3 Author: ajnonaka Date: Fri Nov 18 13:44:22 2011 -0800 fortran version of WaveEquation_C. fully working (I think) Tutorials/WaveEquation_F/GPackage.mak Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/inputs_3d Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit a629751a4b96aad37f28560d2f85ddb5797b4e57 Author: ajnonaka Date: Fri Nov 18 12:31:43 2011 -0800 remove unused variables Tutorials/WaveEquation_C/init_data_2d.f90 commit 9731fa67be693a1c12999f392074a63c7ff2962e Author: lijewski Date: Fri Nov 18 12:30:09 2011 -0800 datalog is now a Managed PArray instead of UnManaged so it gets properly cleaned up on exit. Src/C_AMRLib/Amr.cpp commit 9567086c28bdf44d55432ab8c045b88b3b16d068 Merge: 41489c15e 4dcea09fe Author: Weiqun Zhang Date: Fri Nov 18 12:14:32 2011 -0800 Merge branch 'hypre' commit 4dcea09fedeb51cdb0d12155f75147641e476fc2 Author: Weiqun Zhang Date: Fri Nov 18 12:13:36 2011 -0800 Minor changes in input file Tests/LinearSolvers/ComparisonTest/inputs.3d commit 41489c15efd49cc32a79b32e48f053157973113e Merge: e1fb94758 daac099fe Author: Weiqun Zhang Date: Fri Nov 18 12:12:02 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e1fb9475804d2e39c83a28a10e300688f272dd81 Author: Weiqun Zhang Date: Fri Nov 18 12:10:51 2011 -0800 Collect more timing info. Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit daac099fed4ba413db21973f833d5bef93a45ad7 Merge: 4a39731a2 f6dd2da64 Author: lijewski Date: Fri Nov 18 10:58:18 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4a39731a2d5d8e27ef698226f9da3637265354cb Author: lijewski Date: Fri Nov 18 10:58:02 2011 -0800 Minor performance tweak to copyassoc_check(). Src/F_BaseLib/layout.f90 commit 7294c7fca57ba27f42a6074c8deac5314c458e41 Author: Weiqun Zhang Date: Fri Nov 18 10:37:56 2011 -0800 Minor changes for the case when some processors have no grids. Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp commit 3b84370d933aca0ecd56ed8837d8385fdcf9d190 Author: Weiqun Zhang Date: Fri Nov 18 10:35:32 2011 -0800 Remove a useless statement. Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit c66fe8dbb731b2f82e83726d8ed2de3932b08ec0 Merge: cb2c8d4cf f6dd2da64 Author: Weiqun Zhang Date: Fri Nov 18 10:19:41 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit cb2c8d4cf4947b358a1ecdb25d3df2a1d2131275 Author: Weiqun Zhang Date: Fri Nov 18 10:18:55 2011 -0800 Fix typo in a variable name. Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit f6dd2da64ea441b8f84475508e01fa669a15cdfb Author: Weiqun Zhang Date: Fri Nov 18 10:08:27 2011 -0800 delete BndryData objects in the destructor of HypreABecLap Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp commit 691b789d6d4d8979177ce2dd02d24227d5439809 Author: lijewski Date: Fri Nov 18 09:44:56 2011 -0800 Be a little smarter about which cached copyassocs to delete when the cache hits the maximum size. The max copyassoc cache size now defaults to 25 instead of 50. Src/F_BaseLib/layout.f90 commit 3e504e4bdb4b0edb9bd9cdfe84c9f518e05df94c Author: lijewski Date: Fri Nov 18 09:21:27 2011 -0800 Added -lmpl for my machine. Tools/F_mk/GMakeMPI.mak commit 940bc24e323367c4a3f02279986091465244da68 Merge: 87cd2e93c 5cf2d086b Author: Michael Zingale Date: Fri Nov 18 09:51:56 2011 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 87cd2e93c99d0265d556398847f95ebddd9a57a5 Author: Michael Zingale Date: Fri Nov 18 09:51:08 2011 -0500 shift the gfortran-specific comments into comps/gfortran.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/gfortran.mak commit 5cf2d086bdce4c230f9e924e56beb8d22b4b70d5 Author: ajnonaka Date: Fri Nov 18 06:47:56 2011 -0800 starting new example Tutorials/WaveEquation_F/GNUmakefile Tutorials/WaveEquation_F/GPackage.mak Tutorials/WaveEquation_F/inputs_2d Tutorials/WaveEquation_F/main.f90 commit 6a7d62d32e4f2aeb8672a4547a834f8ffa76193c Merge: e9246ca59 0023a3f77 Author: ajnonaka Date: Thu Nov 17 17:51:10 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit e9246ca59cf7e14fea7827770516b194421d035d Author: ajnonaka Date: Thu Nov 17 17:50:49 2011 -0800 tidy this tutorial up a biZ Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/inputs_2d Tutorials/WaveEquation_C/inputs_3d commit 0023a3f77ae93b6552754e2da334db8337ddc9a5 Merge: 8cff4acd3 947045eb3 Author: Weiqun Zhang Date: Thu Nov 17 17:14:10 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 8cff4acd3e8498985f87701d311e3aa6d4786d11 Author: Weiqun Zhang Date: Thu Nov 17 17:13:39 2011 -0800 Fix a bug in setBndryConds. It now uses FabSetIter to loop over local boxes. Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit 947045eb36dd4c458694d6462036353fea608cff Author: ajnonaka Date: Thu Nov 17 15:34:58 2011 -0800 deleting old copies Docs/BoxLib/Overview.tex Docs/BoxLib/boxlib.tex Docs/BoxLib/boxlib_directory_bw2.eps Docs/BoxLib/castro_scaling.eps Docs/BoxLib/data_loc.odg Docs/BoxLib/data_loc2.eps Docs/BoxLib/index_grid.odg Docs/BoxLib/index_grid2.eps Docs/BoxLib/lmc_scaling.eps Docs/BoxLib/maestro_scaling.eps Docs/preface/preface.tex commit f12a8cb248a2bed5064b0ecfb50a44d8e61e876f Author: lijewski Date: Thu Nov 17 15:31:36 2011 -0800 Added mgt_flush_copyassoc_cache(). This is now called on Finalize() to remove any cached copyassoc objects. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit e8c68a5d5d8dfcd6f9fca167ff8d3e5d13cc4481 Merge: 170c02e1b ced020f11 Author: ajnonaka Date: Thu Nov 17 15:29:33 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 170c02e1befeaf1b3f62dc3d27a7a74e6a7f9fa8 Author: ajnonaka Date: Thu Nov 17 15:29:17 2011 -0800 more re-org Docs/GNUmakefile Docs/Overview/Overview.tex Docs/UsersGuide.tex commit d15ec3edceaf4660427f9fac18c0860d91551350 Author: ajnonaka Date: Thu Nov 17 15:24:24 2011 -0800 new section Docs/GettingStarted/GettingStarted.tex commit fbc7cc038df5e4ddf7cb15f7c603eb3d82f7f060 Author: ajnonaka Date: Thu Nov 17 15:23:02 2011 -0800 re-org Docs/GNUmakefile Docs/UsersGuide.tex commit e5a8ad66e39529dcb4a0d6ac4adf10ff972ce882 Author: ajnonaka Date: Thu Nov 17 15:22:14 2011 -0800 re-org Docs/Preface/Preface.tex commit a0175e5f85f3fbe774382f920a1477d8d22f4804 Author: ajnonaka Date: Thu Nov 17 15:21:41 2011 -0800 re-org Docs/Preface/preface.tex commit f2e2fb9f7ae56bc91e953a1612234a29c12ab33d Author: ajnonaka Date: Thu Nov 17 15:21:22 2011 -0800 re-org Docs/Overview/Overview.tex Docs/Overview/boxlib_directory_bw2.eps Docs/Overview/castro_scaling.eps Docs/Overview/data_loc.odg Docs/Overview/data_loc2.eps Docs/Overview/index_grid.odg Docs/Overview/index_grid2.eps Docs/Overview/lmc_scaling.eps Docs/Overview/maestro_scaling.eps commit 9726b2114027aa24c749c5049a981ba140466f2d Author: ajnonaka Date: Thu Nov 17 15:20:58 2011 -0800 re-org Docs/BoxLib/Overview.tex commit e812d483bd81eed387d025c61c0d0cedd93cd182 Author: ajnonaka Date: Thu Nov 17 14:52:06 2011 -0800 updates Docs/BoxLib/boxlib.tex commit ced020f11778901f65071772571035b3c12466c7 Merge: b477712da 4cb57b57d Author: Weiqun Zhang Date: Thu Nov 17 12:59:37 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b477712dae103e99ea98aa03d9e2f5906c68e69e Author: Weiqun Zhang Date: Thu Nov 17 12:58:49 2011 -0800 Add timing information Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit 4cb57b57dd79bc6c2e71a7e131c8119eebf7196f Author: ajnonaka Date: Thu Nov 17 12:19:35 2011 -0800 updates Docs/BoxLib/boxlib.tex Docs/preface/preface.tex commit a72614f3c8ffaf284acdd2698aeaf20e11ce12a2 Author: ajnonaka Date: Thu Nov 17 12:17:52 2011 -0800 scaling figs Docs/BoxLib/castro_scaling.eps Docs/BoxLib/lmc_scaling.eps Docs/BoxLib/maestro_scaling.eps commit 101a2afb68c1fcb938ded2458313dac3808d84d4 Author: ajnonaka Date: Thu Nov 17 11:06:43 2011 -0800 moved file Src/C_AMRLib/OpenSource.txt commit 8e821376ffc815f95b64a76a568762f1d44c7b45 Author: ajnonaka Date: Thu Nov 17 11:05:45 2011 -0800 boxlib tree figure Docs/BoxLib/boxlib_directory_bw2.eps commit f835a4fa42e1b89725d971072e32ae9e552d3402 Author: ajnonaka Date: Thu Nov 17 11:05:19 2011 -0800 updating doc Docs/BoxLib/boxlib.tex Docs/GNUmakefile Docs/README Docs/UsersGuide.tex Docs/preface/preface.tex commit 4097d56af5b1ca9feb6e3883c7371ccd0a4e18a4 Author: ajnonaka Date: Thu Nov 17 11:04:12 2011 -0800 moved license from C_AMRLib license.txt commit 8a423e751e7dff9650bc442f6ef6270af7829370 Author: ajnonaka Date: Thu Nov 17 10:15:31 2011 -0800 renamed UsersGuide.tex Docs/paper.tex commit 11b523fd2fa901ec1b32ce910c17459c309f0e2c Author: ajnonaka Date: Thu Nov 17 10:11:52 2011 -0800 updating in progress... Docs/BoxLib/boxlib.tex Docs/BoxLib/maestro_directory.odg Docs/GNUmakefile Docs/UsersGuide.tex commit e3f1268666dd9049ad97a7a0d8f7054b7906789f Author: ajnonaka Date: Thu Nov 17 09:27:55 2011 -0800 eliminating option for building sub-directories within the main documentation. someone can add this back in if they actually see a reason for this Docs/BoxLib/GNUmakefile commit 7ad9b38bac2c14d37bf1a8ba5a65f51dc6fc67d4 Author: ajnonaka Date: Thu Nov 17 09:27:24 2011 -0800 git rid of these too Docs/BoxLib/mac.odg Docs/BoxLib/mac2.eps commit 069cb441110b4356ccff020f49a9d252a1d43781 Author: ajnonaka Date: Thu Nov 17 09:24:39 2011 -0800 get rid of this too Docs/BoxLib/maestro_directory2.eps commit 147faa639710c94792ce1f67d178b727d930a8d0 Author: ajnonaka Date: Thu Nov 17 09:23:27 2011 -0800 no idea why this was here Z Docs/BoxLib/paper.tex commit 16a8bb528455de9de1a2154b03f90169d6c058b3 Author: lijewski Date: Thu Nov 17 07:44:42 2011 -0800 Just a little code rearrangement & reformatting in InitFromAscii(). Src/C_AMRLib/Particles.H commit bac25312b71921638dac357f093f4bc9325fc0af Author: Michael Zingale Date: Thu Nov 17 09:18:38 2011 -0500 add xrb Tools/F_mk/GMakeMPI.mak commit bbd689988f4d08238a60820b1790c84438d62eb5 Author: Michael Zingale Date: Wed Nov 16 22:25:03 2011 -0500 add defaults for the input param strings -- this is needed for CASTRO Tools/F_scripts/write_probin.py commit 8447147227cd02c89d94071514e17e5c006dec27 Merge: 12243b211 8b1ce0ac5 Author: Ann Almgren Date: Wed Nov 16 18:16:06 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 12243b211085434acfae2f64d0c5691fd5a32422 Author: Ann Almgren Date: Wed Nov 16 18:15:07 2011 -0800 In InitFromAsciiFile in Particles:H, we now read the file using at most 64 processors; this speeds things up dramatically for nprocs > 64. Src/C_AMRLib/Particles.H commit 8b1ce0ac5f10096c5acb4dfcf0f09737ef4d6b9c Author: lijewski Date: Wed Nov 16 16:19:32 2011 -0800 A little optimization & cleanup. Src/C_AMRLib/Particles.H commit 6085f0a5042fdc1789efa9c26b438cf573b37f9b Author: Ann Almgren Date: Wed Nov 16 14:41:13 2011 -0800 We were not calling post_regrid when using regrid_on_restart with finest_level = 0. Now we are. Src/C_AMRLib/Amr.cpp commit fab8a926d3f984aa6a7d16cf4437fbc702aaa9ce Merge: 80a2041b2 354e7b1bd Author: Weiqun Zhang Date: Wed Nov 16 10:52:57 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 80a2041b2ef24c0c9da792ad657a4d8dd3fd9582 Author: Weiqun Zhang Date: Wed Nov 16 10:51:26 2011 -0800 Add Hypre to the comparison test Tests/LinearSolvers/ComparisonTest/COMP_NORM_1d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_3d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_3D.F Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/Make.package Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp commit 354e7b1bd3a6370fe56c7b043141a5aff6731c2b Author: lijewski Date: Wed Nov 16 10:25:02 2011 -0800 Removed some unused variables and some prettification. Src/C_AMRLib/Particles.H commit 5c38de3b061f356d8ead8bb80f2a272c2db30f64 Author: vince Date: Tue Nov 15 13:48:59 2011 -0800 added the IOBenchmark. Tests/IOBenchmark/GNUmakefile Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/README commit a3edbdafe72006871fba6d7811ac3943bbd9b535 Author: Ann Almgren Date: Tue Nov 15 13:03:19 2011 -0800 Add new routine -- set_const_gravity_coeffs -- that does not take an array as an argument. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit ad380bacda1918494efc361a667ab64f257399ee Author: Weiqun Zhang Date: Mon Nov 14 10:30:14 2011 -0800 untrack tag files .gitignore commit 82e72ceb19c9ae61597e0e017f02bc94187077ea Merge: a897c50da 13b86ff7f Author: Weiqun Zhang Date: Mon Nov 14 10:27:38 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a897c50da7b7859e0946f9625508c54b5f9130f3 Author: Weiqun Zhang Date: Mon Nov 14 10:23:20 2011 -0800 Add 1D case. Tests/LinearSolvers/ComparisonTest/main.cpp commit eb8512a1874168a223b292e9daf25115fcf14177 Author: Weiqun Zhang Date: Mon Nov 14 10:21:15 2011 -0800 Add 1D test. Tests/LinearSolvers/ComparisonTest/COEF_1D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_1d.f90 commit 5c0a65d845d8d341cff435c57e685d0cbe8ad008 Author: Weiqun Zhang Date: Mon Nov 14 10:18:33 2011 -0800 Minor changes to make it more generic, in case the physical dome is not from 0 to 1. Tests/LinearSolvers/ComparisonTest/COEF_3D.F commit 930f1a3926adfdd49cbe5ec7455af5092ce5f786 Author: Weiqun Zhang Date: Mon Nov 14 10:15:41 2011 -0800 Add 1D case to mg_tower_print. Src/LinearSolvers/F_MG/mg.f90 commit 6bf0fa264e41303d8b16361a3aa521f5868df873 Author: Weiqun Zhang Date: Mon Nov 14 10:06:43 2011 -0800 Fix the subroutines names in the calls to mgt_verify. Fix the size of arrays in a 1D routine. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 13b86ff7fe32c7a4591eae0ca3fa944581705a03 Author: Ann Almgren Date: Fri Nov 11 08:37:07 2011 -0800 1) Modify default stencil_order (sets order of boundary condition stencils) to be 2 instead of 1 when the F90 solver is called from C++. 2) Removed commented lines from stencil routine. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 commit e6e909b789982f814a73c15bacbc8bffd876b3fc Author: Ann Almgren Date: Thu Nov 10 10:27:26 2011 -0800 These are changes for how the Hypre solver is called -- from Rob Falgout. Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/inputs.3d commit 764ea54149ac81fbefe50d9c8e58d54980c75953 Author: Ann Almgren Date: Wed Nov 9 15:42:35 2011 -0800 Made the test in AmrData.cpp on whether the grids fit in the domain be an explicit test rather than a BL_ASSERT. Src/Extern/amrdata/AmrData.cpp commit a6970ca22d14fa88a259ea814681c3065f17113b Author: lijewski Date: Mon Nov 7 19:37:16 2011 -0800 Applied patches supplied by Steffen Klemer. Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 70a53183edc97308101719c3b869b835e77009a2 Author: lijewski Date: Fri Nov 4 15:07:26 2011 -0700 eps from 1.e13 => 1.e-13. Src/C_AMRLib/Particles.cpp commit 0e6a5a92743da175d6b4451b21e872b344be92ed Author: lijewski Date: Fri Nov 4 10:31:33 2011 -0700 Made some loops more memory-access efficient. Src/LinearSolvers/F_MG/coarsen_coeffs.f90 commit f4bbaa53654f24c627ae661a575affe3ff97604d Author: lijewski Date: Fri Nov 4 10:15:12 2011 -0700 1000.0 => 1000.0D0 Src/F_BaseLib/interp.f90 commit 50d17791598f62fa98e28310dcfdabfadcd886d9 Merge: 4a4ce0baf b96cb3c77 Author: Ann Almgren Date: Thu Nov 3 22:12:15 2011 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 4a4ce0bafcc02573fef916eb1daef3f71db4a54a Author: Ann Almgren Date: Thu Nov 3 22:11:34 2011 -0700 Split subroutine mg_tower_smoother and jac_smoother out of mg.f90 and into mg_tower_smoother.f90 in the F_MG directory. Src/LinearSolvers/F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit b96cb3c773443efc1e08ae8d79389702cf4c5a51 Author: Michael Zingale Date: Thu Nov 3 21:11:47 2011 -0400 add a check whether we defined a parameter already in the previous set of runtime parameters Tools/F_scripts/write_probin.py commit 1101fbcb38828830f8b9095a72a4c9d0e321c861 Author: Michael Zingale Date: Thu Nov 3 20:14:55 2011 -0400 add the ability to have 2 separate groups of runtime parameters. This allows them to be split into different modules. Tools/F_scripts/write_probin.py commit a681cca0f28e94a07a363c90b0a55636163767ef Author: Michael Zingale Date: Thu Nov 3 19:44:06 2011 -0400 add comments Tools/F_scripts/findparams.py commit d96d9229e4cd2b71f4c524868354893d07b7a504 Author: Michael Zingale Date: Thu Nov 3 15:53:02 2011 -0400 slight prettification Tools/F_scripts/findparams.py commit 086f2b63e8ab3781df2f94dfe8cd4fccb123089f Author: Michael Zingale Date: Wed Nov 2 14:23:06 2011 -0400 a simple script to search a list of directories for _parameters files and print the resulting list to stdout. This is used by makefiles to provide the list of dependencies for write_probin.py Tools/F_scripts/findparams.py commit 0f18810afeced831b2dcc53e14457c0864a3a4d8 Author: Michael Zingale Date: Wed Nov 2 10:28:27 2011 -0400 move the write_probin.py script from the MAESTRO source to here so it can be used by other BoxLib codes (like CASTRO) Tools/F_scripts/write_probin.py commit 5c9e6f2f8178efb3e6e78a77682d8e609176b715 Author: Matthew Emmett Date: Sat Oct 29 09:06:56 2011 -0400 PyBoxLib: Silence some warning, minor tweaks to build system. Src/Python/GMakerules.mak Src/Python/mkpyfboxlib Src/Python/src/boxlib_numpy.c commit 5e09d3144c7363f68c07056184e0fc1e961510b4 Author: lijewski Date: Fri Oct 28 09:33:43 2011 -0700 Moved the initialization of "ss" in s_minion_full_fill_3d() to before the OMP PARALLEL DO loop. Src/LinearSolvers/F_MG/cc_stencil.f90 commit d805c660acda187267ddf2dc4a5f3962fa6b92eb Author: lijewski Date: Fri Oct 28 08:53:21 2011 -0700 A little note explaining why this directory exists. Tests/LinearSolvers/C_CellMG/dumpi/NOTE commit df608fe047404c1cb0f7a8754da105495e548b15 Author: lijewski Date: Fri Oct 28 08:44:53 2011 -0700 A little cleanup. Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.4096core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.512core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.64core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.8core commit 7447e8ee92cfe16af6f98d26c5601c0be7456e17 Author: lijewski Date: Fri Oct 28 08:42:24 2011 -0700 Now accepts n_cells and max_grid_size. If n_cells is defined will make a domain that long in each direction and then split it up based on max_grid_size. Otherwise expects to read in a file containing the initial BoxArray. Tests/LinearSolvers/C_CellMG/main.cpp commit 80b74ba89fd705fcd1f4db192f8e73322db65f48 Author: lijewski Date: Thu Oct 27 14:32:51 2011 -0700 Renamed the exascale directory -> dumpi since I really used these inputs files for the dumpi test with Joe Kenny. Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.4096core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.512core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.64core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.8core commit 7d782ba2d3d7ed9c72f0453e06437be4fb58ac6e Author: lijewski Date: Thu Oct 27 14:30:49 2011 -0700 I meant to put these input files into the exascale directory. Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.4096core Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.512core Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.64core Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.8core commit a310b4fdb1393814733a9383c186026cfe719c95 Author: lijewski Date: Thu Oct 27 14:25:29 2011 -0700 Inputs files I used when running the MG test for dumpi that I passed to Joe Kenny. Tests/LinearSolvers/C_CellMG/inputs.3d.4096core Tests/LinearSolvers/C_CellMG/inputs.3d.512core Tests/LinearSolvers/C_CellMG/inputs.3d.64core Tests/LinearSolvers/C_CellMG/inputs.3d.8core commit db724aa293b448ef86e43136df5b41f06b24bcc1 Merge: aa8ac787c 4ab338a4e Author: vince Date: Wed Oct 26 15:35:03 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit aa8ac787c94b9fe3e65c6ed207c386658e8d342f Author: vince Date: Wed Oct 26 15:33:29 2011 -0700 added Amrvis namespace. updated files to use the namespace. fixed memory leak. Src/Extern/amrdata/AmrData.H Src/Extern/amrdata/AmrData.cpp Src/Extern/amrdata/AmrvisConstants.H Src/Extern/amrdata/DataServices.H Src/Extern/amrdata/DataServices.cpp Tools/C_mk/Make.mpi Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp commit 03168769aea413110a56e83e284febc3f207be01 Author: vince Date: Wed Oct 26 15:25:57 2011 -0700 fixed boxlib path. Tools/C_util/Convergence/GNUmakefile Tools/C_util/Statistics/GNUmakefile commit 4ab338a4e10d62d9810a93a326039cf4e360c329 Author: Ann Almgren Date: Wed Oct 26 14:38:56 2011 -0700 Fix Redistribute so that empty boxes do not generate seg faults. Src/C_AMRLib/Particles.H commit 3e70985b8e675820c5a5d66ef0581066b4d9db24 Merge: 4ff705ed4 bf62007d6 Author: lijewski Date: Mon Oct 24 14:01:48 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4ff705ed4e94be43e1d76b9ba95096c59c49d6c7 Author: lijewski Date: Mon Oct 24 14:01:01 2011 -0700 Deprecate CrseInit(FArrayBox&,...); spew a warning if used. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 5c4044f2765be887fae63718391e481cf72aa93a Author: lijewski Date: Mon Oct 24 14:00:24 2011 -0700 If blocking_factor or max_grid_size are not explicitly defined, use supplied defaults. Src/C_AMRLib/Amr.cpp commit bf62007d6ad77a07b363eb079bd68af71a7f2f5f Author: Ann Almgren Date: Mon Oct 24 13:29:11 2011 -0700 Get this Tests/LinearSolvers/F_MG test code to compile again. No guarantee that it works correctly. Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_single.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_single.f90 commit 0430b38c754fc7d99d7da879554e5e31ac019eb7 Author: lijewski Date: Mon Oct 24 12:23:30 2011 -0700 Closer to compiling with new GIT layout. Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/GPackage.mak Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_single.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_single.f90 Tests/LinearSolvers/F_MG/t_smoother.f90 Tests/LinearSolvers/F_MG/t_stencil.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit adb4f1c892b0dceacc055bd1525aad13976df971 Author: lijewski Date: Mon Oct 24 12:22:59 2011 -0700 Add t/ to ignore list. .gitignore commit 59ce88b96fdd393fcc02a6b3bb321fce50718a4c Merge: c4e458d88 ee5feaf4b Author: lijewski Date: Mon Oct 24 10:42:50 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c4e458d887162b941940ec18eb86ea6fdd7e1acb Author: lijewski Date: Mon Oct 24 10:41:41 2011 -0700 Replaced saxpy(a,ONE,b) with plus_plus(a,b) calls. Replaced saxpy(a,-ONE,b) with sub_sub(a,b) calls. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit ee5feaf4b2d8b17bfe53b03eaabfc6bc993c161f Author: Ann Almgren Date: Mon Oct 24 10:20:19 2011 -0700 Fix bug in reading max_grid_size and blocking_factor arrays -- we need to read max_level+1 values, but we were only reading max_level values (when number of values > 1 in the inputs file) Src/C_AMRLib/Amr.cpp commit 20cf71c6b31668a9f7f8aaf6c8b37f5be944c554 Author: lijewski Date: Fri Oct 21 15:57:38 2011 -0700 Modest speedup to simplify_doit(). Src/C_BaseLib/BoxList.cpp commit 4f7680ceef24c13b9b56f8d1eb6d230ceb4facfd Author: lijewski Date: Fri Oct 21 14:44:20 2011 -0700 Got MPI working on my upgraded machine. Tools/C_mk/Make.mpi commit 6dabdfb614cdea80f13be8a6626643057594add8 Merge: 48de16eaa ea67ef579 Author: lijewski Date: Fri Oct 21 13:56:20 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 48de16eaac007b1e4c400abd3418321d9adac04f Author: lijewski Date: Fri Oct 21 13:55:43 2011 -0700 Added .gitignore that ignores d f o directories as well as *o *a and a few other things. .gitignore commit ea67ef579942da1287eac5d4a790a147b8564500 Author: Ann Almgren Date: Fri Oct 21 13:54:16 2011 -0700 Add the line p_n_comp[i].simplify(); inside the grid_places() routine. This reduces the number of grids dramatically when doing regridding with low lbase and high finest_level. Saves a factor of over 100 in test with lbase=2 and finest_level=7. Src/C_AMRLib/Amr.cpp commit ba0a1ead341fbc6f2b943fd15d3f38742db2610d Author: lijewski Date: Fri Oct 21 13:47:26 2011 -0700 Use BoxList::catenate() instead of BoxList::join() when possible. The former is more memory efficient. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/Extern/amrdata/AmrData.cpp commit b0c9b71b4ff2638c4ff15339fdeac64ac85c4dbe Author: Matthew Emmett Date: Thu Oct 20 15:35:40 2011 -0400 PyBoxLib: Add ml_layout wrapper. Src/Python/GMakerules.mak Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/layout.py Src/Python/src/blobjects.py Src/Python/src/fboxlib.f90 commit 4779042149c8ca6e411163c39224c75c9b6a4354 Author: Matthew Emmett Date: Thu Oct 20 14:26:07 2011 -0400 PyBoxLib: Change makefile structure to mimic BoxLib, remove extraneous files. Src/Python/GMakerules.mak Src/Python/GPackage.mak Src/Python/Makefile Src/Python/mkpyfboxlib Src/Python/src/blobjects.f90 Src/Python/src/boxlib_numpy.c Src/Python/src/fboxlib.pyf Src/Python/src/pyfboxlib.m4 Src/Python/src/pyfboxlib.pyf commit dbe72636e184599609745959c75a762ee0740671 Author: Matthew Emmett Date: Thu Oct 20 11:36:12 2011 -0400 PyBoxLib: Add Src/Python. Src/Python/Makefile Src/Python/README Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/base.py Src/Python/pyboxlib/boxarray.py Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/layout.py Src/Python/pyboxlib/multifab.py Src/Python/src/blobjects.f90 Src/Python/src/blobjects.py Src/Python/src/boxlib_numpy.c Src/Python/src/boxlib_numpy.f90 Src/Python/src/fboxlib.f90 Src/Python/src/fboxlib.pyf Src/Python/src/pyfboxlib.m4 Src/Python/src/pyfboxlib.pyf Src/Python/test.py commit 8a813a0175935fbc21a04683732eabaf5d9b8d8e Author: Ann Almgren Date: Wed Oct 19 19:27:05 2011 -0700 Add options for Zarija's machine, stribog. Tools/C_mk/Make.mpi commit 232bf71dda22e7e40db72fc594240688cb2010ee Author: Weiqun Zhang Date: Tue Oct 18 11:28:19 2011 -0700 Add a space to the ouput message Tools/C_util/regtests/testnew.py commit ff26b7a115c04859c2f07f8f32ea75c67cc2ef6c Author: Ann Almgren Date: Mon Oct 17 14:20:41 2011 -0700 This has latest greatest InitCosmo from Jan Frederik. Src/C_AMRLib/Particles.H commit 4a497e85d94ddebacfefa03a90f9aa064b511c19 Author: gilet Date: Mon Oct 17 12:27:53 2011 -0700 added -lmpl for orga Tools/F_mk/GMakeMPI.mak commit 2e0224ad058c0dddb93e7fc54a4e1f4a5a50ac40 Author: Ryan Orvedahl Date: Sat Oct 15 17:59:29 2011 -0400 add support for sn.astro.sunysb.edu Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 1810cea785b161cbcc90b0fdc29054e6cdb696d3 Merge: b1758478f e765074d3 Author: Michael Zingale Date: Fri Oct 14 15:12:40 2011 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit b1758478f53c6ebad90b941cfac68fdf9ea9e66c Author: Michael Zingale Date: Fri Oct 14 15:12:06 2011 -0400 add MPI stuff for sn Tools/F_mk/GMakeMPI.mak commit e765074d3d4754cf309eb08cb53a6593caa510ec Author: Ann Almgren Date: Fri Oct 14 12:11:54 2011 -0700 Change int to long in i = 0 to truesize in clear (already did this in define). Src/C_BaseLib/BaseFab.H commit 5cd85707cc2e84ffcb05f2252044e55f27e79c95 Author: Ann Almgren Date: Fri Oct 14 11:35:09 2011 -0700 Replace int by long in BaseFab::define so that it can handle very large (e.g, 1024^3) boxes. Src/C_BaseLib/BaseFab.H commit 9f4efbb09054dd9739babbfd816e899e70d8ee6d Author: Ann Almgren Date: Fri Oct 14 11:34:39 2011 -0700 Fix mpi for manda. Tools/C_mk/Make.mpi commit 2b3ddfea66872833062f1f36a6b74995ab49f4ae Author: lijewski Date: Thu Oct 13 14:26:03 2011 -0700 Un-inlined some stuff that didn't need to be inlined. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/UseCount.H Src/C_BaseLib/UseCount.cpp commit e93dcabc5d2f7279d0b83ab9668a64feab30282c Author: lijewski Date: Thu Oct 13 13:59:03 2011 -0700 Merged the std::stable_sort() and std::reverse() into a static function Sort(). Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit e234a263019a7493e1f583a348035faafb8091f3 Author: lijewski Date: Thu Oct 13 12:59:39 2011 -0700 More protected => private for some data members. Un-inlined some stuff. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Orientation.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit d7e0849e1ae7c4261e2adf15d2ae0580b017b4c8 Merge: 78263f806 85433f302 Author: lijewski Date: Wed Oct 12 13:54:36 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 78263f8069a9b03ef79532018036298b4ab1704b Author: lijewski Date: Wed Oct 12 13:53:40 2011 -0700 Made as much "protected" data "private" as possible. Removed unneeded "virtual" on some member functions. Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/BCRec.H Src/C_AMRLib/Derive.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateDescriptor.H Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/RealBox.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/FabSet.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/MultiGrid.H commit 85433f30258a646be57a514a930aaa7f35a0895c Author: lijewski Date: Tue Oct 11 15:08:30 2011 -0700 Use -O3 instead of -Ofast with PathScale to work-around current 4.0.9 bug in IPA on hopper. Tools/C_mk/Make.Linux commit acb8a7143f8e069a49c10bd2a33e514b70638f4e Author: lijewski Date: Tue Oct 11 15:01:01 2011 -0700 -Ofast no longer works on latest PathScale on hopper. Use -O3 instead. Tools/F_mk/comps/Linux_pathscale.mak commit 3c32e3231a257791c6505a222f7a7a0d79e9e1f0 Author: lijewski Date: Mon Oct 10 13:16:59 2011 -0700 Changes to work around PathScale bug. PathScale has problems with file scope C++ standard strings in MPI programs. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Tools/C_mk/Make.Linux commit e117ae6860ed5327369f5118e3e5e743f1e5e79f Merge: c80ff4cae 55f0965b5 Author: Marc Day Date: Fri Oct 7 16:34:47 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Tools/C_mk/Make.defs commit c80ff4caee9e950dbf2c2d028d1a2fa0638c7080 Author: Marc Day Date: Fri Oct 7 16:26:22 2011 -0700 update for ascem with sub-comm in fBox BoxLib_Version.txt Tools/C_scripts/gen_release_tarball.txt commit 55f0965b5809c0bd595bb5f7e14e8711ad1e6233 Author: lijewski Date: Fri Oct 7 15:59:15 2011 -0700 std::snprintf() => snprintf() to get to compile with PGI. Src/C_BaseLib/ParallelDescriptor.cpp commit 2ca9e892ac3e9501a7dc4006d9ebfa38e2671da9 Author: lijewski Date: Fri Oct 7 15:12:55 2011 -0700 Now always calls the mgt_init() that takes a single argument. We want to support George Pau who needs the ability to pass in an MPI_Communicator that is not MPI_COMM_WORLD. Added Finalize() that gets called on BoxLib::Finalize() which'll reset initialized to false. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 92ee6be23ab697ade5a76b02375a67592707df94 Author: lijewski Date: Fri Oct 7 15:10:02 2011 -0700 mgt_init() now takes a single integer argument "comm". Removed the saved logical variable that only called parallel_initialize() on the first call. Instead MGT_Solver only calls mgt_init() when it needs to. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 78f6039275d8de2f97ebb03f1a2927f18ae76159 Author: lijewski Date: Fri Oct 7 15:06:21 2011 -0700 parallel_initialize() now takes an optional integer "comm" argument. If it's present we use it instead of MPI_COMM_WORLD as the MPI communicator. Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 77f0a22199b530579b2348a42611085b9f7d7786 Author: Michael Zingale Date: Fri Oct 7 15:10:57 2011 -0400 add the compilation and execution commands to the web output Tools/C_util/regtests/testnew.py commit 4ed8bd9c465a26870448a9883941e62dcad50c03 Author: lijewski Date: Thu Oct 6 14:38:59 2011 -0700 More tweaking on removeOverlap(). There's got to be a better way to do this but I don't see it just yet. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 2064452d0cf9b05a6cd538c4270fa6c4b2f747b1 Author: lijewski Date: Thu Oct 6 12:40:52 2011 -0700 Instead of just calling std::list::clear() our version of clear() employs the swap() trick to really get rid of any extra memory hanging around due to stray Boxes. Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit e119b641d2ba69a0c448eaf5610e3df32d8321d1 Author: lijewski Date: Thu Oct 6 12:30:18 2011 -0700 removeOverlap() no longer returns a BoxList. Instead it's a void function. We now though fix up the resultant BoxArray so it doesn't have holes. We then can use the boxList() function to get a good non-overlapping list of boxes. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp commit 6671bfab7ee035ce1286876381dd47e00319a383 Author: lijewski Date: Thu Oct 6 11:06:58 2011 -0700 This has most of the previous tweeks put back in. What I broke was something in removeOverlap() which I'm still thinking about. It's weird. Src/C_BaseLib/BoxArray.cpp commit 1f46c539e53bd5569a2b1fa4614b47133589a25e Author: lijewski Date: Thu Oct 6 10:34:33 2011 -0700 I broke BoxArray somehow. I'm reverting to this earlier copy from Parallel/BoxLib till I figure out what I did. Src/C_BaseLib/BoxArray.cpp commit c87f9e17501bafb684ee6e643cddbfac6f64553e Author: Ann Almgren Date: Wed Oct 5 20:03:05 2011 -0700 Changes to InitCosmo in Particles.H only. Src/C_AMRLib/Particles.H commit ca3a12101f670cc452ae24af6685daa246051e75 Author: lijewski Date: Wed Oct 5 16:15:48 2011 -0700 A little tidying of for() loops. Src/LinearSolvers/C_CellMG/LinOp.cpp commit 2c4856d89e67cc6210da1240e0512e0164bf4453 Author: lijewski Date: Wed Oct 5 16:07:20 2011 -0700 Some more tidying of for() loops. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 6d1066a58a79a487ec88a1f7a3946e7f73181ab4 Author: lijewski Date: Wed Oct 5 15:39:01 2011 -0700 Some tidying up of for() loops. Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.cpp commit 5d639e8833bca1e4f9e7f00e239979785e7c83be Author: lijewski Date: Wed Oct 5 15:31:39 2011 -0700 Some tidying up of for() loops. When possible moved function calls from the test portion to the init portion. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp commit 8bb2cea3204b500b37f05e452ca94db0690ad2cb Author: lijewski Date: Wed Oct 5 14:07:33 2011 -0700 Merged the guts of the two define() functions into a new function called by both. Src/C_BaseLib/FabArray.H commit 3487a95fbd15e557b7902d82f1b567eb6edd1ae3 Author: lijewski Date: Wed Oct 5 12:57:09 2011 -0700 Removed remnant embedded CVS $Id strings. Src/LinearSolvers/C_TensorMG/DivVis_F.H Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/main.cpp Tools/C_mk/Make.OSF1 Tools/C_scripts/strip72 Tools/C_util/Make.package commit 7bd56dac285294361c7857d15be56d5518dea6ac Author: lijewski Date: Wed Oct 5 12:51:43 2011 -0700 Use <> on include files not "" for consistency. Src/C_AMRLib/DatasetClient.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/COORDSYS_F.H Src/Extern/amrdata/AmrData.H Src/Extern/amrdata/AmrData.cpp Src/Extern/amrdata/DataServices.H Src/Extern/amrdata/DataServices.cpp Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_cg.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Tests/LinearSolvers/C_NodalMG/proj.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/PltFileFluxAve.H Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.H Tools/C_util/Statistics/PltFileXAve.cpp Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/mfMinMax.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFcol.cpp Tools/C_util/ViewMF/viewMFdiff.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.H Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/WaveEquation_C/main.cpp commit 54943ca8443aba26a0e1047196c09d9e73d8291d Author: lijewski Date: Tue Oct 4 14:25:51 2011 -0700 Simplified how AuxBoundary are built. We no longer have to explicitly force'm to not use the MinimizeCommCosts code. That code no longer exists. Src/C_AMRLib/AuxBoundaryData.cpp Tests/C_BaseLib/tMinCommCosts.cpp commit 41b34604968184823a013bb08ee1234f7fb9b400 Author: Ann Almgren Date: Tue Oct 4 11:09:54 2011 -0700 Move the definition of r1 so that even when we don't need to solve the "Solve Time" output is defined. Src/LinearSolvers/F_MG/ml_cc.f90 commit 271fb8f0b77a75c4604b63893f36c6ec83553768 Author: Ann Almgren Date: Tue Oct 4 09:42:49 2011 -0700 Replace FOPTF += -mp1 fOPTF += -mp1 by FOPTF += -mp1 -fltconsistency fOPTF += -mp1 -fltconsistency in Make.defs for Intel verion 11.* Without the -fltconsistency, the loss of precision with Intel optimization causes multigrid to fail. Tools/C_mk/Make.defs commit ca1c69b1dcb0b5ff8c40195beebbd359a05768f9 Author: lijewski Date: Mon Oct 3 12:58:46 2011 -0700 Replaced Cray vector merge routines with fortran 90 merge() calls. Src/Extern/amrdata/FABUTIL_2D.F Src/Extern/amrdata/FABUTIL_3D.F commit e053836198f314de905320c1b603dd2a799c7210 Author: lijewski Date: Mon Oct 3 11:04:17 2011 -0700 I'm changing BL_NOFAST => BL_FAST. I'm don't want the "fast" optimization options to be the default when DEBUG=FALSE. If you want to try using the "fast" optimization options you now have to set BL_FAST=TRUE in you GNUmakefile. Buyer beware. This tends to expose bugs in compilers. Tools/C_mk/Make.Linux commit 53e049152759675948ca022640c0cfc5478d568f Author: lijewski Date: Sat Oct 1 08:33:25 2011 -0700 Fix to multi-level AssignDensity(). We never should have tried to reuse the BoxArray in fmf that way. Weird thing is this code used to work. I think what happened is that I "fixed" MultiFab::clear() a while back. Previously all it did was get rid of the memory. The new improved version also clear()d the BoxArray among a few other things. Src/C_AMRLib/Particles.H commit 762f19e25d39a828f010324f050585887fd331b1 Merge: 575b68be1 e40f6a170 Author: Weiqun Zhang Date: Fri Sep 30 11:43:25 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 575b68be1fe4ee06d59ebf108f1da0a44a1907aa Author: Weiqun Zhang Date: Fri Sep 30 11:35:12 2011 -0700 If the link files are absolute path, the old version would fail. This is now fixed. The link files can now be either absolute path or just basename. The old version used gmake. But on some systems the GNU amke is just "make". In the new version, MAKE is a variable that can be changed in the input file for the script. Also, numMakeJobs is added so that several make jobs can run simultaneously. Tools/C_util/regtests/testnew.py commit e40f6a17089439e23c6da66959845fbdae0adbc2 Author: lijewski Date: Thu Sep 29 16:08:02 2011 -0700 Quiet compiler warning. Src/C_AMRLib/DatasetClient.cpp commit 9edd2256f3574b434186750431d3f4f23aa4f272 Author: lijewski Date: Thu Sep 29 13:42:06 2011 -0700 Removed all the wrappergen stuff. This is a third-party library for profiling MPI calls. The only reason it was in our original CVS repository was because Chuck made some modifications to it. Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/PROTO Tools/C_util/wrappergen/README Tools/C_util/wrappergen/args.c Tools/C_util/wrappergen/args.h Tools/C_util/wrappergen/doc.c Tools/C_util/wrappergen/doc.h Tools/C_util/wrappergen/driver.c Tools/C_util/wrappergen/expandingList.h Tools/C_util/wrappergen/mpifn Tools/C_util/wrappergen/petsccfg.h Tools/C_util/wrappergen/prof.c Tools/C_util/wrappergen/prof_wrapper.c Tools/C_util/wrappergen/readproto.c Tools/C_util/wrappergen/sample.c Tools/C_util/wrappergen/sample.w Tools/C_util/wrappergen/system.c Tools/C_util/wrappergen/system.h Tools/C_util/wrappergen/tools.h Tools/C_util/wrappergen/wrappergen.c Tools/C_util/wrappergen/wrappergen.h Tools/C_util/wrappergen/write_proto.c commit 6d5b893593d27b6e0495cf1c70045856000bc5c0 Author: lijewski Date: Thu Sep 29 09:17:09 2011 -0700 sprintf() => snprintf() This allows us to specify the size of the buffer into which we're writing so that we don't overflow the buffer & write arbitrary memory. We also can tell when the buffer when the buffer is too small to contain everything we wanted to write and abort if necessary. Src/C_AMRLib/DatasetClient.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp Src/Extern/amrdata/AmrData.cpp Src/Extern/amrdata/DataServices.cpp Src/F_BaseLib/fabio_c.c commit 4450f4050d07e634a0154f5109870549bceb22e2 Author: lijewski Date: Wed Sep 28 15:48:15 2011 -0700 Oops. Forgot a semi-colon. Src/C_AMRLib/Particles.H commit 0642a68626998b9b5d1b49c2ac8a08aa2e530ecf Author: lijewski Date: Wed Sep 28 15:40:36 2011 -0700 Changed as many sprintf() calls to BoxLib::Concatenate() as possible. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/StationData.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/BndryRegister.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp Tools/C_util/WritePlotFile.cpp Tutorials/MultiGrid_C/writePlotFile.cpp Tutorials/WaveEquation_C/writePlotFile.cpp commit 20d78f69bcba04dd0fbb37d62c4077ef7f375528 Author: lijewski Date: Wed Sep 28 15:40:11 2011 -0700 Cut at new GNUmakefile for GIT. Tools/C_util/Statistics/GNUmakefile commit f7fb52b6ca12860ba5a262381213c036cc8216cf Author: lijewski Date: Wed Sep 28 15:36:08 2011 -0700 Cut at working GNUmakefile for new GIT repositories. Will needs to be fixed a tad once AmrData stuff is in it's correct place. Tools/C_util/Convergence/GNUmakefile commit 3d524a4eba9aba0833b3817c718be8a4a16ef656 Author: lijewski Date: Wed Sep 28 15:10:18 2011 -0700 Change [fF]DEBF from -O0 => -O1 for gfortran. Some version of gfortran get internal compiler error with -O0 on some hgproj code. Tools/C_mk/Make.defs commit fa44de59c67c8e5373f88fb3215d98eec30f1785 Author: lijewski Date: Wed Sep 28 14:56:14 2011 -0700 Removed some unused variables. Tutorials/WaveEquation_C/main.cpp commit 82a5224cb43b60bb00b7091e9b705260f4a231cc Author: lijewski Date: Wed Sep 28 09:16:56 2011 -0700 -O -> -O0 when debugging. Will produce slower but "truer" code. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit cbd22c57acb6341bf8024962cb71b7c82e8d64c6 Author: Weiqun Zhang Date: Tue Sep 27 16:15:24 2011 -0700 BoxLib_F with Dirichlet boundary works for both level solve and composite solve. Periodic and Neumann boundaries do not work yet. Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp commit f39c92fad3e5f1931b7fdbf4190d01b9f4a9a13f Author: Weiqun Zhang Date: Tue Sep 27 16:12:01 2011 -0700 MGT_Solver::set_vis_coefficients(PArray& aa, Array >& bb, const Real& beta, Array< Array >& xa, Array< Array >& xb, int index_order=0); Add an optional argument index_order. If index_order == 0, bb[dim][level] else, bb[level][dim] The second way is consistent with other set_?_coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit fcd3f86e12e08daa646fd386e0eb8301261d5749 Author: Weiqun Zhang Date: Tue Sep 27 14:23:50 2011 -0700 add routines for computing norms to makefile Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/main.cpp commit eb6676d19d1c25edfbcfed31005e36f0db7fe5f3 Merge: b7bceb7eb 21fcaa5ea Author: Weiqun Zhang Date: Tue Sep 27 14:21:39 2011 -0700 Merge branch 'boxarray' commit 21fcaa5ea828ba3e4eed54e8eb7c9fd19993eb2b Author: Weiqun Zhang Date: Tue Sep 27 14:20:52 2011 -0700 compute 2-norm and max-norm Tests/LinearSolvers/ComparisonTest/COMP_NORM_3d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tests/LinearSolvers/ComparisonTest/compute_norm.cpp commit b7bceb7eb605dc39f98d70bf82f78a5c3021403a Merge: ed9ac7d2b 4cba38c6a Author: lijewski Date: Tue Sep 27 14:02:34 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ed9ac7d2b421529a54f12e1cb99f3d95292d33f5 Author: lijewski Date: Tue Sep 27 14:01:29 2011 -0700 Removed a couple gfortran warning flags on the f90 debug line that weren't supported by gfortran version 4.3.3 or anything earlier. Tools/C_mk/Make.defs commit 13612c2e0edd9c5c8fa4dac30ae0dc68f6826e29 Author: lijewski Date: Tue Sep 27 13:58:53 2011 -0700 Removed some new/deletes and replaced with Array operations. Src/C_AMRLib/TagBox.cpp commit d769f319706bd0569219278015fd514bcbc6fc45 Author: lijewski Date: Tue Sep 27 13:58:24 2011 -0700 Disabled the copy assignment operator and copy constructor. We don't want folks copying BaseFabs. Src/C_BaseLib/BaseFab.H commit 4cba38c6ab1734ba880cec316fef2f4bce24eb21 Merge: a1958f23d 09ae66c72 Author: Weiqun Zhang Date: Tue Sep 27 12:49:41 2011 -0700 Merge branch 'master' into boxarray commit a1958f23d47e8458b060ec97d302f2170ae62290 Author: Weiqun Zhang Date: Tue Sep 27 12:48:23 2011 -0700 a file containing calls to BoxLib_F Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp commit 09ae66c723770c10c378b2236490c92de7756115 Merge: 5a95abba6 0dc127fac Author: Weiqun Zhang Date: Tue Sep 27 12:37:10 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5a95abba693f279cc26bba7dc8801a06c3d7365f Author: Weiqun Zhang Date: Tue Sep 27 12:36:50 2011 -0700 write plotfile Tutorials/MultiGrid_C/writePlotFile.H Tutorials/MultiGrid_C/writePlotFile.cpp commit e868b40f69c327d67ab611682099be04b1748e6a Author: Weiqun Zhang Date: Tue Sep 27 10:35:16 2011 -0700 Fix a bug: phys_bc was created by new BCRec, but was deleted. Tutorials/MultiGrid_C/main.cpp commit 0dc127fac63182502e924e13e4e96f387aa04b09 Merge: a2c5fa15c fe822a6be Author: Ann Almgren Date: Tue Sep 27 08:55:49 2011 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit a2c5fa15cebe72f984cf5fb6dac71bf5e2521233 Author: Ann Almgren Date: Tue Sep 27 08:54:25 2011 -0700 Make_defs: Turns out franklin does not like having two else statements in an "ifeq" sequence. We have replaced the else ... else by a nested if statement inside the first else. Tools/C_mk/Make.defs commit 930178f852184489e696fe59d4c8871a09e09aa1 Author: Weiqun Zhang Date: Mon Sep 26 17:26:16 2011 -0700 Fix a comment about copy constructor and copy assignment operator. Src/C_BoundaryLib/InterpBndryData.H commit fe822a6be67230a264f31399bd24cb5a0e8238ed Merge: cd4ae62d9 d4e1b7f37 Author: Weiqun Zhang Date: Mon Sep 26 15:55:59 2011 -0700 Merge branch 'master' into boxarray commit cd4ae62d9b67f2e3785769a0a5ff1e7c6b4c92bd Author: Weiqun Zhang Date: Mon Sep 26 15:54:59 2011 -0700 BoxLib_F runs. But not sure whether or not the boundaries are set correctly. Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp commit d4e1b7f37dddf3c7cf3dd864fe7ee5b15f914ff5 Author: lijewski Date: Mon Sep 26 13:47:06 2011 -0700 Changed the way Arenas are allocated. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/FabArray.H Tests/LinearSolvers/C_NodalMG/proj.cpp commit 18e302e158866b0d2dc2f1f02a9dac23a6c78f1f Author: Weiqun Zhang Date: Fri Sep 23 18:28:37 2011 -0700 Started the linear solver comparison test The setup of multilevel grids, coefficients, rhs and exact solutions are done. It can also write a plotfile. Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp commit 0d0064cdfea64e0a1b5082262be537a0f7970b00 Merge: bc82cc698 c98917c8a Author: Ann Almgren Date: Fri Sep 23 10:15:21 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bc82cc69870754a9380dcf55d9b117dea0e93831 Author: Ann Almgren Date: Fri Sep 23 10:14:56 2011 -0700 We now pass vel_fac into Particles::InitCosmo() instead of computing it inside. Src/C_AMRLib/Particles.H commit c98917c8a4aedec04e9b1989454708438056fc6f Author: Michael Zingale Date: Fri Sep 23 12:09:08 2011 -0400 add support for link files (link1File, link2File, link3File). These are linked into the run directory instead of copied. Tools/C_util/regtests/testnew.py commit a75359f4c40e155023058c193d976fbbd6b32b52 Author: Michael Zingale Date: Fri Sep 23 10:43:06 2011 -0400 do a symlink for helm_table.dat instead of copying it Tools/C_util/regtests/testnew.py commit a470ea6228e2518345d2874babc3d9a6e7480bac Author: Michael Zingale Date: Thu Sep 22 22:42:45 2011 -0400 update for testnew.py Tools/C_util/regtests/Castro-tests.ini commit 9dae2b1ed543875da392c68f5a46a4c9ec268bf8 Author: Michael Zingale Date: Thu Sep 22 22:14:08 2011 -0400 update to work with the latest version of the test suite Tools/C_util/regtests/Maestro-tests.ini commit d472258203827ee674aa4ea12cbfd4ba28c5e8a2 Author: Michael Zingale Date: Thu Sep 22 22:00:12 2011 -0400 add git pull and changelogs for the boxlib directory Tools/C_util/regtests/testnew.py commit 4b3d3b33c15b12b7571e5d76953db145151a6ee4 Author: Weiqun Zhang Date: Thu Sep 22 14:33:12 2011 -0700 MG tutorial now writes plotfiles so that they can be read by Visit. Tutorials/MultiGrid_C/Make.package Tutorials/MultiGrid_C/main.cpp commit ffac0acf8f8750ac352798682afdb5a3f091eb35 Author: Weiqun Zhang Date: Thu Sep 22 14:32:56 2011 -0700 Make writePlotFile more general for an arbitary number of components. Tutorials/WaveEquation_C/writePlotFile.cpp commit e012e685b4c9a9256ebe176bf28635ad12f51646 Author: Weiqun Zhang Date: Thu Sep 22 13:45:52 2011 -0700 slight cleanup of the Hypre driver Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H commit c2ce66dcc30f5fa60f4c4e59d41b1a5e1fe2d5a9 Merge: a1e25beb5 6a9107e64 Author: Michael Zingale Date: Thu Sep 22 15:20:44 2011 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit a1e25beb56977500f94b56ea09adc5b2a72521d7 Author: Michael Zingale Date: Thu Sep 22 15:20:00 2011 -0400 add more checks Tools/C_util/regtests/testnew.py commit 6a9107e642e9f3d44a08c9bfd3a17bf08f5e69a0 Author: Weiqun Zhang Date: Wed Sep 21 16:41:36 2011 -0700 Give warning when both of the following are true: ifndef CG_USE_OLD_CONVERGENCE_CRITERIA mg. use_Anorm_for_convergence = 0. This appears to be a bad combination at least for the hard test in MG tutorial. Src/LinearSolvers/C_CellMG/MultiGrid.cpp Tutorials/MultiGrid_C/GNUmakefile commit 3b7df33d067889b40b258597aad35a2a5bc6eef6 Merge: 955bdf4cf d08341105 Author: Weiqun Zhang Date: Wed Sep 21 15:56:53 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 955bdf4cfa80d72c8d8a7eee6115c20293b2c6cd Author: Weiqun Zhang Date: Wed Sep 21 15:53:40 2011 -0700 It seems too verbose that all the grids are printed out when mg.verbose>2. The threshold is now >4. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 3df724a2e122b3f9f9f64ddd28179dca738b1081 Author: Weiqun Zhang Date: Wed Sep 21 15:52:49 2011 -0700 delete a space in write(*,*) Src/LinearSolvers/F_MG/itsol.f90 commit f4408cc28ae1157c6bd1daa73df546ae5af80488 Author: Weiqun Zhang Date: Wed Sep 21 15:39:52 2011 -0700 In the bottom CG solver, A and RHS are rescaled first. So the initial error printed out is different from the error printed out before bottom. To avoid confusion, a note is added. Src/LinearSolvers/F_MG/itsol.f90 commit 3bee73c44893be673497637a7ded8cdee21b6c47 Author: Weiqun Zhang Date: Wed Sep 21 15:24:44 2011 -0700 Add CPPFLAGS += -DCG_USE_OLD_CONVERGENCE_CRITERIA This makes BoxLib_C bottom CG solver to use the old convergence criteria. Using the new criteria, BoxLIb_C will fail at the hard test. Tutorials/MultiGrid_C/GNUmakefile commit d08341105b5ecc5f370d5b54822c73618e1698a8 Merge: 89a73d635 a8c40c6ce Author: Aleks Donev Date: Wed Sep 21 17:26:17 2011 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 89a73d635e7e5f131dd7cbc85b4ba9d722d5c508 Author: Aleksandar Donev Date: Wed Sep 21 16:28:33 2011 -0400 Added Courant systems to Makefile Tools/F_mk/GMakeMPI.mak commit a8c40c6ce3262a41076040e33cc1e77372735968 Author: Michael Zingale Date: Wed Sep 21 12:22:57 2011 -0400 add support for BOXLIB_HOME. Finish cleaning things up. Tools/C_util/regtests/testnew.py commit 2ef7324293435edfcc9ac54d5460477423068cb7 Author: Michael Zingale Date: Wed Sep 21 12:00:08 2011 -0400 add BOXLIB_DIR to the list of information held by this module. Tools/F_scripts/make_build_info commit 03f8a7e9e3b53ade94a35c64983b59cbd1e18cfe Author: Weiqun Zhang Date: Tue Sep 20 11:08:18 2011 -0700 Added SMG solver for Hypre Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/inputs.3d commit dbfd9afea1a273516de53f5b54d4fca4b9807e99 Merge: 2d6f5756c 346fac64e Author: Marc Day Date: Mon Sep 19 17:19:18 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2d6f5756c44812f3ee2a0aca08c5403c2378d1f0 Author: Marc Day Date: Mon Sep 19 17:18:55 2011 -0700 Replace Wall with everything but unused-dummy-arguments Tools/C_mk/Make.defs commit e6d5944abc0f57c0b56cadf0c2b14177b249f8c9 Author: Weiqun Zhang Date: Mon Sep 19 15:18:40 2011 -0700 Two parameters are introduced in the setup of problems. We now can run test problems with variable diffusion coefficient. Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/RHS_3D.F Tutorials/MultiGrid_C/RHS_F.H Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit 346fac64e24d4ef2681ff7f801c4c36c518cebd8 Merge: 550b78cca 177d4d0b4 Author: Ann Almgren Date: Mon Sep 19 13:50:40 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 550b78cca3314487fffa6b8909b7823a98e6aec5 Author: Ann Almgren Date: Mon Sep 19 13:49:30 2011 -0700 Tests/StencilOrder: Add this new test program (with accompanying README file) to demonstrate the difference in timings that we see by simply modifying the ordering of the indices in multigrid stencils, from ss(i,j,k,n) to ss(n,i,j,k) demonstrates a roughly factor 5 speedup for this example stencil with 21 entries. Tests/StencilOrder/README Tests/StencilOrder/program.f90 commit 177d4d0b493cc5901da8a84295ad9467550e55f2 Merge: b6bb2ef9b 4a5989f96 Author: lijewski Date: Mon Sep 19 13:07:46 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b6bb2ef9b2377786d56ae1d8e59bd4793c45d2a9 Author: lijewski Date: Mon Sep 19 13:07:14 2011 -0700 Some endian test stuff for Darwin from Chris Malone. Tools/F_mk/GMakedefs.mak commit 4a5989f9622093fd1e9c79d3793dcb8e23b76d17 Merge: c09ab80de b69d6b480 Author: Michael Zingale Date: Mon Sep 19 15:22:40 2011 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c09ab80decc09a92a909d1a53e5fa1cdd2dd2846 Author: Michael Zingale Date: Mon Sep 19 15:21:54 2011 -0400 new version of the test suite. This uses test and suite objects to make things clearer and more managable. Start of the changes to get git into things Tools/C_util/regtests/testnew.py commit b69d6b480ab0ea6a830e2761131014148bafd0b9 Author: Ann Almgren Date: Mon Sep 19 11:48:06 2011 -0700 Changes in Src/LinearSolvers/F_MG only: These files use the new stencil ordering: ss(n,i,j,k) instead of ss(i,j,k,n). This requires a new type of multifab (type stencil) which orders the data this way, but this new type does *not* currently support all the regular multifab operations, so care must be used. Only the stencil arrays ("ss") are re-ordered this way. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 6dbdd1ae374461de4aa776c0e842cd79b56e01d6 Author: Ann Almgren Date: Sun Sep 18 07:05:39 2011 -0700 Add more output so it will be easier to see which test was run. Tutorials/MultiGrid_C/main.cpp commit 2bff14bdf3314da78b6fb47ce5a526ce9a0a7011 Author: Ann Almgren Date: Fri Sep 16 18:27:38 2011 -0700 Add new flag to control BoxLib_C convergence criteria. Tutorials/MultiGrid_C/inputs.3d commit 2dda8dc5f6facac56b6296e392a00debb8beb8e1 Author: lijewski Date: Fri Sep 16 16:45:14 2011 -0700 Removed some duplicate code in Make.mpi. In vector_i, removed the built data member and use associated() instead. Use BUMP=1.5 as the exponential growth factor. Some cleanup as well. Src/F_BaseLib/vector_i.f90 Tools/C_mk/Make.mpi commit 7107777ca5c7c2dedfcba999a8dac73b5041bd76 Merge: 66772967e 5deff2267 Author: Weiqun Zhang Date: Fri Sep 16 16:19:56 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 66772967e4e71940033578cd7093acbdb0d281d1 Author: Weiqun Zhang Date: Fri Sep 16 16:12:54 2011 -0700 fix a problem in inputs Tutorials/MultiGrid_C/inputs.3d commit 5deff22675e3e76af5ac3f9ea6027473fc9cc622 Author: Ann Almgren Date: Fri Sep 16 15:38:59 2011 -0700 Add a flag "use_Anorm_for_convergence" that allows us to control whether or not we use the Anorm in the convergence test. This allows us to test convergence against the F90 solver and the Hypre solver. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 9c3b83de913a5639debb97e5f5c7f014f7940b5f Author: Ann Almgren Date: Fri Sep 16 15:26:15 2011 -0700 Fix test for print statements regarding convergence Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 6e8bee67512a04e9a319d4ef4db61e85d2926eb3 Author: Ann Almgren Date: Fri Sep 16 15:04:57 2011 -0700 Clean up print statements for convergence test. Src/LinearSolvers/F_MG/ml_cc.f90 commit 58acdf886c8966cf224e128669daccbdd28e677a Author: Ann Almgren Date: Fri Sep 16 14:33:24 2011 -0700 Add additional output (if verbose > 0) so we know what convergence criterion was used. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit fa32f3527ac2725224799c40a2d5b016684a65d7 Author: Ann Almgren Date: Fri Sep 16 14:31:23 2011 -0700 GNUmakefile: Add much more commentary about how to set variables so this will compile. Tutorials/MultiGrid_C/GNUmakefile commit 374b87908e80c5c4b2f832a027c674be809f4fc8 Author: Weiqun Zhang Date: Fri Sep 16 13:13:06 2011 -0700 pass high-order boundary parameter to Fortran Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F commit 133cefb6868f06b58a974713290d53e9f8218eb9 Author: Weiqun Zhang Date: Fri Sep 16 12:04:40 2011 -0700 make the stencil index in hypre consistent with what returned by BoxLib bndlib Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H commit 386964b7a0ce7fa405d360938d6004fc23120e9a Merge: c7010a1d6 d6044764e Author: Weiqun Zhang Date: Fri Sep 16 10:45:48 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c7010a1d686afbfef07e25a61a6143e282771c60 Author: Weiqun Zhang Date: Fri Sep 16 10:45:40 2011 -0700 minor cleanup Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp commit 2cac522671e933846590cd5c141a132550937520 Author: Weiqun Zhang Date: Fri Sep 16 10:44:38 2011 -0700 remove redundant soln.setVale(0.)'s Tutorials/MultiGrid_C/main.cpp commit d6044764e232d125215adf86588a49e9eaba2210 Author: Ann Almgren Date: Fri Sep 16 10:17:41 2011 -0700 Separate out the Fortran code for the RHS from the Fortran code for the coefficients. Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/Make.package Tutorials/MultiGrid_C/RHS_3D.F Tutorials/MultiGrid_C/RHS_F.H Tutorials/MultiGrid_C/main.cpp commit 160d3fd26f6b7a86112e48f9970b83b60b36b17c Author: Ann Almgren Date: Fri Sep 16 10:08:28 2011 -0700 Explicitly set cg.v = 0 so we don't get CG messages from BoxLib_C solver. Tutorials/MultiGrid_C/inputs.3d commit 5db3cfa011e60c28bd21b352bf78d212df92bcf2 Author: Ann Almgren Date: Thu Sep 15 21:37:36 2011 -0700 1) Set solution to zero before each solve. 2) Wrap one more solve_with_hypre by ifdef USEHYPRE Tutorials/MultiGrid_C/main.cpp commit 4ea2d43473eb4bf5c0ac690fa59b45263464bf25 Author: Weiqun Zhang Date: Thu Sep 15 17:40:32 2011 -0700 fix a typo in a string for output file name Tutorials/MultiGrid_C/main.cpp commit f37b356785ae8710cd773ab2d76bcb5bbc9bdc92 Merge: 3c8c721af 8763c6cdc Author: Weiqun Zhang Date: Thu Sep 15 17:35:53 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Tutorials/MultiGrid_C/main.cpp commit 3c8c721af336d4098b6b869b7cbdb8933e2f2be7 Author: Weiqun Zhang Date: Thu Sep 15 15:55:46 2011 -0700 Make bc_type and solver_type enum type rather than string type. Using string is more error-prone due to typos in the string. Move to the part that sets boundaries to a function. Bot BoxLib_C and Hypre use it. Tutorials/MultiGrid_C/main.cpp commit 8763c6cdc475447b7372e1611edf8c4f384378f2 Merge: 93028fd6b 18d138c28 Author: Ann Almgren Date: Thu Sep 15 15:35:43 2011 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 93028fd6b346ab53ce116edc8094c8af278ebdb2 Author: Ann Almgren Date: Thu Sep 15 15:35:25 2011 -0700 Add solver_type = "All" and additional print statements. Tutorials/MultiGrid_C/main.cpp commit 18d138c28a55cd818686e1c2a8df6f77dfaba40e Author: Ann Almgren Date: Thu Sep 15 13:53:35 2011 -0700 1) Replace 1e40 by 1e200 in test in fillpatch.f90 whether region is completely covered 2) Modify print statement to be more informative. Src/F_BaseLib/fillpatch.f90 commit 5b20fe6fd8629c36cebf3650f8036ff1486ab43b Author: Weiqun Zhang Date: Thu Sep 15 10:37:03 2011 -0700 The index for dimension was sometimes "n", sometimes "dir", and sometimes "i". It is now changed to "n" for consistency. Tutorials/MultiGrid_C/main.cpp commit 765f5b6faa8fb9b5fef0efac8ecb90fbbc898641 Author: Weiqun Zhang Date: Thu Sep 15 10:25:27 2011 -0700 Fix a bug. dx[i] should be dx[n], where i is MFIter index, n is dimension index. update the setup of boundaries before calling hypre Tutorials/MultiGrid_C/main.cpp commit 71c926a99daf3f5ef1dedfef830b23a76a407223 Author: lijewski Date: Thu Sep 15 10:15:24 2011 -0700 Changes from Chris Malone. Src/F_BaseLib/GPackage.mak Tools/C_mk/Make.Darwin Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit dd6c3e154402334dab6b60872949374e7f510eb4 Merge: 4d5cd28b8 3d33d18e6 Author: Marc Day Date: Thu Sep 15 08:46:57 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4d5cd28b89f47b5fb9c36f593f460bb89b6a6acf Author: Marc Day Date: Thu Sep 15 08:46:44 2011 -0700 Clean up screen dump during build using C_mk stuff: if the GNUmakefile (or make cmd line) contains VERBOSE=FALSE or VERBOSE=OFF, the build line will not be echoed to the screen. Added a line to simply say ...Building XXX... , commented out strip72 warning text, removed warning about unused dummy arguments in gfortran. Comment out silly echo SUCCESS, since it reports success regardless - tests based on the presence of this string should be restructured. Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/C_scripts/strip72 commit 3d33d18e690fcca4ffda78d8d235986388eee588 Author: lijewski Date: Thu Sep 15 08:44:40 2011 -0700 A little simplification; make the swap() call for clearing memory one liners. Src/C_AMRLib/Particles.H commit ce3f8101122f9ddc2e19a2857b5f26003798b8f1 Author: Ann Almgren Date: Wed Sep 14 21:28:46 2011 -0700 1) Fix boundary conditions for BoxLib_C solver in Tutorials/Multigrid_C 2) Change multifab_remote --> remote in all places for consistency Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Tutorials/MultiGrid_C/main.cpp commit 67e2adadf4bf64b6265de30a5b22c8f40fe43282 Merge: b8fcdaf7c f24274ced Author: Weiqun Zhang Date: Wed Sep 14 18:20:48 2011 -0700 merge commit b8fcdaf7cfe73b7cb64c2efc271cb72393e98bc5 Author: Weiqun Zhang Date: Wed Sep 14 18:12:03 2011 -0700 hypre A matrix is no longer symmetric Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit f24274cedeb6001fcde72afadf445563ad13db51 Author: lijewski Date: Wed Sep 14 17:11:11 2011 -0700 More mods from Chris Malone. Tools/F_mk/GMakedefs.mak commit 0c2f5e2857f3610e630858d278683dd4b74eb799 Author: lijewski Date: Wed Sep 14 16:51:48 2011 -0700 Added Darwin_intel.mak from Chris Malone. Tools/F_mk/comps/Darwin_intel.mak commit c66f71a3d3665962cad36cedbb0fc4849b663d8d Author: Ann Almgren Date: Wed Sep 14 14:19:49 2011 -0700 Add comments about verbosity flags. Tutorials/MultiGrid_C/inputs.3d commit f0ba7df0ac2ce7b5d94ced84f9d93fc07a8132f9 Merge: a466011f8 3c236289b Author: Ann Almgren Date: Wed Sep 14 13:29:35 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3c236289b211a773f276f2c93921f8e3bf82d6d8 Author: Weiqun Zhang Date: Wed Sep 14 12:51:39 2011 -0700 fix default BOXLIB_HOME Tutorials/MultiGrid_C/GNUmakefile commit a8dd99a45d594bc49e1797096f6ec21cc86263b6 Author: Weiqun Zhang Date: Wed Sep 14 12:08:01 2011 -0700 clean up Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit 80cd5771a15d9c445b7d7a25a182fda8905db0de Author: Weiqun Zhang Date: Wed Sep 14 10:19:25 2011 -0700 add the iostream and iomanip headers to HypreABecLap Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H commit ddb68f90d67cce601666e40bb7fbd3c5ad087de6 Author: Weiqun Zhang Date: Wed Sep 14 10:14:54 2011 -0700 Add USE_HYPRE to GNUmakefile so that the code can be compiled without hypre. Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/main.cpp commit a466011f8e0bec42cae37f2829f796ca9d7c7494 Merge: 895f426a9 90b45e11c Author: Ann Almgren Date: Wed Sep 14 08:29:26 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 90b45e11c0a22c9473e5ad910440fc5cfd5f0a07 Author: Weiqun Zhang Date: Wed Sep 14 06:18:21 2011 -0700 rename solvers to BoxLib_C and BoxLib_F Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit f9595a74421155c88b6911bef017cd7b1664028e Merge: f3255977e 82803c556 Author: Weiqun Zhang Date: Wed Sep 14 05:38:55 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f3255977e18211ded75d33e45f6b9b6b763a472b Author: Weiqun Zhang Date: Wed Sep 14 05:38:15 2011 -0700 check in hypre driver Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H Tutorials/MultiGrid_C/HypreABecLap/Make.package commit 895f426a99eeff269c6608c0ded4d76864f92361 Merge: e5ded45cb 82803c556 Author: Ann Almgren Date: Tue Sep 13 22:08:12 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1103bccbee3a53451d7d8b84ca10753e75b81135 Author: Weiqun Zhang Date: Tue Sep 13 18:12:45 2011 -0700 8 combinations work. The one doesn't work is C++ with periodic boundary. Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit 82803c55679f36b57d0c1e8671fe26f702e62de6 Author: Marc Day Date: Tue Sep 13 13:40:31 2011 -0700 modify install procedure to clean up how an external code might link to the libraries CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/ParmParse.H Src/C_BoundaryLib/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/Extern/gslib/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Tools/CMake/CCSEConfig-install.cmake.in Tools/CMake/CCSEConfigReport.cmake Tools/CMake/CCSEConfigVersion-install.cmake.in Tools/CMake/CCSELinkLine.cmake Tools/CMake/CCSEOptions.cmake Tools/CMake/InstallManager.cmake Tools/CMake/MakefileConfig.export.in Tools/CMake/ParseLibraryList.cmake Tools/CMake/TransformVersion.cmake Tools/C_scripts/boxlib-build.sh commit e5ded45cb11f631ba1525ca86e7872d83cc8b17e Author: Ann Almgren Date: Tue Sep 13 13:15:18 2011 -0700 This now has the working 3d 4th order variable coefficient stencil. Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 commit 3af8df5f9f287d0564c57cac5c7616437b9cfe7d Author: lijewski Date: Tue Sep 13 11:05:04 2011 -0700 Do a maxSize() on the BoxArrays to get more grids. Tests/C_BaseLib/tMFcopy.cpp commit cceb168908c23dab03377181b0294ef295b24efc Author: lijewski Date: Tue Sep 13 10:51:34 2011 -0700 More work on parallel copy test. Tests/C_BaseLib/tMFcopy.cpp commit 20afe70790529b9587ccefd6284a218caef75a29 Author: Ann Almgren Date: Tue Sep 13 07:00:35 2011 -0700 Fix the 3d 4th order variable coefficient stencil. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 7f39bd501590f08a243085dcab29a0f0e5941868 Author: Ann Almgren Date: Mon Sep 12 18:21:20 2011 -0700 More trying to get the 3D variable coefficient 4th order solver to work. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 commit 434edf0c6a192b23e9368e0c1cc7b00d23903ce3 Author: Weiqun Zhang Date: Mon Sep 12 16:38:08 2011 -0700 fixed a couple of bugs. C++ & F90 solvers work for Dirichlet boundary. Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit 312a9b3daf7a5add12c3b3a3c5bd3542d0407f75 Merge: 158146557 4564b07bf Author: Ann Almgren Date: Mon Sep 12 14:53:52 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 158146557a521f7f3720aaff8e64b7c99719b81d Author: Ann Almgren Date: Mon Sep 12 14:53:00 2011 -0700 1) Broke cc_stencil.f90 into two files -- cc_stencil.f90 and cc_stencil_apply.f90 2) Added 4th order stencil for variable coefficients in 3d (61 terms in stencil) Src/LinearSolvers/F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 4564b07bf55d7dfdc9dccd8cfb01e9834b17f9a5 Merge: 34808451d 7873d5fec Author: lijewski Date: Mon Sep 12 14:31:11 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 34808451dc4a3c653fe50f1b8c69b6f9b637e192 Author: lijewski Date: Mon Sep 12 14:30:59 2011 -0700 Fixed typo in comment. Tests/C_BaseLib/tMFcopy.cpp commit 12880bb7e044f58d6cbab28540a5cd5dd2d5f98e Author: lijewski Date: Mon Sep 12 14:30:02 2011 -0700 Added SFC_Threshold() functions to set/get the sfc_threshold. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 41c5d33574e27e98f51e03624020740fc8298949 Author: lijewski Date: Mon Sep 12 14:28:23 2011 -0700 Added new test routine that tests parallel copy between two multifabs whose boxarrays cover the same area but have different number of boxes and hence different distribution. Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tMFcopy.cpp commit 7873d5fec28af829416466a858545238502b5189 Author: Ann Almgren Date: Mon Sep 12 12:55:35 2011 -0700 Remove extra arguments so this compiles. Src/LinearSolvers/F_MG/cc_stencil_fill.f90 commit 37ec61afdb0592a46de314e126d830810e4fada7 Author: Ann Almgren Date: Mon Sep 12 12:54:41 2011 -0700 Need to declare the new variables so this compiles (though still not working) Src/LinearSolvers/F_MG/cc_stencil.f90 commit 269105e601df000c58af1cc709e0c2a08012b45d Author: Ann Almgren Date: Mon Sep 12 12:06:36 2011 -0700 1) New improved version of subroutine minion_fill_full_2d 2) Introduced subroutine minion_fill_full_3d but it is not yet complete. 3) Modified call to minion_full_fill_3d to test on whether ns = 61, not 125. Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 commit b153170d2a1db58790833f7f4323c3fd70e530a5 Author: Ann Almgren Date: Sat Sep 10 09:32:52 2011 -0700 Latest version -- added choice of bc_type -- still not fully working. Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit 2da2316aa8250009a64891daa50cad0f2f82e1e4 Author: Ann Almgren Date: Fri Sep 9 21:54:36 2011 -0700 New Tutorials directory -- a C++ MultiGrid driver that will call the C++ solver, the F90 solver and the Hypre solver. Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/Make.package Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit c6eb615f1c91e61b03aa1d808caf2a991c827dbe Author: Ann Almgren Date: Fri Sep 9 17:25:13 2011 -0700 No need to copy mf into plotMF Tutorials/WaveEquation_C/writePlotFile.cpp commit 98092bb26e12850b94ba27b3b1568be7244e4048 Author: Ann Almgren Date: Thu Sep 8 11:10:30 2011 -0700 Keep this file here but don't put it in GPackage.mak Signed-off-by: Ann Almgren Src/F_BaseLib/mt19937ar.f90 commit 329f995ff2adfbd01228e0bb65e50b72ea21e115 Author: Ann Almgren Date: Thu Sep 8 09:49:30 2011 -0700 Include options for the Gottingen machines. Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi Tools/F_mk/GMakedefs.mak commit a16fd652bfddc6d5a70d458bd82c4d3d10bac606 Author: Marc Day Date: Wed Sep 7 19:15:59 2011 -0700 version/release info BoxLib_Version.txt Tools/C_scripts/gen_release_tarball.txt commit b322708519e191d37f8594aaddd548dabda6c749 Author: Marc Day Date: Wed Sep 7 18:41:58 2011 -0700 Add gslib files here to simplify distribution for ASCEM Src/Extern/gslib/CMakeLists.txt Src/Extern/gslib/acorni.f Src/Extern/gslib/backtr.f Src/Extern/gslib/beyond.f Src/Extern/gslib/blue.f Src/Extern/gslib/chknam.f Src/Extern/gslib/chktitle.f Src/Extern/gslib/cova3.f Src/Extern/gslib/dlocate.f Src/Extern/gslib/dpowint.f Src/Extern/gslib/dsortem.f Src/Extern/gslib/gauinv.f Src/Extern/gslib/gcum.f Src/Extern/gslib/getindx.f Src/Extern/gslib/getz.f Src/Extern/gslib/green.f Src/Extern/gslib/hexa.f Src/Extern/gslib/ksol.f Src/Extern/gslib/ktsol.f Src/Extern/gslib/locate.f Src/Extern/gslib/nscore.f Src/Extern/gslib/numtext.f Src/Extern/gslib/ordrel.f Src/Extern/gslib/picksupr.f Src/Extern/gslib/powint.f Src/Extern/gslib/psfill.f Src/Extern/gslib/psline.f Src/Extern/gslib/pstext.f Src/Extern/gslib/rand.f Src/Extern/gslib/red.f Src/Extern/gslib/resc.f Src/Extern/gslib/scal.f Src/Extern/gslib/setrot.f Src/Extern/gslib/setsupr.f Src/Extern/gslib/sortem.f Src/Extern/gslib/sqdist.f Src/Extern/gslib/srchsupr.f Src/Extern/gslib/strlen.f commit 00834825b1ceaed39edbf631c20b01ed22fc6f5a Author: Marc Day Date: Wed Sep 7 18:40:50 2011 -0700 Add some amrdata files here as a temporary measure until amrvis available elsewhere Src/Extern/amrdata/AmrData.H Src/Extern/amrdata/AmrData.cpp Src/Extern/amrdata/AmrvisConstants.H Src/Extern/amrdata/CMakeLists.txt Src/Extern/amrdata/DataServices.H Src/Extern/amrdata/DataServices.cpp Src/Extern/amrdata/FABUTIL_2D.F Src/Extern/amrdata/FABUTIL_3D.F Src/Extern/amrdata/Make.package commit 35073eb8f00d83637d2c7f1d034d9cd008b51419 Author: Marc Day Date: Wed Sep 7 18:38:40 2011 -0700 Add support for CMake builds CMakeLists.txt Src/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Src/C_BoundaryLib/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Tools/CMake/CCSEConfigReport.cmake Tools/CMake/CCSEOptions.cmake Tools/CMake/CMakeParseArguments.cmake Tools/CMake/ExampleBoxLibConfig.cmake Tools/CMake/ExampleCMakeLists.txt_CCSEApp Tools/CMake/PreprocessBoxLibFortran.cmake Tools/CMake/TestManager.cmake Tools/C_scripts/boxlib-build.sh commit 5f65fa2a6ccc455e52eaeddff2b2d2a32be73a60 Merge: 25be55a57 1872ad5d5 Author: Marc Day Date: Wed Sep 7 18:34:43 2011 -0700 Merge branch 'master' of /home/marc/src/CCSE/BoxLib commit 25be55a5720ab3e923c3655d057f7cddc2e73f93 Author: Marc Day Date: Wed Sep 7 18:32:09 2011 -0700 Add Utility.H Src/C_AMRLib/SlabStat.cpp commit 1872ad5d5b61ea1bcc98d75a092afba92c2d45b6 Author: lijewski Date: Tue Sep 6 09:51:38 2011 -0700 Got rid of explicit copy constructors and copy assignment operators. Use the compiler generated ones. Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/Orientation.H commit 6bdd8ca145a028cf0da5ef0ed3f6870cb65507a4 Author: cmalone Date: Tue Aug 30 15:04:33 2011 -0700 get rid of all the *.mod files in the CWD Signed-off-by: lijewski Tools/C_mk/Make.Darwin commit 05d6ea6c8518320d9fe0c1d3a98f8fc9f3573583 Author: lijewski Date: Tue Aug 30 13:52:19 2011 -0700 workd with USE_F90_MG=TRUE Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 8c4b2719949fb36bc17c6bf7af213823423ff83e Author: lijewski Date: Tue Aug 30 12:59:41 2011 -0700 A wad of simplification and consolidation. Removed BL_USECLOSE -- always assume true. Removed BL_USEOLDREAD -- always assume false. Always use the ReadAndBcastFile() stuff whether or not USE_MPI=TRUE. Always use the fancy probin reader regardless of whether or not USE_MPI=TRUE. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/VisMF.cpp commit 4fc226e9c37a7661cc820e178a3c343c226edd52 Author: Ann Almgren Date: Tue Aug 30 09:03:02 2011 -0700 Added Tutorials directory with first example: WaveEquation_C, a simple program that uses BoxLib stuff with the C++ make system to run a single-level wave equation evolution routine. Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/Make.package Tutorials/WaveEquation_C/advance_2d.f90 Tutorials/WaveEquation_C/advance_3d.f90 Tutorials/WaveEquation_C/init_data_2d.f90 Tutorials/WaveEquation_C/init_data_3d.f90 Tutorials/WaveEquation_C/inputs_2d Tutorials/WaveEquation_C/inputs_3d Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp commit 9c85fdb6ad65d19f5b13369625f7f5e4f25b0902 Author: lijewski Date: Mon Aug 29 14:51:27 2011 -0700 Added Initialize()/Finalize() functions to ensure static variables are initialized properly. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 81cbb868c2e6012b6ab77502b3f668f72209f4fe Merge: ccf6f7b20 2369ea7c6 Author: ajnonaka Date: Fri Aug 26 16:12:38 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ccf6f7b203c878e2261386fd76527220f74a31e6 Author: ajnonaka Date: Fri Aug 26 16:11:59 2011 -0700 Chris' mod for macs Tools/F_mk/GMakeMPI.mak commit 51a9bfd921ad5d80f15621850cbb3d4927a8eae1 Author: ajnonaka Date: Fri Aug 26 16:11:37 2011 -0700 Chris' mod for mac's Tools/C_mk/Make.Darwin commit 2369ea7c65aa91ee76cc747e7e0a9dae81c202a1 Author: lijewski Date: Fri Aug 26 16:11:27 2011 -0700 0.0 -> 0.0d0 in a few places. Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/LinearSolvers/C_TensorMG/DV_2D.F commit 782319319ecff0729dcee2b9a069df8c52558150 Author: Theodore Kisner Date: Thu Aug 25 15:58:55 2011 -0700 Had to modify this commit because BoxLib.f90 was named FBoxLib.f90 in Ted's work and boxlib_f.f90 in Ann's work. We kept it as boxlib_f.f90. Old message: Rename BoxLib.f90 to FBoxLib.f90 to avoid name conflicts in the output object files when building outputs in the top level of the source tree. Signed-off-by: lijewski Src/F_BaseLib/GPackage.mak commit da21ffe648c5028b4309d48ea73c0cd3ec437646 Author: Theodore Kisner Date: Thu Aug 25 15:15:03 2011 -0700 Convert Cray vector merge functions to modern fortran merge syntax. Signed-off-by: lijewski Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/LinearSolvers/C_CellMG/ABec_1D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LO_1D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_1D.F Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_TensorMG/DV_2D.F Src/LinearSolvers/C_TensorMG/DV_3D4.F commit 5de41c7e1794ed6f992b6b6fdd90cbd2a2f61e2f Author: lijewski Date: Fri Aug 26 13:58:49 2011 -0700 Removed some unused routines. Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f commit 2eea0ea5796552380e70cd4fc7222944b90b8063 Author: lijewski Date: Fri Aug 26 10:48:51 2011 -0700 Wrapped plotfile and checkpoint file timings in (verbose > 0). Also removed the probStartTime member from Amr.H. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 9481c869e2c173d5c2b11ff3cb8652b19d8423ec Author: Ann Almgren Date: Thu Aug 25 15:16:41 2011 -0700 Before these lines were commented out -- now they have been removed. Src/LinearSolvers/F_MG/FParallelMG.mak commit 298a3086de930e3d3c1b293ef8cb9c08bd176016 Author: Ann Almgren Date: Thu Aug 25 15:13:51 2011 -0700 1) Rename six files so they no longer have name conflicts with the C++ file. So ... box.f90 --> box_f.f90 boxarray.f90 --> boxarray_f.f90 cluster.f90 --> cluster_f.f90 BoxLib.f90 --> boxlib_f.f90 multifab.f90 --> multifab_f.f90 particles.f90 --> particles_f.f90 Note that this does not affect other files as these are included by module name, not file name. 2) Also remove from F_MG/FParallelMG.mak the files which are in F_BaseLib/FParallel.mak Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/box_f.f90 Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/particles_f.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit b39c67c43d9bd443667b737eeb9c660998b56645 Author: lijewski Date: Wed Aug 24 12:33:20 2011 -0700 A simple commit to check that email notices are working. Docs/GNUmakefile commit f55d31b00b3e98fc25ab530415cb6e6e407b5f56 Author: Ann Almgren Date: Tue Aug 23 14:04:30 2011 -0700 Update the GNUmakefile in Tests/LinearSolvers/ComparisonTest Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 089a0b50e96ed0fecd703226ea6741a2b54686af Author: vince Date: Tue Aug 23 14:00:08 2011 -0700 email push test 0. v. Tests/C_BaseLib/tVisMF.cpp commit bc88ee6744323ad929f421326d53b1c2ac52d643 Author: lijewski Date: Thu Aug 18 14:12:34 2011 -0700 Quieted some warnings. Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp Src/C_BaseLib/BoxLib.cpp commit 4adfaa3b222ac6369cd42ac44b288098571163b3 Author: lijewski Date: Thu Aug 18 13:44:14 2011 -0700 Cleaned up the Make stuff. Removed all hints of installing things since we don't do that anymore. Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/C_scripts/install-sh commit d83c6c2c7f4058e237edf893998933d1b9bf6167 Author: lijewski Date: Thu Aug 18 13:23:14 2011 -0700 Removed all .dsp stuff for generating Microsoft-compatible Makefiles. Also got rid of ckread.pl since we no longer generate tranfiles from ChemKin itself. Tools/C_mk/Make.rules Tools/C_scripts/ckread.pl Tools/C_scripts/dsp.lib.mak Tools/C_scripts/dsp.mak commit f13aa0a7dba2262425f490164be2c56f845ad5ee Author: Ann Almgren Date: Wed Aug 17 13:14:08 2011 -0700 Fixed comments to refer to new directory structure. Src/F_BaseLib/FParallelMG.mak commit 97b765e7df9acbc9ca06f3d8f290b477bb19403e Author: Ann Almgren Date: Wed Aug 17 13:10:37 2011 -0700 Make Tests/C_BaseLib and Tests/F_BaseLib both up to date. Tests/C_BaseLib/GNUmakefile Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/mt19937ar.f90 commit 3264097b8e6de6c84a042090bd56c1ae3ec5a0e9 Author: Ann Almgren Date: Wed Aug 17 13:03:39 2011 -0700 This now compiles. Tests/LinearSolvers/C_TensorMG/GNUmakefile commit a79f09e35eeaa83533f011a414e919217457f625 Author: Ann Almgren Date: Wed Aug 17 13:01:56 2011 -0700 Remove reference to iamrlib. Tests/LinearSolvers/C_CellMG/GNUmakefile commit 17ead3845e4184bc0d9d00358046be3eaac98fa3 Author: Ann Almgren Date: Wed Aug 17 12:59:09 2011 -0700 No more reference to fboxlib. Tests/LinearSolvers/C_CellMG/main.cpp commit 1f1d8621ab85a081d7780eea24f1ae2a1a4014d3 Author: Ann Almgren Date: Wed Aug 17 12:58:13 2011 -0700 Need a bunch of Mac* files, copied from IAMR/Source, to compile the macproj test. Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/MACOPERATOR_2D.F Tests/LinearSolvers/C_CellMG/MACOPERATOR_3D.F Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 4a354f72e846fcb8d34ae4de564fbfee22dbffa0 Merge: 9bd48775e 3c6f2d0bc Author: Ann Almgren Date: Wed Aug 17 12:38:39 2011 -0700 Merge branch 'master' of almgren@gamera:/usr/local/gitroot/BoxLib commit 9bd48775efba69a33d0e3f8a993f73de532a47c6 Author: Ann Almgren Date: Wed Aug 17 12:38:23 2011 -0700 slight clean-up Tests/LinearSolvers/ComparisonTest/main.cpp commit 3c6f2d0bcb12c782af3ddd1f8fbdf047f3c163f7 Merge: 1cbd04d30 d49d32a18 Author: Marc Day Date: Wed Aug 17 12:37:05 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d49d32a1893f2aa93341655a8e6788823d8e6ab8 Author: Ann Almgren Date: Wed Aug 17 12:36:02 2011 -0700 Dont need our own copies of MacBndry* -- they're in C_BoundaryLib. Tests/LinearSolvers/ComparisonTest/MacBndry.H Tests/LinearSolvers/ComparisonTest/MacBndry.cpp commit 25f52d0263779327b79bb4aac3ceaa4bc3dea8e6 Author: Ann Almgren Date: Wed Aug 17 12:33:48 2011 -0700 Now compiles with F90 solvers turned on as well. Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/main.cpp commit dfd4431bdea513b306b9f41a6887b3827de33d51 Author: Ann Almgren Date: Wed Aug 17 12:27:53 2011 -0700 This now compiles with the new BoxLib format. Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/main.cpp commit 305cea277cbb0ae6e8cab964423b275de1382a64 Author: Ann Almgren Date: Wed Aug 17 12:12:03 2011 -0700 Changes to try to get this to compile. Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 1cbd04d306cad2f598d56ebb2f87e65972a0b541 Author: Marc Day Date: Wed Aug 17 11:00:33 2011 -0700 Remove bibtex command Docs/GNUmakefile commit 77c09bc60dd1d14e55135bce9e51d1da2bad0ea3 Author: lijewski Date: Wed Aug 17 08:32:12 2011 -0700 Removed a couple weird Crutchfield scripts. Tests/LinearSolvers/C_TensorMG/doit Tests/LinearSolvers/C_TensorMG/dotest commit 9d3e82d48c27dadf74c2805e1dcff91f4dc6c699 Author: lijewski Date: Wed Aug 17 08:22:21 2011 -0700 Removed instances of PROFILE={TRUE,FALSE} in GNUmakefiles. Left the PROFILE rule in Make.rules. Tests/C_BaseLib/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile Tools/C_mk/Make.T3E Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/GNUmakefile.temp Tools/C_util/Statistics/GNUmakefile Tools/C_util/ViewMF/GNUmakefile Tools/C_util/dbgTools/GNUmakefile commit 35c472835bf150c2bf1fe47a6337f80767177f96 Merge: 8b5f4329b c55a4fe5f Author: lijewski Date: Wed Aug 17 08:10:59 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c55a4fe5fe536c12605f6adfdc6aeb34a8237404 Author: Ann Almgren Date: Tue Aug 16 20:59:36 2011 -0700 PBOXLIB_HOME --> BOXLIB_HOME Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile commit fd66beae8f556694c3022baceb25568439f0f25f Author: Ann Almgren Date: Tue Aug 16 20:58:33 2011 -0700 1) PBOXLIB_HOME --> BOXLIB_HOME 2) Get rid of ComparisonTest from Src/LinearSolvers/C_CellMG -- it is already in Tests/LinearSolvers/C_CellMG Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_3D.F Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_F.H Src/LinearSolvers/C_CellMG/ComparisonTest/GNUmakefile Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.H Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.cpp Src/LinearSolvers/C_CellMG/ComparisonTest/Make.package Src/LinearSolvers/C_CellMG/ComparisonTest/inputs.3d Src/LinearSolvers/C_CellMG/ComparisonTest/main.cpp commit 615dc20009304dbfe967a1a5a9d09e884ebbda3f Author: Ann Almgren Date: Tue Aug 16 20:53:16 2011 -0700 PBOXLIB_HOME --> BOXLIB_HOME Tests/C_BaseLib/GNUmakefile commit 462d9e780160e396f564e856fe8ab374ba4d3a7d Author: Ann Almgren Date: Tue Aug 16 20:51:40 2011 -0700 Change PBOXLIB_HOME --> BOXLIB_HOME Src/LinearSolvers/F_MG/GPackage.mak Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/GNUmakefile.temp Tools/C_util/Statistics/GNUmakefile Tools/C_util/ViewMF/GNUmakefile Tools/C_util/dbgTools/GNUmakefile commit 5db4f008d15744ac3129d520154bc420c1bc5513 Author: Ann Almgren Date: Tue Aug 16 20:48:37 2011 -0700 PBOXLIB_HOME --> BOXLIB_HOME. Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 9efd70f60e9aacb6546b7cb575f1b123d8846777 Author: Ann Almgren Date: Tue Aug 16 18:18:00 2011 -0700 Better for new BoxLib structure... Tools/F_mk/GMakedefs.mak commit 8b5f4329bfb9a046bfcd4aaab7653040c7dce06f Author: lijewski Date: Tue Aug 16 16:34:11 2011 -0700 No longer keeping around the POSIX Pthread stuff. Src/C_BaseLib/Thread.H commit 43b1440f7c8003b3d2e9920ba7f4b6475b4b3c57 Merge: a735b5a94 2b05c2450 Author: lijewski Date: Tue Aug 16 16:25:05 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a735b5a940f301744fde675f7834da76ce20d6e3 Author: lijewski Date: Tue Aug 16 16:24:09 2011 -0700 Removed all BL_PROFILE stuff. Left a bare-boned Profiling.H so code that still have BL_PROFILE stuff in them will compile. Also got rid of the POSIX Pthread stuff. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BLMpi.cpp Src/C_BaseLib/BLMpi.w Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Tests/C_BaseLib/tMinCommCosts.cpp commit 2b05c2450554b1ebe1ab9aa01c26afba0cfe69a7 Author: ajnonaka Date: Tue Aug 16 15:36:49 2011 -0700 progress toward getting fParallel stuff to compile Tools/F_mk/GMakedefs.mak commit d58c411426abb80c2b6083d442920581f7a7d4f2 Author: Ann Almgren Date: Tue Aug 16 15:06:03 2011 -0700 Removed all references to fParallel/extern/mpi, BL_USE_FARG, etc -- these were only needed for hive and harmonic. Tools/F_mk/GMakeMPI.mak commit 2d43f80b3fc47cf8f38521bbef01b24941f294f8 Author: Ann Almgren Date: Tue Aug 16 14:11:51 2011 -0700 Change FPARALLEL --> . or .. (i.e. fix paths) Tools/F_mk/GMakedefs.mak commit 0134d9bbb811e0d502dfd41e0ee151baf2da6330 Author: mjlijewski@lbl.gov Date: Tue Aug 16 08:56:28 2011 -0700 Cleaned up some header file comments. Removed some embedded TeX and turned it into text. Src/C_BoundaryLib/InterpBndryData.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.H commit d030d176dcabe00887e9c0f0950c2905861ce0e1 Author: mjlijewski@lbl.gov Date: Mon Aug 15 15:51:28 2011 -0700 Removed all .cvsignore files. Use .git/info/exclude instead. Src/C_AMRLib/.cvsignore Src/C_BaseLib/.cvsignore Src/C_BoundaryLib/.cvsignore Src/LinearSolvers/C_CellMG/.cvsignore Src/LinearSolvers/C_NodalMG/.cvsignore Tests/C_BaseLib/.cvsignore Tests/F_BaseLib/.cvsignore Tests/LinearSolvers/C_CellMG/.cvsignore Tests/LinearSolvers/F_MG/.cvsignore Tools/C_util/wrappergen/.cvsignore commit e941baef6a423134827309678c40e7578acf23c9 Author: Ann Almgren Date: Mon Aug 15 15:32:10 2011 -0700 Moved these to Tests/LinearSolvers/C_NodalMG/test_grids. Src/LinearSolvers/C_NodalMG/tests/3d_4_level.grids Src/LinearSolvers/C_NodalMG/tests/gr.11 Src/LinearSolvers/C_NodalMG/tests/gr.15 Src/LinearSolvers/C_NodalMG/tests/gr.16 Src/LinearSolvers/C_NodalMG/tests/gr.19 Src/LinearSolvers/C_NodalMG/tests/gr.19l3 Src/LinearSolvers/C_NodalMG/tests/gr.19s2 Src/LinearSolvers/C_NodalMG/tests/gr.19s2.4 Src/LinearSolvers/C_NodalMG/tests/gr.19s4 Src/LinearSolvers/C_NodalMG/tests/gr.19s4.1 Src/LinearSolvers/C_NodalMG/tests/gr.292.11 Src/LinearSolvers/C_NodalMG/tests/gr.292.25 Src/LinearSolvers/C_NodalMG/tests/gr.7 Src/LinearSolvers/C_NodalMG/tests/gr.8 Src/LinearSolvers/C_NodalMG/tests/gr.8a Src/LinearSolvers/C_NodalMG/tests/gr.ann.1 Src/LinearSolvers/C_NodalMG/tests/gr.sstanley.1 Src/LinearSolvers/C_NodalMG/tests/gr0 Src/LinearSolvers/C_NodalMG/tests/gr0a Src/LinearSolvers/C_NodalMG/tests/gr0b Src/LinearSolvers/C_NodalMG/tests/gr1 Src/LinearSolvers/C_NodalMG/tests/gr1mike.thin Src/LinearSolvers/C_NodalMG/tests/gr1rick2 Src/LinearSolvers/C_NodalMG/tests/gr2 Src/LinearSolvers/C_NodalMG/tests/gr2.0 Src/LinearSolvers/C_NodalMG/tests/gr2.1 Src/LinearSolvers/C_NodalMG/tests/gr2.inf Src/LinearSolvers/C_NodalMG/tests/gr2a2 Src/LinearSolvers/C_NodalMG/tests/gr2a4 Src/LinearSolvers/C_NodalMG/tests/gr2ann Src/LinearSolvers/C_NodalMG/tests/gr2ann.l0 Src/LinearSolvers/C_NodalMG/tests/gr2ann.l1 Src/LinearSolvers/C_NodalMG/tests/gr2ann.l2 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p1 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p2 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p3 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p4 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p5 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p6 Src/LinearSolvers/C_NodalMG/tests/gr2b Src/LinearSolvers/C_NodalMG/tests/gr2c Src/LinearSolvers/C_NodalMG/tests/gr2cross Src/LinearSolvers/C_NodalMG/tests/gr2d Src/LinearSolvers/C_NodalMG/tests/gr2d2 Src/LinearSolvers/C_NodalMG/tests/gr2d4 Src/LinearSolvers/C_NodalMG/tests/gr2dave Src/LinearSolvers/C_NodalMG/tests/gr2e Src/LinearSolvers/C_NodalMG/tests/gr2f Src/LinearSolvers/C_NodalMG/tests/gr2g Src/LinearSolvers/C_NodalMG/tests/gr2h Src/LinearSolvers/C_NodalMG/tests/gr2mike Src/LinearSolvers/C_NodalMG/tests/gr2mike1 Src/LinearSolvers/C_NodalMG/tests/gr2mike2 Src/LinearSolvers/C_NodalMG/tests/gr2mike3 Src/LinearSolvers/C_NodalMG/tests/gr2r1 Src/LinearSolvers/C_NodalMG/tests/gr2r2 Src/LinearSolvers/C_NodalMG/tests/gr2r3 Src/LinearSolvers/C_NodalMG/tests/gr3.rz Src/LinearSolvers/C_NodalMG/tests/gr3a Src/LinearSolvers/C_NodalMG/tests/gr3ann Src/LinearSolvers/C_NodalMG/tests/gr3ann2 Src/LinearSolvers/C_NodalMG/tests/gr3b Src/LinearSolvers/C_NodalMG/tests/gr3c Src/LinearSolvers/C_NodalMG/tests/gr3mike Src/LinearSolvers/C_NodalMG/tests/gr3mike.3 Src/LinearSolvers/C_NodalMG/tests/gr3rick Src/LinearSolvers/C_NodalMG/tests/gr3rick2 Src/LinearSolvers/C_NodalMG/tests/gr4 Src/LinearSolvers/C_NodalMG/tests/gr4level Src/LinearSolvers/C_NodalMG/tests/gt.32 Src/LinearSolvers/C_NodalMG/tests/gt.bill1 Src/LinearSolvers/C_NodalMG/tests/gt.inputs.3d.spin.grids Src/LinearSolvers/C_NodalMG/tests/gt.jbb.1 Src/LinearSolvers/C_NodalMG/tests/gt.sas Src/LinearSolvers/C_NodalMG/tests/gt.scott.1 Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_2.32 Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_2.64 Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_3 Src/LinearSolvers/C_NodalMG/tests/gt0 Src/LinearSolvers/C_NodalMG/tests/gt010 Src/LinearSolvers/C_NodalMG/tests/gt012 Src/LinearSolvers/C_NodalMG/tests/gt016 Src/LinearSolvers/C_NodalMG/tests/gt05 Src/LinearSolvers/C_NodalMG/tests/gt1 Src/LinearSolvers/C_NodalMG/tests/gt12 Src/LinearSolvers/C_NodalMG/tests/gt12.2 Src/LinearSolvers/C_NodalMG/tests/gt12.3 Src/LinearSolvers/C_NodalMG/tests/gt2 Src/LinearSolvers/C_NodalMG/tests/gt2t1 Src/LinearSolvers/C_NodalMG/tests/gt2t3 Src/LinearSolvers/C_NodalMG/tests/gt2t4 Src/LinearSolvers/C_NodalMG/tests/gt3 Src/LinearSolvers/C_NodalMG/tests/gt3ann Src/LinearSolvers/C_NodalMG/tests/gt3ann2 Src/LinearSolvers/C_NodalMG/tests/gt4 Src/LinearSolvers/C_NodalMG/tests/gt4s2 Src/LinearSolvers/C_NodalMG/tests/gt4s2.4.4 Src/LinearSolvers/C_NodalMG/tests/gt4s2a Src/LinearSolvers/C_NodalMG/tests/gt4s4 Src/LinearSolvers/C_NodalMG/tests/gt4s4.2.4 Src/LinearSolvers/C_NodalMG/tests/gt4s4.4.2 Src/LinearSolvers/C_NodalMG/tests/gt5 Src/LinearSolvers/C_NodalMG/tests/gt5s2 Src/LinearSolvers/C_NodalMG/tests/gt5s4 Src/LinearSolvers/C_NodalMG/tests/gt6 Src/LinearSolvers/C_NodalMG/tests/gt6s Src/LinearSolvers/C_NodalMG/tests/gt6s2 Src/LinearSolvers/C_NodalMG/tests/gt6s4 Src/LinearSolvers/C_NodalMG/tests/gt7a Src/LinearSolvers/C_NodalMG/tests/gt7aa Src/LinearSolvers/C_NodalMG/tests/gt8 Src/LinearSolvers/C_NodalMG/tests/gt8a Src/LinearSolvers/C_NodalMG/tests/gt8b Src/LinearSolvers/C_NodalMG/tests/gt8c Src/LinearSolvers/C_NodalMG/tests/gt8ms2 Src/LinearSolvers/C_NodalMG/tests/gtbig Src/LinearSolvers/C_NodalMG/tests/gtbig2 Src/LinearSolvers/C_NodalMG/tests/gtbig3 Src/LinearSolvers/C_NodalMG/tests/gtbig4 Src/LinearSolvers/C_NodalMG/tests/gtbig5 Src/LinearSolvers/C_NodalMG/tests/gtclearlarge Src/LinearSolvers/C_NodalMG/tests/gtclearsmall Src/LinearSolvers/C_NodalMG/tests/gtgrav2 Src/LinearSolvers/C_NodalMG/tests/gtgrav4 Src/LinearSolvers/C_NodalMG/tests/gtjbb Src/LinearSolvers/C_NodalMG/tests/gtjbb2 Src/LinearSolvers/C_NodalMG/tests/gtpfail Src/LinearSolvers/C_NodalMG/tests/gtrick commit 50a44ca32be5e074daacc3ff28db8d4fcbfa13a0 Author: Ann Almgren Date: Mon Aug 15 15:29:05 2011 -0700 Move test directories out of Src. Src/LinearSolvers/C_CellMG/Test/.cvsignore Src/LinearSolvers/C_CellMG/Test/COEF_2D.F Src/LinearSolvers/C_CellMG/Test/COEF_3D.F Src/LinearSolvers/C_CellMG/Test/COEF_F.H Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/Palette Src/LinearSolvers/C_CellMG/Test/amrvis.defaults Src/LinearSolvers/C_CellMG/Test/grids/gr.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/gr.2_256squared Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/gr.2_big Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_d Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_e Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_d Src/LinearSolvers/C_CellMG/Test/grids/gr.3_128cubed Src/LinearSolvers/C_CellMG/Test/grids/gr.3_256cubed Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2boxes_a Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2x3x4 Src/LinearSolvers/C_CellMG/Test/grids/gr.3_512cubed Src/LinearSolvers/C_CellMG/Test/grids/gr.3_big Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/gr.3_mac_tst Src/LinearSolvers/C_CellMG/Test/grids/gr.3_shiftedUp Src/LinearSolvers/C_CellMG/Test/grids/gr.3_small_a Src/LinearSolvers/C_CellMG/Test/grids/gr.3_stack_a Src/LinearSolvers/C_CellMG/Test/grids/grids.15456.REMOVED.git-id Src/LinearSolvers/C_CellMG/Test/grids/grids.213 Src/LinearSolvers/C_CellMG/Test/grids/grids.25600.REMOVED.git-id Src/LinearSolvers/C_CellMG/Test/grids/grids.5034 Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/in.2_big Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b 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Src/LinearSolvers/C_TensorMG/Test/Palette Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.H Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Src/LinearSolvers/C_TensorMG/Test/amrvis.defaults Src/LinearSolvers/C_TensorMG/Test/doit Src/LinearSolvers/C_TensorMG/Test/dotest Src/LinearSolvers/C_TensorMG/Test/grids/gr.3_2x3x4 Src/LinearSolvers/C_TensorMG/Test/grids/gr16.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr16x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr2D Src/LinearSolvers/C_TensorMG/Test/grids/gr32.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr32x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr64.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr8.dog Src/LinearSolvers/C_TensorMG/Test/inputs Src/LinearSolvers/C_TensorMG/Test/inputs2D Src/LinearSolvers/C_TensorMG/Test/inputs3D Src/LinearSolvers/C_TensorMG/Test/inputs8 Src/LinearSolvers/C_TensorMG/Test/main_2D.F Src/LinearSolvers/C_TensorMG/Test/main_3D.F Src/LinearSolvers/C_TensorMG/Test/main_F.H Src/LinearSolvers/C_TensorMG/Test/probin Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Src/LinearSolvers/C_TensorMG/Test/vpramps.dat commit 54ed991765c9d5afcbaa157f7d90c9fc369cae64 Author: Ann Almgren Date: Mon Aug 15 15:27:19 2011 -0700 This test directory is now in Tests/F_BaseLib. Src/F_BaseLib/test/.cvsignore Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/ball_def.14656 Src/F_BaseLib/test/conn_defs Src/F_BaseLib/test/def_knapsack.out Src/F_BaseLib/test/fornberg_weights.f90 Src/F_BaseLib/test/inputs.domain Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/makefile Src/F_BaseLib/test/t_bl_prof.f90 Src/F_BaseLib/test/t_bx.f90 Src/F_BaseLib/test/t_bxasc.f90 Src/F_BaseLib/test/t_cls.f90 Src/F_BaseLib/test/t_knapsack.f90 Src/F_BaseLib/test/t_main.f90 Src/F_BaseLib/test/t_particles.f90 commit 754866e8bb1152b0f6a10a5e2c369b887474d994 Author: Ann Almgren Date: Mon Aug 15 15:26:16 2011 -0700 This test directory is now in Tests/C_BaseLib. Src/C_BaseLib/test/.cvsignore Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/ba.15456.REMOVED.git-id Src/C_BaseLib/test/ba.15784.REMOVED.git-id Src/C_BaseLib/test/ba.213 Src/C_BaseLib/test/ba.23925.REMOVED.git-id Src/C_BaseLib/test/ba.25600.REMOVED.git-id Src/C_BaseLib/test/ba.3865 Src/C_BaseLib/test/ba.5034 Src/C_BaseLib/test/ba.60 Src/C_BaseLib/test/ba.95860.REMOVED.git-id Src/C_BaseLib/test/ba.mac.294 Src/C_BaseLib/test/mt19937int.out Src/C_BaseLib/test/t8BIT.cpp Src/C_BaseLib/test/tBA.cpp Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tDM.cpp Src/C_BaseLib/test/tDir.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tMF.cpp Src/C_BaseLib/test/tMinCommCosts.cpp Src/C_BaseLib/test/tParmParse.cpp Src/C_BaseLib/test/tRan.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BaseLib/test/tVisMF2.cpp Src/C_BaseLib/test/tread.cpp commit 577d5fbad921db7ba48c60fcac3e12350983b17e Author: mjlijewski@lbl.gov Date: Mon Aug 15 14:56:47 2011 -0700 Removed all Doc++ junk. Also removed some extraneous GNUmakefiles. Reformatted some stuff to make it easier to read. 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Src/C_AMRLib/FLUXREG_2D.F Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/t8BIT.cpp Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tDir.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tMF.cpp Src/C_BaseLib/test/tParmParse.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BaseLib/test/tread.cpp Src/F_BaseLib/fabio_c.c Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/timer_c.c Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_NodalMG/GNUmakefile commit 0f525b53e52c5e7eeda826d7f736525c905b5e74 Author: mjlijewski@lbl.gov Date: Mon Aug 15 11:26:00 2011 -0700 Removed BLVERSION.H file. Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package commit 2af0139f0dd53013343b205900ab6abf1d7f513b Author: mjlijewski@lbl.gov Date: Mon Aug 15 11:18:02 2011 -0700 Removed some WorkQueue and Thread stuff. All the WorkQueue stuff is gone. Most of the POSIX Thread stuff is gone, but not the files themselves. BLProfiler still used the THread stuff. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/WorkQueue.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tProfiler.cpp Src/C_BaseLib/test/tWorkQueue.cpp Src/LinearSolvers/C_CellMG/ComparisonTest/main.cpp Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tWorkQueue.cpp commit ae458c259904afec5ea81bebbcc3124f170b49d0 Author: Ann Almgren Date: Sat Aug 13 15:55:47 2011 -0700 Remove all Banner.html commit f70616485b4c1ca10a7f40a0e93814e7e114cb01 Author: Ann Almgren Date: Sat Aug 13 15:54:32 2011 -0700 Remove cvs tags. Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/t8BIT.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tDir.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tread.cpp commit aed27a28da2f426b20b50122e1c621c3ef87a8b3 Author: Ann Almgren Date: Sat Aug 13 15:52:51 2011 -0700 Removed cvs tags. Src/C_BaseLib/Arena.H Src/C_BaseLib/Arena.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/BLassert.H Src/C_BaseLib/BLutil_F.f Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/GNUmakefile Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Looping.H Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/REAL.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BaseLib/SPACE.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Thread.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/UseCount.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/WorkQueue.H Src/C_BaseLib/ccse-mpi.H commit c0afd4c2f8f63c6ca97e233e08fe7e59be45bdf2 Author: Ann Almgren Date: Sat Aug 13 15:47:39 2011 -0700 Remove cvs tags. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_F.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/LO_BCTYPES.H Src/C_BoundaryLib/LO_UTIL.F Src/C_BoundaryLib/MacBndry.cpp Src/C_BoundaryLib/Mask.H Src/C_BoundaryLib/Mask.cpp commit b99c93e70f30e9030966c18c080ab691b01ef9f0 Author: Ann Almgren Date: Sat Aug 13 15:45:28 2011 -0700 Remove cvs tags. 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Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/DivVis_F.H Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Make.package commit d5a76c45c1d62123180f13c03c634d573e029f3b Author: Ann Almgren Date: Sat Aug 13 15:28:11 2011 -0700 Remove cvs tags. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_1D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/ABec_UTIL.F Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F Src/LinearSolvers/C_CellMG/MG_F.H Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/lo_bctypes.fi Src/LinearSolvers/C_NodalMG/Make.package commit 0913989631f878eb8f302c8dac508f3636ded639 Author: Ann Almgren Date: Sat Aug 13 15:26:58 2011 -0700 Deleted Banner and removed CVS Id's from other files. commit fd67c03dcf1a0e696f0d3e6c30da84876bfd23fc Author: Ann Almgren Date: Sat Aug 13 15:18:45 2011 -0700 Remove reference to FBOXLIB_HOME. Src/LinearSolvers/C_to_F_MG/Make.package commit df8ccd217cf847d659ccffa89003e218a11f99d1 Author: Ann Almgren Date: Sat Aug 13 14:51:36 2011 -0700 Fix $(TOP) --> $(PBOXLIB_HOME) for Tools/... Tools/C_mk/Make.rules commit 8cf56858f1ac3a21866829e1f8dd226d22f2538e Author: Ann Almgren Date: Sat Aug 13 14:48:42 2011 -0700 Fix the paths and names of mk and scripts Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit cfb2885f4d45045397346476b244d7f087a0e93f Author: Ann Almgren Date: Fri Aug 12 19:32:57 2011 -0700 changed script Tools/C_mk/Make.rules commit 448215f1a389a95a35b9cd1f050d92a061879f47 Author: Ann Almgren Date: Fri Aug 12 19:28:33 2011 -0700 changed script location Tools/C_mk/Make.rules commit 1a787ad15cc9f726db9ccff460503726efdab63e Author: Ann Almgren Date: Fri Aug 12 18:57:18 2011 -0700 Needed to fix the paths for mk and scripts. Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 7c211b6efd1d285c98f8ef98ad626fbeb22028bc Author: Ann Almgren Date: Fri Aug 12 18:17:15 2011 -0700 Modifying C_mk/Make* to reflect the new path for C_mk Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 746e104f29eafbfe5a60074748de932ba2804872 Author: almgren Date: Thu Aug 11 13:47:16 2011 +0000 This now includes the particles. Src/C_AMRLib/Make.package commit b03c56306bfe14888b8430f4a6ccb19cfc4c769f Author: almgren Date: Wed Aug 10 22:11:31 2011 +0000 Fix oops. Src/C_BaseLib/Make.package commit 5d9abf01a75ed8d085475879512dbeb3620b3716 Author: ajnonaka Date: Wed Aug 10 20:33:52 2011 +0000 added support for Intel12 on hopper Tools/F_mk/comps/Linux_intel.mak commit 7e325f4ec111937a02367406f118da46617b8268 Author: almgren Date: Wed Aug 10 20:19:41 2011 +0000 Remove RealBox, CoordSys and Geometry stuff. Src/C_BoundaryLib/Make.package commit ce4223dc5a93853a220423968e0a80925da9661d Author: almgren Date: Wed Aug 10 20:18:57 2011 +0000 Added RealBox, CoordSys, Geometry stuff. Src/C_BaseLib/Make.package commit 796921e14c27405afcfe87afb910952420679076 Author: almgren Date: Wed Aug 10 19:40:14 2011 +0000 Remove reference to Minion stencil in nodal stencil. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 1c30afd90d6c7cb41edcc0094fe4be596df45231 Author: almgren Date: Wed Aug 10 19:27:09 2011 +0000 Comment out all SPARSKIT files since we no longer build in the sparse solver capability. Src/LinearSolvers/F_MG/FParallelMG.mak commit 4fbebe8a2bba7917dcc459d09626482fb30eaeb5 Author: lijewski Date: Tue Aug 9 21:47:18 2011 +0000 more Initialize()/Finalize() foo fah Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit a84a627647a350b9e41b9cfba137d939bd22ae86 Author: lijewski Date: Tue Aug 9 21:32:45 2011 +0000 added clear() to DeriveList Src/C_AMRLib/Derive.H commit 052a82345c32cf5cacfef7fa47edf666172e8591 Author: lijewski Date: Tue Aug 9 16:36:54 2011 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit 2f343ae655cd49c2e5f83605dc05fa1bb0d08638 Author: lijewski Date: Tue Aug 9 16:30:16 2011 +0000 fix to clear(); have to also do a resize(0) to fully clear a StateDescriptorList Src/C_AMRLib/StateDescriptor.cpp commit dfce75119ac2c3acb9a9b06cf495dd6f71bbee7a Author: lijewski Date: Tue Aug 9 15:51:53 2011 +0000 yet more work on Initialize()/Finalize() Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 70b700c75802f5335e7f0c6f85375a19cc63c700 Author: lijewski Date: Tue Aug 9 00:00:01 2011 +0000 yet more work on Initialize()/Finalize() Src/C_BaseLib/Arena.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit aa25a6789e0a22b92fd55a9576edae09d886e457 Author: lijewski Date: Mon Aug 8 21:23:34 2011 +0000 more work on Initialize()/Finalize() Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit 3576dd57b123a14aa1721e64ac737bf2e19c0ca0 Author: lijewski Date: Mon Aug 8 20:47:45 2011 +0000 more work on Initialize()/Finalize() Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 0a185b8eea4f1d4347f9f2abe87607dce9be9ed5 Author: lijewski Date: Mon Aug 8 20:37:25 2011 +0000 more work on Initialize()/Finalize() Src/C_AMRLib/Amr.cpp commit 59c2fffcebec595aeed8b6469d85f6776bb51e37 Author: lijewski Date: Mon Aug 8 17:24:24 2011 +0000 put 'initialized' into unnamed namespace instead of static member Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 64758c4cb5cf444646a4336459d2e23dae4d7cdd Author: lijewski Date: Mon Aug 8 16:58:44 2011 +0000 add clear() to ErrorList Src/C_AMRLib/ErrorList.H commit ecec93f42d402a179cd944a41538751b2a439f92 Author: lijewski Date: Sat Aug 6 02:57:14 2011 +0000 turn on/off cache statistics with geometry.verbose Src/C_BaseLib/Geometry.cpp commit 39f08d3e873e3a03551de0c0f192c6da628de33a Author: lijewski Date: Sat Aug 6 02:56:31 2011 +0000 turn on/off cache statistics with fabarray.verbose Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit e6ad17efeb528c7af9f8c40259a52ff514e15e93 Author: almgren Date: Sat Aug 6 00:34:08 2011 +0000 Allow us to use DistributionMapping.v as well as DistributionMapping.verbose to control the verbosity. Src/C_BaseLib/DistributionMapping.cpp commit 8aec9a5c8c993a62489b337b05c024fd1c983e7a Author: lijewski Date: Fri Aug 5 23:14:10 2011 +0000 new way of doing Finalize() Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 9b50a56e40b735729ffc7c323c2f375ffa7ffd84 Author: lijewski Date: Fri Aug 5 22:56:49 2011 +0000 new way of doing Finalize() Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 55626e797bbf530e459372e02d17670998f5add4 Author: almgren Date: Fri Aug 5 22:28:02 2011 +0000 Needed ParmParse.H ... Src/C_AMRLib/Particles.H commit 419cac73379b4e7fad5a3e14440fad4ed2f0c75d Author: lijewski Date: Fri Aug 5 22:21:16 2011 +0000 some cleanup Src/C_BoundaryLib/InterpBndryData.cpp commit 6d7c94cb0d9336b4f0a65455265bafa5f91e12cf Author: lijewski Date: Fri Aug 5 22:21:05 2011 +0000 new way of doing BoxLib::Finalize() Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 419d3a60b8b3f2583d1d1a1bbdfa0d22d5997cd2 Author: lijewski Date: Fri Aug 5 22:20:28 2011 +0000 BoxLib now maintains a stack of functions that should be called on BoxLib::Finalize(). Initialization functions that set defaults or that build global data that needs to be cleared out on BoxLib::Finalize() should define a function of the form: void (fp) () that performs necessary cleanup, and then register those functions via BoxLib::ExecOnFinalize(fp). Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParmParse.cpp commit ce8f5af4e8141aae67bffed6a6171e4b849bf681 Author: almgren Date: Fri Aug 5 22:04:38 2011 +0000 Allow a new type of ErrorFunc so that we can have different argument lists for the error tagging functions. Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit c62073e5401f8f5ce541d2d10517f575acb28454 Author: lijewski Date: Thu Aug 4 21:13:49 2011 +0000 more Initialize()/Finalize() foo fah Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit dabc57be25d4483e925ba3f667f8d96df110feb2 Author: lijewski Date: Thu Aug 4 20:25:44 2011 +0000 Added Initialize()/Finalize() but not yet integrated into BoxLib.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 4e1a554eac7e0815dc981a4060053301128b0290 Author: lijewski Date: Thu Aug 4 19:36:57 2011 +0000 flush the CPC cache in Finalize() Src/C_BaseLib/FabArray.cpp commit 241873b4d01708f140ff93264b2e060012d0592e Author: almgren Date: Tue Aug 2 18:47:14 2011 +0000 Put central copy of MacBndry.{H,cpp} here instead of all applications carrying their own copy. Src/C_BoundaryLib/MacBndry.H Src/C_BoundaryLib/MacBndry.cpp Src/C_BoundaryLib/Make.package commit 04ce8dd1f72debbbff51d3d1b74ee5a50e382eb2 Author: lijewski Date: Mon Aug 1 20:32:12 2011 +0000 more regularization of Initialize()/Finalize() calls Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParmParse.cpp commit 66320a05be8f0c31b057e655267ef37042f1500c Author: lijewski Date: Thu Jul 28 18:10:15 2011 +0000 MultiFabs can now be clear()d and define()d again Src/C_BaseLib/FabArray.H commit 7c5e157151183a1aedf8efd6cd1d7d1dc68e0c08 Author: almgren Date: Thu Jul 28 05:39:50 2011 +0000 get rid of minion_stencil_fill routines, they were identical to the s_simple_2d_cc and s_simple_3d_cc but with order hard-wired to 2. Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 commit da7ad8a3c3dea9e08a379de703829a938a44b683 Author: almgren Date: Thu Jul 28 01:29:08 2011 +0000 Fix loop indices in Minion 4th order variable density stencil. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 353d37da6260b72d21898f70599a3700cb054501 Author: lijewski Date: Wed Jul 27 19:48:05 2011 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 5d9f92c1ce5d87cfb0d810f34e1483e2d651f362 Author: marc Date: Mon Jul 25 18:10:11 2011 +0000 Add ability to augment pp table externally, used in Amanzi, for example to init via Teuchos::ParameterList Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit dd800052673cc8fe96995e77ee292fd3f4500207 Author: lijewski Date: Wed Jul 20 23:17:44 2011 +0000 Added "stencil" optional logical that implies this multifab is to be used as a stencil. This puts the "ncomps" components of the stencil into the first component of the multifab instead of the fourth component. Use this at your own risk. Almost all of the multifab routines will fail on such a multifab. Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit bdddafdee2c5fb3c695814f0687807c231d3310e Author: mzingale Date: Wed Jul 20 15:33:44 2011 +0000 local declarations of ZERO and ONE conflict with versions coming in from a module. Explicitly include bl_constants_module now. Some other module needs a private statement somewhere... Src/LinearSolvers/F_MG/itsol.f90 commit 9a33fbc94bd4c42730fedb4429a31af33a864d5e Author: lijewski Date: Wed Jul 20 15:28:28 2011 +0000 defined some constants to get code to compile Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 commit d3eb8955e35333789bb22c86c96c3234d5fe2a7a Author: mzingale Date: Wed Jul 20 15:21:02 2011 +0000 use bl_constants_module to get this compiling Src/LinearSolvers/F_MG/cc_stencil.f90 commit a3def08adb8684317efc2386f9e3c511f50aadaf Author: almgren Date: Wed Jul 20 14:50:08 2011 +0000 Don't need to define these here. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 1f41b218ed43a202b789d2ffeaeb5508582e80b6 Author: almgren Date: Wed Jul 20 14:40:03 2011 +0000 Move definition of BC_GEOM from cc_stencil.f90 to bc_functions.f90 Src/LinearSolvers/F_MG/bc_functions.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 commit f198d1cab607ec25f176ec1154c9e0172591f42a Author: almgren Date: Wed Jul 20 14:37:52 2011 +0000 Add BC_GEOM. Src/LinearSolvers/F_MG/bc_functions.f90 commit c181c1f2ca3373cc8a1bd1f92fdf81f5d510615f Author: mzingale Date: Wed Jul 20 14:10:56 2011 +0000 add missing "implicit none". No longer compiles. Src/LinearSolvers/F_MG/bc_functions.f90 Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 commit f34c61898782cac30eb5eb1a1d723628d185bdaf Author: almgren Date: Wed Jul 20 05:25:44 2011 +0000 Separate restriction modules. Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_restriction.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 640106ca7bea598e94db57ee68e65bdf462cfe50 Author: almgren Date: Wed Jul 20 05:20:47 2011 +0000 Add edge_restriction file. Src/LinearSolvers/F_MG/edge_restriction.f90 commit 7216cf41026662cf1d2a6df3e586627a17794d15 Author: almgren Date: Wed Jul 20 05:06:12 2011 +0000 Fix some modules...now compiles with CASTRO. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit d1afee040022dd602c1ea1f9ef50cfaa08ec43a8 Author: almgren Date: Wed Jul 20 04:44:52 2011 +0000 Extracting ml_resid type stuff from ml_cc.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit b5d476f15f4f428c647cefdab5665922f20ddd50 Author: almgren Date: Wed Jul 20 04:32:44 2011 +0000 Move applyop stuff into separate file. Src/LinearSolvers/F_MG/ml_cc.f90 commit 6ae50d8274975d577c3d471354bd3404c1a6504b Author: almgren Date: Wed Jul 20 04:23:58 2011 +0000 Add cc_applyop.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 commit 6e4356c4f6aac45fadf104d3c7adfb5a10b8d120 Author: almgren Date: Wed Jul 20 04:06:00 2011 +0000 Forgot multifab_module. Src/LinearSolvers/F_MG/ml_norm.f90 commit 09a35a6053729bc89cb3bfd4758a1f3dc86f9cf5 Author: almgren Date: Wed Jul 20 04:04:35 2011 +0000 Catch these up with other changes. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit fd6be8ba1bcd5bd47c2d4e39b3075425d322a1ba Author: almgren Date: Wed Jul 20 04:04:08 2011 +0000 ml_util.f90 --> ml_norm.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/ml_norm.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit d433a62c5052656bce51c464f5c7aa6bf3acf52a Author: almgren Date: Wed Jul 20 03:54:05 2011 +0000 Keep up with new files. Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak commit 44fd970a900fa132c5930b34ef2622241d934b49 Author: almgren Date: Wed Jul 20 03:53:53 2011 +0000 Break up ml_interface_stencil.f90 into nodal and cc. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 commit 52300e8e6741fc741e97cb1dd6a318dee9c4542d Author: almgren Date: Wed Jul 20 01:51:56 2011 +0000 Get ml_prolongation started to separate. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 9253b80cd88b0d12e7c8722d0d428d75760b7649 Author: almgren Date: Wed Jul 20 01:43:24 2011 +0000 mg_nodal_cpp --> nodal_mg_cpp Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak commit 025b18c03557e5294c72f483cba519b99d1159cc Author: almgren Date: Wed Jul 20 01:42:44 2011 +0000 Changed name. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit d187360580ad86cbd35a43c467955dbb0caa96d5 Author: almgren Date: Wed Jul 20 01:40:31 2011 +0000 add bl_error_module... Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/tridiag.f90 commit bc2b7586c0f846f26512bcf21d69d0b1963df0a8 Author: almgren Date: Wed Jul 20 01:36:49 2011 +0000 Fix nodal_newu... Src/LinearSolvers/F_MG/GPackage.mak commit 7fe9caeb434a20be7a0176fecbe7c10dd3119dfe Author: almgren Date: Wed Jul 20 01:34:45 2011 +0000 Clean up ... Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 55a4243d588cc6be0147224fa7baf40ba964d08c Author: almgren Date: Wed Jul 20 01:32:31 2011 +0000 Remove ST_FILL... they were never used. Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 326fa0d658de6f3d9384783aa197a8a6e4c5dd93 Author: almgren Date: Wed Jul 20 01:29:44 2011 +0000 stencil --> ... Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit c6ca04f98d29aa5b3e3834cabc9c4807e3d90808 Author: almgren Date: Wed Jul 20 01:29:18 2011 +0000 stencil_module --> ... Src/LinearSolvers/F_MG/mg_tower.f90 commit 7ee88d7e420e901188d0b1e212e0cf6192c5bfe5 Author: almgren Date: Wed Jul 20 01:28:43 2011 +0000 stencil -->... Src/LinearSolvers/F_MG/ml_util.f90 commit 1afe4e3bd0f8a588663175afc8450a48fa01cbd8 Author: almgren Date: Wed Jul 20 01:27:28 2011 +0000 fix oops. Src/LinearSolvers/F_MG/bc_functions.f90 commit bda2966d589eb9c63ff32cd70a14760f1a912715 Author: almgren Date: Wed Jul 20 01:26:43 2011 +0000 add bl_spacedim. Src/LinearSolvers/F_MG/bc_functions.f90 commit cb83d9545768a27bd38780e3c31643578add34d0 Author: almgren Date: Wed Jul 20 01:25:21 2011 +0000 move BC_BIT... Src/LinearSolvers/F_MG/bc_functions.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 commit d5488a87cec8cbed4ad698e7c795df7fcb2afc51 Author: almgren Date: Wed Jul 20 01:23:43 2011 +0000 Extra bc_neumann, bc_dirichlet, etc, from cc_stencil.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/bc_functions.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit b7a8dc1c43c06925bdd2a9c75c18fc085ff6461e Author: almgren Date: Wed Jul 20 01:11:02 2011 +0000 *** empty log message *** Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 commit b3991c0530077171b4a3a6da083804ce2e12b4ae Author: almgren Date: Wed Jul 20 01:10:22 2011 +0000 stencil_module --> cc_stencil_module or nodal_stencil_module Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 1e965085e004180de91eb465ac9e5546b1492a36 Author: almgren Date: Wed Jul 20 00:59:59 2011 +0000 impose_neumann_bcs.f90 --> nodal_neumann_bcs.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/tridiag.f90 commit 3e94d9580d74ac4c7420f9e14b1a62604fa9f6dd Author: almgren Date: Wed Jul 20 00:56:30 2011 +0000 Separate cc from nodal in the stencil* files. Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 commit e3031b86e7ac4a08a25ae1d1f188810e6bceb01c Author: almgren Date: Wed Jul 20 00:44:13 2011 +0000 Clean up from previous changes.. this now compiles with CASTRO... Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/tridiag.f90 commit 0f08304627f6cdd60c3da28bef29b4bec1f9c63f Author: almgren Date: Wed Jul 20 00:36:27 2011 +0000 Forgot to fix module name. Src/LinearSolvers/F_MG/cc_smoothers.f90 commit f14ba5418681b353ec5ef553c5ed52c3607c2de4 Author: almgren Date: Wed Jul 20 00:36:06 2011 +0000 Include cc_smoothers_module and nodal_smoothers_module instead of mg_smoother_module Src/LinearSolvers/F_MG/mg.f90 commit 19bc810d73d496d6b001c195de11c95523f6b5ee Author: almgren Date: Wed Jul 20 00:35:38 2011 +0000 Separate mg_smoother.f90 into separate files -- cc_smoothers.f90 and nodal_smoothers.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 9e9b9898540e9e129e769fb740a12248bd5afb96 Author: almgren Date: Wed Jul 20 00:32:58 2011 +0000 Separate mg_smoother.f90 into nodal_smoothers.f90 and cc_smoothers.f90, and separate tridiag.f90 into a separate file. Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/tridiag.f90 commit 82049104a2c467b633de1db40056b759e0c56bfb Author: lijewski Date: Tue Jul 19 21:12:32 2011 +0000 use -O3 for optimizing with gfortran instead of -O2 Tools/C_mk/Make.defs commit 3c5bcb5b1652bd7b3cf50298b30ca1aeb9638f36 Author: almgren Date: Tue Jul 19 17:17:29 2011 +0000 These are the files I'm using to compare C++ to F90 solvers. Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_3D.F Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_F.H Src/LinearSolvers/C_CellMG/ComparisonTest/GNUmakefile Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.H Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.cpp Src/LinearSolvers/C_CellMG/ComparisonTest/Make.package Src/LinearSolvers/C_CellMG/ComparisonTest/inputs.3d Src/LinearSolvers/C_CellMG/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/MacBndry.H Tests/LinearSolvers/ComparisonTest/MacBndry.cpp Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/main.cpp commit ef882f8c1bee54c84bb22418866d64d69593c990 Author: marc Date: Tue Jul 19 17:11:07 2011 +0000 Fix up fParallel calls Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit 7090ad431ac3afdd46bbe3d862af8400f71bc92a Author: almgren Date: Tue Jul 19 00:07:05 2011 +0000 Remove unused variables in George's new stencils to quiet warnings... Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 4133b3bd3c9591f4c37c4e023776f16e0a1573e8 Author: almgren Date: Mon Jul 18 23:45:01 2011 +0000 Remove unused variables. Src/LinearSolvers/F_MG/stencil.f90 commit 7d7c56e3164869afa8655b8da9efff67df60fe14 Author: lijewski Date: Mon Jul 18 20:51:17 2011 +0000 substitute istringstream for deprecated istrstream Src/C_AMRLib/Amr.cpp commit fc95967cccfde8652c8d2a69e338b60bc62ee20a Author: lijewski Date: Mon Jul 18 19:52:05 2011 +0000 substitute istringstream for deprecated istrstream Src/C_BaseLib/VisMF.cpp commit 78e07f1b626239c610d4c9ef828cd5d2f88e9cbb Author: lijewski Date: Mon Jul 18 16:39:54 2011 +0000 deal with losing an AmrLevel on a regrid() in Redistribute() Src/C_AMRLib/Particles.H commit 5689e17209ae7c928c7f7416cea4de06d4f3aa06 Author: lijewski Date: Sat Jul 16 16:02:14 2011 +0000 in Redistribute() must remove from the level map empty particle containers Src/C_AMRLib/Particles.H commit 577f3254f932bf38006b09ba16c45d48508ff59c Author: lijewski Date: Sat Jul 16 04:10:21 2011 +0000 added m_particles.reserve() calls to the various init routines Src/C_AMRLib/Particles.H commit de40cfb1e43dd275a6356332530da5068adfd87a Author: almgren Date: Sat Jul 16 04:01:36 2011 +0000 Change tcmf -> new_cmf so that we dont re-use MultiFab after clear -- turns out that clear does not delete the boxarray... Src/C_AMRLib/Particles.H commit a3b610e79ed2325b991d28b64b6178606911eb7d Author: almgren Date: Sat Jul 16 03:50:17 2011 +0000 Add m_particles.resize() in Redistribute if m_particles.size() < m_amr.finestLevel()+1. Src/C_AMRLib/Particles.H commit 34e3f8ffc1fa2134da4de05f9dd83cf78ace7aa7 Author: lijewski Date: Thu Jul 14 23:32:18 2011 +0000 cut scalar time in Redistribute() by roughly a factor of two Src/C_AMRLib/Particles.H commit 12dd6593fea6619bdaefe59e24f384b736b019bf Author: gilet Date: Thu Jul 14 22:13:07 2011 +0000 add note that this script is not for use on Jaguar Tools/F_scripts/extract.parallel commit 7565e65ca405ed5d9500a54c51ebcb7e059d6264 Author: almgren Date: Thu Jul 14 21:24:35 2011 +0000 Move LO_UTIL.F to bndrylib. Src/LinearSolvers/C_CellMG/Make.package commit 95cb2ad19bdf6752c52a94996a0deafc886ffd27 Author: almgren Date: Thu Jul 14 21:24:11 2011 +0000 Add LO_UTIL.F Src/C_BoundaryLib/Make.package commit 36e082819ca48c8e7fd88cee0e111d13754f20ba Author: lijewski Date: Thu Jul 14 16:53:26 2011 +0000 ByteSpread() now also prints out total particle count. Src/C_AMRLib/Particles.H commit 4a44a3d222a6eeb7ce0cba4b61fe33cb2937dabf Author: lijewski Date: Wed Jul 13 22:42:01 2011 +0000 Bypass the MPI_Alltoall() calls in Redistribute() if there's no parallel work to do by doing a ReduceLongMax() on the number of particles I have that aren't mine. Src/C_AMRLib/Particles.H commit 021624fe281153b1c5414e73f83fb5d6152a1330 Author: mzingale Date: Wed Jul 13 21:31:22 2011 +0000 have the timestamp routine that an optional argument, vel_mf, which contains the velocites. If this mf is present, then output the velocity of the zone where the particle lives along with the other data Src/F_BaseLib/particles.f90 commit bc864535a7f6281f8bd5f1dbc74fbd2889cdd943 Author: almgren Date: Wed Jul 13 21:28:03 2011 +0000 No longer need Make_nyx.package since we've moved those files into bndrylib. Src/LinearSolvers/C_CellMG/Make_nyx.package commit 15050de7169c681f45426d87527443c633a10bd1 Author: almgren Date: Wed Jul 13 21:27:31 2011 +0000 Move files from mglib to here. Src/C_BoundaryLib/Make.package commit d3201d2d9394396bff1d0ed47be5737a9828cc7e Author: almgren Date: Wed Jul 13 21:26:24 2011 +0000 Revised Make.package since we moved a bunch of files into bndrylib. Src/LinearSolvers/C_CellMG/Make.package commit aa9c9b3a9daae813b272b6bb346c945c459fd2b1 Author: lijewski Date: Wed Jul 13 21:16:48 2011 +0000 now output time spent in scalar and parallel parts of Redistribute() Src/C_AMRLib/Particles.H commit fe349bc59a8e791fa436e499777796a0a92ee0b4 Author: gpau Date: Wed Jul 13 00:17:26 2011 +0000 added the general stencil for DIM=3: look for simpleg Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 669681cbdd024e8f1b37cbcca89c124ed0f1f292 Author: lijewski Date: Tue Jul 12 18:02:55 2011 +0000 use memory a bit more efficiently in Redistribute() Src/C_AMRLib/Particles.H commit 3d98131dccdef5a2250aaa3fa7784036ed09c01c Author: lijewski Date: Tue Jul 12 16:54:30 2011 +0000 beefed up OK() a bit more Src/C_AMRLib/Particles.H commit 3dda83c309cab3500d95cd1ed6983f78d4a46715 Author: lijewski Date: Mon Jul 11 20:29:08 2011 +0000 Modest speedup to Redistribute(). Previously we only passed m_cpu and m_id via MPI and recalculated m_lev, m_grid and m_cell using Where(). Now Redistribute() sends all the integral data via MPI and recalculates nothing. For large numbers of particles this is a modest speedup. Src/C_AMRLib/Particles.H commit aeeb49285c32f1eb7cc3df8f46228de40458491e Author: lijewski Date: Fri Jul 8 21:34:26 2011 +0000 modest speedups and simplifications to estTimestep() Src/C_AMRLib/Particles.H commit d737696a38e6d4799801c154cfe8923a501ec662 Author: lijewski Date: Fri Jul 8 20:20:49 2011 +0000 figured out issue with MoveRandom(); should now scale perfectly with threads Src/C_AMRLib/Particles.H commit 41510f9f612b55feb7aeb312434181ad482c2a89 Author: lijewski Date: Fri Jul 8 19:59:06 2011 +0000 added parallel keyword to pragma omp so estTimestep() and MoveRandom() really threads Src/C_AMRLib/Particles.H commit 30afb773a25c4c0019e171e4f909b62f088ea603 Author: lijewski Date: Fri Jul 8 17:15:56 2011 +0000 quiet some compiler warnings Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 49a670cffb77ff978bced9546cf0c23e0508f737 Author: lijewski Date: Fri Jul 8 16:42:38 2011 +0000 quiet some compiler warnings Src/C_BaseLib/Looping.H commit a5e99816663634e16b422bc9797b2fda70a0a479 Author: lijewski Date: Fri Jul 8 16:19:06 2011 +0000 quiet some compiler warnings Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 5d9235910482d035c88de86c91df6b27dd74fe8b Author: lijewski Date: Fri Jul 8 16:03:40 2011 +0000 removed some unused variables Src/C_BaseLib/BaseFab.H commit 4776a48626e6d1d36e72b982b74360e7083feeb7 Author: lijewski Date: Fri Jul 8 16:02:51 2011 +0000 cut number of random number calls in MoveRandom() by half Src/C_AMRLib/Particles.H commit c412077965943bb11cf02b7ef80480f2f4b1149e Author: mzingale Date: Fri Jul 8 15:54:28 2011 +0000 add a function particle_global_numparticles to return the total number of active particles -- for diagnostics Src/F_BaseLib/particles.f90 commit 4b4dc85f703e49b30e6acf72cbf267680baa60aa Author: marc Date: Wed Jul 6 23:19:58 2011 +0000 Add + and - to allowed characters in identifiers Src/C_BaseLib/ParmParse.cpp commit 3c5253a1ffcb74df9049104b9905109923a32f95 Author: almgren Date: Wed Jul 6 22:37:55 2011 +0000 Make sure to do a copyplus instead of a pure copy for the case of a particle on a fine grid next to another fine grid -- without this a zero ghost cell could overwrite a non-zero ghost cell. Src/C_AMRLib/Particles.H commit 537fcdc119791628537ef0714d233e9f3bc428ef Author: lijewski Date: Wed Jul 6 22:27:53 2011 +0000 The parallel multifab -> multifab copy() can now also do add. The default is as before; i.e. if you want to copy src to dst: dst.copy(src) If you want you want to add src into dst: dst.copy(src,FabArrayBase::ADD); Src/C_BaseLib/FabArray.H commit c01b4323dfa10eb9052f51433a2de16878ecfd46 Author: almgren Date: Wed Jul 6 21:31:14 2011 +0000 Fix periodic wraparound in multilevel AssignDensity. Src/C_AMRLib/Particles.H commit 34b8c297619084b8ffec0e763eac417b6602803f Author: almgren Date: Wed Jul 6 17:13:28 2011 +0000 Fix the case in AssignDensity where we need to copy from fine ghost cells onto coarse valid regions. Src/C_AMRLib/Particles.H commit 92ccde940a30e2a623aaf7ef05a99319ed3c43f9 Author: almgren Date: Wed Jul 6 07:31:34 2011 +0000 Allow us to enforce solvability even for multilevel solves -- just enforce it at amr level = 0, not the higher levels. Src/LinearSolvers/F_MG/ml_cc.f90 commit 64eac4b7236ee88d9a74c9e0acca4a8d89a6f452 Author: almgren Date: Wed Jul 6 02:59:40 2011 +0000 Eliminate GetRhoFromParticles -- this was replaced by AssignDensity and other source in CastroParticles.cpp Src/C_AMRLib/Particles.H commit 3b2e8648a8ecea9b149e9022e04b8a96819dc846 Author: almgren Date: Wed Jul 6 02:58:57 2011 +0000 Add new routine -- MultiplyParticleMass -- used in SantaBarbara initialization. Src/C_AMRLib/Particles.H commit 898f35a0ce9cd2270c140a1168e2e9842bd9c870 Author: almgren Date: Tue Jul 5 20:43:16 2011 +0000 Fix to GetRhoFromParticles when lev > 1 -- we need to count the contributions from particles at level lev-1 which might contribute to the density at level lev. Src/C_AMRLib/Particles.H commit 6c068f68a5341599677549202b7c58c001c971e2 Author: almgren Date: Tue Jul 5 20:41:01 2011 +0000 Add new subroutine part_sumdensup, which is just like subroutine part_summassup, but differs in that it does not multiply the coarse contributions by volfrac since it works with density instead of mass. Src/C_AMRLib/Particles_1D.F Src/C_AMRLib/Particles_2D.F Src/C_AMRLib/Particles_3D.F Src/C_AMRLib/Particles_F.H commit 3b643baeb26e324dd3a08884d606ec726f823e10 Author: almgren Date: Mon Jul 4 18:48:19 2011 +0000 Fix initialization of multilevel Santa Barbara problem Src/C_AMRLib/Particles.H commit f8f29b6c6060f1f9f57475626a0963907f18721b Author: gpau Date: Sat Jul 2 14:09:47 2011 +0000 added a generic stencil that constructs the entries to matrix directly. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 632cff8cfff09779165811f284b7fd38ea1443e9 Author: gpau Date: Sat Jul 2 13:54:39 2011 +0000 changes made to handle a generic linear system solve. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 1b32b7b9a2cc99b0f078e43063364572985ffe81 Author: marc Date: Fri Jul 1 23:10:54 2011 +0000 to facilitate derivation, if necessary Src/C_BaseLib/ParmParse.H commit 4a0efd0239cff7d81fce9a7793949b59d1f24a2d Author: marc Date: Fri Jul 1 22:50:54 2011 +0000 add hedorah to the list of special cases Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit a7e0ae177f6afe5cfe91203fd6a26c7a33150491 Author: almgren Date: Fri Jul 1 19:11:24 2011 +0000 Fix ml_layout_build_la_array so instead of copying the entire mba, we only copy nlevel levels of it (as is done in ml_layout_build_n). Src/F_BaseLib/ml_layout.f90 commit c8a7b55aedc22266db5652213e3ed8aff73ed4de Author: almgren Date: Fri Jul 1 06:06:03 2011 +0000 Don't print all the particles in InitFromAscii. Src/C_AMRLib/Particles.H commit 41c7e4ddb223386fedbaa1e20d64c00474b96fdf Author: almgren Date: Thu Jun 30 21:59:46 2011 +0000 Add new way of building ml_layout -- ml_layout_build_la_array -- which allows us to copy existing la_array(n) instead of making new ones. Src/F_BaseLib/ml_layout.f90 commit 0f1ea092b3edfb9e5fc5753fa084948460a536c5 Author: almgren Date: Thu Jun 30 21:24:09 2011 +0000 Destroy ba_new once we're done with it (elminated leftover layout in MEMORY STATS) Src/F_BaseLib/make_new_grids.f90 commit 43eb61dcba569767b6ec2eba8f125760500f8435 Author: lijewski Date: Wed Jun 29 16:10:50 2011 +0000 Fixed bug in InitFromAscii() when running in parallel. There was in essence an off-by-one counting bug which caused the last particle read in by cpu 0 to be the first particle read in by cpu 1, and the last particle in the file to not be read in by cpu N was not read in at all. Src/C_AMRLib/Particles.H commit ce3b584f3a3d08b0e9a4e7f78ffb8b1f386aa9f5 Author: lijewski Date: Wed Jun 29 15:10:42 2011 +0000 got rid of some unused variables in Timestamp() Src/C_AMRLib/Particles.H commit 96fd03a37fbc65e4a21f965e57606b8d36da6eda Author: mzingale Date: Wed Jun 29 13:31:30 2011 +0000 store .mod files in o/ on nan Tools/C_mk/Make.Linux commit d3b342ab5ac906ba3e2cb6656a355a1c29fdb95c Author: mzingale Date: Wed Jun 29 13:12:13 2011 +0000 switch to latest MPI for nan Tools/C_mk/Make.mpi commit 9934f9e8eabec309790cea31ca40ffa8d599e4d6 Author: lijewski Date: Wed Jun 29 05:23:51 2011 +0000 remove some debugging I/O Src/C_AMRLib/TagBox.cpp commit 02f62ac286a358d1841913f24efefafd4239f540 Author: lijewski Date: Wed Jun 29 05:21:17 2011 +0000 fix to previous mod when USE_MPI=FALSE Src/C_AMRLib/TagBox.cpp commit 64e791dcacc298cdcd0c2a0e38d5badcea37b4f8 Author: lijewski Date: Wed Jun 29 04:40:38 2011 +0000 remove potential problem with send/recv args to MPI_Gatherv() being the same on the root processor Src/C_AMRLib/TagBox.cpp commit b5c6b68fb6eb34e41ddb944c50effd338b0cdc04 Author: mzingale Date: Tue Jun 28 21:51:33 2011 +0000 no -module flag for nan Tools/C_mk/Make.Linux commit 3b1e7ee5222a5553ca862772c608ff28b8bcc73c Author: mzingale Date: Tue Jun 28 21:15:01 2011 +0000 add MPI instructions for nan. Need -DMPICH_SKIP_MPICXX to make things happy Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit c27b9ca88972109d520c02e944fe6dc26633ad6b Author: almgren Date: Tue Jun 28 19:09:34 2011 +0000 Remove characters from word. Src/F_BaseLib/tag_boxes.f90 commit bb5ff56052a689bf9ae0cd32147248276e0c461b Author: marc Date: Fri Jun 24 23:13:09 2011 +0000 Add some arguments for parallel stuff Src/C_BaseLib/.cvsignore Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H commit 58b0d0437d79cedac481064c5e6396e4cfb9059c Author: marc Date: Fri Jun 24 22:59:07 2011 +0000 add hg file to list Src/C_BoundaryLib/.cvsignore commit 0e14ea0ef970ec927ae5b656b9f58458a01f979f Author: marc Date: Fri Jun 24 22:40:28 2011 +0000 stupid cast that seems to be needed for idiotic GNU compiler Src/C_BoundaryLib/BndryData.cpp commit 83e5754447b14b92e0cd9b7f248b5361d834a105 Author: lijewski Date: Fri Jun 24 21:03:23 2011 +0000 more OMPing Src/LinearSolvers/F_MG/ml_prolongation.f90 commit ae2cdea752e158a0accb067bfd078a3004769ae9 Author: lijewski Date: Fri Jun 24 21:01:36 2011 +0000 some more OMPing Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit c0f3c9107b6566c77ac526780bc54cff4d4bbdbc Author: lijewski Date: Fri Jun 24 21:01:02 2011 +0000 some more OMPing and moved temp from stack to allocatable Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 56e13a67d92a70d53ce349b12c073c6882a09dc2 Author: lijewski Date: Fri Jun 24 21:00:21 2011 +0000 make lr, tb and fb allocatable instead of building on the stack Src/LinearSolvers/F_MG/mg_smoother.f90 commit beaf25a00f9a74d7c892cc466f7317b5ad8933b6 Author: lijewski Date: Thu Jun 23 23:42:44 2011 +0000 little more OMPing Src/LinearSolvers/F_MG/mg_prolongation.f90 commit f64e983f2f6e3fdc6e1b4a44ef4cdf499553ed13 Author: lijewski Date: Thu Jun 23 20:10:33 2011 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_restriction.f90 commit d818f94223b04b83cf6ea87360210be09cbd135e Author: lijewski Date: Wed Jun 22 23:13:49 2011 +0000 single-precision constants -> double-precision constants Src/F_BaseLib/fourth_order_interp_coeffs.f90 commit f648dc3534a685c1d016ffe40d5d323185d1e6aa Author: lijewski Date: Wed Jun 22 22:11:27 2011 +0000 0 -> 0.0_dp_t in a few places Src/F_BaseLib/multifab.f90 commit d149b7e11ac11c278792a5689da7521dc7e63169 Author: lijewski Date: Wed Jun 22 21:19:15 2011 +0000 More work on periodic_add_copy(): Replace array assignments w/ calls to cpy_d() and additions with calls to cpy_d() using ml_restrict_copy_sum() as a filter. Likewise replace saxpy() calls with multifab_copy() calls using ml_restrict_copy_sum() as a filter. Src/LinearSolvers/F_MG/ml_restriction.f90 commit 6de0035cbbc259e9a107b0b1e3ea9205ebbce261 Author: lijewski Date: Wed Jun 22 18:11:33 2011 +0000 little more simplificaton to periodic_add_copy(); can't be readily cached due to synced argument Src/LinearSolvers/F_MG/ml_restriction.f90 commit 38e5bad88b05a92c7a4877d3593e9ce01f04a1d3 Author: almgren Date: Wed Jun 22 01:27:02 2011 +0000 max --> std::max Src/C_AMRLib/Particles.H commit dafa932e266711554c97e64f9d0c034ac89811cd Author: almgren Date: Wed Jun 22 01:24:55 2011 +0000 Fix typo. Src/C_AMRLib/Particles.H commit 2ae51226a26b44e4fe2195aa04a3a7c02049e515 Author: almgren Date: Wed Jun 22 01:20:58 2011 +0000 Change estTimestep so that we satisfy dt = cfl * a * dx / mag_vel where mag_vel is the maximum of a component in any one direction, not the magnitude of the velocity. Src/C_AMRLib/Particles.H commit ae91d6ee3d5a8e0c7c05b1cf66dfb010c53bbc0c Author: almgren Date: Wed Jun 22 00:51:11 2011 +0000 estTimestep now takes a CFL in the argument list which specifies what maximum fraction of a cell the particle can cross in a timestep. Src/C_AMRLib/Particles.H commit bd13bb01d7b74c6ebf653561fab29ce7c7033cbe Author: lijewski Date: Wed Jun 22 00:01:51 2011 +0000 use O2 when optimizing Tools/F_mk/comps/gfortran.mak commit c9392e1affcccd3132615017158f5cb29e07bf77 Author: gilet Date: Tue Jun 21 19:16:42 2011 +0000 add script to extract multiple files from HSI at a time Tools/F_scripts/extract.parallel commit 616924dfa3e77bd9893d9db91616aed53834a1cb Author: lijewski Date: Tue Jun 21 19:05:17 2011 +0000 early exit from periodic_add_copy() when not periodic Src/LinearSolvers/F_MG/ml_restriction.f90 commit 827380be8ccd698cb39879e6bb3a85cab5ab33f7 Author: lijewski Date: Tue Jun 21 19:04:51 2011 +0000 removed comment Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit 7b3adfd8f8ff1fcf5304b74ab6f47f019ca745c0 Author: celdred Date: Tue Jun 21 18:25:32 2011 +0000 added gojira entry Tools/F_mk/GMakeMPI.mak commit 6e58d0ea603a72403de9e2d96f31aec9f22ec1b3 Author: lijewski Date: Thu Jun 16 16:30:26 2011 +0000 removed some unused code Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 5a794d5a88c797935956c0c69434600335a65492 Author: lijewski Date: Thu Jun 16 15:51:30 2011 +0000 removed some XT3 junk Src/C_BaseLib/Utility.cpp commit 07e71c29483d3f4619d0f948ee8ef39a835b1ede Author: lijewski Date: Tue Jun 14 20:35:53 2011 +0000 remove option for calling bicubic interp on state data Src/C_AMRLib/Particles.H commit 727675e50de4500d8f616fea30e7b84ffc77c9ba Author: lijewski Date: Tue Jun 14 20:35:35 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles_2D.F commit da656a839af41494237b65a2203b03d4cc46bcb8 Author: ajnonaka Date: Tue Jun 14 16:44:03 2011 +0000 now printing lo/hi/avg FAB byte spread Src/F_BaseLib/fab.f90 commit 1d37f3052cca0bd7a80a43c8c45c86631d4721bf Author: almgren Date: Mon Jun 13 20:20:35 2011 +0000 Need more files than we thought. Src/LinearSolvers/C_CellMG/Make_nyx.package commit 8fd27b25e3bd44ecb15555e08b35b8741364adfb Author: almgren Date: Mon Jun 13 20:03:47 2011 +0000 Only include what we need for running NYX. Src/LinearSolvers/C_CellMG/Make_nyx.package commit b15a456c11b299a679ede5485ce7249f581a46b8 Author: lijewski Date: Fri Jun 10 23:48:03 2011 +0000 quiet some unsed variable warnings Src/C_AMRLib/Particles.H commit 36f82ffb08dc1463b38a628a03e66cb7d2a1fad6 Author: lijewski Date: Fri Jun 10 23:45:29 2011 +0000 we store the average advected velocity in particles that use AdvectWithUmac() for LMC Src/C_AMRLib/Particles.H commit e23e26ca206ccbf67677238dd043ad7235199ac0 Author: lijewski Date: Fri Jun 10 23:39:54 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles_2D.F commit 7f7bd95300cdbe9d52bea3db0ce215d63e98b84a Author: lijewski Date: Fri Jun 10 17:43:22 2011 +0000 make it explicit that we are using cell-centered data in bicubic Src/C_AMRLib/Particles_2D.F commit 1ee40d60598d67620c60e7ca9417fcc790ab1a82 Author: wqzhang Date: Fri Jun 10 16:23:59 2011 +0000 more radiation benchmarks added Tools/C_util/regtests/radiation-tests.ini Tools/C_util/regtests/test-Ubuntu.py commit 1b4385464790db152b9187abecf5401cad7a4007 Author: lijewski Date: Thu Jun 9 23:25:54 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles_2D.F Src/C_AMRLib/Particles_F.H commit 74fb42d05ac95127ab32edfc2db4266cdcd7ff83 Author: lijewski Date: Wed Jun 8 21:40:33 2011 +0000 more work on AdvectWithUmac(); now Redistribute between predictor and corrector Src/C_AMRLib/Particles.H commit efce3be00b153b400aa80390824c297291613af1 Author: lijewski Date: Wed Jun 8 19:50:12 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.cpp commit f769638176c85ab916a3f95dd79ab563564994fc Author: mzingale Date: Wed Jun 8 17:46:17 2011 +0000 add a generic catch for a linux machine with the generic localhost name (like a typical laptop), with an MPIHOME defined to an mpich directory. Tools/F_mk/GMakeMPI.mak commit 32c25b24858b8a704d3b6c548c657670c332ab05 Author: lijewski Date: Tue Jun 7 21:53:57 2011 +0000 just a little tidying up of things ... Src/C_AMRLib/Particles.H commit c1d348773be0fd2a5208a7730f8da7ad7b0e3571 Author: gilet Date: Mon Jun 6 23:49:26 2011 +0000 module name was too long for PathScale on hopper Src/F_BaseLib/fourth_order_interp_coeffs.f90 Src/F_BaseLib/interp.f90 commit 102bc876c1c36fc22657967baef22457c95981f4 Author: lijewski Date: Mon Jun 6 22:39:17 2011 +0000 added optional finalize_parallel arg to Finalize() for George Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp commit 2e36c8f7a7e48c2c24d160e30038cc3a8ea3b4b6 Author: almgren Date: Mon Jun 6 22:15:21 2011 +0000 oops. Src/F_BaseLib/interp.f90 commit 86279bbb4514725add330ce5c6445ad3d60e19bd Author: almgren Date: Mon Jun 6 22:13:37 2011 +0000 fix name of interp_coeffs_module -> fourth_order_interp_coeffs_module. Src/F_BaseLib/interp.f90 commit f028adbb6f5072891e6d2b3886c0b7eb0f355ee9 Author: lijewski Date: Mon Jun 6 21:38:58 2011 +0000 didn't have vel interp quite right in AdvectWithUmac() Src/C_AMRLib/Particles.H commit 01d188c7fd2dd1ea27709fc46e0f174b3b320183 Author: lijewski Date: Mon Jun 6 19:51:29 2011 +0000 Pulled the core of Interp() into InterpDoIt() which is now called by AdvectWithUmac(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 057f981fb0e25be2b755f65e03dc4d4fa818b394 Author: almgren Date: Mon Jun 6 18:52:27 2011 +0000 Add fourth_order_interp_coeffs.f90 Src/F_BaseLib/GPackage.mak commit ae419e2f6bae513124896d38fce230f5fdd0c146 Author: almgren Date: Mon Jun 6 18:51:45 2011 +0000 Change name of module Src/F_BaseLib/fourth_order_interp_coeffs.f90 commit 9c5902239e5165322e597b9577ab7d59d1199f1d Author: almgren Date: Mon Jun 6 18:51:27 2011 +0000 Add Matt's implementation of fourth-order interpolation, which requires fourth_order_interp_coeffs_module Src/F_BaseLib/fourth_order_interp_coeffs.f90 Src/F_BaseLib/interp.f90 commit 4c2c6b5897c2d2545d801ea843dbefbda38b0c3a Author: almgren Date: Mon Jun 6 18:46:27 2011 +0000 Fix calling sequence for fourth_order_interp_2d, and replace calls by bl_error calls for 1d and 3d. Src/F_BaseLib/fillpatch.f90 commit 2854b6a2e0d07e119a9b9c317b1415659c259691 Author: lijewski Date: Fri Jun 3 22:45:13 2011 +0000 use scientific notation in Timestamp() and force 10 digits of accurracy Src/C_AMRLib/Particles.H commit e293e0cab1ab1a3f0a54c9b41f67a6b1d8154dc8 Author: ajnonaka Date: Fri Jun 3 17:45:41 2011 +0000 rennamed a bl_prof_timer to avoid conflict Src/LinearSolvers/F_MG/stencil.f90 commit 9876f01f8d2d37ccf78ac73263379fc6703f01a4 Author: ajnonaka Date: Thu Jun 2 21:44:31 2011 +0000 fix error in ghost cell checking in multifab_sub_sub_c Src/F_BaseLib/multifab.f90 commit 3108c3cb97e81cc2af46b2f1f4bacc8ec95717bf Author: mzingale Date: Tue May 31 21:40:20 2011 +0000 add .SDC to the suffix -- this way the build system uses separate files for the SDC and non-SDC versions of the code, and doesn't confuse object files if you switch. Tools/F_mk/GMakedefs.mak commit 55d10eea9e337d83da44b150b5e0e8791ad8e55c Author: lijewski Date: Fri May 27 17:41:13 2011 +0000 a little simplification Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 95c7f354360bcdec07a0ff46301e4214481d3ae7 Author: lijewski Date: Thu May 26 21:11:27 2011 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit da99b8611851fcb02b417aa0aa1b1791717ad2ba Author: lijewski Date: Thu May 26 20:57:34 2011 +0000 don't build lasrctmp in fluxassoc_build() if not really needed Src/F_BaseLib/layout.f90 commit e3576a97ad2597bc421da8348b1ba2fc259afcc7 Author: lijewski Date: Thu May 26 20:30:27 2011 +0000 don't build latmp in boxassoc_build() if not really needed Src/F_BaseLib/layout.f90 commit b8260b5b7f8b843fdd471a895f1b0b365dfad381 Author: lijewski Date: Thu May 26 19:29:57 2011 +0000 multifab_sum_boundary() now used layout_get_box_intersector() stuff Src/F_BaseLib/multifab.f90 commit cacfaca645e18ce3c2d8421805744571e26edc6a Author: lijewski Date: Thu May 26 17:01:35 2011 +0000 initial cut at multifab_sum_boundary() Src/F_BaseLib/multifab.f90 commit bfda22d0c685713af39448cdee5e262b8a6bf24e Author: lijewski Date: Wed May 25 21:59:17 2011 +0000 Don't forget to call set_particle_id() in checkpoint() after get_particle_id(). The latter increments our internal particle_id counter and the former sets it back to where it should be. Otherwise we "lose" a particle_id every time we write a checkpoint file. Src/F_BaseLib/particles.f90 commit c1f9dd5cbc452570d46d657216ca077b2446ea3c Author: almgren Date: Mon May 23 22:33:00 2011 +0000 Add new subroutine make_particle_count which fills a multilevel multifab with the number of particles per cell. Src/F_BaseLib/particles.f90 commit ef60a2fe01fb6e59b29fb589f75ed0f141f80414 Author: almgren Date: Mon May 23 20:52:14 2011 +0000 Fix error message. Src/F_BaseLib/particles.f90 commit a781a22b0eafe7b621defeeecbcc39108d9b15d6 Author: lijewski Date: Mon May 23 20:30:21 2011 +0000 added Tokenize() Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 01641db35e5adc86a2f188ce7456b74f6f19ff07 Author: almgren Date: Mon May 23 18:42:30 2011 +0000 Add comment. Src/F_BaseLib/particles.f90 commit 64f8ae8c8629deeb6e36f3258b94e446421c9966 Author: almgren Date: Thu May 19 19:47:51 2011 +0000 Added some debugging to InitCosmo. Src/C_AMRLib/Particles.H commit 0c514b84e3899e8b8109bd3d6166fcc0acae0804 Author: almgren Date: Thu May 19 18:21:52 2011 +0000 New version of InitCosmo(). Src/C_AMRLib/Particles.H commit 549eacb04ed385efd02e054193b283ae2952d1e5 Author: lijewski Date: Wed May 18 20:49:11 2011 +0000 IncrementWithTotal() now returns a long not an int. Ints are only guaranteed to hold numbers up to 2^31-1. All callers of this routine should change their return value from int to long as well. Src/C_AMRLib/Particles.H commit 9165a3e939f50b7eea7c02073ef6969394fbab71 Author: almgren Date: Wed May 18 19:19:22 2011 +0000 Make a version of MoveRandom that takes level as an argument. Src/C_AMRLib/Particles.H commit 4cea52d9d5e36a8e84c6ad57ac05c80fd7899cd2 Author: lijewski Date: Wed May 18 16:07:38 2011 +0000 AdvectWithUmac() now assumes we have at least one ghost cell in umac. This means we only have to do one Redistribute() per call instead of two. It also means that particles that cross a periodic boundary work properly. Src/C_AMRLib/Particles.H commit 986a600d2c1408b2c3c7cfb27e0581580873b6f6 Author: lijewski Date: Mon May 16 22:54:34 2011 +0000 delta in move_advect() didn't take into account a non-zero problo Src/F_BaseLib/particles.f90 commit 081540255269208e362f5bc560c75f2b9c51ac6f Author: lijewski Date: Mon May 16 22:47:19 2011 +0000 delta in MoveKick[Drift] routines didn't take account of possibility of non-zero problo Src/C_AMRLib/Particles.H commit e70ec87c64f4db29405928f4a5fcecdeb89b950e Author: lijewski Date: Mon May 16 21:48:02 2011 +0000 fixed my typo Src/C_AMRLib/Particles.H commit b06d7409a6f36ef29ab97b1c669dba525d22407c Author: almgren Date: Mon May 16 21:13:58 2011 +0000 Remove unused "grid" Src/C_AMRLib/Particles.H commit c67c9a01ce7f9d1a72c7c3794502fc2d1a2ab40b Author: lijewski Date: Mon May 16 17:25:21 2011 +0000 removed unused variable Src/C_AMRLib/Particles.H commit 561f36801c8e033dd679f8ede6d2a947f3033316 Author: lijewski Date: Sun May 15 18:29:36 2011 +0000 added assert that DeriveFunc != 0 in derive() Src/C_AMRLib/AmrLevel.cpp commit 3de83c6c1ffd8c29c8407d2629af186d9e30f389 Author: lijewski Date: Sun May 15 17:08:14 2011 +0000 removed some crufty KCC and Cfront stuff Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/winstd.H Tools/C_mk/Make.AIX Tools/C_mk/Make.CRAY Tools/C_mk/Make.CYGWIN_NT Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.Linux Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit e234707f011f2102bf09f4a07a3897ec89aee6dd Author: lijewski Date: Sun May 15 15:24:12 2011 +0000 think I've finally got Timestamp doing what I want Src/C_AMRLib/Particles.H commit 4ab15b16b4ebee457a49cd0cb32d776c8524b455 Author: almgren Date: Fri May 13 21:54:27 2011 +0000 Make the two Increment routines have separate names. Src/C_AMRLib/Particles.H commit ec049a0d4aa8ed8b45a1a11cbcf3ca09814cf7b5 Author: almgren Date: Fri May 13 21:46:06 2011 +0000 Add a version of Particles that return the total number of particles in the domain at this level. Src/C_AMRLib/Particles.H commit 257ac64428d3f40f03073e21f8937cd5c8dd303d Author: almgren Date: Fri May 13 20:58:31 2011 +0000 Clean up the Fortran-less Derive stuff. Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 4502e8a3afcb41c1369bc606aaf33e84821315c6 Author: almgren Date: Fri May 13 20:35:05 2011 +0000 Allow us to defined derived quantities without associated Fortran functions -- these must be defined entirely in the C++. Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 1fe503fa451aa15b4f5113f976ab6ae2ec7fef27 Author: almgren Date: Fri May 13 17:52:25 2011 +0000 If particle is right on a domain boundary then move it just inside the boundary. Also add print statements about bad particle if initialization fails. Src/C_AMRLib/Particles.H commit 111dcd634de9529e6485ae15b4f95276c188216b Author: lijewski Date: Thu May 12 22:20:33 2011 +0000 removed names from Timestamp Src/C_AMRLib/Particles.H commit 0cc3c0ce723e85794c7f865a2b8033884e376f47 Author: lijewski Date: Thu May 12 20:58:44 2011 +0000 close() Timestamp file after flush() Src/C_AMRLib/Particles.H commit e3306725292a3903f64cab8b9ecfcccad0ea9910 Author: lijewski Date: Wed May 11 17:55:40 2011 +0000 exist ASAP from Timestamp() if no work to do Src/C_AMRLib/Particles.H commit 8483ac48a9b9c65b3e1acd81e585735699281e53 Author: lijewski Date: Tue May 10 22:36:04 2011 +0000 make AssignDensityDoIt() work with non zero-based prob domain like Interp() Src/C_AMRLib/Particles.H commit ca9ef50163a7be357801cce99b525f090646832a Author: lijewski Date: Tue May 10 22:34:35 2011 +0000 make sure frac is in [0,1] in a floating-point way Src/C_AMRLib/Particles.cpp commit 0d423ba5921ef1713aade3b773abe23ac9c1f7e0 Author: lijewski Date: Tue May 10 18:56:30 2011 +0000 frac calculation in Interp now works with non zero-based prob domain Src/C_AMRLib/Particles.cpp commit f5b2a5b865fee47a54e2e9807d5f8df6fda3348e Author: lijewski Date: Tue May 10 04:55:21 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.H commit 2fa73845aec986aa253870e7624163d8ac8f9d9a Author: lijewski Date: Mon May 9 20:03:29 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.cpp commit d62424634f2e2920128a3d3f1868f356a1525931 Author: lijewski Date: Mon May 9 19:48:36 2011 +0000 just use MyProc when setting initial m_cpu Src/C_AMRLib/Particles.H commit 14b0c8b112245a0412bf6654a9ff10dcb4cab4f1 Author: lijewski Date: Mon May 9 17:27:45 2011 +0000 removed lev argument from Interp() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit cfc92c2b00f6546ca75ebe23161c8e53ca20bd89 Author: lijewski Date: Mon May 9 16:43:30 2011 +0000 Timestamp() must now be passed the MultiFab to be sampled Src/C_AMRLib/Particles.H commit e8dd76fc105e5c41d77729de990aa4ca16e970ba Author: lijewski Date: Mon May 9 05:51:58 2011 +0000 some I/O mods Src/C_AMRLib/Particles.H commit e0f2191a4c7d55b8d0a80f31e2aae27b02860ebe Author: lijewski Date: Mon May 9 05:51:03 2011 +0000 removed some I/O Src/C_AMRLib/Particles.cpp commit e127fcee11e9646465e7d23705d72037ec0d24af Author: lijewski Date: Mon May 9 04:35:50 2011 +0000 print count of particles removed in RemoveParticlesNotAtFinestLevel() Src/C_AMRLib/Particles.H commit c65a387b0319380846baa4c397c89f17042b341f Author: lijewski Date: Mon May 9 02:02:41 2011 +0000 no longer remove zero length files in Timestamp; can't happen since each file gets a header Src/C_AMRLib/Particles.H commit 2d310c38011c6c7636ef6e33146936a7584f7b70 Author: lijewski Date: Mon May 9 01:25:38 2011 +0000 fixed some debug output when DIM=2 Src/C_AMRLib/Particles.H commit 635258f02972b40893e0232233c0c7beaa57bb8c Author: lijewski Date: Mon May 9 00:09:20 2011 +0000 refinement to Timestamp() Src/C_AMRLib/Particles.H commit bd88647ca029ad8c3f80e6386c73be9908a7568c Author: lijewski Date: Sun May 8 20:04:49 2011 +0000 Undefaulted the second argument to InitFromAsciiFile(). This way is someone updates to the latest code and tries to use it, they'll get an error, until I've gotten around to fixing all calling sequences. Src/C_AMRLib/Particles.H commit 2d75d5171cb2901a97c96e32f2bbe0f539321627 Author: lijewski Date: Sun May 8 19:37:15 2011 +0000 Apparently InitFromAsciiFile() has changed since I wrote it. Instead of just reading in the position data, N bytes of m_data where also being read it. Not sure how reading in all those bytes could possibly make sense since some of those bytes are there only to hold temporary position data in AdvectWithUmac(), but I had to change it a bit in order to make the routine work when I only want to read in positions: I added a default integer argument "extradata", that defaults to zero, which is the number of bytes of data in m_data to read in for each particle. It MUST be <= N. The default way to use InitFromAsciiFile() is now to read in just positions. If you want to get "extra" data read in for each particle, you must specify the count as the second argument of the call. Src/C_AMRLib/Particles.H commit b984fa5c9c9835dde13cc093efdfbd69ecd86a5a Author: lijewski Date: Sun May 8 19:02:58 2011 +0000 remainder of particles in InitFromAscii() needs to go to last CPU not IOProc Src/C_AMRLib/Particles.H commit 7fd55e972cda178b5c5ad7d9969535d0ee07a863 Author: lijewski Date: Sat May 7 00:16:22 2011 +0000 InitFromAsciiFile() is now much faster in parallel Src/C_AMRLib/Particles.H commit 12ed44dfbb5445ac7d8d146153463d4d6ce87903 Author: lijewski Date: Fri May 6 21:52:07 2011 +0000 changed AdvectWithUmac() to John's satisfaction Src/C_AMRLib/Particles.H commit 34ef9ff6b49c43b9b2ade4e5c7b6ed0ca04091a9 Author: lijewski Date: Fri May 6 21:21:07 2011 +0000 modest speedup to InitFromAsciiFile(); more to come ... Src/C_AMRLib/Particles.H commit 5758965ae597e044af1384e7ac668a39ec60c40f Author: almgren Date: Fri May 6 21:03:11 2011 +0000 Add new routine -- GetRhoFromParticles which defines a grid-based density and modifies the mass of the particles so that the total mass of grid+particles remains the same. Src/C_AMRLib/Particles.H commit 54be97ea6599ef8bd8b7630d49f6704554a146f3 Author: almgren Date: Fri May 6 00:06:04 2011 +0000 If we call AssignDensity, then now allow domains that have no periodic boundaries as long as none of the particles are within one cell of the domain boundary. Src/C_AMRLib/Particles.H commit 1d29c22ec266497ab71d619f169c265edbc06cd5 Author: lijewski Date: Thu May 5 22:49:45 2011 +0000 GetGravity() now calls Interp() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 84c10585cb069b75e6b2b34676a588445fe52ec2 Author: lijewski Date: Thu May 5 17:35:39 2011 +0000 added ParticleBase::Interp() -- called by Timestamp() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit b55b5fedda6ac452d418dc1839c8e4501921fd01 Author: lijewski Date: Wed May 4 19:46:04 2011 +0000 early exit from Increment() Src/C_AMRLib/Particles.H commit 110b4b10ff81121bfcca5c03144aab5d30a8f30b Author: lijewski Date: Wed May 4 17:10:37 2011 +0000 added RemoveParticlesNotAtFinestLevel() needed by HeatTransfer Src/C_AMRLib/Particles.H commit 52bde8ac565d7e6602be41dba3c1d0c1691ce649 Author: lijewski Date: Tue May 3 21:01:37 2011 +0000 removed some excess whitespace when printing in verbose Src/C_AMRLib/Particles.H commit 5bf196e35f12467c3df6b4b894d36d065a5f894b Author: lijewski Date: Tue May 3 20:00:00 2011 +0000 no longer force Timestamp() to have non-empty names and indices Src/C_AMRLib/Particles.H commit a28e619171853bc4bee64c52399bce2938077421 Author: lijewski Date: Tue May 3 19:21:09 2011 +0000 refinement to how we reset NextID() Src/C_AMRLib/Particles.H commit 5264abb3c3ae3672ca390f07e953fabc125a6a03 Author: almgren Date: Mon May 2 18:45:30 2011 +0000 Only enforce periodicty in AssignDensity if there are actually particles present. Src/C_AMRLib/Particles.H commit de52900600575a74b978497e2e4f96fb13ef3e5f Author: almgren Date: Fri Apr 29 22:24:46 2011 +0000 Modify fill_boundary so that it doesn't kick out if ng = 0. Src/F_BaseLib/multifab.f90 commit 4d178a6a1951e240a2bda182fa41097d2bcfb9f8 Author: lijewski Date: Fri Apr 29 17:57:19 2011 +0000 slightly different rules for libraries from Gunther for VisIt usage Tools/C_mk/Make.rules commit abb81b4a3ff6f2fbe446a0776509b961dd62bd90 Author: almgren Date: Thu Apr 28 21:59:53 2011 +0000 Correct criterion for destroying gcrse. Src/F_BaseLib/fillpatch.f90 commit 5d33678f63cd2f0006fc71d2abb8445aedf5c7a2 Author: almgren Date: Thu Apr 28 20:56:38 2011 +0000 Changes by Ann & Mike L. which hopefully fix the problems we were seeing. Still not clear if this will work in all cases; we are assuming that proper nesting covers situations. Src/F_BaseLib/fillpatch.f90 commit 9060a21d7b17fdf9ba93c641c4fc2410d8d578b9 Author: almgren Date: Thu Apr 28 19:33:36 2011 +0000 If ng = 0 define ncomp(crse) components of gcrse (used to default to 1). Src/F_BaseLib/fillpatch.f90 commit 56d3e69141ce3e750b1bf7712af4b4dfef6aa215 Author: almgren Date: Sun Apr 24 21:17:11 2011 +0000 Allow for fourth order stencil with stencil_width = 2. Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 88c932351e3fbc9c0db117ffba3c8c3c49766d0c Author: almgren Date: Sun Apr 24 21:09:14 2011 +0000 If fourth_order = .true. then call fourth_order_interp instead of lin_cc_interp. Src/F_BaseLib/fillpatch.f90 commit 524d5a0a5c082b21476548702f89c4f195d6610e Author: almgren Date: Sun Apr 24 21:08:15 2011 +0000 Add stubs for fourth order interpolation routines. Src/F_BaseLib/interp.f90 commit 041917e70f7d9a5b76bf5c7d3c223bf66b837399 Author: lijewski Date: Fri Apr 22 23:05:21 2011 +0000 a little more OMP work Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 013ece29e83aff808a949b1adc9ecbed65e0ff61 Author: lijewski Date: Fri Apr 22 21:37:17 2011 +0000 changed some 0 -> ZERO Src/LinearSolvers/F_MG/stencil.f90 commit cca17799f6362ba521bbcaaf2f29b384e2dff3ec Author: almgren Date: Fri Apr 22 21:35:20 2011 +0000 1) Pass through optional argument stencil_width_input. 2) Send ng=0 to fillpatch -- no need to create ghost cells of the buffer region mf's around the fine grids. Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit c1183891ac6c24dafaa65a92397ffc7e0bb1793e Author: almgren Date: Fri Apr 22 21:29:06 2011 +0000 Allow for a more general stencil_width (still defaults to one) Src/F_BaseLib/fillpatch.f90 commit b68e06f67b2b3e10bf705cfcd5c67abfb5246d54 Author: almgren Date: Fri Apr 22 20:18:52 2011 +0000 Fix test on whether coeffs sum to zero (used for whether we enforce solvability) Src/LinearSolvers/F_MG/ml_cc.f90 commit d034d7be7616b55df6db196b8cf1e26912b14676 Author: almgren Date: Fri Apr 22 20:07:27 2011 +0000 Add new function -- "max_of_stencil_sum" that looks just like stencil_norm but doesn't take the absolute value of each component before summing. Src/LinearSolvers/F_MG/stencil.f90 commit dd3d3cee2912f9f30ebceb8a1e0d5c4e7ac099c9 Author: almgren Date: Fri Apr 22 18:49:40 2011 +0000 Adding additional print statement. Src/LinearSolvers/F_MG/ml_cc.f90 commit d34370b6f07baf8bbf2c0d50d646a1a75a4624a6 Author: ajnonaka Date: Thu Apr 21 20:12:24 2011 +0000 prevent the grid iteration code from running during initialization if you have supplied a grid file. This prevents multiple redundant calls to initData at level 1 and greater if you have supplied a fixed grid file Src/C_AMRLib/Amr.cpp commit 46e3c4397cc060e34cfd4cbb3a0cde3ecf597dc7 Author: lijewski Date: Wed Apr 20 20:08:44 2011 +0000 use CC wrapper instead of crayc++ for Cray Tools/C_mk/Make.Linux commit a0beb4049f3a5e6d223d37541f7bb6427c0cc5e1 Author: lijewski Date: Mon Apr 18 16:43:03 2011 +0000 now print out number of OMP threads if BL_USE_OMP=TRUE Src/C_BaseLib/BoxLib.cpp commit a9135de36ea88c01344ca626a7a9016896f5dfa8 Author: marc Date: Thu Apr 14 22:25:22 2011 +0000 Fix up the logic for BL_NO_FORT Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 6045aceba361a9e4a089bf4fd2198f5c87532968 Author: lijewski Date: Wed Apr 13 21:15:20 2011 +0000 some OMP Src/C_AMRLib/FLUXREG_3D.F commit 8aac6a4ec330e49f2e43c7b7e07ec2e662bb05d0 Author: lijewski Date: Wed Apr 13 21:03:26 2011 +0000 minor performance improvement Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit b32c306f3f8a64d35e35e823e71ae82e63e11f3a Author: almgren Date: Fri Apr 8 18:46:32 2011 +0000 Get rid of extra characters. Src/F_BaseLib/make_new_grids.f90 commit 8574335147d76ba18c1a5845333ff8de12ad1389 Author: marc Date: Fri Apr 8 01:34:01 2011 +0000 *** empty log message *** Tools/C_util/ViewMF/viewMFcol.cpp commit c6229704b14dd4ac5170a1f79474500f409b0124 Author: lijewski Date: Thu Apr 7 21:18:19 2011 +0000 removed all references to USE_THREADS Src/C_BaseLib/test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/C_BaseLib/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tools/C_mk/Make.AIX Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs commit e93c256015e86da9263de88a6c43b5367820a682 Author: lijewski Date: Sat Apr 2 23:26:07 2011 +0000 minor simplification of AssignDensity() Src/C_AMRLib/Particles.H commit 9ef548b36e08aebf25d10ba35acac2cc2a57c936 Author: lijewski Date: Fri Apr 1 23:15:23 2011 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit ba907cfbf64a8903c3ba92cd6112fe6860c6eb94 Author: lijewski Date: Fri Apr 1 17:36:21 2011 +0000 added GPROF stuff Tools/F_mk/comps/gfortran.mak commit cd14ba9a71fe938ed2b00d92214126c11d79c818 Author: almgren Date: Thu Mar 31 18:03:47 2011 +0000 Add comments about which MoveKick or MoveKickDrift function we're calling -- the one with gravity at cell centers or the one with the normal components of gravity on faces. Src/C_AMRLib/Particles.H commit 4b70af736f7d76c2f965c65134d6c604df02fbe8 Author: lijewski Date: Thu Mar 31 16:59:12 2011 +0000 added a little commented out debugging code Src/C_BaseLib/Geometry.cpp commit c88db5d9b7107b46aa77a896c367a2a1d447d320 Author: lijewski Date: Thu Mar 31 16:17:04 2011 +0000 got to call new SumPeriodicBoundary() with correct Geom Src/C_AMRLib/Particles.H commit 614af5d6c9f0fe31a69471fd15fbef5de1f4cce0 Author: lijewski Date: Wed Mar 30 23:59:27 2011 +0000 integrated in new SumPeriodicBoundary(dstmf,srcmf) Src/C_AMRLib/Particles.H commit ee1b80d10263a38252c6a4d845bcb9b6ffd6b424 Author: lijewski Date: Wed Mar 30 23:58:51 2011 +0000 Wrote SumPeriodicBndry() taking a srcmf and dstmf. Still needs to be tested. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 4419c69a20a9dbe8b617c4bcef08a4425f9c488b Author: lijewski Date: Wed Mar 30 21:42:56 2011 +0000 more work on AssignDensity(); still not right for level 1 grid abutting periodic boundary Src/C_AMRLib/Particles.H commit 1333972a72ffe5d48693e2818729f6f5537f603d Author: almgren Date: Wed Mar 30 19:27:13 2011 +0000 1) Change verbosity threshhold. 2) If there are no particles at a level then return a negative est_dt for that level. Src/C_AMRLib/Particles.H commit f8b12073a406c043747f8be29bf65eac7f9d3a9a Author: almgren Date: Wed Mar 30 18:28:55 2011 +0000 if particles.verbose > 0 then print out total number of particles when reading from ascii file. Src/C_AMRLib/Particles.H commit 5d7de367133f32b4298ce027a8453e31ac96ef7e Author: lijewski Date: Wed Mar 30 18:16:59 2011 +0000 modest improvement to bndry_reg_copy() Src/F_BaseLib/bndry_reg.f90 commit 716631ab0f0ae4ae6815fdad9d9c4734527ccb0b Author: almgren Date: Wed Mar 30 17:44:22 2011 +0000 Add setval of tcmf. Src/C_AMRLib/Particles.H commit 7b9dfdfdf697536b0f1ada09a065f83a66227df4 Author: almgren Date: Wed Mar 30 17:08:00 2011 +0000 Make sure to call multifab_fill_boundary on crse mf when filling bndry_reg. Src/F_BaseLib/bndry_reg.f90 commit 6e605c640b88c217c46e86222a29178ef4d0f88f Author: lijewski Date: Tue Mar 29 20:48:25 2011 +0000 yet more work on multi-level AssignDensity() Src/C_AMRLib/Particles.H commit 97e565ff3ed983f36016f16f86b8d8b72a10dab4 Author: lijewski Date: Tue Mar 29 20:35:46 2011 +0000 more work on multi-level AssignDensity() Src/C_AMRLib/Particles.H commit a4db7937acde2720565d9192be6bba8fe7812e7d Author: lijewski Date: Tue Mar 29 20:24:20 2011 +0000 more work on multi-level AssignDensity() Src/C_AMRLib/Particles_1D.F Src/C_AMRLib/Particles_2D.F Src/C_AMRLib/Particles_3D.F commit 4457897b2873c7151e7de540d8eb93bedfeeee4f Author: lijewski Date: Tue Mar 29 17:43:39 2011 +0000 more work on multi-level AssignDensity() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles_F.H commit 81d8358487c7aa069c4b95f70fd4b85a2d459aa3 Author: lijewski Date: Tue Mar 29 17:28:13 2011 +0000 some work on multi-level AssignDensity() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles_1D.F Src/C_AMRLib/Particles_2D.F Src/C_AMRLib/Particles_3D.F Src/C_AMRLib/Particles_F.H commit 2c92cf131d544fc50bacf24e9ea57698fd9386de Author: lijewski Date: Mon Mar 28 23:00:26 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles_3D.F commit 2f5dea77a020749b1baabb010dd426a1c0664e4f Author: lijewski Date: Mon Mar 28 23:00:13 2011 +0000 added AssignDensityDoIt() Src/C_AMRLib/Particles.H commit 1db4bdea075d95ab374e617437ddd88bb0450b73 Author: lijewski Date: Mon Mar 28 22:37:45 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles_1D.F Src/C_AMRLib/Particles_2D.F commit 5ae45db8c61006f07600dd7bf3ad614e187d8a37 Author: lijewski Date: Mon Mar 28 22:20:08 2011 +0000 added part_summassup() Src/C_AMRLib/Particles_3D.F Src/C_AMRLib/Particles_F.H commit 9ea1c8eb6c5abb5b5d53128ad2963ae23553c030 Author: lijewski Date: Mon Mar 28 20:32:42 2011 +0000 added part_sumdown() Src/C_AMRLib/Particles_3D.F Src/C_AMRLib/Particles_F.H commit 017cd78c7014c27a706251c4f1365239022108a7 Author: lijewski Date: Mon Mar 28 16:19:35 2011 +0000 mod to quiet g++ Src/C_AMRLib/Particles.H commit 1503348ff3228c0203c504c96f8a3519bfcd0ba3 Author: lijewski Date: Fri Mar 25 18:01:48 2011 +0000 some OMP refinement Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 0f5999c1322522f3d84db5a70bd7a25961ecf311 Author: lijewski Date: Fri Mar 25 17:11:38 2011 +0000 some OMP refinement Src/F_BaseLib/fab.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab.f90 commit 731234bf48973e8200bb7d7867e72a1964b471a6 Author: lijewski Date: Thu Mar 24 21:27:31 2011 +0000 some OMP refinement Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit eecf6c81d397e512d3f20b8734027be767a16be8 Author: lijewski Date: Thu Mar 24 20:50:43 2011 +0000 some OMP refinement Src/C_AMRLib/INTERP_3D.F commit 0f244370fb7979854900797701a0872e94c10113 Author: lijewski Date: Thu Mar 24 20:37:37 2011 +0000 some OMP refinement Src/C_BaseLib/SPECIALIZE_3D.F commit 2c3839d4b0c86f6b22973fd290cdcbd6b099ee44 Author: lijewski Date: Tue Mar 22 20:24:56 2011 +0000 some cleanup Src/C_AMRLib/Amr.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/interface.cpp commit 049b34833ba5b2c3843879d913959eef82a8477d Author: lijewski Date: Tue Mar 22 20:02:48 2011 +0000 No longer need to call AddToCache() to recache some MultiFabs. DistributionMapping::FlushCache() now only removes DMs that are not referenced by any MultiFabs. Src/C_AMRLib/Amr.cpp commit d781e4d7264c5e46d2ae1944c90f7ae0020ee358 Author: lijewski Date: Tue Mar 22 20:01:39 2011 +0000 The cache is now a std::map instead of a std::vector. FlushCache() now only removes DMs that are not referenced by any MultiFabs. Removed AddToCache(). Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 373d14eb15a5b8f8fac1b4e0579a8c87a692e494 Author: almgren Date: Sun Mar 20 17:42:38 2011 +0000 Make the minion smoother be GSRB, for now anyway. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit b759a8fb43b7adf4ecd4df0ed6a65e68de9ef732 Author: almgren Date: Sun Mar 20 15:36:34 2011 +0000 Add crse flux construction for Minion's 2D cross stencil (ns = 9 as opposed to 7). Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 92b106b4ed8c7f76be78bed45bd4af0894057aab Author: almgren Date: Sun Mar 20 15:35:56 2011 +0000 Add flux construction for Minion's 2D cross stencils (ns = 9 as opposed to 7) Src/LinearSolvers/F_MG/stencil.f90 commit 8f2d33ef89c58e0a977c78e4afc2c1fffd6a22e5 Author: almgren Date: Sun Mar 20 15:29:42 2011 +0000 Fix typo. Src/LinearSolvers/F_MG/ml_cc.f90 commit 0a9c55df74c4b3e27248f951078820952a4fa386 Author: almgren Date: Sun Mar 20 15:26:43 2011 +0000 Clean up how we test whether we should enforce solvability. Src/LinearSolvers/F_MG/mg.f90 commit 856ff3d37e09393e0ef64c4c172b302d3d03cfe7 Author: almgren Date: Sun Mar 20 15:25:59 2011 +0000 Use new coeffs_sum_to_zero flag to decide whether to enforce solvability. Src/LinearSolvers/F_MG/ml_cc.f90 commit 579594a99b1aff4269b9f61ccff72993d5a2fc2d Author: almgren Date: Sun Mar 20 15:25:33 2011 +0000 Add coeffs_sum_to_zero flag in mgt Src/LinearSolvers/F_MG/mg_tower.f90 commit 383000cd5b40e4856c1075b3daaf309f719a02fd Author: almgren Date: Sun Mar 20 02:51:00 2011 +0000 Need to allow for nghost > 1. Src/F_BaseLib/create_umac_grown.f90 commit 3ed535aa9b96eb0a1026180fa7d0c1eb1a9fc46f Author: almgren Date: Sat Mar 19 20:15:17 2011 +0000 Grow the fine region by ng_fill instead of 1 so that we fill the right zone of ghost cells. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit c9549dcafd368fad05744ecb93a6fc23cb4a4385 Author: almgren Date: Sat Mar 19 01:24:04 2011 +0000 Remove unused variable. Src/LinearSolvers/F_MG/ml_cc.f90 commit 665f09d440ae25c09eae97e7357f01ff10eb54f9 Author: almgren Date: Fri Mar 18 23:59:32 2011 +0000 Comment out the making of bottom_singular until I figure out how to differentiate MAC solves from viscous/diffusive solves. Src/LinearSolvers/F_MG/mg.f90 commit ae8a745513d5bfcd6276b576fa627a0dc7da3322 Author: lijewski Date: Fri Mar 18 16:40:29 2011 +0000 removed some too-little-work OMP loops Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 8fd8622d0e66d03975ef1b907b9fbd69adbe2728 Author: lijewski Date: Fri Mar 18 16:03:41 2011 +0000 removed some too-little-work OMP loops Src/F_BaseLib/fab.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab.f90 commit 36683cda860921c3cb8c0ba85cbea36fcf5d15d8 Author: lijewski Date: Thu Mar 17 22:11:14 2011 +0000 removed some too-little-work OMP loops Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/hg_avg3d.f commit 90fca2c8a777de4149f2e99e4f70274f96fe6352 Author: lijewski Date: Thu Mar 17 21:13:01 2011 +0000 removed some too-little-work OMP loops Src/C_BaseLib/COORDSYS_3D.F commit a4fda83f9393b888179438715b2cb9c8d5ec0b15 Author: lijewski Date: Thu Mar 17 21:00:23 2011 +0000 removed some too-little-work OMP loops Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/INTERP_3D.F commit 7a11c523d6770ecb71b7a654ecb8b294d985f36c Author: lijewski Date: Thu Mar 17 20:52:50 2011 +0000 removed some too-little-work OMP loops Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit 2cc3c2606cb200ae5c5d28e5c6aa43802ea4ebc9 Author: almgren Date: Wed Mar 16 19:50:38 2011 +0000 We now allow crse to have more than one ghost cell (before required exactly one) and we only copy what is needed for interpolation. Src/F_BaseLib/create_umac_grown.f90 commit e9bb87ebdfa4cf82e2cfff48a1d871393a752139 Author: almgren Date: Wed Mar 16 17:56:35 2011 +0000 Convert is_singular from integer to logical. Src/LinearSolvers/F_MG/mg.f90 commit 723ffd9c624b77a2c2366fb62f8cfc1e7c88e1ae Author: almgren Date: Wed Mar 16 17:34:59 2011 +0000 Add "is_singular" optional argument to mg_tower_build so that you can over-ride the local test for solvability. Src/LinearSolvers/F_MG/mg.f90 commit a1f709cc893818d09af1e34280b9921ffa834890 Author: nazgul Date: Tue Mar 15 23:56:12 2011 +0000 Adding ability to specify DistributionMapping when defining FluxRegisters. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 2f91d691bbc009969e6e136a271c508f536ff33e Author: nazgul Date: Tue Mar 15 23:55:15 2011 +0000 Adding ability to specify DistributionMapping when defining these objects, in case the correct map has been flushed from the cache. Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit c4172d61a8b89742f8cd6b60ab93fcbe848fbccd Author: almgren Date: Thu Mar 10 23:42:04 2011 +0000 Add pleiades stuff. Tools/C_mk/Make.mpi commit 0dca7de44729be768e002ce2d61554961361b17e Author: wqzhang Date: Wed Mar 9 23:54:05 2011 +0000 Some new features. If one types "touch dump_and_continue" in the run directory, a checkpoint file and a plot file will be generated and then the run will continue. The "dump_and_continue" file will be deleted. If one types "touch stop_run" in the run directory, the run will stop without generating a checkpoint. The "stop_run" file will be deleted. If one types "touch dump_and_stop" in the run directory, a checkpoint file and a plot file will be generated and then the run will stop. The "dump_and_stop" file will be deleted. Src/C_AMRLib/Amr.cpp commit fbeca23a12ef5502590cd5bd84972fd3bdb7e5bf Author: ajnonaka Date: Wed Mar 9 13:32:07 2011 +0000 typo in output string Src/F_BaseLib/fab.f90 commit c2661dfa951b3a355896a8d9d975e4d7ebfab51f Author: almgren Date: Tue Mar 8 21:04:50 2011 +0000 Modify the verbosity tests so that the "particles added per processor" print only happens if verbosity > 1. Src/C_AMRLib/Particles.H commit ae0874d88fe6c8bc901460b6d2076281ddda75dd Author: marc Date: Tue Mar 8 18:47:47 2011 +0000 *** empty log message *** Tools/C_util/ViewMF/GNUmakefile Tools/C_util/ViewMF/mfMinMax.cpp commit dc69ba3831b51fceccb093fe371ae5d49ad0b865 Author: lijewski Date: Tue Mar 8 02:09:14 2011 +0000 little mod to previous OMP reorg of estTimestep() Src/C_AMRLib/Particles.H commit 3f6b1b01ac7f8a62d7dbdf3de125aad9931257e2 Author: almgren Date: Tue Mar 8 01:32:18 2011 +0000 Mike L's fixes to estTimestep make this work with PGI + OMP. Src/C_AMRLib/Particles.H commit 48107b8f1d2a698e81b9ff19ed9c2edf12269604 Author: almgren Date: Mon Mar 7 03:39:11 2011 +0000 Add additional solvability enforcement -- *before* we start the V-cycle. We might even be able to use this only and eliminate the tests inside the V-cycles .... but for now we'll leave them in. Src/LinearSolvers/F_MG/ml_cc.f90 commit 9bb23368b351065bd3c5e2b10e1e3cc62024be0e Author: almgren Date: Sun Mar 6 16:20:48 2011 +0000 Move ParallelReduceMin call out of verbose test. Src/C_AMRLib/Particles.H commit adf4672587f1898240287fb163195d82576d8226 Author: lijewski Date: Sat Mar 5 00:18:09 2011 +0000 version of contains_nan() and contains_inf() that take scomp ncomp and ngrow Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 7a5147b4455256acbfb7b70700c9e0799d7cc43b Author: almgren Date: Fri Mar 4 02:03:50 2011 +0000 Add Amr::NumDataLogs to tell you how many data streams you have opened. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 4ed5a936c975a3cc2af9d557cf3f49b6214b066a Author: almgren Date: Thu Mar 3 23:19:38 2011 +0000 Verbose --> SetVerbose Src/C_AMRLib/Particles.H commit b493d19bb0c55d74c52db604f4d3c471e016a4b4 Author: lijewski Date: Thu Mar 3 21:49:55 2011 +0000 some simplification Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 7653303114c4343c66fe40fb19167207506856ec Author: lijewski Date: Thu Mar 3 17:57:22 2011 +0000 added minIndex() and maxIndex() Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit a9c0ca7690c9e15188cc6962f29ff9bac8380f8c Author: almgren Date: Wed Mar 2 23:21:49 2011 +0000 Comment out print statement. Src/LinearSolvers/F_MG/mg.f90 commit c59081121057e589ba9609b881c3955673f0e2f0 Author: almgren Date: Wed Mar 2 23:21:08 2011 +0000 Make the cell-centered single-level solver solvable if singular -- EACH V-cycle. Src/LinearSolvers/F_MG/ml_cc.f90 commit 7af67a0bdbbaf968feffc03dc6d910d9b0e787d0 Author: almgren Date: Wed Mar 2 23:20:11 2011 +0000 Fix print statement. Src/LinearSolvers/F_MG/itsol.f90 commit f75c7ed57f3052b5beea317c54434e8cf42bb663 Author: lijewski Date: Tue Mar 1 17:12:29 2011 +0000 simplified AdvectWithUMac() Src/C_AMRLib/Particles.H commit e9f7644949a578bfecf1e39b4fee1d71830c7aed Author: lijewski Date: Tue Mar 1 17:09:07 2011 +0000 simpler but equivalent formulas for delta and vel in move_advect Src/F_BaseLib/particles.f90 commit 72d738b23c63c6848f6ff182cd278e78963a535c Author: wqzhang Date: Mon Feb 28 23:10:19 2011 +0000 test.py does not work on Ubuntu (at least 10.04 LTS) because os.system calls dash instead of bash Tools/C_util/regtests/test-Ubuntu.py commit ccb86d391ca8b63bd5420aa0f3a9dd8cff03d69f Author: wqzhang Date: Mon Feb 28 23:05:34 2011 +0000 *** empty log message *** Tools/C_util/regtests/radiation-tests.ini commit 012fe5a155e87f1f0f5ec3fc555c3daa5702cd3f Author: lijewski Date: Mon Feb 28 21:17:26 2011 +0000 removed an assertion Src/C_AMRLib/Particles.H commit 25296e269faa327cfca3f0cbbaf9711e346a222b Author: mzingale Date: Mon Feb 28 21:06:53 2011 +0000 the predictor and corrector in the advection were both doing almost the same thing -- remove redundant code by looping over the velocity interpolation and redistribution Src/F_BaseLib/particles.f90 commit 496491c2adc369c457dedab74d488d6dbf06f549 Author: lijewski Date: Mon Feb 28 19:03:52 2011 +0000 bit more simplification Src/C_AMRLib/Particles.H commit f0454b82806cd98bc5aa8b79b8b391077e54c947 Author: lijewski Date: Mon Feb 28 18:29:09 2011 +0000 made AdvectWithUMac mirror the one in fParallel Src/C_AMRLib/Particles.H commit a53786d8446ff7637d134aadf78ea5566772c5d5 Author: lijewski Date: Mon Feb 28 18:23:43 2011 +0000 some cleanup & speedups Src/C_AMRLib/Particles.H commit 62999c433ee108a5bbc4263bd684f05ce47e0565 Author: lijewski Date: Mon Feb 28 17:49:31 2011 +0000 added code to check to infs mirroring nan code Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio_c.c commit ad98b2fe441be68c89326fdb061d0e116fcc68d7 Author: almgren Date: Sat Feb 26 01:59:18 2011 +0000 Remove extraneous definition. Src/C_AMRLib/Particles.H commit d986f63e1fe93242fb83d85f7a3f4af8035a032c Author: almgren Date: Sat Feb 26 01:50:11 2011 +0000 Change default in estTimeStep to be 0.5 rather than 0.1 Src/C_AMRLib/Particles.H commit 6a23aa0bcd43ae6c2398211b31d67f75d48101d8 Author: almgren Date: Sat Feb 26 01:45:33 2011 +0000 Added another version of moveKick and moveKickDrift that takes edge-based gravity components rather than cell-based. Src/C_AMRLib/Particles.H commit da3432de0b624308e46e13f8bca8701351480567 Author: almgren Date: Sat Feb 26 00:03:02 2011 +0000 Remove print statement. Src/LinearSolvers/F_MG/itsol.f90 commit aae3d367a865a9bbcb9bb31b100523fe69cf6c31 Author: lijewski Date: Fri Feb 25 22:39:33 2011 +0000 FAB_CONTAINS_NAN now works for gcc; need to test on __GNUC__ macro Src/F_BaseLib/fabio_c.c commit 068e39a15556a5cb57cf341ab854571a14b0c8d2 Author: lijewski Date: Fri Feb 25 22:13:25 2011 +0000 contains_nan_bx_c() Src/F_BaseLib/fab.f90 commit 668db550a17db4460b9200345a4e87fce31f82de Author: lijewski Date: Fri Feb 25 21:17:51 2011 +0000 contains_nan_allc() calls contains_nan_c() Src/F_BaseLib/fab.f90 commit 2155523d6aba608219458be4fda3c668dc2a00aa Author: lijewski Date: Fri Feb 25 21:10:52 2011 +0000 added contains_nan_c() Src/F_BaseLib/fab.f90 commit bca9b562f8d2de1e7a4ca95eb78827ddb9c99d88 Author: lijewski Date: Fri Feb 25 18:47:10 2011 +0000 some simplification of add_point() Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit e0321505d84e5262fd3ce3bc86c6b3a5f0dd4412 Author: mzingale Date: Fri Feb 25 16:52:21 2011 +0000 remove the conditional_add routine -- it required that all processors call it at the same time -- this is not how we do the particle adds in MAESTRO. Instead, implement a less ambitious version by adding the "conditional" logical optional argument to the normal pointwise add routine. If true, then this will only add the particle if there is not already one in the same zone/level. Src/F_BaseLib/particles.f90 commit b69a93965713cc66a755dc053ecc73caa152c2b0 Author: marc Date: Thu Feb 24 01:06:52 2011 +0000 *** empty log message *** Tools/C_util/ViewMF/viewMF.cpp commit 21eb835bb344e18212015ec8f8799d7b76bf8393 Author: almgren Date: Tue Feb 22 23:53:07 2011 +0000 Make sure to do singular adjustment *before* diagonal preconditioning. Src/LinearSolvers/F_MG/itsol.f90 commit 0c595a1680fede756ee51e4c28cfb4c1168dc0d9 Author: almgren Date: Tue Feb 22 23:35:14 2011 +0000 Fix test for mgt%bottom_singular. Src/LinearSolvers/F_MG/mg.f90 commit b804f7e779129cdd0fb81ccfa02bf82a00ac0545 Author: almgren Date: Tue Feb 22 21:48:34 2011 +0000 Change Init --> InitFromAsciiFile Src/C_AMRLib/Particles.H commit f15497b2a4a416aa7195d2bda362782c2f695e91 Author: mzingale Date: Sun Feb 20 15:45:19 2011 +0000 first cut at a "conditional add" routine -- only add a particle if it is some distance (dr) away from any existing particle. Needs more testing, but seems to work. Src/F_BaseLib/particles.f90 commit 51ea5ec9ceefb180774a87271c113cf2ae991083 Author: almgren Date: Fri Feb 18 21:28:34 2011 +0000 1) Wrapped printing of read time for PROBINIT inside verbose>1 test. 2) Added sanity checks when restarting to check n_cell and ref_ratio from inputs file against what is in checkpoint file. If the index-space domains at all levels don't match then the code aborts on restart. Src/C_AMRLib/Amr.cpp commit b44a287f155f549aae05205926f028cc005c3db3 Author: lijewski Date: Thu Feb 17 17:14:24 2011 +0000 more specialized versions of contains_nan() and contains_inf() Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit 35d118157d232b51a17c3dcaf03884fb05002d58 Author: lijewski Date: Thu Feb 17 00:02:18 2011 +0000 changes to debugging interface Src/F_BaseLib/particles.f90 commit b7a2de5af9a4d3f57577b90c15cad04b70bc81bd Author: almgren Date: Tue Feb 15 22:38:43 2011 +0000 Forgot commas. Src/C_AMRLib/Particles.H commit bf5e15b97908259d7a7105bb3a150952cf951d40 Author: almgren Date: Tue Feb 15 22:33:16 2011 +0000 Fix typos. Src/C_AMRLib/Particles.H commit 6b648d6a8f1c06149a5dd245b833a8cb764a472e Author: almgren Date: Tue Feb 15 20:55:18 2011 +0000 This has the correct time stepping now (fingers crossed) Src/C_AMRLib/Particles.H commit eac71640515973573f2ad770bc4eaf435d03d0a7 Author: almgren Date: Mon Feb 14 22:54:12 2011 +0000 Add adot/a term to velocity update. Src/C_AMRLib/Particles.H commit d24109c37d3330bc1291ab386c516c9aeb396da3 Author: almgren Date: Mon Feb 14 02:48:02 2011 +0000 This version includes new options for JFE's machine (Jan Frederik Engels). Tools/C_mk/Make.defs commit e397d0aef3fbc7b718fbff16ab157497195b3861 Author: almgren Date: Sat Feb 12 03:17:19 2011 +0000 Integrate changes from Test_90Mpc version. Src/C_AMRLib/Particles.H commit 65b34564bf63e0f2c610c7392bb5fdacf3f9a337 Author: lijewski Date: Fri Feb 11 22:30:02 2011 +0000 some cleanup Src/C_AMRLib/Particles.H commit bcc4cd903dc842c81890fa37ab8ca89ff02e7900 Author: lijewski Date: Fri Feb 11 21:50:34 2011 +0000 added WriteAsciiFile() Src/C_AMRLib/Particles.H commit 6ee908d8f35084b203f446213f51edc82e7b1d29 Author: marc Date: Thu Feb 10 19:15:21 2011 +0000 adjust usage of numLevelsMAX to be consistent with its name, was allowing one extra level Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit c07bbd987f7a67b07b23ebc78260293e0e35e003 Author: lijewski Date: Thu Feb 10 00:06:50 2011 +0000 fixed issue with Timestamp() Src/C_AMRLib/Particles.H commit 83a340e632ced515920385460ca9e0d3b417ce37 Author: lijewski Date: Wed Feb 9 23:42:03 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.H commit 45ee144c1242efd02f4ebcd453b9aef321677b0e Author: lijewski Date: Wed Feb 9 23:21:15 2011 +0000 some work on advectWithUMac() Src/C_AMRLib/Particles.H commit a5035b6e157da7af51d318d8bf1373efc16199c6 Author: lijewski Date: Tue Feb 8 23:01:50 2011 +0000 bit more work on Timestamp() -- appears to be working Src/C_AMRLib/Particles.H commit 4a6ffacd2f3455767cb842c166269e08b92d7a4b Author: lijewski Date: Tue Feb 8 22:17:50 2011 +0000 redistribute() now also does the origpos member Src/F_BaseLib/particles.f90 commit e91c4b7dab6924e8073b11753206ed02a0ff1568 Author: lijewski Date: Tue Feb 8 19:19:01 2011 +0000 more work on Timestamp() Src/C_AMRLib/Particles.H commit 678e89fa59ba47e894cf4e509ac389f31b84f6e7 Author: lijewski Date: Tue Feb 8 19:05:22 2011 +0000 some work on Timestamp() Src/C_AMRLib/Particles.H commit 09d8d31009ebaf8d68a78e2f95604f096ede2873 Author: mzingale Date: Sun Feb 6 03:07:39 2011 +0000 first attempt at doing second-order in time advection of the particles. A new field, origpos(), was added to the particle datatype to store the position of the particle at the start of the time integration. Redistribution is now done twice -- once at the half-time and then after the final movement of the particle. Src/F_BaseLib/particles.f90 commit 6a807169af16243cde1b1ee6c665022adcf88a62 Author: lijewski Date: Fri Feb 4 23:20:33 2011 +0000 we now checkpoint/restart the max value of particle_id Src/F_BaseLib/particles.f90 commit 9a9cbc5e193b0ce79889bfd719a521fa446407b5 Author: lijewski Date: Fri Feb 4 22:46:21 2011 +0000 we now checkpoint/restart the max value of NextID() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit eff3d8f2a2d034ab1d657ec69597f74c1ff5e926 Author: lijewski Date: Fri Feb 4 22:30:24 2011 +0000 Init() can now be called on restart too - doesn't assume there are no existing particles in container Src/C_AMRLib/Particles.H commit 398c68202ecffc3a8ff9a08022294c72d6bdf12c Author: lijewski Date: Fri Feb 4 21:32:06 2011 +0000 do NOT use the update arg to Where() after PeriodicShift() Src/C_AMRLib/Particles.H commit e3e18fc5fd320b2721a6bca249deb102b5f3a225 Author: lijewski Date: Fri Feb 4 21:31:25 2011 +0000 PeriodicShift() now only tries a particular dir if you're periodic in that dir Src/C_AMRLib/Particles.cpp commit 35fc616c11226a2e36001fcdb7855299ca5d02f2 Author: lijewski Date: Fri Feb 4 20:25:50 2011 +0000 deal with N==0 in InitRandom() Src/C_AMRLib/Particles.H commit 03ee8e1f8a0f49885a76b3af6cecbe06495f5e87 Author: lijewski Date: Fri Feb 4 19:08:15 2011 +0000 integrated in ParticleBase::NextID() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 212f9409ff3c61299a0671f6fbb023826b74c9fb Author: lijewski Date: Fri Feb 4 18:47:34 2011 +0000 Particles can now be invalidated. Their ID is negated. Algorithms must ignore invalid particles. Redistribute() gets rid of them. Checkpoint() doesn't write'm to disk. Src/C_AMRLib/Particles.H commit 3c28a31fd8de658bce72477e9209963e6f675417 Author: lijewski Date: Fri Feb 4 16:44:00 2011 +0000 added a BL_ASSERT() Src/C_AMRLib/Particles.H commit 61ec0ffd7461c3aee2b8efceb27c2f699cd3f6fe Author: lijewski Date: Wed Feb 2 22:15:45 2011 +0000 removed do_not_minimize_comcost stuff Src/C_BaseLib/DistributionMapping.cpp commit 31368e35fc04faaeb60507dfda3a6476be778317 Author: marc Date: Wed Feb 2 01:42:16 2011 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit 2aefc92ff5fc85ba4c6d1545f18e545b323386c2 Author: mzingale Date: Sun Jan 30 02:45:07 2011 +0000 change the header names to contain no spaces so it is easier to parse Src/F_BaseLib/particles.f90 commit ec0adc991c15bda05933cde9b1fa5e9668317c26 Author: mzingale Date: Sat Jan 29 20:13:12 2011 +0000 add a header to the top of the timestamp files that lists the name of each column. This requires that a names() array is passed through giving the name of each data field. Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit bb4541229038fc5273b75bed51b90a1539e6866f Author: ajnonaka Date: Sat Jan 29 01:59:27 2011 +0000 created a tidy interface for adding a single particle at a point Src/F_BaseLib/particles.f90 commit e11a6d4091d9c8bff2682696eedef2b5ad99be80 Author: ajnonaka Date: Fri Jan 28 18:12:27 2011 +0000 generalized piecewise bilinear advection of particles using mac velocities to 1d/2d/3d Src/F_BaseLib/particles.f90 commit 5b2aec51b77be75c33394fe5bd02eada3767250c Author: ajnonaka Date: Fri Jan 28 00:41:26 2011 +0000 bilinear advection using MAC velocities (2d only) Src/F_BaseLib/particles.f90 commit ffabe8eee93e25737daf52c05b8d2683e66320d2 Author: ajnonaka Date: Fri Jan 28 00:23:49 2011 +0000 particle_move_advect now takes mac velocities as input. Still using 1st order approximation to velocity at a point, which will be upgraded soon. moved advection of particles to advance.f90, immediately following the second call to macproject Src/F_BaseLib/particles.f90 commit 34670e4bf4216be0e45542987f5c2983b7d61d85 Author: lijewski Date: Thu Jan 27 23:39:44 2011 +0000 *** empty log message *** Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 1098ba2a72c47700a46ac75e487f31d805037045 Author: ajnonaka Date: Thu Jan 27 23:38:52 2011 +0000 made particle_id a saved variable added global accessor for particle_id Src/F_BaseLib/particles.f90 commit 85084dfa4e3e028bac86ec84a84dd60bad727569 Author: lijewski Date: Thu Jan 27 23:19:50 2011 +0000 more error checking Src/F_BaseLib/vector_i.f90 commit 3deda67ed26709146ea51e0cc93fdde5e8e6e935 Author: ajnonaka Date: Thu Jan 27 22:53:08 2011 +0000 changed problo/hi -> prob_lo/hi to make consistent with VARDEN and MAESTRO Src/F_BaseLib/fabio.f90 Src/F_BaseLib/particles.f90 commit 95903767f1397d839a30a194d3670045034f9a28 Author: ajnonaka Date: Thu Jan 27 22:46:20 2011 +0000 added an advect function Src/F_BaseLib/particles.f90 commit 709e44dc7ad9846a89ec24a262e10819ee8c0094 Author: lijewski Date: Thu Jan 27 22:31:22 2011 +0000 more error checking Src/F_BaseLib/particles.f90 commit 072082e9f81dc41fcbad6797ea710ae1b92d01f2 Author: lijewski Date: Thu Jan 27 22:13:30 2011 +0000 brought up-to-date with latest particle changes Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit cd06bbad69c79ac3269559836cfd41a14258290a Author: lijewski Date: Thu Jan 27 21:27:57 2011 +0000 mods for MAESTRO Src/F_BaseLib/particles.f90 commit 284f34ccefaf84b7594205c133dabba34cdec835 Author: lijewski Date: Wed Jan 26 22:51:02 2011 +0000 now used PARTICLES Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile commit 089aa9a988b70d9001146417ed964e74fd751671 Author: lijewski Date: Wed Jan 26 22:47:07 2011 +0000 added PARTICLES macro to get particles.f90 Src/F_BaseLib/GPackage.mak commit cad9ef451f9da5865f993cce474a3d17004b92df Author: ajnonaka Date: Wed Jan 26 21:12:13 2011 +0000 add f90sources += particles.f90 Src/F_BaseLib/GPackage.mak commit 671a40933dab97b9c6c4ed72daa0a69338edbe14 Author: lijewski Date: Wed Jan 26 17:11:47 2011 +0000 added dataptr() Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit dd2a8fc2d82f19f4758f1d30528523ec3d6842b8 Author: marc Date: Tue Jan 25 23:50:22 2011 +0000 Add placeholder for max_order...ordre of tangential interpolant...supporting only 1 and 3 at the moment Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_F.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp commit ce2ac33663ffbaf08d909b3de58843db66ecddd0 Author: lijewski Date: Tue Jan 25 23:26:33 2011 +0000 some simplification Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit cc93ac78488aad402454bd5f0fbb891224333f49 Author: lijewski Date: Tue Jan 25 22:26:54 2011 +0000 2D now appears to work also Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit d73b353da95d42b040632e716b6cda6f7d2bf7c9 Author: lijewski Date: Tue Jan 25 18:44:57 2011 +0000 some simplification Src/F_BaseLib/particles.f90 commit 35329ed0d7a6d9c62714846067638c82a39e6c70 Author: lijewski Date: Tue Jan 25 17:16:44 2011 +0000 particle_vector -> particle_container Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 5d4604190b8fa85c1cc8e139c47a1f84da57e6be Author: lijewski Date: Tue Jan 25 00:04:21 2011 +0000 little more cleanup Src/F_BaseLib/particles.f90 commit 4872091dd1f9e730cb110597104f8e3db4cc1227 Author: lijewski Date: Mon Jan 24 23:56:30 2011 +0000 remove empty timestamp files after each series of writes Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit fe747390417ec3a0ba9f40dad831c2012228a986 Author: lijewski Date: Mon Jan 24 23:55:59 2011 +0000 added some unlink() code for empty files used by particle code Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c commit f41cce267b76f6f44f96cd1834133753a0aa4b90 Author: lijewski Date: Mon Jan 24 23:08:26 2011 +0000 can now set/unset verbosity and debugging via function calls Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 807b15c1b35c52b1824daa52e6674383ca8ab573 Author: lijewski Date: Mon Jan 24 23:07:58 2011 +0000 some cleanup Src/F_BaseLib/particles.f90 commit 50bb96c0e17d6e4124639ace729e92d07e40e731 Author: lijewski Date: Mon Jan 24 22:36:05 2011 +0000 added some timestamp() tests Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit d9db99ce329fa848f32cdf234c30ee3006aeed8c Author: lijewski Date: Mon Jan 24 22:35:42 2011 +0000 timestamp() appears to be working Src/F_BaseLib/particles.f90 commit c7cf0b46b3e409d4678a4778b3ba3ad48dd0e2c1 Author: lijewski Date: Mon Jan 24 22:22:58 2011 +0000 timestamp() closer to working Src/F_BaseLib/particles.f90 commit db5904c26d33d4eac959aca7d32ee20b1b375f81 Author: lijewski Date: Mon Jan 24 21:06:56 2011 +0000 *** empty log message *** Src/F_BaseLib/fabio_c.c commit 911e4a3c6cfb2b4bf5cfd85b8289e45922957a97 Author: lijewski Date: Mon Jan 24 21:06:42 2011 +0000 some work on timestamp() Src/F_BaseLib/particles.f90 commit 43b2304595deb07abe77dfe1a48f20776a74c1a2 Author: lijewski Date: Fri Jan 21 21:23:59 2011 +0000 added couple more functions needed by particle code Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c commit 3eb3d9e01aba89b650d46ae75ac48555119f5037 Author: lijewski Date: Fri Jan 21 21:22:03 2011 +0000 some cleanup Src/F_BaseLib/particles.f90 commit 38cfb2358c6f068123668aca9c2a6cec95de928e Author: lijewski Date: Fri Jan 21 20:59:15 2011 +0000 *** empty log message *** Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit f2d3a04c1ac86b62094b3789af198e431b75156a Author: lijewski Date: Fri Jan 21 20:52:04 2011 +0000 some code to test restart() Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit a13abc933aedba82806aa393abe602a58a9b08da Author: lijewski Date: Fri Jan 21 20:51:52 2011 +0000 restart appears to be working Src/F_BaseLib/particles.f90 commit c5d4d351caba94ae4e6fd4eaeb2b272fd31fa07c Author: lijewski Date: Fri Jan 21 01:21:27 2011 +0000 *** empty log message *** Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 8d1e0d408591fddbe9bc0f3acd543aabbbf4dad7 Author: lijewski Date: Fri Jan 21 01:21:16 2011 +0000 some work on restart() Src/F_BaseLib/particles.f90 commit a1741c876cb3b0ac672ec9f45be1eb84aee70f49 Author: lijewski Date: Thu Jan 20 21:35:32 2011 +0000 checkpoint() appears to work; on to restart() Src/F_BaseLib/particles.f90 commit b486092867b7b47f4e0a72f310b2ec82deceb5e0 Author: lijewski Date: Thu Jan 20 17:45:26 2011 +0000 checkpoint() is that much closer to working Src/F_BaseLib/particles.f90 commit b5947b9cee06b1d629ac53311f38e60faa7111de Author: lijewski Date: Wed Jan 19 23:51:18 2011 +0000 yet more work on checkpoint() Src/F_BaseLib/particles.f90 commit 454b5a39277aa8e3965eb922dec500717b40fdf8 Author: lijewski Date: Wed Jan 19 23:50:27 2011 +0000 moved interface for particle write routines from particles.f90 to here Src/F_BaseLib/fabio.f90 commit b1d6b2348f08704c4165b8cb979f8a7aaaf36a3a Author: lijewski Date: Wed Jan 19 23:37:33 2011 +0000 added couple C I/O functions needed by particle code Src/F_BaseLib/fabio_c.c commit e8650168165eff1286f5fb5fbb42b1ad7aab24bd Author: lijewski Date: Wed Jan 19 23:37:09 2011 +0000 yet more work on checkpoint() Src/F_BaseLib/particles.f90 commit 2f2f2379c8571ca08cd8cf8e096a2bc793b1a0c3 Author: lijewski Date: Wed Jan 19 22:26:51 2011 +0000 some more work on checkpoint() Src/F_BaseLib/particles.f90 commit c7c397455c482f4373e8b671a86b0734941b6046 Author: lijewski Date: Wed Jan 19 21:43:22 2011 +0000 some work on checkpoint() Src/F_BaseLib/particles.f90 commit aee91af68d949710c4bdd9639add89620345485f Author: lijewski Date: Fri Jan 14 21:25:30 2011 +0000 comment out particles.f90 for the moment Src/F_BaseLib/GPackage.mak commit 3cef6e5a7475bc89cf2975a0f470b0e5de96ab44 Author: lijewski Date: Thu Jan 13 19:13:20 2011 +0000 redistribute() appears to be working Src/F_BaseLib/particles.f90 commit 8b364887455ae1bc2f033bd82e437864d63bfaa7 Author: lijewski Date: Thu Jan 13 19:12:58 2011 +0000 *** empty log message *** Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 61fbbbb8a14b2fb87091425eb123ee4c1185d088 Author: lijewski Date: Thu Jan 13 18:15:16 2011 +0000 redistribute() is closer to being working code ... Src/F_BaseLib/particles.f90 commit 39f168a93fd3e2b7689684233bb8768da2605093 Author: lijewski Date: Thu Jan 13 18:14:54 2011 +0000 more testing for redistribute() Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit bdfa002e10c9249448a5675764c50a4da9534037 Author: lijewski Date: Thu Jan 13 00:18:13 2011 +0000 some work on redistribute() - not finished Src/F_BaseLib/particles.f90 commit 7ba867837db22e1e670b9f130d4f580f4bf1f660 Author: lijewski Date: Wed Jan 12 22:12:29 2011 +0000 Figured out the Intel -vs- gfortran issue. I wasn't setting the rr(n,:) component of the ml_boxarray. That should really be passed as part of build_n(). Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit c5d47669764012c60b5f468cb410230fe2d46e7a Author: lijewski Date: Wed Jan 12 21:49:57 2011 +0000 move_randomo() implemented; works with gfortran but not Intel 11.1 ??? Src/F_BaseLib/particles.f90 commit 5df1388eca23b3c4f9af0d5f7e401ca67e389643 Author: lijewski Date: Wed Jan 12 21:49:24 2011 +0000 test code for move_random() Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit cc5b4593be664d9b5858bd8c498ee1c64b8d8867 Author: lijewski Date: Wed Jan 12 17:55:14 2011 +0000 multi-level mla's appear to work OK Src/F_BaseLib/particles.f90 commit c4272b91797f1119fa3387801160d54bd39f3d0f Author: lijewski Date: Wed Jan 12 17:54:41 2011 +0000 added test for multi-level mla Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 150b06d94fe1c76094288bc6fb89dda289f1aef1 Author: lijewski Date: Wed Jan 12 03:09:37 2011 +0000 fixed bug -- how did it work for me before? Src/F_BaseLib/particles.f90 commit 6062518c92d6404f91031636fa45f3cf73ca2f4c Author: lijewski Date: Wed Jan 12 00:27:26 2011 +0000 init_random() seems OK in serial Src/F_BaseLib/particles.f90 commit 94a623cff0a1621c917b8a044c8644402c0c0980 Author: lijewski Date: Wed Jan 12 00:26:52 2011 +0000 testing init_random() Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit f8124f2b76abde7e6c3183883f4973c3a522fb7f Author: lijewski Date: Tue Jan 11 23:56:23 2011 +0000 wrote init_random() -- untested yet Src/F_BaseLib/particles.f90 commit 3f2f9c28d8ea2f5738247d7d74ad192feb4b6649 Author: lijewski Date: Tue Jan 11 22:24:08 2011 +0000 wrote particle_index() and particle_where(); now to test ... Src/F_BaseLib/particles.f90 commit 41eb3592aab5b8e3fea66e3858e09f72ce93d7fd Author: lijewski Date: Tue Jan 11 20:30:22 2011 +0000 particle_vector knows about valid/invalid particles Src/F_BaseLib/particles.f90 commit 223ffc6eabf384a31ad9641a949ed5c056d50a2e Author: lijewski Date: Tue Jan 11 20:30:01 2011 +0000 *** empty log message *** Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 6d26eef25be786fc1af0aeecad12341dfb837945 Author: lijewski Date: Tue Jan 11 18:25:28 2011 +0000 added particle_vector Src/F_BaseLib/particles.f90 commit e64deb07f9d85a3ca819fbb10f6d62e4ef928174 Author: lijewski Date: Tue Jan 11 17:02:19 2011 +0000 added particles stuff Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 commit 4ab911788d8c8183988f3640c19f607f4af4f1a9 Author: lijewski Date: Tue Jan 11 17:01:50 2011 +0000 particles test code Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 37e7fdcf9b3eb3d97161bdfb7e029e4d6021bfb8 Author: lijewski Date: Tue Jan 11 17:01:11 2011 +0000 added particles.f90 Src/F_BaseLib/GPackage.mak commit 2b7bd76ac6865fd440aa9292ff019138b86e7341 Author: lijewski Date: Tue Jan 11 17:00:47 2011 +0000 Just getting started ... Src/F_BaseLib/particles.f90 commit 94ed7421e9fbea49676e18e6d360825668b4ddcd Author: almgren Date: Thu Jan 6 23:05:44 2011 +0000 Add JFE's InitCosmo() routine which sets up initial conditions a la Martin White. Src/C_AMRLib/Particles.H commit a1398f84a3f5df10890e14579191771959855b2a Author: almgren Date: Mon Jan 3 21:35:05 2011 +0000 Add a to estTimestep. Src/C_AMRLib/Particles.H commit 550be76fa9a6587cb60b73ebe86a8f8a157154db Author: almgren Date: Mon Jan 3 20:49:31 2011 +0000 Fix... Src/C_AMRLib/Particles.H commit 8bc34dede449830a0398da207112491b4e99c15c Author: almgren Date: Mon Jan 3 20:48:00 2011 +0000 Add versions of moveKick and moveKickDrift that include the comoving coordinate stuff. Src/C_AMRLib/Particles.H commit 7efe4e360feef4cd0e6d09d3a54ae89cf8b995cd Author: almgren Date: Mon Jan 3 20:26:30 2011 +0000 This doesn't compile. Src/C_AMRLib/Particles.H commit 4dea81541ab142460efca12278c4d3c7b80a2cc1 Author: gpau Date: Wed Dec 22 23:46:58 2010 +0000 *** empty log message *** Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile commit 31f5c0dde6ea182d5f12a5a4d3776e8aeedb1a8c Author: ajnonaka Date: Tue Dec 21 18:38:02 2010 +0000 added ability to pass in aux multifab to tagging routines Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/tag_boxes.f90 commit 057b35332743b620cd9ec03baf6e6a9de52d15fe Author: mzingale Date: Tue Dec 21 15:08:41 2010 +0000 add toy_convect, diffusion tests Tools/C_util/regtests/Maestro-tests.ini commit e30646f4460726be9fda154612686a1bfd92c429 Author: ajnonaka Date: Mon Dec 20 20:34:35 2010 +0000 fixed bug in calls to multifab_fill_boundary and multifab_physbc_edgevel for problems where nlevs > 2 Src/F_BaseLib/create_umac_grown.f90 commit 4032ed90a05cbcf8d8f9ff89386485b8ce18a434 Author: mzingale Date: Wed Dec 15 03:30:51 2010 +0000 trap uninitalized variables in debug mode Tools/F_mk/comps/gfortran.mak commit d7402f076dbc81b7538f5aaca760ba69033678fd Author: mzingale Date: Tue Dec 14 03:23:35 2010 +0000 add support for MPI for fParallel-based runs Tools/C_util/regtests/test.py commit 9b4094cdbc4481b7d1cb1eda03d160b62c5d8b5a Author: gpau Date: Thu Dec 9 00:53:21 2010 +0000 fix for pgCC oddity Src/C_BaseLib/BaseFab.cpp commit 033dc34047f66366ad548e1ca9a63f291235edd5 Author: lijewski Date: Wed Dec 8 23:07:06 2010 +0000 mods for compiling VisIt with Microsoft Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/winstd.H commit 950f94545746286486f9e6619afffe0cdbbd6a9d Author: lijewski Date: Wed Nov 24 02:50:25 2010 +0000 Yet another downgrade of the Cray optimization options. I've finally managed to get Castro/ParticleTest working with the Cray compiler on grace. The C++ used "-O 1 -h noexceptions" and the Fortran "-O 1,vector0 -h noomp". This is strictly with MPI not with OMP. It takes roughly twice as long per timestep as does PGI. Tools/C_mk/Make.Linux commit 6962caea5fb723674cc6c246b84f33e3e5008bc1 Author: lijewski Date: Sat Nov 20 21:50:29 2010 +0000 Downgrade Cray optimization from -O 2 -> -O 1. Still can't get Castro/ParticleTest to run. It's dying in the first gravity solve. Weird since MAESTRO/wdconvect works with -O 1. Tools/C_mk/Make.Linux commit 0e4dbd8b468a5f96c3abf8925fce4f605c1ca333 Author: lijewski Date: Sat Nov 20 20:21:26 2010 +0000 Downgrade optimization from -O2 -> -O1. -O2 hits an OMP bug though -O2 works fine with just MPI. Weirdly -O1 appears to produce slight faster code (just a few percent). Tools/F_mk/comps/Linux_cray.mak commit 8a61abad95f56d977d43af121b2e97f0c2eff5e5 Author: mzingale Date: Sat Nov 20 01:42:58 2010 +0000 add a 1-d version to get flame_1d running again Src/F_BaseLib/multifab_physbc_edgevel.f90 commit 03ed0297ce3835f2c423ae6bef945e6f3713a852 Author: lijewski Date: Fri Nov 19 18:06:59 2010 +0000 dm wasn't being initialized Src/F_BaseLib/test/t_bxasc.f90 Tests/F_BaseLib/t_bxasc.f90 commit 2ff3e01c168ebe3312726b3303d8a5c8fb6b621c Author: lijewski Date: Thu Nov 18 20:14:12 2010 +0000 tweaks to Cray options to work around a bug Tools/C_mk/Make.Linux commit 990052328ce02c7ba2e7f4578edfaf32d8ccd267 Author: ajnonaka Date: Mon Nov 15 20:50:51 2010 +0000 default max_bottom_nlevel=3 instead of 1024 Src/LinearSolvers/F_MG/mg_tower.f90 commit def1f343d24768d9f03ba01e40a571b308f1bbf1 Author: lijewski Date: Mon Nov 15 19:23:57 2010 +0000 speedup to InitRandom() Src/C_AMRLib/Particles.H commit f854c9188d19620c2dea43f94871a4f16dd7f222 Author: vince Date: Mon Nov 15 19:13:37 2010 +0000 couts. Src/C_AMRLib/StationData.cpp commit f94798eca8a6f9b9e4d1cb69ff68adae23e902da Author: lijewski Date: Thu Nov 11 21:08:56 2010 +0000 parallel_abort() was ignoring the optional string argument Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit ed4ff64e0c166e71c3e3f9daf28a2a5a700531f7 Author: ajnonaka Date: Thu Nov 11 17:54:39 2010 +0000 fixed USE_OLDPLOTPER Tools/C_mk/Make.defs commit a8e291ad7e133fd5a4cd9af7dd7d32725417f65d Author: ajnonaka Date: Thu Nov 11 17:48:44 2010 +0000 add support for USE_OLDPLOTPER=TRUE in makefile Tools/C_mk/Make.defs commit 3ee111ca09ad657e7d572cb10f4e2ed5dcd25057 Author: ajnonaka Date: Thu Nov 11 17:48:24 2010 +0000 change "BL_USEOLDPLOT_PER" to "BL_USE_OLDPLOTPER" to be consistent with other cases Src/C_AMRLib/Amr.cpp commit 25aa4e267ad91619b09b7b67887249f5d23fcd9b Author: lijewski Date: Wed Nov 10 23:46:48 2010 +0000 tweaked g++ and gfortran debug options Tools/C_mk/Make.defs commit 1be67525fcaba9a04e19aced0b79248e0d09bc15 Author: lijewski Date: Wed Nov 10 23:46:09 2010 +0000 quiet -Wall warnings Src/C_AMRLib/Amr.cpp Src/C_AMRLib/MAKESLICE_3D.F Src/C_BaseLib/COORDSYS_3D.F commit 4296cdee4e648908100f22e4b12e2a0d5f84ea83 Author: lijewski Date: Wed Nov 10 22:10:08 2010 +0000 more IPM tweaks for hopper and franklin Tools/C_mk/Make.Linux commit 97d94a64a641e98968547a5ebb7660a501b25dfc Author: lijewski Date: Tue Nov 9 21:16:51 2010 +0000 short-circuited some parallel routines when nprocs()==1 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 70d605cd12bb721255d16fb5145e26877f50321c Author: lijewski Date: Tue Nov 9 20:37:41 2010 +0000 added MPI_Gatherv() capability to parallel_gather() Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit e3b107317186363d249ff5eed58c6dde1277db1b Author: lijewski Date: Tue Nov 9 20:36:44 2010 +0000 added simple parallel_gather() test Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit a8aa41270e527e3bd6f6f57661082169c15b7cab Author: almgren Date: Tue Nov 9 20:08:24 2010 +0000 Cleanup... Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F Src/C_BaseLib/COORDSYS_F.H commit 56e798f2d72dfd7545c7a1fe1d181b9cb587e6d6 Author: lijewski Date: Tue Nov 9 17:16:07 2010 +0000 compiles again Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bx.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bx.f90 Tests/F_BaseLib/t_main.f90 commit 716cff18a6b869352010969245c5f344932f7520 Author: almgren Date: Tue Nov 9 16:56:07 2010 +0000 Replace 1e-20 by 1d-50 -- we were bumping into this limit in very low density astrophysics problems. Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit a5b578b8d3fd9659015dfa8a6d7199a849255d5b Author: vince Date: Mon Nov 8 20:19:22 2010 +0000 fix for stationdata with capped finest level. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit ac8af0fdd83b7380c483053376d4749b35472b12 Author: vince Date: Fri Nov 5 21:22:19 2010 +0000 fixed station bug. modified plot_per to adjust timestep. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit c764015ca52678c9ca909f72645d494a725859a6 Author: lijewski Date: Fri Nov 5 21:00:44 2010 +0000 fixed bug I just introduced Src/C_AMRLib/Particles.H commit 415f008f4ead783ad011b3632dc1535815a6d5eb Author: lijewski Date: Fri Nov 5 20:13:53 2010 +0000 trimmed memory use in Redistribute() a tad Src/C_AMRLib/Particles.H commit a4b653f41f510ccc0363eb36888eb8149e7aa0de Author: lijewski Date: Fri Nov 5 18:04:54 2010 +0000 call mgt_use_alltoallv() if fabarray.do_alltoallv is true Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 12e65418b40105ff9358af648499244762301952 Author: lijewski Date: Fri Nov 5 18:04:09 2010 +0000 added mgt_use_alltoallv() which sets Do_AllToAllV in multifab_module to true Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 013be99bb28620dd7a76a4f6e2c4444bbcc629f6 Author: lijewski Date: Fri Nov 5 16:47:15 2010 +0000 Twiddle particles by some epsilon in PeriodicShift() in the case where they lie exactly on the domain boundary. We do this to make sure the particles when periodically shifted is back in the domain. I don't trust floating point arithmetic to always do the right thing. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 18cc719270cbe8a2e086d81f2fe82e8fab8346ce Author: lijewski Date: Thu Nov 4 16:53:00 2010 +0000 wrapped some stray I/O statements in m_verbose > 0 Src/C_AMRLib/Particles.H commit d7d12fe342effbcbb35628b9f60a3df3df904e90 Author: lijewski Date: Thu Nov 4 16:24:40 2010 +0000 some more error checking Src/C_AMRLib/Particles.H commit 75871fa48db802c9e7dc7c92629907c6c6b18a4f Author: lijewski Date: Wed Nov 3 06:01:07 2010 +0000 changed the byte spread output to refer to MPI processes instead of CPUs Src/F_BaseLib/fab.f90 commit ed569a9a2267feabbfb5e660ca180a9c5e5ebe04 Author: almgren Date: Tue Nov 2 16:05:37 2010 +0000 oops -- still need variable "vol" Src/LinearSolvers/F_MG/mg.f90 commit b43f6b7c28840b46a83b933e41e04b700f96ef59 Author: almgren Date: Tue Nov 2 16:00:35 2010 +0000 Change box_volume to box_dvolume so we can handle really big numbers (too big for an integer) Src/LinearSolvers/F_MG/mg.f90 commit af4b464e0d8736fe321f4037c989853ea9e90809 Author: lijewski Date: Mon Nov 1 23:01:49 2010 +0000 Added timer to InitRandom(). Added some more error checking. Unroll the last of simple BL_SPACEDIM loops. Src/C_AMRLib/Particles.H commit 545021dc840810b2b9f8235df3a448dac4fbb8ef Author: lijewski Date: Mon Nov 1 21:26:59 2010 +0000 we no longer send/recv m_lev, m_grid or m_cell -- the receiving MPI process just recalculates Src/C_AMRLib/Particles.H commit 127ecb6a5fb89cd63fcace209c9986032096e27b Author: lijewski Date: Mon Nov 1 20:57:00 2010 +0000 some performance tweaks Src/C_AMRLib/Particles.H commit 62ec42d2cece7915dd88b767bb9727c7f0f6b470 Author: lijewski Date: Mon Nov 1 18:04:36 2010 +0000 no longer write p.m_lev and p.m_grid to disk -- they can be easily recreated given how we write checkpoint files Src/C_AMRLib/Particles.H commit 46c2b8f4c6d077b4554150089d202c92d379e3a3 Author: lijewski Date: Mon Nov 1 17:22:41 2010 +0000 I've redone how particles are stored. Instead of a single deque we now have a deque per grid per level. This makes most of the algorithms that operate on particles containers more memory efficient since they almost always work on a level by level and grid by grid basis. Src/C_AMRLib/Particles.H commit b7ed5d0ba8846314edc8dd1ff3d09e4757702277 Author: lijewski Date: Mon Nov 1 17:16:55 2010 +0000 some IPM stuff for hopper Tools/C_mk/Make.Linux commit c4e8ce23c67943cf2beaaf9a6926c9e09255f2ae Author: lijewski Date: Fri Oct 29 22:50:41 2010 +0000 added ability to sort particles -- not yet used Src/C_AMRLib/Particles.H commit eea5383c38e730f6c1b0950b2c7ca49fb580f622 Author: lijewski Date: Fri Oct 29 21:39:15 2010 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_cc.f90 commit 55e74ccd0cafe8c6111e2e8be54e02a0507573c9 Author: almgren Date: Fri Oct 29 21:16:41 2010 +0000 Add code to print "sum of rhs" *only* for all periodic bc's and cell-centered. Src/LinearSolvers/F_MG/ml_cc.f90 commit 2cc61686ef3da8b78e23f0d11eb6f9d4dc21bd68 Author: lijewski Date: Fri Oct 29 20:36:14 2010 +0000 added serialize option to InitRandom() Src/C_AMRLib/Particles.H commit 754200a895dfe5ec209b0861297504194479cc2d Author: lijewski Date: Fri Oct 29 17:22:04 2010 +0000 *** empty log message *** Src/C_AMRLib/Particles.cpp commit 15721de0e0a9dad08da6ca8280a212cf879ddc17 Author: lijewski Date: Thu Oct 28 15:56:43 2010 +0000 AssignDensity() wasn't quite right for 3D Src/C_AMRLib/Particles.H commit 944e7d0e90a571d1e032928f9a32f404d22c45a2 Author: lijewski Date: Wed Oct 27 22:11:54 2010 +0000 tweak to OMP in sumParticleMomentum() to satisfy PathScale Src/C_AMRLib/Particles.H commit 551331575feb4429104d0556dd7e98a04f10ae05 Author: lijewski Date: Wed Oct 27 22:04:34 2010 +0000 simplified the OMP scheme for sumParticleMomentum() Src/C_AMRLib/Particles.H commit 54fb4499a48ba4b0272f977bfff8e110d480824a Author: lijewski Date: Wed Oct 27 21:56:03 2010 +0000 OMPd sumParticleMomentum() Src/C_AMRLib/Particles.H commit c9a81e72d1e8b44f2da18a1d956df1ed97045a6d Author: lijewski Date: Wed Oct 27 21:25:55 2010 +0000 came up with a way to OMP AssignDensity() Src/C_AMRLib/Particles.H commit dce5d5e3f2372d2ce12f4ed9bf189d9247a5289d Author: lijewski Date: Wed Oct 27 20:45:39 2010 +0000 sumParticleMomentum() now calculates all BL_SPACEDIM momemtums at once Src/C_AMRLib/Particles.H commit fcbd1ebfad975f80a280143f449503411f19fdc4 Author: lijewski Date: Wed Oct 27 19:41:04 2010 +0000 mods for PathScale Tools/C_mk/Make.Linux commit 471aed64db6172faaef31a778f56121484d3ae7b Author: lijewski Date: Wed Oct 27 17:44:22 2010 +0000 added -h noexceptions to CXXFLAGS for Cray Tools/C_mk/Make.Linux commit 9b59dd4bdfcba87ba23161dfbe150f388b10a629 Author: lijewski Date: Tue Oct 26 23:25:02 2010 +0000 Decreased the optimization in BL_NOFAST for PathScale to just -O. Looks like I have to use BL_NOFAST on the current version of hopper. Else I get Bottom solver failures in the gravity solve. Tools/C_mk/Make.Linux commit 8b5839d99adc87cd11ee4a1a168a92d42e4285b3 Author: lijewski Date: Tue Oct 26 22:09:17 2010 +0000 decrease Cray optimization intensity Tools/F_mk/comps/Linux_cray.mak commit 22c3c5f646e61a4fb0c2d186ef92dae92ab8994b Author: lijewski Date: Tue Oct 26 20:32:29 2010 +0000 decreased Cray optimization strenght a bit Tools/C_mk/Make.Linux commit 945075534541e153555bf4f56af74c2b5f678cfa Author: lijewski Date: Tue Oct 26 20:21:33 2010 +0000 mods to quiet Cray compiler Src/C_AMRLib/Particles.H commit 98d67453f686d7479181c1c8d8bf65ddea62864c Author: lijewski Date: Mon Oct 25 23:36:18 2010 +0000 OMPd estTimestep() Src/C_AMRLib/Particles.H commit 8d550d3d86dea3b2bd7f1ed9dce2e6f60e00225d Author: almgren Date: Mon Oct 25 22:10:07 2010 +0000 Fix indexing of cell vs csect in AssignDensity... Src/C_AMRLib/Particles.H commit 31275dbab36d2079dfa350fbf1020b8f6367f20e Author: almgren Date: Mon Oct 25 22:01:54 2010 +0000 Fix up getGravity Src/C_AMRLib/Particles.cpp commit 57411ae0f65f918b3d138375cd9a74d7a884c226 Author: lijewski Date: Mon Oct 25 20:06:33 2010 +0000 getParticleGrav() -> ParticleBase::GetGravity() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit e2a004d4986a88609c9662cd31354b9b1cc087d1 Author: almgren Date: Mon Oct 25 18:47:48 2010 +0000 This now includes Jan's updates which use getParticleGrav to interpolate the gravity onto particle locations instead of using the cell-centered value. Src/C_AMRLib/Particles.H commit 176e0b4cace3e6151a1c3b05224b805ed786dcce Author: lijewski Date: Mon Oct 25 03:43:11 2010 +0000 little cleanup Src/C_AMRLib/Particles.H commit 2d221cf1dee7d4b183d752444b6f19f9730f6738 Author: lijewski Date: Mon Oct 25 01:59:43 2010 +0000 std::list -> std::deque as the latter is more amenable to OMPing Src/C_AMRLib/Particles.H commit 56ff56e51736f21b0c673246676dfaae48080bbd Author: lijewski Date: Sun Oct 24 23:41:46 2010 +0000 some OMPing Src/C_AMRLib/Particles.H commit 3355039a9d33c026fc56e56c35e1f20beb083256 Author: lijewski Date: Sun Oct 24 22:45:29 2010 +0000 minor performance tweaks Src/C_AMRLib/Particles.H commit 35a31c1cde9e8383d0915967689df83b90b33f7a Author: lijewski Date: Sun Oct 24 22:07:10 2010 +0000 add some more timers Src/C_AMRLib/Particles.H commit c25c23d11faddae30a9995074b089fd4b2d3426d Author: lijewski Date: Fri Oct 22 23:25:30 2010 +0000 more Cray tweaks Tools/C_mk/Make.Linux commit ce42be1b5a80229d079faf9d29d226145192febe Author: lijewski Date: Fri Oct 22 22:26:31 2010 +0000 fixed bug in AssignDensity() when DIM=3 - be good if Jhon could confirm Src/C_AMRLib/Particles.H commit eb2bbd75e48c3f9ff790ac8650fe73d340eca789 Author: wqzhang Date: Fri Oct 22 21:10:12 2010 +0000 added my desktop baragon Tools/C_mk/Make.defs commit 816c636f18a1ee149d79fcc5b1bf82ea1dccd24c Author: ajnonaka Date: Fri Oct 22 20:31:36 2010 +0000 if USE_LEVELSET=T, at .LevelSet suffix to executable name Tools/C_mk/Make.defs commit 1bd6264156584ce28a37929be977b175b1883517 Author: lijewski Date: Fri Oct 22 20:26:10 2010 +0000 more Cray stuff Tools/C_mk/Make.Linux commit 8fa04dd8d1fc4001df945ef6da2e4ab1c450d0f8 Author: lijewski Date: Fri Oct 22 16:48:51 2010 +0000 some work adding Cray Tools/C_mk/Make.Linux commit e8eec6dba102548db2a6386b4093caae42100e4b Author: lijewski Date: Fri Oct 22 15:34:29 2010 +0000 added -Minline flag Tools/F_mk/comps/Linux_pgi.mak commit af9b83e866c26c2767955df18855e92659345218 Author: lijewski Date: Thu Oct 21 20:59:14 2010 +0000 for Cray compilers Tools/F_mk/comps/Linux_cray.mak commit 980fa4ba43088597c7ee05a0e50b4c058f1e0073 Author: lijewski Date: Thu Oct 21 20:58:15 2010 +0000 some work for Cray compiler suite Tools/F_mk/GMakedefs.mak commit 95efbdb385cd47b44812b72f24dbb281b0c02945 Author: lijewski Date: Thu Oct 21 18:21:39 2010 +0000 added grace Tools/F_mk/GMakeMPI.mak commit 4bfb8680a9702744650520cc6a22acc6ceeac803 Author: lijewski Date: Wed Oct 20 23:17:09 2010 +0000 tweaked the PGI optimization flags Tools/C_mk/Make.Linux commit e52a73ea1102af26b5a8b0a287489577f05435e3 Author: lijewski Date: Wed Oct 20 23:15:22 2010 +0000 added GRACE Tools/C_mk/Make.defs commit 4e6f9e04d29292305b855ffdfc5ec2f3027b2bca Author: ajnonaka Date: Wed Oct 20 13:58:53 2010 +0000 mpi for my home machine Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 6322fc185db0eac690b9669518063014fefa3a54 Author: mzingale Date: Wed Oct 20 13:54:55 2010 +0000 add support for kraken Tools/F_mk/GMakeMPI.mak commit 3a44d87c42bec8809de74b3c2b8185afdcbe93d4 Author: wqzhang Date: Tue Oct 19 22:48:32 2010 +0000 *** empty log message *** Tools/C_mk/Make.rules commit 353a919764eaa4f9b370579901be4193ef0598b8 Author: ajnonaka Date: Tue Oct 19 00:04:05 2010 +0000 MPI for ebirah Tools/F_mk/GMakeMPI.mak commit e6958bfef8b4822e41a86685f25326be762a469e Author: almgren Date: Mon Oct 18 21:48:52 2010 +0000 We do not need those lines for compiling with intel on ranger. Tools/C_mk/Make.mpi commit e884ce44abc6cb83c6e10417a355227a1e6dd06f Author: lijewski Date: Mon Oct 18 21:09:32 2010 +0000 introduced version string for checkpoint/restart files Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit b18c0b7cb88439325a30b68ead22879a9b2fc277 Author: lijewski Date: Mon Oct 18 20:02:18 2010 +0000 some performance tweaking Src/C_AMRLib/Particles.H commit 806338863d9c02be68187bbbb43707104dea05f6 Author: lijewski Date: Mon Oct 18 19:18:49 2010 +0000 a little cleanup Src/C_AMRLib/Particles.H commit 9f26609da780754e20bb4ffc0699644f6fcd2f73 Author: lijewski Date: Mon Oct 18 18:26:32 2010 +0000 now unlink() zero-length data files but not directories Src/C_AMRLib/Particles.H commit e5cffd200820c1bec4a5d6950827b11f0f60ddf6 Author: lijewski Date: Mon Oct 18 17:14:17 2010 +0000 non-backward compatible performance change to particle checkpoint/restart files Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit e5bd5964223759b9a4d1515214e62c5fee5a5456 Author: almgren Date: Fri Oct 15 22:55:19 2010 +0000 Add orion. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 28138ffc67b0f89eb12ca891e8002612c00ffb3a Author: lijewski Date: Fri Oct 15 21:33:53 2010 +0000 some cleanup and additional error checking Src/C_AMRLib/Particles.H commit ea094d1748f061a33d9500da8c96f353702c5d0e Author: ajnonaka Date: Fri Oct 15 20:45:02 2010 +0000 bugfix - using && instead of .and. didn't work with my gfortran Src/LinearSolvers/F_MG/mg.f90 commit 85a9f0f467f03c68b9fa56a16edd73fb991ae26f Author: lijewski Date: Fri Oct 15 20:42:51 2010 +0000 Restart() appears to be working. Will need to be updated when Vince's IntRealDescriptor-style stuff is ready. Src/C_AMRLib/Particles.H commit 8e96f5615e8ae0e76848e395358d5f431077677b Author: almgren Date: Fri Oct 15 20:35:40 2010 +0000 Add "if verbose > 1" before print statement re bottom_solver=4 coarse domain size Src/LinearSolvers/F_MG/mg.f90 commit c1f14a8083dfaa1da5574a0c6c970a1c6a220747 Author: adonev Date: Fri Oct 15 20:21:27 2010 +0000 Added flag BL_FAST_COMP Tools/F_mk/comps/Linux_intel.mak commit 9e6c485130c9a653ef80d8248a0006c6673f93d1 Author: lijewski Date: Fri Oct 15 17:03:47 2010 +0000 Now writing out particles in native binary. Needs to eventually to brought up to date with Vince's IntDescriptor stuff when he's done with it. Src/C_AMRLib/Particles.H commit 5da107bf47d9e8f27768de0a37cc270285112fe3 Author: lijewski Date: Thu Oct 14 23:50:37 2010 +0000 a little cleanup Src/C_AMRLib/Particles.H commit 5bb69d9f86498ef909abc58d51487d628b8fb39a Author: lijewski Date: Thu Oct 14 23:34:34 2010 +0000 OK() is now more thorough Src/C_AMRLib/Particles.H commit 002cdbbc30edef26294a71f4f584d56ad9403ba9 Author: lijewski Date: Thu Oct 14 23:13:04 2010 +0000 yet more work on Checkpoint() Src/C_AMRLib/Particles.H commit 668a45595796d8f6dae6bd70b12edec0564643be Author: lijewski Date: Thu Oct 14 22:37:31 2010 +0000 more work on Checkpoint() Src/C_AMRLib/Particles.H commit 4ecb3abc6cc1f49ee3c9321cfc2af1981968b5ae Author: lijewski Date: Thu Oct 14 21:51:03 2010 +0000 initial work on Checkpoint(); more needed Src/C_AMRLib/Particles.H commit 67ed9bd8bb3e078971d6aa5f4584b26f08790831 Author: lijewski Date: Thu Oct 14 17:34:43 2010 +0000 some optimization Src/C_AMRLib/Particles.H commit 0f0eb8fb5268c3e006327ef938fa209f211af975 Author: lijewski Date: Wed Oct 13 23:11:33 2010 +0000 some cleanup and more error checking Src/C_AMRLib/Particles.H commit ec649a3cf333076e4388aa408cfa4dd9942f9ac8 Author: almgren Date: Sat Oct 9 19:16:31 2010 +0000 Add verbose to test for output... Src/C_AMRLib/Particles.H commit 29ef6f8de26fc66cd302977d7f389294a4d44a2b Author: almgren Date: Sat Oct 9 16:31:01 2010 +0000 Make sure to set bottom_singular = .true. if the boundary conditions for the current solve are all periodic. Src/LinearSolvers/F_MG/mg.f90 commit 0c937af5e164e2ac1c0a2d0f0317fcd1aa8cc33b Author: almgren Date: Fri Oct 8 20:50:57 2010 +0000 These appear to actually work with clumping particles in 2d. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 3c0a480080c35c18b6ee1e305a786d67cffb4338 Author: almgren Date: Fri Oct 8 17:03:28 2010 +0000 Latest updates from JF. Src/C_AMRLib/Particles.H commit 429daf4af9ba5276e0f8f72b6d5c8cf655527a38 Author: almgren Date: Thu Oct 7 16:49:54 2010 +0000 Change the default particle to have the first real component have value = 1 (and all the others are zero). Src/C_AMRLib/Particles.H commit b7c9b3e4b6e4e3bda5efd3acb7170d0b97e393f8 Author: almgren Date: Wed Oct 6 22:05:14 2010 +0000 Add Particles_F.H Src/C_AMRLib/Particles_F.H commit cd581f37de87a765ec222a8fbb08cb320ccdd113 Author: almgren Date: Wed Oct 6 21:14:44 2010 +0000 This is a merge of Mike's latest and Jan's latest -- it has everything as of now. Src/C_AMRLib/Particles.H commit 2dcab77f432c15b38282066e7a3233eb6f2102a8 Author: almgren Date: Wed Oct 6 20:17:48 2010 +0000 Moved Particles.* from amrlib to particles directory. Src/C_AMRLib/Make.package Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit a4a51da96ba6f3ffea4c00c501e136d0494ebf7b Author: vince Date: Wed Oct 6 20:01:22 2010 +0000 added new machines. Tools/C_mk/Make.mpi commit 0ed17248de77ba5d954f58b4531244f80674550c Author: lijewski Date: Wed Oct 6 15:44:20 2010 +0000 little code rearrangement Src/C_BaseLib/FabArray.H commit 35b6b8a4093164fd1cb95ca2a822a69373ff05ec Author: lijewski Date: Wed Oct 6 15:38:30 2010 +0000 little code rearrangement in SumPeriodicBoundary() Src/C_BaseLib/Geometry.cpp commit ef7a4a9f9daa1c33dea2c4b8fff0613a49eee8bd Author: lijewski Date: Wed Oct 6 15:31:30 2010 +0000 use intersections() in SumBoundary() Src/C_BaseLib/MultiFab.cpp commit 7ab858e9481089a76b1da2cc4fc549e4821245d9 Author: lijewski Date: Wed Oct 6 15:14:27 2010 +0000 minor code motion Src/C_BoundaryLib/BndryData.cpp commit 41d7df28cd5da797c8a4e897caa931af8c90cdc5 Author: lijewski Date: Wed Oct 6 15:14:27 2010 +0000 minor code motion Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 062b0c6cc9e2a6d2cd82886d881d1847d4e6a0b5 Author: lijewski Date: Tue Oct 5 23:00:00 2010 +0000 added initial cut of SumBoundary() Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 696fc700323c502ad7afa4d3e44ab676bb7e7e2d Author: lijewski Date: Tue Oct 5 21:40:47 2010 +0000 added SumPeriodicBoundary() Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit b197069a44d76214ca25caf3ef6214bd3097840f Author: lijewski Date: Mon Oct 4 16:47:42 2010 +0000 ParmParse can now deal with longs Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit ead690e1c43b5289aa54b62d917d8180645f69fb Author: adonev Date: Sun Oct 3 23:32:29 2010 +0000 donev in Makefile Tools/C_mk/Make.mpi commit 5388e4e556820030d821ceaabdb706a4b1031d19 Author: ajnonaka Date: Fri Oct 1 23:13:06 2010 +0000 more makefile hacking Src/F_BaseLib/GPackage.mak Src/F_BaseLib/multifab_physbc_edgevel.f90 commit 627f8e56293246ffcb21e25744e8cabdec57864e Author: ajnonaka Date: Fri Oct 1 22:41:37 2010 +0000 in progress hacking to get the initial model stuff to compile Src/F_BaseLib/GPackage.mak Src/F_BaseLib/multifab_physbc_edgevel.f90 commit d5aef03c8bdeca3b9ae50c327e3b4dea87b0df65 Author: marc Date: Fri Oct 1 21:55:40 2010 +0000 Add win include Src/C_BaseLib/IntVect.H commit f23b7b9764a6ee47da36aae1df27b2f6321cca2a Author: marc Date: Fri Oct 1 21:54:57 2010 +0000 Rename macro for excluding fortran functions from boxlib build Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package commit 2f9722a46e6cee3417836fa6c458e9451b27dcaa Author: ajnonaka Date: Fri Oct 1 21:54:18 2010 +0000 moved MAESTRO/Source/impose_phys_bcs_on_edge_vels into /boxlib/ and rennamed it multifab_physbc_edgevel. create_umac_grown.f90 now calls multifab_physbc_edgevel on the coarsest and the current fine level Src/F_BaseLib/GPackage.mak Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 commit 116bab0663f725d7c56cf1c9ca12367de1c5e172 Author: lijewski Date: Fri Oct 1 21:44:47 2010 +0000 brought back from the dead Src/C_BaseLib/GNUmakefile commit 8bcf8dc9c8f0e6cbaf183554e0b69f0d30cd2bd8 Author: ajnonaka Date: Fri Oct 1 21:14:33 2010 +0000 need to pass the_bc_level into create_umac_grown so we can call impose_phys_bcs_on_edges Src/F_BaseLib/create_umac_grown.f90 commit d19c785753689c6db8c760f356f1082a7f512ba3 Author: ajnonaka Date: Fri Oct 1 20:40:21 2010 +0000 it would help if i actually added this file to the repository Src/F_BaseLib/create_umac_grown.f90 commit 45ed05189fa130b54d69811888cefcd93a1dd0ae Author: ajnonaka Date: Fri Oct 1 19:34:31 2010 +0000 move create_umac_grown.f90 into /boxlib/ and removed these local copies Src/F_BaseLib/GPackage.mak commit ad64007e090db8073b6a6bf8937d314663bb3832 Author: almgren Date: Fri Oct 1 17:40:07 2010 +0000 We need to back out this change from v1.36 to v1.37 or the CASTRO codes don't build anymore Tools/C_mk/Make.rules commit ed8da9f3dd2653c5d72ef1ac93770f40c25cfe80 Author: lijewski Date: Thu Sep 30 22:41:03 2010 +0000 some VisIt changes from Gunther Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/FPC.cpp Src/C_BaseLib/Make.package Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 6f3cf23ca034db3dd50a10dba8518e2ed5fc69e1 Author: ajnonaka Date: Thu Sep 30 05:00:39 2010 +0000 remove unused variables Src/F_BaseLib/fab.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 04acb3dc767c634f2a14a8dd558225f2a17da2bf Author: ajnonaka Date: Thu Sep 30 01:08:20 2010 +0000 turn on gfortran compiler warnings if you are in debug mode. it will warn you about uninitialize and unused variables Tools/F_mk/comps/gfortran.mak commit c81c74a6bda85a8821ce3eef0894ef6913b33861 Author: marc Date: Wed Sep 29 23:16:18 2010 +0000 removing files that were renamed to avoid name collisions Src/LinearSolvers/C_NodalMG/cg.cpp Src/LinearSolvers/C_NodalMG/cg_2d.f Src/LinearSolvers/C_NodalMG/cg_3d.f commit 77e2721a80c22bfc5539f8dd57d2bab22077b987 Author: marc Date: Wed Sep 29 23:14:21 2010 +0000 Incorporate name changes into filelist Src/LinearSolvers/C_NodalMG/Make.package commit 20de950baca4681a5f1391eafafbb9bf5ed2db19 Author: marc Date: Wed Sep 29 23:13:40 2010 +0000 Renamed from cg_3d.f to avoid name collision in case-insensitive environments Src/LinearSolvers/C_NodalMG/hg_cg3d.f commit d59ab580c9ac5b38e49c4f5920b676fb5c90accf Author: marc Date: Wed Sep 29 23:12:54 2010 +0000 Renamed from cg_2d.f to avoid name collision in case-insensitive environments Src/LinearSolvers/C_NodalMG/hg_cg2d.f commit 9e832b00e19ba99406dcb0273edd889c05c8ebe0 Author: marc Date: Wed Sep 29 23:11:30 2010 +0000 Renamed from cg.cpp to avoid name collision in case-insensitive environments Src/LinearSolvers/C_NodalMG/hg_cg.cpp commit 78ca7d97fb4343145709ccf6cc70785967bf02c8 Author: marc Date: Wed Sep 29 03:46:35 2010 +0000 *** empty log message *** Tools/C_mk/Make.CYGWIN_NT commit 9c9b0172961b3fe4edd250203e56364cb553f49e Author: adonev Date: Mon Sep 27 23:28:22 2010 +0000 Added host donev Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit a14c34f0ed4f5cc3a29b268e03a5c10063ce4a74 Author: adonev Date: Mon Sep 27 21:22:18 2010 +0000 Added host donev Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit c8c0c53f76e4dd6e9d7feb6251c52741a9ecb2da Author: lijewski Date: Mon Sep 27 21:11:33 2010 +0000 more particle stuff Src/C_AMRLib/Make.package commit 8ecd29c99534af0f8eb9ff9edd5c11fa86ee0f63 Author: gpau Date: Wed Sep 22 04:47:04 2010 +0000 Doing function provided by ViscBndry differently: do not need ViscBndry in solve. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit c5b1ac310b2b9736052602ee087a83aff18ff641 Author: gpau Date: Tue Sep 21 22:01:10 2010 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 1c92891c28a49ff750ef592169e3563f43fc7e7d Author: wqzhang Date: Thu Sep 16 21:29:17 2010 +0000 Fixed a comment Src/C_BaseLib/IntVect.H commit f40d8a7edb38714e7f650b383ffc52a1e91b574b Author: ajnonaka Date: Thu Sep 16 17:56:36 2010 +0000 Chris' fix to get PathScale working on atlas Tools/F_mk/GMakeMPI.mak commit 0d83a8a33e207b1dc64a065b11f13feba10ecfa7 Author: marc Date: Mon Sep 13 20:33:30 2010 +0000 fix PathScale second underscore thing Tools/C_mk/Make.Linux commit 30aea3be16d352aa08af49b3a2250f99f081a04f Author: lijewski Date: Fri Sep 10 23:05:34 2010 +0000 beefed up FULLWARN for g++ Tools/C_mk/Make.defs commit 7f716bb081b5f418c89fecf20dcf4010fe3e9265 Author: lijewski Date: Fri Sep 10 22:34:20 2010 +0000 now passes g++ -pedantic -Wall Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 1460228a1e0690fa19135fbc68053590d48fcda9 Author: lijewski Date: Fri Sep 10 20:24:52 2010 +0000 added -fbacktrace flag when debugging with gfortran Tools/F_mk/comps/gfortran.mak commit 2cb89b71f6708672ea7073b357b7dfcc76667c12 Author: lijewski Date: Thu Sep 9 16:47:29 2010 +0000 unOMPd setval() Src/F_BaseLib/fab.f90 commit 6f4170bdcefa76e259473558eb8bb038d2f60268 Author: lijewski Date: Thu Sep 9 16:27:10 2010 +0000 removed some unused dummy arguments and unOMPd SETVAL Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit a2c182ce998082f668fdb3ae398c2806bd40413e Author: almgren Date: Wed Sep 8 16:47:35 2010 +0000 Add kraken stuff. Tools/C_mk/Make.Linux commit f480a1a50715280b79de525defd18ce6681d7504 Author: almgren Date: Wed Sep 8 16:46:48 2010 +0000 Add kraken info. Tools/C_mk/Make.defs commit 27cbcc3b59f99cb695776c65b0a49c3c549106e3 Author: gpau Date: Tue Sep 7 18:03:14 2010 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 4e0ec6f19f2e4030d5f0b8f7ff02a6844d4cf916 Author: almgren Date: Thu Sep 2 23:35:06 2010 +0000 Fix bug in stencil_norm inside if present(mask) test. Src/LinearSolvers/F_MG/stencil.f90 commit 7c3b7406e900c2be914e4e4c8a01427dbe8b0749 Author: ajnonaka Date: Tue Aug 31 15:21:08 2010 +0000 MPI on my home machine Tools/F_mk/GMakeMPI.mak commit 6e5b85fb04c5ba50afdcb0b779d40263a82ec4fd Author: ajnonaka Date: Tue Aug 31 15:21:01 2010 +0000 MPI on my home machin Tools/C_mk/Make.mpi commit f7ccb72d04eb349cece0193d8f9f4fa6b6d8e047 Author: ajnonaka Date: Fri Aug 27 23:02:54 2010 +0000 added -fno-range-check for gfortran to get the fParallel/extern/random/mt19937ar.f90 stuff to compile Tools/C_mk/Make.defs commit f15f10b6db6f843da4941f912975fe36d8058474 Author: ajnonaka Date: Fri Aug 27 22:43:02 2010 +0000 new install of mpi. Fixed to work with gfortran on atragon Tools/C_mk/Make.mpi commit d2e0b9a0d7196be0fa25d4d9ac903555b2f74622 Author: ajnonaka Date: Fri Aug 27 22:32:11 2010 +0000 new install of mpi. Fixed to work with gfortran on atragon Tools/F_mk/GMakeMPI.mak commit 9d02c3d103733af067174ed46aab973b8569c746 Author: almgren Date: Fri Aug 27 21:54:47 2010 +0000 This modifies the convergence criterion for the solver in ml_cc so that it stops when res < eps * MAX(bnorm,tres0) instead of res < eps * bnorm. Here bnorm = norm(rhs) and tres0 = norm(resid0). Src/LinearSolvers/F_MG/ml_cc.f90 commit 75f8f1c32caee746d9bb21eab588ab903055f708 Author: ajnonaka Date: Thu Aug 26 21:33:27 2010 +0000 printing out fancy bottom solver grids even when mg_verbose=0 Src/LinearSolvers/F_MG/mg.f90 commit 0ffdf6f243ef0635f199f699624d138dd2d6d561 Author: nazgul Date: Thu Aug 26 00:15:56 2010 +0000 Commenting out iters.f, as it causes build problems for Castro and does not appear to be used. Louis Src/LinearSolvers/F_MG/FParallelMG.mak commit 977e74398b627a5673c2cd402c4c052f46e20354 Author: lijewski Date: Wed Aug 25 21:40:17 2010 +0000 no longer include sparse_solve.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit 878ff03a602a4bd30c8a7126624b1dfc5c1ee945 Author: lijewski Date: Wed Aug 25 20:37:51 2010 +0000 removed some dubiously useful OMP constructs Src/LinearSolvers/F_MG/ml_util.f90 commit c66a102082b733c1823c1b0599cb5a6bd00811ee Author: lijewski Date: Wed Aug 25 19:51:11 2010 +0000 remove OMP stuff on faces -- not enough work Src/LinearSolvers/F_MG/impose_neumann_bcs.f90 commit 43d9d681b8410a9eab71e8f7eda06e71d062915c Author: lijewski Date: Wed Aug 25 19:35:15 2010 +0000 OMP'd stencil_norm() when present(mask) Src/LinearSolvers/F_MG/stencil.f90 commit 3f636502de11d6a63787d685a40a9deb48495c59 Author: lijewski Date: Tue Aug 24 23:08:25 2010 +0000 some cleanup Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 commit 1c5fd530ede896aa4b939de9a57aadf3ac6916a2 Author: ajnonaka Date: Tue Aug 24 21:41:34 2010 +0000 fixed the 12 thread multilevel bug. now it gives the same answer as 6 threads to machine precision Src/LinearSolvers/F_MG/stencil.f90 commit 4c6ecaa9d5406d25db2da8dcddd198a5f4cd3314 Author: almgren Date: Tue Aug 24 20:30:31 2010 +0000 end if --> endif Src/C_BaseLib/BoxLib.cpp commit 67bdbd7159578d9f28d74dac685cf2e9bb4f7546 Author: almgren Date: Tue Aug 24 20:12:38 2010 +0000 Print out many MPI processes even if only one. Src/C_BaseLib/BoxLib.cpp commit 6d99f244be8acba98719526a3cd59453a371b799 Author: lijewski Date: Tue Aug 24 20:12:00 2010 +0000 removed all nocomm stuff and some OMP loops of dubious usefulness Src/F_BaseLib/multifab.f90 commit 4c113f1c7a900c76f07b545fdfa15bdc4c844f17 Author: almgren Date: Tue Aug 24 20:08:19 2010 +0000 Wrap the statement "MPI initialized..." with #ifdef BL_USE_MPI Src/C_BaseLib/BoxLib.cpp commit 3490e3861204069e41bcc5787540cae081187ae7 Author: lijewski Date: Tue Aug 24 17:46:28 2010 +0000 removed ml_layout_build_la() -- not used by any current code Src/F_BaseLib/ml_layout.f90 commit 333fba55dc9d6bf703460fb7fa8c7561065b0726 Author: lijewski Date: Tue Aug 24 17:31:57 2010 +0000 Added destroy_all_layouts member to ml_layout. This is so we can distinguish between the two main ways of building ml_layouts. In most f90 code we use build() which forces the layouts of higher levels to be owned by the one at the coarsest level, via proper nesting. In the MGT code however the layouts are build level by level and hence in destroy() we must destroy all of them, not just the one at the coarsest level. Src/F_BaseLib/ml_layout.f90 commit f36b4162d5ee3d361a5340501c5a60bf846850a3 Author: ajnonaka Date: Mon Aug 23 23:36:14 2010 +0000 upgraded the fancy bottom_solver_type 4 to allow an even coarsen bottom solve for this bottom solver. ultra complicated and will get some details in the user's guide when I figure out a clean way of describing it Src/LinearSolvers/F_MG/mg.f90 commit 4c9018aeb100c0e69eaaa5c73a5e905570968811 Author: lijewski Date: Mon Aug 23 23:30:51 2010 +0000 got rid of OMP shared variable warnings via firstprivate Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 5a9c0857cdc686c7466574db4921ae00340fbe44 Author: ajnonaka Date: Mon Aug 23 20:35:00 2010 +0000 some cleanup - preparing to make the new bottom solver more robust by allowing more levels in certain cases. Example: we would like a 20^3 problem to be able to go down to a 5^3 rather than the 10^3 it would currently do. Src/LinearSolvers/F_MG/mg.f90 commit cf0b5fc486e5f1c50e95b6065ccb71bf4f6a0d8b Author: lijewski Date: Fri Aug 20 17:30:30 2010 +0000 some cleanup Src/LinearSolvers/F_MG/ml_solve.f90 commit ac9658e952dc9ccecd62c9dc8bb923f0178c58c1 Author: lijewski Date: Fri Aug 20 17:03:27 2010 +0000 unOpenMPd set_faces_edges_corners_3d - probably not a win Src/LinearSolvers/F_MG/stencil_nodal.f90 commit f041aff891e8b9d591e3e56154fd5d765d108c02 Author: lijewski Date: Fri Aug 20 16:46:50 2010 +0000 some more OpenMPing Src/LinearSolvers/F_MG/stencil.f90 commit 7e000bffccf7e375183abe8dd031a97a395e64b4 Author: lijewski Date: Thu Aug 19 23:45:25 2010 +0000 removed some unused routines & made some private Src/LinearSolvers/F_MG/stencil.f90 commit 4e8d9b5366e29ed7620925c23e8e9ec0f621dd99 Author: lijewski Date: Thu Aug 19 22:56:32 2010 +0000 refined public interface Src/LinearSolvers/F_MG/nodal_mask.f90 commit 672c09741d6a1866d3e28a6b9b8d1c83b01a29f5 Author: lijewski Date: Thu Aug 19 22:36:40 2010 +0000 fixed up public/private stuff Src/LinearSolvers/F_MG/ml_restriction.f90 commit 43cf26a01e81ac1c3f3f4ecf5c22e0e753cd5f9a Author: lijewski Date: Thu Aug 19 22:29:44 2010 +0000 made only those routines that need to be public Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 109737e73a596f4fbdfe5f3dfe2d740982184302 Author: lijewski Date: Thu Aug 19 22:20:46 2010 +0000 made only those functions used outside this module public Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 311e51850a88f017e4cf80382c17957a7afcc36b Author: lijewski Date: Thu Aug 19 22:12:30 2010 +0000 make scale_residual_[123]d private Src/LinearSolvers/F_MG/ml_cc.f90 commit 77cf804cc67e37103f9a7b5ac7fbd40bcce6e5b3 Author: ajnonaka Date: Thu Aug 19 21:51:52 2010 +0000 output number of threads and MPI processes to job_info and at the beginning of each run Src/F_BaseLib/BoxLib.f90 Src/F_BaseLib/GPackage.mak Src/F_BaseLib/omp.f90 Src/F_BaseLib/omp_stubs.f90 commit a64875a56a0bf77a312e1d62ec94fbea56b03ec2 Author: lijewski Date: Thu Aug 19 21:30:06 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/itsol.f90 commit a15eb4a8da49eb3674c9e540e02faec2531006a0 Author: lijewski Date: Thu Aug 19 21:19:17 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/nodal_newu.f90 commit 2b18dc3a3cf43c5054d6cb6c99c5c7edca24f930 Author: almgren Date: Thu Aug 19 00:37:34 2010 +0000 Modified the nodal solver output to more closely match the MAC solver -- specifically, it now prints F90mg: Final Iter. 7 resid/resid0 = 0.33106928E-11 rather than MG finished at 7 iterations at the end of the solve. Src/LinearSolvers/F_MG/ml_nd.f90 commit 75a0bb3429421e6dd8594a0cf054fae37f868389 Author: lijewski Date: Wed Aug 18 22:10:12 2010 +0000 attempt to shut up 'possible uninitialized variable' msgs Src/F_BaseLib/multifab.f90 Src/F_BaseLib/plotfile.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 5507c1419343ef8d160678242dcb2bc238ee2341 Author: lijewski Date: Wed Aug 18 20:15:12 2010 +0000 0 -> 0_dp_t and removed a print statement Src/F_BaseLib/multifab.f90 commit 84b59d00d1d4e5af8a292bac01ff1cce7f296b96 Author: ajnonaka Date: Tue Aug 17 13:44:07 2010 +0000 in MAESTRO/Source/ rennamed cluster_min_width to minwidth so it matches what's in boxlib/cluster.f90 now you can set blocking_factor in the inputs file both blocking_factor and minwidth default to 8 in both MAESTRO and cluster.f90 Src/F_BaseLib/cluster.f90 commit cbf4965300053c747a3ba0cdad41bcd8a9c53160 Author: ajnonaka Date: Tue Aug 17 13:09:04 2010 +0000 output says "MPI initialized with XXXX MPI processes" instead of CPUs Src/F_BaseLib/BoxLib.f90 commit a79632c38697af60da5ee7842c68f94dae52bf59 Author: lijewski Date: Mon Aug 16 20:02:11 2010 +0000 plugged memory leak Src/F_BaseLib/fabio.f90 commit 7eb887eb0f1265f82c69b5f5e3c4454e0166403f Author: lijewski Date: Mon Aug 16 19:26:22 2010 +0000 shut up some valgrind warnings Src/F_BaseLib/bndry_reg.f90 commit 50c2eb9b115ed6cb900957fb7ff29a01dd8e9b5c Author: mzingale Date: Mon Aug 16 13:22:09 2010 +0000 get make_benchmarks working again if there are self-tests defined Tools/C_util/regtests/test.py commit 44dc6d1e985cd8015dcf95a9c42f6e75eff01f41 Author: lijewski Date: Fri Aug 13 21:44:26 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/nodal_divu.f90 commit 66e740cfd836168e56a84728eb7a4fa98cc6f899 Author: lijewski Date: Fri Aug 13 20:30:07 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 6bd7744d6450b1457bed28d4eb553cbdc2327cb7 Author: lijewski Date: Fri Aug 13 20:18:08 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 47fb4ce512f7426cbd4e851dbd31389d3e4e84ec Author: lijewski Date: Fri Aug 13 17:21:51 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/mg_restriction.f90 commit 5b59025c16170f3ca46fc0f13791bd492c321163 Author: lijewski Date: Fri Aug 13 17:05:32 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/coarsen_coeffs.f90 commit 838e620a7131d60f822b3eb5d0a15cfe57f9876e Author: lijewski Date: Fri Aug 13 16:33:13 2010 +0000 some code rearrangement Src/F_BaseLib/sort_box.f90 commit c34c05e31f8964c9a3a58118a0e9251c443242ff Author: lijewski Date: Fri Aug 13 16:24:31 2010 +0000 some OpenMPing Src/F_BaseLib/interp.f90 commit 2a4a01b1833bf72891f30a5278c5b3c2dac361e9 Author: ajnonaka Date: Fri Aug 13 15:16:41 2010 +0000 test commit for cvs email notifications Src/F_BaseLib/make_new_grids.f90 commit fb65c719648c53128589828e2329c990048a7a93 Author: ajnonaka Date: Fri Aug 13 14:38:54 2010 +0000 New probin variables that let you set max_grid_size as a function of level. They are max_grid_size_1, max_grid_size_2, and max_grid_size_3. Note max_grid_size_base has been replaced by max_grid_size_1. These default to max_grid_size if they are not set. max_grid_size_1 is max_grid_size for the coarsest level, "level 1" max_grid_size_2 is max_grid_size for the first level of refinement, "level 2" max_grid_size_3 is max_grid_size for the second level of refinement and beyond, "level 3 and beyond" Modified inputs files to reflect this. Also, setting the default value of cluster_min_width to 8. 16 gave horrifically blocky looking grid structures, even for very hi-res problems. The averaging procedure just works better if you get more form-fitting grids. Still need to update local copies of initialize.f90, regrid.f90, and make_new_grids.f90 Src/F_BaseLib/make_new_grids.f90 commit 83cd9088ab59f476327b4e5176aa4670b889a201 Author: lijewski Date: Thu Aug 12 23:36:20 2010 +0000 removed pc_cc_interp and pr_cc_interp routines Src/F_BaseLib/interp.f90 commit f4ec43b3934c3ba7385c7a2862e19b8d19d2bc8a Author: lijewski Date: Thu Aug 12 23:18:05 2010 +0000 removed bl_nd_interp_[23]d Src/F_BaseLib/interp.f90 commit af6dd476b806094949f51e20164ad761b55e43df Author: ajnonaka Date: Thu Aug 12 22:23:27 2010 +0000 use lbound/ubound instead of 1,size for fab/multifab loops Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit b53ab2beb8c1c18b814eb368975a89535564624f Author: lijewski Date: Thu Aug 12 21:04:28 2010 +0000 workaround for dumb IBM xlf bug Src/F_BaseLib/fillpatch.f90 commit 93ae903df568769b8122ac1b4a36df21d6ee23d5 Author: almgren Date: Thu Aug 12 19:45:38 2010 +0000 Anything to do with the sparse solver is now commented out in mg.f90 and mg_tower.f90 and we no longer include sparse_solve.f90 in GPackage.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 commit 66d8e047f2b7d9a5913631f6ee4814a21c74e1fc Author: lijewski Date: Thu Aug 12 19:33:22 2010 +0000 OpenMP'd min_val and max_val routines Src/F_BaseLib/fab.f90 commit 07514d755ad217cf90d02a4b5640b9dfdcc7b4d1 Author: lijewski Date: Thu Aug 12 17:41:18 2010 +0000 OpenMP'd sub_sub and plus_plus routines Src/F_BaseLib/multifab.f90 commit de0c9af114b22b5d78e44eccc58409803e2b31be Author: lijewski Date: Thu Aug 12 17:27:38 2010 +0000 OpenMP'd mult_mult routines Src/F_BaseLib/multifab.f90 commit 2a022aeeecf4543c69035304c52e15d60cd1322c Author: lijewski Date: Thu Aug 12 17:18:03 2010 +0000 OpenMP'd div_div routines Src/F_BaseLib/multifab.f90 commit dd061d14688fb697331dad4326dad3e1d1372e17 Author: lijewski Date: Thu Aug 12 16:06:17 2010 +0000 some code simplification Src/F_BaseLib/multifab.f90 commit d0b938b646b8f792e12a847850df1039e9a5df28 Author: ajnonaka Date: Thu Aug 12 13:47:07 2010 +0000 -O for franklin, -Ofast for everyone else, regardless of what the OMP flag is set to Tools/F_mk/comps/Linux_pathscale.mak commit d311f9fdd6c8bacfafd15b44d2aec9ae30040db1 Author: gpau Date: Thu Aug 12 00:12:50 2010 +0000 *** empty log message *** Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNorm.cpp commit 36dda58ddc03e71b0de2da4f333fef607b7bb782 Author: gpau Date: Wed Aug 11 22:46:45 2010 +0000 added multilevel support for visc_coefficients Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 32e16bbd4486b6677142ad7ee0d37a6ab808ac95 Author: mzingale Date: Fri Aug 6 19:31:13 2010 +0000 update to new file and dir locations Tools/C_util/regtests/Maestro-tests.ini commit 9f4f4f239e9932cfc149559e36206111bdc4e97d Author: lijewski Date: Thu Aug 5 15:53:24 2010 +0000 compiles now Tools/C_util/Convergence/DiffSameGrid2.cpp commit 1ddaf92208e99c4d246283ad92cb933cd98ce7e8 Author: mzingale Date: Tue Aug 3 15:32:19 2010 +0000 add support for NYBlue -- note, now we do COMP=xlf Tools/F_mk/comps/xlf.mak commit 05305f69f88463b70fe38864d8847c332d0c975d Author: almgren Date: Fri Jul 30 23:25:33 2010 +0000 rho_xy,rho_yz,rho_xz were not being used. Src/LinearSolvers/C_CellMG/ABec_3D.F commit 0b47a14740f9bc5e706da0a019e2fb986297c057 Author: almgren Date: Fri Jul 30 21:41:06 2010 +0000 Fix an oops. Src/C_AMRLib/INTERP_1D.F commit 8ba0e33ed5ae2492c8ac7974e82b51637cae5535 Author: almgren Date: Thu Jul 29 16:33:28 2010 +0000 Reused "actual_state" twice, first should have been "actual_comp" Src/C_AMRLib/INTERP_F.H commit 63ebb521ed0627e1d9be9bb97303da6a50c499f1 Author: almgren Date: Wed Jul 28 01:21:08 2010 +0000 Fix another oops. Src/C_AMRLib/INTERP_2D.F commit 0a5212ffa665ddcbc3e59f605bfe0467b427d2bc Author: almgren Date: Wed Jul 28 01:17:57 2010 +0000 Typo before. Src/C_AMRLib/INTERP_2D.F commit 5da7ef1415421455932c77088b9054e1a141e91c Author: almgren Date: Wed Jul 28 01:07:23 2010 +0000 Pass actual_comp and actual_state to the Fortran interp routines, through the Interpolater::interp(...) routines. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit 7eef840d7ff3be3d0735e74897ca43c7717e5adc Author: gilet Date: Wed Jul 28 00:50:55 2010 +0000 Change MPIHOME for orga so things work again Tools/F_mk/GMakeMPI.mak commit 182ad6ea343867e02823686becc9856f75d769c2 Author: almgren Date: Mon Jul 26 23:56:09 2010 +0000 Moved ml_fill_all_fluxes back from mg_cpp.f90 into stencil.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 7149216fbe4d7a9597a2b1b695a7bb118ea4f507 Author: almgren Date: Mon Jul 26 16:54:04 2010 +0000 Start to put use_hypre option in. Src/LinearSolvers/F_MG/mg.f90 commit 740eec39971ac2c72f42d20ad4bbfcb7f1bf2d3c Author: lijewski Date: Fri Jul 23 23:14:46 2010 +0000 some g++ and gfortran mods Tools/C_mk/Make.defs commit 5e2d59fbbe28cfe3237c5f0da7f2c2dfbf3f594b Author: lijewski Date: Fri Jul 23 18:21:28 2010 +0000 some cleanup prompted by gfortran -Wall Src/F_BaseLib/interp.f90 Src/F_BaseLib/list_box.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 commit 0f17e775671c71478b23a2db32886619ac78605e Author: lijewski Date: Fri Jul 23 17:00:40 2010 +0000 add -fopenmp if OMP Tools/F_mk/comps/gfortran.mak commit 79a1001d7e973e427167b3737477a50c8e3b1c1c Author: almgren Date: Fri Jul 23 16:31:01 2010 +0000 Modify to let this work on hicegate0, Wolfram Schmidt's machine. Tools/C_mk/Make.mpi commit 7a8a2bee16c07b604a1399597efd8633f8952293 Author: almgren Date: Fri Jul 23 16:24:28 2010 +0000 Fix the eps stuff we pass in to ml_nd_solve and ml_cc_solve. Src/LinearSolvers/F_MG/ml_solve.f90 commit 2f7936a18bf2653cfd0dd9b630cb02f98261e841 Author: almgren Date: Fri Jul 23 03:19:20 2010 +0000 Fix oops in previous commit. Src/LinearSolvers/F_MG/ml_nd.f90 commit 7c05054a6adb8f5a92c03024bfcef8ba944308c3 Author: almgren Date: Fri Jul 23 03:15:47 2010 +0000 Add print statement if already converged Src/LinearSolvers/F_MG/ml_nd.f90 commit ed11557ec2c1aec65bf9d23aee9c7a80dbab87d9 Author: almgren Date: Thu Jul 22 23:49:52 2010 +0000 Don't force the Intel compilers when MPI is defined. Tools/F_mk/GMakeMPI.mak commit 3123b1083603e4a3dbe32400c66d1e30367e7136 Author: almgren Date: Thu Jul 22 14:34:43 2010 +0000 Removed quotes around included files. Tools/F_mk/GMakedefs.mak commit 49ff4250a5178c834a5d92e6c28c9c3c3f4e742f Author: almgren Date: Wed Jul 21 21:46:16 2010 +0000 Put each compiler's options into a separate file in comps/*.mak Tools/F_mk/GMakedefs.mak commit e1f97d7535667320584b6d065453c7efde4bdce2 Author: almgren Date: Wed Jul 21 21:44:11 2010 +0000 Use this to simplify the makefile system -- these are included in Gmakedefs.mak Tools/F_mk/comps/Darwin_ibm.mak Tools/F_mk/comps/Linux_catamount.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_lahey.mak Tools/F_mk/comps/Linux_nag.mak Tools/F_mk/comps/Linux_pathscale.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/Linux_sunstudio.mak Tools/F_mk/comps/Linux_xt4.mak Tools/F_mk/comps/aix.mak Tools/F_mk/comps/crayx1.mak Tools/F_mk/comps/g95.mak Tools/F_mk/comps/gfortran.mak Tools/F_mk/comps/irix64.mak Tools/F_mk/comps/osf1.mak Tools/F_mk/comps/xlf.mak commit 1999fb539f31adce58de402946fcd8fdaa24eb53 Author: lijewski Date: Wed Jul 21 19:28:28 2010 +0000 fix where to find mpi stuff for my machine Tools/F_mk/GMakeMPI.mak commit 728aab835dc53c1a932cb0af89b01b4277d677cc Author: lijewski Date: Wed Jul 21 19:03:55 2010 +0000 fix for when not all levels defined Src/F_BaseLib/ml_layout.f90 commit fb82cda7c5fe551dd0a939b07b9f00da4cf8ac27 Author: almgren Date: Tue Jul 20 21:35:12 2010 +0000 Need this to compile from C++ Src/LinearSolvers/F_MG/mg_cpp.f90 commit ce298b90068d9c966f3c75d68cfe5711c78d777f Author: almgren Date: Tue Jul 20 20:59:33 2010 +0000 Use local form of dnrm2 so we don't have to link with LAPACK. Src/LinearSolvers/F_MG/sparse_solve.f90 commit 8ddfbabbaca025cdf1fd2c2223d4f69dde378afd Author: almgren Date: Tue Jul 20 19:58:40 2010 +0000 More clean-up of use modules... Src/LinearSolvers/F_MG/ml_solve.f90 commit 2d387426775bca1f50399c5ce24cc0995197390a Author: almgren Date: Tue Jul 20 19:56:50 2010 +0000 More clean-up... Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit e16c8a885900e2023206bf6ceb220a7db5836c14 Author: almgren Date: Tue Jul 20 19:54:26 2010 +0000 Clean up "use" statements. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit 4125108dff9cd5739b3db75e666048d983e14888 Author: almgren Date: Tue Jul 20 19:35:22 2010 +0000 Moved ml_fill_all_fluxes from ml_util into mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit bdd0edb444d759ab87b61beee8bc0886382d2d75 Author: almgren Date: Tue Jul 20 19:32:44 2010 +0000 No more mlmg.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak commit fa20e42e02fad65a211a2b3c8eaddaef207d9690 Author: almgren Date: Tue Jul 20 19:22:48 2010 +0000 Fix oops. Src/LinearSolvers/F_MG/ml_nd.f90 commit 2c17475397fd126f44e3bc29b26232c114c7a8e0 Author: almgren Date: Tue Jul 20 19:03:17 2010 +0000 Fix oops... Src/LinearSolvers/F_MG/ml_nd.f90 commit 9c51d17459012909715cbea09ca212312b357cdf Author: almgren Date: Tue Jul 20 19:00:09 2010 +0000 Moved grid_res into ml_nd. Src/LinearSolvers/F_MG/mg.f90 commit 8540e67fbd021a9ceb69c19a3fbbb6d704548730 Author: almgren Date: Tue Jul 20 18:59:07 2010 +0000 Move files from mg_defect.f90 (which no longer exists) into ml_nd.f90 Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/ml_nd.f90 commit af62c2a6625b9cb26c5d163fa84bd4247f5f3e84 Author: almgren Date: Tue Jul 20 17:59:52 2010 +0000 Renamed eps --> rel_eps Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 7df677b2803601d99b44ee103f6bf3b0dd744a23 Author: almgren Date: Tue Jul 20 03:31:20 2010 +0000 Add eps_in as optional argument to ml_cc_solve. Src/LinearSolvers/F_MG/ml_solve.f90 commit 3ebe992b7dd776ec7294870ae59f27d272e4829d Author: almgren Date: Mon Jul 19 22:11:17 2010 +0000 Need to remove "pure" to compile with Intel 10.1 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 commit 6cbff8c358d94e48e0519098183c84f76a12fc71 Author: almgren Date: Mon Jul 19 20:46:04 2010 +0000 Change the print statement: MPI initialized with xx CPUs to MPI initialized with xx MPI Processes since they are no longer the same with threading. Src/C_BaseLib/BoxLib.cpp commit 0e986e3f27f686607701c6e86fd84f70f52bf19d Author: lijewski Date: Mon Jul 19 20:09:44 2010 +0000 some cleanup including making functions with no side-effects pure Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/sort_d.f90 Src/F_BaseLib/sort_i.f90 Src/F_BaseLib/tag_boxes.f90 Src/F_BaseLib/vector_i.f90 commit d52881e16017bfdc509c0ba15290fe209a30d9ae Author: almgren Date: Mon Jul 19 19:40:08 2010 +0000 Change default for max_iter from 20 to 50. Src/LinearSolvers/F_MG/mg_tower.f90 commit 73921a01dbb428b4b2b377cb9198c35ae4fe0d74 Author: almgren Date: Mon Jul 19 18:14:02 2010 +0000 Make the default for RANGER be for PGI so we don't need the special intel stuff. Tools/C_mk/Make.mpi commit 5bf1381b920178417acaddc5163a4d9d3cfbd992 Author: almgren Date: Mon Jul 19 18:10:08 2010 +0000 Works now for ranger. Tools/C_mk/Make.Linux commit f19073ec4aaff4052066d1301442dee4325cadc7 Author: lijewski Date: Mon Jul 19 16:56:47 2010 +0000 mods in preparation for making the components of multifabs private Src/LinearSolvers/F_MG/ml_nd.f90 commit dee2a81b165036d7866b19608f111a55df4e908b Author: lijewski Date: Sat Jul 17 00:51:01 2010 +0000 mods to quiet gfortran std=f95 warnings Src/F_BaseLib/fabio_c.c Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/system_util_c.c Src/LinearSolvers/F_MG/stencil_nodal.f90 commit d30ef740088d89f5b9b9602f9a380485bcb56c81 Author: lijewski Date: Sat Jul 17 00:05:27 2010 +0000 mods in preparation of making the components of multifabs private Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 6e573cd66d5e190975f813d7af470da3639383aa Author: lijewski Date: Thu Jul 15 20:29:51 2010 +0000 the components of type fab are now private and only accessible via function calls Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 34135e109867778279a34943dcd97cc4ba52a572 Author: almgren Date: Thu Jul 15 04:01:29 2010 +0000 Add Amr::blockingFactor (int lev) which returns blocking_factor[lev]. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 788d861073f285ad4231fff8aa5b6c2418605cf0 Author: lijewski Date: Wed Jul 14 23:27:45 2010 +0000 the components of type boxarray are now private and only accessible via function calls Src/F_BaseLib/box.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/list_box.f90 Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 42828dd5975ec1c33c9590fdd58ff2782d3be001 Author: lijewski Date: Wed Jul 14 20:16:18 2010 +0000 made get_dim() a pure function Src/F_BaseLib/box.f90 commit 8711b2bbe9cc4d0d72ed102b4e1377392bd0c02f Author: lijewski Date: Tue Jul 13 22:16:48 2010 +0000 made component types private Src/F_BaseLib/bl_stream.f90 commit 5c7264fa69d3257cab3163d2b6144a6c1fbae54c Author: lijewski Date: Tue Jul 13 21:22:53 2010 +0000 made a couple module variables private Src/F_BaseLib/plotfile.f90 commit cee2ecb7f6caef452c7a79ca88f7f9ebe1e2cb43 Author: lijewski Date: Tue Jul 13 21:22:33 2010 +0000 removed pingpong.f90 Src/F_BaseLib/GPackage.mak commit 0cef45f0bdaefdd7b2d34466607c43f35027e3d5 Author: lijewski Date: Tue Jul 13 21:15:56 2010 +0000 made sfc_greater_i() private Src/F_BaseLib/knapsack.f90 commit 08ab0e512d3d5df3ded07a0af3bd103899a5f577 Author: lijewski Date: Tue Jul 13 21:04:17 2010 +0000 made a module variable private Src/F_BaseLib/bl_timer.f90 commit fa588b7c587d85f524d621b2c70c8fee733bfb85 Author: lijewski Date: Tue Jul 13 20:58:19 2010 +0000 removed unused module variables and made others private Src/F_BaseLib/bl_IO.f90 commit 7bdfb9ebed8aa8eb2f38073d02bae45b6cb77dc7 Author: lijewski Date: Tue Jul 13 20:50:49 2010 +0000 removed unused module variable Src/F_BaseLib/box.f90 commit c7ef4b2c7f66ea61ab7eedad817589ed6f5ebe99 Author: lijewski Date: Wed Jun 30 22:50:53 2010 +0000 only call simplify() if too few grids Src/C_AMRLib/AuxBoundaryData.cpp commit 0b9ee5106f014b9c8371646853bbbfb001bf73f8 Author: lijewski Date: Wed Jun 30 22:35:46 2010 +0000 add back in KnapSack to initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit 850d35968b9ed22d987c643f1e390a0f7fc2cb4c Author: lijewski Date: Wed Jun 30 22:16:36 2010 +0000 do a maxSize() after the simplify() in initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit 76606b0813833eb10ae279f445875a49bce2dc05 Author: lijewski Date: Tue Jun 29 20:19:45 2010 +0000 sped up boxlist_simplify() and boxarray_simplify() Src/F_BaseLib/list_box.f90 commit bbddffd6bbebb7f196e9f23dba8942d58c829a2c Author: ajnonaka Date: Tue Jun 29 15:25:44 2010 +0000 changed the plot_per functionality to print the plotfile *after* you pass plot_per, rather than before. This matches the MAESTRO functionality and also prevents the code from printing two plotfiles in a row at the end of a simulation. Src/C_AMRLib/Amr.cpp commit 79e7714a5caf9a7097c45df7e73b56bcdead2c71 Author: lijewski Date: Mon Jun 28 20:44:24 2010 +0000 do NOT force the use of KnapSack in initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit 2a0d24c3f3b363f951865f372effe0f99f35d38a Author: lijewski Date: Mon Jun 28 18:25:12 2010 +0000 initialize() now calls GetBndryCells() Src/C_AMRLib/AuxBoundaryData.cpp commit e84a86abf8d94442f1465db3d443395477eb80ec Author: lijewski Date: Mon Jun 28 18:24:45 2010 +0000 make better use of faster simplify() in GetBndryCells() Src/C_BaseLib/BoxArray.cpp commit e4b3a2caf580e875be5b71f2bdc689cc54dec2ee Author: lijewski Date: Mon Jun 28 17:43:50 2010 +0000 call simplify() at end of GetBndryCells() Src/C_BaseLib/BoxArray.cpp commit d787f94e3ac07470a191e54f04415f374e7fed76 Author: lijewski Date: Mon Jun 28 17:33:48 2010 +0000 users can choose the best simplify() or the fast one Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 339b28e070357b83c4a849f93a175069514a0807 Author: lijewski Date: Mon Jun 28 16:17:48 2010 +0000 limit how far afield we look for abutting boxes in simplify_doit() Src/C_BaseLib/BoxList.cpp commit 8ba9c0df4372ca74331606af276308a88cad4f86 Author: vince Date: Fri Jun 25 22:36:07 2010 +0000 added some diagnostics and a sync. Src/C_BaseLib/VisMF.cpp commit 57ebb28de9210a20404206623e722c3b0a5f6b85 Author: lijewski Date: Wed Jun 23 22:02:06 2010 +0000 use std::fabs() instead of std::abs() in a couple places Src/C_BaseLib/FArrayBox.cpp commit b9225915e5a080d13588e44408bf26d1f4c9f212 Author: almgren Date: Sun Jun 20 00:47:24 2010 +0000 Get rid of daxpy.f and ddot -- these are in BLAS... Src/LinearSolvers/F_MG/FParallelMG.mak commit bddf8a447488b83e742000ddbca6bbb7f9eec011 Author: almgren Date: Sun Jun 20 00:23:19 2010 +0000 Change the interface for set_mac_coefficients, set_visc_coefficients, set_porous_coefficients so we don't have to pass a MacBndry, instead we pass xa and xb directly. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 4e14c2a0485e7df56a72fedc8a399f0ea5a7c350 Author: almgren Date: Sun Jun 20 00:15:07 2010 +0000 Add these files so we can stop including the Make.package from LAPACK, SPARSKIT and BLAS. Hope this works! Src/LinearSolvers/F_MG/FParallelMG.mak commit d693dae62f40e12cda0ad013ef2519b055b168ef Author: lijewski Date: Fri Jun 18 22:22:05 2010 +0000 more refinement of refine_grid_layout Src/C_AMRLib/Amr.cpp commit 7ad1715ec5a91c653119bbf088fc1ee3ad06edfb Author: lijewski Date: Wed Jun 16 20:49:27 2010 +0000 Attempt to minimize the number of new grids built in refine_grid_layout by refining each dimension at a time until we've got more than NProcs grids. Src/C_AMRLib/Amr.cpp commit 348af522e515bd8218f6907706c599a2c47ff527 Author: lijewski Date: Wed Jun 16 20:17:55 2010 +0000 added version of maxSize() taking an IntVect to mirror the version in BoxList Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 046b1e51d79b801856f1252cb52a770e889f7cc8 Author: almgren Date: Fri Jun 11 19:48:58 2010 +0000 Add kiryu. Tools/F_mk/GMakeMPI.mak commit c2a8bbd3c8a3a557b2a6c76b2b3a2d08ec6810f5 Author: marc Date: Thu Jun 10 20:29:13 2010 +0000 Mods for marcs account on the TUe computer Tools/C_mk/Make.mpi commit f6c9308127ccd617425a1efec151a868454b244b Author: almgren Date: Thu Jun 10 00:34:46 2010 +0000 Remove unused variable. Src/LinearSolvers/F_MG/ml_cc.f90 commit cbb0f20b8aeb80bc98cf1678d19160b1073106d0 Author: almgren Date: Wed Jun 9 19:59:36 2010 +0000 Modified amr.regrid_int so that we only need max_level values of it (instead of max_level+1), and we don't need it at all if max_level = 0. Also add print statement that says "Successfully read inputs file" (analogous to "Successfully read probin...") Src/C_AMRLib/Amr.cpp commit 38ac663f514bd375a83b3d7da9bf45ac3759ae5e Author: mzingale Date: Wed Jun 9 16:57:12 2010 +0000 update to allow for the cvs updates to work when fParallel is not in the top level directory Tools/C_util/regtests/test.py commit 6e8f1870bca3c285092dac67156d38f94dc6283c Author: gpau Date: Wed Jun 9 16:56:26 2010 +0000 added an optional argument for Reflux function that allows the flux to be multiplied by a fixed value regardless of the face direction. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit ca00a6b5496c068199be318ca81ee13961aa50fc Author: mzingale Date: Wed Jun 9 00:48:16 2010 +0000 remove the old NMake stuff Tools/F_mk/NMakedefs.mak Tools/F_mk/NMakerules.mak commit 64039fdd74a70df9e56e160a5f2793fa5b512ba9 Author: almgren Date: Tue Jun 8 21:34:32 2010 +0000 Dont maintain NPackage.mak anymore. Src/F_BaseLib/NPackage.mak commit 8e364fda454711bf4a13e39ff0f44bef9aa808ce Author: ajnonaka Date: Tue Jun 8 20:05:38 2010 +0000 back of compiler optimization for franklin with pathscale and openmp. -Ofast won't even compile so going back to -02 Tools/F_mk/GMakedefs.mak commit 8f0d8ce7c287f3b5da43813c7e077ea36da52d8b Author: almgren Date: Mon Jun 7 19:59:39 2010 +0000 Remove unused variable. Src/LinearSolvers/F_MG/stencil.f90 commit dc30d85e35f0b756d44eccd8e93fa323f5c2141d Author: ajnonaka Date: Mon Jun 7 19:41:23 2010 +0000 added a .MAESTRO to the executable suffix list if we are building with USE_MAESTR_INIT=TRUE Tools/C_mk/Make.defs commit b0a7103432e1c2d4ba250704a816ede089361d2f Author: almgren Date: Sun Jun 6 20:07:22 2010 +0000 Fix this. Src/LinearSolvers/F_MG/FParallelMG.mak commit d8c278dbe35f429eb0bd90c6d8981a5c9cf47503 Author: gpau Date: Sat Jun 5 02:10:53 2010 +0000 updated to handle new operator Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit fb7fd70eda0e8febae4218e68f5ca902ac40ae1b Author: gpau Date: Sat Jun 5 02:06:46 2010 +0000 updated to handle new operator. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit d496158231ce305b9ead559f82d9cf3b0c25412a Author: adonev Date: Fri Jun 4 23:16:23 2010 +0000 Added host angilas Tools/F_mk/GMakeMPI.mak commit baf8ffd5b2ce0af830890f70899bf2e23224c288 Author: almgren Date: Fri Jun 4 21:42:45 2010 +0000 Latest ... Docs/BoxLib/boxlib.tex Docs/paper.tex commit 5dca9c30819f24ef328b9191f4b4572adaac77f6 Author: almgren Date: Fri Jun 4 21:39:28 2010 +0000 We just keep making it better... Docs/BoxLib/boxlib.tex commit 3a80fcf4c01f88457385838a8c62418c3acb5884 Author: almgren Date: Fri Jun 4 21:39:15 2010 +0000 These are just the framework for building the docs. Docs/GNUmakefile Docs/paper.tex commit cc1d3f4793c64394494f2a44cb251c0f52ed4180 Author: almgren Date: Fri Jun 4 21:16:00 2010 +0000 Copied from MAESTRO/docs/architecture then modified. Docs/BoxLib/GNUmakefile Docs/BoxLib/boxlib.tex Docs/BoxLib/data_loc.odg Docs/BoxLib/data_loc2.eps Docs/BoxLib/index_grid.odg Docs/BoxLib/index_grid2.eps Docs/BoxLib/mac.odg Docs/BoxLib/mac2.eps Docs/BoxLib/maestro_directory.odg Docs/BoxLib/maestro_directory2.eps Docs/BoxLib/paper.tex commit 5dd18f376cbd9ef04222947facef95d306c161ac Author: almgren Date: Fri Jun 4 21:15:33 2010 +0000 For now this holds the copyright info. Docs/preface/preface.tex commit 099cdb05068cf6e5e17ca9ab4c862cf5661cce7f Author: ajnonaka Date: Fri Jun 4 17:14:31 2010 +0000 works now for array of regrid_int's Src/C_AMRLib/Amr.cpp commit 0c4fe056d1bcc53ac4bb657966a268464eb00489 Author: almgren Date: Thu Jun 3 20:22:07 2010 +0000 Turns out regrid_int was being stored as an array over nlevels but was only being read in as a single integer which was assigned to all levels. Now we have the option of reading in a single integer for all levels or an array (nlevels long) of values. Src/C_AMRLib/Amr.cpp commit 67364655bf30582d19ba4534217b2ad21ec9443d Author: lijewski Date: Wed Jun 2 19:49:57 2010 +0000 added stuff for ORANGE Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 796f5be1eff57f06e8653144fa1e5d03c9ecfa4f Author: lijewski Date: Wed Jun 2 02:59:42 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit d24636fef3e83adb3624b5782d317f3a6cec6aba Author: lijewski Date: Wed Jun 2 02:43:50 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit da3dbedefc31eefb290739a16bdbe25a30731b9c Author: lijewski Date: Wed Jun 2 02:33:28 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 093e73801ef65ce0f8ff4f1051e1f9422a0284e1 Author: lijewski Date: Wed Jun 2 02:15:41 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 1bc676136872c55ad99cdb8971705757e07627ee Author: lijewski Date: Wed Jun 2 02:00:01 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/mg.f90 commit 7da8fcc38530241f5fc22c91078956dae50d3a3e Author: lijewski Date: Wed Jun 2 01:49:57 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 6c9509ea865fb99824aaea604a5b6f9f92e82499 Author: lijewski Date: Wed Jun 2 01:25:23 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/mg.f90 commit d9ee3cde690bde9a8c6bff3efe06172673385d48 Author: ajnonaka Date: Wed Jun 2 00:53:13 2010 +0000 backing out of a previous change which mysteriously breaks the multigrid on Ann's and my machine Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit b17daf618a518c4d784a97ebe338ddbc6973fa3c Author: vince Date: Tue Jun 1 21:50:06 2010 +0000 paths for kiryu. Tools/C_mk/Make.mpi commit 97c00579d2800134e8f6c61075035a35f5cce3d7 Author: almgren Date: Mon May 31 19:40:23 2010 +0000 Modify the amr.verbose > 1 option so that it calls printGridSummary instead of not printing any grid info. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit d861b22d9b94cfb924ceb8c866408c60bae2ba6d Author: almgren Date: Mon May 31 18:33:06 2010 +0000 Replace "verbose" by "verbose > 0" in most cases, but "verbose > 1" in cases which controlled a call to printGridInfo. Src/C_AMRLib/Amr.cpp commit 4b4a0325a4f3bcf5b4bb6dfd12ef983e6e9fe51d Author: lijewski Date: Mon May 31 15:52:09 2010 +0000 plugged memory leak Src/F_BaseLib/cluster.f90 commit 30108129b510a6809d3f4e701bd229a0c77eae10 Author: almgren Date: Mon May 31 03:38:54 2010 +0000 Add checkpoint_on_restart flag which only happens if doing regrid_on_restart. Src/C_AMRLib/Amr.cpp commit 93687b24aad98b03afc9d47818c1a0ed1ee6f245 Author: almgren Date: Mon May 31 03:29:16 2010 +0000 Fix indentation. Src/C_AMRLib/Amr.cpp commit 4e70f27ab274d4d55330fc0545cc0eeaf047368b Author: almgren Date: Sun May 30 23:07:43 2010 +0000 I believe that this version of cluster correctly uses blocking_factor when making grids, both in serial and in parallel. It works for a simple 2d test in varden anyway. Src/F_BaseLib/cluster.f90 commit e3b3f021e2bdc6da304dfeefc5481e4a4a7bbc82 Author: lijewski Date: Fri May 28 23:39:28 2010 +0000 removed some unused variables Src/F_BaseLib/pingpong.f90 commit 7c184483c573ea7e3d65c5028e1602d3d8de9492 Author: lijewski Date: Fri May 28 23:31:09 2010 +0000 cleaned up some unused variables Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 8977241f6d3f6ec5920550e170dedcd2e6ed8bb6 Author: lijewski Date: Fri May 28 21:58:13 2010 +0000 removed some unused variables Src/F_BaseLib/box_util.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bx.f90 Src/F_BaseLib/test/t_bxasc.f90 Src/F_BaseLib/test/t_cls.f90 Src/F_BaseLib/test/t_knapsack.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bx.f90 Tests/F_BaseLib/t_bxasc.f90 Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_knapsack.f90 Tests/F_BaseLib/t_main.f90 commit 7a0e000e6374bba9e58677ad878e2526505fe083 Author: lijewski Date: Thu May 27 22:23:32 2010 +0000 moved tagboxes_coarsen() from tag_boxes.f90 -> cluster.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/tag_boxes.f90 commit 33756cc9b71e6af0a5a7e4b4685270f69c4aabfd Author: lijewski Date: Thu May 27 22:16:30 2010 +0000 bit more cleanup Src/F_BaseLib/tag_boxes.f90 commit 27bd8a1f1616fb8c8ec118cd75d524550ea274d6 Author: lijewski Date: Thu May 27 22:15:02 2010 +0000 got rid of some unused variables Src/F_BaseLib/make_new_grids.f90 commit fd083b1c8b22932792754427fad135a65e73d76d Author: lijewski Date: Thu May 27 22:13:57 2010 +0000 tagboxes_coarsen() appears to work Src/F_BaseLib/tag_boxes.f90 commit 5744a7408e36a7d67b954dfff43ec34891ab7f7e Author: lijewski Date: Thu May 27 21:37:55 2010 +0000 initial cut of tagboxes_coarsen(); compiles but hasn't been tested Src/F_BaseLib/tag_boxes.f90 commit c43127d3118b5c4583fd97e49c590b239ca6ff03 Author: lijewski Date: Thu May 27 16:32:50 2010 +0000 now compiles again after recent code changes Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bxasc.f90 Src/F_BaseLib/test/t_cls.f90 Src/F_BaseLib/test/t_knapsack.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bxasc.f90 Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_knapsack.f90 Tests/F_BaseLib/t_main.f90 commit 0ca1a46d70ad73a80ccb2ba1595ecdb27c5ef53e Author: almgren Date: Wed May 26 03:25:12 2010 +0000 SPARSKIT stuff needs ddot which is now in BLAS. Src/LinearSolvers/F_MG/GPackage.mak commit 9e1e9456d505b48241cc1575031799b770506e7a Author: almgren Date: Wed May 26 00:47:58 2010 +0000 Replace a comma by a semicolon so we now compile again with USE_MPI = TRUE. Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp commit 52c132c39accd505eed78a930e224a25817fab0f Author: almgren Date: Tue May 25 21:56:21 2010 +0000 One more fix... Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit 21c3832b996919c9d8960e21598c32ef80b07402 Author: almgren Date: Tue May 25 21:47:45 2010 +0000 Try again... Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit 8e63620e554cd3f95d2a99dc9944f92be90e05e4 Author: almgren Date: Tue May 25 21:39:24 2010 +0000 Fix mistakes. Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit 3db71d39d3a3da01daefa3945ce091e0e418608c Author: almgren Date: Tue May 25 21:24:14 2010 +0000 Allow different number of state variables. Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit 2e9a4eb810b7b665af19ce7c712b832e96f90d4b Author: almgren Date: Tue May 25 21:12:18 2010 +0000 If nComp differs then choose the min of the two files. Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit e2d9b789aa3ac9ebbd2b9b55f3a56c9f0f07a6fc Author: almgren Date: Tue May 25 19:09:30 2010 +0000 Fix countval arguments. Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp commit ecd832be75d8779c842549b6553440d3262f9cc5 Author: almgren Date: Tue May 25 19:08:24 2010 +0000 This version is derived from DiffSameGridRefined but does *not* require that the two plotfiles have the same boxarray at each level being compared, only that they have the same region of space covered. We do a multifab copy to fill a boxarray at the coarse resolution instead of comparing directly to the multifab in the plotfile. Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit 692e6f93bea1d3e4586231b3bd49afb72d316ea9 Author: mzingale Date: Tue May 25 00:28:36 2010 +0000 also store the compilation flags in the job_info file. That should pretty much cover it all. Tools/F_scripts/make_build_info commit a3013dd3d1190b95820ab62310f7579292a26f5a Author: mzingale Date: Sat May 22 18:26:58 2010 +0000 allow for the list of modules to be longer, but we need to break it over 2 lines in the source to get it to compile. Tools/F_scripts/make_build_info commit 37aebea02f2959bf72452e03a4d87034c5c554e2 Author: mzingale Date: Fri May 21 23:13:57 2010 +0000 get Castro building again -- daxpy and ddot are not in this directory Src/LinearSolvers/F_MG/FParallelMG.mak commit 9bdffb47f8122b40d6206d52f01d3a3074140c06 Author: almgren Date: Fri May 21 22:36:02 2010 +0000 Remove unused variable. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 4a912254ab8a6ae5d60ee11dcea3ee4583cc88f2 Author: mzingale Date: Fri May 21 18:59:26 2010 +0000 comment tweaks Tools/F_scripts/make_build_info commit 06547fc74e444188e92fdc27b8dab05478b2f53a Author: mzingale Date: Fri May 21 17:20:07 2010 +0000 change how build_info works. It is now a module (which is safer for the string length matching) and therefore, it now needs to be detected by the moddep.pl script, so the dependences in GMaestro.mak are updated. This seems to work. When you recompile, it rewrites build_info.f90 and recompiles it (as we want). Note that now build_info.f90 is deleted once it is built. Tools/F_scripts/make_build_info commit 9eab2efdd162a158c18272639e9af3c3328da823 Author: mzingale Date: Thu May 20 23:50:48 2010 +0000 fix a line-length issue -- should really wrap the modules line Tools/F_scripts/make_build_info commit 5d871a112220ba873e969ac4fca951cdf1d9a35d Author: mzingale Date: Thu May 20 22:10:41 2010 +0000 store the list of "modules" (e.g. reaction network, EOS, ...) compiled into the code in the job_info file. Tools/F_scripts/make_build_info commit b14bf4c6b2afca87359ca4386985f010faf8dd3a Author: mzingale Date: Thu May 20 19:52:54 2010 +0000 move the stuff that makes build_info.f90 out of the general mk/ stuff and into GMaestro.mak, since this is only used by Maestro. This will give us more control over it. Tools/F_mk/GMakerules.mak commit 398f8bc1d404af9d4dc886e4caa02fdf47a47720 Author: ajnonaka Date: Mon May 17 22:46:49 2010 +0000 OMP fix Src/LinearSolvers/F_MG/itsol.f90 commit d4f3cd5e7ed10651d26ced1f38e3ccc1312970f4 Author: almgren Date: Sat May 15 01:12:56 2010 +0000 Fix the way max_bottom_nlevel is handled. Src/LinearSolvers/F_MG/mg.f90 commit 9b8352d8e8bec1df997a95694f82972f0632591e Author: lijewski Date: Fri May 14 18:06:17 2010 +0000 intel icc does not support -fltconsistency :-( Tools/F_mk/GMakedefs.mak commit 333ec4ce7edf27030c569f2a932fe50a2a5cfb21 Author: ajnonaka Date: Thu May 13 17:00:07 2010 +0000 amr.plot_per and amr.check_per now do not alter the time step, and print the plot/check file immediately before you hit the period you specify Src/C_AMRLib/Amr.cpp commit 662f7d6b96f62a70aaea4bf03e20262877a14f36 Author: lijewski Date: Wed May 12 22:19:16 2010 +0000 removed omp.f90 and omp_stubs.f90 Tests/LinearSolvers/F_MG/cc_single.f90 Tests/LinearSolvers/F_MG/nodal_single.f90 commit 4ec2f8ae6d196d231f9efe0799ccc0695c0808a4 Author: lijewski Date: Wed May 12 22:19:08 2010 +0000 removed omp.f90 and omp_stubs.f90 Src/F_BaseLib/GPackage.mak Src/F_BaseLib/NPackage.mak Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/tag_boxes.f90 commit 97a509648d7e119224eab8e02fc249eec72b08a8 Author: lijewski Date: Wed May 12 22:16:08 2010 +0000 not needed Src/F_BaseLib/omp.f90 Src/F_BaseLib/omp_stubs.f90 commit 6853a906811534207243f11d714043121c0371e7 Author: lijewski Date: Wed May 12 21:18:43 2010 +0000 removed boxlist_intersection() for boxes and boxlists -- not needed anywhere Src/F_BaseLib/list_box.f90 Src/F_BaseLib/test/t_knapsack.f90 Tests/F_BaseLib/t_knapsack.f90 commit feba6340057cf6285ae731850f77b987d24127e4 Author: lijewski Date: Wed May 12 20:48:04 2010 +0000 removed some unused drek Src/F_BaseLib/box.f90 commit f0150d03bbd42c88f96056f255b4bc6eb59ad3d1 Author: lijewski Date: Wed May 12 20:35:26 2010 +0000 removed some unused drek Src/F_BaseLib/boxarray.f90 commit 8373fbf06a8ce92be1a2c3aec7e4cc88209e4d62 Author: almgren Date: Wed May 12 18:05:46 2010 +0000 Put print statements before and after reading probin so that we can tell if we die there -- dying while reading probin always just gives an Abort with no error message, so this at least lets you know you are there. Only prints with amr.v >= 1. Src/C_AMRLib/Amr.cpp commit da24461fca0b3f91e0e9ff30dc2607fec2767df0 Author: lijewski Date: Wed May 12 16:45:22 2010 +0000 removed aveassoc stuff - no longer used by average.f90 Src/F_BaseLib/layout.f90 commit 7fb05cd8e80a614a87630455bca148480783e17e Author: lijewski Date: Wed May 12 16:29:17 2010 +0000 removed mcc stuff -- SFC is the way to go Src/F_BaseLib/knapsack.f90 commit a3dfadda908b890441df9f81af05042e4dc2da97 Author: almgren Date: Tue May 11 02:16:20 2010 +0000 Fix comment for subroutine mg_defect. Src/LinearSolvers/F_MG/mg.f90 commit 24c42c0cd5f53e6ddbfb83fef2f37657e12b04d8 Author: marc Date: Fri May 7 22:19:03 2010 +0000 Add support for euclid at nersc Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit c8fd80077ee1bf65a9323e6dd3900ced383bc44d Author: almgren Date: Fri May 7 20:44:26 2010 +0000 Add one line of comment... Src/LinearSolvers/F_MG/mg.f90 commit cd3c9b4a8fccbe5ca7ee54a2251e6331ad5adc0d Author: almgren Date: Fri May 7 20:13:52 2010 +0000 Fix print statement for convergence. Src/LinearSolvers/F_MG/ml_nd.f90 commit 5b8bcbd632c01564c9197eb8c8900e0e0cee44f5 Author: almgren Date: Fri May 7 20:04:03 2010 +0000 Change in what is printed, not what is done. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 16ce697823de7423dce3408e1d278e8355fc8a4d Author: lijewski Date: Fri May 7 16:31:20 2010 +0000 added assert to make sure folks don't ask for more grow cells than they have valid region Src/C_BaseLib/Geometry.H commit c87e04fd013c3d0e60924dac339dc85a47661688 Author: almgren Date: Thu May 6 20:31:13 2010 +0000 1) Do singular adjustment for cell-centered as well as nodal. 2) Set solution to zero if rnorm > bnorm at end of bicg. Src/LinearSolvers/F_MG/itsol.f90 commit ec2ec4df21b39851c5d58a7875838d04e70f798c Author: almgren Date: Thu May 6 01:59:20 2010 +0000 More clean up -- also adding mgt%st_type as a member of mg_tower, so we can test on that instead of on ns. Src/LinearSolvers/F_MG/mg.f90 commit 45f3e0df05143d0247adf7028e7dde6970564b7d Author: almgren Date: Thu May 6 01:58:28 2010 +0000 Fix definitions of hi. Src/LinearSolvers/F_MG/mg_smoother.f90 commit a27b9c19ba61ed452f3b239c782f2308c42de781 Author: almgren Date: Thu May 6 01:58:04 2010 +0000 Add st_type as a member of mg_tower. Src/LinearSolvers/F_MG/mg_tower.f90 commit 61a962dcd4a897e9de6c12c96d0454cc5f472ae5 Author: almgren Date: Thu May 6 01:38:58 2010 +0000 Fixes for minion routines plus getting rid of more "stencil" stuff. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil.f90 commit a90cf6261c50c2cf79421a5e142cd67900626436 Author: almgren Date: Wed May 5 21:38:45 2010 +0000 AmrLevel::computeNewDt now takes post_regrid_flag as a final argument. Src/C_AMRLib/AmrLevel.H commit 1859ac414a9658456724460e52611f7e4d04065a Author: almgren Date: Wed May 5 21:38:24 2010 +0000 1) Amr::timeStep now takes stop_time as the final argument. 2) There is a new flag, compute_new_dt_on_regrid (default=0) which, if true, tells the code to call computeNewDt after a regrid with base level 0. This is needed in particular in codes like CASTRO which call an EOS routine to compute the sound speed which is used in computing dt. 3) AmrLevel::computeNewDt now takes an integer flag, post_regrid_flag, which tells the routine whether it is being called after a regrid. If so, then dt_min[i] is "minned" with dt_level[i], rather than change_max*dt_level[i]. Src/C_AMRLib/Amr.cpp commit 431b5542a4f2b3019c1a0c82f1ed689e6c6da4d9 Author: almgren Date: Wed May 5 21:36:11 2010 +0000 Amr::timeStep now takes stop_time as the final argument. Src/C_AMRLib/Amr.H commit c059da7481a52e418ae1da445156223baca40bf0 Author: lijewski Date: Wed May 5 20:17:25 2010 +0000 got rid of some duplicate printing Src/C_AMRLib/Amr.cpp commit 5967f6876766371abb13791077b4b990f58125ab Author: almgren Date: Sat May 1 02:54:58 2010 +0000 Add hypre_libraries to the link line in the right way. Tools/F_mk/GMakedefs.mak commit 41e5d5e58a6f378c869afdfbea668ab9b62f1727 Author: almgren Date: Fri Apr 30 19:48:04 2010 +0000 Need mg_tower.f90 as well as mg.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit 1584ec78b9365a6c2bb1ad37162658ce72fdcfdc Author: almgren Date: Fri Apr 30 19:07:19 2010 +0000 Change the print statements for bottom_solver = 4 Src/LinearSolvers/F_MG/mg.f90 commit 41f46e7eaad43ddf827fece865041c753912443f Author: almgren Date: Fri Apr 30 17:37:46 2010 +0000 Move mg_tower type definition into mg_tower.f90 Src/LinearSolvers/F_MG/mg.f90 commit 8592d1c17f2a5a5a2efe8173d25e4b47b4c85711 Author: almgren Date: Fri Apr 30 17:37:01 2010 +0000 Remove unused mg_tower_v_cycle_c. Src/LinearSolvers/F_MG/mg.f90 commit e1d6094400278ba7b2d16925a8e3737b1a322c8f Author: almgren Date: Fri Apr 30 17:34:52 2010 +0000 Move the definition of mg_tower out of mg.f90 so that we don't have to remake as many files when we play with mg. Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 7c6321fbca7c362685b2ef33952ea181132455da Author: mzingale Date: Fri Apr 30 15:05:03 2010 +0000 no, really add inf... Tools/F_mk/GMakeMPI.mak commit 2498600a6ee5fe904dfb843da69652cfc6f4893a Author: mzingale Date: Fri Apr 30 15:03:55 2010 +0000 add inf Tools/F_mk/GMakeMPI.mak commit e87c6b6e9ec3033352475c363043e0821a1411d6 Author: almgren Date: Thu Apr 29 21:38:05 2010 +0000 Modify print statement to be more similar to Initial error print. Src/LinearSolvers/F_MG/mg.f90 commit b12c4c6c5fc813f1f549a022d389c3ed6aba2be3 Author: almgren Date: Thu Apr 29 21:34:40 2010 +0000 Fix typo in previous commit. Src/LinearSolvers/F_MG/itsol.f90 commit c0fb2504a2bbc58410025b61699326906c9bf879 Author: almgren Date: Thu Apr 29 21:33:37 2010 +0000 Add diagonal preconditioning to the CG solve as well. Src/LinearSolvers/F_MG/itsol.f90 commit 2658461e42b519513ae7deedf3cece1deb8dde79 Author: almgren Date: Thu Apr 29 21:31:45 2010 +0000 1) Add diagnoal preconditioning to the BiCG so that we set a = a/a(:,0) and res = res/a(:,0) before starting to solve -- this reduces the number of BiCG iterations needed. 2) Change convergence test to *only* return true if res < eps*bnorm Src/LinearSolvers/F_MG/itsol.f90 commit 9eb962034101c0c4305f477cc4415adcc7a88edd Author: almgren Date: Thu Apr 29 21:30:27 2010 +0000 Change convergence test to *only* return true if res < eps*bnorm Src/LinearSolvers/F_MG/ml_cc.f90 commit 4346d7728f8e7885757969af12422b5ab7a9a335 Author: almgren Date: Thu Apr 29 21:30:17 2010 +0000 1) Add print statement for Initial(rhs) and Initial(error) 2) Change convergence test to *only* return true if res < eps*bnorm Src/LinearSolvers/F_MG/ml_nd.f90 commit bb677be3aff5b5dbfaffaf9286b25eb8b5a594a0 Author: almgren Date: Thu Apr 29 19:11:16 2010 +0000 Remove itsol_BiCGStab_solve_st, itsol_CG_solve_st, itsol_precon_st -- no one was using these... Src/LinearSolvers/F_MG/itsol.f90 commit b1ca7d3e110d79dcd704938235c6435255a9971c Author: mzingale Date: Wed Apr 28 23:34:43 2010 +0000 mgt_bottom_solver -> mgt%bottom_solver line-wrap some comments Src/LinearSolvers/F_MG/mg.f90 commit 550d8d7a1912717809a4c1223c7e690dc7ffa833 Author: almgren Date: Wed Apr 28 21:47:32 2010 +0000 If we're at a higher AMR level don't create all the bottom_solver stuff. Src/LinearSolvers/F_MG/mg.f90 commit a3a730fe7bc7e3d125dd6c64ededc4fa08261099 Author: ajnonaka Date: Wed Apr 28 13:57:29 2010 +0000 now testing the new email list... Src/LinearSolvers/F_MG/stencil_fill.f90 commit 0903180d7919dedadca00dbe85c889a3068108d4 Author: ajnonaka Date: Wed Apr 28 13:53:36 2010 +0000 FINAL TEST COMMIT Src/LinearSolvers/F_MG/stencil_fill.f90 commit f69567dd24ae4fb063af4626e21fea50b8b188a9 Author: ajnonaka Date: Wed Apr 28 13:52:00 2010 +0000 TEST COMMIT 3 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 3a68e13b4cb0998e84febc72d09e3746d1196d81 Author: ajnonaka Date: Wed Apr 28 13:49:48 2010 +0000 TEST COMMIT 2 (almost done - sorry for the spam) Src/LinearSolvers/F_MG/stencil_fill.f90 commit 6096481bdc8ac01a0ec471e42a1a8d40d70e7ad4 Author: ajnonaka Date: Wed Apr 28 13:46:45 2010 +0000 TEST COMMIT Src/LinearSolvers/F_MG/stencil.f90 commit 3f1915958f73a767c778646dba2bd68119276df8 Author: ajnonaka Date: Wed Apr 28 13:40:49 2010 +0000 commit to test log messages - no changes Src/LinearSolvers/F_MG/stencil.f90 commit 55f4281a2d4fa307fdd1f92995ba4aeb7d9221e0 Author: almgren Date: Wed Apr 28 00:01:43 2010 +0000 If doing XGRAPH stuff (1d) then allow Amr::init to call setPlotVariables so we can use it in the xgraph stuff. Src/C_AMRLib/Amr.cpp commit 83ed0cda0ce522d7ffa84dc9ba702977951d1610 Author: lijewski Date: Tue Apr 27 23:01:54 2010 +0000 plugged memory leaks in bottom_solver==4 Src/LinearSolvers/F_MG/mg.f90 commit e634ad044faa300ea330da6339078533a9105a93 Author: mzingale Date: Tue Apr 27 19:18:31 2010 +0000 add a routine write_a_hgproj_grid to complement read_a_hgproj_grid. This is useful for dumping out a grid structure from MAESTRO for debugging in the test_average problem. Src/F_BaseLib/box_util.f90 commit 1cb4db49970a92f921166186e510e1d60701447a Author: almgren Date: Mon Apr 26 21:26:15 2010 +0000 There was duplication of code that didn't need to be there, inside the bottom solver stuff. Src/LinearSolvers/F_MG/stencil_fill.f90 commit 636e58b4a8870f2638ce959b80df838b977e3b2f Author: gpau Date: Mon Apr 26 19:13:01 2010 +0000 updated the porous stuff Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit b826541bb978c2f22d43dbd4a46e6e9bd87e034a Author: almgren Date: Mon Apr 26 19:10:26 2010 +0000 This version compiles... Src/LinearSolvers/F_MG/mg_cpp.f90 commit 3457b2de9663cb8ca716a96a8a70afa3b5531346 Author: almgren Date: Mon Apr 26 19:00:08 2010 +0000 Fix the definition of nlevel -- it's number of mglevels, not amr levels, when used for cell_coeffs and edge_coeffs. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 8efed4f50b60bed1b6078c6351c434e94e0ad3b7 Author: almgren Date: Mon Apr 26 17:23:07 2010 +0000 st_coeffs --> coarsen_coeffs Src/LinearSolvers/F_MG/FParallelMG.mak commit 41039936b0a6ae149d367ad955b5ce3b72b4e42d Author: almgren Date: Mon Apr 26 17:21:55 2010 +0000 edge_coeffs should be (:,:), not (:) Src/LinearSolvers/F_MG/mg_cpp.f90 commit 7f4471de00cae6a0f5aa679090fd2c8ceeea59dc Author: mzingale Date: Sat Apr 24 13:42:12 2010 +0000 line wrap error Src/LinearSolvers/F_MG/stencil.f90 commit f462d96e9b5010a9b47ee2836f9cf04a128daa6d Author: almgren Date: Sat Apr 24 05:13:53 2010 +0000 Fix bug in 3d averaging of x-edge coefficients. Src/LinearSolvers/F_MG/coarsen_coeffs.f90 commit 200403bf6d5cee425db5582b7544529ea96fcc8b Author: almgren Date: Sat Apr 24 01:34:49 2010 +0000 Remove print statement. Src/LinearSolvers/F_MG/stencil_fill.f90 commit e3ec8212dc242831c0901ce972b377bb63fb1eb9 Author: almgren Date: Sat Apr 24 01:16:13 2010 +0000 We no longer have a single coeffs(:) array, we now have cell_coeffs and edge_coeffs. Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 46574f4c2b51fa824514df16b31897da0ad87f16 Author: almgren Date: Sat Apr 24 01:08:53 2010 +0000 Remove unused "cross" in extrap_1d. Src/LinearSolvers/F_MG/stencil.f90 commit ef0e467b977cd715639454806900a93b0deb5454 Author: almgren Date: Sat Apr 24 00:59:37 2010 +0000 Fix calls to ml_restriction to no longer pass "face_type" Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 0b10be5dba5582ee03924717e9a04856c0eecea3 Author: almgren Date: Sat Apr 24 00:59:16 2010 +0000 Removed unused variable "face_type" from ml_restriction and ml_nodal_restriction Src/LinearSolvers/F_MG/ml_restriction.f90 commit 9f6ecafa52414e24511003b7f07e757d644e4f50 Author: almgren Date: Sat Apr 24 00:27:30 2010 +0000 Get rid of unused variable "vol" Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit fd8d4f02654ea99eb501b9e7d44228f9f93cec0c Author: almgren Date: Sat Apr 24 00:07:01 2010 +0000 Typo ex --> dx Src/F_BaseLib/tag_boxes.f90 commit 6adfb5d8b401c8da8cad63ff1bad24827dbd91d0 Author: ajnonaka Date: Fri Apr 23 23:41:55 2010 +0000 for intel 9, reverting to a less optimized mode, which actually runs faster (go figure) and is less susceptible to the plotfile pi bug I've been struggling with Tools/F_mk/GMakedefs.mak commit 08c5d1d17ce626fa8ecced67c2190092761cec9d Author: ajnonaka Date: Fri Apr 23 22:36:32 2010 +0000 rewritten in gfortran-friendly way Src/F_BaseLib/layout.f90 commit 9918c8846b8f7769edd3949bbf3d2b8ead6d6871 Author: ajnonaka Date: Fri Apr 23 22:29:28 2010 +0000 pass in dx to tag_boxes so you can refine based on location Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/tag_boxes.f90 commit 3ce13fba9c37b8810aab4203690789a1f5ba8930 Author: almgren Date: Fri Apr 23 21:34:20 2010 +0000 Add multifab_build_edge routine. Src/F_BaseLib/multifab.f90 commit ccc2d4c4b8d5097e0c5e9eeec009f27a0f6e698a Author: lijewski Date: Fri Apr 23 20:16:46 2010 +0000 removed some dead code Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 75ea8460969a7d230976686ba6549dfb4c1f38fc Author: almgren Date: Fri Apr 23 18:33:18 2010 +0000 Renamed st_coeffs.f90 --> coarsen_coeffs.f90 Src/LinearSolvers/F_MG/GPackage.mak commit 762770eb3a93ae03da7dc3d31b39189e7ec5b681 Author: almgren Date: Fri Apr 23 18:24:47 2010 +0000 Rename st_coeffs.f90 --> coarsen_coeffs.f90 and modify it to put in more comments and make it work for the porous media stencils. Src/LinearSolvers/F_MG/coarsen_coeffs.f90 commit e082129eb916b9632925c6c1c4d2d4ce243e7a72 Author: almgren Date: Fri Apr 23 18:24:00 2010 +0000 1) Include coarsen_coeffs_module instead of coeffs_module. 2) Start to make the number of components more general so we can accomodate the porous media stuff. Src/LinearSolvers/F_MG/stencil_fill.f90 commit 2d6025901ea7e5332319e57d52819b59ee60de65 Author: almgren Date: Fri Apr 23 18:21:05 2010 +0000 Doesn't need to include coeffs_module. Src/LinearSolvers/F_MG/nodal_mask.f90 commit 528f54aa36c9d43907ebdc437bd4ae71c52973ba Author: mzingale Date: Fri Apr 23 15:29:17 2010 +0000 mgt%dh was being indexed incorrectly when initializing coarse_dx Src/LinearSolvers/F_MG/mg.f90 commit 8d05ad40816bcf474a3b71c2cab571b769551e41 Author: gilet Date: Wed Apr 21 16:30:17 2010 +0000 added stuff for orga Tools/F_mk/GMakeMPI.mak commit 38940c48a4d74a3abe2e42840796d91109decf25 Author: almgren Date: Wed Apr 21 04:00:44 2010 +0000 Pass in bottom_solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 8dd4a39059f5a128be3da9c9bdfb50cd7750e0cf Author: almgren Date: Wed Apr 21 03:58:56 2010 +0000 Fix a buggy part. Src/LinearSolvers/F_MG/stencil_fill.f90 commit 84fdbacb037c17395db58aaffdf56008001d287e Author: almgren Date: Wed Apr 21 03:57:48 2010 +0000 Remove unused statements. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 7fe617e67ffd1db7288fb8de6399b233c8b8a51d Author: ajnonaka Date: Tue Apr 20 21:55:41 2010 +0000 xlf library location mysteriously moved in the last hour Tools/C_mk/Make.mpi commit 5a6a23c3839a8d9d05d8e15820c676343ffaea5d Author: almgren Date: Tue Apr 20 21:36:42 2010 +0000 Need to set coeffs%nc equal to coeffs(maxlev)%nc, NOT ss%nc. Src/LinearSolvers/F_MG/stencil_fill.f90 commit c7e46e6882cdd3088def45d3ed105d7262ef888e Author: almgren Date: Tue Apr 20 21:30:33 2010 +0000 One more call to fix. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit aa1a3229f93cbaa84d5bcd42fe01213dc7955a93 Author: almgren Date: Tue Apr 20 21:29:35 2010 +0000 Fix interface for porous... Src/LinearSolvers/F_MG/mg_cpp_f.h commit d5d5083ad1659c1133334092dbda4d4ada12678e Author: almgren Date: Tue Apr 20 21:26:54 2010 +0000 Make this work with the C++ interface. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit f107f19de3602329e5e19310f48828e59dd0dbf4 Author: almgren Date: Tue Apr 20 21:26:36 2010 +0000 Make the number of components more general so this will work with the multicomponent porous media stencil. Src/LinearSolvers/F_MG/stencil_fill.f90 commit 72b52cb310eb0cd0e166dff7ec7b01ab07e6eb4d Author: almgren Date: Tue Apr 20 20:34:37 2010 +0000 Also need to include stencil_fill.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit 43758a95f037bbf9ffb5947f92537705136959dd Author: almgren Date: Tue Apr 20 20:33:14 2010 +0000 Dont use optional dh to define the dimension of another array. Src/LinearSolvers/F_MG/mg.f90 commit 6d728269f7bc5f216d6b8f724cbde5c2b406d930 Author: almgren Date: Tue Apr 20 20:31:06 2010 +0000 Fix line 157. Src/LinearSolvers/F_MG/mg.f90 commit 876a80d351eb57375869dd4b2ffce0a74a1bfc1c Author: ajnonaka Date: Tue Apr 20 20:22:34 2010 +0000 forgot to include impose_neumann_bcs.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit 8cb0b2ecc2a3d8f4c311b4d212c16aa76f6d33dc Author: almgren Date: Tue Apr 20 20:12:56 2010 +0000 Dont need to pass pd into stencil_fill. Src/LinearSolvers/F_MG/stencil_fill.f90 commit 445e3dcd52d0da1117cba32094bfb79d2775c1ce Author: ajnonaka Date: Tue Apr 20 19:43:52 2010 +0000 omp now compiles on intrepid with xlf; whether it works or not is currently unknown Tools/C_mk/Make.mpi commit 2e21f171a63de21a761edae9233cdafd4bb63051 Author: ajnonaka Date: Tue Apr 20 19:35:49 2010 +0000 oops, guess it doesn't work yet, but this fixes one library Tools/C_mk/Make.mpi commit 45986cd52dc3008250d13ca5875ae35a8d7a0f49 Author: ajnonaka Date: Tue Apr 20 19:34:27 2010 +0000 omp now compiles on intrepid with xlf; whether it works or not is currently unknown Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit af3f696d55a9e9e9051c274576eadee748d935d9 Author: almgren Date: Tue Apr 20 19:31:59 2010 +0000 Add stencil_fill_minion_all_mglevels which enables bottom_solver=4 for the minion stencil as well. Src/LinearSolvers/F_MG/stencil_fill.f90 commit b9885a9edac4dedab92b1b2d8da10b7db449a03a Author: almgren Date: Tue Apr 20 18:59:55 2010 +0000 Added some new files. Src/LinearSolvers/F_MG/GPackage.mak commit c6a07deba1c08682b36985c3b81f234128d9d95f Author: almgren Date: Tue Apr 20 18:53:58 2010 +0000 Changes so that all of the bottom_solver=4 stuff is now created in files in this directory rather than needing to be passed in. Src/LinearSolvers/F_MG/impose_neumann_bcs.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 8d72fd9b59dd041f9bcd4d1f848cbb2bd8974bec Author: ajnonaka Date: Tue Apr 20 16:42:16 2010 +0000 added some non-mpi support for interpid Tools/C_mk/Make.Linux commit e06744660ae7a989e5354e524675202733d4433d Author: ajnonaka Date: Tue Apr 20 16:19:13 2010 +0000 OMP compiler options for xlf compilers on intrepid Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 2f46f2b065ded104009b0f38fef5c07ee8a7e941 Author: lijewski Date: Mon Apr 19 23:16:09 2010 +0000 fixed bug in init() -- copy()s weren't correct in parallel Src/C_BoundaryLib/BndryData.cpp commit a5923fa5ecf70bc94b37210aad16abbc0cf2c1f7 Author: almgren Date: Sun Apr 18 18:35:05 2010 +0000 Fix spelling of error message -- incommesurate --> incommensurate Src/F_BaseLib/layout.f90 commit dc8483e7d0e0e3a110033247957c0dd12457a4fe Author: almgren Date: Sat Apr 17 00:20:12 2010 +0000 Put a & to break up a long line so hopefully Minion's compiler will be ok with it. Src/F_BaseLib/layout.f90 commit 0b127e3ee9133ac1aa363b26a3b03b54a9876a2d Author: gpau Date: Fri Apr 16 19:55:46 2010 +0000 added some functions to handle multilevel solve for the porous media code Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit e5724fec724f30c817900a7f8889c12e984e2f19 Author: gpau Date: Fri Apr 16 19:55:04 2010 +0000 added a subroutine to handle multilevel solve for the porous media code Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 79dd717edb3c77c770814eb15de92f8332f56fbd Author: lijewski Date: Thu Apr 15 21:17:10 2010 +0000 carver.nersc.gov stuff Tools/F_mk/GMakeMPI.mak commit 652edd0b91092131bd2fead15ba09ead26318a44 Author: lijewski Date: Thu Apr 15 21:16:38 2010 +0000 more junk for carver.nersc.gov Tools/C_mk/Make.Linux commit 445dc3cb32cedc924c58579c7dfbef77ae57c139 Author: lijewski Date: Tue Apr 13 23:16:33 2010 +0000 now works with full pathname instead of just relative Tools/C_scripts/moddep.pl commit 118c249065ae8304db4ba7b701b573758218318d Author: lijewski Date: Tue Apr 13 23:15:30 2010 +0000 now works with full pathname for FPARALLEL instead of just relative Tools/F_scripts/moddep.pl commit d83162a8f1b79b5fe1d5d3f79ccd400f1f7e2983 Author: lijewski Date: Tue Apr 13 23:14:54 2010 +0000 added extern/random stuff Tests/LinearSolvers/F_MG/GNUmakefile commit c70e5bc205c2fd5bc8e3d98d072e3c534a6102f0 Author: almgren Date: Mon Apr 12 18:39:33 2010 +0000 Move mt19937ar.f90 from boxlib to extern/random so we don't have to compile it every time -- it takes a long time. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/mt19937ar.f90 commit 671158057677ca6013cb1d569a5b693bd233b07e Author: adonev Date: Fri Apr 9 22:15:57 2010 +0000 stochastic_varden now compiles OK Src/F_BaseLib/GPackage.mak commit dbd7a6934bd9122596bc72a7f81127f7afa6e807 Author: ajnonaka Date: Wed Apr 7 19:03:39 2010 +0000 xlf on interpid with omp now compiles Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 8a1f397995aa9e16e679a904c41c00cae4f52c6a Author: vince Date: Tue Apr 6 20:48:05 2010 +0000 fixed default MPI_HOME. Tools/C_mk/Make.mpi commit efc16db5d7e8042990f203079093dc457e270a41 Author: ajnonaka Date: Tue Apr 6 20:41:44 2010 +0000 turned of auto threading on intrepid Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 66866f6516e40b196f7a507e2fb6811beed13419 Author: ajnonaka Date: Tue Apr 6 20:14:57 2010 +0000 for some reason the mpi compiler on intrepid needs its own OMP statements Tools/F_mk/GMakeMPI.mak commit 535418ea1885479534e9f41bf3e370cbba07c521 Author: ajnonaka Date: Tue Apr 6 19:45:36 2010 +0000 OMP flags for xlf compiler on intrepid Tools/F_mk/GMakedefs.mak commit ff75457ac562e606b5cc9ad4bbb420c9e51df065 Author: almgren Date: Fri Apr 2 21:43:37 2010 +0000 1) Define a RegridOnRestart function that returns regrid_on_restart (called only by main.cpp at this point) 2) Define a RegridOnly(time) function which does regridding only if we restart but don't take a timestep. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit fb8d620bad5220b2940d207143b40234d63149f0 Author: almgren Date: Fri Apr 2 20:29:13 2010 +0000 Now allow us to have StateData that is not stored in the checkpoint. If store_in_checkpoint = false then the statedata multifabs will not be written to the checkpoint diretory (though the times, domain, etc will be written in the header). We set "nsets" = 0 when we write. Then when we read, for each statedata we read "nsets" to know whether to read 0, 1, or 2 multifabs (1 if only new data, 2 if both old and new data). Src/C_AMRLib/StateData.cpp commit 1819a6e12a57febf3e0dfc545dad5729bc0d3296 Author: almgren Date: Fri Apr 2 20:27:18 2010 +0000 Undo the previous stuff I added in AmrLevel for controlling the StateData::store_in_checkpoint. This is now entirely used inside StateData, in the checkPoint and restart routines. Src/C_AMRLib/AmrLevel.cpp commit 4f36613631cb5a5702d365ce9036591358847215 Author: almgren Date: Wed Mar 31 23:43:33 2010 +0000 Added Minion 2nd order stencils -- these are identical to the standard 2nd order cell-centered stencil except the dimensioning of the incoming arrays is different. Eventually we should merge these routines. Src/LinearSolvers/F_MG/stencil.f90 commit 38ac6a41c8da3d34fbae0d1f57beda92b0f8ff5a Author: lijewski Date: Mon Mar 29 21:01:38 2010 +0000 got 2D working again Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit adb92fafd88e22d4413a2d827b0d7a521572987b Author: almgren Date: Fri Mar 26 21:43:08 2010 +0000 If the desc_lst[i].store_in_checkPoint() is not true then we 1) dont write this statedata to a checkpoint 2) dont read this statedata from a checkpoint. Note that the first StateData must be read/written so that we can get "time" from it. We also assume that the StateData being defined has the same TimeType as the first StateData. Src/C_AMRLib/AmrLevel.cpp commit f417581e84b768508fc7598613f2859754d6cd70 Author: almgren Date: Fri Mar 26 21:34:23 2010 +0000 StateDescriptor now has a member called store_in_checkpoint. If this is true then this StateData will be written to the checkpoint file via AmrLevel::checkPoint and will be read from checkpoint via AmrLevel::restart. If it is false then the data will be allocated in restart but set to 0, and it won't be written to a checkpoint file. Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 1e57d642448a5fc7a9fda9daaf769e930390d3d2 Author: lijewski Date: Fri Mar 26 20:33:02 2010 +0000 fixed parallel bug Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit e721ec6ceaed507847cde7958ecf3c385e6d99d5 Author: almgren Date: Thu Mar 25 21:44:46 2010 +0000 Allow a "dump_old" flag to be passed through AmrLevel into StateData so we have the option not to write both the old and new data. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 164c2519ea4160e9999d7108a6a019051331bc75 Author: lijewski Date: Thu Mar 25 20:33:42 2010 +0000 mods for carver.nersc.gov Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 02a1c52e79251d32edfeff0217f166d09ba0f819 Author: gpau Date: Wed Mar 24 23:53:44 2010 +0000 fixed an error with the pressure solve Src/LinearSolvers/F_MG/stencil.f90 commit 02ec51ef7fdf45c0dce051e76facc92cab34b765 Author: gpau Date: Wed Mar 24 19:29:43 2010 +0000 fixed the stencil to loop over ncomp of density Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 0f06e11cdd6d0d46fbe702ef57aed84f1bc0ed3c Author: gpau Date: Wed Mar 24 19:28:47 2010 +0000 updated the porous Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit a563781fff58be4edc9c4cb08bc1853aec3ec689 Author: lijewski Date: Tue Mar 23 19:17:33 2010 +0000 hmmmm Src/C_BaseLib/BoxList.cpp commit 70b79786a7f83aeb102b86f4fc1e3ca42d3f7708 Author: gpau Date: Tue Mar 23 19:10:35 2010 +0000 removed bad BL_ASSERT() Src/C_BaseLib/BoxList.cpp commit 1195a8474503e563236274a0ff9c1ee2c553f0a2 Author: mzingale Date: Sun Mar 21 20:55:41 2010 +0000 add support for self-tests (like Maestro's test_advect). These are tests that diagnose themselves, so no comparison to a benchmark is needed. Tools/C_util/regtests/Maestro-tests.ini Tools/C_util/regtests/test.py commit 12722230aa85297fc5416646689dcde198131fd8 Author: mzingale Date: Fri Mar 19 20:21:00 2010 +0000 add -fltconsistency to the -mp1 for Intel 10 and 11 -- this fixes errors that test_advect showed. Tools/F_mk/GMakedefs.mak commit 451af8379f7d44e0ad73bffd7d45f5e724841610 Author: ajnonaka Date: Fri Mar 19 19:23:06 2010 +0000 mods for PGI and jaguar Tools/C_mk/Make.Linux commit c458c7d740ec8bf79455ec0631707870fe6cca2f Author: gpau Date: Fri Mar 19 18:05:17 2010 +0000 fixed a bug in the simplen_2d Src/LinearSolvers/F_MG/stencil.f90 commit 408f3f68d015b490191422c06cd0173d28138415 Author: mzingale Date: Fri Mar 19 14:01:08 2010 +0000 add some error handling for the visualization if no output file is produced Tools/C_util/regtests/test.py commit a7a3fb82f5b6606578b7d1261992d492adbce015 Author: almgren Date: Thu Mar 18 21:48:00 2010 +0000 Move "finest_level = new_finest_level" to be before the call to amr_level->post_restart in Amr::restart. Src/C_AMRLib/Amr.cpp commit c77c1f6bc30599fea2d58d11d94bbbbeb06728f1 Author: almgren Date: Thu Mar 18 21:14:42 2010 +0000 Fixing spacing in print statements. Src/LinearSolvers/F_MG/mg.f90 commit b6eee8deb588add635e65e8511c58e476108373d Author: almgren Date: Thu Mar 18 20:56:16 2010 +0000 We now define the stencil terms based on (alpha - sum_i beta0_i div dot beta_i grad) Src/LinearSolvers/F_MG/stencil.f90 commit 22de052bc2b8c4b7290e3c71a7b18fe36f81e4ee Author: almgren Date: Thu Mar 18 20:51:02 2010 +0000 We now pass a cell-centered beta0 in for the porous media stuff -- the new stencil is (alpha - sum_i beta0_i div dot beta_i grad) Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit d8081503cb84b503a085936cf3f7bc9a17e85f94 Author: almgren Date: Thu Mar 18 20:47:48 2010 +0000 1) Pass abs_tol into ml_nd 2) Need to pass a "nc" argument into coarsen_coeffs now. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 8d22f0386ec8e0b348923098da26fab475112384 Author: almgren Date: Thu Mar 18 20:46:14 2010 +0000 Pass in abs_eps and use as appropriate. Src/LinearSolvers/F_MG/ml_nd.f90 commit a3d09c8ec6a4b27a6382837ace0bcf23a9ba3e4d Author: almgren Date: Thu Mar 18 20:42:31 2010 +0000 Modify set_porous_coefficients to take a cell-centered beta0 such that the stencil looks like (alpha - sum beta0_i del dot beta_i grad). Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 545e627ffb310d2f28351a8337102968d81a4577 Author: mzingale Date: Thu Mar 18 16:52:49 2010 +0000 latest test suite Tools/C_util/regtests/Maestro-tests.ini commit 4d0dfe5fb61f43645b7a2054701b84938570c286 Author: mzingale Date: Thu Mar 18 16:52:14 2010 +0000 pretty-up the output (now in color) Tools/C_util/regtests/test.py commit deca8d9f59ed8c7631824b1508abc2e592badeff Author: almgren Date: Tue Mar 16 23:44:51 2010 +0000 Wrap BoxLib::Warning inside if IOProcessor test. Src/C_AMRLib/Amr.cpp commit abe2c859cc2f61310e925b33f2996b618b55ecf1 Author: almgren Date: Tue Mar 16 19:38:23 2010 +0000 Remove unused variables. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit b6bd20c2c4ffc668e21447e632db25c2a774fa9f Author: almgren Date: Tue Mar 16 19:23:23 2010 +0000 Clean up unused variables. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit a536d08c60f6f348e00f214b6a7fc202953244e4 Author: ajnonaka Date: Tue Mar 16 19:16:12 2010 +0000 syntax fix Src/LinearSolvers/F_MG/mg.f90 commit dc6cbda7ea1112c1a2ba271f0b9d6b5f550bef51 Author: almgren Date: Tue Mar 16 19:10:32 2010 +0000 Fix bottom_solver_type = 4 so that it now works with PGI on franklin -- problem before was that mg_tower_bottom_solve was effectively called recursively from mg_tower_cycle --> mg_tower_cycle --> mg_tower_bottom_solve --> mg_tower_cycle --> mg_tower_bottom_solve. We have fixed this by renaming the routine that is called when bottom_mgt is present -- that is now "do_bottom_mgt", and the routine mg_tower_bottom_solve only does bottom_solver_type = 1,2 or 3. Src/LinearSolvers/F_MG/mg.f90 commit fe032b7cc52e584d5d33bafbeddc30b00559da0e Author: lijewski Date: Mon Mar 15 21:24:19 2010 +0000 removed commented out vestiges of OMP in hgrlxu() Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit e312b0e7595d7a3896ca5443e8d8ef385ec3b8f8 Author: lijewski Date: Mon Mar 15 19:56:16 2010 +0000 added levelCount() Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 85fca65a8f59e39c93f73b964d970772efcdbf60 Author: lijewski Date: Mon Mar 15 01:15:22 2010 +0000 added fredom stuff Tools/C_mk/Make.Linux commit 53383a9ffff462a60054a63817ecc0a8c2b52a12 Author: lijewski Date: Mon Mar 15 01:13:15 2010 +0000 removed some OMP stuff that PGI gets wrong Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 6254d754e8c1a4da868ae44716eeba8208b1e703 Author: lijewski Date: Sun Mar 14 22:01:46 2010 +0000 freedom added Tools/C_mk/Make.defs commit 804c69d9c7109e863869e756e40e03a620be4769 Author: lijewski Date: Sat Mar 13 01:24:22 2010 +0000 OMP mods to compile with PGI Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 043c91c07c737e615e84e79615051fd84f0ab79a Author: lijewski Date: Fri Mar 12 21:07:59 2010 +0000 changed -O -> -fast for PGI Tools/F_mk/GMakedefs.mak commit 332fa9027d5b00f9b38ffaba5169d6f0441936a2 Author: lijewski Date: Thu Mar 11 22:28:09 2010 +0000 remove OMP loop -- Intel didn't like it :-( Src/LinearSolvers/F_MG/mg_restriction.f90 commit b45819b5bbd78b7c3ae4b1250e2c5c104b2b8eef Author: mzingale Date: Thu Mar 11 03:38:22 2010 +0000 fix a bug introduced during an optimization Src/LinearSolvers/F_MG/stencil.f90 commit 9516d785bb68cab154aeaa3883f84417d3bc1cf7 Author: ajnonaka Date: Wed Mar 10 21:18:08 2010 +0000 get rid of SMP stuff so nobody gets the (false) impression that it actually works Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit a8d4fee5889ff6609b389ba0046e1743ff413a6f Author: almgren Date: Tue Mar 9 18:23:25 2010 +0000 Remove print statements. Src/LinearSolvers/F_MG/mg_cpp.f90 commit c4b0308d6077a6a4eda7f58a73018dcd506b5435 Author: lijewski Date: Tue Mar 9 17:01:01 2010 +0000 fixed something I broke Src/LinearSolvers/F_MG/nodal_mask.f90 commit 0c6c63a77eb69b91fa0105beca915967450d4245 Author: lijewski Date: Mon Mar 8 19:02:52 2010 +0000 *** empty log message *** Tests/LinearSolvers/F_MG/nodal_multi.f90 commit 5ab18f200e4f6bf1d5ace7abbce5c4f5ede91f02 Author: almgren Date: Sat Mar 6 22:40:05 2010 +0000 Now allow multicomponent coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 163b58e80402168d77a61387e7c08c2d9722bf54 Author: almgren Date: Sat Mar 6 22:39:38 2010 +0000 Now allow multicomponent betax, betay. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/stencil.f90 commit 56112f93857682c39574ef2dbf2bf044b86701ff Author: almgren Date: Sat Mar 6 04:25:35 2010 +0000 Remove unused variables. Src/F_BaseLib/multifab.f90 commit dce71441378ab3deb9a974271fc9171504cb1e9c Author: lijewski Date: Sat Mar 6 00:15:55 2010 +0000 use our cpy_[dilz] routines instead of compiler generated ones Src/F_BaseLib/multifab.f90 commit 3a3b4043a8b337aa5ba386ef8d2ef7bd1635dfa4 Author: lijewski Date: Fri Mar 5 23:46:58 2010 +0000 bit more OMP Src/F_BaseLib/multifab.f90 commit 15e66cb4c0fb3b4315d47035a06602ba194ff1a5 Author: lijewski Date: Fri Mar 5 23:28:10 2010 +0000 OMPd fab_setval_c() Src/F_BaseLib/fab.f90 commit e253ed0d364755d55c1ab6f2094c6a53f1c18530 Author: lijewski Date: Fri Mar 5 23:05:05 2010 +0000 OMP'd norm_inf Src/F_BaseLib/multifab.f90 commit 69194a6d04273835c9355c585becc1390da9e9da Author: lijewski Date: Fri Mar 5 21:52:58 2010 +0000 more OMPing Src/F_BaseLib/multifab.f90 commit 31c1478390a76ab0af93740652b59d2959e9b85a Author: lijewski Date: Fri Mar 5 20:40:21 2010 +0000 little code rearrangement Src/LinearSolvers/F_MG/stencil.f90 commit b42a0d121e60ab6e7f46dcfec941d5ebc6a261de Author: lijewski Date: Fri Mar 5 18:58:48 2010 +0000 some code consolidation Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 347e9524425fa75d69a35e476575595bac5f9ca9 Author: lijewski Date: Fri Mar 5 18:19:11 2010 +0000 some more OMPing Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 286de7a8e4de4edb20533a0d414c24ab134444eb Author: lijewski Date: Fri Mar 5 17:46:01 2010 +0000 removed some duplicate code Src/LinearSolvers/F_MG/mg_smoother.f90 commit 8a07f08f92839f10627099e7f559de68fc32c526 Author: lijewski Date: Fri Mar 5 00:03:13 2010 +0000 more OMP tweaking Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 0c2afa953d81cbf8e17176fb1c99fa5dd23aa060 Author: lijewski Date: Thu Mar 4 22:03:50 2010 +0000 removed itsol_breakdown() -- not used Src/LinearSolvers/F_MG/itsol.f90 commit 5e5fd7b7aaf0b21cf88b42aa10479770dce08a35 Author: lijewski Date: Thu Mar 4 22:00:53 2010 +0000 some cleanup Src/F_BaseLib/multifab.f90 commit 7706e7a7a6ed537ea896b33ed7dee77d260f3c2b Author: lijewski Date: Thu Mar 4 17:35:13 2010 +0000 Commented out a bunch of OMP directives that Chuck put in. They were over boxes which is not the right way to do things. Got to eventually go back over these and OMP over the fortran instead. Src/F_BaseLib/multifab.f90 commit 89ac65a11d84098285a05f261ce6cb1370849bbc Author: lijewski Date: Thu Mar 4 17:33:36 2010 +0000 OCVS: ---------------------------------------------------------------------- Removed couple OMP directives on loops over boxes that Chuck put in some time ago. It's not the right way to do things. It was leading to nested thread calls which was killing PathScale. Src/LinearSolvers/F_MG/mg.f90 commit 206edffaa77a60c540adcef2916a8944af9ea092 Author: lijewski Date: Thu Mar 4 00:05:18 2010 +0000 more eliding of function calls Src/LinearSolvers/F_MG/nodal_mask.f90 commit bd6becc7be6f80d59624fcc21b2b349c8e271811 Author: lijewski Date: Wed Mar 3 23:59:12 2010 +0000 some cleanup Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit ee56089a7c394a8f1a46af20596d373e3e6361af Author: lijewski Date: Wed Mar 3 23:17:39 2010 +0000 some OMPing Src/LinearSolvers/F_MG/nodal_divu.f90 commit e6410fc36f2d6c841a4e7235fabe31a5a263a1a6 Author: lijewski Date: Wed Mar 3 23:13:07 2010 +0000 OPM'd Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 5032baf79b86dd69c5b7aeacae33ac94f4589505 Author: lijewski Date: Wed Mar 3 21:15:01 2010 +0000 Removed bunch of duplicate functions by making single module private version. Src/LinearSolvers/F_MG/itsol.f90 commit dbb9dcd8974cd46bbb9be7b0e87e15c68b17caa8 Author: lijewski Date: Wed Mar 3 21:06:03 2010 +0000 more OMP and cleanup Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 40109797cdfaf5f231d7eec31e9f176c14ebaf96 Author: lijewski Date: Wed Mar 3 18:11:03 2010 +0000 OMP 7-point jacobi Src/LinearSolvers/F_MG/mg_smoother.f90 commit f6e9a189b7026f984f3f9daf9f99bf22e44baa7c Author: lijewski Date: Wed Mar 3 17:57:28 2010 +0000 more OMP stuff Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit fe5593b142f9c79aff56f5bd07be98cd6974d4f1 Author: lijewski Date: Tue Mar 2 23:49:03 2010 +0000 some OPMing Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 39914b8fd38b8299ea3cd6255d31230e21ee3cdd Author: lijewski Date: Tue Mar 2 23:20:41 2010 +0000 some OMP Src/LinearSolvers/F_MG/mg_restriction.f90 commit 797d6da6a334a8f80b0eb866f26bd52d7c23c304 Author: lijewski Date: Tue Mar 2 23:08:27 2010 +0000 more function eliding Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/stencil.f90 commit efd30b24610554ce1eafde6d93c2e93d694d05a1 Author: lijewski Date: Tue Mar 2 21:06:00 2010 +0000 yet more eliding of bc_neumann() and bc_dirichlet() Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 4c5d0fd0dc99dd48e6e5c348bbf726720cca8d31 Author: lijewski Date: Tue Mar 2 19:05:19 2010 +0000 more eliding of bc_neumann() and bc_dirichlet() Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 58c4d32a536750e42e1cd26c72cc231fc92a075f Author: lijewski Date: Tue Mar 2 18:16:47 2010 +0000 Rearranged code to remove bunch of bc_neumann() calls. More to be done ... Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit fcb350bc3dedb9a6d27bb1a69b5c55d9bac316f4 Author: lijewski Date: Mon Mar 1 23:45:37 2010 +0000 removed some OMP loops that crashed Intel Src/F_BaseLib/multifab.f90 commit c70cc22b777a5ab146811c7c4d5e5fd3c7d87e56 Author: lijewski Date: Mon Mar 1 23:10:17 2010 +0000 some OMP Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 2bbe1d8133cd1e15f7137e20773b92fbcd239bc1 Author: lijewski Date: Mon Mar 1 22:43:58 2010 +0000 yet more OMP Src/LinearSolvers/F_MG/stencil.f90 commit 2166e1b3505f53a72f09713952cbdb83a039124e Author: lijewski Date: Mon Mar 1 22:22:02 2010 +0000 some OMP Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 249014c8f1dcf3cbf90bb8b97ef59eaa22898aef Author: lijewski Date: Mon Mar 1 22:15:57 2010 +0000 some OMP Src/LinearSolvers/F_MG/mg_smoother.f90 commit ee4ac73aff413b14268caf3493d203633b5458f2 Author: lijewski Date: Mon Mar 1 22:02:03 2010 +0000 brought up-to-date Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit c71cd67454116ac0a8fbdcd4386cb01b60505a7a Author: lijewski Date: Mon Mar 1 22:00:11 2010 +0000 Got rid of -stand f95 for intel; complains about OMP loops. Added appropriate stuff for OMP with Intel. Changed -mp --> -mp1 Tools/F_mk/GMakedefs.mak commit 7b3b4bbdce4ef1af3cf1a1da65a619b0bab07c51 Author: lijewski Date: Mon Mar 1 20:12:14 2010 +0000 speedup to gs_rb_smoother_3d Src/LinearSolvers/F_MG/mg_smoother.f90 commit e8da78520ed4108a5a8064905c039d80f1b5c1fe Author: almgren Date: Fri Feb 26 22:23:37 2010 +0000 Remove unused variable: IntVect b1_length = b1.size(); Src/C_AMRLib/TagBox.cpp commit 9bc1ed8228fb412e8846542d172d08ccfe83e361 Author: almgren Date: Fri Feb 26 21:57:04 2010 +0000 Modify Amr, AmrLevel and Make.package so that we don't generically include SlabStat and StationData stuff. You must now define USE_SLABSTAT or USE_STATIONDATA to get those (respectively). Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Make.package commit f066e95e7bf6828621b7de52e6a739312568aa4f Author: lijewski Date: Fri Feb 26 21:33:58 2010 +0000 minor efficiency tweaks Src/C_BaseLib/BoxList.cpp commit f97aeb710e27e9aa877b6357fba77058c60375a7 Author: lijewski Date: Fri Feb 26 21:14:00 2010 +0000 minor tweaks to add() Src/C_BaseLib/BoxDomain.cpp commit 321b38acdf934271f3ea02c938ea62f7dbaa68c6 Author: lijewski Date: Thu Feb 25 22:34:34 2010 +0000 use LnClassPtr instead of CpClassPtr Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit a8c4cd2d1e576f9353ebd50e37ec5252b8a90f0e Author: lijewski Date: Thu Feb 25 20:59:23 2010 +0000 undrrelxr now uses LnClassPtr instead of CpClassPtr Src/LinearSolvers/C_CellMG/LinOp.H commit b20ab92d21df8f9d0757475d43b3926cb3f516a1 Author: lijewski Date: Tue Feb 23 21:37:42 2010 +0000 minor tweak to how intersections() is used Src/C_AMRLib/AuxBoundaryData.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit c85db87eab07f2d2cf64fa6c39090c9075e4018f Author: lijewski Date: Tue Feb 23 21:08:02 2010 +0000 remove unused constructor & use reserve() on vector members Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit 008d668f54555e09a72fb4aa8f890b8525fbcf8d Author: lijewski Date: Tue Feb 23 20:09:48 2010 +0000 use a std::list instead of std::vector for PIRMList type Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit c373ecc11199942b6f1b8abc3baacca979ed70b2 Author: lijewski Date: Tue Feb 23 18:36:07 2010 +0000 added swap() Src/C_BaseLib/BaseFab.H commit 2c80ce5e6096489ac77e3da4ac46a2fd24978621 Author: almgren Date: Mon Feb 22 00:53:12 2010 +0000 Removed empty loop in Amr::restart Src/C_AMRLib/Amr.cpp commit 6f93bfa722676468d4bcf3ec336b3f1d69e19d73 Author: lijewski Date: Sun Feb 21 16:28:19 2010 +0000 efficiency mods to simplify() Src/C_BaseLib/BoxList.cpp commit 0c0c5a4709b10da4d50461ffdddd2c6aec575f29 Author: almgren Date: Fri Feb 19 23:40:10 2010 +0000 These now compile. Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp commit 10ddef716b96a49be0f2b17b137df73014353e6d Author: ajnonaka Date: Fri Feb 19 23:04:42 2010 +0000 prints out norms now - that are properly normalized as well (as noted in the output stream)! Tools/C_util/Convergence/DiffFab.cpp commit ce1f42e056386570fe875a780510acc816817537 Author: almgren Date: Fri Feb 19 22:45:04 2010 +0000 Start to make these compile again. Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp commit 273ec2566ffa63b34d82917529c58ad05547b815 Author: almgren Date: Fri Feb 19 22:44:51 2010 +0000 Default COMP to Intel, not g++. Tools/C_util/Convergence/GNUmakefile commit 8fe144acd66b9be222d06c829e8949cf36c7a3f5 Author: ajnonaka Date: Fri Feb 19 22:36:05 2010 +0000 compiles again Tools/C_util/Convergence/DiffFab.cpp commit 1affa13cb658e0976532579b745c939f2410d982 Author: lijewski Date: Fri Feb 19 21:19:34 2010 +0000 minor refinement of execute() Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 96c916151dcb2278624b2cf1444b64dbff91493b Author: lijewski Date: Fri Feb 19 18:18:34 2010 +0000 a bit more const-correctness Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 537d266e68039ae8c9da03154b1f9b586106ad3b Author: almgren Date: Fri Feb 19 18:16:11 2010 +0000 Add -DBL_PLEIADES so we know if we are on pleiades. Tools/C_mk/Make.Linux commit bd4348f0ccd20e09e8a368decee88ca61778aadc Author: lijewski Date: Fri Feb 19 17:59:07 2010 +0000 removed BFProxy stuff Src/C_BaseLib/BaseFab.H commit 8c900fa9ed7156dff7619d3d79c53230e13184c4 Author: almgren Date: Thu Feb 18 17:49:08 2010 +0000 Fix print statements. Src/LinearSolvers/F_MG/mg.f90 commit effe8cd4bdbc51ecd3bf6fd3bf77f7e30a7744b9 Author: lijewski Date: Wed Feb 17 16:49:54 2010 +0000 integrated back in FORT_HGRESU and FORT_HGRLXU for the time being Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit b4efa0046f0e2a85b8f13ca6cef5c52c8f8d4c97 Author: lijewski Date: Tue Feb 16 18:41:07 2010 +0000 removed some virtuals -- FabArrayBase is a concrete class Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 76a8d5a9439f235c48b8ee7f2b53f8b3fa6fd187 Author: lijewski Date: Tue Feb 16 18:15:50 2010 +0000 remove some temporaries Src/C_BaseLib/BoxList.cpp commit 2a27bc7569ba524642e50e62da2a709378fa14b1 Author: lijewski Date: Tue Feb 16 18:15:17 2010 +0000 enforce stricter const-correctness Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H commit a3321cc4c6b35a2065e2dad67c4637108ac6d472 Author: lijewski Date: Tue Feb 16 18:07:00 2010 +0000 fix for more const-correct BoxLib Src/LinearSolvers/C_NodalMG/interface.cpp commit 960d98e4fc7086b647be827baae436b04cb6f522 Author: lijewski Date: Tue Feb 16 18:02:58 2010 +0000 Uninlined constructors/destructor. Removed "virtual" on destructor. Src/C_BoundaryLib/Mask.H Src/C_BoundaryLib/Mask.cpp commit 94fd978b971dacb92698ae3ca2681c7134d7b8a0 Author: lijewski Date: Tue Feb 16 17:54:23 2010 +0000 uninlined constructors Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp commit d5276cf2a082d7ed48ade9f0c6e55076d322c12a Author: lijewski Date: Tue Feb 16 17:52:34 2010 +0000 moved constructor/destructor to .cpp file instead of inlining Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp commit 7072ff560908fdcc9f87c8992f3efe96c97206d8 Author: lijewski Date: Tue Feb 16 17:42:46 2010 +0000 *** empty log message *** Src/C_AMRLib/Cluster.cpp commit 86f53ef18a111f22381b12ce5d9405a29517146f Author: lijewski Date: Sat Feb 13 23:06:18 2010 +0000 added cg.cpp Src/LinearSolvers/C_NodalMG/Make.package commit 0a8d767d29a66588da01f61648489cf501097199 Author: lijewski Date: Sat Feb 13 22:50:17 2010 +0000 some efficiency mods Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AuxBoundaryData.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.cpp commit 2a36501f1969fd3dcfeecb432dfbd1acffc94e6a Author: almgren Date: Sat Feb 13 01:41:39 2010 +0000 Remove unused variables. Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit aa11fdc528e975ab7a30ef4b427f2ee7fb8b6e04 Author: almgren Date: Sat Feb 13 01:17:54 2010 +0000 Moved gt_breaks_27pt to the Test directory. Src/LinearSolvers/C_NodalMG/Test/gt_breaks_27pt Tests/LinearSolvers/C_NodalMG/gt_breaks_27pt commit 3adf9176ff364f48f25af67ae987a5942b207d5a Author: almgren Date: Sat Feb 13 01:15:26 2010 +0000 Moved 3d_4_level.grids to the tests directory. Src/LinearSolvers/C_NodalMG/tests/3d_4_level.grids Tests/LinearSolvers/C_NodalMG/test_grids/3d_4_level.grids commit 2c1575dba8595f031dee012f876ca7cb6009fcde Author: almgren Date: Sat Feb 13 01:14:08 2010 +0000 Moved files.2d and files.3d to the Test directory. Src/LinearSolvers/C_NodalMG/Test/files.2d Src/LinearSolvers/C_NodalMG/Test/files.3d Tests/LinearSolvers/C_NodalMG/files.2d Tests/LinearSolvers/C_NodalMG/files.3d commit 3f2e088c43bfdca69cfe28257f0ab18c70de5924 Author: almgren Date: Sat Feb 13 01:12:33 2010 +0000 Moved proj.cpp and inputs to the Test directory. Src/LinearSolvers/C_NodalMG/Test/inputs Src/LinearSolvers/C_NodalMG/Test/proj.cpp Tests/LinearSolvers/C_NodalMG/inputs Tests/LinearSolvers/C_NodalMG/proj.cpp commit b42a9ddc5e039b1066107f22ede3f383bee59dcf Author: almgren Date: Sat Feb 13 01:10:35 2010 +0000 No clue what hgproj.pg was for. Src/LinearSolvers/C_NodalMG/hgproj.pg commit eee1c2e385fbf44f780c96220c43b5519d51283f Author: almgren Date: Sat Feb 13 00:53:07 2010 +0000 Move cgsolve out of hg_multi3.cpp and into a separate file, cg.cpp Src/LinearSolvers/C_NodalMG/cg.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit bc7e855655e81ccf76eea6bec5810229cbe4cb24 Author: almgren Date: Sat Feb 13 00:47:47 2010 +0000 Removed unused subroutines and renamed HGRESUR to HGRES_CROSS. Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 29f7accccc7c0c8f8198429f2c84b6b59d53a3cb Author: almgren Date: Sat Feb 13 00:47:07 2010 +0000 Moving subroutines around to make it easier to keep track of things. Created cg_2d.f and cg_3d.f to hold the subroutines used for the CG bottom solve. Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/cg_2d.f Src/LinearSolvers/C_NodalMG/cg_3d.f Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f commit 520bc3588d2ddd93e158275588e4097eea006590 Author: almgren Date: Fri Feb 12 23:36:42 2010 +0000 Added more print statements to make it look more like f90 version. Doesn't change execution and should be the same with Pcode = 0 or 1. Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 85dcb13ffb334f92abe53f842fcdd582e739db13 Author: almgren Date: Fri Feb 12 23:34:40 2010 +0000 Remove unused routines (ones with unrolled loops) and modified print statements. Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 155fb0f883515fb5372d66c67908647bacf5fd80 Author: almgren Date: Fri Feb 12 23:34:04 2010 +0000 Remove unused variables, unused subroutines, and the unrolled versions of the cross-stencil relaxation routines. Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 98bb50dbb8c70a2518f3cf2bca8199e5194f256f Author: lijewski Date: Thu Feb 11 23:38:05 2010 +0000 some inlining Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp commit a85e2bb416647af415fe9b962fc5195a0f8d037c Author: lijewski Date: Thu Feb 11 23:15:08 2010 +0000 some inlining Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit b52d6390fca4d7fe72c033e81a4c1e176fb0a0a3 Author: lijewski Date: Thu Feb 11 22:22:34 2010 +0000 some inlining Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/UseCount.H Src/C_BaseLib/UseCount.cpp commit 1b922d62c0fcf9723ec6e9672f3ed08d576260a8 Author: almgren Date: Wed Feb 10 22:19:52 2010 +0000 1) Back out the introduction of "just_solve" 2) Add an extra argument (Rhs) to nodal_project. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 014165552476977c2cc6d43695d5473ef81a1cfb Author: almgren Date: Wed Feb 10 21:46:57 2010 +0000 Add additional option for solve which doesn't take a BndryData Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 7deca33ed236961cd853673fb021c7dacacddf13 Author: lijewski Date: Wed Feb 10 21:22:23 2010 +0000 some refinement to Distribute() Src/C_BaseLib/DistributionMapping.cpp commit 5367f307867ae0aec20c0086cde5ccafd46bcf6d Author: almgren Date: Wed Feb 10 20:44:49 2010 +0000 Modified print statements to be more aligned with current mglib. Src/LinearSolvers/F_MG/mg.f90 commit 0386aa07297c2f58590bc692fad4cafb950ef9c4 Author: almgren Date: Wed Feb 10 20:42:24 2010 +0000 Modified verbosity controls to make output more similar to that of F90 solvers. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 98040fe40ac5c208084763e105950057276c4052 Author: almgren Date: Wed Feb 10 20:31:43 2010 +0000 Remove unused variable. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 63802dbefc1f271a3e7739f55121ccb3037e2d71 Author: lijewski Date: Wed Feb 10 17:32:03 2010 +0000 some simplification Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 30dbd1204d64962b281ed187e5c647fa645448ec Author: lijewski Date: Tue Feb 9 23:04:49 2010 +0000 added to get sprintf() Src/C_BoundaryLib/BndryRegister.cpp commit ed78307b4fa834ae149289d1d587a16a228fdc33 Author: lijewski Date: Tue Feb 9 22:15:36 2010 +0000 shut up some compiler warnings on franklin Src/C_AMRLib/FluxRegister.cpp commit 3ad7a098c76ae00dc6f33ed254f5b1f7e50c38f2 Author: aaspden Date: Tue Feb 9 21:00:42 2010 +0000 Hopper Tools/F_mk/GMakeMPI.mak commit cd156dfe35b3b82dfb0bb2faa65bcff0e827ca4d Author: lijewski Date: Tue Feb 9 20:29:04 2010 +0000 use a std::map instead of a std::vector for the cache Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit cc7813fc182f8f4eb681a3075befb2e0594f2a3d Author: lijewski Date: Tue Feb 9 18:22:09 2010 +0000 removed unused BL_ASSERT() Src/C_AMRLib/TagBox.cpp commit 0bb268f5f9ee06e4740ed181791674ce67bb7f51 Author: lijewski Date: Tue Feb 9 18:19:35 2010 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp commit fbe08482f078ccf1b22347cc8261393586f901ba Author: lijewski Date: Tue Feb 9 17:33:59 2010 +0000 added some reserve() calls Src/C_BoundaryLib/FabSet.cpp commit f107790823b87430b10a2e8c5a8c9d0dced10dc0 Author: lijewski Date: Tue Feb 9 17:32:44 2010 +0000 added reserve() call in intersections code Src/C_BaseLib/BoxArray.cpp commit 7bcaa91f8ace0a9112afd6c3096ab48f0cec0209 Author: lijewski Date: Tue Feb 9 06:32:27 2010 +0000 some memory consolidation Src/C_AMRLib/TagBox.cpp commit 3d33070d37dbe488af42caaa9174b3dc936bfe8f Author: lijewski Date: Tue Feb 9 06:05:55 2010 +0000 use vector::reserve() Src/LinearSolvers/C_NodalMG/interface.cpp commit 152aea1242bd4ff8fd865bd1bb530341b0ab2202 Author: lijewski Date: Tue Feb 9 03:59:25 2010 +0000 removed unused function Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 9b73857b778dc44136f544190833b21338d941b7 Author: lijewski Date: Tue Feb 9 01:08:39 2010 +0000 now use vector::reserve() Src/C_AMRLib/AuxBoundaryData.cpp commit 6224af89550833ca1a4b77ec8b828aaaacbcc943 Author: lijewski Date: Tue Feb 9 00:50:26 2010 +0000 use vector::reserve() a bit Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit a9a35f2ddae3a4e4c45a3cc5569e81a7206b9d04 Author: lijewski Date: Mon Feb 8 23:39:53 2010 +0000 use std::vector::reserve() in places Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit bc738d945df42a902f8d31f98f801ede490e29ab Author: lijewski Date: Mon Feb 8 23:39:13 2010 +0000 some simplification Src/C_BaseLib/BoxList.cpp commit e516da4b4b8e6b1557ac478a4daa194ac3d4f379 Author: lijewski Date: Mon Feb 8 21:05:04 2010 +0000 replace std::vector with std::list in a number of places Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 9394cd59eaff1ad4fc30fa671397faeaec559d32 Author: almgren Date: Mon Feb 8 19:01:38 2010 +0000 Add shift operator for BoxArray that takes an IntVect. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 59a982acb519b8a4688791d2a917491646441a3f Author: ajnonaka Date: Tue Feb 2 19:15:06 2010 +0000 turn on Ann and Andy's unused variable warnings for C++ and fortran Tools/C_mk/Make.defs commit ced34dd8a8aa90413b5de907d211da2a746db26f Author: ajnonaka Date: Tue Feb 2 14:45:19 2010 +0000 turn on unused variable check in debug mode using gfortran Tools/C_mk/Make.defs commit beeced10a7fd58bcc94d48eb29d052443bb7c705 Author: ajnonaka Date: Tue Feb 2 14:10:58 2010 +0000 when compiling in debug mode with intel 9, you now get unused variable warning messages Tools/F_mk/GMakedefs.mak commit 351c159892819d2d450bd280373deca892437445 Author: ajnonaka Date: Tue Feb 2 13:01:47 2010 +0000 reverting back to 1/29/10 - otherwise Castro doesn't compile with Intel10 in DEBUG mode Src/C_BaseLib/CArena.cpp commit 205544e1b53445cd43dbcaf2f3dbf75944fae0bd Author: ajnonaka Date: Tue Feb 2 12:56:23 2010 +0000 need to declare freeblock before using - was causing compiler error in debug Src/C_BaseLib/CArena.cpp commit 9bd9703fe4aec1e9b7cebe382bba09a406c87acd Author: lijewski Date: Fri Jan 29 21:14:02 2010 +0000 additional optimization options for PathScale Tools/C_mk/Make.Linux commit 166763b966b056812dc5d45c6573cf8d31a8cbb8 Author: lijewski Date: Fri Jan 29 20:42:04 2010 +0000 some cleanup Src/C_AMRLib/Amr.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/VisMF.cpp commit f4393a701e4d35499e0c8cf597883d34dddf32ae Author: mzingale Date: Thu Jan 21 17:53:51 2010 +0000 add xmin, ymin, ... to the coordinates vector to account for domains that don't start at 0 Tools/F_scripts/idlbl/rawread.pro Tools/F_scripts/idlbl/rawread3d.pro commit 6f633b68ae6e15efe6db4668b09df83a574041df Author: nazgul Date: Wed Jan 20 19:21:49 2010 +0000 Added read and write functions to support FluxRegister checkpoint/restart. Louis Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 112d83aff147a2f2701d2d96b0fe5a6ff17c8cdb Author: nazgul Date: Wed Jan 20 19:20:11 2010 +0000 Read and write functions to support flux register checkpoint/restart. Louis Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 38c3029c1289ad9f701ac2616b0654fe553d52c3 Author: almgren Date: Tue Jan 12 22:51:34 2010 +0000 Make sure to set abs_eps based on what we've defined in the mgt. Src/LinearSolvers/F_MG/ml_cc.f90 commit a7a22db8be634eef22601e344e695a542cfacc4d Author: almgren Date: Tue Jan 12 20:34:42 2010 +0000 Fix print statement. Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 499e651bac98d43e8d5248095648b5ed9c4f9b41 Author: gilet Date: Wed Jan 6 01:11:50 2010 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit 385f181838c97ddbf65f90f81a9dd0d93cab1ab5 Author: lijewski Date: Wed Dec 23 04:34:56 2009 +0000 disabled (again) FAST optimization for PathScale Tools/C_mk/Make.Linux commit e963bc492280213877d555cb48e00d94de30f3f2 Author: gpau Date: Mon Dec 21 21:52:11 2009 +0000 add new files so that we can calculate fluxes at any location and direction Tools/C_util/Statistics/PltFileFluxAve.H Tools/C_util/Statistics/PltFileFluxAve.cpp commit 87fb961f8e4dd3a64b12d2ae97c54ee7935197a5 Author: gpau Date: Mon Dec 21 21:51:12 2009 +0000 make changes to flux calculations Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileStat.cpp commit 2d08d3eaa73992f2b006af741e33ad1ee2df4696 Author: lijewski Date: Mon Dec 21 20:36:20 2009 +0000 removed stdnormal_cdf() Src/C_BaseLib/Utility.cpp commit 4086842e2392175cfd388ebf6d444dc954eda6f4 Author: lijewski Date: Mon Dec 21 20:36:04 2009 +0000 removed Output_CPU_Comm_Costs() Src/C_BaseLib/DistributionMapping.cpp commit 2f421623b49531bce3c7514babd6ab22939c5d63 Author: almgren Date: Mon Dec 21 17:44:10 2009 +0000 Added stuff for ranger, a machine that Jason Nordhaus uses. Tools/C_mk/Make.mpi commit 8740b09d32c3e8afdeab48c8e319ab467ee389d8 Author: almgren Date: Mon Dec 21 17:42:40 2009 +0000 Added ranger (a Texas machine which Jason Nordhaus uses). Tools/C_mk/Make.defs commit eed94342cf5300d3c3731462f1a17b5a56d90e15 Author: lijewski Date: Mon Dec 21 16:07:03 2009 +0000 disable fast stuff for PGI -- breaks LLNS Tools/C_mk/Make.Linux commit c29c228c32d2e86b8deef6273a1a664247b3b319 Author: lijewski Date: Fri Dec 18 19:04:17 2009 +0000 put back some of the not NOFAST stuff Tools/C_mk/Make.Linux commit 36717f3cc7a1257a723c41e54944c694c570161c Author: lijewski Date: Fri Dec 18 18:41:34 2009 +0000 don't print MFRead::: stuff by default Src/C_AMRLib/Amr.cpp commit 3bfaf52ac8d17bf7cbc04e08662775b92ca142d3 Author: lijewski Date: Mon Dec 14 21:13:58 2009 +0000 disable the MFRead:: output Src/C_BaseLib/VisMF.cpp commit 96b176bb6558d137fb6d991bac830ca7e3d44907 Author: lijewski Date: Fri Dec 11 03:05:08 2009 +0000 some cleanup of InvNormDistBest() Src/C_BaseLib/Utility.cpp commit 0153cfdf92bbff627ee394b674b82c40b2030789 Author: lijewski Date: Fri Dec 11 01:06:49 2009 +0000 Added InvNormDistBest(). This is used instead of the previous "best" option to InvNormDist(). The algorithm is from Applied Statistics Algorithm 241 by Michael Wichura and the C++ implementation by John Burkardt. It provides machine precision and is much faster than the previous "best" option. It's only about 30% slower than InvNormDist(). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit ebd33c4ae4038a11082280ba80ed092c4f6c5ca1 Author: vince Date: Thu Dec 10 22:49:30 2009 +0000 added code for more file system friendly restarts. Src/F_BaseLib/fabio.f90 commit 70d4e1fd61d22e65ebea46373125be1b67bf0c4d Author: almgren Date: Thu Dec 10 22:18:47 2009 +0000 We need to delete fluxes which we have created through a call to mgt_compute_flux. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 180e9a6a7baad84652e1865b9da1923038d5ffe7 Author: almgren Date: Thu Dec 10 22:18:27 2009 +0000 We need to be able to delete fluxes which are built in mgt_compute_fluxes. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 4547fab1eb121dfa803dd6fd41748e6ee737ffb7 Author: almgren Date: Wed Dec 9 19:15:15 2009 +0000 Allow us to read in a single value for n_error_buf, to be used for all levels, or an array for n_error_buf with a distinct value for each level. Src/C_AMRLib/Amr.cpp commit 31a965cfc0905107ab17c1cb8ee463cbcf97615d Author: lijewski Date: Wed Dec 9 17:41:57 2009 +0000 Added d2_value() from latest MT folks. Faster implementation of d[12]?_value() according to latest MT stuff. Changed names: d1_value -> d_value and d_value -> d1_value to match MT. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit cf56abeb6d856494f10707e39d210d54ad9d77b5 Author: lijewski Date: Wed Dec 9 06:37:50 2009 +0000 modest speedup to mt19937 code Src/C_BaseLib/Utility.cpp commit f6fe84224730b4f486322bafe39442ec676f3b86 Author: lijewski Date: Tue Dec 8 22:36:42 2009 +0000 increased a buffer size by a tad Src/C_BaseLib/VisMF.cpp commit 8614490a558ae451a1bff4817d77cbd0202a70ff Author: lijewski Date: Tue Dec 8 21:20:35 2009 +0000 added save()/restore() for mt19937 Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit e804a8ae6ec8bf26e326bff98c7509d949abf9e3 Author: lijewski Date: Tue Dec 8 19:23:14 2009 +0000 added blinitrand() entry point Src/C_BaseLib/Utility.cpp commit 761d12241090d16ef59607c5069a246e62e088ef Author: almgren Date: Fri Dec 4 20:18:50 2009 +0000 Add empty line after Final Iter print statement for easier readability. Src/LinearSolvers/F_MG/ml_cc.f90 commit f9d941abab706162186ba7553aab36e56269579d Author: lijewski Date: Fri Dec 4 18:21:56 2009 +0000 fixed bug I introduced yesterday Src/C_BaseLib/Geometry.cpp commit ffcc320685dc325dece0007f38da87d43bf4008c Author: lijewski Date: Fri Dec 4 17:35:13 2009 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit 70af7fd46ff5df6a1f7b9eed8f82cfb8879b5ff0 Author: lijewski Date: Thu Dec 3 19:12:28 2009 +0000 can now set periodicity on construction Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit a322b68ace9a1a1ab133d1b0ee94e4c403d24596 Author: mzingale Date: Thu Dec 3 02:25:59 2009 +0000 fix the C compiler on Atlas, add optimizations for Intel 11 Tools/F_mk/GMakedefs.mak commit e5fbcb50f579caebc361f6dda4255cd88d80d597 Author: lijewski Date: Sat Nov 28 07:27:53 2009 +0000 up rMAX to 16 from 8 Src/C_AMRLib/INTERP_3D.F commit 8b8dd3704c9df05249509a9882cdba12d3f9bf30 Author: almgren Date: Sat Nov 28 04:28:45 2009 +0000 Should have 1/hx^2 in filling the Minion stencil... Src/LinearSolvers/F_MG/stencil.f90 commit 3dd4da2ae73ba15dcf1a0073fd85ca555ad08b11 Author: minion Date: Sat Nov 28 00:23:19 2009 +0000 fixed stencil Src/LinearSolvers/F_MG/stencil.f90 commit f13af5f49cf75288a958298182f49e00d8927893 Author: minion Date: Wed Nov 25 18:14:11 2009 +0000 var density mg still not working Src/LinearSolvers/F_MG/stencil.f90 commit 98789ca5509f52072511f5c4b95ea05f9f4021b6 Author: lijewski Date: Wed Nov 25 05:28:18 2009 +0000 refine_grid_layout yet again defaults to true Src/C_AMRLib/Amr.cpp commit 4645679a3d03b5256ae3341873eb067fb18efe3c Author: lijewski Date: Tue Nov 24 18:37:17 2009 +0000 mods for hopper Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 13fdc62c441b14be936db7d51576bf6781232769 Author: lijewski Date: Sat Nov 21 03:46:42 2009 +0000 Dug up an old version of FORT_NBINTERP that didn't have the "vectorization" crap in it and then OpenMP'd it. Src/C_AMRLib/INTERP_3D.F commit 673eea439b52d229dd14c0aeaaa255c07894bf7b Author: lijewski Date: Fri Nov 20 21:46:35 2009 +0000 more OpenMPing Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/INTERP_3D.F commit c6a51097d6603fa55cc9693a94bb444c151e5965 Author: lijewski Date: Fri Nov 20 17:41:11 2009 +0000 -fno-exceptions doesn't play well with MPICH2 header files at the moment Tools/C_mk/Make.defs commit 988546ca88e832807ca52d88369c65177adc9b1e Author: lijewski Date: Thu Nov 19 20:59:26 2009 +0000 Get rid of the -Ofast stuff for PathScale. Now you get same options w/wo BL_NOFAST=TRUE. Tools/C_mk/Make.Linux commit 3e6baee96b1db544b2b63d67f4cbf98f3cb93761 Author: lijewski Date: Wed Nov 18 17:11:48 2009 +0000 some cleanup Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 92884feb775d7d4b2c92b7a4811c25012cb687aa Author: lijewski Date: Tue Nov 17 22:14:46 2009 +0000 yet more OpenMP Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 34174cefdfc39c01716d83f4c391fe6d222d8f0b Author: lijewski Date: Tue Nov 17 21:52:53 2009 +0000 yet more OpenMP Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 112fd8bee555c35fcb2709c75f773854883eb799 Author: lijewski Date: Tue Nov 17 21:40:58 2009 +0000 more OpenMP Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 304066fd69df64e609c627e384a10d887cb8f7db Author: lijewski Date: Tue Nov 17 21:19:20 2009 +0000 more OpenMP Src/LinearSolvers/C_NodalMG/hg_avg3d.f commit 201843aa24db294695dc5691c138dc92a0d8fa30 Author: lijewski Date: Tue Nov 17 18:57:50 2009 +0000 changed FAB byte string to say MPI nodes not CPUs Src/C_AMRLib/Amr.cpp commit c524f74b0d3b40dc0d9fc36d9727ebff8466c10d Author: mzingale Date: Tue Nov 17 04:39:36 2009 +0000 get create_nodal_mask_1d to compile Src/LinearSolvers/F_MG/ml_solve.f90 commit d47052d152b813c484572fa8ddc0eeb1ad0ee737 Author: almgren Date: Tue Nov 17 03:04:27 2009 +0000 Add 1d versions. Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 commit 28ca8a09b7717bda8e56ecf8816e5809733e114b Author: almgren Date: Tue Nov 17 03:01:00 2009 +0000 Add 1d version. Src/LinearSolvers/F_MG/nodal_newu.f90 commit 801b48e79a1bd2b9f2af0c12fdd29008c35e8168 Author: gpau Date: Mon Nov 16 18:16:27 2009 +0000 *** empty log message *** Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileStat.cpp commit 15e205a90bc76949d229d7b3078494189b89ca72 Author: gpau Date: Sun Nov 15 17:01:53 2009 +0000 added functionality to PltFileList: now reads in multifab instead of just plotfiles. Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileList.cpp commit ddb3c5f2bc96ecb3950218643d094725e535f52d Author: gpau Date: Sun Nov 15 00:06:43 2009 +0000 update the outputfile Tools/C_util/Statistics/PltFileStat.cpp commit c4d1def7a2c2763ea276628f9ef01e8ca7bc1672 Author: almgren Date: Sat Nov 14 01:17:23 2009 +0000 Hack the mg driver so that in 1d the code calls the line solve at the top level and does not enter the V-cycle or call the bottom solver. Src/LinearSolvers/F_MG/mg.f90 commit 4f7711075a98dadb147348f5b30bdfc8cc58a42f Author: almgren Date: Sat Nov 14 01:16:39 2009 +0000 Fix the Neumann boundary conditions in the nodal_line_solve_1d. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 7394edc051faec682a65144326b583ce0ce2966c Author: gpau Date: Fri Nov 13 22:47:04 2009 +0000 handles multifab variogram Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/PltFileStat.cpp commit 8a8cbc220795fc0f8fc5190788d11af2eb4cf77e Author: gpau Date: Thu Nov 12 21:57:09 2009 +0000 *** empty log message *** Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileStat.cpp commit b2722597a377b362b3f9d958ecaa97f4e20d7994 Author: almgren Date: Wed Nov 11 22:26:38 2009 +0000 Replaced cycle by cycle_type. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit fad336fb610df0a0d7bca3d7cc1bc24b12a03023 Author: almgren Date: Wed Nov 11 22:19:52 2009 +0000 Just a cleanup.. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 50461ff9f9728dbdb7bc1d2fbe92ebbaeb480e23 Author: ajnonaka Date: Wed Nov 11 21:53:06 2009 +0000 fixed the pesky bottom_solver=4 once and for all Src/LinearSolvers/F_MG/mg.f90 commit e96ea9639f14ddc96435efdd65b37b8ab756e52a Author: lijewski Date: Wed Nov 11 20:37:02 2009 +0000 add -fpconstant to Intel fortran and some simplification Tools/C_mk/Make.defs commit 085ae0376bbcedc5cc945422c6439f1ed5201f54 Author: lijewski Date: Wed Nov 11 20:20:36 2009 +0000 decrease Intel optimization -O3 and -ip are buggy Tools/C_mk/Make.defs commit 504b171fc94b030761910a93b5fced57efd8d32f Author: gpau Date: Tue Nov 10 23:26:05 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileList.cpp commit 78a19761f053c4b7fb6addbfad035fda9af252dc Author: gpau Date: Tue Nov 10 22:19:48 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileList.cpp commit e5322e0c9a9a5d3ceefa52a1171a788b3a24d6d9 Author: lijewski Date: Tue Nov 10 21:44:13 2009 +0000 now use a map instead of a PArray to hold FABs Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.H commit 6fbab7b061c355811660e2267dc56575a1c4950e Author: lijewski Date: Tue Nov 10 21:43:44 2009 +0000 now us a map instead of a PArray to hold FABs Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 43371cc6924d0518ee0308cb385e897e97f6f677 Author: gpau Date: Tue Nov 10 21:39:32 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileList.cpp commit 3ac953cbec8df6eeb5f1b31bc11ce1a066e3e765 Author: gpau Date: Tue Nov 10 21:10:53 2009 +0000 *** empty log message *** Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileList.cpp commit 2b343d9de01d41cdceb419b08695af7d1ff76446 Author: gpau Date: Tue Nov 10 20:42:17 2009 +0000 updated with some GSLIB stuff Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileStat.cpp commit 71d8c1ea67468685c77d176160b4b18f1837b362 Author: nazgul Date: Tue Nov 10 19:45:40 2009 +0000 For della, use mpich by default. openmpi version commented out. Louis Tools/C_mk/Make.mpi commit 78c1a8ade7f95f727fb14651740b00d9e1bdbe39 Author: almgren Date: Tue Nov 10 02:32:38 2009 +0000 This version should now work with della. Tools/C_mk/Make.mpi commit e79eebad76ec63a0691f675c8327057e0a6e3bd8 Author: lijewski Date: Fri Nov 6 22:51:47 2009 +0000 added some if clauses to OpenMP directives Src/LinearSolvers/C_NodalMG/hg_proj3d.f commit 1c0abed8b4a342aa5c149bc8d6177cc631861213 Author: lijewski Date: Fri Nov 6 22:39:49 2009 +0000 added some if clauses to OpenMP directives Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 2b501040ca56a93c697a076cd1298bb75329e873 Author: lijewski Date: Fri Nov 6 22:03:02 2009 +0000 added some if clauses to OpenMP directives Src/LinearSolvers/C_NodalMG/hg_avg3d.f commit 186bfc89d3d4fd2452c2cb1b937a0bd00f2a3567 Author: lijewski Date: Fri Nov 6 21:55:50 2009 +0000 added some if clauses to OpenMP directives Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 8e4d07af34a52cf92c68c477dfd95d27e26e418c Author: lijewski Date: Fri Nov 6 21:00:18 2009 +0000 more OpenMP stuff Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/CG_3D.F commit 457bc3657c4478489f71ed594b5da6d5ef4b53d3 Author: lijewski Date: Fri Nov 6 20:34:20 2009 +0000 wrapped pragma omp with BL_USE_OMP to shut up warnings Src/C_AMRLib/FluxRegister.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit d052fc119e39dffaad97e0ef8ce521e42bca061d Author: lijewski Date: Fri Nov 6 20:06:43 2009 +0000 replaced some usages of MFIter::fabbox() Src/C_AMRLib/FluxRegister.cpp commit c604300e6db34c7234c13a2d6eb6e0ca15a2ef5a Author: lijewski Date: Fri Nov 6 18:33:23 2009 +0000 some cleanup Src/C_BaseLib/FabArray.cpp commit 94957e65ee280ced403e03867ba68ba2984da310 Author: lijewski Date: Fri Nov 6 16:44:43 2009 +0000 g++ 4.4.1 thinks strrchr() returns const char* Src/C_BaseLib/VisMF.cpp commit 40e39786ee048413df7de0d58a5ec0914c9675ad Author: lijewski Date: Thu Nov 5 23:41:37 2009 +0000 more OpenMP mumbo-jumbo Src/LinearSolvers/C_CellMG/LP_3D.F commit 1f3eea5235342e40d350c9b61ab5975c6d4de943 Author: lijewski Date: Thu Nov 5 23:34:18 2009 +0000 more OpenMP mumbo-jumbo Src/LinearSolvers/C_CellMG/LO_3D.F commit 797b2d67656e2e1a6632d2cb0169f19f7c603f13 Author: lijewski Date: Thu Nov 5 23:23:24 2009 +0000 more OpenMP mumbo-jumbo Src/LinearSolvers/C_CellMG/ABec_3D.F commit 68ed80f60d7eabbf1e809cfaadc930b0f7954dad Author: almgren Date: Thu Nov 5 23:07:06 2009 +0000 Ann's changes in gridding parameters (blocking_factor, max_grid_size) as detailed in an email to CCSE. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit d174236ad755d2d371ad848caabca71385b28923 Author: lijewski Date: Thu Nov 5 22:45:37 2009 +0000 OpenMP'd Src/C_BaseLib/COORDSYS_3D.F commit 3a1ae54f5957a26bc5dd629de0bb7f7867b6dbfa Author: lijewski Date: Thu Nov 5 22:33:23 2009 +0000 OpenMPing FASTCOPY() is a lose Src/C_BaseLib/SPECIALIZE_3D.F commit 579bf293c9077ed19af24956c4d3a1744d89bc41 Author: lijewski Date: Thu Nov 5 21:30:53 2009 +0000 more OpenMPing Src/C_BaseLib/SPECIALIZE_3D.F commit d0896a0ebf0c1e88d6164f424b8219a894255312 Author: lijewski Date: Thu Nov 5 07:50:40 2009 +0000 commented out one pragma omp that kills PathScale Src/C_AMRLib/FluxRegister.cpp commit dda7ea5cebd90b3b0ae5474528acc3b95eb2084a Author: almgren Date: Thu Nov 5 04:01:13 2009 +0000 Modify the test on max_grid_size vs blocking_factor -- we now only require that max_grid_size >= blocking_factor, not . *not* that max_grid_size >= blocking_factor*ref_ratio Src/C_AMRLib/Amr.cpp commit 5d4dbd8800a8a4716f8a2a9dc3d6005b8ee0151d Author: lijewski Date: Wed Nov 4 21:35:24 2009 +0000 OpenMP the .cpp not the .F when possible Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FluxRegister.cpp commit 3401f654c984dd954cc0a3df69e645b16e10204c Author: lijewski Date: Wed Nov 4 18:50:35 2009 +0000 now thread across FABS in applyBC() Src/LinearSolvers/C_TensorMG/DV_3D4.F Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 49f9fc278357261c9298edf44be668b821ee129b Author: lijewski Date: Wed Nov 4 18:14:56 2009 +0000 now do all faces of given FAB at a time in applyBC() Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit c5953b60934f3f66f6a0ce023edbdc06ecb27ea3 Author: lijewski Date: Wed Nov 4 17:11:39 2009 +0000 now thread applyBC() across FABs Src/LinearSolvers/C_CellMG/LinOp.cpp commit df2ff0ce0b479f07b6dc07853b4951739104cfda Author: lijewski Date: Wed Nov 4 16:55:37 2009 +0000 OpenMP stuff Src/LinearSolvers/C_CellMG/MG_3D.F Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit f10ede1435960e0112ca6eab585434bf5df33705 Author: lijewski Date: Wed Nov 4 02:30:19 2009 +0000 modified MFITer internals for some OpenMP work to come Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b5e371533c1ff3a78303a77afe3c3055d949f4a0 Author: lijewski Date: Wed Nov 4 02:28:22 2009 +0000 OpenMP'd solves across FABs and removed advance() and update() Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 0fa1638f7dc936671528a8920e9b151136471def Author: lijewski Date: Tue Nov 3 21:37:29 2009 +0000 more OpenMP stuff Tools/C_mk/Make.defs commit 84ca88bc14e6881ce17455cf4cafc33532efbe9d Author: lijewski Date: Tue Nov 3 16:35:22 2009 +0000 OpenMp LinOp::applyBC() over face calls to FORT_APPLYBC() Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LinOp.cpp commit 9e154248980905217fb963cc6f1a5a9d899c775e Author: nazgul Date: Fri Oct 30 23:51:19 2009 +0000 Using what appears to be the preferred mpi on della. Louis Tools/C_mk/Make.mpi commit 0f3f3ae9302c841bc9db28de7c4ac1334d16b61d Author: almgren Date: Wed Oct 28 20:18:31 2009 +0000 Minor tweaks for 1d. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit a2d8b5477603bea055eda646d37949d6f920b118 Author: mzingale Date: Wed Oct 28 00:37:14 2009 +0000 add support for different compilers for CASTRO Tools/C_util/regtests/Castro-tests.ini Tools/C_util/regtests/test.py commit f59da16728d8c5f1791ec08af81a6f00cc160839 Author: lijewski Date: Tue Oct 27 21:05:48 2009 +0000 more OpenMPing Src/LinearSolvers/C_NodalMG/hg_proj3d.f commit dab320250cefc633de1bf5656a6c3cdfcbdb145e Author: lijewski Date: Tue Oct 27 20:45:56 2009 +0000 some cleanup Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f commit 075e2b0ee89977f271120aeeeffb1f3753652303 Author: lijewski Date: Tue Oct 27 20:06:01 2009 +0000 more OpenMPing Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 1c60f18646eba92cdb53cd186ba67132d33af52a Author: lijewski Date: Tue Oct 27 19:37:59 2009 +0000 more OpenMPing Src/LinearSolvers/C_NodalMG/amr_real3d.f commit aab15187414404cf5ab15f88888ae17ea30ef206 Author: lijewski Date: Tue Oct 27 19:09:12 2009 +0000 more OpenMPing Src/C_AMRLib/FLUXREG_3D.F commit 34c856816e2f1ba7bf4b77d2edfee5a540570b64 Author: lijewski Date: Tue Oct 27 04:55:45 2009 +0000 some OpenMP Src/LinearSolvers/C_NodalMG/hg_avg3d.f commit 9a5fccd6354ed7633ec775f7a9d30cbfa365d240 Author: lijewski Date: Tue Oct 27 04:43:04 2009 +0000 some OpenMPing Src/C_AMRLib/FLUXREG_3D.F commit 41aa6723777aa74e39284da1448cbfc6739ccb7d Author: lijewski Date: Mon Oct 26 21:58:40 2009 +0000 print out size as well as initialize() time Src/C_AMRLib/AuxBoundaryData.cpp commit 7661605829bca2af733d2f3939fd5e22d0348095 Author: lijewski Date: Mon Oct 26 20:26:53 2009 +0000 add some PathScale options for when BL_NOFAST=TRUE Tools/C_mk/Make.Linux commit bbdaa44ecd0135908f23a450e20e479bd324f04c Author: lijewski Date: Fri Oct 23 20:12:29 2009 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 16cd2e325016ab14c21eb1c32fff859aa6107f97 Author: lijewski Date: Fri Oct 23 19:57:50 2009 +0000 OpenMP mods for Intel 11 Tools/C_mk/Make.defs commit 8f8e2678a49d0e32f13c8885f4dda65207bb2ef3 Author: lijewski Date: Thu Oct 22 21:00:30 2009 +0000 removed OpenMP directives from FORT_NBINTERP() - buggy Src/C_AMRLib/INTERP_3D.F commit 065d8111437e333b3cb73ffb36e4dca8d7a1c113 Author: vince Date: Thu Oct 22 19:24:32 2009 +0000 added the new mothra. Tools/C_mk/Make.mpi commit 0e08a5277339f1171f5fc8a8bfb3490ab93e08ec Author: lijewski Date: Tue Oct 20 22:47:35 2009 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit 911a6159c2925f1c888f0704cf908540036427d2 Author: lijewski Date: Tue Oct 20 02:37:46 2009 +0000 rearranged OpenMP directives for Intel 11.1 Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit 4fef3d1783abdfb0968f078c9c6d0c9cc13dce16 Author: lijewski Date: Fri Oct 16 18:17:21 2009 +0000 OpenMP mods to quiet PathScale Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit 18c0203086af329465b2da2c363bb7b2e12283e9 Author: lijewski Date: Fri Oct 16 17:04:09 2009 +0000 OpenMP tweaks to quiet PathScale Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 2d412fd700f75dc79d85813687ccf58dbfd07475 Author: almgren Date: Thu Oct 15 21:57:39 2009 +0000 Remove print statement. Src/LinearSolvers/F_MG/mg_restriction.f90 commit 228facb311e995a46df665cdde07ef6942b84863 Author: almgren Date: Thu Oct 15 21:57:21 2009 +0000 Fix 1d version. Src/LinearSolvers/F_MG/mg_restriction.f90 commit 46e5242f6c0058666bee240b8ec0ec5bdcb1cff3 Author: almgren Date: Thu Oct 15 21:57:10 2009 +0000 Add impose_neumann_bcs_1d. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 6af8a7eb948f63ef86823449b6b74c929bac200a Author: lijewski Date: Mon Oct 12 21:40:17 2009 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H commit 56dc460619ef85b55b3631a6ec207e060e94aa2d Author: lijewski Date: Mon Oct 12 21:37:41 2009 +0000 New versions of fortran-specialized functions that can be OpenMP'd in 3D. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 98622516503f3bbcc27bb466eaa6ef04ecc0240a Author: mzingale Date: Sat Oct 10 20:54:02 2009 +0000 add Intel 11, and support for atlas Tools/F_mk/GMakedefs.mak commit 7a0b8fac78461a6b206930f32b68a02487a1854d Author: gpau Date: Thu Oct 8 22:50:52 2009 +0000 removed a bug Tools/C_util/Statistics/PltFileXAve.cpp commit 30b4f0bbe3dfe8187b9b72690d4a954173de09c7 Author: lijewski Date: Thu Oct 8 22:10:56 2009 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.f commit b74ff527da1e19daa4fd9d1aebc4e13ee8ce897f Author: lijewski Date: Thu Oct 8 21:50:46 2009 +0000 more OpenMP Src/LinearSolvers/C_NodalMG/hg_proj3d.f commit 163c226b7ad64c3179b687a906f0617a2a049c33 Author: lijewski Date: Thu Oct 8 21:38:47 2009 +0000 more OpenMP stuff Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 7afa5d3efcbf4fa26a31e4e8a903ddfd78a5b175 Author: lijewski Date: Thu Oct 8 21:05:19 2009 +0000 redo of OpenMP stuff Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 7d2876cf51531836b212fb55f6c4195f028d35bc Author: lijewski Date: Thu Oct 8 20:35:29 2009 +0000 OpenMP Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit d602ecfbc352ff7bbeec6ea0482288a417438554 Author: lijewski Date: Thu Oct 8 20:29:52 2009 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit d1d6eae0e3b65ce5d371db0dc9347322d9beb1b4 Author: lijewski Date: Thu Oct 8 17:58:43 2009 +0000 mods to work with PGI OpenMP Src/LinearSolvers/C_TensorMG/DV_3D4.F commit d3fbff33ab813920f9f4ed072dd6596487b95ea4 Author: lijewski Date: Thu Oct 8 17:41:02 2009 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/DV_3D1.F commit 69017ef9246f277e2a8ef5ebb80513a467b69293 Author: lijewski Date: Thu Oct 8 17:40:47 2009 +0000 more OpenMP Src/LinearSolvers/C_TensorMG/DV_3D2.F commit e1de999d814187b9bbaefca8ec1be35afd686524 Author: lijewski Date: Wed Oct 7 22:14:01 2009 +0000 more OpenMP directives Src/LinearSolvers/C_TensorMG/DV_3D1.F commit adfb6e008ae7bc6a8aa6389fc978d9b87ee99f9d Author: gpau Date: Wed Oct 7 21:24:49 2009 +0000 updated file reflect variable phi Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileXAve.H Tools/C_util/Statistics/PltFileXAve.cpp commit 73cccdc37e4a689fee98d01ad525b3eed7f3135f Author: lijewski Date: Wed Oct 7 21:19:17 2009 +0000 more OpenMP junk Src/LinearSolvers/C_TensorMG/DV_3D4.F commit 5154ba21be0c1510cd777f11e13483920464e8b9 Author: lijewski Date: Wed Oct 7 21:00:43 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/DV_3D4.F commit f081c31654b0b4d2cf32ac023ecabac4f690c000 Author: lijewski Date: Wed Oct 7 20:24:37 2009 +0000 more OpenMP directives Src/LinearSolvers/C_TensorMG/DV_3D3.F commit ea6bd912f7b9d26680ba79dda8909559043f4f8f Author: lijewski Date: Wed Oct 7 18:06:04 2009 +0000 added some d0's on constants Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit 82980c56b811c2dacbca649fb30d3610ca162cbf Author: lijewski Date: Wed Oct 7 17:58:54 2009 +0000 added some d0's on constants Src/LinearSolvers/C_TensorMG/DV_3D4.F commit a54a1233dbdd021e110cbec48cb05cb624eb8ab1 Author: lijewski Date: Wed Oct 7 17:58:29 2009 +0000 little simplification Src/LinearSolvers/C_CellMG/LO_3D.F commit c3afbd1cdf9f287fb6b2318a39d055da68df5a6c Author: lijewski Date: Wed Oct 7 17:31:01 2009 +0000 workaround for PGI OpenMP bug Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit fb01e4673a3e8275aa8e6ec5cf69a5186e465ef7 Author: lijewski Date: Wed Oct 7 17:30:20 2009 +0000 bug fix -- misspelled couple private() variables for OpenMP Src/LinearSolvers/C_TensorMG/DV_3D3.F commit 204cd91eb60fce5b57654d80582152a98433b1bf Author: gpau Date: Wed Oct 7 17:03:51 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileXAve.H Tools/C_util/Statistics/PltFileXAve.cpp commit e6b48ef0e4dcd28e0b949ed9182cb3f25dedae4b Author: gpau Date: Wed Oct 7 16:35:31 2009 +0000 added some functionalities Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.H Tools/C_util/Statistics/PltFileXAve.cpp commit c526b79ebb13794d92e56822a90264158e78674a Author: lijewski Date: Tue Oct 6 21:40:30 2009 +0000 removed FORT_SCALADDTO() -- doesn't appear to be used Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H commit 14fe6165b30987e146c2c7232ef7439637611633 Author: lijewski Date: Tue Oct 6 21:37:14 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/DV_3D3.F commit f848933bd030b82fc85bea886b513ed6fbff4716 Author: lijewski Date: Tue Oct 6 20:30:16 2009 +0000 added FORT_FASTONENORM() and FORT_FASTZERONORM() Src/C_BaseLib/SPECIALIZE_1D.F commit 30a0ab6509d2aa0efbb12a83c30179c44a52c493 Author: vince Date: Tue Oct 6 20:00:31 2009 +0000 addend angilas support for mpi. Tools/C_mk/Make.mpi commit cab02bc5b42604b077a9b7de41010dd911a9a3f2 Author: lijewski Date: Tue Oct 6 16:02:18 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/DV_3D2.F commit 856313cdb7944a25e459322bc4b2ef0453672e56 Author: lijewski Date: Mon Oct 5 22:49:21 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/DV_3D1.F commit 3de92ff738ace578516063104bcb4b47a389e4b2 Author: almgren Date: Mon Oct 5 21:51:07 2009 +0000 Added 1D versions of all the routines. Src/LinearSolvers/F_MG/nodal_divu.f90 commit f93a35553e888c7bbecd959dab91740369a240d5 Author: lijewski Date: Mon Oct 5 21:47:50 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit f523c10bb71eaad8bbfec094b43a231a268abd02 Author: lijewski Date: Mon Oct 5 21:13:20 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit 8f843b51fe373c502e16fa35ad32a5de2c8deb33 Author: lijewski Date: Mon Oct 5 20:42:30 2009 +0000 more OpenMP stuff Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_proj3d.f commit 23d74f51420c0b7ed2457df440ac60d67799d787 Author: lijewski Date: Mon Oct 5 16:41:30 2009 +0000 OpenMP'd hgints() hgrlxu() & hgresu() Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 89355c93c455c9ea971a1e1688544e4abaf23e6d Author: gpau Date: Fri Oct 2 00:36:14 2009 +0000 added pdf function. Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp commit 4af32fa290957e1c7f20d5e9bdcf0dcbf5047efd Author: lijewski Date: Thu Oct 1 21:20:40 2009 +0000 OpenMP'd node_bilinear_interp Src/C_AMRLib/INTERP_3D.F commit a2a1ab6f0d0a0656c0423170731f8c3916bef379 Author: lijewski Date: Thu Oct 1 20:51:08 2009 +0000 *** empty log message *** Src/C_AMRLib/INTERP_3D.F commit 9b1df818863c64af8499354c74ccb1a5b81f64d9 Author: lijewski Date: Thu Oct 1 19:30:58 2009 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit 8cda9b7b56d1d8067e4c927550994f123aab2da3 Author: lijewski Date: Thu Oct 1 18:18:10 2009 +0000 Added specialized version of 0 & 1 norms for Real in Fortran Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 6be3eccc5ae9af20c6b218a67a69de37f691d3c8 Author: lijewski Date: Tue Sep 29 20:42:36 2009 +0000 removed WorkQueue stuff Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit de6ef6dbb5f20e5d624841601e51e2d3ec5727da Author: lijewski Date: Mon Sep 28 21:29:25 2009 +0000 removed all BL_THREAD junk Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit e5a5d0134f994cb435a46272d7928712797b0bed Author: lijewski Date: Mon Sep 28 21:13:32 2009 +0000 SELECT instead of IF Src/LinearSolvers/C_CellMG/LO_3D.F commit 18b873055090fb42fa6e89e2bcbb2ffa7b52f066 Author: lijewski Date: Mon Sep 28 21:13:06 2009 +0000 removed FORT_CGPRECND() Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_F.H commit 6e680886fca4e744f54a528a9cb4f6e6463ef72d Author: lijewski Date: Mon Sep 28 20:29:59 2009 +0000 use SELECT instead of IF Src/LinearSolvers/C_CellMG/LO_3D.F commit 800dfc71c75570ec06618ad13892acbf39e08652 Author: lijewski Date: Mon Sep 28 20:14:48 2009 +0000 some simplification of APPLYBC() Src/LinearSolvers/C_CellMG/LO_3D.F commit fe1895451dde40a1010142c1a444e3ca272cedea Author: lijewski Date: Mon Sep 28 19:23:01 2009 +0000 more OpenMP tweeking Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit 92cab89a0c40fc11cc155ad0309f9ddcbe7eb76f Author: lijewski Date: Mon Sep 28 19:13:53 2009 +0000 OpenMP'd Src/LinearSolvers/C_CellMG/ABec_3D.F commit 8304e9cf2f1761a275457ae48493d02edb086418 Author: lijewski Date: Mon Sep 28 18:09:11 2009 +0000 yet more OpenMP tweeking Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit 48a819b69d5aded6d0a685804bb7ef44d2207999 Author: lijewski Date: Mon Sep 28 17:57:54 2009 +0000 more OpenMP tweeking Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit ee17182b5900120aad0077833b9687bc982da715 Author: lijewski Date: Mon Sep 28 17:51:35 2009 +0000 OPenMP'd Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit 2c58407b3767c3c3700e6e618b31082458e44ca7 Author: nazgul Date: Mon Sep 28 17:06:21 2009 +0000 Updated compiler options for Atlas. -mp is deprecated. Using -fp-model fast=2 instead. Louis Tools/C_mk/Make.Linux commit 233d5536f3a6329ff3836febd7489ec4373393c6 Author: lijewski Date: Mon Sep 28 17:05:50 2009 +0000 removed OpenMP directives -- slowed down test case Src/LinearSolvers/C_CellMG/CG_3D.F commit d3f560a49ba9ea9ac33caeb0bdabad9afa5e3fe7 Author: lijewski Date: Mon Sep 28 16:46:16 2009 +0000 added some OpenMP macros Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit e2eec3918bb0ba6a06186d3a4c9036800cba2822 Author: lijewski Date: Fri Sep 25 23:18:53 2009 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 0dbe06b78006d93746a9376321726387937d3236 Author: lijewski Date: Fri Sep 25 21:24:22 2009 +0000 disable -Ofast for PathScale C++ compiler - causes bug in mglib on franklin Tools/C_mk/Make.Linux commit e55cc43b6437f4cd0d773b6b0948ac942e5413e1 Author: lijewski Date: Fri Sep 25 18:04:31 2009 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/inputs.3d Tests/LinearSolvers/C_CellMG/inputs.3d commit 78ab25819a885c18ce281ded321072e16207b423 Author: lijewski Date: Fri Sep 25 03:50:56 2009 +0000 rearranged some OpenMP stuff Src/C_AMRLib/INTERP_3D.F commit e4a3d304e1d6686bf01e22ff39c44841115a4ffc Author: lijewski Date: Thu Sep 24 21:48:47 2009 +0000 added some OpenMP directives linccinterp Src/C_AMRLib/INTERP_3D.F commit ce195cc6e41a8900a7a51b1f6d529b6266a74065 Author: lijewski Date: Wed Sep 23 21:59:07 2009 +0000 some OMP stuff Tools/C_mk/Make.Linux commit 3e4c3aff2520d88213f0d3e7f42a2bbd0c0aa5d9 Author: lijewski Date: Fri Sep 18 22:10:33 2009 +0000 some OpenMP stuff Tools/C_mk/Make.defs commit 8b9c3b09fb9cbe49c6a45beabd9cf61e79d5383d Author: ajnonaka Date: Fri Sep 11 23:26:57 2009 +0000 OMP=t option for PGI on franklin Tools/F_mk/GMakedefs.mak commit 0c9e3e2092be5b6c5450100c9172123a498f9c6e Author: vince Date: Fri Sep 11 18:20:09 2009 +0000 more 11.1. Tools/C_mk/Make.defs commit a845ca1e1403982321ba0cfd70a2061994deeb77 Author: vince Date: Fri Sep 11 18:13:19 2009 +0000 intel 11.1. Tools/C_mk/Make.defs commit 3146307098c040dd3d40c932df5e98f26f37c3aa Author: ajnonaka Date: Thu Sep 10 22:20:02 2009 +0000 on franklin with pathscale, now you can turn on openmp with OMP=t in your make line Tools/F_mk/GMakedefs.mak commit 2f22cc503b5806f30bf8f29a7099c82c30304a12 Author: lijewski Date: Wed Sep 2 17:50:59 2009 +0000 now pass problo and probhi optionally to ml_multifab_write Src/F_BaseLib/fabio.f90 commit 692cce43310274e14e28e732fa1fdce504513b84 Author: mzingale Date: Wed Sep 2 16:27:58 2009 +0000 no longer abort if a plotfile variable is not found in plotfile_var_index, instead just return -1. The calling program should test on the output. This allows you to test for the presence of variables. Src/F_BaseLib/plotfile.f90 commit ac85f01322d3b255d3d4762cc7cdac7c796d4156 Author: lijewski Date: Fri Aug 28 16:55:31 2009 +0000 default refine_grid_layout to false Src/C_AMRLib/Amr.cpp commit d2d3379dd9b5aff3faad56b263ef464120054e6d Author: ajnonaka Date: Wed Aug 26 22:24:39 2009 +0000 got rid of the nx,ny,nz stuff by passing in hi(:) instead Src/F_BaseLib/tag_boxes.f90 commit afeeeae7396be0ff6d9d4928c2ad596ad14e354b Author: mzingale Date: Sun Aug 23 15:42:59 2009 +0000 add a routine that calls the C getcwd function to return the output directory -- for logging purposes. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_system.f90 Src/F_BaseLib/system_util_c.c commit 62a42f9f7ef63102051de5501e029c7ffc761bc8 Author: almgren Date: Thu Aug 20 20:52:56 2009 +0000 oops -- left in print statement by accident. Src/LinearSolvers/F_MG/mg.f90 commit 382d692ba0de1b809948fcc2f6938ca1910fb32e Author: almgren Date: Thu Aug 20 20:49:35 2009 +0000 Redefine "lcross" and call nodal_smoother_1d instead of nodal_line_solve_1d. Src/LinearSolvers/F_MG/mg.f90 commit 7e07dd5e8ef38df671ba753b25c6d9580772c7d7 Author: almgren Date: Thu Aug 20 20:48:56 2009 +0000 1) Add nodal_line_solve_1d. 2) Modify nodal_smoother_1d to be red-black. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 410aadd0346e47d6fbfc5d9b6c5f42b211ef38ba Author: almgren Date: Thu Aug 20 20:48:18 2009 +0000 Add call to fine_edge_resid_1d instead of aborting. Src/LinearSolvers/F_MG/ml_util.f90 commit 7c58a40dfe122b7ed606a3eeb2cdf61e4927677e Author: almgren Date: Thu Aug 20 20:47:53 2009 +0000 Fix fine_edge_resid_1d. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit df33e3f00bbbe8ecfd666d5b5b0946dac7ec6c6a Author: almgren Date: Tue Aug 18 02:05:31 2009 +0000 Add 1d version of subtract_divu_from_rhs. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 17cc21e18b3a81b42c271d0756448d1153ce9ff4 Author: almgren Date: Fri Aug 14 22:28:31 2009 +0000 Fix indexing in 1d. Src/LinearSolvers/F_MG/stencil.f90 commit 50a9a8adfcbb31f1549c5840e9765e82c0d1de26 Author: almgren Date: Fri Aug 14 22:21:48 2009 +0000 Fix typo. Src/LinearSolvers/F_MG/stencil.f90 commit 743ceb63f678848868e038223e44dad5b19c417a Author: almgren Date: Fri Aug 14 22:21:05 2009 +0000 Fix stencil_apply_1d. Src/LinearSolvers/F_MG/stencil.f90 commit 5484d0b623a555fa658713f751cb114ec61f2ba0 Author: almgren Date: Fri Aug 14 22:20:18 2009 +0000 1) Fix bug in stencil_1d_apply 2) Modify stencil_1d_apply and stencil_2d_apply to take lo and hi as inputs so we can more easily debug with the actual indices. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/stencil.f90 commit b2d7afcb713565822499ee4463cd3f64b09959b8 Author: almgren Date: Fri Aug 14 22:09:47 2009 +0000 Added 1d capability. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 commit ab657f19139e0fb8f607a9d8a068e09548ba3f63 Author: almgren Date: Wed Aug 12 22:38:28 2009 +0000 Use lo(:),hi(:) instead of nx,ny,nz for easier debugging. Src/LinearSolvers/F_MG/stencil.f90 commit 43fbacb7d1feb6653522979e48aa2fd77d629ed5 Author: almgren Date: Tue Aug 11 20:28:28 2009 +0000 Explicitly add climits. Src/C_AMRLib/TagBox.cpp commit 7b4bdd9709fefe549a4ba7945f0566d110cdc5cc Author: almgren Date: Tue Aug 11 17:11:19 2009 +0000 Fixed a bug -- we didn't use to call crse_fine_residual from applyop so the coarse grid cell next to a fine grid had the wrong residual. Src/LinearSolvers/F_MG/ml_cc.f90 commit aef96086fc2d7e2f92b6591c89941f140f0caa2e Author: ajnonaka Date: Fri Aug 7 17:16:29 2009 +0000 added .smp to executable if smp is true Tools/F_mk/GMakedefs.mak commit e135151ab74d0dbf4c00104267ac4629b39c6ef4 Author: mzingale Date: Fri Aug 7 15:15:04 2009 +0000 add some error checking to the copying of inputs, probin, and the auxfiles Tools/C_util/regtests/test.py commit b2936eb471362c05ae43f01281a69cd3766ad03c Author: almgren Date: Thu Aug 6 21:51:36 2009 +0000 Fixed the Minion "full" stencil which is used for variable density. Src/LinearSolvers/F_MG/stencil.f90 commit 6ce45c515b0921b32ef041cdf6a6f5f7bdebe764 Author: mzingale Date: Tue Aug 4 19:17:19 2009 +0000 update to reflect new directory locatios Tools/C_util/regtests/Castro-tests.ini commit 5e3494fc35ecdeacc6781a805fefe95215c91290 Author: mzingale Date: Tue Aug 4 18:58:49 2009 +0000 on second thought, update -d for CASTRO is a bad idea Tools/C_util/regtests/test.py commit 63adde2b360c7039c462262c9d8bc20e0d4bbf40 Author: mzingale Date: Sun Aug 2 14:37:03 2009 +0000 do a CVS update -d to capture new directories. only take the file name (not relative path) for the auxFiles when copying to the web directory Tools/C_util/regtests/test.py commit 53096042efa0fb8c34e5f5306dbbe5d87ebd6eff Author: mzingale Date: Sun Aug 2 00:59:32 2009 +0000 update to reflect new directory structures and no more grid files Tools/C_util/regtests/Maestro-tests.ini commit c01a45803842890156dff1646925229ee0c74e0c Author: mzingale Date: Thu Jul 30 19:44:28 2009 +0000 add a check that if there is a floating point constant that it be a double precision constant. At the moment, it catches a bunch, but has too many false positives Tools/F_scripts/fcheck.py commit dafbbb5faad0c335e3ac53f08b5c66891b361c7b Author: mzingale Date: Thu Jul 30 17:19:13 2009 +0000 the start of a simple script to check that quantities are allocated correctly in our Fortran code. At the moment, it looks for all the 'real' variables that aren't 'dp_t'. Next up is checking all the constants. Tools/F_scripts/fcheck.py commit a6dfeb036d5a83c2fe637c1fd92832d2813577e3 Author: ajnonaka Date: Thu Jul 30 15:58:14 2009 +0000 on franklin, hpctoolkit will compile in if you add "USE_HPCTOOLKIT=t" when you make Tools/F_mk/GMakedefs.mak commit b3c0a0b446985e6f9d690a56ad3a77bfec6b195c Author: ajnonaka Date: Thu Jul 30 15:40:58 2009 +0000 mpi stuff for surveyor at argonne Tools/F_mk/GMakeMPI.mak commit de806a853632d6fb456674b93cdf78851e5e1292 Author: almgren Date: Mon Jul 27 21:50:16 2009 +0000 Remove unused variable. Src/LinearSolvers/F_MG/ml_cc.f90 commit c111ed4badf4e9bd74eb2f9c7858076e4bb6f779 Author: almgren Date: Mon Jul 27 21:48:37 2009 +0000 Remove extra print statement. Src/LinearSolvers/F_MG/ml_cc.f90 commit 1dbb1becf35729a1a328862012689fcad614a10f Author: almgren Date: Mon Jul 27 20:55:17 2009 +0000 Shouldn't have had print statement and stop in there. Src/LinearSolvers/F_MG/ml_cc.f90 commit 733c9df5ab2119bbf1f3201155656092698a982f Author: almgren Date: Mon Jul 27 20:28:31 2009 +0000 Dont need to restrict rh(n) onto rh(n-1) in applyop since rh is identically zero. Src/LinearSolvers/F_MG/ml_cc.f90 commit a799ef17c94f14045aea67d8edce7d2fb7333a91 Author: lijewski Date: Fri Jul 24 19:14:09 2009 +0000 removed cache junk Src/C_AMRLib/Amr.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 19b4551134682222d5c68bf90462faef08ec7213 Author: lijewski Date: Fri Jul 24 17:46:18 2009 +0000 default copy cache back to on with max size to 10 Src/C_BaseLib/FabArray.cpp commit cbe8c29fe1a84bb9a21bd20b7fb6b587d1e96745 Author: lijewski Date: Thu Jul 23 22:26:01 2009 +0000 refine_grid_layout only does grids below new_finest Src/C_AMRLib/Amr.cpp commit c424c1e4c55db25952c27d7770c5adaa021b0ec1 Author: mzingale Date: Thu Jul 23 16:50:07 2009 +0000 add some useful debugging flags, commented out Tools/F_mk/GMakedefs.mak commit 39d0aaaa342dee7183b2dbb40096dadd75c8e7ed Author: lijewski Date: Tue Jul 21 21:19:21 2009 +0000 fixed bug in grid_places() Src/C_AMRLib/Amr.cpp commit df9a4535b6695bb0511b0025e809d509b18a1ae8 Author: lijewski Date: Thu Jul 16 18:01:27 2009 +0000 break up crse domain using maxSize() Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp commit 6eee76e2dd65121cc76bd577ee1d446f5178b67e Author: lijewski Date: Thu Jul 16 17:37:20 2009 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/Test/inputs3D Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/inputs3D Tests/LinearSolvers/C_TensorMG/testVI.cpp commit e763480dc18879480108714d8c19e8f4a349f239 Author: lijewski Date: Thu Jul 16 16:59:51 2009 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/Test/grids/gr.3_2x3x4 Src/LinearSolvers/C_TensorMG/Test/grids/gr16.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr16x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr2D Src/LinearSolvers/C_TensorMG/Test/grids/gr32.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr32x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr64.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr8.dog Src/LinearSolvers/C_TensorMG/Test/inputs3D Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/grids/gr.3_2x3x4 Tests/LinearSolvers/C_TensorMG/grids/gr16.dog Tests/LinearSolvers/C_TensorMG/grids/gr16x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr2D Tests/LinearSolvers/C_TensorMG/grids/gr32.dog Tests/LinearSolvers/C_TensorMG/grids/gr32x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr64.dog Tests/LinearSolvers/C_TensorMG/grids/gr8.dog Tests/LinearSolvers/C_TensorMG/inputs3D Tests/LinearSolvers/C_TensorMG/testVI.cpp commit 974f1ca7a197bc86502d0cb16e3171c50dd934c5 Author: lijewski Date: Thu Jul 16 16:32:44 2009 +0000 first cut at bringing up-to-date Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/Make.package Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Src/LinearSolvers/C_TensorMG/Test/main_F.H Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/C_TensorMG/testVI.cpp commit e998bb1459e14eba409f3a30ab0ec13b5469cb70 Author: lijewski Date: Mon Jul 13 20:18:28 2009 +0000 removed simplify() in initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit 9f2b21fa47f009e8cc3b4fe49120e51785f1dd7a Author: lijewski Date: Mon Jul 13 20:17:24 2009 +0000 removed simplify() in GetBndryCells Src/C_BaseLib/BoxArray.cpp commit 2da1b61382fe2cc88e19059bad30aff98e6a1977 Author: lijewski Date: Sun Jul 12 00:38:32 2009 +0000 fpb_cache_max_size now defaults to 10. Src/C_BaseLib/Geometry.cpp commit 0691b8449fb83b8976819432edb94957d400982c Author: lijewski Date: Sat Jul 11 03:01:19 2009 +0000 max_live_tasks now defaults to 50. Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit df8da84c11747be6f7b6151a2029a21f93d2cf61 Author: lijewski Date: Sat Jul 11 00:49:21 2009 +0000 use_copy_cache now defaults to false. Src/C_BoundaryLib/FabSet.cpp commit 594b59f2e860bf8a655f57d467dacdb18cd548dd Author: lijewski Date: Sat Jul 11 00:45:49 2009 +0000 use_copy_cache now defaults to false. fb_cache_max_size now defaults to 10 instead of being unlimited. Src/C_BaseLib/FabArray.cpp commit 9bbb18111bfccfa2ec3db1dc12c5e43538ec3235 Author: ajnonaka Date: Fri Jul 10 19:27:56 2009 +0000 allocate arrays at runtime instead of on the stack Src/F_BaseLib/interp.f90 commit 9da504dbb56ec1a9f94e34f213a3d0bf54e20055 Author: ajnonaka Date: Fri Jul 10 19:27:45 2009 +0000 fix a copy statement which was not compatible with intel 9.1.043 Src/F_BaseLib/fillpatch.f90 commit 322c9ce684e52a2c234b1f582ea6af4335d2572f Author: mzingale Date: Mon Jul 6 20:57:53 2009 +0000 for intel, in debug mode, also set -u, which enforces 'implicit none' -- just in case we missed one somewhere Tools/F_mk/GMakedefs.mak commit 54fb9bc9ca5e1b7aebf526bc0172fb0f2938a751 Author: ajnonaka Date: Fri Jun 19 22:45:25 2009 +0000 got USE_SMP to compile on intrepid Tools/C_mk/Make.mpi commit 0aa6f11b17e4fa58a9e987f432171ef2a733558c Author: ajnonaka Date: Fri Jun 19 22:32:03 2009 +0000 compiles now with SMP on intrepid Src/LinearSolvers/F_MG/mg_smoother.f90 commit 9e2b2d99b946f282226418301e135ef5c8813123 Author: lijewski Date: Fri Jun 19 21:07:13 2009 +0000 SMP -> USE_SMP=TRUE Tools/C_mk/Make.mpi commit 256723f4a06c3311e28f8f3bd45beb98ebab66c3 Author: lijewski Date: Fri Jun 19 19:20:17 2009 +0000 added simplify() and maxSize() to GetBndryCells() Src/C_BaseLib/BoxArray.cpp commit e564aa84b6950efec91ba94eb6ee3c8ed2d3cad2 Author: lijewski Date: Thu Jun 18 17:16:36 2009 +0000 more work on intrepid Tools/C_mk/Make.mpi commit 7741caab76cfd3dd310d930e0d69a97c13d09fd3 Author: lijewski Date: Thu Jun 18 16:54:34 2009 +0000 some work getting HyperCLaw to compileon intrepid Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 5cd003ef8ed703dd7facc36088c9dcdc1317151d Author: lijewski Date: Wed Jun 17 15:54:28 2009 +0000 *** empty log message *** Src/C_AMRLib/AuxBoundaryData.cpp commit 031bb5a250882a0e41d3c2b3b2da79a4b9313b68 Author: almgren Date: Tue Jun 16 23:04:38 2009 +0000 Add Barrier calls at the end of Amr::writePlotFile and Amr::checkPoint. Hopefully this fixes the problems we've been having on della.princeton.edu Src/C_AMRLib/Amr.cpp commit 0ee8ecdb48b6d9d1dfe4fe6ec5302f206e37210f Author: mzingale Date: Wed Jun 3 21:02:03 2009 +0000 update to reflect current problem setups Tools/C_util/regtests/Maestro-tests.ini commit 90a8d03be924217988205afd707fd248174cf439 Author: ajnonaka Date: Wed Jun 3 16:34:09 2009 +0000 added parallel_barrier call to parallel_initialize to give timers better performance Src/F_BaseLib/parallel.f90 commit d5fe0c040af14a8ed008b5578f6ae3e8a339b815 Author: ajnonaka Date: Tue Jun 2 21:38:51 2009 +0000 made timer output much more readable added additional timers in put_1d_array_... Src/F_BaseLib/bl_prof.f90 commit 37d7652d9a7e9734e943cdb8671a6258ccbe80f4 Author: lijewski Date: Tue Jun 2 02:51:02 2009 +0000 Added new version of CrseInit() that takes a single MultiFab. This is meant to replace the weird version that takes a FArrayBox and has to be followed by a call to CrseInitFinish(). Codes should set themselves up to use this version, as the FArrayBox version appears to use too much memory in high CPU/high grid count scenarios. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 85a4df50ca133d76788298447b16527b53f05ff8 Author: lijewski Date: Fri May 29 23:38:59 2009 +0000 default verbose to false for CrseInitFinish() Src/C_AMRLib/FluxRegister.cpp commit 8085995aed6539d36845b86070cb05fb7f1635e1 Author: lijewski Date: Fri May 29 23:15:57 2009 +0000 some instrumentation for CrseInitFinish() Src/C_AMRLib/FluxRegister.cpp commit 1da5a38714e6e65a5e71e5af6a82d71f62f30391 Author: ajnonaka Date: Fri May 29 21:57:03 2009 +0000 #pathscale friendly Src/C_BaseLib/FabArray.H commit f6ff4077e58b83ab5516da7d349aadf4f6d619e1 Author: lijewski Date: Fri May 29 21:54:15 2009 +0000 more instrumentation Src/C_BaseLib/FabArray.H commit 99d6f761e17842d953ece0b7ff4c742ceb1380ff Author: lijewski Date: Fri May 29 21:13:35 2009 +0000 added some instrumentation to CollectData() Src/C_BaseLib/FabArray.H commit bda7b8118f78d256bc5e8b693dc017ac834b8311 Author: lijewski Date: Wed May 27 21:36:59 2009 +0000 parallel speedup to linComb() Src/C_BoundaryLib/FabSet.cpp commit 024a0157d18d2cbb080f061758f35ee75eac1f3e Author: lijewski Date: Wed May 27 21:08:21 2009 +0000 parallel speedups for Reflux() and CrseInit() Src/C_AMRLib/FluxRegister.cpp commit cf7f5cd4274db0df6027a3c4ec08c36553e21aff Author: lijewski Date: Tue May 26 21:02:40 2009 +0000 added timer to initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit f7de295d31c0ead4e4dd32cfe98681d19647d6ed Author: lijewski Date: Tue May 26 20:40:00 2009 +0000 verbose flag and some timers Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit f8b29412b67cc326f96cadb20b530d742d4fa80b Author: lijewski Date: Tue May 26 20:20:52 2009 +0000 some timers Src/C_AMRLib/AmrLevel.cpp commit 677cd16dfd3567b4340838087b2911604d7aed22 Author: almgren Date: Tue May 26 17:19:02 2009 +0000 Remove unused variables bxa_src and bxa_dst. Src/F_BaseLib/layout.f90 commit 9656d87a05a795f58192bfa552633709e282b2c3 Author: lijewski Date: Mon May 18 16:51:25 2009 +0000 removed unused code in TagBox::coarsen() Src/C_AMRLib/TagBox.cpp commit 73dfac0c21a064036be7896d364afac880d9506f Author: gpau Date: Fri May 15 16:51:34 2009 +0000 MultiFab::Initialize() called in BoxLib::Initialize() Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit af4d4cd94756b1f981e9ff93bc6e38638cc6027f Author: ajnonaka Date: Mon May 11 20:57:52 2009 +0000 added f90sources += mt19937ar.f90 Tests/LinearSolvers/F_MG/GPackage.mak commit 329a24a91a81157ed85fbe116e4b2d6f89a7ea24 Author: almgren Date: Sun May 10 05:11:16 2009 +0000 Added 3d Minion stencil. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/stencil.f90 commit a296ed03e5364afbd69c0cb93c6cdb59dbb18dbb Author: lijewski Date: Fri May 8 18:07:31 2009 +0000 attempt to deal with empty case Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/AuxBoundaryData.cpp commit 6289cda4dffa74f575c50c88d64b9cd69a743c19 Author: almgren Date: Wed May 6 23:50:04 2009 +0000 Put the minus sign back into minion_full_fill_2d. Src/LinearSolvers/F_MG/stencil.f90 commit 53b7400ce572d00c2fc00d1f50572a38feef0d9f Author: almgren Date: Wed May 6 23:40:12 2009 +0000 Fix up stencil... Src/LinearSolvers/F_MG/stencil.f90 commit 7a2919f92441d1d81cf919d4b6dca66a2068b439 Author: almgren Date: Wed May 6 22:50:02 2009 +0000 Generalize to coeffs having more than one ghost cell. Src/LinearSolvers/F_MG/stencil.f90 commit 64edf3ab2c0fea76d44a58c39da0d7e552fd84eb Author: almgren Date: Wed May 6 21:49:33 2009 +0000 Uncomment lines. Src/LinearSolvers/F_MG/stencil.f90 commit 0b000400628a6a00fe920341bf58bcd54a93aa49 Author: almgren Date: Wed May 6 21:37:40 2009 +0000 Fix stencil in stencil_minion_full_fill. Src/LinearSolvers/F_MG/stencil.f90 commit 0317b0185c6e2572b934f700d248f80b37971ee4 Author: almgren Date: Wed May 6 20:56:00 2009 +0000 Add stencil for 25-point minion solve. Src/LinearSolvers/F_MG/stencil.f90 commit bcd0b66f6efb70348cb5554a2b7a576a487c2d76 Author: almgren Date: Wed May 6 17:27:54 2009 +0000 Adding stencil_minion_full_fill_2d... Src/LinearSolvers/F_MG/stencil.f90 commit 07a9571c662d47e972c13d641364089476d38aba Author: almgren Date: Wed May 6 16:50:23 2009 +0000 Added new MINION type -- full vs cross. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/stencil.f90 commit f87c96e2386349f33302db3ee6cec045cd15d7d1 Author: mzingale Date: Mon May 4 17:21:21 2009 +0000 define a new method, plotfile_var_index that returns the index in the fab corresponding to a plotfile name. Rewrite fwdconvect to use this. Src/F_BaseLib/plotfile.f90 commit d42b178acafc20cccbd26cfec46a8b2b7ea67473 Author: gpau Date: Sat May 2 00:40:33 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileXAve.cpp commit e9f220ef0ca9176d69517d317d1eb357612786fe Author: almgren Date: Thu Apr 30 22:04:28 2009 +0000 Fix print statement for going down in V-cycle. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit efa99c1059bdec0e3cf67fb775035849d36a78a7 Author: lijewski Date: Thu Apr 30 17:34:34 2009 +0000 disallowed copy constructor & assignment operator Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit 3d4f3f39769cc63e9438db3a3f27efbb9cee3711 Author: gpau Date: Fri Apr 24 19:21:35 2009 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit e57e5ad810d0300c9976e78b2f17b347cf2df8dc Author: almgren Date: Tue Apr 21 19:40:00 2009 +0000 Fixed verbosity again. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 45bcfcb78772aa6e54ade822ea9f937986a8554a Author: almgren Date: Tue Apr 21 19:21:16 2009 +0000 Modified verbosity -- added extra verbosity to Multigrid when verbose > 1.Z Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 622b579bbf4a996677c13893c2dc7a307dac0817 Author: ajnonaka Date: Tue Apr 21 17:22:08 2009 +0000 boxassoc deallocate statements weren't being counted properly Src/F_BaseLib/layout.f90 commit d310552aa9c26e69e853fc2bb10b23477d0ddc37 Author: ajnonaka Date: Tue Apr 21 17:04:25 2009 +0000 plugged memory leak Src/LinearSolvers/F_MG/mg.f90 commit 75ae9a4657d0629e17cfbf4b4946b98001416906 Author: ajnonaka Date: Mon Apr 20 22:07:06 2009 +0000 PathScale with MPI works on jaguar Tools/C_mk/Make.mpi commit 56c88b2ed1e4b43e256b4e5ad0fcdc52460283f1 Author: almgren Date: Mon Apr 20 21:44:03 2009 +0000 We need i3 not i2 to print nboxes in layout_print. Src/F_BaseLib/layout.f90 commit 54a1353e4cf3e1cc0fd0599787710ce55b4e7ceb Author: almgren Date: Mon Apr 20 19:41:19 2009 +0000 Need to have a ghost cell for rh when nodal. Src/LinearSolvers/F_MG/mg.f90 commit 66f84d07ba1d41f290b14325709d1e4746f3baf1 Author: almgren Date: Mon Apr 20 17:38:34 2009 +0000 Formatting only. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 837f1a9d0db7bbcff2c54075f8d31d74746181a8 Author: almgren Date: Sat Apr 18 03:21:20 2009 +0000 Dont think we need to include mlmg.f90 in a make... do we? Src/LinearSolvers/F_MG/GPackage.mak commit ea898a3775e37dcbec1ed6c5be6f481f2b8a55d8 Author: almgren Date: Sat Apr 18 03:20:11 2009 +0000 Fix case where we set bottom_solver_eps = eps when only one mg_level -- we only want this in the case when it's not being called as a bottom solver for another mgt, so here we test on volume ... this should work well enough for now. Src/LinearSolvers/F_MG/mg.f90 commit 47c76a0f45c536a1ee72bc8e0d2a5a7599dfe83d Author: almgren Date: Fri Apr 17 21:36:12 2009 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit ef063901016ee129a40f49e4a9e65411300b7b9a Author: almgren Date: Fri Apr 17 21:20:46 2009 +0000 IF nodal and using CG or BiCG as bottom solver then build the nodal mask at the bottom solver level ahead of time and pass it in to the BiCG or CG routine so that they can pass it into the multifab_dot routine so we don't build it every time the dot routine is called. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 commit 5ce340f53976b6e48fb5bc2285c738a22ecb72cf Author: almgren Date: Fri Apr 17 21:19:14 2009 +0000 Added optional nodal_mask argument to multifab_dot which computes a dot product. Without the nodal_mask argument present the multifab_dot function still builds and destroys the nodal mask every time it is called. Src/F_BaseLib/multifab.f90 commit 2c639c65a9d4b202bca45d0e5855c4d10333901c Author: ajnonaka Date: Thu Apr 16 22:20:08 2009 +0000 plugged memory leak Src/LinearSolvers/F_MG/mg.f90 commit 6098ec080a21191af0afe9b90e5282b1108298eb Author: almgren Date: Thu Apr 16 21:44:46 2009 +0000 Make sure to allocate bottom_uu and bottom_rh as nodal if need be. Src/LinearSolvers/F_MG/mg.f90 commit d56a1d4b3acdf720a33817f33cdd5f09826ffd9d Author: ajnonaka Date: Thu Apr 16 20:38:46 2009 +0000 added timer for build_nodal_dot_mask Src/F_BaseLib/multifab.f90 commit 728504d5409cb9681b6b3be21a2db20a3b39d8f0 Author: almgren Date: Thu Apr 16 17:30:46 2009 +0000 Put in the interface for bottom_solver = 4 option with the nodal solver. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit b95cd5946289566597eab554215d43fff0f95924 Author: almgren Date: Thu Apr 16 17:24:07 2009 +0000 New stuff for bottom_solver = 4. Src/LinearSolvers/F_MG/mg.f90 commit 51ebe9f074d74fd2beb183f1d667f59ba2409fde Author: almgren Date: Thu Apr 16 17:22:11 2009 +0000 Pass bottom_mgt through as an optional argument. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 0ef7e75c190276c3fda905cb42fb4c73d04e7a6c Author: lijewski Date: Tue Apr 14 17:03:04 2009 +0000 try to print out something useful when trees unbalanced Src/F_BaseLib/bl_prof.f90 commit 49febc0bd73770f71600047f2918dc22ce955f2c Author: lijewski Date: Mon Apr 13 23:07:29 2009 +0000 removed uses of reshape() Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 37476df877b81013160e141b6377adfd7566959e Author: lijewski Date: Mon Apr 13 17:17:03 2009 +0000 removed av member of comm_dsc type Src/F_BaseLib/layout.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 78bd2dbc8c0cd47587c37f47e715d8341449e2d6 Author: vince Date: Tue Apr 7 20:39:54 2009 +0000 added def for HOST if not set. Tools/C_mk/Make.mpi commit 0992475d704b6cbcd10e00c023e5018b6de4d1f7 Author: vince Date: Tue Apr 7 17:37:20 2009 +0000 updated gojira. Tools/C_mk/Make.mpi commit fa539e3d84035468cb64f3eb59044c50d3871af1 Author: gpau Date: Sun Apr 5 15:28:42 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileXAve.cpp commit 482343aae49f83e8a50787e54d82aea0b8e725f4 Author: ajnonaka Date: Fri Apr 3 20:38:04 2009 +0000 better job with timer formatting Src/F_BaseLib/bl_prof.f90 commit 06545e741fa6fdb26859e0dc20922cdbe5a949ed Author: lijewski Date: Fri Apr 3 20:19:05 2009 +0000 *** empty log message *** Tests/LinearSolvers/F_MG/inputs commit c4cafc5eea9df771630b00141a00f0dc8c24114c Author: lijewski Date: Fri Apr 3 20:15:11 2009 +0000 some simplification Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit c5374325b4f2f16a8ccc1660b4718d9ea52dfb77 Author: ajnonaka Date: Fri Apr 3 20:02:53 2009 +0000 changed the bl_timer output width to 40 characters so you can actually see what's being called... Src/F_BaseLib/bl_prof.f90 commit 860d90b66cc5dfdf7cc926a16c4e5e22da121edd Author: lijewski Date: Thu Apr 2 19:31:52 2009 +0000 more verbose output Src/F_BaseLib/layout.f90 commit 79cfe78bbb56aabc67de372fdad0863bb2586e04 Author: lijewski Date: Thu Apr 2 17:20:29 2009 +0000 added simple hash to speed up copyassoc matches Src/F_BaseLib/layout.f90 commit c417aa575c2a9fed33e4b9d6d605f6d966a97bff Author: lijewski Date: Thu Apr 2 05:10:18 2009 +0000 back to simpler way of limiting copyassoc cache size Src/F_BaseLib/layout.f90 commit a9458d126db414e2a90a4d0124114ad2f654451e Author: lijewski Date: Wed Apr 1 20:54:14 2009 +0000 more sophisticated cache clearing strategy Src/F_BaseLib/layout.f90 commit 298b5598d7a0835f83badb7c64eacee5486ee6a2 Author: lijewski Date: Wed Apr 1 20:24:24 2009 +0000 smarter about what to delete from copy cache Src/F_BaseLib/layout.f90 commit 21011b165efceddc99a07bce743cce975d37cc5c Author: lijewski Date: Wed Apr 1 18:23:20 2009 +0000 print copy cache stats on flush Src/F_BaseLib/layout.f90 commit 41174bcdbb4c85d4eb430fa44403a14089efd155 Author: lijewski Date: Wed Apr 1 18:12:35 2009 +0000 copyassoc cache refinements Src/F_BaseLib/layout.f90 commit 29901d43abdf45edc766004bd11348ee6c059850 Author: almgren Date: Tue Mar 31 17:37:06 2009 +0000 Don't need to compute residual on the way back up the V-cycle *after* the relaxation at that level -- we can compute it later when we need it. Left in that we do compute it if do_diagnostics is on. Src/LinearSolvers/F_MG/ml_cc.f90 commit 5846eb54b2d65b3f2a98a97db301faa43747ad27 Author: ajnonaka Date: Tue Mar 31 17:24:05 2009 +0000 fix comment Src/F_BaseLib/make_new_grids.f90 commit 84397f68e3564417a95126f61579963ff5e8bea5 Author: ajnonaka Date: Tue Mar 31 17:09:01 2009 +0000 fixed a comment Src/F_BaseLib/ml_boxarray.f90 commit 9d365a4aa6c5e4dbff0ed9eb7f308b415dd0dc3c Author: lijewski Date: Mon Mar 30 22:01:29 2009 +0000 bypass distribution mapping calculation when possible Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/ml_boxarray.f90 commit 43259fc232a14b3187c10618aa9c9a7c4bd96031 Author: lijewski Date: Mon Mar 30 21:49:55 2009 +0000 bypass distribution mapping calculation when possible Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 29eed1d6a1ebde4b35db9d87f8e91b9ea0d44d45 Author: ajnonaka Date: Mon Mar 30 21:34:59 2009 +0000 modified calls to multifab_fill_ghost_cells to not call multifab_fill_boundary for the crse data when the ghost cells have previously been filled. no change to results. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit ac370a47825434afa0ad788b0b04e2389238515b Author: almgren Date: Mon Mar 30 21:12:12 2009 +0000 Move call to multifab_fill_boundary out of ml_interp_bcs and into ml_cc which is calling ml_interp_bcs 2*BL_SPACEDIM times. Should reduce the time in multifab_fill_boundary by factor of 2*BL_SPACEDIM. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit d99aa3bc5a351d7a7bceaad6f16b0648b682c03d Author: ajnonaka Date: Mon Mar 30 19:31:19 2009 +0000 sfc_threshold=4 actually is a better idea now that we have turned off the knapsack minimize communication cost optimization Src/F_BaseLib/layout.f90 commit 353b9bcb694c8c04ae58c2c1f8aa0ea4ebbac5b6 Author: almgren Date: Mon Mar 30 17:56:57 2009 +0000 Add new smoother type -- "efficient GSRB" -- doesn't do a fill boundary between the red and black sweeps. Src/LinearSolvers/F_MG/mg.f90 commit 39843b0521ca4caa096a93c647ec4d48c1bfe756 Author: lijewski Date: Mon Mar 30 17:51:45 2009 +0000 set sfc_threshold default to 0 Src/F_BaseLib/layout.f90 commit 559e9acd577f246661c1afd37906a267aae19fba Author: lijewski Date: Mon Mar 30 17:47:33 2009 +0000 turn off do_mcc by default Src/F_BaseLib/knapsack.f90 commit 1b6467c106e1a0e8d3466873abd5eeabd17e56fa Author: lijewski Date: Mon Mar 30 16:03:20 2009 +0000 reverted out the removal of profile timers Src/LinearSolvers/F_MG/mg_smoother.f90 commit 6a9dbeadd3fc5554716e5ae39f84af820da1ae6f Author: lijewski Date: Sat Mar 28 22:19:10 2009 +0000 commented out some print statements Tests/LinearSolvers/F_MG/cc_multi.f90 commit a45e974fb85c0a8c0b21063131704c0e85bb7fa7 Author: ajnonaka Date: Fri Mar 27 20:26:57 2009 +0000 make sure to destroy bpt if you return out of a function early Src/F_BaseLib/cluster.f90 commit 8cd4c3c5525d1a1e0d1bc9771fb6e5bc9ccdcda3 Author: lijewski Date: Fri Mar 27 20:06:42 2009 +0000 remove bl_prof_timers Src/LinearSolvers/F_MG/mg_smoother.f90 commit 449009227fd617993f81bd4a702e8827692a6c46 Author: lijewski Date: Thu Mar 26 21:58:34 2009 +0000 modest speedup to SSFC stuff Src/C_BaseLib/DistributionMapping.cpp commit 1b7dfc1f1aa517bc60f892c7d0e7644634e68565 Author: lijewski Date: Thu Mar 26 17:51:53 2009 +0000 modest optimization to sfc_greater_i() Src/F_BaseLib/knapsack.f90 commit 295c2be658536a52f6f6977da3d19b6f32f6a97b Author: lijewski Date: Wed Mar 25 19:57:25 2009 +0000 minor tweeks to previous fix Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 6791710a0caed2313cc02b913f22051308b86cc1 Author: lijewski Date: Wed Mar 25 19:04:30 2009 +0000 added box_get_intersector stuff to ml_interface_c() -- big speedup Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit df006f82f2ceabf31a4148b83957c46eba3ea5ad Author: ajnonaka Date: Tue Mar 24 21:45:48 2009 +0000 make modules go to correct directory on jaguar Tools/F_mk/GMakedefs.mak commit 6923e3647b818f3ba25701eb710b8922c44b541b Author: lijewski Date: Tue Mar 24 20:23:35 2009 +0000 efficiency mods to layout_get_box_intersector Src/F_BaseLib/layout.f90 commit 0deb53510e2b4a474edc56ad8ae5a3875b06c29f Author: lijewski Date: Mon Mar 23 19:16:59 2009 +0000 test for out-of-bounds in layout_get_box_intersector() Src/F_BaseLib/layout.f90 commit f25d5774b569ef5f135daf28ba6ab9c853d74fa2 Author: ajnonaka Date: Mon Mar 23 18:25:26 2009 +0000 split up ba_new so the number of intersections per box isn't to big. i.e., there is more than one box in ba_new Src/F_BaseLib/make_new_grids.f90 commit 664c61ed4465aa741531da2990d2c9878c82dbcd Author: ajnonaka Date: Sat Mar 21 00:07:10 2009 +0000 made knapsack verbosity false by default Src/F_BaseLib/knapsack.f90 commit aeb763ac4000ce75d87ee099f6d907528bda3034 Author: lijewski Date: Fri Mar 20 22:20:59 2009 +0000 plot_nfiles=-1 or checkpoint_nfiles=-1 ==> really use ParallelDescriptor::NProcs(). Src/C_AMRLib/Amr.cpp commit 2c4c66de5c71dea76daceb7403a51b2c436e2752 Author: almgren Date: Tue Mar 17 17:03:10 2009 +0000 This DiffPlot is obsolete -- has been replaced by other Diff... routines. Tools/C_util/Convergence/DiffPlot.cpp commit 24879bccac47784ff9507829a1d59bcc8aee68db Author: vince Date: Fri Mar 13 20:32:58 2009 +0000 added hyperion. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 66331b045a1f31c81338b48d9191eebdb5cbb050 Author: almgren Date: Fri Mar 13 18:01:25 2009 +0000 Add a new routine -- tags_and_untags, which copies both the CLEAR and the SET values instead of just the SET values. Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit bb15619cd1492e4082e6f4591cec206619324ce3 Author: vince Date: Thu Mar 12 01:11:37 2009 +0000 squished denorm mins to zero when writing the header. this is for aix. Src/C_BaseLib/VisMF.cpp commit d832cc84b3f70cd68c6fc63b068819e94fb5d2a4 Author: lijewski Date: Wed Mar 11 16:44:17 2009 +0000 Removed the grid_loc data member of AmrLevel. Also the corresponding accessory function gridLocations(). Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StationData.cpp commit 4656082d044b37294874f8da6b5943667d11cd73 Author: almgren Date: Tue Mar 10 20:09:21 2009 +0000 Make the derive functions virtual. Src/C_AMRLib/AmrLevel.H commit 4ba409f88ecc3c5f598b3cc37b35a1baf3acd240 Author: lijewski Date: Mon Mar 9 16:05:03 2009 +0000 mods for yana at LLNL from Mike Singer Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit fa14688f483ead2ba060a87bf98f2a1ab0f640a8 Author: lijewski Date: Tue Mar 3 20:34:29 2009 +0000 some cleanup Src/C_BaseLib/DistributionMapping.cpp commit 4e2c6d9d029c0a1221e67f0f82752dbfbc1a0fa3 Author: lijewski Date: Mon Mar 2 23:23:13 2009 +0000 more namespace cleanup Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BoundaryLib/FabSet.cpp commit 396c486e400f406c26ce96e97297bb45284d044d Author: lijewski Date: Mon Mar 2 22:38:56 2009 +0000 some namespace cleanup Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BoundaryLib/FabSet.cpp commit 590123df905d15284c5b8d0204238774513cae49 Author: lijewski Date: Mon Mar 2 21:18:37 2009 +0000 put FSRec in unnamed namespace Src/C_BoundaryLib/FabSet.cpp commit e0617cf2446acfd8f39d3b226c47b5fbb7e5b595 Author: lijewski Date: Mon Mar 2 21:17:55 2009 +0000 use IntVect::Compare instead of IntVectComp Src/C_AMRLib/TagBox.cpp commit 44cae48ef7fed462129293b35716c64f9f7507bc Author: lijewski Date: Mon Mar 2 21:17:29 2009 +0000 put struct in unnamed namespace Src/C_AMRLib/FluxRegister.cpp commit 8eafd9119f37373edd4222cdcc2a37661d56b387 Author: lijewski Date: Mon Mar 2 21:04:12 2009 +0000 put BoxCmp in unnamed namespace Src/C_BaseLib/BoxList.cpp commit 9448d180e4cd37e9e81c251d900913c60cc85577 Author: lijewski Date: Mon Mar 2 21:00:59 2009 +0000 put SFCToken in unnamed namespace Src/C_BaseLib/DistributionMapping.cpp commit e874a951fc1614fa7c0be8651c7921d0bfa863d1 Author: ajnonaka Date: Fri Feb 27 23:31:54 2009 +0000 mpi works in 3d now on lawrencium Tools/C_mk/Make.mpi commit 4134e75d5df22bd17b123d82a4d204b30590a883 Author: ajnonaka Date: Fri Feb 27 23:21:11 2009 +0000 catch mpi for lawrencium Tools/C_mk/Make.mpi commit 101751bccf7c77599ca4fd31f5e1f14f49634385 Author: marc Date: Fri Feb 27 00:44:10 2009 +0000 CYGWIN does support the -f option, move HOSTNAME call Tools/C_mk/Make.defs commit 653988e91feb0c349b5f9505afe7aaccc1811e77 Author: ajnonaka Date: Tue Feb 24 18:49:43 2009 +0000 Our makefiles for MAESTRO and MAESTRO_paper4 were starting to diverge. Brought these almost back into sync now - one more possible change coming Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 7feab5f39725213e54b568b612d6f4dfd8dbe299 Author: mzingale Date: Mon Feb 23 18:51:57 2009 +0000 if making benchmarks + compileTest, nothing to report Tools/C_util/regtests/test.py commit 29d5da84b79efba7b636c671640accae3ce08ff7 Author: mzingale Date: Fri Feb 20 20:43:53 2009 +0000 for some reason the BL_AIX flag never made it in for intrepid Tools/F_mk/GMakeMPI.mak commit 945a1c75745e7b1486ddf2fb916df88159321993 Author: lijewski Date: Fri Feb 20 18:20:15 2009 +0000 update for pleiades Tools/C_mk/Make.Linux commit 66ee1ddc7eb8ad27dae67045b2cab595b90564a7 Author: almgren Date: Thu Feb 19 18:34:45 2009 +0000 Fixed settings for pleiades. Tools/C_mk/Make.mpi commit 69c73a4c1582098b178253aa9ef9124fec7cfc85 Author: lijewski Date: Wed Feb 18 22:03:19 2009 +0000 can now use space-fill-curves instead of knapsack Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 commit 445415ec5157e53386dc7d74986f94fd63ed66e5 Author: lijewski Date: Tue Feb 17 23:50:36 2009 +0000 some work on implementing space-filling-curves Src/F_BaseLib/knapsack.f90 commit 49009d43b3a82a47c2bc96df4cc561128dce104c Author: lijewski Date: Fri Feb 13 18:57:01 2009 +0000 remove OMP stuff intrepid complained about Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 commit c64200c37b4e21609c2e713a5d51ef29dbc232cc Author: lijewski Date: Fri Feb 13 16:39:52 2009 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit 27b0a5ab49979a5ecf249e7336c60632d31838f5 Author: almgren Date: Thu Feb 12 21:13:02 2009 +0000 Add BL_USECLOSE for pleiades. Tools/C_mk/Make.mpi commit 25b39214dd3e1f0a027211a8efaca282c93b5236 Author: almgren Date: Thu Feb 12 21:11:32 2009 +0000 Add special case for pleiades. Tools/C_mk/Make.Linux commit 5e388c5f8fb43ab543cda14ee70f73bb94fc46f9 Author: vince Date: Thu Feb 12 20:51:51 2009 +0000 added option for explicit file closing. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit a06800b5e0ea6add60be60e68ad0246093c9be6a Author: mzingale Date: Thu Feb 12 19:48:47 2009 +0000 fix the logic for deciding if a test is successful Tools/C_util/regtests/test.py commit e02e8cda218a0b248cb579cd84dfe0630f6d8750 Author: marc Date: Wed Feb 11 23:06:50 2009 +0000 fix data type Src/C_BaseLib/ParallelDescriptor.cpp commit 6d529949d42ff1659640d1bfe1ce60c536347484 Author: mzingale Date: Wed Feb 11 22:02:16 2009 +0000 add support for compile-only tests Tools/C_util/regtests/test.py commit a856bcb9b11fbce8315aecc25f6e84c2b043a58f Author: lijewski Date: Wed Feb 11 01:44:06 2009 +0000 replaced STOP with bl_abort() Src/C_BaseLib/BLutil_F.f commit a5748fc73429953000cbf8584ed19bf653c9de5f Author: lijewski Date: Tue Feb 10 21:49:11 2009 +0000 added some xlC/xlf stuff for intrepid Tools/C_mk/Make.Linux commit c244a8896d2d5b31aa74cb91d96c034e683ed825 Author: mzingale Date: Mon Feb 9 21:09:30 2009 +0000 fix a restart comparison bug if the file names are too long Tools/C_util/regtests/test.py commit db20140fb3cef55b65bcf36994d60772cefc2d62 Author: gpau Date: Mon Feb 9 21:09:08 2009 +0000 Fixes for Lawrencium. Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 4b9c7ec1b51dabe3505d48ed1289ecb87f7b5578 Author: ajnonaka Date: Mon Feb 9 20:30:54 2009 +0000 works for Lawrencium mpi Tools/F_mk/GMakeMPI.mak commit e4883b382269ab3828a67cb77c353a71d5308f77 Author: mzingale Date: Mon Feb 9 15:09:26 2009 +0000 archive the output fix a restart issue for Parallel rename chk files for fParallel jobs using the new commandline setting Tools/C_util/regtests/test.py commit 2213d666d9678399b829172e64930f1f38eb8a8f Author: mzingale Date: Fri Feb 6 23:10:50 2009 +0000 add xlf stuff so we can compile analysis routines on the Intrepid frontend Tools/F_mk/GMakedefs.mak commit 337bd1b2c567d078fd7db0c1bf083f94dfb32592 Author: vince Date: Fri Feb 6 22:57:03 2009 +0000 changes for lijewski. Tools/C_mk/Make.mpi commit 5581d467ce07251dcc4db84a53414daa4bd518c9 Author: lijewski Date: Fri Feb 6 22:14:38 2009 +0000 Do_AllToAllV is now settable Src/F_BaseLib/multifab.f90 commit 576fee341d9933c3f5c7ad10f553fb55884a8de4 Author: lijewski Date: Fri Feb 6 21:30:57 2009 +0000 some rearrangement Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 4b34db192c3ecbb0835086f37b948b0c2212dfdb Author: mzingale Date: Fri Feb 6 20:58:08 2009 +0000 Chris's Intrepid changes to get Amrvis compiling Tools/C_mk/Make.defs commit 408e09a46632797462f82ef5dbee5d2b7ba024ca Author: almgren Date: Fri Feb 6 20:46:19 2009 +0000 Fix previous fix. Src/C_BaseLib/ParallelDescriptor.cpp commit 17f147924bcf69c1e5adb34659dbf2f371a7dfe9 Author: lijewski Date: Fri Feb 6 19:17:04 2009 +0000 added allreduce() operations on vectors Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 7e718eaf8e31cfd275b7a2015f6b018f9c5d1e59 Author: mzingale Date: Fri Feb 6 16:30:50 2009 +0000 more clean-ups Tools/C_util/regtests/test.py commit c95307df2118b382fd8c918879460c15416a50df Author: mzingale Date: Fri Feb 6 16:02:04 2009 +0000 -module and -I are now picked up from the PathScale entry in GMakedefs.mak so we don't need to repeat them here Tools/F_mk/GMakeMPI.mak commit 3f12d4c20c4286a4533a8c3bbe44d85c091fcbac Author: mzingale Date: Fri Feb 6 15:03:50 2009 +0000 some code clean up + add the ability to override the compiler for fParallel. Tools/C_util/regtests/test.py commit 080b2abfc1d1d22d4567b29579cf3bb576706e5b Author: mzingale Date: Thu Feb 5 20:22:04 2009 +0000 neither $HOST nor uname contain "intrepid" on intrepid, so define HOSTNAMEF which is the output of hostname -f, which does contain "intrepid". THis is used in GMakeMPI.mak to define the compilers. Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit c9a2cea47a314e96a241206b3f49898fedf8a638 Author: mzingale Date: Thu Feb 5 19:49:36 2009 +0000 for some reason, on jaguar with PathScale, we were explicitly not putting in the module path and include path flags for compiling. This means that any .mod files were in the . instead of in t/XXX/m/. We don't need a special case for jaguar here. Note: this doesn't affect an MPI build, since that uses the jaguar stuff setup in GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 8d75fe58818efed0fb57859e21f3e74cf67ef9bb Author: lijewski Date: Tue Feb 3 17:08:10 2009 +0000 note in comments that if you want Array use std::vector Src/C_BaseLib/Array.H commit f759e8d1578b6f96d5f1a02894a9c73ebd911bef Author: vince Date: Mon Feb 2 20:50:44 2009 +0000 intel 11. Tools/C_mk/Make.defs commit aad7090e016c91f6c0ded97acac8fb78ad5ad341 Author: mzingale Date: Sat Jan 31 20:04:00 2009 +0000 add a comment Tools/F_scripts/make_build_info commit 21f7fd907319dc13a14a818564cb7f2fd5b2d7ad Author: mzingale Date: Sat Jan 31 19:13:25 2009 +0000 switching over to uname instead of relying on setting HOST in a makefile automagically makes MPI compiling work on nan Tools/F_mk/GMakeMPI.mak commit cf0e993ff0ab14034eecbf2dbc5127d94d3b2c46 Author: lijewski Date: Thu Jan 29 21:13:24 2009 +0000 added BL_NOFAST to turn off maximum optimization Tools/C_mk/Make.Linux commit 3206c015a0a794e184364063a658852c002018b6 Author: lijewski Date: Thu Jan 29 17:47:15 2009 +0000 removed STRCTLY stuff Tools/C_mk/Make.defs commit af6a6c11c26fcc414c04ad0591d088f78bb5e42c Author: mzingale Date: Thu Jan 29 15:02:31 2009 +0000 make realclean before building the comparison and vis tools Tools/C_util/regtests/test.py commit 2bb002043c98fe84a4730e27b5ab42ba92c7eb68 Author: mzingale Date: Wed Jan 28 18:00:20 2009 +0000 make the vis stuff more robust Tools/C_util/regtests/test.py commit f64db38b5a45ad923f49f44af66d1dad41e48cdb Author: almgren Date: Tue Jan 27 18:21:43 2009 +0000 We can now set max_level to be smaller than before on restart. Src/C_AMRLib/Amr.cpp commit c94e891e0d8e449d6bc70b3907939ee76cbd290f Author: almgren Date: Mon Jan 26 21:26:05 2009 +0000 Added Real Geometry::ProbSize() Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 289b0583534126d5cf3cb3568d70b13c6f6a80fc Author: almgren Date: Mon Jan 26 21:06:18 2009 +0000 Added bool Geometry::isAllPeriodic() to return true only if domain is periodic in all directions, otherwise false. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 5ebbc058077986e6cdcd9c319dbc7886cc31b10d Author: mzingale Date: Thu Jan 22 21:21:02 2009 +0000 f90 -> f95 on intrepid Tools/F_mk/GMakeMPI.mak commit 1ecb4cb997de2f7f89b6e30abaf4f7395e862e7b Author: mzingale Date: Fri Jan 16 20:28:01 2009 +0000 add Chris's ANL Intrepid fixes Tools/F_mk/GMakeMPI.mak commit 8456acea47ec4ae609a58689f0267cf2fcd1bb1f Author: lijewski Date: Wed Jan 14 23:13:36 2009 +0000 made single private definition of ilut_build() Src/LinearSolvers/F_MG/sparse_solve.f90 commit 00de1c37dcc3a2cabf5583fc14be983f632d5a1c Author: almgren Date: Mon Jan 12 22:19:31 2009 +0000 Removed unused variable. Src/LinearSolvers/F_MG/ml_cc.f90 commit ed7912f80813225c5277b712f6b3e3d63565aac8 Author: gpau Date: Sat Jan 10 00:05:56 2009 +0000 parallelized PltFileXAve.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp commit 31a7b5025cc80332bfc3f757d52cff3ed86aa8ec Author: ajnonaka Date: Fri Jan 9 23:41:34 2009 +0000 forgot to declare a variable Src/F_BaseLib/fabio_c.c commit 99e9e26ae6c27810fca312d847855ca30e7a641b Author: vince Date: Mon Jan 5 21:12:15 2009 +0000 added varan. Tools/C_mk/Make.mpi commit 482763e76fa7b685b6d956417d3f3f9ccd0a1b65 Author: mzingale Date: Sat Jan 3 19:39:33 2009 +0000 for nan, if we are doing mpi, use mpif90 and mpicxx Tools/F_mk/GMakeMPI.mak commit e3babc9f0819ea3dd32d1eaaa5490cc7b34dd930 Author: lijewski Date: Fri Jan 2 18:13:04 2009 +0000 plugged some memory leaks Src/LinearSolvers/F_MG/mg_cpp.f90 commit ceeb3807c63643a3756af480e4dc51d02ac59df6 Author: almgren Date: Sat Dec 27 01:47:51 2008 +0000 Clean up some memory. Src/LinearSolvers/F_MG/mg_cpp.f90 commit b179bd9496c3837dd72d0b8cca3bc36cade11d54 Author: lijewski Date: Fri Dec 19 22:48:51 2008 +0000 added contains_nan() Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio_c.c commit b985c054b153a91d6cad9b19d4deff4247aff0bf Author: vince Date: Wed Dec 17 21:52:22 2008 +0000 added F90 for franklin. Tools/C_mk/Make.Linux commit ab6ad5d3a7ff54c021ebbdfd2ad7bc8c17bdf302 Author: lijewski Date: Wed Dec 17 21:00:35 2008 +0000 *** empty log message *** Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit a1fc7edd70a0f98ec9bc21a56efeeae04af71c00 Author: almgren Date: Mon Dec 8 21:41:59 2008 +0000 Let us call CellBilinear if not in 3-d -- it appears to work in 2d anyway. Src/C_AMRLib/Interpolater.cpp commit 6d95a087a98adcb17399831bd69874ccd7e91f6c Author: ajnonaka Date: Thu Dec 4 18:54:14 2008 +0000 need to specify which optional argument is going into ml_cc() Src/LinearSolvers/F_MG/ml_solve.f90 commit 7502ab90aef9a488ec038d1430e0852dc15d2bca Author: almgren Date: Thu Dec 4 18:41:11 2008 +0000 Actually use abs_eps for a change. Src/LinearSolvers/F_MG/ml_cc.f90 commit 095eb10131bd20fddee669a12c5e035f88768259 Author: almgren Date: Thu Dec 4 18:40:43 2008 +0000 Pass abs_tol through into solver. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 43d493374a652d3dbcb3e3b01145b6f59eb97db9 Author: almgren Date: Tue Dec 2 01:51:59 2008 +0000 Cleaned up SETAREA. Src/C_BaseLib/COORDSYS_1D.F commit 1eab40784a839ea8e15e0e5502d604469e075aef Author: almgren Date: Tue Dec 2 01:51:28 2008 +0000 Cleaned up SETAREA Src/C_BaseLib/COORDSYS_2D.F commit 95371d2073ab564885fd4032cabb352be26a723c Author: almgren Date: Tue Dec 2 01:49:30 2008 +0000 Cleaned up SETDLOGA. Src/C_BaseLib/COORDSYS_2D.F commit 9925c5fe634d23a9444f62d432b5692d20712284 Author: almgren Date: Tue Dec 2 00:46:54 2008 +0000 Fix SETDLOGA and improve the formatting of the others. Src/C_BaseLib/COORDSYS_1D.F commit 1eee9a41a5108378f54f250ea52e888238219a79 Author: lijewski Date: Mon Nov 17 23:45:55 2008 +0000 ParmParse do_full_knapsack Src/C_BaseLib/DistributionMapping.cpp commit 7b283d7f5a1d93b1d1227792fc1bd2e3807fb435 Author: lijewski Date: Mon Nov 17 23:45:39 2008 +0000 set copy_cache_max_size default to 100 Src/C_BaseLib/FabArray.cpp Src/C_BoundaryLib/FabSet.cpp commit 6497378dad890759c21cf69652f122875ff781eb Author: lijewski Date: Thu Nov 13 16:57:52 2008 +0000 print out reusage rate of various caches Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit ef65bcb5db04b894a8ef4da62843cabd532b1987 Author: lijewski Date: Wed Nov 12 21:34:52 2008 +0000 -1 implies no limit on cache size Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit 64dd74de9c95ffa6c1a4ea49ac6f26b3208fefef Author: lijewski Date: Wed Nov 12 04:27:32 2008 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Geometry.cpp commit 12f41f92c499a009e60e5b8f291180097b31f5d3 Author: almgren Date: Tue Nov 11 00:53:56 2008 +0000 Only define final_resnorm from ni_res if it's been included in the calling sequence. Src/LinearSolvers/F_MG/ml_cc.f90 commit 442c46bc990277a940a5bd4262a84cc6c7264bd9 Author: almgren Date: Mon Nov 10 22:56:26 2008 +0000 Add final_resnorm to calling sequence for mgt_solve and ml_cc. This can be used to pass the final resnorm back to the calling routine -- this can be used later as a test for correction solves. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 commit 78e5fb88fac800c16158445cb6539faeb8ec922e Author: almgren Date: Mon Nov 10 22:54:38 2008 +0000 Add final_resnorm to calling sequence for mgt_solve. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 61aff7c72d46a0c51fd93972096bb446360ff21f Author: almgren Date: Thu Nov 6 17:26:10 2008 +0000 Add additional verbosity about which convergence criterion was satisfied. Src/LinearSolvers/F_MG/ml_cc.f90 commit 094e2a29eed2ed72c9d1e6f5379a3062f58a3176 Author: lijewski Date: Thu Nov 6 17:14:49 2008 +0000 Added do_full_knapsack flag which defaults to false. The default implies that we skip the triply nested loop which swaps boxes trying to get the efficiency above the threshold. We just sort the boxes and pass them out in the most efficient manner we can and let that suffice. Src/C_BaseLib/DistributionMapping.cpp commit 0c4b0a28a9da805483ce809f4644c17ed08b146d Author: almgren Date: Wed Nov 5 18:07:36 2008 +0000 In gs_rb_smoother_1d, do lexicographical rather than GSRB smoothing -- GSRB just wasn't working... Src/LinearSolvers/F_MG/mg_smoother.f90 commit 371653ae860d349b09caf83da8ccc872ee1c3cd6 Author: almgren Date: Wed Nov 5 18:07:08 2008 +0000 Don't call line solve for DIM=1 and more than one box -- call gs_rb_smoother_1d instead. Src/LinearSolvers/F_MG/mg.f90 commit d7f74cb600c20f464f801d1a7174cf79d5f20451 Author: lijewski Date: Wed Nov 5 00:10:43 2008 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 80c6c4d26e72b067e717049c4ac1225f0f3f74ea Author: lijewski Date: Mon Nov 3 23:33:30 2008 +0000 Now count & output # of passes thru core of knapsack() algorithm. max_efficienty now defaults to 0.9 and sfc_threshold to 6. Src/C_BaseLib/DistributionMapping.cpp commit 56b6721eea39712d3ffe8aa7daca681b568eaec6 Author: lijewski Date: Mon Nov 3 20:22:52 2008 +0000 refine_grid_layout now defaults to true. ---------------------------------------------------------------------- removed automatically CVS: CVS: Committing in . ---------------------------------------------------------------------- Src/C_AMRLib/Amr.cpp commit 48d57db7a4629ba451ba3210e9ee8fcd76b2216c Author: lijewski Date: Fri Oct 31 20:40:02 2008 +0000 Moved template statics set via ParmParse into FabArraBase & set'm via BoxLib::Initialize(). Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit ab8108f51de0387b886f60b49f925d973af7bc46 Author: lijewski Date: Thu Oct 30 20:03:31 2008 +0000 Added refine_grid_layout, but it defaults to false for the time being. Src/C_AMRLib/Amr.cpp commit 1ae0f3972219eeb98a5f76403391e1a00d6694cb Author: sepp Date: Wed Oct 29 16:50:44 2008 +0000 1) add MultiFab Divide operation similar to Subtract Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit eb6316693b843f620a08709dd89a46b2570da3ca Author: sepp Date: Tue Oct 28 21:51:50 2008 +0000 1) add a Multiply operation similar to Subtract Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit e6af54e676510c958bbb43b9c4beae10c7707641 Author: lijewski Date: Fri Oct 24 21:05:35 2008 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit b127ca9cb4efb1213b55e20eeffb5c6a4ff29ca2 Author: lijewski Date: Fri Oct 24 03:47:29 2008 +0000 skip over orphaned DMs in GetMap() Src/C_BaseLib/DistributionMapping.cpp commit 2dd0f7044ed1bd34fb2e30156502dd5e66fbd208 Author: vince Date: Thu Oct 23 19:56:37 2008 +0000 added gigan. Tools/C_mk/Make.mpi commit 3f1a4a9d9e8d9286e6d510ec5e045f02fe0a8c35 Author: ajnonaka Date: Wed Oct 22 22:45:44 2008 +0000 fixed bug in index-ing Src/LinearSolvers/F_MG/nodal_divu.f90 commit 4505f4697aaa993a507a35814450e673d6f5f9b9 Author: lijewski Date: Wed Oct 22 19:56:38 2008 +0000 Fixed bug in build_copy() routines that Candace found. Src/F_BaseLib/multifab.f90 commit b8d09d253d3bd3470d014ce5acdbad0d0f627b4a Author: almgren Date: Tue Oct 21 17:47:58 2008 +0000 Switched order of lines -- no functional change. Src/LinearSolvers/F_MG/ml_nd.f90 commit 8202f31ed6461ab672f5c1d18c3555053df44825 Author: almgren Date: Mon Oct 20 18:24:40 2008 +0000 Dont need to print the RHS on the way back up the V-cycle ... it hasn't changed since the start of the V-cycle... Src/LinearSolvers/F_MG/mg.f90 commit 1e42451bb0465922254486fa79a3a13b3d16678d Author: almgren Date: Mon Oct 20 18:23:10 2008 +0000 Fixed formatting of print statements for easier reading when debugging. (Numbers now line up...) Src/LinearSolvers/F_MG/mg.f90 commit fe4436e0bb5bf550052f073b8f111cef35d2a0be Author: lijewski Date: Thu Oct 16 18:13:23 2008 +0000 reverted back out recent GetBndryCells() changes Src/C_BaseLib/BoxArray.cpp commit 398d578c060363c8d8215c2191db18108e1f0c66 Author: lijewski Date: Thu Oct 16 16:03:01 2008 +0000 Do a maxSize(64) after simplify() in GetBndryCells(). Src/C_BaseLib/BoxArray.cpp commit 0fb1ab30496c993f74f29812c7e552765678f2f7 Author: lijewski Date: Thu Oct 16 16:02:32 2008 +0000 Do a maxSize(64) after simplify() in initialize(). Src/C_AMRLib/AuxBoundaryData.cpp commit 35a6b3e28bb14c901029941d3cf932825646e3e3 Author: lijewski Date: Wed Oct 15 22:45:30 2008 +0000 GetBndryCells() now does a simplify(). Src/C_BaseLib/BoxArray.cpp commit 8d223e40d3c1e30370139b26ee8d5714b077ccae Author: lijewski Date: Wed Oct 15 22:43:34 2008 +0000 now do a simplify() in initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit 808495d83a2b5880e8ee78a67176a0e1c65ccc4a Author: marc Date: Sat Oct 11 00:23:53 2008 +0000 Add default flag to Mikes FPB code interface Src/C_BaseLib/Geometry.H commit 2ecad1689d2c207feb420abd313be95d2e8785c3 Author: lijewski Date: Fri Oct 10 23:31:57 2008 +0000 now use Ofast for PathScale optimization Tools/C_mk/Make.Linux commit ea6dd82c6d561b14f142a28b3f268878c82c1116 Author: lijewski Date: Fri Oct 10 22:35:41 2008 +0000 FillPeriodicBoundary() is now a template in BoxLib namespace on FabArray ---------------------------------------------------------------------- automatically CVS: CVS: Committing in . CVS: CVS: Modified Files: CVS: Geometry.H Geometry.cpp CVS: ---------------------------------------------------------------------- Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 375bf5eb505a4303e710de7ebc20bc2744e0b603 Author: lijewski Date: Mon Oct 6 20:22:09 2008 +0000 use 'fast' instead of 'O' for optimization with PGI Tools/C_mk/Make.Linux commit 383b33dbd9dacecb01b2f914267db904442b5b69 Author: ajnonaka Date: Mon Oct 6 17:13:07 2008 +0000 using -Ofast optimization - seems to give a few more percent speed bonus Tools/F_mk/GMakedefs.mak commit 3a843ee02a359118f84a8cd6371d4ca780c189f4 Author: ajnonaka Date: Mon Oct 6 16:33:38 2008 +0000 adding -ipa flag back in, so that means you need to module swap pathscale pathscale/3.2 on franklin before next week, when 3.2 becomes the default. Testing shows -ipa runs faster Tools/F_mk/GMakedefs.mak commit 5398a0d5a8ed5cf89a737e0bd6b0b02c97f70ddc Author: ajnonaka Date: Sun Oct 5 00:05:26 2008 +0000 i've permanently disabled the -ipa flag. now the default pathscale compilers (3.1) work on jaguar AND franklin. 3.2 should work as well, but I'm going back to the default 3.1 Tools/F_mk/GMakedefs.mak commit 78fca4e7f488f24275883a6f122f6d61c20afafd Author: ajnonaka Date: Sat Oct 4 23:12:47 2008 +0000 oops; franklin's hostnane is nid*. works now Tools/F_mk/GMakedefs.mak commit ba43b98ee1d58d590dfd2fc3d6a6951dc2dfad1b Author: ajnonaka Date: Sat Oct 4 23:05:39 2008 +0000 if franklin, disable -ipa flags. after a make realclean, MAESTRO compiles on franklin again Tools/F_mk/GMakedefs.mak commit 54794f0ac83cd4339403e1d27df3cea5b5d539dd Author: almgren Date: Thu Oct 2 19:10:33 2008 +0000 Impose a limit on how many times you regrid on initialization. Previously one could go on regridding indefinitely; now there's a limit of 4 times through the regridding process. The integer MaxCnt is locally defined and arbitrarily set to 4; we could ParmParse this later if needed. Src/C_AMRLib/Amr.cpp commit 20c347c3945b6e058dacde809b9cb6c1d2484e70 Author: almgren Date: Wed Oct 1 18:20:07 2008 +0000 Added an option to generate a runlog_terse which prints only the step number, time and dt, with no words. It is set by amr.run_log_terse = filename in the inputs file. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 0d3bce175e3190fdaad32c7a5430a5417c2bd9ff Author: lijewski Date: Tue Sep 30 20:48:29 2008 +0000 mods for when there are no bndry cells; i.e. triply periodic Src/C_AMRLib/AuxBoundaryData.cpp commit 1c37a999bb1410117d38c665c79327cd97bc2a13 Author: lijewski Date: Tue Sep 30 17:17:04 2008 +0000 FillBoundary() is now in FabArray Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit b9dab17ad19cd8789d131cf3aff56039004db413 Author: mzingale Date: Tue Sep 30 14:28:49 2008 +0000 an updated version of the changelog script (taken from http://www.red-bean.com/cvs2cl/). This version seems to work better with recent CVS changes. Tools/F_scripts/cvs2cl.pl commit 02f6c735d587407ccc97b2a9a03bbdee46bba23d Author: almgren Date: Fri Sep 26 21:01:27 2008 +0000 For nodal_smoother_3d, Jacobi iteration, only update uu = uu_temp if we've actually defined uu_temp. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 667a2d4011430d5419e01e320be187bf8e027a21 Author: vince Date: Thu Sep 25 22:50:21 2008 +0000 strstream update. Src/C_AMRLib/DatasetClient.cpp commit d766fd0b5c20d10f0c123adb7f5d6ce425ecd8ca Author: sepp Date: Tue Sep 23 14:45:01 2008 +0000 1) reverse Ann's change that turns off icc for v 9.0 of compiler Tools/C_mk/Make.defs commit 892fa6df3d6eae6d36af04b58264abc2d8f73778 Author: ajnonaka Date: Mon Sep 22 18:40:03 2008 +0000 #f90sources += mt19937ar.f90 putting local copy in wdconvect instead since this sompiles so slowly Src/F_BaseLib/GPackage.mak commit 9e6d0cd0becb47c3dbdddcec29b48e7e1ba39542 Author: ajnonaka Date: Mon Sep 22 18:35:33 2008 +0000 f90sources += mt19937ar.f90 Src/F_BaseLib/GPackage.mak commit e6f179cea2e41bb385949b2274b547f664acbf60 Author: ajnonaka Date: Wed Sep 17 20:49:05 2008 +0000 added mpi capabilities for atragon Tools/F_mk/GMakeMPI.mak commit 6f83689e0ad5efd94e18060c747c38bd45327285 Author: vince Date: Wed Sep 17 20:01:52 2008 +0000 added atragon and gojira. Tools/C_mk/Make.mpi commit 23f078aef33bff19a27f27731051bb16a669b75f Author: ajnonaka Date: Thu Sep 11 15:19:00 2008 +0000 aligned the tabs so the logic reads easier Src/LinearSolvers/F_MG/mg.f90 commit e72c55c8d622fd99794a26677f50207bb54ae671 Author: ajnonaka Date: Wed Sep 10 21:11:44 2008 +0000 fixed a line of code that didn't work with intel compiler version 9.1.043 Src/F_BaseLib/fillpatch.f90 commit 6a009601099d8431ec97659e2654f230c2d34690 Author: ajnonaka Date: Wed Sep 10 21:11:17 2008 +0000 made the cpy_ functions public Src/F_BaseLib/multifab.f90 commit f5afb812ab9fe80b1958b00698f89b90d86114db Author: ajnonaka Date: Mon Sep 8 19:39:20 2008 +0000 works for ng = 0 Src/F_BaseLib/fillpatch.f90 commit 2f8768296bd80af36268a2a331e920c2801c39dd Author: lijewski Date: Mon Sep 8 19:26:20 2008 +0000 fix for case when ng==0 Src/F_BaseLib/fillpatch.f90 commit a5d85147d92ff54e82c03ed9da14198d5a28308b Author: marc Date: Thu Sep 4 17:14:28 2008 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/inputs.2d Src/LinearSolvers/C_CellMG/Test/inputs.3d Tests/LinearSolvers/C_CellMG/inputs.2d Tests/LinearSolvers/C_CellMG/inputs.3d commit c948ebac1caf8f10b4541813e5ed225b1e8e6dae Author: marc Date: Thu Sep 4 17:00:04 2008 +0000 Added arguments to COEF call to satisfy compiler Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit a0fc4d1a1fc3f47e3c55c87d19e9a69dfb735f56 Author: ajnonaka Date: Wed Sep 3 00:16:03 2008 +0000 including tag_boxes.f90 and make_new_grids.f90 in the boxlib GPackage.mak instead of modifying all of my local directories. Src/F_BaseLib/GPackage.mak commit de30a123510a6556602fe0bc869e2ba43fe84bcc Author: ajnonaka Date: Tue Sep 2 22:12:23 2008 +0000 tag_boxes no longer relies on a "ng_cell" from probin. ng is computed within this function Src/F_BaseLib/tag_boxes.f90 commit c2bd368700ea98de78599f5936e41621d85bef07 Author: almgren Date: Mon Sep 1 22:58:40 2008 +0000 Add scale_residual_1d call so that 1d does the same thing as 2d and 3d. Src/LinearSolvers/F_MG/ml_cc.f90 commit 114c78887bf2495f29013787bd997ee67633dba5 Author: ajnonaka Date: Thu Aug 28 17:41:48 2008 +0000 made 2d consistent with 3d Src/F_BaseLib/tag_boxes.f90 commit 58f2c01ec3937263cfaeb4c86a1939d877467c87 Author: ajnonaka Date: Wed Aug 27 23:04:11 2008 +0000 Every instance of tag_boxes.f90 that was not in boxlib was identical. So I removed them all from the local directories and made the default version in boxlib the same as the removed copies. Src/F_BaseLib/tag_boxes.f90 commit 6e8d34f178d31634a535a2a50b54d31310feb47a Author: ajnonaka Date: Wed Aug 27 22:57:30 2008 +0000 Fixed a bug where nothing would ever be tagged for level 4 or greater. Also, the comments did not match the code. The code did a nonsensical tagging, so I made the code match the comments, which did make sense. Src/F_BaseLib/tag_boxes.f90 commit 2e5ae3b3dd7e47ddf2e90b4e1093ce98c014f447 Author: mzingale Date: Tue Aug 26 15:18:39 2008 +0000 add the 2-d gaussian diffusion problem Tools/C_util/regtests/Castro-tests.ini commit 159a4ca3f6775509b3db1fc48f3bc7ce9d2bda79 Author: almgren Date: Mon Aug 25 23:08:04 2008 +0000 Replace "area" by "coeffs" in set_gravity_coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 61f3cff25ac1196d7213c347dcb3bf83478f04bc Author: almgren Date: Mon Aug 25 23:07:31 2008 +0000 Replace "area" by "coeffs" Src/LinearSolvers/C_to_F_MG/MGT_Solver.H commit 769db6da23636a0f1e373168580554dd39f87512 Author: almgren Date: Mon Aug 25 23:06:52 2008 +0000 Remove geom from call to set_gravity_coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit ed045ff040927194ac938f48b84735b2e3f1a94a Author: mzingale Date: Mon Aug 25 20:56:41 2008 +0000 fix a crash if the benchmark file was not found Tools/C_util/regtests/test.py commit d4538e9a2cb32d3e287ae20326f6b2492d24261b Author: almgren Date: Mon Aug 25 20:12:10 2008 +0000 Add mgt_applyop. Src/LinearSolvers/F_MG/mg_cpp_f.h commit be3eff82684339c11f241e691ea94908c0fb00d6 Author: almgren Date: Mon Aug 25 19:57:32 2008 +0000 Add mgt_applyop() to be called from MGT_Solver. Src/LinearSolvers/F_MG/mg_cpp.f90 commit d06a9c57f032ef3f25850e2334aa3e8164897629 Author: almgren Date: Mon Aug 25 17:38:35 2008 +0000 Add applyop interface (modeled on compute_residual interface). Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 739774c229edd5405a1684eb672d84a50d6d8218 Author: almgren Date: Mon Aug 25 17:30:54 2008 +0000 ml_cc_applyop didn't need fine_mask to be passed in - it was used in defining Anorm and bnorm which were unused. Src/LinearSolvers/F_MG/ml_cc.f90 commit df0356bf2ce39767dcac8a974b56e022fce1377b Author: ajnonaka Date: Thu Aug 21 18:19:56 2008 +0000 fixed a bug in ml_restriction_c where we were filling the boundary on all the components, not lnc. Src/LinearSolvers/F_MG/ml_restriction.f90 commit 4b11ae02b2a11a00a191b88190dd6a8c1786b04f Author: mzingale Date: Mon Aug 18 19:33:11 2008 +0000 don't do vis if we are making benchmarks Tools/C_util/regtests/test.py commit fe32486c6ab13bb109b75cb14f542ff92c26dca3 Author: mzingale Date: Mon Aug 18 14:26:12 2008 +0000 add the vis image to the report page Tools/C_util/regtests/test.py commit 810d5a1b07a5933638b0510dd93964be5779611c Author: mzingale Date: Mon Aug 18 03:10:01 2008 +0000 start adding the framework for visualization Tools/C_util/regtests/test.py commit afd5955cfc561e6a6ac5ce10f170539a82382dc9 Author: mzingale Date: Sun Aug 17 23:19:46 2008 +0000 update to reflect dx = dr changes Tools/C_util/regtests/Maestro-tests.ini commit 377b1530dd35527597d57ee2da14ea08088778df Author: vince Date: Tue Aug 12 00:09:49 2008 +0000 added battra. Tools/C_mk/Make.mpi commit 91a8250ba81a934de2334cac04518260b5b06632 Author: vince Date: Mon Aug 11 19:18:06 2008 +0000 changes for manda. Tools/C_mk/Make.mpi commit d49646397c57d3b80f0bcd6b3b36c4a314352511 Author: almgren Date: Thu Aug 7 21:30:12 2008 +0000 Create pmask from la_array(1), not la_array(nlevs) Src/F_BaseLib/make_new_grids.f90 commit 05a31180cdd311fd68b34be8d40f1f40998ea2e3 Author: almgren Date: Thu Aug 7 21:18:52 2008 +0000 1) Fix regridding and proper nesting. 2) Move min_eff and minwidth to cluster and add functionality to set them through probin. Src/F_BaseLib/cluster.f90 Src/F_BaseLib/make_new_grids.f90 commit 822ac78a0aea0a83d996a5881b05735afdf7b43d Author: almgren Date: Thu Aug 7 21:15:22 2008 +0000 Don't need cluster_2d.f90 anymore -- we use cluster.f90 for 2d and 3d. Src/F_BaseLib/cluster_2d.f90 commit 8670e15b3c8748c0ac4cb72b33e2f61c0904941d Author: almgren Date: Wed Aug 6 21:58:09 2008 +0000 Move the test on being close to the domain boundary *after* instead of *before* the proper nesting test. Src/F_BaseLib/make_new_grids.f90 commit 81660235761719f2ec2bfa9acd33806d3c8fc3fa Author: almgren Date: Wed Aug 6 21:43:05 2008 +0000 If a fine grid is within 2 fine cells of a physical non-periodic boundary, then make the grid touch the boundary instead of staying 2 cells away. We don't know how to fillpatch the third ghost cell if it's outside the domain but the grid doesn't touch the domain boundary. Src/F_BaseLib/make_new_grids.f90 commit c6098553f14939a723f9e5d184d91e1964e7f864 Author: vince Date: Wed Aug 6 19:38:44 2008 +0000 changes for naphta. Tools/C_mk/Make.mpi commit f54f2a0014bb116c33240f4d5876ddd44378cfea Author: almgren Date: Wed Aug 6 19:35:26 2008 +0000 Only do proper nesting test if there are in fact grids at the finer level. Src/F_BaseLib/make_new_grids.f90 commit e404ef00456e73c001efb3d797d46a54e3f609e9 Author: almgren Date: Wed Aug 6 19:29:38 2008 +0000 Dont call cluster if there are no tagged points. Src/F_BaseLib/make_new_grids.f90 commit 5d45bf21207d022d3b1ba320eb018a9fa9bb10de Author: vince Date: Wed Aug 6 18:30:25 2008 +0000 change for naphta. Tools/C_mk/Make.mpi commit bb0431a95517172e20f24485c4bc8e476afc5cbe Author: lijewski Date: Wed Aug 6 16:16:23 2008 +0000 destroy() tagboxes in enforce_proper_nesting() Src/F_BaseLib/make_new_grids.f90 commit 7aa52e52149a58b13adef9b78b13f52295c63bc1 Author: almgren Date: Wed Aug 6 03:09:43 2008 +0000 1) Removed probin_module from enforce_proper_nesting. 2) Modified enforce_proper_nesting so it calls the clustering algorithm to create the new grids, instead of just adding small grids to the existing one. This allows us to use the minwidth criteria already in cluster. Src/F_BaseLib/make_new_grids.f90 commit c840d16110276d04e11d91030d9da8f6ff2619b7 Author: almgren Date: Wed Aug 6 00:03:57 2008 +0000 Modify the call to the proper_nested routine. Src/F_BaseLib/ml_boxarray.f90 commit 56234e6b739f6b07de50a440f79e17abb0c68cde Author: almgren Date: Wed Aug 6 00:03:36 2008 +0000 Moved enforce_proper_nesting into here. Src/F_BaseLib/make_new_grids.f90 commit 8b59d08bca5c2485d8673c3e81943593bd5a8835 Author: almgren Date: Tue Aug 5 23:01:46 2008 +0000 Set minwidth = 4 instead of 2. Src/F_BaseLib/make_new_grids.f90 commit 9bbb2b384d03b9ca065a12935ed3495142408aea Author: almgren Date: Tue Aug 5 21:10:22 2008 +0000 Hopefully we fixed the case where multifab_fill_ghost_cells asks fillpatch to fill a box which is completely outside the domain. Src/F_BaseLib/fillpatch.f90 commit 25d8e3b7e5dfe37acd7e4616d2e2e18a26f505d2 Author: gilet Date: Tue Aug 5 18:08:43 2008 +0000 mpich now works on gigan Tools/F_mk/GMakeMPI.mak commit 5e497bd81a9c95ec8ac0af8d704d86ee9bae3278 Author: almgren Date: Mon Aug 4 23:19:06 2008 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit ac860ad274039c9ad1e93d43cec75f6fd078eb60 Author: almgren Date: Mon Aug 4 23:13:02 2008 +0000 Fix a typo. Src/LinearSolvers/F_MG/stencil.f90 commit 68e48b55bea10ad578490d7b0cf9f7331d660de5 Author: almgren Date: Mon Aug 4 23:09:49 2008 +0000 1) Use the beta's since they carry the viscous coefficients for the viscous/diffusive solves. 2) Add the alpha -- forgot that last time. Src/LinearSolvers/F_MG/stencil.f90 commit 6d2fd2989c5a576e01ce8d2f788078c0db917f97 Author: almgren Date: Mon Aug 4 22:59:43 2008 +0000 Put full 9-pt cross stencil back in. Src/LinearSolvers/F_MG/stencil.f90 commit e3d60dd262d80abd7515820b69302c57289f0d8e Author: almgren Date: Mon Aug 4 22:45:16 2008 +0000 I have added the functionality to do Minion's 4th order constant density stencil -- the coefficients are independent of beta for now, and the 1-d stencil would be (i-2,j), (i-1,j), (i,j), (i+1,j) (i+2,j) and analogously in 2d. Only 2d is coded. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/stencil.f90 commit bd758e0109283441b91b9c3daebe43360adfda58 Author: almgren Date: Fri Aug 1 23:11:45 2008 +0000 Remove unused "proc" Src/F_BaseLib/cluster.f90 commit 93c7fac93048fa5abda08827d25130d9e5c4ed7a Author: almgren Date: Fri Aug 1 23:11:02 2008 +0000 Remove unused ibxs(:) Src/F_BaseLib/cluster.f90 commit 24bd14f0fe3b452b1bb96b6a47ee025705e636d2 Author: mzingale Date: Fri Aug 1 17:49:14 2008 +0000 the C99 standard moves std::abort into cstdlib and std::strerror into cstring, so these header files need to be added in the appropriate places. This allows Castro to compile with GCC 4.3 Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit ff69775c3e3e1e26f708d9028ca0666de1dd163a Author: lijewski Date: Thu Jul 31 21:55:48 2008 +0000 added version of GetVolume() taking a FArrayBox Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit c0250fefe8326f3debd5e0873a2379d9e5303ff7 Author: almgren Date: Thu Jul 31 20:42:51 2008 +0000 Replace bl_abort by bl_error. Src/LinearSolvers/F_MG/mg.f90 commit 333a02938b61f17ee63996c2ae00ee984fddc82a Author: almgren Date: Thu Jul 31 19:43:41 2008 +0000 This changes the default scheme for 1-d cell-centered solves. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit 5e1b9f4afcea7ac044eebae3f460b91625da300a Author: lijewski Date: Thu Jul 31 18:05:48 2008 +0000 added GetFaceArea() taking FArrayBox & grid index parallel one taking MultiFab and grid Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 68fc28aae036f93ee319e69a7b5a4dd8b6361227 Author: almgren Date: Thu Jul 31 17:54:27 2008 +0000 Put new mpi link for manda only. Tools/C_mk/Make.mpi commit 5e59022010ff1892e849e84dbf2d39dc01f42447 Author: almgren Date: Wed Jul 30 20:48:10 2008 +0000 Don't pass in the default value of omega when defining the solver; instead let mg.f90 define an appropriate value. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 0562d68c650fde20db4873de31c1573d14799e40 Author: almgren Date: Wed Jul 30 20:47:10 2008 +0000 Add omega default for 1-d : by trial and error, 0.6 seems to work well. Src/LinearSolvers/F_MG/mg.f90 commit 8af542607bce7030c015f84a0acbaf5aa43fa70e Author: lijewski Date: Wed Jul 30 01:10:47 2008 +0000 littlea cleanup Src/C_BaseLib/BaseFab.H commit b061a04a7f6f724ee897313029a2647383e9f248 Author: lijewski Date: Wed Jul 30 00:54:45 2008 +0000 fixed bug related to calculating FAB byte spread and clear() calls Src/C_BaseLib/BaseFab.H commit 87da79b5ccc60497668e79f1518968878820f248 Author: almgren Date: Tue Jul 29 19:32:04 2008 +0000 Remove stray line -- no change in functionality (caught by Candace G) Src/F_BaseLib/multifab.f90 commit a43a2b059f7f7676c2ac1530713ec70ef7df2191 Author: lijewski Date: Tue Jul 29 16:28:08 2008 +0000 modest simplification Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit e5ccb158db0c1dd97ad135704c70ac1cd4facaf1 Author: lijewski Date: Wed Jul 23 21:38:57 2008 +0000 some memory cleanup Src/C_AMRLib/AmrLevel.cpp commit 415c0a247654c429fb8a2de125d8a493978ed5dc Author: lijewski Date: Wed Jul 23 17:18:34 2008 +0000 *** empty log message *** Tools/C_mk/Make.defs commit ce1f87bf8056a78f313a12a8b1113623442b43d9 Author: mzingale Date: Mon Jul 21 19:45:46 2008 +0000 use the new compare tool Tools/C_util/regtests/Castro-tests.ini commit f08e4ca050cfae6cde1c15ba26322fcdb32a5c88 Author: mzingale Date: Mon Jul 21 19:32:45 2008 +0000 do the cvs update on fParallel still Tools/C_util/regtests/test.py commit 7f7d54ef398bfa33324cb67bbfc1e6cf195afcfd Author: mzingale Date: Mon Jul 21 19:28:27 2008 +0000 new compare tool Tools/C_util/regtests/Maestro-tests.ini commit 91605dbc5aae03889742aef8fae5392db55b5a71 Author: mzingale Date: Mon Jul 21 19:27:59 2008 +0000 switch over to using fParallel/data_processing/fcompare to do the comparisons -- this works even if the list of variables changes, so a better comparison can be done on those that remain. It also does 1-,2-, and 3- all in one executable. Tools/C_util/regtests/test.py commit 4cf2c2ae111219aeac2454621310a88ff8c620d4 Author: almgren Date: Fri Jul 18 23:57:31 2008 +0000 1) Added gs_rb_smoother_1d as well as line solve -- use gsrb if more than one grid at the level, it works better with V-cycle. 2) Moved defn of mgt%dim to the top because it was getting used before it was defined. Src/LinearSolvers/F_MG/mg.f90 commit ac96e1bd59a79dad316d9f6a51b1914c551a19c1 Author: almgren Date: Fri Jul 18 23:45:30 2008 +0000 Add gs_rb_smoother_1d for 1d gsrb relaxation -- need to use this instead of line solve for multiple grids, otherwise mg v-cycles seem to have a hard time. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 07b334e82ffe753eba13cc35d323cbf9af337db5 Author: ajnonaka Date: Thu Jul 17 14:10:14 2008 +0000 fixed multilevel, 3d, out-of-bounds bug Src/LinearSolvers/F_MG/ml_prolongation.f90 commit c8de02dfe79396efc00e5e8f484883eaf2a18d06 Author: marc Date: Wed Jul 16 22:48:41 2008 +0000 marc hacking for gigan Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 85ff82403033e64276542a734800c5394e09328a Author: almgren Date: Wed Jul 16 20:57:52 2008 +0000 Made same changes for 1d as already done for 2d and 3d in setting stencils at interior grid boundaries. Src/LinearSolvers/F_MG/stencil.f90 commit 908cb27c25e4c8e40741da38f5cef36062fc71bd Author: almgren Date: Wed Jul 16 17:48:57 2008 +0000 Introduced new integer member of Amr : file_name_digits. This defaults to 5, but can be set in parmparse. This is the number of digits used in plotfile names and checkpoint file names. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 91f134043afcd4240e300f4d2348a5a70c2e2db6 Author: lijewski Date: Wed Jul 16 17:40:24 2008 +0000 added mindigits 3rd arg to Concatenate() that defaults to 5 Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 868724a66616793573533460b54ae08cf2ef39a5 Author: lijewski Date: Tue Jul 15 20:58:20 2008 +0000 mods for intel -- needs more stuff than xlf95 says it should Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/layout.f90 commit 53a43144c794630f236998fb5d9c68c2583fa185 Author: lijewski Date: Tue Jul 15 20:30:49 2008 +0000 now compile with no complaints with xlf95 -qlanglev=95std Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 9783467307ab19c99b0c88c5aeca2786a059d5d0 Author: lijewski Date: Sat Jul 12 18:51:45 2008 +0000 plugged memory leak found by Candace Src/LinearSolvers/F_MG/mg.f90 commit 16beda084a441ed3e25597fa1e76f14e10c8ece1 Author: lijewski Date: Thu Jul 10 23:24:16 2008 +0000 removed unneeded module usage Src/F_BaseLib/make_new_grids.f90 commit cab0f0f101215bd847e44e355140efb87da98a64 Author: lijewski Date: Thu Jul 10 20:17:39 2008 +0000 plugged memory leak & make boxes via copy() Src/F_BaseLib/make_new_grids.f90 commit df8871418459a084e349d9d65d83755c328799d7 Author: lijewski Date: Thu Jul 10 20:08:47 2008 +0000 added a TODO and a timer Src/F_BaseLib/cluster.f90 commit ef155deaa46f5c557c7bd4e7cac842962fcf4ee4 Author: almgren Date: Thu Jul 10 19:29:20 2008 +0000 Warning on no point flagged is now in make_new_grids instead of in cluster. Src/F_BaseLib/cluster.f90 commit 47407998c9f4080a020a52b1fdfadae2e3fe76a7 Author: almgren Date: Thu Jul 10 19:28:49 2008 +0000 Put warning statement in make_new_grids if no points are tagged for refinement. Src/F_BaseLib/make_new_grids.f90 commit 467bf9bfcd906ee46e15ba8d9c15fa986b32cc5d Author: lijewski Date: Thu Jul 10 17:42:18 2008 +0000 *** empty log message *** Src/F_BaseLib/test/t_knapsack.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_knapsack.f90 Tests/F_BaseLib/t_main.f90 commit 39ea09e004ba2a2ec9fb943ac27e15333caff430 Author: lijewski Date: Thu Jul 10 17:41:59 2008 +0000 can now intersect a boxlist with a box or another boxlist Src/F_BaseLib/list_box.f90 commit d8feffb0482ba61282389c382fef2621bd58fb07 Author: mzingale Date: Thu Jul 10 17:12:32 2008 +0000 get this working for fParallel runs again Tools/C_util/regtests/test.py commit 5a791f1e7d5a8ff894eb110b797f1fa405b8ec0d Author: mzingale Date: Thu Jul 10 16:55:57 2008 +0000 document the MPI stuff Tools/C_util/regtests/test.py commit aa5b93db4226a83196e953b0f392dfbc6c4fafe3 Author: lijewski Date: Thu Jul 10 16:10:14 2008 +0000 Moved some list_box routines that were private in boxarray to list_box. More could be done but I'm hitting an Intel compiler error. Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/list_box.f90 commit a085533a78aabcdacf2707081756ef1ad76aa62b Author: mzingale Date: Thu Jul 10 14:21:17 2008 +0000 add parallel: Tools/C_util/regtests/Castro-tests.ini commit f8a7765ffa31c9804c0e1549270072b24047b790 Author: mzingale Date: Thu Jul 10 14:20:52 2008 +0000 get initial MPI stuff in the test suite to do parallel tests Tools/C_util/regtests/test.py commit 45025557c951afee098e89e33f46f92d4d3da02d Author: mzingale Date: Thu Jul 10 13:48:18 2008 +0000 only store ChangeLog.Parallel if we are doing a Parallel/ test Tools/C_util/regtests/test.py commit c838ecf9d216b0fbc2b4cf99a7a8303327059ba7 Author: lijewski Date: Thu Jul 10 05:57:52 2008 +0000 removed couple unused & broken routines Src/F_BaseLib/boxarray.f90 commit 9f35b545023d3da43e670dff3fa0ddb7ebd0f75e Author: almgren Date: Thu Jul 10 01:25:37 2008 +0000 Fixed subroutine buffer. Src/F_BaseLib/make_new_grids.f90 commit 6d6cbd5a4bb319989fdad8f3b53cda62e34370a1 Author: almgren Date: Wed Jul 9 22:32:28 2008 +0000 Set the setval back to true in subroutine buffer. Src/F_BaseLib/make_new_grids.f90 commit e44c6288363705cd0e1ebbc90d133fe55eacc8b5 Author: almgren Date: Wed Jul 9 22:30:44 2008 +0000 Added machine della (Adam Burroughs' machine at Princeton) as an option. Tools/C_mk/Make.defs commit 251fb59d4a2e3aa1b4d742e62054f2b666d8319d Author: almgren Date: Wed Jul 9 22:28:57 2008 +0000 Add machines manda and DELLA as new options. Tools/C_mk/Make.mpi commit 97e8fb8fc49d0a76b4e6c062e67c225eadea21af Author: lijewski Date: Wed Jul 9 20:16:26 2008 +0000 some cleanup & memory leak squashing Src/F_BaseLib/make_new_grids.f90 commit cc4745a6e4545df9a88656300e46097f13d2e6b0 Author: lijewski Date: Wed Jul 9 19:48:05 2008 +0000 changes a setval(.true.) to setval(.false.) Src/F_BaseLib/make_new_grids.f90 commit 59babc59c3ac13b6308a519b9c2c34e72331570f Author: almgren Date: Wed Jul 9 00:04:58 2008 +0000 Renamed regrid.f90 --> make_new_grids.f90 Src/F_BaseLib/make_new_grids.f90 commit db42c5c3425607e96725b32343f3f8737f831f8f Author: almgren Date: Tue Jul 8 23:53:01 2008 +0000 Separated the tag_boxes functionality out of regrid -- new files tag_boxes.f90 Src/F_BaseLib/regrid.f90 Src/F_BaseLib/tag_boxes.f90 commit edca25d116ddb9cd6a8fb743eebed5cfca386819 Author: almgren Date: Tue Jul 8 23:39:52 2008 +0000 Remove commented line. Src/F_BaseLib/boxarray.f90 commit ec84735085dd74010bdac40a1a83c12def472e59 Author: lijewski Date: Tue Jul 8 23:08:13 2008 +0000 tiny bit of cleanup Src/F_BaseLib/multifab.f90 commit 5cafdd09b2f8f64e4ed57058b0d08767b356822e Author: lijewski Date: Tue Jul 8 21:54:12 2008 +0000 first cut at map_periodic() Src/F_BaseLib/cluster.f90 commit 954dd032a6335be910cd2f293846d2af2f1bef6c Author: almgren Date: Mon Jul 7 18:05:26 2008 +0000 This takes max_grid_size as an argument to make_new_grids, and some other changes.. Src/F_BaseLib/regrid.f90 commit d08eac4d58ad542ae0a48a625bad4f528a7ce97e Author: almgren Date: Thu Jul 3 21:32:39 2008 +0000 Replace set_const_gravity_coefficients by a flagged version of set_gravity_coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 81e7a26958aa1b0d48f72b067ac446cbdf4ee12f Author: almgren Date: Thu Jul 3 00:05:28 2008 +0000 Add another sanity check for proper nesting. Src/F_BaseLib/ml_boxarray.f90 commit 7cea7eacf4ce7c5bbf9ea47269e677cc25be98c1 Author: almgren Date: Thu Jul 3 00:04:30 2008 +0000 Modify properly nested test to take optional arguments: min_level and max_level, so can test just between two levels. Src/F_BaseLib/ml_boxarray.f90 commit b245b3c170aabfd18feff80addb9b7213b1a513f Author: almgren Date: Wed Jul 2 23:15:57 2008 +0000 Removed commented line. Src/F_BaseLib/fabio.f90 commit c8d07d382e98d5c15550b4df9d67f702ff2e2bec Author: almgren Date: Wed Jul 2 22:52:15 2008 +0000 Fix ml_layout_restricted_build. Src/F_BaseLib/ml_layout.f90 commit 400a307668f0007585835f306e0b74c64df98858 Author: almgren Date: Wed Jul 2 22:18:16 2008 +0000 Added new "subroutine ml_layout_restricted_build(mla, mba, nlevs, pmask)" which builds a ml_layout from the first nlevs levels of the mba. Src/F_BaseLib/ml_layout.f90 commit 0c309f608deee0b8bd3ddeff308a11f760a48328 Author: ajnonaka Date: Wed Jul 2 16:13:31 2008 +0000 plugged a very sneaky memory leak Src/LinearSolvers/F_MG/mg.f90 commit 7e488348382406a5c9ac679fda3a032298fae1c6 Author: lijewski Date: Tue Jul 1 18:00:10 2008 +0000 now contains GetBndryCells() Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit e9e648abe35f35834f6b512de26a016ac7c7a817 Author: lijewski Date: Tue Jul 1 17:59:33 2008 +0000 moved GetBndryCells() to BoxArray Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit bb98e058a210d16fe9a341f16d6c56b4dc91ba30 Author: lijewski Date: Mon Jun 30 22:05:03 2008 +0000 minimize copy()ing Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit d97ca14aa36a5653fbdf3125f12112d93d63f3b9 Author: lijewski Date: Thu Jun 26 23:04:34 2008 +0000 slight reworking of ml_boxarray_properly_nested() Src/F_BaseLib/ml_boxarray.f90 commit d71845dc0630a90f1203454121cd12b8ded98a2c Author: lijewski Date: Thu Jun 26 21:02:48 2008 +0000 more efficient periodic tests in properly_nested() Src/F_BaseLib/ml_boxarray.f90 commit bffa60a879beb169be02b9d25d5985eed1cee480 Author: lijewski Date: Thu Jun 26 20:45:21 2008 +0000 no need to grow box by ng before passing to box_periodic_shift() Src/F_BaseLib/fillpatch.f90 commit 09f2e0572bec60f287427a2a193f01c039bfde9f Author: lijewski Date: Thu Jun 26 15:58:19 2008 +0000 *** empty log message *** Src/F_BaseLib/boxarray.f90 commit eccb019a5c5872ebcdc8015b293fef095d23ea79 Author: lijewski Date: Thu Jun 26 15:57:56 2008 +0000 added couple uses of boxarray_contains() Src/F_BaseLib/test/t_knapsack.f90 Tests/F_BaseLib/t_knapsack.f90 commit 8e02e21edcce7b8094cd8e3cc72262ee1168c3a6 Author: almgren Date: Thu Jun 26 05:38:50 2008 +0000 I believe we now have a correct implementation of ml_boxarray_properly_nested. Only limited testing has been done, but it seems good. Src/F_BaseLib/ml_boxarray.f90 commit a7a23c5f3f7022b86e0df8bceb8dc7fc48f34b25 Author: ajnonaka Date: Thu Jun 26 03:51:35 2008 +0000 added "use_bl_error_module". Code compiles again. Src/F_BaseLib/boxarray.f90 commit 277a9424a2fbe46b5e401b7ac68065694348c4b6 Author: almgren Date: Wed Jun 25 23:31:30 2008 +0000 New functions added: 1) function boxarray_boxarray_contains(ba1,ba2) returns true if ba1 contains ba2 2) function boxarray_box_contains(ba1,ba2) returns true if ba contains bx Src/F_BaseLib/boxarray.f90 commit 69d154998f165199b830f6c37d415797f0ac89eb Author: almgren Date: Wed Jun 25 22:11:05 2008 +0000 Replace the box_grow_i_m function by box_grow_n_m which actually makes the lo lower and the hi higher, unlike the previous box_grow_i_m, which made the lo lower and the hi lower (go figure). Src/F_BaseLib/box.f90 commit 53a1edfb22633414220d71c0348924728f5f8114 Author: almgren Date: Wed Jun 25 21:19:50 2008 +0000 Fix ml_boxarray_properly_nested so that it correctly works *except* for periodic cases. It takes an integer, nproper, which is how many grow cells are needed at the fine level to be contained by the coarser boxarray. Src/F_BaseLib/ml_boxarray.f90 commit 1d5cdefddfc51f987d73572667838ddcce17f13b Author: almgren Date: Wed Jun 25 19:14:47 2008 +0000 Change ml_boxarray_properly_nested_new --> ml_boxarray_properly_nested and ml_boxarray_properly_nested --> ml_boxarray_properly_nested_old Src/F_BaseLib/ml_boxarray.f90 commit be42b2561364a1fd65a06cb0108bc9be8b519ec3 Author: almgren Date: Wed Jun 25 18:04:29 2008 +0000 Slight change in the test for creating maximum number of multigrid levels. One of the criteria for stopping the coarsening is now if the volume of the entire boxarray is less than or equal to 2**dim. This makes the single-base-grid XRB initial divu iterations converge. Hopefully it won't break anything else (?). Src/LinearSolvers/F_MG/mg.f90 commit 35141da3193b58fea2f66b670aa13a700f2f8459 Author: lijewski Date: Wed Jun 25 17:25:51 2008 +0000 some cleanup Src/F_BaseLib/cluster.f90 commit 9ffeffda76c2a58ba814c7541eaa1e6eb42b62dd Author: almgren Date: Wed Jun 25 15:12:05 2008 +0000 Should use bchi instead of bclo in test on whether is BC_INT -- oops! Src/LinearSolvers/F_MG/stencil.f90 commit 42c006b1e1cc20c7a1286689e2bb87922061325e Author: almgren Date: Wed Jun 25 05:25:05 2008 +0000 Changed the way we define the stencil at interior boundaries of grids -- this only changes the stencil values at the level of machine precision, but it helps in debugging ... now the stencils will be identical whether there is a single grid or multiple grids covering the same region. Src/LinearSolvers/F_MG/stencil.f90 commit ffa8dfc18a95e4633ac510842023f7c52456bcaa Author: lijewski Date: Tue Jun 24 22:29:58 2008 +0000 fixed another parallel gotcha -- seems OK but more testing required Src/F_BaseLib/cluster.f90 commit 129c4d783d8633bd549c37175cca5f4279a48d82 Author: almgren Date: Tue Jun 24 20:09:01 2008 +0000 Fix ml_edge_restriction to correctly handle the periodic fix. Src/LinearSolvers/F_MG/ml_restriction.f90 commit f3ff013bc732fe7854ee9d0e6cde8587b369f547 Author: almgren Date: Tue Jun 24 17:03:08 2008 +0000 Remove fillpatch and multifab_fill_ghost_cells -- returning to previous approach where these are included in the directory where define_bc_tower lives... Src/F_BaseLib/GPackage.mak commit 615dab16fd637ddbca34112c7577a87bb4fac0e0 Author: almgren Date: Tue Jun 24 05:29:58 2008 +0000 Divide max_grid_size by ref_ratio since we create the new grids at the coarser resolution but we want max_grid_size to hold at the fine resolution. Src/F_BaseLib/regrid.f90 commit 7d7ce5ac9fb186200e8dfdf47e3b13e79c4615b4 Author: almgren Date: Mon Jun 23 23:29:56 2008 +0000 Impose boxarray_maxsize on the new boxarray before making the new multifabs. Src/F_BaseLib/regrid.f90 commit 07eeff2438ad0b88071b7ad83cbd63777aa4d0bc Author: almgren Date: Mon Jun 23 22:00:19 2008 +0000 Take max_grid_size as an input into make_new_grids. Src/F_BaseLib/regrid.f90 commit b398ff8064c6d7f6a9ce953440fcd29b5db2965b Author: lijewski Date: Mon Jun 23 21:54:35 2008 +0000 removed setval_mask() functions - not apparently used anywhere Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit 38a194777523f042d5ece4ac18b7eab5f8e6c924 Author: almgren Date: Mon Jun 23 21:42:34 2008 +0000 Added fillpatch.f90 and multifab_fill_ghost_cells.f90 to GPackage.mak since we took them out of varden/GPackage.mak Src/F_BaseLib/GPackage.mak commit 0d55d87bdcbcfa1446213f53dec234cbeaa8e6d3 Author: lijewski Date: Mon Jun 23 21:29:27 2008 +0000 removed potentially troublesome where constructs Src/F_BaseLib/box.f90 commit 6b61a8e229ffdc7b372b10c58d8868d2140fb3ec Author: ajnonaka Date: Mon Jun 23 20:07:52 2008 +0000 in function box_grow_i_m, loop over dimensions instead of assuming dim=3 Src/F_BaseLib/box.f90 commit b7c9c0d9eefa2095767a7ef81c71412aae7ac716 Author: ajnonaka Date: Mon Jun 23 19:41:05 2008 +0000 loop over l(i) instead of using where construct Src/F_BaseLib/box.f90 commit ef78a96cdde29d8f89e80815bd0db52c2d9bcd8b Author: lijewski Date: Sun Jun 22 18:02:27 2008 +0000 *** empty log message *** Src/F_BaseLib/cluster.f90 commit b273b88a0ba217bf71025bff2a3a97a1da427200 Author: lijewski Date: Fri Jun 20 16:34:52 2008 +0000 clustering now works in parallel Src/F_BaseLib/cluster.f90 commit 06776fcd768d19c05fb035102c292a3f131e67cc Author: lijewski Date: Fri Jun 20 16:33:50 2008 +0000 changed verbosity defaults Src/F_BaseLib/knapsack.f90 commit 81e61e36dd914ee29646b2e5a876c727ea98c9ce Author: lijewski Date: Mon Jun 16 20:50:56 2008 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 128fb7d7c04fe7ae859b6feb53bb7f8cf4554275 Author: lijewski Date: Mon Jun 16 17:46:12 2008 +0000 plugged some memory leaks Src/LinearSolvers/F_MG/ml_restriction.f90 commit c4a8a4e26eedff2891898b15dcd5eb34dc7ab5a4 Author: almgren Date: Sat Jun 14 01:56:54 2008 +0000 Added new routine -- subroutine multifab_copy_on_shift -- called only by ml_edge_restriction -- this enables copies across periodic edges. Src/F_BaseLib/multifab.f90 commit 240c0d0ede8f67d3f7a7aa1f4cdf56d8b1162160 Author: almgren Date: Sat Jun 14 01:56:09 2008 +0000 Enable periodic averaging-down in ml_edge_restriction. Src/LinearSolvers/F_MG/ml_restriction.f90 commit ba0b725bf865f1ae616d77cfe1b402648a5b19d4 Author: almgren Date: Wed Jun 11 22:27:53 2008 +0000 Fix for periodic -- where divu is not zero on the periodic edge. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 2371ebf6bc2fdd5ee302cd4a392c490a25a732f6 Author: lijewski Date: Wed Jun 11 17:03:38 2008 +0000 mods to enable writing plotfiles in single precision Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c commit be4755e974ae40a5c5c2796412b7916fb329c8b6 Author: mzingale Date: Mon Jun 9 23:50:40 2008 +0000 fix a model file Tools/C_util/regtests/Maestro-tests.ini commit e8a90f4eb3d3ab003b75f3cb829247a6fd444ab8 Author: almgren Date: Mon Jun 9 17:40:02 2008 +0000 1) Cleaned up the crse/fine resid routine. 2) We now include fine fluxes on periodic boundaries -- this seems to work for now. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 4f5fe45f32b65758b256e54de8fda704df334ef7 Author: mzingale Date: Sun Jun 8 22:30:57 2008 +0000 update to reflect changes to the spherical problems Tools/C_util/regtests/Maestro-tests.ini commit c8193f3659314491d52ce1fb512e7261d77988cb Author: lijewski Date: Tue Jun 3 23:45:09 2008 +0000 some simplification of VisMF::Write Src/C_BaseLib/VisMF.cpp commit e5ce8eae5f68ecaa21b8ee5baee702e4b34bccc7 Author: aaspden Date: Tue Jun 3 20:09:14 2008 +0000 Added a Barrier to prevent running out of PER_PROC message packets (happened on Jagwar) Src/C_BaseLib/VisMF.cpp commit 166d4b78845c851d26d0bff18284f15bd6da9efd Author: almgren Date: Tue Jun 3 19:44:30 2008 +0000 Change mla and la from intent "inout" to intent "in" Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 1fa362b7c438d25fad9763df0daa0aea4694f9cc Author: almgren Date: Tue Jun 3 19:44:00 2008 +0000 Change la to "in" from "inout" Src/F_BaseLib/bndry_reg.f90 commit c20ae4014dfe7b9cc91ace2d77bebc97dc8b53f1 Author: mzingale Date: Fri May 30 17:41:58 2008 +0000 for jaguar, if we are doing PathScale don't include the -module part twice Tools/F_mk/GMakedefs.mak commit 555c3d7a0e5866c0b522f992eba9b7dd7c78323e Author: jbb Date: Wed May 28 17:04:25 2008 +0000 Fix the print statements for the case where the initial guess solves the problem. Also, in this case, don't even enter the iteration loop. Src/LinearSolvers/F_MG/ml_cc.f90 commit 5b219d90f0488b51eb082c42f92782b2971431b1 Author: gpau Date: Sat May 24 14:57:42 2008 +0000 some files for statistical analysis Tools/C_util/Statistics/AVGDOWN_2D.F Tools/C_util/Statistics/AVGDOWN_3D.F Tools/C_util/Statistics/AVGDOWN_F.H Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/Make.package Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp commit c464672caa3be9c0ed1983be2b6fd8c09e14dea3 Author: lijewski Date: Thu May 15 16:54:02 2008 +0000 Vince's nOutFile and lUsingNFiles modifications Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c commit d67bd13ae5320a47e61d3d38a4102185b0734434 Author: lijewski Date: Tue May 13 21:52:48 2008 +0000 Added a couple tests for a mismatch between the size of integer and size of off_t in routines writing raw FAB data to disk. The offset of the start of the FAB is an off_t, but is passed back to FORTRAN as an integer. If this is ever hit we'll have to redo how I/O is done. The offset itself is stored in the header of the MultiFab on disk so reading proceses know where to go on disk to get the data. Src/F_BaseLib/fabio_c.c commit e387ee0394f64b5cb10e2ae3091318dbc6330815 Author: mzingale Date: Tue May 13 15:22:35 2008 +0000 Castro now uses 5 digits in the plotfile names Tools/C_util/regtests/test.py commit a5e740e9a22f289482269f772040e13cef1bb53e Author: mzingale Date: Tue May 13 15:07:07 2008 +0000 have homer put the module files into the o/ directory Tools/C_mk/Make.Linux commit 26c341a3f73f07a413e5aa9e21738f09b523b8d9 Author: lijewski Date: Mon May 12 22:34:16 2008 +0000 now print out number of CPUs MPI initialized with Src/F_BaseLib/BoxLib.f90 commit 0d74ac3894b7cded693fc77f93ce6a78952a8aeb Author: almgren Date: Fri May 9 17:28:58 2008 +0000 Remove unneeded variables. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 9b9c8689db47c4d3f30b892d65b8b3bc48ed1556 Author: almgren Date: Fri May 9 17:26:17 2008 +0000 Small code cleanup. Src/LinearSolvers/F_MG/stencil.f90 commit f1f4f8e5432946acde6d743414b90ce522d03561 Author: almgren Date: Wed May 7 20:20:10 2008 +0000 Removed unused variables. Src/C_BaseLib/COORDSYS_1D.F Src/F_BaseLib/layout.f90 commit fe7af46f827d37f72bdd56d9eb9b06f3d800aee2 Author: almgren Date: Wed May 7 20:19:34 2008 +0000 Removed unneeded "lenx". Src/C_AMRLib/FLUXREG_1D.F commit 61c49443938c0c88df02c756fb877f595bbcb369 Author: almgren Date: Fri Apr 25 21:06:54 2008 +0000 Changed the length in BoxLib::Concatenate from 4 to 5 -- this will make pltfiles and chkfiles now use 5 spaces instead of 4 for the step number. Src/C_BaseLib/Utility.cpp commit c6a247cabfc2dba4dd9a1dc92562ded1c7977f14 Author: almgren Date: Fri Apr 25 20:45:49 2008 +0000 Can't use 0.d0 Src/C_BaseLib/MultiFab.cpp commit 4152b96c0f99e3087232e479074e1a10abd5f6d2 Author: almgren Date: Fri Apr 25 19:30:49 2008 +0000 Added a norm2 function to MultiFab (analogous to norm0). Doesn't use ghost cells. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 6646fb78e53ff9ad85c3c1f96778077daf349e7d Author: lijewski Date: Mon Apr 21 20:02:00 2008 +0000 added build_random_boxarray to public interface Src/F_BaseLib/mt19937ar.f90 commit 44771ad7cba6c2d1862a7d925d5f4fb9b2cea5d2 Author: lijewski Date: Fri Apr 18 20:09:07 2008 +0000 atlas updates from Mike Singer Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit d486f2374cc7ba4f7b6e32e6c163fc37b53ff41e Author: aaspden Date: Thu Apr 17 23:10:54 2008 +0000 Gimantis update Tools/C_mk/Make.defs commit 6876fdcf6c255f047cfa806553708c9439080e78 Author: mzingale Date: Tue Apr 15 14:43:23 2008 +0000 Castro uses a different # of digits in the plotfile name Tools/C_util/regtests/test.py commit e50d195dce3c37ad61a4bfa11dd39e32cb827b5f Author: mzingale Date: Mon Apr 14 21:07:09 2008 +0000 get the Castro test suite back up to date with the latest changes Tools/C_util/regtests/Castro-tests.ini commit 0bd96169dce2c59b81dae357c4f6f40217d4ad0d Author: mzingale Date: Mon Apr 14 21:04:33 2008 +0000 don't generate Parallel Changelog for an fParallel run remove useFParallel for Parallel builds -- it is always needed now. Tools/C_util/regtests/test.py commit 47aab0be0fcebaa46f9f7273cbae597838e1aea4 Author: almgren Date: Fri Apr 11 20:30:10 2008 +0000 Another fix of sign error on lo side in stencil_all_flux_3d. Src/LinearSolvers/F_MG/stencil.f90 commit a4944f01e496977ca41a373b25704494bc43c79e Author: almgren Date: Fri Apr 11 20:28:32 2008 +0000 Fill sign error for lo side in stencil_all_flux_3d. Src/LinearSolvers/F_MG/stencil.f90 commit 1c5bcdaeb0beac04e01de2258b365fc7111a65e5 Author: lijewski Date: Thu Apr 10 21:14:48 2008 +0000 now print out # CPUs MPI initialized with Src/C_BaseLib/BoxLib.cpp commit 1edf91d0a940b5888449962baf51e359f71082db Author: almgren Date: Thu Apr 10 20:31:23 2008 +0000 Moved GetBndryCells to be member function of Geometry. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit ad0f4562cc06702648dee3e7c5f744d173e1db7b Author: almgren Date: Wed Apr 9 19:54:35 2008 +0000 We need this in order to include the right fParallel/boxlib files when compiling in the Parallel/Castro subdirectories. Src/F_BaseLib/FParallelMG.mak commit 1eebc4cae7d82d491e11dfa79641c64834e264c3 Author: ajnonaka Date: Tue Apr 8 23:27:17 2008 +0000 at the end of ml_restriction_c, changed the call to multifab_fill_boundary to multifab_fill_boundary_c Src/LinearSolvers/F_MG/ml_restriction.f90 commit 9004a2e767b7e11437bc54505587c67265f762e5 Author: lijewski Date: Wed Apr 2 20:39:43 2008 +0000 modest touch-up to norm0() Src/C_BaseLib/MultiFab.cpp commit cd5b894e2bbe38bd1a568264d3018b66d217a0ea Author: almgren Date: Wed Apr 2 19:21:23 2008 +0000 Added norm0 function which takes the inf norm of a multifab using no ghost cells. Optional comp argument (defaults to zero). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 7d24b8ed98bd9560dfec49ddd946e3a022b7fba3 Author: almgren Date: Tue Apr 1 20:02:11 2008 +0000 1) Move the functions which call the mt19937ar random stuff from box_util.f90 into mt19937ar.f90 2) Remove mt19937ar.f90 from GPackage.mak and NPackage.mak so that they are not included in general. They can still be included as needed in the boxlib/test directory (the only place I can found where the make_random_box routines are actually called) Src/F_BaseLib/GPackage.mak Src/F_BaseLib/NPackage.mak Src/F_BaseLib/box_util.f90 Src/F_BaseLib/mt19937ar.f90 commit 713ff52886631c61abc24215ce77e554eb59f312 Author: almgren Date: Mon Mar 31 20:39:13 2008 +0000 Changes by Candace in making varden truly adaptive. Src/F_BaseLib/fabio.f90 Src/F_BaseLib/regrid.f90 commit 8b175ebd99e098dba9c25f3b45d1bb1856e58454 Author: vince Date: Fri Mar 21 22:24:16 2008 +0000 i/o float fix. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit 5e4c883bd37102f5eefa17e16da0fbb9d7e984dd Author: vince Date: Fri Mar 21 22:07:37 2008 +0000 i/o fix. Src/C_BaseLib/RealBox.cpp commit 1f205d789d9188e09c7b50c1cddaa718db18bdfa Author: almgren Date: Tue Mar 18 19:54:58 2008 +0000 Candace's changes to regrid -- buffer subroutine not complete, but this does multiple levels. Src/F_BaseLib/regrid.f90 commit 06cbf8ac73a337881e450fb72a1f31ea38b94c66 Author: almgren Date: Tue Mar 18 19:54:35 2008 +0000 Candace found missing destroy -- fixed here. Src/F_BaseLib/cluster.f90 commit a68e979cffe464a026c87fdfb415a563a2a6c603 Author: jbb Date: Sat Mar 8 00:56:53 2008 +0000 added mpi link for gimantis Tools/F_mk/GMakeMPI.mak commit 8551edd439d3b44b9ac9ab0b7c9bc8331ca9f53c Author: mzingale Date: Tue Mar 4 20:03:12 2008 +0000 fix jaguar compiling -- now it handles modules correctly. Tools/F_mk/GMakeMPI.mak commit 64b111a7515387a87fb974cb219fbc3a5f83ee6c Author: lijewski Date: Tue Mar 4 18:41:19 2008 +0000 removed some profilers Src/F_BaseLib/multifab.f90 commit 0a3a0114bac9ea8606c194b9907b596f11b1a491 Author: ajnonaka Date: Mon Mar 3 22:07:23 2008 +0000 fixed a comment Src/LinearSolvers/F_MG/ml_nd.f90 commit 24d2d750d8bddec8fb5b2b5c390c777be2403353 Author: mzingale Date: Mon Mar 3 20:51:19 2008 +0000 update homer to use MPICH2 Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit a74c631f193822b2fc976c1f99e491cfb8067009 Author: almgren Date: Mon Mar 3 18:03:07 2008 +0000 Remove print statement. Src/LinearSolvers/F_MG/nodal_divu.f90 commit f5c32f101673bcd5719be3ee89a20f17ce699c97 Author: jbb Date: Mon Mar 3 17:38:15 2008 +0000 Add case for mothra. Tools/F_mk/GMakeMPI.mak commit ac00fff324ec5e7eaa4ac082cd91afc299da8be5 Author: almgren Date: Mon Mar 3 03:13:43 2008 +0000 Add subtract_divu_from_rh. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 3de5ba2ad54e6bec80d97a4cb9b46668e39e065a Author: almgren Date: Fri Feb 29 22:55:56 2008 +0000 Oops - forgot to destroy the multifab zero_rh which I'd added. Src/LinearSolvers/F_MG/ml_nd.f90 commit a2916c53ec854019c35889b896c38200018c10f3 Author: almgren Date: Fri Feb 29 22:30:02 2008 +0000 Fix the crse_fine_nodal_residual -- before it was passing in the fine grid rh and using that in computing the crse/fine residual -- but in fact the crse/fine rhs already sits on the crse grid, so we only want to modify that with the crse/fine L(phi), not the full crse/fine (f - Lphi), since the f at the crse/fine boundary has been constructed to be the right crse/fine f. Src/LinearSolvers/F_MG/ml_nd.f90 commit 488e6bf5989568af7cd8baef3aa045b2f9423eb6 Author: lijewski Date: Thu Feb 28 17:48:01 2008 +0000 BL_PGI no longer needed Src/C_BaseLib/Thread.H Src/C_BaseLib/Utility.H Tools/C_mk/Make.Linux commit fdfa38758e2ab2d618bdae78d53d8ee6764a770b Author: jbb Date: Wed Feb 27 20:27:21 2008 +0000 Make the include c.depends and include f90.depends fail if cant be built. Tools/F_mk/GMakerules.mak commit 2643d9b8b7514c5aa6fdc39883738f300046cadb Author: ajnonaka Date: Wed Feb 27 05:12:18 2008 +0000 fixed the format of "Header" so it looks the same regardless of compiler and machine. Src/F_BaseLib/fabio.f90 commit 8704cdf6fd886f7cef14b47dd00ccae5b6f2351c Author: ajnonaka Date: Tue Feb 26 21:08:47 2008 +0000 Modified the pltXXXX/Header output so it compatible with visIt as well as amrVis. In particular: -Any line that begins with an integer cannot have any blank spaces before that first integer. -We had our grid definitions divided up by line, i.e., ((0,0) (15,63) (0,0)) ((0,0) (31,127) (0,0)) ((0,0) (63,255) (0,0)) where they need to be continuous on one line, i.e., ((0,0) (15,63) (0,0)) ((0,0) (31,127) (0,0)) ((0,0) (63,255) (0,0)) There was also a bug in how we computed the physical coordinates of each box above the lines "Level_X/Cell". It was a dx scaling problem which is now fixed. Src/F_BaseLib/fabio.f90 commit e2179e2fe21e277b528d3ce45594eff0d69a2b6c Author: ajnonaka Date: Tue Feb 26 16:55:33 2008 +0000 remove dx from call to multifab_phybc Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit de918157b46ecf89edfcac553086bd3e1ec62923 Author: ajnonaka Date: Mon Feb 25 23:28:56 2008 +0000 some comments about what the inputs to itsol_stencil_apply, mg_defect, and itsol_defect are Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 commit 130ebd9f7f2376d2d3919384a9dd2aaf85304c28 Author: ajnonaka Date: Thu Feb 21 21:06:52 2008 +0000 works for jaguar now Tools/F_mk/GMakeMPI.mak commit 6104d6ffd85f75cb0b95c302dffae1d389ebfecd Author: almgren Date: Thu Feb 21 18:44:50 2008 +0000 Add "all = .true." to setval for buf. Src/F_BaseLib/cluster.f90 commit fa8512110ba0497bbfd922cafb9566692206cdc6 Author: almgren Date: Thu Feb 21 18:39:37 2008 +0000 Need to initialize "buf" to false before setting true values in subroutine buffer_nd Src/F_BaseLib/cluster.f90 commit 1a6f106e110fdfb1f422f8e29a4587f384ec2406 Author: mzingale Date: Sun Feb 17 18:33:58 2008 +0000 work with the new plotfile format (plt00000 instead of plt0000). Also if we fail in making a benchmark file (the code crashes before output) then don't report that we've made a benchmark. Tools/C_util/regtests/test.py commit 37b7ad7d96b2f549f4ec37699d352140810bd6d7 Author: vince Date: Wed Feb 13 21:24:57 2008 +0000 more gimantis additions. Tools/C_mk/Make.defs commit d0c5ab64450404ec548a49d97b6297c153a41dcd Author: vince Date: Mon Feb 11 23:54:22 2008 +0000 additions for gimantis. Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit c22c35ed8c28abef5797637dc753803eb48e8e50 Author: marc Date: Fri Feb 8 20:56:10 2008 +0000 *** empty log message *** Tools/C_mk/Make.defs commit ff6fff911d5b71cd145031bede37a6b5d209d874 Author: jbb Date: Fri Feb 8 20:22:31 2008 +0000 make mothra work Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 42fc06dbd32dcfd1982979758e2a69d7b72b6c51 Author: lijewski Date: Fri Feb 8 18:15:11 2008 +0000 added some implicit none statements Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F commit e67a027c50f47c5a9e524bf3460bc7e60439e312 Author: lijewski Date: Fri Feb 8 18:08:01 2008 +0000 added some implicit none statements Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit cebb9da569a5dc924bd76870527d57871561b83b Author: lijewski Date: Fri Feb 8 17:48:46 2008 +0000 added some implicit none statements Src/C_AMRLib/FILCC_1D.F Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/MAKESLICE_3D.F commit ca1653be47b4cff9baaab796c0d81d900bd15d67 Author: lijewski Date: Thu Feb 7 23:48:08 2008 +0000 some cleanup Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit ffc2bd2d2a84f05c6bae1dbaae44d74caa714601 Author: lijewski Date: Tue Feb 5 21:28:18 2008 +0000 make explicit that we use O2 not Ofast with PathScale Tools/F_mk/GMakedefs.mak commit 1d96e73fa4d933c430fc9744edd2d15521300a52 Author: lijewski Date: Tue Feb 5 21:25:50 2008 +0000 use -O2 -ipa with PathScale to be consistent with stuff in fParallel Tools/C_mk/Make.Linux commit 453028a61b629ab0992f054e8a755465671ca00f Author: lijewski Date: Tue Feb 5 20:05:00 2008 +0000 added -mp for Intel 9/10 optimization Tools/F_mk/GMakedefs.mak commit fdc3119bc5e608b321c8b466fde02829e80571fd Author: ajnonaka Date: Thu Jan 31 23:26:41 2008 +0000 commented out code that sets solution to zero. So far, the multigrid appears to behave better; ie, we've seen convergence for 100 grids and haven't tried anything higher yet. Src/LinearSolvers/F_MG/itsol.f90 commit 7172a76015fba5e3005c186d0840d346a9b57826 Author: sepp Date: Thu Jan 31 23:18:18 2008 +0000 1) removed extraneous blank before comma after _l2 in DIMS for dim 2 and 3 Src/C_BaseLib/ArrayLim.H commit 6aef11d06b9e1eed86b52101098395e2cd3356ea Author: almgren Date: Thu Jan 31 21:51:03 2008 +0000 Added options to make mpi work on pleiades. Tools/C_mk/Make.mpi commit f6fe4d2fc2ac774bf6f5f2294e35af377fb84d1c Author: marc Date: Thu Jan 31 18:58:36 2008 +0000 += instead of = Tools/C_mk/Make.Linux commit 1924821ff92a8c6bbfff9fe62b58314936666e75 Author: marc Date: Thu Jan 31 18:50:17 2008 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Make.package commit 5185180d724b4917d552c65e991d7362b5be0681 Author: lijewski Date: Thu Jan 31 18:31:02 2008 +0000 more IO wraps Src/F_BaseLib/multifab.f90 commit 006cfbbbd657ed7aa2b1f1b7054ab411464cbf3c Author: lijewski Date: Thu Jan 31 18:25:46 2008 +0000 parallel_IOProcessor() wraps in print() Src/F_BaseLib/multifab.f90 commit 7504942b3ff6657929264e6864e223f58074ee86 Author: marc Date: Thu Jan 31 18:20:54 2008 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 7f5c5ae11521aecfcd589c8409b15f3b991181c9 Author: almgren Date: Tue Jan 29 17:56:49 2008 +0000 Fix misspelling in command line option. Tools/C_mk/Make.defs commit 25663707d9001128fefd0f8d8bf1e588b65df7ec Author: lijewski Date: Mon Jan 28 20:42:10 2008 +0000 added profiler to ml_nodal_restriction Src/LinearSolvers/F_MG/ml_restriction.f90 commit db262c1706b47a7bcf62588a27d2c2ffc01e8897 Author: lijewski Date: Fri Jan 25 22:17:47 2008 +0000 some cleanup Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 0c09dbfc3be7eec1a5b5776e61bbb8dfa337589e Author: gpau Date: Thu Jan 24 23:54:18 2008 +0000 PathScale bug fix Tools/C_mk/Make.Linux commit 5583219c1d4d968ebfb3385ef2bacecf265c5043 Author: mzingale Date: Thu Jan 24 22:07:34 2008 +0000 fix the permissions at the end of the suite run so other users can see the files Tools/C_util/regtests/test.py commit f2063f5b7cba41ec3ca16ba6eebb6aa9c17a6231 Author: mzingale Date: Thu Jan 24 19:42:45 2008 +0000 update the grid file for test_smallscale Tools/C_util/regtests/Maestro-tests.ini commit f4de399a5a441f569b4454a7beff791da7e4df65 Author: lijewski Date: Thu Jan 24 17:13:30 2008 +0000 reverting out some changes -- not particularly useful Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 48c4f0ba9fb80bb110e3ac74bf444403b290db84 Author: lijewski Date: Wed Jan 23 23:33:42 2008 +0000 got rid of gs_rb_smoother_3d_transpose() Src/LinearSolvers/F_MG/mg_smoother.f90 commit 872c9eab14baa1c3b9e14f361b22ff94fb9a34a3 Author: lijewski Date: Wed Jan 23 22:10:49 2008 +0000 unrolled 3d cross stencil for modest speed improvement Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit ca0b96a90c58944a0d3b10e2066e9294a92afe3b Author: lijewski Date: Wed Jan 23 20:39:13 2008 +0000 couple very modest optimizations Src/LinearSolvers/F_MG/mg_smoother.f90 commit a07a9e0ee7bcf284b5b638af4dc942089f44809a Author: lijewski Date: Tue Jan 22 17:06:31 2008 +0000 added logical do_mpp to allow turning off minimize comm costs Src/F_BaseLib/knapsack.f90 commit 9936b1673ecafdee600eb72ca6ec3ada9c71ea83 Author: lijewski Date: Tue Jan 22 17:05:40 2008 +0000 *** empty log message *** Src/F_BaseLib/test/t_knapsack.f90 Tests/F_BaseLib/t_knapsack.f90 commit ab4117a995087a69bed9146f53c2c331b4f5b557 Author: lijewski Date: Mon Jan 21 17:53:52 2008 +0000 Added the following subroutines: subroutine setval_fabs_on_init(yes_or_no) subroutine set_fab_default_init(val) subroutine set_zfab_default_init(val) subroutine set_ifab_default_init(val) subroutine set_lfab_default_init(val) Previously fabs were always setval()d on being built to a hard-wired value. Src/F_BaseLib/fab.f90 commit 2712252068148c9af82378b95dad50033164e79b Author: mzingale Date: Sun Jan 20 21:46:03 2008 +0000 add compilation rules for homer Tools/F_mk/GMakedefs.mak commit f348c5639c8d197710735f3a9ff44567553d8f4b Author: lijewski Date: Fri Jan 18 21:18:02 2008 +0000 now have minimize communication costs ability in knapsack Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 commit 4141c08ca13a2bf398e26bd54a4fa4df644c2cd9 Author: mzingale Date: Wed Jan 16 21:18:47 2008 +0000 turn on -mp for Intel, and turn on warnings for Intel 10 in debug mode Tools/F_mk/GMakedefs.mak commit 62946bf3e1934681ad25cadfe9f6f817bac4915a Author: mzingale Date: Tue Jan 15 22:53:40 2008 +0000 add support for Intel 10.1 Tools/C_mk/Make.defs commit 8ee5343b7a77f7dc1b10f96c1a8a1f9d27a5fbaa Author: ajnonaka Date: Tue Jan 15 22:01:38 2008 +0000 changed PathScale compiler options to -O2 -ipa Tools/F_mk/GMakedefs.mak commit 0798bb6adc72dd2f88ae6dc948bdbb846c886def Author: almgren Date: Tue Jan 15 22:01:27 2008 +0000 Modify nodal_smoother_2d and nodal_smoother_3d so for the cross stencil: if the domain is periodic in x and odd in x (or periodic in y and odd in y for 3d) then use Jacobi instead of Gauss-Seidel relaxtion. Gauss-Seidel red-black is bad in this case because the multifab_fill_boundary will overwrite new values on the lo side with old values on the hi side, making it not converge. Src/LinearSolvers/F_MG/mg_smoother.f90 commit f144755153af68c8d92aba4e7ab5709fa2515ef6 Author: almgren Date: Tue Jan 15 22:00:08 2008 +0000 1) Modify the number of iterations after a bottom solver failure from 2 to 20. 2) Define pmask to pass into the nodal smoother to test on whether to do Jacobi (if odd and periodic) or Gauss-Seidel (otherwise) for cross stencil. Src/LinearSolvers/F_MG/mg.f90 commit 15170710a07ce224b19c3079314d7d07c02313a0 Author: almgren Date: Tue Jan 15 21:58:58 2008 +0000 Print statement in BiCG if solution is set to zero, also return error stat. Src/LinearSolvers/F_MG/itsol.f90 commit 79f9823492b5fc2716c649ceeaf44329891700d6 Author: almgren Date: Tue Jan 15 18:27:12 2008 +0000 Make it so the CC and the nodal solver call bl_abort if they don't converge in max_iter iterations. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit f0199e022c311498149d6da1cc69c3cc8e77d9d8 Author: lijewski Date: Mon Jan 14 21:00:15 2008 +0000 added back in some stuff I removed -- used by MGT_Solver Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 033266308d990d59ee8a329ccd3773545271b40a Author: lijewski Date: Mon Jan 14 20:54:43 2008 +0000 added sort_i.f90 needed by fab.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit 29e0bfb01849f23aa056d0670290b87189b139df Author: lijewski Date: Mon Jan 14 20:07:31 2008 +0000 tweaked due to bndry_reg.f90 mods Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit de239333eb7212dc85e9c09f48b664b1d02b5fae Author: lijewski Date: Mon Jan 14 20:06:38 2008 +0000 obmf multifabs are now build optionally Src/F_BaseLib/bndry_reg.f90 commit d7ff812d25c04b048ec01f934f2d53faca311102 Author: lijewski Date: Mon Jan 14 04:37:08 2008 +0000 bndry_reg_rr_build_1 -> bndry_reg_rr_build Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit e9456db356ef7775e55d7d1d49a2e52f0d74f7ef Author: lijewski Date: Mon Jan 14 04:35:31 2008 +0000 Removed unused function. Renamed bndry_reg_rr_build_1 -> bndry_reg_rr_build. Some cleanup. Src/F_BaseLib/bndry_reg.f90 commit 9a0ab5c56ed9220dde08de8766d75cc2cc35b50a Author: lijewski Date: Sat Jan 12 04:44:21 2008 +0000 fixed parallel bug in bndry_reg_build() Src/F_BaseLib/bndry_reg.f90 commit 7e72496b2f5f02bedf9490baa5eff876fcdf4d12 Author: lijewski Date: Fri Jan 11 22:52:28 2008 +0000 *** empty log message *** Src/F_BaseLib/fab.f90 commit 535b4bd3792d3fb9ecaacaca47c45aa74aef0b93 Author: lijewski Date: Fri Jan 11 22:30:06 2008 +0000 use least_used_cpus() when assigning boxes to CPUs Src/F_BaseLib/layout.f90 commit 162e402c899a4d3f427ed6375d1bba2ba18bc9b4 Author: lijewski Date: Fri Jan 11 22:29:36 2008 +0000 added least_used_cpus() Src/F_BaseLib/fab.f90 commit 35faa988a44cc3b542ba64ccaf0aa9c94b391e51 Author: lijewski Date: Fri Jan 11 18:23:57 2008 +0000 added MPI_Allgather functionality Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit d69b56f768819f18e1ec7e0cfcbde60146c518a2 Author: mzingale Date: Tue Jan 8 21:45:23 2008 +0000 make the restart work again (i.e. we need to keep the checkpoint files around) Tools/C_util/regtests/test.py commit 0fa5e7840843e7ca6715c399f78f51a8d96bea67 Author: mzingale Date: Mon Jan 7 21:13:27 2008 +0000 enable bounds checking for gfortran Tools/F_mk/GMakedefs.mak commit 2c01c32be0b39e3316c86c8b530d4fdaa555052f Author: lijewski Date: Thu Jan 3 23:44:21 2008 +0000 fabs no longer have an ng component Src/LinearSolvers/F_MG/stencil.f90 commit 0c825dfb0d94b7d24a35eba9ca651c36564e75ad Author: lijewski Date: Thu Jan 3 23:43:59 2008 +0000 Removed multifab_debug_fill(). Src/F_BaseLib/multifab.f90 commit 3702b6d6dd657721d6002091ea5f1e217daf2bcc Author: lijewski Date: Thu Jan 3 23:43:37 2008 +0000 Removed the "ng" component of fabs. Removed the set_border_val() routines & fab_debug_fill(). Src/F_BaseLib/fab.f90 commit 515d00c8ec639400822416727f8d0e9a8c2c74a1 Author: lijewski Date: Thu Jan 3 23:39:22 2008 +0000 removed multifab_debug_fill() call Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit a7ccd9bacd8c229d9156b79dc5a7dca851ccd092 Author: lijewski Date: Thu Jan 3 06:11:53 2008 +0000 *** empty log message *** Src/F_BaseLib/fab.f90 commit 9392c053b68f6eb8b9a51b2989e8924cf4ec9f4b Author: lijewski Date: Thu Jan 3 05:35:29 2008 +0000 code for calculating & printing fab byte spread Src/F_BaseLib/fab.f90 commit 92963385d9be62140d8c3809ca8cdb2d65688259 Author: lijewski Date: Tue Jan 1 21:04:37 2008 +0000 fixed more parallel bugs Src/LinearSolvers/F_MG/itsol.f90 commit 748d852507ec56934fd27d5524684edfdf4a1cdd Author: lijewski Date: Tue Jan 1 17:15:53 2008 +0000 added aveassoc stuff Src/F_BaseLib/layout.f90 commit 12d549a6da7b810ffad13bdcc423f4eb163c3829 Author: lijewski Date: Tue Jan 1 16:28:45 2008 +0000 added sort_i.f90 Src/F_BaseLib/GPackage.mak commit d14db2cea588f993b5fe7cd1a385d561f47ec302 Author: mzingale Date: Mon Dec 31 15:44:18 2007 +0000 switch to realclean instead of clean don't output checkpoint files (to save space) Tools/C_util/regtests/test.py commit f23eca42c7ae22871d8fa1a98e08d194ffc4e450 Author: lijewski Date: Sat Dec 29 04:13:52 2007 +0000 removed the bound member -- not used Src/F_BaseLib/multifab.f90 commit 45c334e91b6209b693eaf1293621435093fb69b0 Author: lijewski Date: Wed Dec 26 20:32:02 2007 +0000 more mem_stat refinement Src/F_BaseLib/fab.f90 commit 696f7d40963100b46e5bd332dfc218032b73f7ca Author: lijewski Date: Wed Dec 26 19:49:18 2007 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 2a87d86c073170780cbcf948c369a9885e463099 Author: lijewski Date: Wed Dec 26 19:32:31 2007 +0000 more work on mem_stats for cached data Src/F_BaseLib/layout.f90 commit 0b312f77f619e656d669427356a12c7b91ed7103 Author: lijewski Date: Wed Dec 26 02:25:05 2007 +0000 more mem_stats stuff Src/F_BaseLib/layout.f90 commit 992ba8b51a24677dd6f62d7f6dfc4d6fc7cb402d Author: lijewski Date: Wed Dec 26 01:05:31 2007 +0000 now calculates min/max cnt & min/max alloc across CPUs Src/F_BaseLib/bl_mem_stat.f90 commit f59d75a0db475f1552911be757059faa57df295d Author: almgren Date: Wed Dec 26 00:50:36 2007 +0000 Need bl_constants_module now that we're using "ZERO" Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit d245c094e70c9e27ec701a548199e452fc6f0702 Author: lijewski Date: Wed Dec 26 00:19:25 2007 +0000 mem_stats was NOT taking number of components into account Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit a37e564d8cfdb6d0de71ee9e0ac9a171863512c4 Author: lijewski Date: Tue Dec 25 20:40:27 2007 +0000 added flags to put modules in correct place for PGI Tools/F_mk/GMakeMPI.mak commit 65ee2e7e4b9746fdcb7a1e72ad5fc6eaec3083c1 Author: lijewski Date: Mon Dec 24 20:36:34 2007 +0000 run boxarray_maxsize() on boxarray stored in fgassoc Src/F_BaseLib/layout.f90 commit 8e9281b195d11d4242eabcbd10377ac40cf36a3a Author: lijewski Date: Mon Dec 24 18:09:48 2007 +0000 removed unimplemented routine Src/F_BaseLib/list_box.f90 commit 083b73f8837f774bd0d09dc9753ce8a05eee3d28 Author: lijewski Date: Mon Dec 24 18:09:23 2007 +0000 stop -> bl_error() calls Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 10636d87af386c0ffd1b573ed5631cb65f8998e5 Author: lijewski Date: Mon Dec 24 06:41:46 2007 +0000 wrapped some output in parallel_ioprocessor() Src/LinearSolvers/F_MG/mg.f90 commit ab3cc9bc227fb428771f7b9b5607ab356a09842d Author: lijewski Date: Fri Dec 21 21:46:04 2007 +0000 fixed box_intersector stuff; needed to make tmp layout w/nodalized boxarray Src/LinearSolvers/F_MG/ml_solve.f90 commit 2f733a4486be20e0a9c57a8f526bc6a4f7774dc3 Author: lijewski Date: Fri Dec 21 21:33:05 2007 +0000 added check that flux is cell-centered so box_intersector stuff is valid Src/LinearSolvers/F_MG/nodal_divu.f90 commit 7d62907fe2dcd6e008495cfa82f0b8461f5d272d Author: lijewski Date: Fri Dec 21 21:18:39 2007 +0000 fixed box_intersector stuff; needed to make tmp layout w/nodalized boxarray Src/LinearSolvers/F_MG/ml_restriction.f90 commit 1eb7407550580f22dfeb00839cef2316ecb4d9c4 Author: lijewski Date: Fri Dec 21 17:26:29 2007 +0000 moved from varden/MAESTRO directories Src/LinearSolvers/F_MG/ml_solve.f90 commit 786faa454405bae50d0c1ac10fe3334889ad1957 Author: almgren Date: Wed Dec 19 22:52:54 2007 +0000 Need to use ml_util_module in order to call ml_fill_all_fluxes in mgt_compute_flux. Src/LinearSolvers/F_MG/mg_cpp.f90 commit b3c515fff4a137be15f3f0661c26cf8e039a0123 Author: lijewski Date: Wed Dec 19 20:42:10 2007 +0000 needed bl_constants_module Src/LinearSolvers/F_MG/nodal_newu.f90 commit 215b6a984e95eb28e47dc69e0ad245c2f21e74a4 Author: lijewski Date: Wed Dec 19 20:38:27 2007 +0000 ml_norm_inf() and ml_norm_l2() are now in ml_util_module Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit 36cd349fb348e70b24df17442bbe1e4ebccb0196 Author: lijewski Date: Wed Dec 19 17:20:51 2007 +0000 mods to compile with Intel 9.0 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/layout.f90 commit 6f35f094c44634ab6b5ac9d2afed4a9047402edf Author: lijewski Date: Wed Dec 19 06:11:09 2007 +0000 some cleanup of use statements Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 0642ab879c2e947be59a1f4f97bb83e422d1d90d Author: lijewski Date: Wed Dec 19 04:47:27 2007 +0000 more careful with use statements Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_parmparse.f90 Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/cluster_2d.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/list_box.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/mt19937ar.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/ppm_util.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/t_bx.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/t_bx.f90 Tests/F_BaseLib/t_main.f90 commit 7db50ac9d3d20344843bd4f4cb85324853e07f86 Author: lijewski Date: Wed Dec 19 02:54:45 2007 +0000 some franklin/PathScale mods Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 19e6fd890791f96cef066ee57e2241219ced244c Author: lijewski Date: Wed Dec 19 02:52:19 2007 +0000 mods to compile on franklin with PathScale Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit 899584887cd5a1646b53d0b796bcd7f3d8205c4d Author: lijewski Date: Tue Dec 18 17:40:05 2007 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit a33d8138bf3d8d1396a80990d6e34903a72f6d11 Author: lijewski Date: Tue Dec 18 17:24:37 2007 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 592b6074ee8a556c72c78451e2c08807421b50fb Author: lijewski Date: Tue Dec 18 00:22:47 2007 +0000 fixed test in internal_sync_unique_cover() Src/F_BaseLib/layout.f90 commit 1d9abe773329d69bd1b81147187ba0b4fbcecf7a Author: lijewski Date: Mon Dec 17 23:10:53 2007 +0000 fixed bug in boxarray_same_q() Src/F_BaseLib/boxarray.f90 commit c52edd0e950c959929ca9ed931c44d0d2d6b213e Author: lijewski Date: Mon Dec 17 21:40:00 2007 +0000 used new fgassoc stuff from layout Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 1f2e4f5eef244707c54cc1c0fe858da1673c0416 Author: lijewski Date: Mon Dec 17 21:39:43 2007 +0000 added fgassoc to cache ghost cell boxarray used by mf_fill_ghost_cells() Src/F_BaseLib/layout.f90 commit 459b7cbec0b8db4fc9811953bd62b1de27eb1c01 Author: lijewski Date: Mon Dec 17 21:39:11 2007 +0000 more cleanup Src/F_BaseLib/boxarray.f90 commit 5be48a3c9a2e24752965fda1dba76ca02e86feb6 Author: lijewski Date: Mon Dec 17 19:22:07 2007 +0000 came up with simpler way to remove overlap Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit b660d40be2336ed677f1cc8302772074edd46d3f Author: lijewski Date: Mon Dec 17 19:11:40 2007 +0000 removed some unused stuff Src/F_BaseLib/boxarray.f90 commit 425670ec1e2d21a0d835a8b6ea87700696a2eb49 Author: lijewski Date: Mon Dec 17 18:24:07 2007 +0000 cleanup & bug fix in boxarray_add_clean_boxes() Src/F_BaseLib/boxarray.f90 commit f6f65c3e77ad0de0cf5042fc60446ac5591529c0 Author: lijewski Date: Mon Dec 17 18:23:41 2007 +0000 remove overlap in internal ghost multifab Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 0a7d6fa250f3b04df4f7dd37e229318c943d707d Author: ajnonaka Date: Fri Dec 14 21:13:10 2007 +0000 a couple minor 3d bugs fixed. cslope_lo and hi need to have 3 components a reference to fvcy has been changed to fvcz for a dm=3 case Src/F_BaseLib/fillpatch.f90 commit 6efeb0c8a945b1d8de521f8e6919dacae61af4b0 Author: ajnonaka Date: Fri Dec 14 20:55:21 2007 +0000 inverted the meaning of lim_slope so lim_slope .eq. .true. means use limited slopes. Change the behavior of the code by leaving the default value as true. Added lim_slope_input and lin_limit_input as optional input arguments to fillpatch to change the behavior Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 50b729ff9c4f678daa661a17d13cb95e1b3beae5 Author: ajnonaka Date: Fri Dec 14 20:33:46 2007 +0000 fillpatch now takes icomp_fine and icomp_coarse as inputs instead of just icomp. The old way, which used just icomp, didn't work if the coarse and fine components didn't have the same index Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 9e3fda958669e79759cc1a1bd817e5e3bd576cd8 Author: lijewski Date: Thu Dec 13 18:24:23 2007 +0000 call bl_error when proc trees are NOT identical Src/F_BaseLib/bl_prof.f90 commit a549184b2049a93603e047dd7961534a43021e55 Author: lijewski Date: Thu Dec 13 18:23:58 2007 +0000 removed some profilers Src/F_BaseLib/interp.f90 commit a0e05cdad61f07a0eb8bf1c9e07b3e7567a6d038 Author: lijewski Date: Wed Dec 12 20:28:07 2007 +0000 added TODO note Src/LinearSolvers/F_MG/nodal_divu.f90 commit fce2aaf7295b81666bcfc83a951fcaa81e1e5a0c Author: lijewski Date: Wed Dec 12 00:12:03 2007 +0000 use box_intersector stuff in periodic_add_copy() Src/LinearSolvers/F_MG/ml_restriction.f90 commit 7cda382cc7fe9b202c2f9570b4f73a4e7e1ef534 Author: lijewski Date: Tue Dec 11 23:47:19 2007 +0000 now use box_intersector in ml_crse_divu_contrib() Src/LinearSolvers/F_MG/nodal_divu.f90 commit 0d58dedde16abfff241f599959c30b467c99492f Author: lijewski Date: Tue Dec 11 22:22:11 2007 +0000 commented out unused norm_inf() call Src/LinearSolvers/F_MG/mg.f90 commit 44a1216238b614ff5bfe4edee95dfcde4e6d550f Author: lijewski Date: Tue Dec 11 22:21:30 2007 +0000 added needed type casts Src/F_BaseLib/mt19937ar.f90 commit 5354d3d2efbed79856038975e62a4827629b9585 Author: lijewski Date: Tue Dec 11 22:21:05 2007 +0000 some type cleanup Src/F_BaseLib/ml_boxarray.f90 commit 9f740bc405737d1433cc9fb5b862757a21449c87 Author: lijewski Date: Tue Dec 11 22:20:44 2007 +0000 some cleanup Src/F_BaseLib/layout.f90 commit 9b3de5759730f5dfe2aea0cd1b688aa9508d9644 Author: lijewski Date: Tue Dec 11 22:20:26 2007 +0000 removed unused declaration Src/F_BaseLib/fillpatch.f90 commit 18c30b01695423094708c5bf2dbca66acf9f4f4f Author: lijewski Date: Tue Dec 11 22:19:38 2007 +0000 fixed type issue Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/cluster.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit 9a4cc8896bff3096e7fc5f1e0335b5eb8a6d65cc Author: lijewski Date: Tue Dec 11 21:19:28 2007 +0000 check for overflow in box_volume; no longer elemental Src/F_BaseLib/box.f90 commit 968f02555481ca92e13914520861cf433681c1e4 Author: lijewski Date: Tue Dec 11 18:52:48 2007 +0000 some cleanup Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/layout.f90 commit 980c11d4f72a9b34b29b7c3d56958ec2322ce2f4 Author: lijewski Date: Tue Dec 11 18:52:34 2007 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit 476d904565252882df627c9f640f90cbf54c7442 Author: lijewski Date: Tue Dec 11 01:13:28 2007 +0000 added some bl_prof timers Src/F_BaseLib/knapsack.f90 commit edbec963bf78eefc1683ca965914f14346a91139 Author: lijewski Date: Tue Dec 11 01:01:23 2007 +0000 added some bl_prof timers Src/F_BaseLib/interp.f90 commit a2310dd4056dfcb8a33b4c846516a3241614190c Author: lijewski Date: Tue Dec 11 00:42:19 2007 +0000 added some bl_prof timers Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 6345a0fc1f8c12eeafe043c43ab55c42a129e583 Author: lijewski Date: Mon Dec 10 23:56:18 2007 +0000 added some profile timers Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit 7d4dca552456582ee93a261d3b0c041524ce1515 Author: lijewski Date: Mon Dec 10 20:36:34 2007 +0000 fixes to bl_prof usage Src/LinearSolvers/F_MG/ml_cc.f90 commit eaab4c7863777676cb039ae35662917da8e50aea Author: lijewski Date: Mon Dec 10 18:59:56 2007 +0000 parallelized ml_crse_divu_contrib Src/LinearSolvers/F_MG/nodal_divu.f90 commit 130ce7f3f6c3165127826841ca7929a0881d4b6d Author: lijewski Date: Sun Dec 9 01:45:20 2007 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit ae3cc91c3e218de8d067e8a0ea77ff0ca5052abf Author: lijewski Date: Sun Dec 9 01:42:25 2007 +0000 some cleanup Src/F_BaseLib/box_util.f90 Src/F_BaseLib/fillpatch.f90 commit a90b838e3798f90bb30eb75fee820f26718c4301 Author: lijewski Date: Sun Dec 9 00:38:44 2007 +0000 some cleanup Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit b81aabadcfaa1e6d24926d4fb2cf6af68fc2b0c6 Author: almgren Date: Sat Dec 8 00:49:01 2007 +0000 Added multifab_fill_boundary(crse) after restriction. Src/LinearSolvers/F_MG/ml_restriction.f90 commit ee8e4773d0b597cc154a7136eab7995632a53d7d Author: almgren Date: Fri Dec 7 21:28:56 2007 +0000 Put prototype regridding algorithm here. Src/F_BaseLib/regrid.f90 commit 0c935e81d6aa2ccf875653f28328c4f321ce043f Author: lijewski Date: Fri Dec 7 21:25:41 2007 +0000 parallelized ml_interface_c() Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit c8599881da4a6b42d3a31c27446c786ce78c423e Author: ajnonaka Date: Fri Dec 7 19:58:14 2007 +0000 mg test commit Src/LinearSolvers/F_MG/GPackage.mak commit a6e68a91f75652bbbbffec1b962306bd95a49c94 Author: lijewski Date: Fri Dec 7 18:00:25 2007 +0000 added parallel check in ml_crse_divu_contrib() Src/LinearSolvers/F_MG/nodal_divu.f90 commit 3318ee8b68c988fd6adf3b4519fcc0f995d9f912 Author: almgren Date: Fri Dec 7 17:39:53 2007 +0000 Need to add multifab_fill_boundary for full_soln after we create it. Src/LinearSolvers/F_MG/ml_cc.f90 commit 244ce020b197b9cebaeaa46af2b96cb3dde3a7b8 Author: almgren Date: Thu Dec 6 21:57:47 2007 +0000 Separated out crse and fine parts of ml_interface_stencil -- only tested in 2d. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit e959f7070076def3bef521ed09d91d7f5a657016 Author: almgren Date: Thu Dec 6 21:41:36 2007 +0000 Needed to add multifab_fill_boundary for multilevel solve to get right convergence -- I think it's only needed for periodic but not 100% sure. Src/LinearSolvers/F_MG/ml_cc.f90 commit e00665ab432fa03ebd28e5fe8897a1d7a2c3d651 Author: almgren Date: Thu Dec 6 20:39:40 2007 +0000 formatting cleanup. Src/LinearSolvers/F_MG/mg.f90 commit 5196769ccb70650389fe51484d181fa172d90f59 Author: almgren Date: Thu Dec 6 20:39:25 2007 +0000 Removed commented line. Src/LinearSolvers/F_MG/ml_cc.f90 commit be0600c0b2fdc778f846072597475bf414b8928e Author: almgren Date: Thu Dec 6 20:38:59 2007 +0000 Fix ml_interface for the periodic case. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 2eaf7989955b84655901c8972e06cc3f42eec7f6 Author: almgren Date: Thu Dec 6 20:38:04 2007 +0000 Fix stuff in ml_prolongation. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 01b938b88b71035431e1ca19673af85cb0f49bcd Author: lijewski Date: Wed Dec 5 22:35:47 2007 +0000 bndry_reg_copy now fills in periodic cells outside of domain Src/F_BaseLib/bndry_reg.f90 commit 0b71860ccf1fef0616f92bf355bd73c11024f78e Author: lijewski Date: Wed Dec 5 19:02:55 2007 +0000 slight change to calling sequence Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 5b25f4e4eda3af0d7504b50784be142f86fe80d1 Author: almgren Date: Wed Dec 5 19:00:27 2007 +0000 Removed commented line. Src/F_BaseLib/layout.f90 commit b440793f3b2887f14de24a33c4436054ec1ef144 Author: almgren Date: Wed Dec 5 18:36:21 2007 +0000 Remove ng from bndry_reg_copy calls. Src/F_BaseLib/bndry_reg.f90 commit 1598b2fbf05aaebbb5ab4c80a32706785f7aba22 Author: lijewski Date: Wed Dec 5 02:23:07 2007 +0000 more work on parallel-aware more efficient version Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit f2bd5aaeb44133a69cfa29e15c883f065cf3da8f Author: lijewski Date: Wed Dec 5 01:41:59 2007 +0000 special case when can fill periodic ghost cells from given fine data Src/F_BaseLib/fillpatch.f90 commit d0808a0c06a60a4f5962d26c552eb801d6ae59f5 Author: lijewski Date: Tue Dec 4 23:48:40 2007 +0000 some cleanup Src/F_BaseLib/fillpatch.f90 commit 539019c583b9ca9b9009be0a7df920e14c1f6cba Author: lijewski Date: Tue Dec 4 23:39:37 2007 +0000 plugged some memory leaks Src/LinearSolvers/F_MG/ml_cc.f90 commit afce25f7d0e69c657347cc1b800c7dfd9c8031de Author: lijewski Date: Tue Dec 4 22:56:18 2007 +0000 bug fix -- only destroy fla & tmpfine if built Src/F_BaseLib/fillpatch.f90 commit 74d80f5ba3356255a948fa6ab20ebc8f89f9d930 Author: lijewski Date: Tue Dec 4 22:26:35 2007 +0000 start on making fillpatch periodically-aware Src/F_BaseLib/fillpatch.f90 commit b5e36656bacd4b92b3dfa3fd118f9eb789a3b08b Author: lijewski Date: Tue Dec 4 00:33:39 2007 +0000 more error checking Src/F_BaseLib/fillpatch.f90 commit e5629cdb6954998808e0cbfed8b8cacc5e12be0a Author: lijewski Date: Tue Dec 4 00:29:26 2007 +0000 start on more efficient parallel version -- more to do ... Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit ed0c816a543f7627df2d90cbb1943a22be0c9e29 Author: lijewski Date: Tue Dec 4 00:27:35 2007 +0000 modest fixes -- still periodic issues Src/F_BaseLib/fillpatch.f90 commit c6507f25a7a6fae1a2a9652803af0433e4d955d3 Author: mzingale Date: Mon Dec 3 22:27:05 2007 +0000 add a "/" to the end of the paths as required Tools/C_util/regtests/test.py commit 2a1b4c4082e3eda4359a6157f0859439000a0b08 Author: lijewski Date: Mon Dec 3 22:18:48 2007 +0000 modest bug fix Src/F_BaseLib/fillpatch.f90 commit bd9e095d4409546ba8cd993de951343a8d822683 Author: lijewski Date: Mon Dec 3 17:37:30 2007 +0000 mods from Mike Singer Tools/C_mk/Make.mpi commit a79ad1edb2ae4f761dba9a42fe3756d00d03bb22 Author: lijewski Date: Mon Dec 3 17:28:39 2007 +0000 mods from Mike Singer Src/C_BoundaryLib/LO_BCTYPES.H commit de67799f97c4c9ed1f4d72ba1b712d49e6fe6552 Author: lijewski Date: Sun Dec 2 00:49:44 2007 +0000 layout_get_box_intersector() now call init_box_hash_bin() automagically if needed Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/layout.f90 commit 12cd49796ccbc69f72281bde945a300026381889 Author: lijewski Date: Sat Dec 1 00:21:44 2007 +0000 little cleanup Src/F_BaseLib/fillpatch.f90 commit 77696298335cce62a221725bfc6a1b46a706b556 Author: almgren Date: Fri Nov 30 22:52:03 2007 +0000 Don't include fillpatch and multifab_fill_ghost_cells in the make stuff because they depend on stuff in the varden/MAESTRO directories. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/NPackage.mak commit cce8b35733e18a6ccd5bbf298f8d356465f8acb3 Author: almgren Date: Fri Nov 30 22:14:18 2007 +0000 Add fillpatch and multifab_fill_ghost_cells to GPackage and NPackage. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/NPackage.mak commit 545bf251cf65e14a3e8f725af709ab99e427f6df Author: almgren Date: Fri Nov 30 22:12:59 2007 +0000 Move fillpatch and multifab_fill_ghost_cells from varden/MAESTRO into boxlib. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 7c9dfda8f223345179dcd31580d326b0facfb544 Author: almgren Date: Fri Nov 30 22:08:59 2007 +0000 Fixed bug in lin_cc_interp_2d -- was using xok(1) instead of xok(2) for yslope. Src/F_BaseLib/interp.f90 commit cd2f200d0b5c55cb726c682e43f377539639f560 Author: mzingale Date: Sun Nov 25 15:34:32 2007 +0000 new main webpage -- now it lists each test up front in separate columns Tools/C_util/regtests/test.py commit ae6336b7132a1153c0f8f76972dabe1bbc927f8e Author: mzingale Date: Mon Nov 19 03:05:24 2007 +0000 add a --note option and also fix a crash when making benchmarks and we have a restart test Tools/C_util/regtests/test.py commit f53cf86a6d8d595cd855b46db33904be7945915b Author: ajnonaka Date: Sun Nov 18 06:08:35 2007 +0000 created ml_edge_restriction_c. ml_edge_restriction calls ml_edge_restriction_c, which loops over all components in the coarse multifab by default. I believe the code only restricted the 1st component of coarse before. Src/LinearSolvers/F_MG/ml_restriction.f90 commit eb40d05df87a94ba788f9484383928d490cc3779 Author: mzingale Date: Sun Nov 18 02:57:06 2007 +0000 add the ability to do restart tests. Make the script behave gracefully when we fail compiling. Tools/C_util/regtests/Maestro-tests.ini Tools/C_util/regtests/test.py commit a8343dbb23501028d5162764f087d218f0fc0356 Author: ajnonaka Date: Sat Nov 17 01:53:49 2007 +0000 cleaned up code for easier reading Src/LinearSolvers/F_MG/ml_restriction.f90 commit 539e29676e702a503f28fe73341691ee26718caf Author: lijewski Date: Wed Nov 14 22:20:53 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 2e6be8a1d71e8602988cdf5cfdf312cfd1b671ea Author: lijewski Date: Wed Nov 14 21:04:25 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 0057427781e3afcadb6d8662e541a482d920ecc9 Author: lijewski Date: Wed Nov 14 20:33:03 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 75b53eb8db211c158ce5fc3b50a6ca29fb3a5e3d Author: lijewski Date: Wed Nov 14 18:42:15 2007 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 5081a8ad8c58fb8913afd856f3e9db7c509867a1 Author: lijewski Date: Wed Nov 14 03:51:45 2007 +0000 centralized PGI and PathScale stuff Tools/C_mk/Make.Linux commit 994d5fb5e61de23d9e474386ea2a6e56b6a5f1ac Author: ajnonaka Date: Tue Nov 13 18:43:25 2007 +0000 plugged a memory leak Src/LinearSolvers/F_MG/ml_cc.f90 commit bd77285197e6ab7796b0501a255f4594a5707e3c Author: mzingale Date: Tue Nov 13 15:48:56 2007 +0000 turn off debugging Tools/C_util/regtests/test.py commit c935e244d70a17c1e746295bf3087f69e9b21cd8 Author: mzingale Date: Tue Nov 13 15:01:34 2007 +0000 add an entry for nan.astro.sunysb.edu Tools/F_mk/GMakeMPI.mak commit 428f1d0f068da69ee35c2710367599207a3a3c87 Author: lijewski Date: Fri Nov 9 23:05:40 2007 +0000 added some commented out options for Franklin Tools/C_mk/Make.Linux commit 6a4fde42f42a15aaf19de99a359ff9f6a7764f10 Author: marc Date: Thu Nov 8 02:37:58 2007 +0000 Near as I can tell, the IFC major and minor version numbers were not properly set because ifc doesn't always exist to give the version. I tried to unwind the logic to do this right...hope I didn't break anything... Tools/C_mk/Make.defs commit 508a653f015b55c2118526464b67000119a78f10 Author: almgren Date: Thu Nov 8 00:09:29 2007 +0000 Correct call to set coefficients for 2d and 3d. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 6f0cfb5f2db8c0ebb4230a4d93e3a714d1d2365b Author: marc Date: Wed Nov 7 00:38:58 2007 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 853db84068d421614456d6aa5cd087f214e2b2bd Author: lijewski Date: Mon Nov 5 23:00:55 2007 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit 086507bb4211f4bc2a135d936eeaa8196e4adb1e Author: almgren Date: Mon Nov 5 19:08:39 2007 +0000 Stuff to debug Castro 1d. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 9b2d896f2d1d77adc1c5503397baa30210936dc1 Author: almgren Date: Mon Nov 5 18:54:41 2007 +0000 New stuff to enable 1d. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit bb318177f9305dfc0ccac40738305a89cde5ba4d Author: ajnonaka Date: Thu Nov 1 17:29:54 2007 +0000 added commented out jacobi option for 7 point 3d nodal smoother Src/LinearSolvers/F_MG/mg_smoother.f90 commit 4fdf0293bb1ae9910089ecf26e22099fb776957c Author: ajnonaka Date: Thu Nov 1 00:45:25 2007 +0000 added some commented out code to give a jacobi option for gs_rb_smoother_3d Src/LinearSolvers/F_MG/mg_smoother.f90 commit 02a2e453d78720377be2edf2c1d285a6555794b2 Author: almgren Date: Wed Oct 31 20:10:15 2007 +0000 Fix in set_uu_1d. Src/LinearSolvers/F_MG/mg_cpp.f90 commit c481f59ecff527c0c32d5829de290702074fe54d Author: almgren Date: Tue Oct 30 21:04:21 2007 +0000 Add more 1d functions. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit c9eb6f21d68f83608e394b033bc035f3cd1560ed Author: almgren Date: Tue Oct 30 20:50:27 2007 +0000 Adding 1d routines. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 22ca924b90042d91a90be7347308183cde17c8dd Author: almgren Date: Tue Oct 30 20:47:09 2007 +0000 Making 1d stuff compile. Src/LinearSolvers/C_CellMG/ABec_1D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LP_1D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/MG_F.H commit d04a867c88e0cc2ea1120c1cfde85ad0c4ca45fb Author: almgren Date: Tue Oct 30 20:29:03 2007 +0000 Need this in 1d. Src/LinearSolvers/C_CellMG/LP_1D.F Src/LinearSolvers/C_CellMG/MG_1D.F commit 8eeb172ad518102df2442aebabacf599dc30fa38 Author: almgren Date: Tue Oct 30 20:28:18 2007 +0000 This version actually compiles. Src/LinearSolvers/C_CellMG/LO_1D.F commit ab1a1151eab388db7de73fa35608b78eec97faf7 Author: almgren Date: Tue Oct 30 20:24:39 2007 +0000 Need one of these in 1d as well. Src/LinearSolvers/C_CellMG/LO_1D.F commit 8984c5f1402c72aaed4beed6c479a6f47e9c4e14 Author: almgren Date: Tue Oct 30 20:10:19 2007 +0000 Need this in 1d. Src/C_BoundaryLib/INTERPBNDRYDATA_1D.F commit 6ae505cf9f01b04d968c8d3ee27ed750eeb9a90e Author: almgren Date: Tue Oct 30 19:59:55 2007 +0000 Need to have one of these in 1d as well. Src/LinearSolvers/C_CellMG/CG_1D.F commit 03c18d0b4d2a3bb92767e0333657c88aa51639cb Author: almgren Date: Tue Oct 30 19:43:55 2007 +0000 New 1-d version of ABec*.F Src/LinearSolvers/C_CellMG/ABec_1D.F commit 2b46d5aa14d8b49f8c546777b80025a947dd5b53 Author: almgren Date: Tue Oct 30 19:33:52 2007 +0000 Add 1-d capability. Src/LinearSolvers/F_MG/mg_cpp_f.h commit f1cafc4a8afa8a4e9d9a7b92f272e32589e89778 Author: almgren Date: Mon Oct 29 04:26:20 2007 +0000 Necessary modifications to let 1-d work. Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.cpp commit a2773e048ff9c8083a85111acbfa68ba1c5b92d0 Author: almgren Date: Mon Oct 29 04:03:02 2007 +0000 Define GetDLogA for 1d as well as 2d. Src/C_BaseLib/Geometry.cpp commit 71df312e2cbd80839e27a8dad0723ed68850b0e1 Author: almgren Date: Sun Oct 28 19:34:25 2007 +0000 Added LINCCINTERP for 1-d. Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.cpp commit d5796256c671c373904ba3f33fcff2ed5987c84a Author: almgren Date: Sun Oct 28 14:46:30 2007 +0000 Need to include ArrayLim.H, not DIMS. Src/C_BaseLib/COORDSYS_1D.F commit 1c0c03066ae5eaa206cd0168826fb6432b1ebb39 Author: almgren Date: Fri Oct 26 04:12:42 2007 +0000 Change min_width from 1 to 2. Src/LinearSolvers/F_MG/mg.f90 commit 8afb1b8d64f216edfdc3ce2d24ff12b747b2624d Author: almgren Date: Fri Oct 26 00:44:39 2007 +0000 Put fill boundary outside of need_grad_phi if test. Src/LinearSolvers/F_MG/ml_cc.f90 commit 4662f735a002d8aacd8274b3ee47cb03c4388ad5 Author: almgren Date: Tue Oct 23 17:48:35 2007 +0000 New coefficient arrays for variable coefficient test problems. Src/LinearSolvers/C_CellMG/Test/COEF_2D.F Src/LinearSolvers/C_CellMG/Test/COEF_3D.F Src/LinearSolvers/C_CellMG/Test/COEF_F.H Tests/LinearSolvers/C_CellMG/COEF_2D.F Tests/LinearSolvers/C_CellMG/COEF_3D.F Tests/LinearSolvers/C_CellMG/COEF_F.H commit ca0d0700d6395f7e9401b9279751c1c0ffd65260 Author: almgren Date: Tue Oct 23 17:42:21 2007 +0000 Fix second call to jacobi_smooth. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 27e05c50690adedbaf51f456eac40a4782d8a507 Author: lijewski Date: Mon Oct 22 20:29:20 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/CGSolver.cpp commit bf301e6ddde8f55bd924c19770d28524d4231df7 Author: almgren Date: Mon Oct 22 20:27:04 2007 +0000 New version of diagonal (aka Jacobi) preconditioning for solve_bicgstab. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit b015deba94f8950100b9c135aecff5a5c29f28bd Author: almgren Date: Mon Oct 22 03:47:32 2007 +0000 Put in commented code which actually should work much better. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 1031f8bd2264382d35206fabc62d060e61786698 Author: almgren Date: Mon Oct 22 02:49:57 2007 +0000 Added the capability for the BiCG solver in CGSolver.cpp to do a Jacobi relaxation as a preconditioner. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit f11c6c50df6f6db49060d16de8390d1ed7cc4c2c Author: almgren Date: Fri Oct 19 21:22:05 2007 +0000 Code was just wrong -- it was computing the diff into a FAB but never putting it into the "error" MultiFab. Tools/C_util/Convergence/DiffUniform.cpp commit 6610a750a49835df82602dbd4993418c478d56c5 Author: marc Date: Thu Oct 18 00:00:02 2007 +0000 fix CVS screwup Tools/C_mk/Make.mpi Tools/C_mk/Make.rules commit 2fec3697a779d1fc837434f09d07020995716ad8 Author: marc Date: Wed Oct 17 23:43:53 2007 +0000 *** empty log message *** Tools/C_mk/Make.mpi Tools/C_mk/Make.rules commit 24a76f8150f25affd9b4a610e0cfeb7b7dd49d24 Author: mzingale Date: Tue Oct 16 18:41:40 2007 +0000 add links to allow for navigation between the test page and individual tests Add ChangeLogs Tools/C_util/regtests/test.py commit b6654ed7efb6b93a60c33269797e7aa28c5fd44c Author: almgren Date: Mon Oct 15 23:07:47 2007 +0000 Fix calls to stencil_apply... Src/LinearSolvers/F_MG/stencil.f90 commit 46892415471a89ceadf68520f1319077219eb1f5 Author: almgren Date: Mon Oct 15 22:49:06 2007 +0000 Allow the "dd" (or "rr") to have non-zero ghost cells by passing in the ng_d as well as the ng_d. This is relevant for all stencil_apply and stencil_dense_apply calls. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 19ead2be8c00558d5d61f0612fadb0e13455bc02 Author: lijewski Date: Mon Oct 15 21:11:12 2007 +0000 added -lrt for FRANKLIN Tools/C_mk/Make.Linux commit 485fbdab2e178880695057e8c9b7640299b6d730 Author: almgren Date: Thu Oct 11 20:33:23 2007 +0000 Commented code which does Jacobi instead of GSRB relaxation for 2d cell-centered and 2d nodal. As is the code does GSRB, but one can uncomment certain lines to do Jacobi instead. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 5a8da8db97a8503f5d48f5390e38bdfc113dbb37 Author: lijewski Date: Tue Oct 9 21:59:01 2007 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit 064865e14fd87e46b3b7d90bd74c0ea816bb66f0 Author: lijewski Date: Tue Oct 9 21:39:45 2007 +0000 *** empty log message *** Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bxasc.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bxasc.f90 Tests/F_BaseLib/t_main.f90 commit c50ac1b25bed59b7e3c9d8d6b318939eb7a8e58d Author: ajnonaka Date: Tue Oct 9 20:22:46 2007 +0000 Ann's changes in cgsolve. Src/LinearSolvers/F_MG/itsol.f90 commit 67e900f310437831da3e39f450903e549094ebc2 Author: marc Date: Tue Oct 9 00:30:39 2007 +0000 *** empty log message *** Tools/C_mk/Make.CYGWIN_NT commit 3ab74caf78138bfbd2eddecde536c8e3884f8eea Author: lijewski Date: Fri Oct 5 21:52:52 2007 +0000 more franklin mods for Castro Tools/C_mk/Make.Linux commit 0c11fe67ca037b0228f255ed8d2efcb99aab4311 Author: lijewski Date: Fri Oct 5 21:09:37 2007 +0000 automagically identify franklin in Make.defs/Make.Linux Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 72b18355c3095c947f83d204a34fcfd5649f1180 Author: lijewski Date: Fri Oct 5 21:04:46 2007 +0000 treat franklin as Linux machine Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 17d8e0079e362759c67e12810de989661e6af37c Author: almgren Date: Fri Oct 5 17:07:30 2007 +0000 Added new mult functions to multifab and ml_multifab. Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 commit 9f377005d105bea9887fd685bec2fd018decee4f Author: lijewski Date: Thu Oct 4 22:44:21 2007 +0000 ansi C++-ified Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 40ee5b728f11654a022447fbb22de0647bd29649 Author: lijewski Date: Thu Oct 4 22:41:20 2007 +0000 commented out pedantic -- conflicts with something in mpi.h Tools/C_mk/Make.defs commit e34ce03cb69786b4794eb7782f7b95c7d363eda2 Author: lijewski Date: Thu Oct 4 22:31:27 2007 +0000 some cleanup Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/TagBox.cpp commit 24f3c047fcc040d1d5de00a3a7e516a830c66686 Author: lijewski Date: Thu Oct 4 22:31:17 2007 +0000 added -pedantic to g++ Tools/C_mk/Make.defs commit 9b0e2211f74bc7c29c917e8070deab4974c215c4 Author: mzingale Date: Mon Oct 1 14:08:04 2007 +0000 add a comment when the benchmarks are updated so we log the reason for the change in the solution Tools/C_util/regtests/test.py commit ef4a5f0a13c0f2228bbf5c456dfa809205547807 Author: almgren Date: Thu Sep 27 18:16:11 2007 +0000 Fix the copy in ml_multifab to match that in multifab, i.e. you can pass number of ghost cells but can no longer pass "all". Src/F_BaseLib/ml_multifab.f90 commit 9c1d562706e5c82b77a6fd613b76e698070146d0 Author: lijewski Date: Tue Sep 25 20:34:13 2007 +0000 AIX mods Tools/F_mk/GMakedefs.mak commit 363d0e81a4a93dcf3840323fdb0cd87e2798ea92 Author: almgren Date: Tue Sep 25 17:57:39 2007 +0000 Replace all by ng in bndry_reg copy functions. Src/F_BaseLib/bndry_reg.f90 commit f3f83ae1a3927a7a37fe2aafa45010b1f21b3467 Author: lijewski Date: Mon Sep 24 21:29:35 2007 +0000 added xt4 block for franklin Tools/F_mk/GMakedefs.mak commit cc4c7375829c2fe6cf02d68367ffe03c8c11d6b6 Author: lijewski Date: Sun Sep 23 18:39:18 2007 +0000 nan & inf stuff work with PATHSCALE Src/C_BaseLib/FArrayBox.cpp commit 8e43cd94459b7f1052422302072e29f18557523e Author: lijewski Date: Sun Sep 23 16:44:06 2007 +0000 inf & nan stuff works on AIX Src/C_BaseLib/FArrayBox.cpp commit 416f25eb0803904146e99d5a825a7f9bd2402500 Author: lijewski Date: Sat Sep 22 15:05:31 2007 +0000 added nan & inf detection code Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 1ef7026b4e7b736d4474a09f1c863d109d17b63c Author: lijewski Date: Sat Sep 22 15:05:12 2007 +0000 removed debug stuff from MFIter Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit dff9211c1530a2095122696d7368d0706ea238bc Author: almgren Date: Tue Sep 18 20:17:22 2007 +0000 Didn't mean to commit all the changes in stopping criteria, just wanted the change in copy calls. Src/LinearSolvers/F_MG/itsol.f90 commit 7ecbbef4495aace10b38f404e7a9f52a5ae2663a Author: lijewski Date: Tue Sep 18 20:03:57 2007 +0000 force Headers to use scientific notation for floating point values Src/C_BaseLib/VisMF.cpp commit 37506464605180194ff3e496396ea7e96f376209 Author: lijewski Date: Tue Sep 18 19:57:29 2007 +0000 floating point format change: es30.20 -> es25.15 Src/F_BaseLib/fabio.f90 commit 94249c16d440c152eb51a104700973d27e3e1cc6 Author: almgren Date: Tue Sep 18 19:42:36 2007 +0000 Replaced "all" argument by "ng" argument in multifab_copy and multifab_copy_c. Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 commit fd45cdc7c0d10b6a24d8adc2f7b6937239381171 Author: lijewski Date: Mon Sep 17 21:37:27 2007 +0000 simplified _nfiles stuff previously added Src/C_AMRLib/Amr.cpp commit f2c56dbabe7f55cafa2fd8e7a58d925eccff243f Author: lijewski Date: Mon Sep 17 17:47:52 2007 +0000 changed defaults for *_nfiles to 64 Src/C_AMRLib/Amr.cpp commit 7cf65215e3f0a696d5c2045e8e059a8806d06ab6 Author: sepp Date: Wed Sep 12 21:32:26 2007 +0000 1) add an Add and a Subtract routine like the Copy already there Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 160b5c852d54d60ef1c6689a8662fe45e8aa7445 Author: lijewski Date: Fri Sep 7 23:01:43 2007 +0000 can now regrid single-level calculation Src/C_AMRLib/Amr.cpp commit 1861bc1ab6aef8f2ce0118d75b095709ec76998c Author: almgren Date: Fri Sep 7 17:09:14 2007 +0000 These versions of mg.f90 and mg_smoother.f90 actually compile. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit 9100e72267065487814a78cb51c758e7832b6a0f Author: almgren Date: Fri Sep 7 17:07:31 2007 +0000 Modify 2d- and 3d- nodal smoother calls so that when using cross stencil, with red-black Gauss-Seidel, we make sure to do a multifab_fill_boundary between the red and black sweeps. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit c000fb8f69873d8c2653ede0ebf9208211494ab4 Author: lijewski Date: Thu Sep 6 20:27:16 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 9dc0b3a6670bbf3b8edbf32cc0f140633c18edcb Author: marc Date: Tue Sep 4 21:31:40 2007 +0000 Do not include wait.h on Columbia...makes Intel compiler unhappy...do we need this elsewhere?? Src/C_BaseLib/Utility.H commit c70510f7ee7a67f13a13030af385edd5a4c5e512 Author: marc Date: Tue Sep 4 21:25:12 2007 +0000 Remove wait.h include, already dealt with in Utility.H Src/C_BaseLib/Utility.cpp commit e3fa055628ff65319a5ed8887d30a379171b0292 Author: lijewski Date: Tue Sep 4 19:50:10 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.3_512cubed Tests/LinearSolvers/C_CellMG/grids/in.3_512cubed commit 2592824a6ce18ccb29a4f8ddcf650641de3d054b Author: lijewski Date: Tue Aug 28 22:18:55 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared Tests/LinearSolvers/C_CellMG/grids/in.2_256squared commit a5f54e97a240915b95f7068b451721d340de71b4 Author: lijewski Date: Tue Aug 28 21:38:13 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared Tests/LinearSolvers/C_CellMG/grids/in.2_256squared commit fbf42cc6c5ae6f6d57f2a3b49570364660c6fcc3 Author: lijewski Date: Tue Aug 28 19:37:45 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 28d5b7429875f44386ab7d2acac76790c4f4c127 Author: almgren Date: Fri Aug 24 19:27:48 2007 +0000 Add option to set variable coefficients in solve, flag is use_variable_coef which defaults to false. Src/LinearSolvers/C_CellMG/Test/COEF_2D.F Src/LinearSolvers/C_CellMG/Test/COEF_3D.F Src/LinearSolvers/C_CellMG/Test/COEF_F.H Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/COEF_2D.F Tests/LinearSolvers/C_CellMG/COEF_3D.F Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/main.cpp commit 019d72dbf5e22a542f5498692ec52a475c0ae9f5 Author: mzingale Date: Fri Aug 24 14:57:43 2007 +0000 add the ability to do only a single test, if desired Tools/C_util/regtests/test.py commit 22080d53d8856f4862cca14a1fa14e8fdf2f6080 Author: mzingale Date: Thu Aug 23 14:10:48 2007 +0000 make it work with python 2.3 switch to inf norm for fParallel builds, feed in MPI= to disable MPI in the make add the time and date of the CVS update to the webpage Tools/C_util/regtests/test.py commit b9e0b8abb1373cbafde5326166cc96c1fac5c474 Author: lijewski Date: Tue Aug 21 21:49:42 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed Src/LinearSolvers/C_CellMG/Test/grids/in.3_256cubed Tests/LinearSolvers/C_CellMG/grids/in.2_256squared Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed Tests/LinearSolvers/C_CellMG/grids/in.3_256cubed commit 7fc3aca9ec8414c4fa13e8f4277c8a30695028ac Author: almgren Date: Tue Aug 21 21:43:42 2007 +0000 Two more 3-d grids with a domain just broken up into same-size boxes. Src/LinearSolvers/C_CellMG/Test/grids/gr.3_256cubed Src/LinearSolvers/C_CellMG/Test/grids/gr.3_512cubed Tests/LinearSolvers/C_CellMG/grids/gr.3_256cubed Tests/LinearSolvers/C_CellMG/grids/gr.3_512cubed commit 93cf3e8eb56f3ffeda46146cf4f520ce8a16b043 Author: mzingale Date: Tue Aug 21 20:36:35 2007 +0000 echo SUCCESS upon a successful build -- this will be seen by the regression test framework (Parallel/util/regtests/) to detect that compilation worked. Tools/C_mk/Make.rules commit 26766d0786e0038ba603f0a57ad5d972bbf02c73 Author: almgren Date: Tue Aug 21 18:21:53 2007 +0000 Clean this up... Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed commit dc99618e28bd52515c29217d01948fc7614c4f65 Author: almgren Date: Tue Aug 21 18:21:10 2007 +0000 These are the ones we're testing superlu with. Src/LinearSolvers/C_CellMG/Test/grids/gr.2_256squared Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared Tests/LinearSolvers/C_CellMG/grids/gr.2_256squared Tests/LinearSolvers/C_CellMG/grids/in.2_256squared commit a65c79a177cf63761a526af57a3a3697b83065f1 Author: almgren Date: Tue Aug 21 17:41:11 2007 +0000 Finished changing mult,div,plus,sub calls take ng instead of "all" now. Src/F_BaseLib/multifab.f90 commit 321612b4309f76353bc14dfcc02707bddd7a82e4 Author: mzingale Date: Tue Aug 21 14:48:28 2007 +0000 add the initial version of the regression testing framework, developed initially for Castro. The Castro-tests.ini file sets up some pure hydro tests. Maestro-tests.ini will setup a single test for Maestro (in the fParallel framework). Tools/C_util/regtests/Castro-tests.ini Tools/C_util/regtests/Maestro-tests.ini Tools/C_util/regtests/README Tools/C_util/regtests/test.py commit 3a1996eadc511aa4601c97a0330f5e68edfeb5c4 Author: ajnonaka Date: Mon Aug 20 23:32:11 2007 +0000 finished Ann's implementation for mandatory ghost cells for plus_plus, div_div, and mult_mult Src/F_BaseLib/ml_multifab.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit b8e6a8de9b4e142838af46c72c3078a5b4be4484 Author: almgren Date: Mon Aug 20 23:05:20 2007 +0000 We are now changing the calling sequence to operations on multifabs which used to take "all" as an optional argument -- they now take ng. Src/F_BaseLib/multifab.f90 commit d0924c9cd4dcc8005a351a288874952dca5452cc Author: mzingale Date: Fri Aug 10 17:59:22 2007 +0000 add the compressor script from the Parallel tree to help tame our plot/chk directories Tools/F_scripts/compressor commit 4e6a50d4bfad7c7809a92513bc4f26778c44945a Author: almgren Date: Mon Aug 6 22:24:41 2007 +0000 Shouldn't test on rnorm in cg or bicg solve if stopping criterion was reached before any iterations. Src/LinearSolvers/F_MG/itsol.f90 commit 302f73984da74c9ca118fe0d9e546a4084d5bbe2 Author: mzingale Date: Sat Aug 4 23:54:40 2007 +0000 determine if the files agree by looking at the absolute norms and print out a message that the regression suite can detect. Tools/C_util/Convergence/DiffSameGrid2.cpp commit 45766b7394be7ed88fc98a05bba685ef79e8407d Author: mzingale Date: Fri Aug 3 17:37:12 2007 +0000 change the make clean rule from $(RM) $(EBASE)$(optionsSuffix).ex to $(RM) $(executable) so it works when we invoke make as gmake executable=Castro.exe to rename the executable. Tools/C_mk/Make.rules commit 0cf740a7294384d3d39ea781fe39f23e6946612d Author: mzingale Date: Thu Aug 2 17:40:00 2007 +0000 switch over to using a lock file to guarantee that build_info.f90 is regenerated and built each time. This now means that at any make invocation, it gets rebuilt (i.e. not only when some other file has changed), but it avoids some circular dependencies that I couldn't track down. Tools/F_mk/GMakerules.mak commit 9f61eaafd894b13b4aab8c04f259469fca3d1543 Author: mzingale Date: Wed Aug 1 21:23:42 2007 +0000 add a new rule for build_info.f90, so that we are sure that it is regenerated any time we recompile. Previously, the script was not rerun when a file changed, so the build info could be out of date. Now there is a new class of files, sf90sources, that do not get the dependency check done to them. Rightnow, build_info.f90 is the only such example of this type of file. This allows it to have as dependencies all of the other files, thus guarranting that it gets regenerated. Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit 7f9c7d807b045b752e860ea1c3a44160f5a82143 Author: mzingale Date: Wed Aug 1 15:19:55 2007 +0000 make this compile with compilers that don't allow > 132 columns Tools/F_scripts/make_build_info commit 1da95f6d008c78c0bf6d84379b91f11a4fd0972e Author: almgren Date: Tue Jul 31 23:56:29 2007 +0000 Added multifab_print_c and fab_print_c which print only a single component of the multifab or fab. Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit c54300acc0080e1c21a3e38d81ce8e7195f11656 Author: almgren Date: Mon Jul 30 18:18:10 2007 +0000 Missed a few places for the BL_ASSERT(num_comp > 0); statement. Src/C_BaseLib/MultiFab.cpp commit 6bc3153d5794f132710c4d77ebddc39ba7fc8ab4 Author: almgren Date: Mon Jul 30 18:10:58 2007 +0000 Added BL_ASSERT(num_comp > 0); to a number of the plus/minus - type calls... Src/C_BaseLib/MultiFab.cpp commit 9bdb42d026febd5e2004a5591657fcd39af00888 Author: almgren Date: Sat Jul 28 22:24:05 2007 +0000 Fixed stencil_all_flux_3d to match sign convention of 2d version. Src/LinearSolvers/F_MG/stencil.f90 commit f6af15d73e79228b45d9db3e8b7b91ad79b734a9 Author: mzingale Date: Wed Jul 25 20:34:31 2007 +0000 make the string length a script parameter Tools/F_scripts/make_build_info commit a9e74b0cc62cf1d7ac197fa27472391f7c5b9707 Author: marc Date: Wed Jul 25 01:07:35 2007 +0000 *** empty log message *** Tools/C_mk/Make.CYGWIN_NT commit 977402bb330241f435bb20e75133c938aca6bc3e Author: almgren Date: Thu Jul 19 21:04:33 2007 +0000 Added function ml_resid. Src/LinearSolvers/F_MG/ml_cc.f90 commit 1782de980752d700a74dda7bb15fabdbd1c5a730 Author: mzingale Date: Thu Jul 19 18:49:58 2007 +0000 add some more comments and documentation Tools/C_util/Convergence/DiffSameGrid2.cpp commit 0013045364cf07dc12307860d30032a91b42dde8 Author: ajnonaka Date: Thu Jul 19 18:04:50 2007 +0000 fixed bug: in ml_cc_applyop, was computing dm before rh was allocated Src/LinearSolvers/F_MG/ml_cc.f90 commit 04faf4d539e868eafc0c3873ff8217f8c473b492 Author: ajnonaka Date: Wed Jul 18 22:52:57 2007 +0000 residual automatically scales by -1,thus, actually returning (alpha - del dot beta grad)phi in the call to mac_applyop->ml_cc_applyop Src/LinearSolvers/F_MG/ml_cc.f90 commit 43b9b35c8498620a1022bbf8083290e3f9cffbc8 Author: ajnonaka Date: Wed Jul 18 22:29:42 2007 +0000 much more progress in thermal conduction solve; I still need to configure the bc's correctly in thermal_conduct.f90 and actually make the residual and solve calls Src/LinearSolvers/F_MG/ml_cc.f90 commit 453f3eae7af98650a0f14fc71f4df929483c90a4 Author: mzingale Date: Wed Jul 18 20:39:01 2007 +0000 add a divide method so we can divide the zones in one multifab by the value in the corresponding zone of the other. This is needed for the regression testing in util/Convergence/DiffSameGrid2 Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 59d6050c5f0b4d8223ff3df6e164a30cd6e89b83 Author: mzingale Date: Wed Jul 18 20:37:45 2007 +0000 new version of DiffSameGrid that does both relative and absolute errors -- this will be used as part of the Castro regression suite Tools/C_util/Convergence/DiffSameGrid2.cpp commit 5f7695e5e77ba827a47bf4691979d50c628e5bb5 Author: ajnonaka Date: Wed Jul 18 17:54:03 2007 +0000 Working on creating a new subroutine, "mac_applyop", which will live in macproject.f90, and simply returns the residual "-(alpha-del dot beta grad)phi". The subroutine "mac_applyop" is based on subroutine "mac_multigrid", but calls a new subroutine, "ml_cc_applyop" rather than "ml_cc". Subroutine "ml_cc_applyop" is based on subroutine "ml_cc", but stops after the residual is computed. Src/LinearSolvers/F_MG/ml_cc.f90 commit 2dc47968a44758805030e6c88d6ecdc195699486 Author: almgren Date: Tue Jul 17 05:15:37 2007 +0000 Fix small typos. Src/LinearSolvers/F_MG/mg_cpp_f.h commit 22f62ede8bb929afbbd27195e96521c2b6946c75 Author: almgren Date: Tue Jul 17 05:06:33 2007 +0000 Needed 3d instead of 2d... Src/LinearSolvers/F_MG/mg_cpp_f.h commit 28f77d10a6c05d3b66c7e4313358ab73b2af5101 Author: almgren Date: Tue Jul 17 04:46:18 2007 +0000 Remove print statement. Src/LinearSolvers/F_MG/stencil.f90 commit c88ec9a28639097bda842c7242d914d8f74f8908 Author: almgren Date: Tue Jul 17 04:42:12 2007 +0000 Add mgt_compute_residual routine which calls new ml_resid. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit dd6962e48a65c7e7a5393cd9cb5c06d94c345a85 Author: almgren Date: Tue Jul 17 04:41:39 2007 +0000 Added compute_residual routine. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 848a5fa925d8bd0e4e16ad0fcb7b31ca53a1d962 Author: almgren Date: Tue Jul 17 04:15:31 2007 +0000 Change name for timing routine. Src/LinearSolvers/F_MG/mg.f90 commit 9021c05e9b52e440f29153ccc8182f5b4a165b56 Author: almgren Date: Mon Jul 16 21:34:38 2007 +0000 Put same minus signs in stencil_all_flux_3d as stencil_all_flux_2d for lo-side fluxes. Src/LinearSolvers/F_MG/stencil.f90 commit 9c1d0bb125c7cde25ea8dc92d58957c4c671ea0e Author: almgren Date: Mon Jul 16 17:32:05 2007 +0000 Make sure all ghost cells of full_soln at fine grid have the correct values before computing the initial residual for residual-correction form. Src/LinearSolvers/F_MG/ml_cc.f90 commit 5357e7041045f6d1f2ed2b865e7e0525463908cd Author: mzingale Date: Mon Jul 16 14:18:39 2007 +0000 when compiling on jaguar (catamount), put the intermediate module files into the m/ directory (as is done on all other platforms), instead of sticking them in the top level directory. This assumes that we are using the PGI compilers with catamount (which is the default) Tools/F_mk/GMakedefs.mak commit 246196b623e580df0bb07e5bce3a52e849c21cfa Author: almgren Date: Sat Jul 14 02:54:12 2007 +0000 Need to pass in xa, xb since we don't know what AMR level we're actually at. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit ffaf7177b8af5959629ad3a30abb4e5745808484 Author: almgren Date: Sat Jul 14 00:35:45 2007 +0000 Remove extra print statements. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit d253f65c655b42f18e3f30f842de32fd642a1868 Author: almgren Date: Sat Jul 14 00:16:46 2007 +0000 Remove print statements. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 885e642af3efae70f10c4a7edd5bd3dd4b77eb95 Author: almgren Date: Fri Jul 13 22:56:49 2007 +0000 New code to work for gravity in Castro. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 2fcdcff6745c98e72076f3f39a87a8271f0afaeb Author: almgren Date: Fri Jul 13 22:56:17 2007 +0000 New stuff to work for gravity in Castro. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit c0443de77662c9a8b0baeea014543d40046ce162 Author: mzingale Date: Fri Jul 13 16:34:39 2007 +0000 create a rule to make build_info.f90. You need to add f90sources += build_info.f90 to your GPackage.mak to get this rule to execute Tools/F_mk/GMakerules.mak commit 0cef191bebd9e386faf51dc83bac88d76ebf8eb0 Author: mzingale Date: Fri Jul 13 15:15:50 2007 +0000 a script that automagically generates a Fortran subroutine that returns the name of the machine we compiled on, the build date/time, and the directory that we built in. Tools/F_scripts/make_build_info commit d7c1235e378cd52b8c297047efd2dedf6a3911ff Author: almgren Date: Tue Jul 10 21:15:06 2007 +0000 When need_grad_phi is true, make sure we fill periodic and fine-fine ghost cells as well as interpolating from crser grid. Src/LinearSolvers/F_MG/ml_cc.f90 commit a6f59e675e48614bd3d4ac063d4124185ed63c86 Author: ajnonaka Date: Mon Jul 9 18:27:27 2007 +0000 This is a dummy checkin to verify my CVS works. Tools/F_scripts/coco/coco.pl commit b9ebe4200572cbd3e979d4c5e0a8199ebfd5b7e8 Author: almgren Date: Fri Jul 6 01:04:01 2007 +0000 Fixed bug for multiple grids per level above 0. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 2cce8a444b1156b5ffe2f99bb62f9065e7d51bf7 Author: lijewski Date: Thu Jul 5 20:59:05 2007 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit a57e388f4fb4f0628adcaee5190c1093503b5546 Author: almgren Date: Thu Jul 5 20:51:20 2007 +0000 Get rid of unused gbox in assertions. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit a6f68e26519dc26d3c782f7e710224fd288a5f5b Author: almgren Date: Thu Jul 5 20:50:32 2007 +0000 Get rid of unused stuff in assertions. Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp commit fd16e2bfc0e08ab3b16711f10bac8a750071424a Author: almgren Date: Thu Jul 5 20:49:18 2007 +0000 Fix up the MyProc stuff. Src/C_BoundaryLib/FabSet.cpp commit d9b64cee142c15dc8c8c3ef2f3177582945e2563 Author: lijewski Date: Thu Jul 5 20:43:08 2007 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StationData.cpp commit 4cb519abcff6c97e16a7e20dfc42a584b0099364 Author: lijewski Date: Thu Jul 5 20:02:11 2007 +0000 *** empty log message *** Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile commit 2a4d31fd7d1b98f35f9e3b148108b96bb27ce147 Author: lijewski Date: Thu Jul 5 17:02:00 2007 +0000 *** empty log message *** Src/C_AMRLib/Amr.H Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/LevelBld.H commit be18f98e38003f9beec2ec036b7b10560bb6f699 Author: lijewski Date: Tue Jul 3 21:54:58 2007 +0000 *** empty log message *** Src/C_BaseLib/COORDSYS_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F commit ccfe65329715bb903e94339b7ba532d9e6057136 Author: lijewski Date: Tue Jul 3 21:22:57 2007 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 7651597c724546650d8dc42d3d59ad14ae4cdb2a Author: almgren Date: Tue Jul 3 21:05:31 2007 +0000 This main.cpp has a RHS that sums to zero, so it is solvable with all-Neumann or all-periodic bc's as well as with Dirichlet. Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 92c3405ca8c4ab3001f9777fe4a6ce33f976f4a7 Author: almgren Date: Tue Jul 3 20:41:45 2007 +0000 New files with 128 cubed divided into 64 patches of 32 cubed. Src/LinearSolvers/C_CellMG/Test/grids/gr.3_128cubed Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed Tests/LinearSolvers/C_CellMG/grids/gr.3_128cubed Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed commit c1a997247879068977dc9d7738f33b02f3c2b5c5 Author: lijewski Date: Tue Jul 3 20:10:56 2007 +0000 g95 stuff Tools/C_mk/Make.defs commit a10cda9d917e1d17558c056e1a3945474cb1b3e4 Author: lijewski Date: Tue Jul 3 19:50:33 2007 +0000 removed extraneous OutOfMemory Src/C_BaseLib/BoxLib.cpp commit 2627d126be4ec8f5b3a37a04017699bbbc3411f0 Author: lijewski Date: Tue Jul 3 03:37:57 2007 +0000 removed stencil_flux_fill_st() Src/LinearSolvers/F_MG/stencil.f90 commit b342af9be7bcfddc168bbaade2c690ef00e5e980 Author: lijewski Date: Tue Jul 3 03:13:09 2007 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 0e933438d3ad6e42b6b10096e8af59a37239fda3 Author: lijewski Date: Tue Jul 3 03:10:38 2007 +0000 some cleanup Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit c40f3f0a57e1618a66036779cafb169d61a4db5a Author: lijewski Date: Mon Jul 2 23:00:14 2007 +0000 some cleanup Src/C_AMRLib/INTERP_2D.F Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_F.H commit ff31d6ec117071fdb51e53c9c8364b9749fcaf21 Author: almgren Date: Mon Jul 2 17:53:31 2007 +0000 Comment out the printing of f90 mg settings (for now) Src/LinearSolvers/F_MG/mg_cpp.f90 commit b79610130191da94efbf12b5b44cbe2d121f7502 Author: almgren Date: Sun Jul 1 21:49:17 2007 +0000 Must take multilevel norm of initial residual. Src/LinearSolvers/F_MG/ml_cc.f90 commit 05b5d4425184298b69c3ffd585c77263a1ab4199 Author: almgren Date: Sun Jul 1 21:14:54 2007 +0000 Need to pass ng into mgt_get_uu so that we can pass the ghost cells of the fine grid solution back from the f90 to the C++. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 84324bba5aa62487c73dedf0121e4b4085f44a37 Author: almgren Date: Sun Jul 1 21:14:09 2007 +0000 Need to pass ng into mgt_get_uu so that we can pass the ghost cells of the fine grid solution back to the C++. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit c99384323994938b993a682fee71b04e89c90b06 Author: almgren Date: Sat Jun 30 00:30:12 2007 +0000 Added need_grad_phi argument to mgt_solve Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 39ec68d7d4136884eda40a7a9b136115d0527959 Author: almgren Date: Sat Jun 30 00:29:58 2007 +0000 Added need_grad_phi argument to MGT_Solver::solve and mgt_solve Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 808dfa4e5084a744bb3da3b14ef569ff4b2e2be8 Author: almgren Date: Fri Jun 29 21:34:45 2007 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 577bd82f23595b9128a12901837fe9d23faf8f6d Author: mzingale Date: Fri Jun 29 17:33:16 2007 +0000 clean up the printing some to now output the variable names Tools/C_util/Convergence/DiffSameGrid.cpp commit c8608caa1fb7a4734586eb0d427bfe8866dfa534 Author: sepp Date: Fri Jun 29 17:06:45 2007 +0000 1) more adjustment of spaces in comments Src/C_AMRLib/BC_TYPES.H commit 49c3490c3e7b9bba5fe0935756af4839bc9d6cb1 Author: sepp Date: Fri Jun 29 17:01:53 2007 +0000 1) adjusted spaces in table so columns line up exactly Src/C_AMRLib/BC_TYPES.H commit 7e5a63684b8c164228bcb566fa4ba6148988452b Author: almgren Date: Thu Jun 28 20:29:56 2007 +0000 Removed another print statement. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 2446b79a48c0b41a829c7786aed6793aa1ea0a5f Author: almgren Date: Thu Jun 28 19:41:20 2007 +0000 Removed write statement. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit b3832b9ba9558ec7ec5445ce47bb877f9abaa5bb Author: almgren Date: Thu Jun 28 19:41:07 2007 +0000 Removed print statement. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 52cb7dc31547a8f47f3337a7a3a8815c380d7cb1 Author: almgren Date: Thu Jun 28 18:46:59 2007 +0000 Get rid of print statements. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 3c981df7599bc574d3ee46ad8027d9614e631a8f Author: almgren Date: Thu Jun 28 17:54:43 2007 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp.f90 commit 2dac7b6e108fffd05b20800571b5c9a3b0ac8e32 Author: almgren Date: Wed Jun 27 23:20:22 2007 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h commit 491736eed7b8aef9819d9d604d8b1a825149b3e7 Author: almgren Date: Wed Jun 27 22:17:34 2007 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 836511b36038736d4b83aa53b95ec4ef0ab02798 Author: almgren Date: Wed Jun 27 17:49:48 2007 +0000 What's needed for level solve_for_phi in Castro, hopefully. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 31819837e6ff4f2912ae6260b87c25d84f3d5982 Author: almgren Date: Tue Jun 26 05:22:49 2007 +0000 Changes in order to more easily set coefficients for a cell-centered gravity solve (a = 0, bx = by = bz = 0) Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 175db13aa538533cfa07a774f02ade5d0c031e13 Author: lijewski Date: Mon Jun 25 22:54:26 2007 +0000 only run f90.depends on f90EXE_sources Tools/C_mk/Make.rules commit cab0d04040c67c40454a3a86cdd0eb281dd1f934 Author: mzingale Date: Fri Jun 22 14:35:56 2007 +0000 add support for Intel 10.0 compilers. Note, with Intel 10.0, there is no longer an ifc command -- it's all ifort. Therefore, we need to switch the shell test that checks the version of the compiler to use ifort. This will work fine for any Intel compiler since 8.0. As a result, we drop the Intel 7.0 support (those compilers are quite old these days anyway). Tools/F_mk/GMakedefs.mak commit 513e18350138ab8c416d7dde2789013dec800029 Author: mzingale Date: Tue Jun 12 12:20:21 2007 +0000 add Intel 10.0 compiler support Tools/C_mk/Make.defs commit 5466618172f565f70cb6e5b395c2aafb7e007296 Author: almgren Date: Thu Jun 7 22:23:07 2007 +0000 Use -mp flag for all Intel compilers -- doesn't allow optimization to screw up the precision. Tools/F_mk/GMakedefs.mak commit 02089336b006439110f5b7ebe74529eb9b6fc8b3 Author: almgren Date: Fri May 11 17:45:04 2007 +0000 mg_jacobi_smoother now does nu1 relaxations instead of 1. Src/LinearSolvers/F_MG/mg.f90 commit b071c9b768d385c9010e843e953617030ec7f10f Author: almgren Date: Wed May 9 21:30:59 2007 +0000 Added mg_jacobi_smoother to be called at end of solve... Src/LinearSolvers/F_MG/mg.f90 commit ccb9519ea793d6de183724239e26b389708d3302 Author: lijewski Date: Wed May 9 19:52:05 2007 +0000 Added reduce_real_sum accessible from Fortran. Src/C_BaseLib/ParallelDescriptor.cpp commit 8be0fc5186dc516c5876417375c12899cb87cac7 Author: lijewski Date: Wed May 9 19:47:14 2007 +0000 Added fortran-acessible calls for ::second() and ::ReduceRealMax(IOProc). Src/C_BaseLib/ParallelDescriptor.cpp commit 5018d015d919c719645d943dda5661224601a659 Author: lijewski Date: Wed May 9 17:55:29 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 85f813e65930583abe8a524f4b6c0d4f80479129 Author: lijewski Date: Tue May 8 21:01:15 2007 +0000 faster sort() in simplify() Src/C_BaseLib/BoxList.cpp commit 328f985fce6d8b9b7fd199d89cbda28900d54969 Author: lijewski Date: Tue May 8 20:08:21 2007 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit ab99c9d6650172eb87b5071db906610023aab510 Author: lijewski Date: Tue May 8 19:28:35 2007 +0000 Added strategically placed simplify()s simplify() scales better than complementIn() in grid_places. Basically we're simplify()ing before complementIn(). Src/C_AMRLib/Amr.cpp commit 7e0d931d74266a1c9a5699557773f6e7d67439b8 Author: lijewski Date: Tue May 8 19:26:35 2007 +0000 now simplify() in batches of 50 not 250 Src/C_BaseLib/BoxList.cpp commit b4ecdd30ba267c094d673636d8424217b6f2b77a Author: lijewski Date: Tue May 8 19:02:45 2007 +0000 assert ngrow>=0 Src/C_BaseLib/FabArray.H commit eb72bf62846368d410bddb855210444da8088acf Author: jbb Date: Tue May 8 16:35:31 2007 +0000 change Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit e1e59bb4d321507c407e0f48e5de638060f5b457 Author: lijewski Date: Tue May 8 03:30:43 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit a7cdc3cb5ff3d5f56be9caf7c5c9b6b029a89193 Author: lijewski Date: Sat May 5 20:54:12 2007 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.cpp commit e15165c3ef364319f8bcdb7d62370d5a4ac02f30 Author: lijewski Date: Fri May 4 23:21:24 2007 +0000 *** empty log message *** Src/C_BaseLib/BoxList.cpp commit 05dc99fa66d23ae93f9a0901f4aad6e91d050cb8 Author: lijewski Date: Fri May 4 23:00:51 2007 +0000 *** empty log message *** Src/C_AMRLib/Cluster.cpp Src/C_BaseLib/BoxArray.cpp commit 4cf13142a9111f628f4519b7a66d06661018bc51 Author: almgren Date: Fri May 4 20:29:49 2007 +0000 This one works on atlas as well as manda (I think). Tools/F_mk/GMakedefs.mak commit f71138f21a5512c3342376b2a18a33417a407110 Author: almgren Date: Fri May 4 20:24:05 2007 +0000 Include specifics for using mpi on manda.lbl.gov Tools/F_mk/GMakeMPI.mak commit 637ac9798c8a4df54e9ea2658716355b77e38182 Author: lijewski Date: Fri May 4 19:08:48 2007 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp commit b06684e5ff4e4463fdab6b1e0b845baf071d5740 Author: lijewski Date: Thu May 3 23:29:59 2007 +0000 changed BL_PROFILE() a bit Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp commit 363b780c01e99d697ce5056fa4a694e79dfba41b Author: lijewski Date: Wed May 2 21:53:15 2007 +0000 added FastContins() Src/C_AMRLib/Cluster.cpp commit 9d13698ed644b363a18325629749592b329d47e3 Author: lijewski Date: Wed May 2 21:49:24 2007 +0000 shortcut for special case of complementIn() Src/C_BaseLib/BoxList.cpp commit 5fedf331523e868b38413bd291e5a747cd4eec5a Author: lijewski Date: Wed May 2 21:48:19 2007 +0000 more profiling Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.cpp commit 1d943463c1abbd32561d6bef5ab843127acf2465 Author: lijewski Date: Wed May 2 16:48:09 2007 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit f300d5a203863a50f825963b16459039b1ff2ab2 Author: lijewski Date: Wed May 2 16:45:27 2007 +0000 added intersections() in setVal() Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 63e120f88d16409f235b10cf34bac41637754579 Author: lijewski Date: Tue May 1 22:42:34 2007 +0000 *** empty log message *** Src/C_BaseLib/BoxList.cpp commit e76e775c2cfbc77ed5cb1e497cd0b25c118919fc Author: lijewski Date: Tue May 1 22:26:03 2007 +0000 comment out simplify in grid_places() for now Src/C_AMRLib/Amr.cpp commit 5f19fcd3c6e932b35a3a50fd7b40e7a1092181e1 Author: lijewski Date: Tue May 1 21:54:43 2007 +0000 commented out simplify() in removeOverlap() for the time being Src/C_BaseLib/BoxArray.cpp commit 2029cc6a789204f39fdd7729fa7639370b78fe50 Author: lijewski Date: Tue May 1 20:11:02 2007 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit 20691dac85d1a27c1593cd9eca6fb227f36192a6 Author: lijewski Date: Tue May 1 03:12:50 2007 +0000 ProjPeriodic() now does a simplify() Src/C_AMRLib/Amr.cpp commit 19b9f4f6ef476ea00b1caa0da79fed0cdc089676 Author: lijewski Date: Tue May 1 02:59:57 2007 +0000 Initialize() now does full simplify() Src/C_AMRLib/AuxBoundaryData.cpp commit 46adc0f35ed766e45792f54b6402ba979642cb4d Author: lijewski Date: Tue May 1 02:59:32 2007 +0000 complementIn() now does full simplify() Src/C_BaseLib/BoxList.cpp commit 4defb19e9ee40e356718e3010875fd10e7c15681 Author: lijewski Date: Tue May 1 02:59:20 2007 +0000 removeOverlap() now does full simplify() Src/C_BaseLib/BoxArray.cpp commit d3cbf2afa6c2a96af819f56dc44af5f2b6641e50 Author: lijewski Date: Mon Apr 30 21:07:14 2007 +0000 a really big HCAll grid Src/C_BaseLib/test/ba.95860.REMOVED.git-id Tests/C_BaseLib/ba.95860.REMOVED.git-id commit 15e6d0e1561513643b5ad3e2486acf02303f7db3 Author: lijewski Date: Mon Apr 30 20:56:30 2007 +0000 added back in simplify(); it's now really fast Src/C_AMRLib/Amr.cpp commit fb31131f95f4f1a685a3fc29a2b1840510f9d172 Author: lijewski Date: Mon Apr 30 20:54:58 2007 +0000 sped up simplify() Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit c46027f408f8229918fd1ec28eeabf9211a2a6b2 Author: lijewski Date: Wed Apr 25 20:02:34 2007 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit c4a15336165483a6cef4e6c0f93ae4763b2739d2 Author: almgren Date: Wed Apr 25 19:38:09 2007 +0000 Change in calling sequence to stencil_fill_nodal (no longer pass h_finest) Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 8fc1d1233277633bee20c07bf36e410114f63593 Author: lijewski Date: Tue Apr 24 21:13:08 2007 +0000 *** empty log message *** Src/C_BaseLib/test/ba.15456.REMOVED.git-id Src/C_BaseLib/test/ba.3865 Src/C_BaseLib/test/ba.mac.294 Src/C_BaseLib/test/tBA.cpp Src/C_BaseLib/test/tDM.cpp Tests/C_BaseLib/ba.15456.REMOVED.git-id Tests/C_BaseLib/ba.3865 Tests/C_BaseLib/ba.mac.294 Tests/C_BaseLib/tBA.cpp Tests/C_BaseLib/tDM.cpp commit 7e762a01e0e9f734036fcb3c2cf7c0f8a1ac2a43 Author: lijewski Date: Tue Apr 24 21:12:42 2007 +0000 improved SFC; sfc_threshold now 10 Src/C_BaseLib/DistributionMapping.cpp commit f0ba0e8c88e0eab253604aae9767e50d72a801b0 Author: lijewski Date: Tue Apr 24 21:05:46 2007 +0000 *** empty log message *** Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/ba.23925.REMOVED.git-id Src/C_BaseLib/test/tDM.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/ba.23925.REMOVED.git-id Tests/C_BaseLib/tDM.cpp commit c4d4cba76595ec16a73786632cfe07461d82502c Author: lijewski Date: Tue Apr 24 19:43:47 2007 +0000 uncomment simplify() till further notice Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp commit 280af56ad7d5ff08b473e7751d3619b6d7c2f140 Author: almgren Date: Tue Apr 24 17:45:28 2007 +0000 Fix in function stencil_norm to workaround bug in Intel compiler for large single arrays. Src/LinearSolvers/F_MG/stencil.f90 commit 6eedd43b787eeb5a44cf38d7555ffdbc7f1a378f Author: lijewski Date: Tue Apr 24 01:13:50 2007 +0000 commented out simplify() in grid_places() Src/C_AMRLib/Amr.cpp commit b7e32f6ae27f0130f975e11f102ba537c265280e Author: lijewski Date: Tue Apr 24 01:13:20 2007 +0000 commented out complementIn() in removeOverlap() Src/C_BaseLib/BoxList.cpp commit 560d9fb605bad393049ba75fcd2bd3c9a2c65406 Author: lijewski Date: Tue Apr 24 01:13:06 2007 +0000 commented out simplify() in removeOverlap() Src/C_BaseLib/BoxArray.cpp commit 9c6d6c416902c0a333b22c8a72d7f03c9c4c87f5 Author: nazgul Date: Mon Apr 23 20:44:48 2007 +0000 Commenting out a section of code that appears to be unnecessary and makes it impossible to have a Tuple. The offending code also conflicts with the comments. If this code really is necessary let me know and we can work something else out. Louis Howell Src/C_BaseLib/Tuple.H commit 961403c906364d83a53a4a2dc2706fa60a32796f Author: nazgul Date: Mon Apr 23 16:46:52 2007 +0000 Minor bug fixes for 1D. (Doesn't look like 1D gets used very much.) Louis Src/C_BaseLib/COORDSYS_1D.F Src/C_BaseLib/CoordSys.cpp commit 0a6107ba9bd2468baefc0d2606d3e655ac774c0a Author: lijewski Date: Sat Apr 21 03:32:11 2007 +0000 yet further refinements to FAB data uniformization Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 6c02d63cd04c806714ea0321e077927b768cbb54 Author: lijewski Date: Sat Apr 21 00:51:57 2007 +0000 further refinements to FAB data uniformization Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 56edbaa75c9539ace339db24085565c859e493eb Author: lijewski Date: Fri Apr 20 21:26:56 2007 +0000 default for sfc_threshold is now 10 Src/C_BaseLib/DistributionMapping.cpp commit 348f8edea5c3ee74d3909d3653ff88971fa565cc Author: lijewski Date: Fri Apr 20 20:55:44 2007 +0000 verbose now defaults to true Src/C_BaseLib/DistributionMapping.cpp commit 89f759a8b169ec24e2070ea88858895ace39857f Author: lijewski Date: Fri Apr 20 19:13:58 2007 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit 251939b5f556303e7b6f39940308ed6f2222c063 Author: lijewski Date: Fri Apr 20 02:49:08 2007 +0000 print out FAB byte high-water-mark at end of timestep Src/C_AMRLib/Amr.cpp commit bcd58fd988c1725d09a59ec969f40ac743a2dadf Author: lijewski Date: Fri Apr 20 02:48:33 2007 +0000 now maintain FAB byte high-water-mark Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 6667dfabf88db1ec6516cf739cb2004b77bd6af4 Author: vince Date: Thu Apr 19 01:23:22 2007 +0000 added a knob for calling probinit. Src/C_AMRLib/Amr.cpp commit 06e5fe920ec9d220246cf149c03b9a56aa8dc8ae Author: vince Date: Thu Apr 19 00:58:17 2007 +0000 some defines for serial. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/VisMF.cpp commit 807ea0b8bb8630feb8663a451d528e4351ff89a8 Author: vince Date: Thu Apr 19 00:19:45 2007 +0000 more efficient version of the multifab reader. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit d4f4d2a98728d48a2b79772f8bb8b66908d992ae Author: vince Date: Thu Apr 19 00:17:49 2007 +0000 added code to limit probin opens. Src/C_AMRLib/Amr.cpp commit 81d6fc55bf8b3d48cb95981e6330142a52bb4bf0 Author: lijewski Date: Wed Apr 18 17:51:08 2007 +0000 Must check DistributionMaps, as well as BoxArrays, when deciding on caching. Src/C_BoundaryLib/FabSet.cpp commit f64cc914382a2c8e0576b0af1dd844a9688666d2 Author: lijewski Date: Wed Apr 18 17:37:08 2007 +0000 Must look at DistributionMapping, not just BoxArray, in FillBoundary(). Src/C_BaseLib/MultiFab.cpp commit 73bed962ca14091f4aefbb0db0e8f1f26794567f Author: lijewski Date: Wed Apr 18 17:29:15 2007 +0000 Need to look at DistributionMapping, in addition to BoxArray, when caching FPBs. Src/C_BaseLib/Geometry.cpp commit 3c39f969094cba927a9f3d6d5205bf700c1fc19f Author: lijewski Date: Wed Apr 18 17:28:03 2007 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit e5e7222f5ea8cc3718268a8e52097efdc5dcc910 Author: lijewski Date: Wed Apr 18 17:27:28 2007 +0000 added -Wno-deprecated for g++ Tools/C_mk/Make.defs commit 51a0da0c3d8fff1eb0bd6094d7df9a763cc5519e Author: lijewski Date: Wed Apr 18 15:40:23 2007 +0000 *** empty log message *** Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/tBA.cpp commit a994b5c1edf5a9bee3d29cddf9ea4e93696368e3 Author: lijewski Date: Tue Apr 17 18:12:14 2007 +0000 added AuxBoundaryData Src/C_AMRLib/Make.package commit 4ece921c4f2ab4cdc05db72f4c0095dad2687b56 Author: lijewski Date: Tue Apr 17 16:56:12 2007 +0000 stripped out of LMC, nova & Castro Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/AuxBoundaryData.cpp commit fcb312b233a5528b224d645ca30a82d7e44a29ea Author: lijewski Date: Tue Apr 10 20:16:27 2007 +0000 needed Src/C_BaseLib/ParallelDescriptor.H commit 35b708e5b091311a5f9b2b61aee58e9fd7900f3e Author: lijewski Date: Mon Apr 9 20:29:45 2007 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 6c3a0338016ebbdd98bb550177a394b4972a0bd5 Author: vince Date: Fri Apr 6 22:31:42 2007 +0000 another friendly read. Src/C_BaseLib/ParmParse.cpp commit 1f1a1975e4c3cb0a0ee6280290b990589a6318d3 Author: vince Date: Fri Apr 6 19:57:12 2007 +0000 implemented a mechanism to limit the total number of open files when reading a multifab. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 57442ad36f281941c99b262fcb5542f649e11130 Author: lijewski Date: Wed Apr 4 05:14:10 2007 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit d333ba9b3644b9ee667ecfb5d7528be4b21f9a4d Author: lijewski Date: Tue Apr 3 23:36:58 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.25600 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034 Tests/LinearSolvers/C_CellMG/grids/in.grids.15456 Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/grids/in.grids.25600 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 commit 5a1f23412c65ac96d90816ea7a65320395ec880c Author: lijewski Date: Tue Apr 3 23:34:55 2007 +0000 add ability to turn off LeastUsedCPUs() Src/C_BaseLib/DistributionMapping.cpp commit 322e3351cc0d56637011f4cb776fdf3978003769 Author: lijewski Date: Tue Apr 3 22:49:59 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit d79a8afd8981df1221e07c2ad7bc0046880bd06d Author: lijewski Date: Thu Mar 29 19:40:57 2007 +0000 removed Cray-isms Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/REAL.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/winstd.H commit 32b1af2e7fe702b225a7f79266e3769d4de10fea Author: lijewski Date: Thu Mar 29 18:12:44 2007 +0000 removed T3E stuff Src/C_BaseLib/FPC.cpp Src/C_BaseLib/Utility.cpp commit 76b0258ce7ad68e39353a3a1d22ebdee00e3e4c9 Author: lijewski Date: Thu Mar 29 18:08:50 2007 +0000 XT3 stuff Src/C_BaseLib/Utility.cpp commit 7c9449d724b1a1900b807f0ac658d2e8e921b611 Author: lijewski Date: Thu Mar 29 17:57:25 2007 +0000 XT3 stuff Src/C_BaseLib/Utility.cpp commit 224bbd14a2d076284fde1e148a7eeb62a76f98fc Author: lijewski Date: Wed Mar 28 21:33:38 2007 +0000 added XT3 stuff Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit a1788d95edadeedab700d19a96d655a8add7950b Author: lijewski Date: Mon Mar 26 17:31:37 2007 +0000 now cognizant of amount of FAB data per CPU Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit e7d48c3bdd90b6964b1574a0f5982fa935ff0849 Author: lijewski Date: Thu Mar 22 16:24:40 2007 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H commit b4d848d8393ec3268be144e530ba84e63a9c0be7 Author: lijewski Date: Thu Mar 22 04:21:20 2007 +0000 add total_bytes_allocated_in_fabs Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit d566a03d76dbba35e81dd66f351ca40ca9b5fe10 Author: almgren Date: Mon Mar 19 19:15:51 2007 +0000 Need this to work on Ann and Andy's machines... Tools/F_mk/GMakedefs.mak commit 7dbbc8d413e14ea93dcc8999177ea5342c7e1b68 Author: lijewski Date: Wed Mar 14 01:17:37 2007 +0000 Knapsack called beneath SFC when too few grids for SFC, can now do MinimizeCommCosts(). Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 0a1f4a5cfeccb547de88a7a896c090a5d9c15c0e Author: lijewski Date: Tue Mar 13 21:35:54 2007 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 2b475b6a8e44b4473415d1074ad8916b7298902d Author: lijewski Date: Tue Mar 13 17:01:23 2007 +0000 SFC is now the default Src/C_BaseLib/DistributionMapping.cpp commit 0f0eb8db4b91018778c0d432b61e4f3788a2597a Author: lijewski Date: Fri Mar 9 04:40:43 2007 +0000 removed nProcsCFD() stuff Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 6c645d8db3a063c141e982994fd36c09feb74b06 Author: lijewski Date: Fri Mar 9 04:21:05 2007 +0000 array versions of REDUCE operators Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit f89681e06d363b684acc0502c7ad95814dd96354 Author: lijewski Date: Thu Mar 8 22:19:39 2007 +0000 XT4/PGI Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 8f62dd9dce857fb2e0f5dde24a7c4bc31e709b29 Author: jbb Date: Wed Mar 7 18:21:02 2007 +0000 atlas changes Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit a8f5c759603363cbed456ccb52d14bc7ae442e49 Author: lijewski Date: Tue Feb 27 22:03:18 2007 +0000 added hacked up version of writePlotFile() Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit f5a975f2edb3d5f499516c36e17f667e77a05897 Author: lijewski Date: Tue Feb 27 19:01:14 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213 Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/main.cpp commit eb3852f48ffd46ece6a237f80ea552935837ad88 Author: lijewski Date: Mon Feb 26 23:21:40 2007 +0000 what we want ANAG to try first Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034 Tests/LinearSolvers/C_CellMG/grids/in.grids.15456 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 commit e8bc4e0d555e7aed9025b5b0405c043c914a8d0a Author: lijewski Date: Sat Feb 24 00:04:59 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/grids.15456.REMOVED.git-id Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034 Tests/LinearSolvers/C_CellMG/grids/grids.15456.REMOVED.git-id Tests/LinearSolvers/C_CellMG/grids/in.grids.15456 Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 commit 5cc15983f71b0b1d331342866853d958fb7b1721 Author: lijewski Date: Fri Feb 23 23:05:57 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 181583f1eaf519d12306fc9dbc571758219a96b6 Author: lijewski Date: Fri Feb 23 22:38:31 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 0f45c6978cfe7a64c3b2b2d54b8a12ec8e63033b Author: lijewski Date: Fri Feb 23 21:42:23 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/grids.15456.REMOVED.git-id Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034 Tests/LinearSolvers/C_CellMG/grids/grids.15456.REMOVED.git-id Tests/LinearSolvers/C_CellMG/grids/in.grids.15456 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 commit 4d809d5176521115b449c1a2839a6566aa6ff5f0 Author: mzingale Date: Thu Feb 22 15:24:37 2007 +0000 some routines for visualizing Maestro data with IDL Tools/F_scripts/idlbl/README Tools/F_scripts/idlbl/batch.pro Tools/F_scripts/idlbl/color.pro Tools/F_scripts/idlbl/color_index.pro Tools/F_scripts/idlbl/colorbar2.pro Tools/F_scripts/idlbl/dump_surface.pro Tools/F_scripts/idlbl/flamelength.pro Tools/F_scripts/idlbl/flash_colors.tbl Tools/F_scripts/idlbl/get_idlbl_path.pro Tools/F_scripts/idlbl/nolabel.pro Tools/F_scripts/idlbl/partvelvec.pro Tools/F_scripts/idlbl/plotflash.pro Tools/F_scripts/idlbl/plotraw.pro Tools/F_scripts/idlbl/rawread.pro Tools/F_scripts/idlbl/rawread3d.pro Tools/F_scripts/idlbl/scale_color.pro Tools/F_scripts/idlbl/start_linux.pro Tools/F_scripts/idlbl/tvimage.pro Tools/F_scripts/idlbl/vcolorbar.pro Tools/F_scripts/idlbl/xaverage.pro commit 20f30ea751dd64154ae23a3534f2eb4f47542cee Author: lijewski Date: Wed Feb 21 21:36:51 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/grids.25600.REMOVED.git-id Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.25600 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034 Tests/LinearSolvers/C_CellMG/grids/grids.25600.REMOVED.git-id Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/grids/in.grids.25600 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 commit 8c12d0a6c30ba7a612bbf167bbfabb2b192523dc Author: mzingale Date: Wed Feb 21 21:28:13 2007 +0000 fix the sub_fab routines -- they were finding the bounds of a null pointer -- not a good thing. Src/F_BaseLib/filler.f90 commit 2071d52eea95d50e89d3123bccd16385c91ef325 Author: mzingale Date: Wed Feb 21 18:15:10 2007 +0000 add support for my cluster (homer) Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit ed710fbeadd863cf5f6817de886e94c1997c1e36 Author: lijewski Date: Wed Feb 21 17:19:34 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/CGSolver.cpp commit a63d3839d4dd8c0a733af9e3531deb751b98f830 Author: lijewski Date: Tue Feb 20 18:30:33 2007 +0000 print out grid distirbution with boxes Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 454067ab72337115db5c5077128edbc5bd41bc60 Author: lijewski Date: Fri Feb 16 21:18:22 2007 +0000 set eps_rel to 1e12 Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 4019bdafbbfc79489bd51afa474342163dbbef9d Author: lijewski Date: Fri Feb 16 00:21:29 2007 +0000 Added version of FillPeriodic that doesn't do any parallelism to support use_jbb_precond in CGSolver.cpp. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit a5e6e494146ca058ca4610b44c8ac05773ff26f5 Author: lijewski Date: Fri Feb 16 00:19:19 2007 +0000 added version of FillBoundary that doesn't do parallel Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit db045847d5bd5f88919bb5e37757ceaea3678c9f Author: lijewski Date: Fri Feb 16 00:15:01 2007 +0000 Hash the mask calculations. Added stuff needed for use_jbb_precond. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit 28c4d23fe39c12a149c9d9264f54ed07195ca1b0 Author: lijewski Date: Fri Feb 16 00:12:58 2007 +0000 Removed CG_Alt and Automatic stuff. Added stuff needed for use_jbb_precond. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 51816af90f5be5d3b3113928e19bb4d8a993d3df Author: lijewski Date: Fri Feb 16 00:09:16 2007 +0000 stuff needed for use_jbb_precond Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp commit dd34825a6cafdf99a497723ce08c92a2da2a2656 Author: lijewski Date: Fri Feb 16 00:03:14 2007 +0000 removed CG_Alt stuff Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 95b9c3a675e3cb8284e146db8f01342a0c07bb4e Author: lijewski Date: Fri Feb 16 00:02:37 2007 +0000 use hash method for calculating masks Src/C_BoundaryLib/BndryData.cpp commit a2dca1278488f1258d37e54843f1511e3c61fdf7 Author: almgren Date: Mon Feb 12 21:11:14 2007 +0000 Added new access functions: const Geometry& getGeom const Real * getDx virtual Real get_alpha virtual Real get_beta virtual const MultiFab& aCoefficients virtual const MultiFab& bCoefficients Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit c753661818d46773d8f446161517513cc93cc649 Author: lijewski Date: Fri Jan 26 20:16:45 2007 +0000 ParmParse'd fpb_cache_max_size Src/C_BaseLib/Geometry.cpp commit 3e4c0aa1b736bfc9c2862ebd3dd088ccced626de Author: lijewski Date: Fri Jan 26 19:23:40 2007 +0000 *** empty log message *** Src/C_BaseLib/MultiFab.cpp commit 7c755d4d37c32a8fab77efd6d8f612bb0644b31d Author: lijewski Date: Fri Jan 26 19:17:09 2007 +0000 ParmParse'd copy_cache_max_size Src/C_BaseLib/MultiFab.cpp commit f647b5b467355acf245194749c9889b2abb8f7e1 Author: lijewski Date: Fri Jan 26 19:03:14 2007 +0000 *** empty log message *** Src/C_BoundaryLib/FabSet.cpp commit 57c72f4563154e06d8725ac98343edfb8cf516c6 Author: lijewski Date: Fri Jan 26 18:47:45 2007 +0000 ParmParse'd copy_cache_max_size Src/C_BoundaryLib/FabSet.cpp commit a0d2dc052dff2cb4e9c8376d8b69182578bb67a9 Author: lijewski Date: Fri Jan 26 18:26:04 2007 +0000 ParmParse'd copy_cache_max_size Src/C_BaseLib/FabArray.cpp commit c7fd94b1c2db4bb0c65d3f07f7773004ad9720bc Author: lijewski Date: Wed Jan 24 18:11:28 2007 +0000 turn on some cache stats Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit 252957236e44fecdbccc915b0f730b722beb2468 Author: lijewski Date: Thu Jan 18 17:22:19 2007 +0000 extra assertion in define() Src/C_BaseLib/FabArray.H commit d0800687749502e65019f287ae61ffd698d261bf Author: lijewski Date: Thu Jan 18 17:22:04 2007 +0000 added copy constructor & assignment operator Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 4c8061aa98ce9d3bc00f2428710f1ba80db89015 Author: almgren Date: Fri Jan 12 20:53:59 2007 +0000 Changed default nub from 0 to 10 so that after CG or BiCG bottom solver the code will do 10 relaxations -- this to deal with case when CG or BiCG just doesn't converge (and I don't know why). Src/LinearSolvers/F_MG/mg.f90 commit 8429abf0eba40ceefcb5e291dba41758b2cf2788 Author: lijewski Date: Thu Jan 4 20:43:26 2007 +0000 oops Src/C_AMRLib/FluxRegister.cpp commit e68eb38e08a37da018c2dbcf4e939c25cea5e6f5 Author: lijewski Date: Thu Jan 4 20:41:18 2007 +0000 fixed bug hitting coalescing memory manager Src/C_AMRLib/FluxRegister.cpp commit 6a937672449b50bde2a40dee5dbd2a41f90301cc Author: almgren Date: Fri Dec 15 00:55:42 2006 +0000 Bring up to date with new BoxLib stuff. Tools/C_util/Convergence/DiffUniform.cpp commit 4b37af90495ff6e03e23ead3a40cc442626d1e66 Author: lijewski Date: Fri Dec 8 20:40:29 2006 +0000 changed some verbose stuff Src/C_BaseLib/DistributionMapping.cpp commit c90513619d531acad5bc4b3c8e17245776e313e5 Author: almgren Date: Mon Dec 4 22:30:08 2006 +0000 Move multifab_remote after loop thru filenames -- checkpoint reading now works in parallel. Src/F_BaseLib/fabio.f90 commit 7d7a4646737416407cfa094fc990c9f67104aca0 Author: almgren Date: Mon Dec 4 20:57:53 2006 +0000 Fix to make ml_multifab_read_d work in parallel... Src/F_BaseLib/fabio.f90 commit b9b678f567e5c1e3ecf4dc843a45690e4d0a4e07 Author: mzingale Date: Fri Dec 1 15:45:33 2006 +0000 some gfortran fixes Tools/F_mk/GMakedefs.mak commit f53a1995968070123bc1f600eb430e0026a09eb9 Author: lijewski Date: Wed Nov 22 21:10:58 2006 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/in.2_big Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d Src/LinearSolvers/C_CellMG/Test/grids/in.2per_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.3_2boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_2x3x4 Src/LinearSolvers/C_CellMG/Test/grids/in.3_big Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.3_mac_tst Src/LinearSolvers/C_CellMG/Test/grids/in.3_shiftedUp Src/LinearSolvers/C_CellMG/Test/grids/in.3_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.3per_2x3x4 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034 Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/in.2_3x2 Tests/LinearSolvers/C_CellMG/grids/in.2_big Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/in.2_small_a Tests/LinearSolvers/C_CellMG/grids/in.2_small_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d Tests/LinearSolvers/C_CellMG/grids/in.2per_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.3_big Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp Tests/LinearSolvers/C_CellMG/grids/in.3_small_a Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a Tests/LinearSolvers/C_CellMG/grids/in.3per_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 Tests/LinearSolvers/C_CellMG/main.cpp commit 9602cf2058199e99568f3c55da304c6e7f6797ef Author: lijewski Date: Tue Nov 21 23:38:57 2006 +0000 changed sfc_threshold: 4 ==> 8 Src/C_BaseLib/DistributionMapping.cpp commit 9e54785b7abe75668500405cb20edb439e24c1db Author: lijewski Date: Tue Nov 21 06:25:50 2006 +0000 more SFC tweaks Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 152b339b6dcad316ff1f25a5a6aec15d015c66b1 Author: lijewski Date: Sun Nov 19 04:09:13 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 0a60f1c849761547c34d8575918fc19e6e576739 Author: lijewski Date: Sat Nov 18 05:07:25 2006 +0000 removed embedded CVS ID Src/C_BaseLib/DistributionMapping.H commit c6a46306cc0688815655a27a3113ed5fc4b03afb Author: lijewski Date: Sat Nov 18 05:05:46 2006 +0000 initial cut at space filling curve mapping; more work to do ... Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 7c025cc98681928697f20ad85dbace33678c1dc0 Author: almgren Date: Sat Nov 11 05:57:26 2006 +0000 Fixed print statement so don't print NaN if res0 = 0. Src/LinearSolvers/F_MG/ml_cc.f90 commit c68d01c028becf6ca2b38428163ec949cb2cc23b Author: marc Date: Thu Oct 12 16:45:12 2006 +0000 *** empty log message *** Tools/C_mk/Make.defs commit e2be34f1e98646abc523d3cb443bab569c1ebd3f Author: lijewski Date: Wed Oct 11 18:15:08 2006 +0000 added defined() Src/C_BaseLib/FabArray.H commit f90d9a944b1e86292b8dcd03ca47e78de2429bdb Author: sepp Date: Tue Oct 10 20:52:16 2006 +0000 1) added stuff for davinci that was checked over my Mike Tools/C_mk/Make.mpi commit 30bbe6953c1a1aad1fb4baadb324cab4a7ec0d52 Author: sepp Date: Fri Oct 6 17:06:30 2006 +0000 1) correct syntax in comment block Src/C_BaseLib/ParmParse.H commit 6bedb4906f29e9ddb7d0df33088522c9a75cb92d Author: lijewski Date: Wed Oct 4 22:27:04 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit cada8d87b97840842747836218d01dc1a82cb847 Author: lijewski Date: Sun Sep 24 00:40:19 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 12c8565d9239845ad8bc1318f4d2548eac9febb1 Author: lijewski Date: Sun Sep 24 00:32:57 2006 +0000 now print out top 5 communicators Src/C_BaseLib/DistributionMapping.cpp commit f86e95a775c6e440b0a7bb4f48b3711afb5b73dc Author: almgren Date: Sat Sep 16 03:20:59 2006 +0000 Fixed extra endif. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 9fd3ecc719c991b654d66102be3dc05abaaf4591 Author: almgren Date: Sat Sep 16 00:52:54 2006 +0000 Fix weighting of different stencils. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 7e1b78cb69eee1f9e1f4f62f141ba88e9975bd09 Author: almgren Date: Sat Sep 16 00:52:35 2006 +0000 Fix weighting of residual for coarsening operations... Src/LinearSolvers/F_MG/ml_nd.f90 commit cbb9cecfbdd5e215788684477823b9b668eb3771 Author: almgren Date: Sat Sep 16 00:52:01 2006 +0000 Fix calling sequence to stencil_one_sided. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 6a4517c4cd8bc31ae68597ddd0ea5656a01809fb Author: almgren Date: Sat Sep 16 00:51:35 2006 +0000 Small cleanup. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 7c2d0a04d34cf726440c652fcad2ea31cb4072d1 Author: almgren Date: Sat Sep 16 00:50:39 2006 +0000 Better write statements, also test in gsrb2d on whether any skewed... Src/LinearSolvers/F_MG/mg_smoother.f90 commit 2ef48f1e6ddd7c0bc825b8cce71c50675d2f3e37 Author: almgren Date: Fri Sep 15 23:57:51 2006 +0000 Fix print statement. Src/LinearSolvers/F_MG/mg.f90 commit 1981dd0d9cc79606f1f92d8c1e021732b8a50cf9 Author: almgren Date: Thu Sep 14 21:03:49 2006 +0000 Remove "NXC" print statement. Src/F_BaseLib/interp.f90 commit 94c9537c216b4c96b38d1970831acd78801a5133 Author: lijewski Date: Thu Sep 14 19:57:27 2006 +0000 *** empty log message *** Tools/C_util/Convergence/GNUmakefile commit d853d3e576f4e018689f2741de07209605b3b4b4 Author: lijewski Date: Thu Sep 14 19:50:46 2006 +0000 *** empty log message *** Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/GNUmakefile commit 2ba8192c7a2b18cce7bdefbc685855b1642414e2 Author: lijewski Date: Wed Sep 13 20:28:00 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit beacb4488c8354ac838e4295d278cfe012469797 Author: lijewski Date: Wed Sep 13 18:03:22 2006 +0000 cleaned up some compiler warnings Src/C_BaseLib/BLThread.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 9d874fcaaf49df2de12526a9002705d3d931e7aa Author: lijewski Date: Tue Sep 12 22:51:04 2006 +0000 refinement to FPB caching Src/C_BaseLib/Geometry.cpp commit fdcce1fc01c31f85fc04b2eac5a40b8100e30ae5 Author: lijewski Date: Tue Sep 12 21:50:09 2006 +0000 refinements to caching Src/C_BoundaryLib/FabSet.cpp commit 660a25936b363faa3df2fd0fd5bbf4167ff2a3b5 Author: lijewski Date: Tue Sep 12 21:38:45 2006 +0000 *** empty log message *** Src/C_BaseLib/MultiFab.cpp commit 1ec56a5db3cfae093505a082e9f402d34a5c2c99 Author: lijewski Date: Tue Sep 12 20:46:46 2006 +0000 refinement to FillBoundary caching Src/C_BaseLib/MultiFab.cpp commit 7bf07f28399b3562bc0e26e799c4af18b53d771c Author: lijewski Date: Tue Sep 12 20:01:16 2006 +0000 refinement to copy caching Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 64d77a4415fab386542c0709dba19ec3b0b618d7 Author: lijewski Date: Mon Sep 11 21:43:39 2006 +0000 flush copy() cache on regrid Src/C_AMRLib/Amr.cpp commit 761b230f52d253f812dabf508a64cbec7c09bb89 Author: lijewski Date: Mon Sep 11 21:43:20 2006 +0000 added copy() caching Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit ebe33c55da5e58b2731bd3a0e933c578e116e839 Author: vince Date: Fri Sep 8 23:17:20 2006 +0000 change for jvn. Src/C_BaseLib/VisMF.cpp commit 2d2475f87d6c07a83467286ce8fb3c8a0539baa6 Author: vince Date: Fri Sep 8 20:44:02 2006 +0000 added support for specifying at run time the number of files written for a multifab. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit c23db4067e73ce966ee7c7fd93bf8ad89707b288 Author: almgren Date: Thu Sep 7 18:30:22 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/GPackage.mak commit 4ce89afd3d9cb7cc8ab39c3fbf44a65abb891d4c Author: lijewski Date: Wed Sep 6 17:26:53 2006 +0000 Box::length() -> Box::size() Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/Looping.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit f0d1ec9dcdb4c51dfac95705542215c66164a31c Author: lijewski Date: Fri Sep 1 23:10:36 2006 +0000 shut up some compiler message Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp commit 554b4e21b5823797cde40c823ae59ced16b69014 Author: lijewski Date: Fri Sep 1 21:28:06 2006 +0000 reverted out fillpatch caching Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit e7e96dc6308ea4e867e5e8edba42f6ffad52400b Author: lijewski Date: Fri Sep 1 21:20:51 2006 +0000 DistributionMappings are now reference counted Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 03664217eea5f6cbd0b40962a45f65c8a827ff31 Author: almgren Date: Fri Sep 1 18:14:39 2006 +0000 Added absolute tolerance as optional argument to itsol_converged. Src/LinearSolvers/F_MG/itsol.f90 commit 958acd65833a83913f9eaa948b8a17becab7603c Author: almgren Date: Fri Sep 1 18:13:54 2006 +0000 Added abs_eps (absolute tolerance) in addition to rel_eps (relative tolerance). Also fixed weighting for dense stencil. Src/LinearSolvers/F_MG/mg.f90 commit ccf6ed0dd5ea4e1456c5dac64ed85a205e8b147a Author: almgren Date: Fri Sep 1 18:09:59 2006 +0000 Hopefully this has correctly weighted stencils for 2d and 3d, cross and dense... Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 9e76bc8ff77baf18893eed27aa57dc080a3f552f Author: lijewski Date: Fri Sep 1 16:24:17 2006 +0000 removed METIS stuff Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit f1e5a2c8c0090274356b502a6f1b8e226791e403 Author: mzingale Date: Fri Sep 1 15:09:29 2006 +0000 a useful script to aggregrate CVS logs into a nice GNU-style ChangeLog format Tools/F_scripts/cvs2cl.pl commit 97534e0df9881d46b57594de2343e7c6d6aed797 Author: mzingale Date: Thu Aug 31 18:57:53 2006 +0000 add nodal_divu.f90 to the list of packages Src/LinearSolvers/F_MG/GPackage.mak commit d1e276910c129f368659e39039c9c4e58043d651 Author: lijewski Date: Wed Aug 30 00:39:20 2006 +0000 some consolidation of caching -v- no caching in CollectData Src/C_BaseLib/FabArray.H commit 154069c0708cd45ec5650a90baf83621c24382b0 Author: lijewski Date: Tue Aug 29 19:52:49 2006 +0000 added ParmParse'd variable to disable caching in CollectData Src/C_BaseLib/FabArray.H commit e6ba936273f21fd927921178cd52eeded3e9cb23 Author: lijewski Date: Mon Aug 28 18:28:42 2006 +0000 some caching of FillPatch stuff Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 6fa49bc959aa57e957b6f0cec6afd8d3fca1b20d Author: lijewski Date: Sat Aug 26 03:47:42 2006 +0000 added amr_real[23]d.2.f to help work around columbia bug Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_real2d.2.f Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.2.f Src/LinearSolvers/C_NodalMG/amr_real3d.f commit d0ed4e00ec1e0069ff399a443bf078fa3e9f0de5 Author: almgren Date: Fri Aug 25 22:04:03 2006 +0000 Modified verbosity and removed extraneous argument "solver" Src/LinearSolvers/F_MG/mg.f90 commit 77b768238ec7699c8ce2992a385bbe38eb0840e1 Author: almgren Date: Fri Aug 25 22:03:29 2006 +0000 Modified verbosity in ml_nd... Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 5e9cb4ced68f432f5b52cb7f81fbf9a548a1cb89 Author: almgren Date: Fri Aug 25 22:02:25 2006 +0000 Modified the scaling for cross-stencil in 2d and 3d. Gives same answers in 3d as in 2d. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 20b2b422156c05ffc3b81d44fa61de341d5ae824 Author: almgren Date: Fri Aug 25 22:01:55 2006 +0000 This nodal_divu is now called from f90 varden codes as well as from mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit 87c5286bd29924d30b1f3951f08536eb35c06d67 Author: almgren Date: Fri Aug 25 22:01:17 2006 +0000 Turned off special nodal stopping criterion in CG solve. Src/LinearSolvers/F_MG/itsol.f90 commit 34880258a58f2874b82ecd08e368e117c9960c99 Author: lijewski Date: Thu Aug 24 21:11:50 2006 +0000 can now choose # of SwapAndTest() calls Src/C_BaseLib/DistributionMapping.cpp commit e7a2f04432b6ae8e43b4ec14d4c761eff226e4af Author: almgren Date: Thu Aug 24 20:57:24 2006 +0000 New version - also called from fParallel/varden and fParallel/nova_varden_heating... Src/LinearSolvers/F_MG/nodal_divu.f90 commit ee27b5c155795bfb25f7d974d44081fd7271acab Author: lijewski Date: Mon Aug 21 00:29:45 2006 +0000 fixed bug in collectdata with do_alltoallv=1 Src/C_BaseLib/FabArray.H commit e2d8ca4e16e1f8e98b812f6ac6b833150a04df88 Author: lijewski Date: Sat Aug 19 03:47:04 2006 +0000 didn't have caching quite right Src/C_BaseLib/FabArray.H commit 0f586d8225c448a4d98b76f6cd7b67ff40b276cb Author: lijewski Date: Sat Aug 19 03:46:18 2006 +0000 print out Box when numPts() overflows Src/C_BaseLib/Box.cpp commit 62532c6f58de1f2b541dd9f4845f1e19bd6e9d6c Author: almgren Date: Fri Aug 18 22:10:47 2006 +0000 Added the diagonal component to ss(i,j,0) in 2d. Also set the coefficient to zero at a Neumann boundary. Src/LinearSolvers/F_MG/stencil.f90 commit af57bd45c03a3c67b8a99d4f8835d04aa6da2fc4 Author: almgren Date: Fri Aug 18 22:05:44 2006 +0000 Small change in formatting. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 2c015e91318d34b2b07c2ea7d9104db9a5e6aebc Author: almgren Date: Fri Aug 18 22:04:38 2006 +0000 Added "save" to mgts declaration. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit b27255493ad84b79e99c960f05adfd2a62a37041 Author: almgren Date: Fri Aug 18 20:29:01 2006 +0000 New interface for bc's. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit e6a83507078b78310b0e2e795d5de3badc4f68a3 Author: lijewski Date: Wed Aug 16 20:41:32 2006 +0000 can now ParmParse between send/recv & alltoallv in copy & collectdata Src/C_BaseLib/FabArray.H commit 4517971111e6a2c1f5c9ce12bb67cc83e5d815a7 Author: almgren Date: Wed Aug 16 19:53:49 2006 +0000 Added new functionality to do diffusive solves as well as MAC solves. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 3c31db4bbcde9516c309b929d2d203bc37720683 Author: almgren Date: Tue Aug 15 19:17:33 2006 +0000 Remove extra print statements... Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 27555f7f4ae903d87149f9563ba177d25122f8c2 Author: almgren Date: Tue Aug 15 19:16:47 2006 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.f commit a79b262489e66780423c29b42bec8d183eb03617 Author: almgren Date: Tue Aug 15 19:14:18 2006 +0000 Fix definition of nx,ny,nz in grid_divu_3d. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 1276be5b053db0fe46d11a8e45288e1813cbf523 Author: almgren Date: Tue Aug 15 19:13:52 2006 +0000 Modify set_vel_2d... Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit c40f94825ef437ae1beb3c59bf0a878fb7b936b6 Author: almgren Date: Tue Aug 15 19:13:07 2006 +0000 Dont need those print statements... Src/LinearSolvers/F_MG/mg_cpp.f90 commit 75aa1439649cbd2e111d964b0ee2fdb0bbc46d52 Author: lijewski Date: Tue Aug 15 19:10:30 2006 +0000 commented out couple prints Src/LinearSolvers/F_MG/mg_cpp.f90 commit aa7a5b643785bbe56859e875f97eb78e0e5e7042 Author: almgren Date: Tue Aug 15 05:31:44 2006 +0000 Fixed diagnostic statements... Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 46fc9bdac37f1b79487fdfbc6aeeac06259cbe43 Author: almgren Date: Tue Aug 15 05:06:59 2006 +0000 Got it right for 3d nodal... Src/LinearSolvers/F_MG/mg_cpp_f.h commit ef153582855b51229d20cf88695c158df23ee4fa Author: almgren Date: Tue Aug 15 04:40:00 2006 +0000 Fixed typo. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit ef3acc9fff49b89adfb075f0b2e3bef6a59ff378 Author: lijewski Date: Tue Aug 15 02:30:43 2006 +0000 Can now ParmParse whether or not to use alltoallv in copy(). Src/C_BaseLib/FabArray.H commit a18e5ce808ba1aa363437f3ed8f72e067ab9bf98 Author: almgren Date: Tue Aug 15 02:18:18 2006 +0000 Latest version which calls cc and nodal multigrid solvers. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H commit 55a86e5a98743c0dd6251d15f4904bcd387184a6 Author: almgren Date: Tue Aug 15 02:17:52 2006 +0000 Latest version which calls nodal as well as cc multigrid solvers. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 0fc8339d4009903646073bb091896028cc28d065 Author: almgren Date: Tue Aug 15 02:15:51 2006 +0000 Latest stuff to enable cc and nodal multigrid calls from IAMR. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit b6d940a4f625b6579fb5da470923174ef2ba1e94 Author: lijewski Date: Tue Aug 15 01:19:15 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit e03cc0b2109451c261f45237aafc32ba296f24e6 Author: almgren Date: Mon Aug 14 21:15:03 2006 +0000 Remove commented line. Src/LinearSolvers/F_MG/mg.f90 commit 7b47787c941c383bce9d7feaab543aed0b054aa9 Author: almgren Date: Mon Aug 14 20:27:02 2006 +0000 Added new files... Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak commit 1ca5a642681ce0bb271e4e9d702d19f6f5a6ad3e Author: almgren Date: Mon Aug 14 20:26:44 2006 +0000 New routines to handle calls from IAMR. Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 commit e208b35e93b48df2c2c148d4ebee3abf29096cec Author: lijewski Date: Mon Aug 14 20:22:12 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_smoother.f90 commit 9234b48657e385b433b0147d70a9ece032671648 Author: almgren Date: Mon Aug 14 20:07:44 2006 +0000 Make mgt%skewed(nlev,ngrids) a member of mgt instead of calculating every time we call the smoother... Src/LinearSolvers/F_MG/mg.f90 commit 0501215564e27b3ea0e47e7ecdd5f345b4169c18 Author: almgren Date: Mon Aug 14 20:06:49 2006 +0000 Tiny modification in function skewed_q. Src/LinearSolvers/F_MG/stencil.f90 commit 82f3caf54af8b24f6485289e3b0e29048bb39946 Author: almgren Date: Mon Aug 14 18:43:05 2006 +0000 Test on skewed-ness at top of gs_rb_smoother_2d and gs_rb_smoother_3d. Also put dd calculation inside if test in these routines. Src/LinearSolvers/F_MG/mg_smoother.f90 commit caecf99d6c6325139efc442f0be5d848dcec315e Author: lijewski Date: Wed Aug 9 18:00:41 2006 +0000 do NOT do alltoallv() by default Src/F_BaseLib/multifab.f90 commit b2f9da880fd4dbe10c77b9063b00aa4ce598b17f Author: lijewski Date: Wed Aug 9 04:20:14 2006 +0000 merged in nocomm=.true. in copy() & fill_boundary() Src/LinearSolvers/F_MG/sparse_solve.f90 commit 6149f3bf48bd7b8fd58ae9b3a1afb2ef0fae8a55 Author: lijewski Date: Wed Aug 9 04:19:38 2006 +0000 added nocomm flag to fill_boundary & copy Src/F_BaseLib/multifab.f90 commit 90f927d39ac09e6aad774b6044feb781c1d846ea Author: almgren Date: Tue Aug 8 21:21:16 2006 +0000 Add the necessary stuff to construct the sparse solver as a bottom solver. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 4d930e5aad48d87659b91cdb7578c8107f5691ce Author: almgren Date: Tue Aug 8 21:20:48 2006 +0000 If mg.usecg = 0, then make the default be the sparse solver, not relaxations. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit b989a0c141c13a36424b68215a00a820a42646d2 Author: almgren Date: Tue Aug 8 18:31:43 2006 +0000 Modified the verbosity to be more in sync with the multigrid verbosity. Src/LinearSolvers/F_MG/sparse_solve.f90 commit a9eb36a5abbe77c92e769b110ebd6ab415b2f9d8 Author: lijewski Date: Mon Aug 7 18:46:45 2006 +0000 added mgt_init() Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 47f5617e1207fd05333a5a508f2d6be31b8bf21f Author: lijewski Date: Mon Aug 7 18:39:51 2006 +0000 added mgt_init() which balls parallel_initialize() Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 649c5d73c655740b168cd5ad656e2099e0b774b4 Author: lijewski Date: Mon Aug 7 18:23:00 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit 44c9c838f7d6b46fd3e0fdf1354605d08bff89b5 Author: lijewski Date: Mon Aug 7 18:22:45 2006 +0000 only call MPI_Init() if MPI_Initialized() is false Src/F_BaseLib/parallel.f90 commit 2019bc4908533169c64d4fbb7c4cea3a6133ec99 Author: lijewski Date: Fri Aug 4 22:33:01 2006 +0000 removed weird embedded comment Src/F_BaseLib/parallel.f90 commit c2625d83e5bcaac02626726aaea83ae87aa0037e Author: lijewski Date: Fri Aug 4 22:26:57 2006 +0000 moved mpi.f into parallel.f90 Src/F_BaseLib/GPackage.mak Src/F_BaseLib/parallel.f90 commit bd1cfff5a0ba24a23563315a5740f9e521cc9860 Author: lijewski Date: Fri Aug 4 22:26:18 2006 +0000 *** empty log message *** Src/F_BaseLib/mpi.f commit e3e5a55a2ee213bb4727de86e0fde641eb89dc78 Author: lijewski Date: Fri Aug 4 22:25:52 2006 +0000 added save to mgts Src/LinearSolvers/F_MG/mg_cpp.f90 commit b0959ba84f4c25495257e3fa07eb771164e9e09c Author: lijewski Date: Fri Aug 4 22:25:34 2006 +0000 removed mpi.f Src/LinearSolvers/F_MG/FParallelMG.mak commit 610b301692dbfbde1f7a0a0cc4a086550e298487 Author: lijewski Date: Fri Aug 4 22:24:03 2006 +0000 f90 stuff Tools/C_mk/Make.AIX Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 631c92e094c4f8f5f4724b3da94651ab6b3a054d Author: almgren Date: Thu Aug 3 20:35:06 2006 +0000 Improve print statements in itsol... Src/LinearSolvers/F_MG/itsol.f90 commit f415cea2183477070ac639f5bc86145e5813f7d6 Author: almgren Date: Thu Aug 3 19:46:42 2006 +0000 Replaced spacing(Anorm) by epsilon(Anorm)*Anorm to be consistent with itsol_converged. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit c48d8aa5928c42df2d45581673c55db115b1757d Author: almgren Date: Thu Aug 3 18:47:06 2006 +0000 Fixed bug in FORT_NORMA for 3D computation of matrix norm. Src/LinearSolvers/C_CellMG/ABec_3D.F commit feafcc70ed0096444f05b29db39df34caee4e963 Author: almgren Date: Thu Aug 3 18:29:29 2006 +0000 Fixed bug in mgt_set_rh_3d. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 8f2a0ac537bcbda0e33f21b9b75411ac51ece926 Author: almgren Date: Thu Aug 3 18:28:11 2006 +0000 Latest greatest, works in 2d and 3d with periodic/Neumann/Dirichlet. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 80482b5d4ec50bf25933c4494811275242cff9b4 Author: almgren Date: Wed Aug 2 21:42:56 2006 +0000 1) Make consistent with mglib again. 2) Set CG and BiCG bottom solvers so that if (rnorm > bnorm) then return solution = 0. Src/LinearSolvers/F_MG/itsol.f90 commit 6dcd8f676629f5a94c32fd27f4668a41ea1f7c3f Author: almgren Date: Wed Aug 2 21:42:16 2006 +0000 Need to reset "final" parameter at end of use. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 48054fd77fc3260f51edc41d4682065ef50e2067 Author: almgren Date: Wed Aug 2 21:41:58 2006 +0000 Dont print out eps as part of mg_tower since it is set only when solve is called. Src/LinearSolvers/F_MG/mg.f90 commit e05874657d68c57abcadbe4908b5da4cf135b57e Author: almgren Date: Wed Aug 2 21:41:39 2006 +0000 Formatting only...make it look like Parallel/mglib. Src/LinearSolvers/F_MG/ml_cc.f90 commit d06335b925c1f1869e176a4035d2df22adb93612 Author: almgren Date: Wed Aug 2 21:41:00 2006 +0000 Modify CG bottom solver so that if (rnorm > bnorm) at end then return solution = 0. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit eeb576d919e6e091f6fffaea4dc9c63177db6cd2 Author: almgren Date: Wed Aug 2 21:37:31 2006 +0000 1) Make consistent with F90 2) In BiCG bottom solver, if (rnorm > bnorm) at end then return solution = 0. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 4073c0f17bc8ca7b5cc115aac7bb068ab3a81dd9 Author: lijewski Date: Wed Aug 2 21:14:14 2006 +0000 *** empty log message *** Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/ba.25600.REMOVED.git-id Src/C_BaseLib/test/tMinCommCosts.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/ba.25600.REMOVED.git-id Tests/C_BaseLib/tMinCommCosts.cpp commit e307ef1e71fe1d61671415deb0ee5572a056589f Author: lijewski Date: Wed Aug 2 21:13:59 2006 +0000 speedup of SwapAndTest(); also only call it once. Src/C_BaseLib/DistributionMapping.cpp commit c6fa38c64def89d3a9f73b2b7bab8448fbd6118c Author: almgren Date: Wed Aug 2 20:13:06 2006 +0000 1) Make consistent with Parallel/mglib for cell-centered solves. 2) Added nu_b and nu_f... Src/LinearSolvers/F_MG/mg.f90 commit 1421132a63bf5392ce5c893e638de1cf7ad4dc46 Author: almgren Date: Wed Aug 2 20:12:20 2006 +0000 Make the output statements consistent with Parallel/mglib. Src/LinearSolvers/F_MG/ml_cc.f90 commit f56d306fff5000529f548847e6081e207519a0a4 Author: almgren Date: Wed Aug 2 20:10:56 2006 +0000 Allow code to reduce order small grids. Src/LinearSolvers/F_MG/stencil.f90 commit 0c8228c3e5052a788ed27a7d739c663180c59744 Author: almgren Date: Wed Aug 2 20:09:53 2006 +0000 Latest greatest...appears to work. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit a815ee1b791a0553f431fbda126033b556d3d4ad Author: almgren Date: Wed Aug 2 20:09:29 2006 +0000 1) Make the formatting consistent with the Parallel/mglib (cell-centered) solves. 2) Add "0" as an argument to mg_precond in the CG and BiCG solves to be consistent with Parallel/mglib - this does a copy rather than a relaxation as the preconditioner. Src/LinearSolvers/F_MG/itsol.f90 commit cb2a2d233b84f4b3cb5ad615506142a021c6b99d Author: almgren Date: Wed Aug 2 20:07:45 2006 +0000 Match the formatting of output statement with the new F90 code. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit d45359860d4dd80f296fb02a8efaafbf66d2475d Author: almgren Date: Wed Aug 2 20:07:22 2006 +0000 Get rid of numiter as a parameter, and always use the update, even if it was bad... Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 8bd7b103b2b427a58a2f0873c499758492f70dc2 Author: almgren Date: Fri Jul 28 21:29:40 2006 +0000 Latest in getting interface with iamr correct. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 510531c0629140a0f72ee440f4b63a4d16b38040 Author: almgren Date: Fri Jul 28 21:29:09 2006 +0000 Trying to pass the variables correctly. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 0b371f69311a8e510b806c8a02d7ad25347775a7 Author: almgren Date: Thu Jul 27 20:57:17 2006 +0000 Appears to work in conjunction with Parallel/iamrlib and fParallel/mg. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit f40fe74e914a2d7268635f96e42c3323b9f3a175 Author: almgren Date: Thu Jul 27 20:56:50 2006 +0000 Appears to work in conjunction with Parallel/iamrlib. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 202db86e1138e5b4a70fbe83512b5e28fbd27332 Author: lijewski Date: Fri Jul 21 22:16:39 2006 +0000 cfe3 -> cfe Tools/C_mk/Make.defs commit 9287e506a566d6381397fbf4db2bd1782e0ba696 Author: lijewski Date: Thu Jul 20 19:54:39 2006 +0000 comment out timer stuff Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 92bb8767b95a72e0dc2f1a2ad6413b4748a1a9f2 Author: almgren Date: Thu Jul 20 19:17:57 2006 +0000 Replaced cout by std::cout and endl by std::endl Tools/C_util/Convergence/DiffSameGrid.cpp commit 80603ba255fe12445d8618510f246cd7a372522c Author: lijewski Date: Tue Jul 18 03:56:30 2006 +0000 optimization flags for columbia Tools/C_mk/Make.Linux commit df6ea7c3d4aee34fa2c11f06e309fb2332210708 Author: lijewski Date: Tue Jul 18 03:55:34 2006 +0000 turn off a bunch of Intel stuff that doesn't always work Tools/C_mk/Make.defs commit 1ecb58cea9c7af47e4c576462461766bb2c05b4d Author: lijewski Date: Thu Jul 13 21:08:56 2006 +0000 ipo -> ip for Columbia Tools/C_mk/Make.Linux commit c884648d888e46b3d23a7c9bcccf5cf3ee00fc96 Author: lijewski Date: Fri Jul 7 18:23:26 2006 +0000 some modest simplification to AddBox() routines Src/C_BaseLib/FabArray.H commit 9b2b233261dcf3e9514f5ab7fa49e2a69eede14d Author: almgren Date: Thu Jul 6 19:01:45 2006 +0000 Fixed the stencils for stencil_order=3 and Neumann bc's: we can't do higher order with Neumann bc's or we will lose solvability. Src/LinearSolvers/F_MG/stencil.f90 commit 8ee03045dca634876242c290df1529e6281eef9c Author: almgren Date: Wed Jul 5 23:33:35 2006 +0000 Moved ml_norm_inf and ml_norm_l2 into ml_nd.f90 from nodal_multi.f90. Also, ml_norm_l2 was just plain wrong for multiple levels. Src/LinearSolvers/F_MG/ml_nd.f90 commit 950613245d02dfc610e6f0ee80a997855d05092d Author: almgren Date: Wed Jul 5 23:29:02 2006 +0000 Moved ml_norm_inf and ml_norm_l2 into ml_cc and no longer have separate copies in cc_multi. Also made the L2 norm do the right thing - it was wrong for multilevel before. Src/LinearSolvers/F_MG/ml_cc.f90 commit 66c4e384ae4cd3f003fb6478c718089bbd7659e2 Author: almgren Date: Wed Jul 5 22:43:01 2006 +0000 bs() around quantities in convergence test *** IN BICGSOLVE ***. (PREVIOUSLY ONLY PUT IN CGSOLVE) Src/LinearSolvers/F_MG/itsol.f90 commit 11d505d6a2e2bbb41816ee67635d0958a1c08c7e Author: lijewski Date: Wed Jun 28 21:07:43 2006 +0000 finally got bndry_reg_rr_build_1() correct? Src/F_BaseLib/bndry_reg.f90 commit 5229488a0a8347812a01e1e351a2420da4b65d7f Author: lijewski Date: Wed Jun 28 16:19:13 2006 +0000 call some fill_boundary()s with cross flag Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 96aa51aba471e3347cbd66eb6ffa90984657c863 Author: lijewski Date: Tue Jun 27 20:24:52 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_smoother.f90 commit 62ed59d86b1ca8860bdf8940f91cd5246d636590 Author: lijewski Date: Tue Jun 27 19:45:04 2006 +0000 cross stuff now appears to work Src/F_BaseLib/layout.f90 commit 7fd51afc3fef4a44e17509d2c32eae7d603963f7 Author: almgren Date: Tue Jun 27 17:30:28 2006 +0000 Put in 21-point stencil option for case where dense but all the dh the same. Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 018f2561dc3f8907db6a03d274c664cd8f13010c Author: almgren Date: Mon Jun 26 21:00:27 2006 +0000 Nodal cross (5pt) stencil now works adaptively Src/LinearSolvers/F_MG/ml_nd.f90 commit ad43a3da305ad5dcd0b2774a05a5bf628bd49d1a Author: almgren Date: Mon Jun 26 21:00:05 2006 +0000 Nodal cross (5pt) stencil now works adaptively... Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 507e44b07976065af1f90303b5262d2d4f49937e Author: lijewski Date: Sat Jun 24 00:00:14 2006 +0000 Uniform DH optimization for nodal_smoother_3d, stencil_apply_3d_nodal & grid_laplace_3d Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 247fde4fba3385639f92b87b55c00619dbb764ad Author: car Date: Fri Jun 23 20:26:51 2006 +0000 tweaked interface to c++/fortran solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 65420a55bfda3170d9bc1e8b0ae8c616a9b5309a Author: almgren Date: Fri Jun 23 18:59:32 2006 +0000 New code for 5-point nodal stencil in 2d. 5-point doesn't work yet but 9-point does still work. Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit f7aae023a57c3f8ad7a3ec6f5162abbff1624544 Author: lijewski Date: Thu Jun 22 22:15:46 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_smoother.f90 commit 07a7e3d30b057e8af91d69107b510e57f20837f6 Author: almgren Date: Thu Jun 22 21:37:01 2006 +0000 Now has capability for 7-point (3d cross) nodal stencil. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 8a86094b89000ad3b9eb5507401705dfea53ca98 Author: almgren Date: Thu Jun 22 21:30:59 2006 +0000 Now has capability for 7-point (cross stencil in 3d) Src/LinearSolvers/F_MG/stencil_nodal.f90 commit bfc9691041ee6c9367e0aa788f096a994fb8419a Author: car Date: Thu Jun 22 19:28:13 2006 +0000 closer Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit afae81b712a8405949753ba7ddf450d8bcc0107f Author: car Date: Thu Jun 22 19:27:37 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 5f75b8c2174323da21a6e95df34a7d9d1d97b42a Author: car Date: Thu Jun 22 19:27:26 2006 +0000 stop using optional unit Src/F_BaseLib/layout.f90 commit cd70bc0f04aa2c2579f277b474487fbce766a95f Author: almgren Date: Thu Jun 22 02:37:12 2006 +0000 Fix calling sequence for first subroutine. Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 88dcdbd4ef431269b9eae2cdf70011116e32d6e6 Author: car Date: Wed Jun 21 22:52:15 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_cpp.f90 commit 6e6e18af71aef142e4d1ccb576c1533ca604ba16 Author: car Date: Wed Jun 21 20:58:25 2006 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 10227526f67b4cc4e3f138c628f2232a2b5db247 Author: lijewski Date: Wed Jun 21 17:40:12 2006 +0000 mods for cfe3 Tools/F_mk/GMakeMPI.mak commit 2650e937eb2a4fb1339a42b963b844d71e69744a Author: lijewski Date: Tue Jun 20 19:36:38 2006 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 22f203ec842100ce55828a76897463bfa12b9130 Author: car Date: Tue Jun 20 16:42:03 2006 +0000 changes for c++/f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_nd.f90 Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp Tools/C_mk/Make.defs commit 5ba13aade4625b1c87df8630521504d4a1f0838c Author: almgren Date: Tue Jun 20 06:50:14 2006 +0000 Put abs() around quantities in convergence test. Src/LinearSolvers/F_MG/itsol.f90 commit 467adf7a1a88beabe2ea46154700ee1342f4a9bf Author: lijewski Date: Mon Jun 19 21:06:57 2006 +0000 removed ml_crse_contrib_easy() Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit b72339bc0abd70d7b4d416a8980fb2e729e0ba94 Author: lijewski Date: Fri Jun 16 22:08:13 2006 +0000 -Ofast => -O2 for PathScale Tools/F_mk/GMakedefs.mak commit 6e1ef31ab569f198ff3392eb7d28fcf2ed12ba00 Author: lijewski Date: Fri Jun 16 21:24:35 2006 +0000 *** empty log message *** Src/F_BaseLib/layout.f90 commit 92e514b1e7995ef2484c25ebbb17da2903bfb577 Author: lijewski Date: Fri Jun 16 20:57:52 2006 +0000 fixed bug in fluxassoc_build Src/F_BaseLib/layout.f90 commit 7040520c6ca22c21da97ac877f10c749f367080a Author: lijewski Date: Thu Jun 15 21:44:40 2006 +0000 sped up fluxassoc_build & copyassoc_build Src/F_BaseLib/layout.f90 commit cb55057a77cfba7053e2a90abcefd64730e18ce5 Author: lijewski Date: Thu Jun 15 20:34:10 2006 +0000 removed all 'easy' functions Src/F_BaseLib/multifab.f90 commit 1665e410ea6b17fbbbc1d13701922bb215cb4e1b Author: lijewski Date: Thu Jun 15 18:12:09 2006 +0000 added cpy_? functions taking filter arg Src/F_BaseLib/multifab.f90 commit a24aa43aaf77b7ab2c0af93123c8eb227103f749 Author: lijewski Date: Thu Jun 15 17:35:57 2006 +0000 Made most communications alltoall. Got rid of all reshape() calls. Src/F_BaseLib/multifab.f90 commit a19a968f87ed80a844ace776369cccfa67f28b2f Author: lijewski Date: Wed Jun 14 22:13:12 2006 +0000 PGI fixes Src/F_BaseLib/layout.f90 commit fe14cba43b03e403eb5a024f024ae23ac37e7390 Author: lijewski Date: Wed Jun 14 22:06:59 2006 +0000 fixes for PGI Src/F_BaseLib/knapsack.f90 commit 31c98ae6ce9a69344e1d6ffb62bfcd40c797a3db Author: lijewski Date: Wed Jun 14 20:55:54 2006 +0000 PGI mods Tools/F_mk/GMakedefs.mak commit 99d552e536a0e2b4108167df8735143cb8b93d36 Author: lijewski Date: Tue Jun 13 22:20:29 2006 +0000 initial cut at XT3 (catamount) Tools/F_mk/GMakedefs.mak commit a3ba97505c2f4fe3f381c6d7b3f8f7335803b2de Author: lijewski Date: Tue Jun 13 22:19:31 2006 +0000 fixes for jaguar (XT3) Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/sort_box.f90 commit 77c45689c1cdc9f7b41a4aba243e0f31fee68a62 Author: lijewski Date: Tue Jun 13 20:45:46 2006 +0000 sped up boxassoc_build Src/F_BaseLib/layout.f90 commit eed0c191e2677c0b8c42503a11962e659cb42676 Author: lijewski Date: Tue Jun 13 18:23:29 2006 +0000 speed up of unique_cover Src/F_BaseLib/layout.f90 commit 3a58b120eb98f1b69103e6d2ed407425a9db58f2 Author: lijewski Date: Tue Jun 13 18:00:48 2006 +0000 added optional sort arg to boxarray_build_l Src/F_BaseLib/boxarray.f90 commit 67da161ae0932e7a7f6a8363ccfeda9aa539efd3 Author: lijewski Date: Tue Jun 13 18:00:10 2006 +0000 *** empty log message *** Src/F_BaseLib/bndry_reg.f90 commit 693149c9a64b43a74b533ab444a4974e35649a2e Author: car Date: Tue Jun 13 17:07:10 2006 +0000 test of knapsack Src/F_BaseLib/test/ball_def.14656 Tests/F_BaseLib/ball_def.14656 commit 00195651789346dda381e36b779fb53f5e88313e Author: car Date: Tue Jun 13 16:46:20 2006 +0000 changes for c++/fortran Src/F_BaseLib/ml_layout.f90 Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 18bfb126aa36a6f25db3bd971078b0cc85710a84 Author: car Date: Tue Jun 13 16:46:04 2006 +0000 changes for fortran/c++ Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 commit 646447d0fd21d3b36b40af65c35071904429db79 Author: lijewski Date: Tue Jun 13 16:39:56 2006 +0000 speed up to build_1 Src/F_BaseLib/bndry_reg.f90 commit 32d74b08adf6bb8d16a019a8b23ffb8c3f1709c6 Author: lijewski Date: Tue Jun 13 15:41:28 2006 +0000 bug fix for hash stuff Src/F_BaseLib/layout.f90 commit 638e6e97f62cccde3b321d6f8efc0e2f1a509869 Author: lijewski Date: Tue Jun 13 03:43:51 2006 +0000 added more timers Src/F_BaseLib/bndry_reg.f90 commit b079894f444b1b21c46bc4d179102a14ca50d0ed Author: lijewski Date: Mon Jun 12 23:25:48 2006 +0000 check (a hack) that call trees are the same across CPUs Src/F_BaseLib/bl_prof.f90 commit f4ef4669b28d7f473f01c28f5ec2be66fa5b5dc2 Author: lijewski Date: Mon Jun 12 22:32:03 2006 +0000 *** empty log message *** Src/F_BaseLib/bl_timer.f90 commit a93974716d08f5fad7a606753ea762af818630cc Author: lijewski Date: Mon Jun 12 22:31:42 2006 +0000 removed ba_bndry_periodic timer Src/F_BaseLib/layout.f90 commit 606c3ca433180060e1826a931847b768f2a11c3a Author: lijewski Date: Mon Jun 12 21:04:10 2006 +0000 commented out private statement Src/F_BaseLib/bl_timer.f90 commit 41d2f719dc90db02063d50adced1ed464e62e777 Author: lijewski Date: Mon Jun 12 17:14:14 2006 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp commit 2b15da424cf2dd4386ab95191508262ef5ee15aa Author: almgren Date: Fri Jun 9 23:06:00 2006 +0000 1) added construction of singular flag 2) added two relaxations at bottom level after the CG solver is called (to match results of Parallel/hgproj code) Src/LinearSolvers/F_MG/mg.f90 commit b9b604ada0f69d0d01457a88fa058d03de84b491 Author: almgren Date: Fri Jun 9 22:34:19 2006 +0000 Modify the CG and BiCG solvers to take a flag which says if the problem is singular. If true, then subtract off the average of the RHS from each value of the residual to make it solvable. The flag is optional. Src/LinearSolvers/F_MG/itsol.f90 commit 8493da246154a8c642780c0b57fbf296eaa8fc56 Author: almgren Date: Fri Jun 9 22:32:50 2006 +0000 In the multilevel convergence test, we were incorrectly computing the residual on the coarsest level if there were more than two levels, because the level 1 residual was averaged down to level 0 before the coarse-fine corrections (from the level 1-2 interface) were used to modify the level 1 residual. This is now fixed. Src/LinearSolvers/F_MG/ml_nd.f90 commit 51efb1261198cfe00bcaac56436677eaee0870ec Author: almgren Date: Thu Jun 8 20:53:12 2006 +0000 This file is a simpler case than gtbig3 of a case that breaks the Parallel/hgproj 3-d 27-point (dense) solver - the solver will not converge because values of the solution on different grids are different. Src/LinearSolvers/C_NodalMG/gt_breaks_27pt commit 9d72ebd5705e72dbe9987ca3f08f13589d55f09d Author: lijewski Date: Wed Jun 7 22:15:40 2006 +0000 added verbose flag Src/F_BaseLib/layout.f90 commit df8194721c8b6d4fd1c1219833400167b57c52c3 Author: lijewski Date: Wed Jun 7 22:15:10 2006 +0000 removed nocomm stuff Src/F_BaseLib/multifab.f90 commit 978642b738ea8549c902d5a9271aa1a55e2e48ca Author: lijewski Date: Wed Jun 7 19:33:11 2006 +0000 cleanup & simplification Src/F_BaseLib/multifab.f90 commit c1c5d29f54b1b50de219d197e7cd8aba6efb99fe Author: lijewski Date: Tue Jun 6 21:53:33 2006 +0000 cache stuff for ml_crse_contrib Src/F_BaseLib/layout.f90 commit 6609cb5778b245807a39270c285c0a06d0736842 Author: lijewski Date: Tue Jun 6 21:53:18 2006 +0000 stubs for alltoall for integer & logicals Src/F_BaseLib/parallel_stubs.f90 commit 329cec038762ce6c2b304779e62b7d7aef7e480c Author: lijewski Date: Tue Jun 6 21:52:53 2006 +0000 ml_crse_contrib() now goes fast in parallel Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit f555d9c6b3964728175df11587aec42178cf2bad Author: lijewski Date: Mon Jun 5 21:39:51 2006 +0000 added alltoall() for integer data Src/F_BaseLib/parallel.f90 commit 79cad7e57f2f0e6258b79ca564dbacbce6945658 Author: car Date: Mon Jun 5 21:25:15 2006 +0000 pointer, intent conflict Src/F_BaseLib/layout.f90 commit fa06b6ab4c79ca9ab4883bf1422f0b9414b1d57f Author: lijewski Date: Sat Jun 3 02:27:43 2006 +0000 tiny bit of cleanup Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 5f44845888628aaad05e79fea4ea1f121d90aad4 Author: lijewski Date: Fri Jun 2 16:35:49 2006 +0000 little cleanup Src/F_BaseLib/bndry_reg.f90 commit aa409ed8e59db133c328b2b3230a6c4e0d220d20 Author: lijewski Date: Thu Jun 1 22:23:37 2006 +0000 fast parallel internal_sync Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 commit d609649c3aee9da070c720cf4fc9ea0e8697a500 Author: lijewski Date: Thu Jun 1 22:23:20 2006 +0000 added alltoall()s for MPI_LOGICAL Src/F_BaseLib/parallel.f90 commit 0f838fdc6b6cc8ac59a86954e4f6facb9d0c4824 Author: lijewski Date: Thu Jun 1 20:18:58 2006 +0000 made a private member public Src/F_BaseLib/boxarray.f90 commit 2a0a673480bb6d32cd04c6addf0fb19209d72c2a Author: lijewski Date: Wed May 31 20:42:49 2006 +0000 AIX mods Tools/F_mk/GMakedefs.mak commit 7efa4b51436756c4b6eea18e7eb4268fb5d7289b Author: lijewski Date: Wed May 31 20:16:49 2006 +0000 tad simplification Src/LinearSolvers/F_MG/ml_restriction.f90 commit 096a90c4f827327c85cc7115e40811d90b6cdff4 Author: lijewski Date: Wed May 31 20:14:45 2006 +0000 some simplification Src/F_BaseLib/box.f90 Src/F_BaseLib/layout.f90 commit d344d662ccbebdb7862a5331139665bc8c069df5 Author: lijewski Date: Tue May 30 23:47:55 2006 +0000 some cleanup Src/F_BaseLib/box.f90 Src/F_BaseLib/multifab.f90 commit e54facbafcdd7d896830dc874beeca66b13bb0ce Author: lijewski Date: Tue May 30 20:07:52 2006 +0000 more speedups to stencil_nodal_fill Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 61895a68b865b73c61150153f060e607441519f8 Author: lijewski Date: Tue May 30 20:05:43 2006 +0000 Added timer to add_clean(). Also added optional argument to turn off calling simplify(). Src/F_BaseLib/boxarray.f90 commit e3aad032d3c4eab045119b42755eeba443d26863 Author: lijewski Date: Tue May 30 17:47:44 2006 +0000 added timer to boxarray_add_clean Src/F_BaseLib/boxarray.f90 commit c65b293f816e998e7b8ebd16ff5ed6f34069cd31 Author: lijewski Date: Tue May 30 17:47:23 2006 +0000 sped up stencil_fill_nodal for periodic Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 32f62a487db0aa3cd96757e1362dea11321761e9 Author: lijewski Date: Sat May 27 17:59:24 2006 +0000 memory management cleanup; expanded copy_sum() Src/LinearSolvers/F_MG/ml_restriction.f90 commit f99fc856b0847599db79145e5ccf125e6193b063 Author: lijewski Date: Sat May 27 05:12:00 2006 +0000 remove dull_copy_d(); use cpy_d(); more remote()s Src/F_BaseLib/multifab.f90 commit 85808ed052aec393d68b2d8903ab51ce90bf7292 Author: lijewski Date: Sat May 27 04:25:05 2006 +0000 added remote() cycle to internal_sync() Src/F_BaseLib/multifab.f90 commit 4b02d86e5b8b7881b74ae4b0dbc1a0e5ce1096a6 Author: lijewski Date: Sat May 27 03:44:25 2006 +0000 added timer to internal_sync Src/F_BaseLib/multifab.f90 commit 03ef6a999a873f273cc9d55c25516d177e732905 Author: lijewski Date: Fri May 26 23:39:18 2006 +0000 added timers Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 3cbee8f52f046e69f7e917215a6fa22fe6c278f4 Author: lijewski Date: Fri May 26 23:20:55 2006 +0000 added a remote() cycle test Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit cfeeb4e9b99fbc29635e7abc79298f20f7aa1341 Author: lijewski Date: Fri May 26 23:20:25 2006 +0000 moved fill_boundary() around Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit 5bfe34320cf661a6600d909d39c2ff4918d58609 Author: car Date: Fri May 26 22:41:37 2006 +0000 don't grow for obmf Src/F_BaseLib/bndry_reg.f90 commit 56cc9d5216b715615b23aa580339c91e11a059d0 Author: lijewski Date: Fri May 26 20:42:44 2006 +0000 changed name of timer Src/F_BaseLib/layout.f90 commit 158015bba2f4c76a63da8a7f271eac7bd004f638 Author: almgren Date: Fri May 26 19:23:21 2006 +0000 Fixed bug in indexing in nodal_restriction_3d (ONLY 3D). Src/LinearSolvers/F_MG/mg_restriction.f90 commit 67aa827a2893d706ca4029fe97ca2fae91e8bb20 Author: lijewski Date: Fri May 26 18:23:43 2006 +0000 removed async stuff & added timers Src/F_BaseLib/multifab.f90 commit b7764f6d229c0ac5e01b17940173e276bfcd7706 Author: lijewski Date: Fri May 26 18:23:16 2006 +0000 added some timers Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 0c0dcf9ebca67c73dcc9912968c82425c6881013 Author: car Date: Fri May 26 18:11:14 2006 +0000 unused variable Src/C_BaseLib/ParmParse.cpp commit 7cb9a765b3661e69d42d46f330c281f5e99d59f3 Author: lijewski Date: Thu May 25 21:50:26 2006 +0000 merged periodic_add_copy()s Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit def5e06def4416f6b4de6ed4e39be8f44c4f8ad0 Author: almgren Date: Thu May 25 20:11:41 2006 +0000 We need to have two different periodic_add_copy routines, depending on whether the multifab src is already synced up at overlapping nodes. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit a19ab9f8aea0cb257a5d8c77acb74b062fa8d594 Author: lijewski Date: Thu May 25 19:19:51 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit 86d186cb44e03a698b22615f83a76b5fe31a0761 Author: lijewski Date: Tue May 23 23:00:33 2006 +0000 parallelized periodic_add_copy() Src/LinearSolvers/F_MG/ml_restriction.f90 commit 7961fa5ab1528b4b1454fbd3e24d42edc8a18df7 Author: almgren Date: Tue May 23 21:36:45 2006 +0000 Got rid of other call to periodic_add_copy(mf); now both places use version in ml_interface_stencil: periodic_add_copy(dest,src) Src/LinearSolvers/F_MG/ml_nd.f90 commit 548c11873def9439ae1614a8acf49b6e444cbe80 Author: almgren Date: Tue May 23 21:31:51 2006 +0000 This is the correct calling sequence for ml_restriction now that a periodic_add_copy has been put into ml_nodal_restriction Src/LinearSolvers/F_MG/ml_nd.f90 commit 444830c4c84a84a66e891875eaeecc13f3283e15 Author: almgren Date: Tue May 23 21:25:44 2006 +0000 Replace destroy by bl_prof_destroy... Src/LinearSolvers/F_MG/mg.f90 commit 12fadcbd91d8ac6332e0136bdcadae7fe99afd44 Author: lijewski Date: Tue May 23 18:03:38 2006 +0000 appears to work in parallel for 2D & no periodic Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 3ad68d16220ca900ae96ccbeb4e71ff8db3a861c Author: lijewski Date: Tue May 23 04:40:22 2006 +0000 some cleanup Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 6e4fc488095191d2773ce71eae425dd137e8202a Author: lijewski Date: Mon May 22 23:20:52 2006 +0000 intent(out) -> intent(inout) Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 3e832d67001de52b47640bf972ac42762002816e Author: lijewski Date: Mon May 22 23:20:05 2006 +0000 wasn't quite right Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 0e8ec7da061630571beead9df3f8dc8078539121 Author: lijewski Date: Mon May 22 23:19:20 2006 +0000 do need to use build_1 Src/LinearSolvers/F_MG/ml_nd.f90 commit fb1196a8bd62b4fcffc700540be8f04dac8499b8 Author: lijewski Date: Mon May 22 20:48:03 2006 +0000 some cleanup Src/LinearSolvers/F_MG/ml_nd.f90 commit fb352d2ee291e8b45a162dab85f077c4599cb3e0 Author: almgren Date: Mon May 22 20:42:53 2006 +0000 Moved periodic_add_copy functionality from ml_nd into ml_restriction for first call anyway...will still need to deal with 2nd call to periodic_add_copy... Src/LinearSolvers/F_MG/ml_restriction.f90 commit 103235da3f822ef267fc9f87902641d55bc1f295 Author: lijewski Date: Mon May 22 20:37:42 2006 +0000 think I got ml_crse_contrib() parallelized Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 1f97df528a68c290383155035552cb2909f416dd Author: lijewski Date: Mon May 22 17:19:21 2006 +0000 some cleanup; not yet parallel-ready Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit b7752562b5f082896291b805b5648bea2d2c770b Author: lijewski Date: Mon May 22 17:03:22 2006 +0000 added neede boxarray_destroy() Src/LinearSolvers/F_MG/stencil_nodal.f90 commit d12b38420a5dffd842acb74c4cbfb67e6e651cee Author: lijewski Date: Sat May 20 00:56:58 2006 +0000 slight rearrangment of code; not yet parallel-ready Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit b2adf0410a64d75b6f13205a9bdff50c978e60ab Author: almgren Date: Fri May 19 21:40:08 2006 +0000 Need another box_nodalize in the counting part... Src/F_BaseLib/bndry_reg.f90 commit 478777d0d55339d9ab58f3cc27e72cf84987e1f3 Author: almgren Date: Fri May 19 18:22:19 2006 +0000 Make sure to box_nodalize inside bndry_reg_build_1. Src/F_BaseLib/bndry_reg.f90 commit 54e48643e75fdbab55f7056cf5c8f2a4fe64fe72 Author: vince Date: Fri May 19 00:14:09 2006 +0000 fixed '>' sign. Src/C_AMRLib/INTERP_3D.F commit 9b403570bc3eccf504e0114271a0e22e3c6ec34d Author: car Date: Thu May 18 21:15:24 2006 +0000 mgt_solver suppt Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit 7b4c8a56de9d72b18157f5c38dcb465f34c4a026 Author: car Date: Thu May 18 21:14:49 2006 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/C_to_F_MG/Make.package commit 9552e7f34a1d1fbe0d638e3bfacff157ad18d999 Author: vince Date: Wed May 17 21:34:13 2006 +0000 gatherv fix for romulus. Src/C_AMRLib/Amr.cpp commit b6517ed94adc062100e97060b3b31b2e91dcaacb Author: almgren Date: Wed May 17 19:53:40 2006 +0000 Necessary corrections to handle periodic bcs. This has been tested for all combinations of bc's with grids in data/hgproj_grids. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 6c9709d2562a987998762a319192cdc8d6b7d1ae Author: lijewski Date: Tue May 16 22:28:37 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_nd.f90 commit b7c5543f4a6ad32871906a957e57f91f16cb1b22 Author: lijewski Date: Tue May 16 21:50:21 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_nd.f90 commit 50d7fe66f205915ac1d6893df3dea39ae6c43190 Author: almgren Date: Tue May 16 21:24:54 2006 +0000 Cosmetic changes only, I think. Src/LinearSolvers/F_MG/mg_restriction.f90 commit c3463354fe54d115c7667f09fa72ec705001301e Author: almgren Date: Tue May 16 21:21:59 2006 +0000 Changes necessary for periodic Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 848d994ef3d359d30f3e425212831212edb1674e Author: lijewski Date: Tue May 16 21:17:59 2006 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit cb474db0005c216076eb30bdd4b0969ab69a7398 Author: almgren Date: Tue May 16 21:04:58 2006 +0000 Changes needed for periodic algorithm. Src/LinearSolvers/F_MG/ml_restriction.f90 commit 7f413cc3d0477435af5c2cdf8eb5028513852ab0 Author: almgren Date: Tue May 16 21:03:14 2006 +0000 Needed correction for periodic. Src/LinearSolvers/F_MG/ml_util.f90 commit bffcfbbfa249571c1f729329e4baa8a999bc86d1 Author: car Date: Mon May 15 21:10:35 2006 +0000 a print function Src/F_BaseLib/ml_layout.f90 commit 10b4116c0d52f129f426ebfebc5c51f8bf17b9c6 Author: car Date: Fri May 12 23:01:24 2006 +0000 needed Src/F_BaseLib/test/t_bl_prof.f90 Tests/F_BaseLib/t_bl_prof.f90 commit e9645b68277850c0b0f5dfa824d1d63e18377325 Author: car Date: Fri May 12 23:01:14 2006 +0000 some parallel support Src/F_BaseLib/bndry_reg.f90 commit 9756b8a96aaa2c61f44fbb5d9476b6a5b5546e37 Author: car Date: Fri May 12 23:01:05 2006 +0000 extra printouts Src/F_BaseLib/layout.f90 commit 72b20b3050f634c5a8d2393477ff0a555b77aba0 Author: car Date: Fri May 12 23:00:48 2006 +0000 should use bnd reg for flux reg Src/F_BaseLib/GPackage.mak Src/F_BaseLib/flux_reg.f90 commit 1d3b3e5ff356fe35d276172afdf2f43b1f17fe09 Author: car Date: Fri May 12 23:00:15 2006 +0000 nil Src/F_BaseLib/flux_reg.f90 commit be7e311976f4b75a317bf85cf7dcc9d3035143f0 Author: car Date: Fri May 12 22:59:38 2006 +0000 accomadate bug in ifort 9.1 Src/F_BaseLib/box.f90 commit 74e4724f90bdc8e627de408ec188d321bfe90b1c Author: car Date: Fri May 12 22:58:46 2006 +0000 changes for cc ml parallel Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit 51a1a96ec9c975ec3cb27ef1b1e9c719ef560c9c Author: lijewski Date: Thu May 11 21:22:31 2006 +0000 yet another bug fix to Gatherv stuff for Hdr Src/C_BaseLib/VisMF.cpp commit 48f4d01d4f7921ef36203c51e5a6d77fbc02ef2e Author: car Date: Wed May 10 18:02:35 2006 +0000 appears that -lguide is not needed in intel link Tools/C_mk/Make.defs commit 217c196d92886f6c98ddd7a397a4fe0900abf8bd Author: car Date: Wed May 10 17:47:55 2006 +0000 maybe a better way to find ifort libraries Tools/C_mk/Make.defs commit e26ee509765651b58443812962e9e000c90d5aca Author: lijewski Date: Mon May 8 22:07:45 2006 +0000 *** empty log message *** Tools/C_util/dbgTools/GNUmakefile Tools/C_util/dbgTools/crsGrids.cpp commit a5f0e572bce12cbde2589cd9b11ec2bd65745589 Author: lijewski Date: Mon May 8 21:59:46 2006 +0000 *** empty log message *** Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/GNUmakefile Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit b2c76362d57d7c236761c22b682272eeca2dd890 Author: lijewski Date: Mon May 8 21:41:33 2006 +0000 *** empty log message *** Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/GNUmakefile commit aef9d43511ec9c07bacb8618ebd6aa13c2a7f5e7 Author: lijewski Date: Fri May 5 18:50:42 2006 +0000 replaced use of std::pow() with D_TERM() Src/C_AMRLib/Interpolater.cpp commit 65196d259986dbe2657c1a5b544de7e88bdcdca5 Author: lijewski Date: Thu May 4 20:07:51 2006 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/grids.213 Src/LinearSolvers/C_CellMG/Test/grids/grids.5034 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034 Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/grids/grids.213 Tests/LinearSolvers/C_CellMG/grids/grids.5034 Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 Tests/LinearSolvers/C_CellMG/main.cpp commit 0090ac0d89716b58053dea0ef00f60f6ef54d241 Author: sepp Date: Thu May 4 19:57:30 2006 +0000 1) to Make.defs, added 2 JFG comments in which CAR explains what changes must be done to run on hive 2) to Make.mpi, added 1 JFG comment pointing out an ifeq block that CAR added to run on hive Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 5ba6767cd65545ce1f5c2d60408e4b89fa823a6f Author: lijewski Date: Wed May 3 18:19:29 2006 +0000 removed length limit on tokens Src/C_BaseLib/ParmParse.cpp commit e925b832695aaf6682ab4b86cfdf6c6b013dfe94 Author: lijewski Date: Tue May 2 21:25:33 2006 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit 47a648ca88e5287c5828cb3b0905fd6764870f96 Author: car Date: Tue May 2 18:41:38 2006 +0000 *** empty log message *** Src/C_BaseLib/SPECIALIZE_1D.F commit e0c0f65c212da0c78c6752b561b552451962bdc1 Author: lijewski Date: Tue May 2 18:01:15 2006 +0000 no Src/C_AMRLib/INTERP_1D.F commit 83adf111b5e0cc4305406ede7fee8905c6b8889d Author: lijewski Date: Tue May 2 16:47:05 2006 +0000 from Greeno Src/C_AMRLib/ARRAYLIM_1D.F Src/C_AMRLib/SLABSTAT_1D.F commit 14eca6e946aab21cf8b8afe9e655d2d9d9ffba02 Author: lijewski Date: Tue May 2 16:39:25 2006 +0000 removed some BL_LANG_CC stuff Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Utility.H commit c253fb635c00d105d734156a2af66b72e85d7277 Author: lijewski Date: Mon May 1 20:26:34 2006 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp commit 88c22c5c4c894920963ee17f2fc281b61775f1bb Author: lijewski Date: Mon May 1 19:19:13 2006 +0000 up from 200 to 100000 to accomodate long material_input entries in geodyne Src/C_BaseLib/ParmParse.cpp commit 58c6ae8b5cdf7dc0ad9a25e67ac604e60566409c Author: car Date: Mon May 1 19:19:12 2006 +0000 not sure i'll need this Tests/LinearSolvers/F_MG/bc_interp.f90 commit 5e5a474fce0d48b24f794357e3fb2f3a0e7f30b5 Author: lijewski Date: Thu Apr 27 21:22:01 2006 +0000 bug fix Src/C_BaseLib/FabArray.H commit a9463b0b819e0ec0d5f551895a52549a3432c7d0 Author: car Date: Thu Apr 27 21:03:08 2006 +0000 gfortran bug work-around Src/F_BaseLib/list_box.f90 commit b487b57e73b00e436545aa1061e091eb7a4ea75f Author: car Date: Thu Apr 27 21:02:33 2006 +0000 discriminate between -pg and BL_PROF Tools/F_mk/GMakedefs.mak commit 5322adf7ee816f580b8b5b720e7d123d6c063ff6 Author: car Date: Thu Apr 27 21:00:26 2006 +0000 no overhead when not profiling Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_prof_stubs.f90 commit bac15b74d7cf8abeee3faf306d7fb93fc967f32e Author: lijewski Date: Mon Apr 24 22:36:31 2006 +0000 more tweaks to CollectData() Src/C_BaseLib/FabArray.H commit 165f82c97eafe946f738df9f708f651db2e86bf9 Author: lijewski Date: Mon Apr 24 21:11:03 2006 +0000 added #ifdef BL_MPI ... #endif Src/C_BaseLib/FabArray.H commit 02ad77896050bc3bdf1eb4289d9d5dd1d5a11a0c Author: lijewski Date: Mon Apr 24 17:27:49 2006 +0000 now uses MPI group operations Src/C_AMRLib/FluxRegister.cpp commit c774a48255f53bbe7c5760d4bea9f19c6e41508c Author: car Date: Fri Apr 21 20:16:57 2006 +0000 parallel safe printing Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit dddec892de8aae79b6a0d6b6c762b7b1d9bf84ca Author: lijewski Date: Thu Apr 20 20:15:38 2006 +0000 slight tweak to CollectData() Src/C_BaseLib/FabArray.H commit f9bc6476cc76b90103fb180f0f56d991ed39e18e Author: lijewski Date: Thu Apr 20 18:21:41 2006 +0000 now use group communication protocols in CollectData() Src/C_BaseLib/FabArray.H commit 25ff108ec49fc9cd13b4a2e1379c968b07416a9b Author: lijewski Date: Wed Apr 19 04:30:29 2006 +0000 substituted alltoallv() for send()/recv() in ::copy() Src/C_BaseLib/FabArray.H commit 05a0ae0ddc4b28e8b2ba5323dd5feb2faca9b764 Author: lijewski Date: Tue Apr 18 23:19:55 2006 +0000 wrapped Gatherv()s in BL_MPI_REQUIRE Src/C_BaseLib/VisMF.cpp commit d5ec6b704be9db5fdd7a663e7305950eb77cf658 Author: lijewski Date: Sat Apr 8 00:01:42 2006 +0000 use MPI_Gatherv() in VisMF::Write() Src/C_BaseLib/VisMF.cpp commit 3c5809db1a26ec899f5d66c64e672824de2417d6 Author: lijewski Date: Fri Apr 7 20:51:59 2006 +0000 use gatherv() instead of send()/recv() for Header build Src/C_BaseLib/VisMF.cpp commit 6b298c76e4b31d6077e21c6be3c92796e9664040 Author: car Date: Thu Apr 6 13:52:53 2006 +0000 reformat Src/F_BaseLib/ml_multifab.f90 commit 9879be386b5f8dcb2b67a8e6bbb4ffb40d7a41e4 Author: car Date: Thu Apr 6 13:52:23 2006 +0000 lall needed to protect all Src/F_BaseLib/multifab.f90 commit 4520a1cfbc724a910989634f3924e0c6bd3ec50e Author: almgren Date: Tue Apr 4 20:15:51 2006 +0000 Made same fixes for 3d as well. Src/LinearSolvers/F_MG/mg_smoother.f90 commit aa2ee478fec7e0664bedb4d4d4c15654c3cf260d Author: almgren Date: Tue Apr 4 20:11:14 2006 +0000 Fix to bug in gs_rb_smoother_2d which caused crash at lowest MG level in non-square grid. Src/LinearSolvers/F_MG/mg_smoother.f90 commit b459194a40c440c6beba8163404a002ab4f364a7 Author: marc Date: Fri Mar 31 22:27:35 2006 +0000 reduce precision Src/C_AMRLib/Amr.cpp commit 94612c2450295178e573cda4c1a84f0aabdb38f2 Author: marc Date: Fri Mar 31 21:48:09 2006 +0000 fix up err in prof statement Src/C_BaseLib/VisMF.cpp commit 76c81d69efcdad8ec4dda144f2a15f908539a189 Author: marc Date: Fri Mar 31 21:42:50 2006 +0000 add a couple of timers Src/C_BaseLib/VisMF.cpp commit 90ac727b4fc1b0eaed3d928c85688f044221857c Author: vince Date: Thu Mar 30 21:52:12 2006 +0000 test for old style box. Src/C_BaseLib/Box.cpp commit 0c997dee62618242a5de9e14cbaab82f79dba644 Author: car Date: Tue Mar 28 00:05:30 2006 +0000 *** empty log message *** Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_knapsack.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_knapsack.f90 commit 99b23bc47fffe886d541945c8a8e267c4a31cabe Author: car Date: Mon Mar 20 20:06:28 2006 +0000 test for ann Src/F_BaseLib/multifab.f90 commit 4f0f921af8c1b7a495778cf25c423d3a7fcf8056 Author: vince Date: Thu Mar 16 19:04:34 2006 +0000 additions for columbia. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit f375e73d1e72942c92aca21cbc34dfdf9e539a02 Author: lijewski Date: Mon Mar 13 21:04:11 2006 +0000 print out distribution with grid log Src/C_AMRLib/Amr.cpp commit 4b98d5bba87a75421a388593578e5baaed450968 Author: car Date: Mon Mar 6 22:23:50 2006 +0000 forward decls needed Src/C_BaseLib/FabArray.H commit db5a93020ea818f6728ddd98657ff35c82e935e2 Author: car Date: Mon Mar 6 19:24:44 2006 +0000 missing declarations Src/C_BaseLib/VisMF.H commit 00c1cc9f55d6f99a24b5799ba8c1a39c76ad08e1 Author: lijewski Date: Wed Feb 15 22:47:12 2006 +0000 more tweaking of min comm cost code Src/C_BaseLib/DistributionMapping.cpp commit 8c2d29b1f954d69f5ec8fc973908fcfd57d21490 Author: lijewski Date: Tue Feb 14 18:56:23 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 46ebda205b0025a998557827b550502c11cc43f1 Author: car Date: Fri Feb 10 22:18:40 2006 +0000 fewer includes when not profiling Src/C_BaseLib/Profiler.H commit 64e6a2f693fe5db4497e28ce379f54e8cdda86e2 Author: car Date: Fri Feb 10 22:18:17 2006 +0000 need string include Src/LinearSolvers/C_NodalMG/RegType.H commit 95410d51b494d3538cc843d3f0ff31c06866d087 Author: car Date: Fri Feb 10 17:22:02 2006 +0000 some code needing further testing Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 69870bace12f177f3bd7c5febe9f382f76d561be Author: car Date: Fri Feb 10 17:20:22 2006 +0000 cleaned up makefile Src/LinearSolvers/C_NodalMG/GNUmakefile commit 27f3189f51f2a24f73d125ab5c089024f32307b2 Author: car Date: Fri Feb 10 17:10:31 2006 +0000 naphta Tools/C_mk/Make.mpi commit a3bf4d26816eb0e95af4aebca8cada9286cbea50 Author: car Date: Fri Feb 10 17:10:11 2006 +0000 BROWSE Tools/C_mk/Make.rules commit 72553443ce7aa09cf9b78e342fb7bab288fcbf6b Author: car Date: Thu Feb 9 23:00:12 2006 +0000 need iostream... Src/C_AMRLib/StateData.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 4cab8d06d2fa5583fbf02bd90693a2034a2afe56 Author: car Date: Thu Feb 9 21:40:58 2006 +0000 can now turn of profiling more completely Src/C_BaseLib/Make.package Src/C_BaseLib/Profiler.H commit 8843742da5c58e3fa5d4775ea6a6dae35c46de88 Author: car Date: Thu Feb 9 21:40:02 2006 +0000 iostream... Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 180ecfdedcca0f98a0b0ec24115267c5e1630872 Author: car Date: Thu Feb 9 21:13:58 2006 +0000 iostream... Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit f9d5083bb29d1752da35b3b17f79f0bd70265328 Author: car Date: Thu Feb 9 21:08:25 2006 +0000 include needed for iostream Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit bbe01d0fad4d3892817f36f6f84a7bad5f1f72a2 Author: car Date: Wed Feb 8 21:38:05 2006 +0000 PGI->BL_PGI Src/C_BaseLib/Thread.H commit 08b1bf77e1637bd5e91a0df0aa265d742b9c3a4d Author: car Date: Wed Feb 8 21:37:26 2006 +0000 wsecond on XT3 Src/C_BaseLib/Utility.cpp commit 5f3137818f504ed04b5b21fd7fbda83c7d085c0d Author: car Date: Wed Feb 8 21:36:12 2006 +0000 PGI flag not needed re template specialization Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 465fbc955a66f821a56deb3fdfc0dfdeb8dc2efa Author: lijewski Date: Mon Jan 30 18:03:18 2006 +0000 commented out some BL_PROFILE()s Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 47527d8177b1c327188c0f2343a2a61ef4f5daba Author: lijewski Date: Fri Jan 27 23:25:38 2006 +0000 *** empty log message *** Src/C_BaseLib/test/tMinCommCosts.cpp Tests/C_BaseLib/tMinCommCosts.cpp commit e611f618dc5b2e5e85346b2763c2a6290ecaa1ac Author: lijewski Date: Fri Jan 27 23:24:38 2006 +0000 speedup of MinimizeCommCosts() Src/C_BaseLib/DistributionMapping.cpp commit 3601dc6a670c509ae29b0c06ead4325cf29823b8 Author: car Date: Thu Jan 26 23:51:58 2006 +0000 machinefile not needed Src/LinearSolvers/C_NodalMG/machinefile.mpi commit 5fdf19b1a9dc952bac99107f266208c816b63627 Author: lijewski Date: Thu Jan 26 00:12:17 2006 +0000 zeroed out Execute() Src/C_BaseLib/Utility.cpp commit 5ea67965fd7dbda544c8d68aaa1642201173ed11 Author: lijewski Date: Thu Jan 26 00:09:26 2006 +0000 *** empty log message *** Src/C_BaseLib/Make.package commit da15ae1b31c3f039fdee6850338541ac28ff6c25 Author: lijewski Date: Wed Jan 25 23:58:03 2006 +0000 more profiling Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 589463ff9e3edaea4f2dcdbef6fa04a7e08c7a1f Author: lijewski Date: Mon Jan 23 22:14:00 2006 +0000 speedup to add() Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit 371ec232f4d30c7a2759fa98b95a536d4261d4e7 Author: lijewski Date: Fri Jan 13 20:26:28 2006 +0000 use O3 with Fortran & PathScale Tools/C_mk/Make.Linux commit 9ef19b43eb474a08db7696ecc8e94dc58aa9f4ab Author: car Date: Tue Jan 10 22:05:28 2006 +0000 Added another assert. Src/C_BaseLib/BoxArray.cpp commit e189c1d565d6f6f68500e3c3fba11b48091eb628 Author: car Date: Tue Jan 10 22:05:08 2006 +0000 Fixed ixType() bug in minimalBox(). Also added a bunch more asserts. Src/C_BaseLib/BoxList.cpp commit 90ecf071b0f17f1bb8e3113b7bca54335eb327fb Author: lijewski Date: Mon Jan 9 19:18:48 2006 +0000 removed some simplify()s Src/C_AMRLib/Amr.cpp commit c9868a3294f6483948eed9d93e6001ef0a5aa187 Author: lijewski Date: Mon Jan 9 19:17:24 2006 +0000 minimize() -> simplify() Src/C_BaseLib/BoxArray.cpp commit be963a490fe1b6893e83bbca57b998a485d269b1 Author: lijewski Date: Mon Jan 9 19:08:58 2006 +0000 *** empty log message *** Src/C_BaseLib/test/ba.15784.REMOVED.git-id Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/ba.15784.REMOVED.git-id Tests/C_BaseLib/tBA.cpp commit 5ee6cb88345bcf7d8a8ce662e50b6d8910d18e10 Author: lijewski Date: Mon Jan 9 18:05:16 2006 +0000 more speedups Src/C_BaseLib/BoxList.cpp commit b72119977b3b1c3c2425addbc86285a1259c3fa5 Author: lijewski Date: Mon Jan 9 05:00:30 2006 +0000 use BoxArray to speed up intersects() Src/C_AMRLib/Cluster.cpp commit 09e6006641f57ac24966269a700ea0d1fd1d3dc3 Author: lijewski Date: Mon Jan 9 04:59:39 2006 +0000 minimize() -> simplify(). Use BoxDomain::add(BoxList) instead of BoxDomain::add(Box). Src/C_AMRLib/Amr.cpp commit 5cf0e8dc3b2e670ff831cbdd3375c039a2c35c16 Author: lijewski Date: Mon Jan 9 04:23:37 2006 +0000 speedup of add(BoxList) Src/C_BaseLib/BoxDomain.cpp commit 381666a58122dd564cf4a2deb7314fe33792379b Author: lijewski Date: Mon Jan 9 02:32:32 2006 +0000 more profiling Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.cpp commit fe65cb3e2d6de7b8feb5561ab8b5fdf1c62c9548 Author: lijewski Date: Sun Jan 8 18:21:23 2006 +0000 aded some profiling Src/C_AMRLib/Cluster.cpp Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.cpp commit 7c9ce6f7e973eefa6896fbc7c2bfd196a080c2eb Author: lijewski Date: Sat Jan 7 20:35:20 2006 +0000 think it's finally right Src/C_BaseLib/BoxList.cpp commit e359a261840b90c6281e01b81b1067850646b435 Author: lijewski Date: Sat Jan 7 18:57:30 2006 +0000 think I fixed complementIn() Src/C_BaseLib/BoxList.cpp commit 001a70a7949bc1b261a202a97c2832387638fb82 Author: lijewski Date: Sat Jan 7 16:27:05 2006 +0000 oops, got some weird recursion to work out Src/C_BaseLib/BoxList.cpp commit cbe8354253ce16a0d37eef68f08917fcc65e6d93 Author: lijewski Date: Sat Jan 7 01:22:09 2006 +0000 more scalable version of complementIn() Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 3e2a1dbca3d886c31999d3240330e241561cf52f Author: lijewski Date: Fri Jan 6 22:58:21 2006 +0000 one complementIn() now calls other Src/C_BaseLib/BoxList.cpp commit a14eb17e8d863d23c29c3337b94c27aa8b320ded Author: lijewski Date: Fri Jan 6 18:47:26 2006 +0000 efficiency back to .95 Src/C_BaseLib/DistributionMapping.cpp commit ba7b4f77d4d3ce0a1e8d32dd41a593ba2d7ccc2d Author: car Date: Fri Jan 6 18:46:57 2006 +0000 newComplementIn Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/tBA.cpp commit 687976c44ce22aa9526eee81c0e214bad2e38543 Author: lijewski Date: Fri Jan 6 17:59:40 2006 +0000 mem improvement for knapsack Src/C_BaseLib/DistributionMapping.cpp commit 1500fae3e7a5a6f3358631c972829e5a6deb026a Author: lijewski Date: Fri Jan 6 05:34:24 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit b60cdf1799ce57af20cbdb976f6177b044565857 Author: lijewski Date: Thu Jan 5 23:53:10 2006 +0000 added timers to grid_places() Src/C_AMRLib/Amr.cpp commit 96e31513ae74c06d4315d522a58d7d2ded8bca46 Author: lijewski Date: Thu Jan 5 23:43:26 2006 +0000 Print out both initial & final knapsack efficiency. Src/C_BaseLib/DistributionMapping.cpp commit f7de3734064e16497bae72b6de34e5b37f58cd7f Author: car Date: Thu Dec 22 23:44:06 2005 +0000 *** empty log message *** Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/t_bx.f90 commit e823a8f461024326f9625a94125e44cfdfffafa3 Author: car Date: Wed Dec 7 17:02:01 2005 +0000 should, but doesn't fix a problem with gfortran Src/F_BaseLib/fab.f90 commit d4261c90e3f4580306fa33bfc97416a7a9b3575a Author: marc Date: Tue Nov 22 22:15:05 2005 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit a2b9808d626a3892ecaae8e13c4514c9ce79641b Author: marc Date: Tue Nov 22 22:14:47 2005 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 7544dd1519f61bf765bb8716e53b7a2748e0a2d9 Author: car Date: Fri Nov 18 22:52:16 2005 +0000 *** empty log message *** Src/F_BaseLib/ml_multifab.f90 commit eec73906c67e8283ad8129eae5be384fd3a02ed9 Author: car Date: Fri Nov 11 18:47:46 2005 +0000 *** empty log message *** Src/F_BaseLib/ml_multifab.f90 commit b89785ddaafe3aac628fa3841edd249ba90762b9 Author: car Date: Thu Nov 10 23:42:16 2005 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit 1fdc00587dfa1a639eda3aaccadd0561121d82bd Author: car Date: Thu Nov 10 23:31:33 2005 +0000 metis is dead Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile commit fb3779c6553deb0d15cb0ed6ca719a099eef9fba Author: car Date: Thu Nov 10 23:24:54 2005 +0000 PathScale fixes Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit e31f0e2dc50aad9c43a7de31e1b3c27761d2ea4c Author: car Date: Thu Nov 10 23:16:32 2005 +0000 greenstreet mpi Tools/F_mk/GMakeMPI.mak commit 6e30f3cffbb1c479136c243cefcb9b2b62314121 Author: car Date: Thu Nov 10 23:11:28 2005 +0000 farg Tools/F_mk/GMakeMPI.mak commit a962239a4f0e4d17665cf64f113dd6a167e39477 Author: car Date: Thu Nov 10 23:03:39 2005 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit 7fc25299cbad0d339c488cb6e45b1f1d93a11e14 Author: car Date: Thu Nov 10 22:51:18 2005 +0000 farg in extern Tools/F_mk/GMakeMPI.mak commit d308b7f6d82362c5c476b3d8a6594894575132da Author: car Date: Wed Nov 9 17:26:29 2005 +0000 fix for parallel stats Src/F_BaseLib/bl_prof.f90 commit 317003ce881bceb1d25c8c28a500eaa63e441d1f Author: car Date: Wed Nov 9 16:53:55 2005 +0000 new MPI config method Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 704001f7ac867f5aef88a08495e05479b0682d58 Author: car Date: Tue Nov 8 16:23:57 2005 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit d0ddeb5c18a89ef390408a956ebde931681f5422 Author: car Date: Tue Nov 8 02:35:19 2005 +0000 debugging Src/F_BaseLib/fabio.f90 Src/F_BaseLib/multifab.f90 commit 49219a96c5230b07469f398573afe8ed4c52f78c Author: car Date: Wed Nov 2 23:49:30 2005 +0000 barrier after mkdir Src/F_BaseLib/fabio.f90 commit 47f908ceeba518497b7058290223e79317cafc77 Author: marc Date: Wed Nov 2 01:41:00 2005 +0000 Add stuff to build on Jacquard Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 4788af3de01e08176b50f1062601a6330ce05730 Author: car Date: Mon Oct 31 17:19:49 2005 +0000 more support for dft; and bl_prof for longer running programs Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 commit ae1bd6c6e263df98b0e6fe8c78f3915ef3027cf2 Author: lijewski Date: Wed Oct 26 18:20:46 2005 +0000 removed sndcnt/rcvcnt args to startup() Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 4b5635bbb7aae582cacb623bf7cebe2923b57be8 Author: lijewski Date: Tue Oct 25 22:13:13 2005 +0000 some simplification of execute() Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit a6cefa42e7bc7c4b766a7be9a761f85874adbfe9 Author: car Date: Mon Oct 24 22:59:40 2005 +0000 timers Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 commit 6ddc25eee92144553e794688527666f06b606c84 Author: lijewski Date: Mon Oct 24 21:16:31 2005 +0000 inlined add_task & depend_on Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit e91d43164dad996872d93023557d89e08595202c Author: lijewski Date: Sat Oct 22 19:41:09 2005 +0000 default for verbose is now false Src/C_BaseLib/DistributionMapping.cpp commit 3a588b62a2441447bdfb34f03701cbfa92a07943 Author: lijewski Date: Fri Oct 21 03:27:42 2005 +0000 removed timer & freshened code Src/LinearSolvers/C_NodalMG/restrictor.cpp commit e32d5f6c37362f924dbc5763e9845124b876059c Author: lijewski Date: Thu Oct 20 22:07:38 2005 +0000 A few more BL_PROFILE calls. Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 1af832ae84c14dcbd677c1615c257bc890092d2e Author: lijewski Date: Tue Oct 18 18:19:57 2005 +0000 some speedups to alloc() Src/LinearSolvers/C_NodalMG/interface.cpp commit 03717febe911155add467a20e367275c8e633b87 Author: lijewski Date: Tue Oct 18 15:57:34 2005 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.cpp commit e6dad106801914f29f6b2069257d6d75d3b365f6 Author: lijewski Date: Tue Oct 18 15:49:57 2005 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.cpp commit aa3daa82e30d0a7737a0e860e7ca69ccd99a05c0 Author: car Date: Mon Oct 17 19:52:48 2005 +0000 *** empty log message *** Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bx.f90 commit e2257c1479917efb7affff42e5ef4c8c190dd6c6 Author: lijewski Date: Mon Oct 17 18:59:00 2005 +0000 removed timer from restrict_level() Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 7fb97991739a78b1cd24723b6acef45afc51ed4e Author: lijewski Date: Mon Oct 17 17:50:34 2005 +0000 merged in intersections() Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 2a5a6d7f63d09e9fca7ee9e9aa7748c891a6f85d Author: lijewski Date: Mon Oct 17 17:50:22 2005 +0000 added some timers Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 140c7e5b70cfae9d065460825d46d8dfffbf6f9e Author: lijewski Date: Mon Oct 17 03:11:14 2005 +0000 a working contains(IntVect) using intersections() Src/C_BaseLib/BoxArray.cpp commit 30ba588aabc93d5d5ce03491d144df9ae6a1b070 Author: lijewski Date: Mon Oct 17 02:21:05 2005 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit 3b6086299986eb8787eb539789935c1716e68a51 Author: lijewski Date: Fri Oct 14 17:22:40 2005 +0000 more polishing Src/C_BaseLib/Box.cpp Src/C_BaseLib/IntVect.cpp commit f2754d2c2ee6d37b97bd8e3d03258f756f30d0c3 Author: lijewski Date: Thu Oct 13 23:04:50 2005 +0000 the previous problem was with the contains(IntVect) -- fixed Src/C_BaseLib/BoxArray.cpp commit 0a8befe81cd6bfd982c4a69c6ad26130c2751c94 Author: lijewski Date: Thu Oct 13 20:14:16 2005 +0000 reverting out some previous mods Src/C_BaseLib/BoxArray.cpp commit 3eae24d944844abdd9d30fb6f7fc761824deb4fe Author: lijewski Date: Thu Oct 13 16:51:04 2005 +0000 oops Src/C_BaseLib/BoxArray.cpp commit 1c5143bc16699a3b9e39a8d73a65601e948c430a Author: lijewski Date: Wed Oct 12 18:01:48 2005 +0000 merged in BoxMSet Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit 71e95a02bffcf56924db9d8c4548626a13cebd7e Author: lijewski Date: Wed Oct 12 04:26:31 2005 +0000 more uses of intersections() Src/C_BaseLib/BoxArray.cpp commit 64217e74d3c7080393a33c72c0aed84022abe609 Author: lijewski Date: Wed Oct 12 02:54:55 2005 +0000 slight speed mods Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 142a63b5ad92acfc0cb0079fc156db9c1eed769f Author: lijewski Date: Tue Oct 11 22:23:26 2005 +0000 use intersections() in restrict_level() Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit a8155c995e160c7c29c328bdf4acd642aecf1465 Author: lijewski Date: Tue Oct 11 19:07:23 2005 +0000 additional constructor Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit a0b975fdb0b591f103caf294f87574edb689dabe Author: car Date: Tue Oct 11 17:12:39 2005 +0000 ready for mike Src/LinearSolvers/C_NodalMG/3d_4_level.grids Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/inputs commit 70f32873bd66d5bf443d0ab8c0ddb150e4e0e5f2 Author: lijewski Date: Tue Oct 11 17:01:08 2005 +0000 use minimize() instead of simplify() in removeOverlap() Src/C_BaseLib/BoxArray.cpp commit 831438722958452eda3eb45b8943649251116cfb Author: lijewski Date: Tue Oct 11 16:07:18 2005 +0000 turned off FillPatch verbosity Src/C_AMRLib/AmrLevel.cpp commit 16d8440e205dae0810dad5f10e07e25dc95c1cea Author: car Date: Tue Oct 11 02:32:09 2005 +0000 added a few timers Src/LinearSolvers/C_NodalMG/interface.cpp commit 06fbc33bb54bcf763290ab743635c764a17a19ba Author: lijewski Date: Mon Oct 10 22:28:51 2005 +0000 *** empty log message *** Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tBA.cpp commit 6cbfff42b0a57feefa3092d0d3af62b63c13f3ae Author: lijewski Date: Mon Oct 10 21:25:33 2005 +0000 added removeOverlap() Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 335976f8f7ab4be16a854d34309215e568048315 Author: lijewski Date: Mon Oct 10 21:00:23 2005 +0000 added timer to FillPatch::Initialize() Src/C_AMRLib/AmrLevel.cpp commit df2c495755596ee597eaecf0cc895d47f0b6257e Author: car Date: Mon Oct 10 18:20:36 2005 +0000 remove inclusion of BoxDomain.H where not needed Src/C_AMRLib/Amr.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/TagBox.H commit 36958112b25a5e62657b25539cfdbbbd99960d80 Author: car Date: Mon Oct 10 18:01:23 2005 +0000 help find g77 library Tools/C_mk/Make.defs commit 71e8458e135e1de3f4643f8f66053477948917e7 Author: lijewski Date: Sun Oct 9 03:08:33 2005 +0000 inlined min()/max() Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp commit aa85ebf8048016bdfa298d6629cf67a6abd98615 Author: lijewski Date: Sun Oct 9 02:23:00 2005 +0000 fix to intersections() for empty BoxArrays Src/C_BaseLib/BoxArray.cpp commit b78e1d3717f41ea1628d5a8797b3058f0c7e2b11 Author: lijewski Date: Sat Oct 8 02:24:48 2005 +0000 *** empty log message *** Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/tBA.cpp commit cc0f19bd82290f06c03be9365efc5348c261e5ed Author: lijewski Date: Sat Oct 8 02:01:05 2005 +0000 *** empty log message *** Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/tBA.cpp commit 0e54be858f9ff3473ea3770850f9e5837779f46a Author: lijewski Date: Sat Oct 8 01:54:46 2005 +0000 added GetBndryCells() Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/tBA.cpp commit eec880d6770d232809c7f430cbc056ac2af83538 Author: lijewski Date: Sat Oct 8 01:53:05 2005 +0000 used by tBA.cpp Src/C_BaseLib/test/ba.213 Src/C_BaseLib/test/ba.5034 Src/C_BaseLib/test/ba.60 Tests/C_BaseLib/ba.213 Tests/C_BaseLib/ba.5034 Tests/C_BaseLib/ba.60 commit 4e1a11abe4e4cd9b1e0734da49058bcce6fc4366 Author: lijewski Date: Fri Oct 7 21:50:29 2005 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.cpp commit 59b8251dbbeb7c67c5bb7ee8c46c444842dbfb6f Author: car Date: Fri Oct 7 17:02:00 2005 +0000 profiler Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Geometry.cpp commit da377106a14aaf99ef88108e9c768e4cbaf7c0f7 Author: lijewski Date: Fri Oct 7 17:01:13 2005 +0000 now use intersections() stuff in one AddBox() Src/C_BaseLib/FabArray.H commit c81dd3e50e2cf3a540968bc5c604d183200940ac Author: lijewski Date: Thu Oct 6 17:59:26 2005 +0000 added/fixed NEEDS_FLUSH_F Tools/C_mk/Make.AIX Tools/C_mk/Make.defs commit ac425c72f696f06c945732ac9047299dd33f4d97 Author: lijewski Date: Thu Oct 6 17:26:16 2005 +0000 now use intersections() in CrseInit(Fab) Src/C_AMRLib/FluxRegister.cpp commit 0b9f5a3b977750b3b6b7f800f7b98c0ab82959f3 Author: car Date: Wed Oct 5 22:45:56 2005 +0000 timers Src/C_AMRLib/FluxRegister.cpp commit e9f3a4cceea9ecf8042f4af067567eafe949c725 Author: lijewski Date: Wed Oct 5 21:44:12 2005 +0000 use intersections() in FillBoundary Src/C_BaseLib/MultiFab.cpp commit 279cd8c63db3d5e1fe690c82313ed57d3bcbc0c6 Author: lijewski Date: Wed Oct 5 21:22:14 2005 +0000 use intersections() in copy() Src/C_BaseLib/FabArray.H commit 7ff28aad9ebfbb1cba47cd3e858d68c8f7342a0a Author: car Date: Wed Oct 5 20:28:48 2005 +0000 pathscale wrong about shared(filter) Src/F_BaseLib/multifab.f90 commit 2430a52dfd06acdac91c428fa715fed6135fdb95 Author: car Date: Wed Oct 5 20:25:05 2005 +0000 shared fcns? Src/F_BaseLib/multifab.f90 commit e56a908a190c20dd97c24a87665f8f9b9ee82975 Author: car Date: Wed Oct 5 19:53:03 2005 +0000 *** empty log message *** Src/F_BaseLib/layout.f90 Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/t_bx.f90 commit e17fc19de6b8fe50d6e119bd8d6e679d506c31c9 Author: lijewski Date: Wed Oct 5 19:25:04 2005 +0000 added intersections() Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 9c2e55d46d2628d5cd0b4b204bec2bbd879e1a01 Author: lijewski Date: Wed Oct 5 19:12:59 2005 +0000 *** empty log message *** Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/tBA.cpp commit 750ced4a0c64a3a1af4d69276d09ac81ecf74f7b Author: car Date: Wed Oct 5 17:06:36 2005 +0000 *** empty log message *** Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/t_bx.f90 commit d3fe79fec3d014fdd2136e2321860e631f512c2e Author: car Date: Tue Oct 4 23:01:36 2005 +0000 *** empty log message *** Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/test/t_bx.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 Tests/F_BaseLib/t_bx.f90 Tools/F_mk/GMakedefs.mak commit c1de8b27e9bcaa4ea62c3f08edc3d05d40a93f3e Author: lijewski Date: Tue Oct 4 17:33:05 2005 +0000 *** empty log message *** Tools/C_mk/Make.defs commit fa86a37b87475f88e9c8456a8ce06392c6e8cac9 Author: lijewski Date: Fri Sep 30 19:26:42 2005 +0000 *** empty log message *** Src/C_BaseLib/bl_flush.f commit 5f7933817e301a4ed439850c10480c6d1c48af1c Author: lijewski Date: Fri Sep 30 17:41:56 2005 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.cpp commit 1a0e860a9ccceabb97cdd3de2884fe4e30467952 Author: lijewski Date: Fri Sep 30 17:41:39 2005 +0000 add flush(6) Src/C_BaseLib/BLBoxLib_F.f commit afd6d42ed49038a490be04a69e1eb86d4e95c400 Author: lijewski Date: Fri Sep 30 17:07:58 2005 +0000 add FORTRAN to bl_ output strings Src/C_BaseLib/BoxLib.cpp commit 636871be43b1b921f989478eed99605dabab4e91 Author: car Date: Fri Sep 30 16:50:20 2005 +0000 cerr message on abort Src/C_AMRLib/StateData.cpp commit 21c5201cc72007853d8bb194f6de554f0e7398e3 Author: car Date: Fri Sep 30 16:47:39 2005 +0000 cout --> cerr Src/C_AMRLib/StationData.cpp commit 6ced8cdca80100d0c691d1bf661801024f4db9f2 Author: car Date: Thu Sep 29 15:56:25 2005 +0000 slight time improvement for boundaries in 3d only at this time Src/LinearSolvers/F_MG/mg_smoother.f90 commit 307ea48916febf658154ac80ce4e0aed5f44f542 Author: car Date: Thu Sep 29 15:55:17 2005 +0000 timer Src/LinearSolvers/F_MG/stencil.f90 commit 01dd546c5f3abae1b6249734bfd12e7eaaba6447 Author: car Date: Thu Sep 29 15:53:54 2005 +0000 *** empty log message *** Src/F_BaseLib/box.f90 Src/F_BaseLib/test/t_bx.f90 Src/LinearSolvers/F_MG/mg.f90 Tests/F_BaseLib/t_bx.f90 commit e4fb6e891c92c9784b1ed120eed9494d2facd3b6 Author: car Date: Wed Sep 28 20:59:07 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bx.f90 commit 0b4bf38f9b96346e189dd0ec625ccd9a7001ba60 Author: car Date: Wed Sep 28 17:48:08 2005 +0000 speed up of boxarray_boxarray_diff; for 5000 box case stencil_fill_cc is 3 x faster Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 commit a903947b84e30eedc31f941a82ba850aeec8d320 Author: car Date: Tue Sep 27 18:12:04 2005 +0000 ba_coarsen Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 851de70edb8c9ea514333b59fb17f903be422bf7 Author: car Date: Tue Sep 27 16:42:11 2005 +0000 gcc 4.0 support Tools/C_mk/Make.defs commit 76dd5a9968f3870d6877172f27fa6626010ac35c Author: car Date: Tue Sep 27 16:40:09 2005 +0000 *** empty log message *** Src/C_BaseLib/.cvsignore commit 1be86432b097c9ad52757382f90fb99220585033 Author: lijewski Date: Fri Sep 23 22:46:07 2005 +0000 added do_alltoallv stuff to copy() Src/F_BaseLib/multifab.f90 commit 1bf0f3e246fcb2a4ed07e5f4cd4bb6d37a4ac752 Author: car Date: Fri Sep 23 15:40:07 2005 +0000 max min and count Src/F_BaseLib/bl_prof.f90 commit cc72d11ab4983aff74f971ab81151d38d6ab05eb Author: car Date: Thu Sep 22 22:39:43 2005 +0000 remove testing smoothers Src/LinearSolvers/F_MG/mg_smoother.f90 commit 09d5e0dfe2e2e0ae00e5b676955fcd3b2886b968 Author: lijewski Date: Thu Sep 22 22:23:40 2005 +0000 optimized copyassoc_build() Src/F_BaseLib/layout.f90 commit 2136c2a9ca7fb91667ba646334375bb59eb56fb4 Author: car Date: Thu Sep 22 22:00:23 2005 +0000 back off the fancy stuff Src/LinearSolvers/F_MG/mg_smoother.f90 commit d02345a0a7c2dde3f6930ebb890c96fad1dcc621 Author: car Date: Thu Sep 22 20:00:01 2005 +0000 in serial, use cpu time Src/F_BaseLib/bl_prof.f90 commit 5009ad68f6532e500cedbc2d24f121a582cb262d Author: car Date: Thu Sep 22 19:59:05 2005 +0000 new smoother, doesn't seem faster Src/LinearSolvers/F_MG/mg_smoother.f90 commit 1384d2882f3206c1e89986587dd6a8233deccd0f Author: car Date: Wed Sep 21 23:01:13 2005 +0000 if not parallel dont reprise numbers Src/F_BaseLib/bl_prof.f90 commit a58216b88c48ff2b1266ddd17f7cef0238cb51f1 Author: car Date: Wed Sep 21 20:11:28 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_prof.f90 commit 3967e95c78e785772dc1365dd045c51909fdacbb Author: car Date: Wed Sep 21 19:52:13 2005 +0000 finally fixed Src/F_BaseLib/bl_prof.f90 commit f0950875138e98b2ab1cf0963932bbfa8ca188ce Author: lijewski Date: Wed Sep 21 19:34:53 2005 +0000 hueristic for chunksize Src/F_BaseLib/layout.f90 commit 7ccaf9ae05cc9933d3735a9eea2aa7a5e63f2ee3 Author: car Date: Wed Sep 21 19:25:54 2005 +0000 better bl_prof Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/test/t_bl_prof.f90 Tests/F_BaseLib/t_bl_prof.f90 commit 02aa4c03911162aed4a5d58b732264569903ecd5 Author: car Date: Wed Sep 21 18:59:20 2005 +0000 *** empty log message *** Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bl_prof.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bl_prof.f90 commit d15f4eaf090d4ae1725ac6bf43d4e6886d4538c5 Author: lijewski Date: Wed Sep 21 17:47:50 2005 +0000 merge two nested loops into one in boxassoc_build() Src/F_BaseLib/layout.f90 commit d086141acb79ec1909a708bc89d541722b4c7d34 Author: car Date: Wed Sep 21 16:22:13 2005 +0000 no more do_atav Src/F_BaseLib/multifab.f90 commit fc9aa3e1087600632d96e2b837949ba8ef340a16 Author: car Date: Wed Sep 21 01:01:21 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_prof.f90 commit 8cdceaf91abda411e2c7d77ab75b0f9fbe596801 Author: car Date: Wed Sep 21 00:27:01 2005 +0000 fix for reduction Src/F_BaseLib/bl_prof.f90 commit c6b3fcc18fec0c51452baddbd37f1873809bf6f8 Author: lijewski Date: Tue Sep 20 22:42:34 2005 +0000 got do_atav working Src/F_BaseLib/multifab.f90 Src/F_BaseLib/parallel.f90 commit 6b94d16b16f7cb3364a87098d6cf68535ab7252c Author: car Date: Tue Sep 20 20:12:15 2005 +0000 parallel_alltoall Src/F_BaseLib/multifab.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 8318ae5aa8cfe06c31934e475358b9d62c1d78a2 Author: car Date: Tue Sep 20 17:22:56 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bxasc.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bxasc.f90 Tests/F_BaseLib/t_main.f90 Tools/F_mk/GMakedefs.mak commit 166fa06b983a4fd84f95a75341a89a39abcd0560 Author: lijewski Date: Tue Sep 20 16:40:30 2005 +0000 added timer around boxassoc_build Src/F_BaseLib/layout.f90 commit 7a223e21b6cc1b15f47250e343a8ae1c051ccd10 Author: car Date: Tue Sep 20 00:09:29 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_smoother.f90 commit 852b4fc3b949ac1a863f3cac1d2d794ad0f731c7 Author: car Date: Tue Sep 20 00:09:04 2005 +0000 cpy_d improves things Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/multifab.f90 commit 31b9ddd81492c0a55a704012647e01883950f93d Author: almgren Date: Mon Sep 19 20:51:01 2005 +0000 Bug fix in ml_interface_stencil_3d. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit d6440b62b4ee7776c182527270893ca41280948f Author: car Date: Mon Sep 19 20:46:33 2005 +0000 norm profiling Src/F_BaseLib/multifab.f90 commit e9ed9fc29b3be4fcc890f70063a0ec6a4b3a48cf Author: car Date: Mon Sep 19 19:50:24 2005 +0000 summary stats Src/F_BaseLib/bl_prof.f90 commit db444b8995f677d195d0436e61cf6f95aa06e376 Author: car Date: Sun Sep 18 23:54:13 2005 +0000 more profiling Src/F_BaseLib/cluster.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 3c38238610c8dcec01c096b7cf9a44a7b32e056d Author: car Date: Sun Sep 18 21:53:11 2005 +0000 profiling Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 2661700bc3def5c650fe399e2530124617c5d0dd Author: car Date: Sun Sep 18 21:52:59 2005 +0000 profiler Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/multifab.f90 commit 7f723798352e4112d10fa772bdea3c74f91b4ea5 Author: car Date: Sun Sep 18 17:54:00 2005 +0000 good first cut of bl_prof Src/F_BaseLib/bl_prof.f90 commit 38a92ed6d5647edaed9fbadeb978806906064e1d Author: car Date: Sun Sep 18 00:21:14 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile commit 940c0d76dc7e593199b5749d24b795160c9260cb Author: car Date: Sat Sep 17 18:35:35 2005 +0000 profiling being added Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 commit 64d844faffba9f82669b871333fb9ad837dc3ca4 Author: car Date: Sat Sep 17 13:58:41 2005 +0000 tweak for reduce Src/F_BaseLib/bl_timer.f90 commit ad65bb9dc4bf383dc5548c0b9072465f7239ba4e Author: car Date: Sat Sep 17 13:57:58 2005 +0000 mg_tower_print Src/LinearSolvers/F_MG/mg.f90 commit 602575526c1f2f90b624495aa8daa773637900fc Author: almgren Date: Fri Sep 16 19:26:41 2005 +0000 Cleaner implementation that looks more like ml_interface_3d_divu in varden/hgproject.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 327d1796ca3d8c85a6fe741ce79676841a0485f2 Author: lijewski Date: Mon Sep 12 16:14:05 2005 +0000 turn off minimize comm costs stuff Src/C_BaseLib/DistributionMapping.cpp commit f7e08f6e3c22a5692552ed0c65ebdd5e088b7989 Author: car Date: Mon Sep 12 14:12:19 2005 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit d015a5915fb97a2e3c36fc5369f22d6a31667db6 Author: car Date: Fri Sep 9 20:35:16 2005 +0000 tweaks for f90 and Intel 9 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit b2971a180b316bcca8c0201f74116f728ed0f9b4 Author: almgren Date: Thu Sep 8 21:55:46 2005 +0000 An attempt to make CG_solve and BiCG_solve not create huge answers when the problem is almost completely solved. Src/LinearSolvers/F_MG/itsol.f90 commit c71de3937ce8a7b10db44f630020298205c62018 Author: car Date: Thu Sep 8 19:35:22 2005 +0000 pure is a stumbling block for PathScale, save for later Src/F_BaseLib/ml_multifab.f90 commit 14d0dc9870af8d7c83ab55ad1c2ba34a2273025f Author: jbb Date: Wed Sep 7 21:13:00 2005 +0000 Oops - typo in previous INTERP_2D.F Src/C_AMRLib/INTERP_2D.F commit 4fecdc3248f073462b304e2de42d79150381652c Author: jbb Date: Wed Sep 7 21:11:47 2005 +0000 Fix in LINCC_INTERP (and set-up for it) so that the routine which sets alpha loops over all of the fine cells in each coarse grid cell, not just the ones to be interpolated. This was needed because of a umac_periodic_bust because regions of different size were setting alpha differently. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/Interpolater.cpp commit 6ea58b46d29cff83e8c7a051b723885c5c5f693e Author: car Date: Wed Sep 7 19:22:31 2005 +0000 added marc's dsp generating code Tools/C_mk/Make.rules commit 5f34dcff25e9694419f5c3cda14c39f4269a3294 Author: car Date: Wed Sep 7 19:01:45 2005 +0000 Got Rid of Lib's added f90 dependencies Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 6e757187e953d7c74a3a25b8dd7d8a06643cda87 Author: car Date: Wed Sep 7 17:27:36 2005 +0000 we don't buid libraries anymore Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_TensorMG/GNUmakefile commit 1f767380abc8bd387fd0c45c6b7f14d97db21c24 Author: car Date: Wed Sep 7 17:02:14 2005 +0000 *** empty log message *** Tools/C_scripts/moddep.pl commit cdc15096801e4ab26f2aa482bbf7514b6ebed656 Author: car Date: Tue Sep 6 22:52:23 2005 +0000 Intel9 support Tools/F_mk/GMakedefs.mak commit 4caade34e3a5748d9b7a0b3ab414b7d2641d20bc Author: car Date: Tue Sep 6 22:51:54 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 0f6ecb8b7553f78967e7ffc4d7d9dd5ea6d8d9b1 Author: car Date: Tue Sep 6 22:06:27 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 63b214527df84716dbc094dce2523d8d0d05c141 Author: car Date: Tue Sep 6 21:06:25 2005 +0000 mg_cpp changes Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 8bb5cf4660d2543c2eb2f653ef5aea848c232966 Author: almgren Date: Thu Sep 1 21:35:00 2005 +0000 Needed to make same index fixed in lin_cc_interp_3d as in lin_cc_interp_2d. Src/F_BaseLib/interp.f90 commit 663283536d904a8a7e44e1962cf28a370fc27db4 Author: almgren Date: Thu Sep 1 19:18:24 2005 +0000 I believe this is the correct scaling for 3-d nodal. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 562960e255d9e279da20e02c96e0da0b1b8ba99e Author: almgren Date: Thu Sep 1 17:57:38 2005 +0000 The ml_layout_build from a ml_boxarray was not correctly passing the problem domain to the layout...instead the problem domain was being defined as the bounding box at that level. Now the problem domain from the ml_boxarray is passed through the layout_build call. Src/F_BaseLib/ml_layout.f90 commit 4f902f1af638a4cd0dbdb9b40f3fcc8e0819039d Author: car Date: Tue Aug 30 20:34:07 2005 +0000 dead code elimination Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/boxarray.f90 commit 674e3c4077f8be3132aee8ae6c7d4dcb25ae810d Author: lijewski Date: Mon Aug 29 16:27:16 2005 +0000 amr.restart=init -> call initialInit() not restart() Src/C_AMRLib/Amr.cpp commit 2297f164e0d163b99b765563fa9213b661725ef6 Author: car Date: Mon Aug 29 15:07:11 2005 +0000 more generics Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/flux_reg.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 4a143096ea66a2c4b664e90b97eef230ea307317 Author: car Date: Wed Aug 24 20:22:46 2005 +0000 added cluster_2d.f90, temporarily Src/F_BaseLib/GPackage.mak commit d3fc959c01f50aff2187b996b8a93c2c15321813 Author: car Date: Wed Aug 24 16:41:02 2005 +0000 one more check for underflow Src/LinearSolvers/F_MG/itsol.f90 commit 3c20ed3b7d93430aa92f5043c1e895941632f0bb Author: car Date: Tue Aug 23 19:02:29 2005 +0000 better error control Src/LinearSolvers/F_MG/itsol.f90 commit 21671775d9fbb51dc083961dcbd182f874af4b96 Author: car Date: Tue Aug 23 18:18:32 2005 +0000 hack to fix cg/bicg when r.a.r is zero Src/LinearSolvers/F_MG/itsol.f90 commit 51ac7a25c9c3f549425ac899e8eb5481df0c2cce Author: car Date: Mon Aug 22 19:19:46 2005 +0000 remove c++ wrapper from compilation Src/LinearSolvers/F_MG/GPackage.mak commit 675f36bd4c6f2c16a6ad0d364a129b34f7dac495 Author: car Date: Mon Aug 22 19:19:16 2005 +0000 some clean up of I/O Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/flux_reg.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/multifab.f90 commit 6f1675893d93e794443ff7264ebb57e3593fddbe Author: car Date: Sun Aug 21 17:13:55 2005 +0000 fleshing out more of the operations on types Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 commit be004338be75ccdc689f5cc2004ee5bc8518c4e8 Author: car Date: Sat Aug 20 19:40:27 2005 +0000 more setvals Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/t_cls.f90 Tests/F_BaseLib/t_cls.f90 commit b991d22391ddf3ca2e150cab99228303069bc11f Author: car Date: Sat Aug 20 19:35:26 2005 +0000 b1 and b2 might be shrunk in recursive call Src/F_BaseLib/cluster.f90 commit 3fa4c88575e63ba68c294970ae0b5c236692cd24 Author: car Date: Sat Aug 20 16:39:57 2005 +0000 cluster should be debugged Src/F_BaseLib/cluster.f90 commit aed40153c00235107f28e812bae7f0fa71679f3c Author: almgren Date: Sat Aug 20 05:27:28 2005 +0000 2D version of cluster.f90 used by Ann until cluster.f90 is debugged. Src/F_BaseLib/cluster_2d.f90 commit 80ead52287c1fd5c6fe42bd3180e1b5d798253bb Author: car Date: Fri Aug 19 23:08:32 2005 +0000 tweaks for mpi Tools/F_mk/GMakedefs.mak commit da9293f3f48ef1b12b6fd81d3f75130343cb6817 Author: car Date: Fri Aug 19 23:08:08 2005 +0000 get_boxarray Src/LinearSolvers/F_MG/mg.f90 commit 441b37079806a801f029cbde13d2f590f51cd08b Author: car Date: Fri Aug 19 23:07:49 2005 +0000 *** empty log message *** Src/F_BaseLib/box.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/t_cls.f90 Tests/F_BaseLib/t_cls.f90 commit 727dd9f170dc113f7d7709b69901fe1d3c32fe6a Author: car Date: Wed Aug 17 13:29:56 2005 +0000 *** empty log message *** Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit ded8071d68edeb14824d4c82271dd1c8be998d9c Author: car Date: Sat Aug 13 15:47:54 2005 +0000 missed some Src/F_BaseLib/parallel.f90 commit e2525278ec281f9bb771237673083ba64da05b54 Author: car Date: Fri Aug 12 17:28:32 2005 +0000 intel is too permissive... Src/F_BaseLib/multifab.f90 Src/F_BaseLib/parallel_stubs.f90 commit f7744131e9c6776f9e6d9812197c58f3f98e301e Author: car Date: Fri Aug 12 17:21:57 2005 +0000 oops Src/F_BaseLib/parallel_stubs.f90 commit 5bca3b1595c678e4399687c86264b81c37f33e7e Author: car Date: Fri Aug 12 16:50:19 2005 +0000 more complex support Src/F_BaseLib/multifab.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit c842ae1e030ae90965db2c28009a58a6555525a7 Author: car Date: Thu Aug 11 23:43:10 2005 +0000 fab, multifab complex for fmm Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit 294d926eb04915a9776689383273bfd0921b4f1d Author: car Date: Wed Aug 3 20:25:32 2005 +0000 oops Src/F_BaseLib/ml_layout.f90 commit 19b4cdb37426d09388c412d27fbc5bd767f444c0 Author: car Date: Wed Aug 3 14:43:43 2005 +0000 extra vars Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/t_cls.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_main.f90 commit fd5d9ed68aa63c644a7490855234dd1ebf6470a1 Author: car Date: Wed Aug 3 14:43:09 2005 +0000 ml_layout Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_layout.f90 commit 6886dc402bef9c6a494accab28ca37e9e13a224d Author: car Date: Fri Jul 29 21:34:27 2005 +0000 fix for 3d Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/t_cls.f90 Tests/F_BaseLib/t_cls.f90 commit 35e65ce7b3db302effe6007e8de3ac89c4811162 Author: almgren Date: Fri Jul 29 20:53:13 2005 +0000 Make sure to set the boxarray%dim = 2 in the 2d case... Src/F_BaseLib/cluster.f90 commit d350889ec96f75c9cb60515ea117a668f2ba4582 Author: car Date: Fri Jul 29 19:13:19 2005 +0000 mask out ghostcells, more debugging Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/t_cls.f90 Tests/F_BaseLib/t_cls.f90 commit e9d1aad29f8666fac989dd810708f1ee1a6613b5 Author: car Date: Fri Jul 29 17:10:05 2005 +0000 i think a fixed cluster Src/F_BaseLib/cluster.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_cls.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_main.f90 commit d336db416c3477d91188881fb10d7b830b211b5f Author: almgren Date: Thu Jul 28 19:34:04 2005 +0000 Dont need to test on (n>1) on the way back up because that code is only called for n = 2,...nlevs. Src/LinearSolvers/F_MG/ml_cc.f90 commit 446171e65a3329fd8de97dc981ef6c0b7e0881e6 Author: almgren Date: Thu Jul 28 19:33:19 2005 +0000 Make sure to use "mini_cycle" instead of mg_tower_cycle when relaxing at a fine AMR level so that the smoother and not the bottom solver will be called. Src/LinearSolvers/F_MG/ml_cc.f90 commit cb2785ebf6550f5f66df0365d02f41ce11d494c4 Author: almgren Date: Wed Jul 27 20:26:09 2005 +0000 Index bug... Src/F_BaseLib/cluster.f90 commit a99e323d08989f0565505a2ee03abbdd1837bf8d Author: car Date: Wed Jul 27 17:12:58 2005 +0000 some fixes Src/F_BaseLib/cluster.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 6d993dd729aa513ae9df52c3d3edabf20badd799 Author: car Date: Tue Jul 26 16:48:37 2005 +0000 lets build boxarrays out of list_boxes Src/F_BaseLib/boxarray.f90 commit 591a8a85854e9bddc38643022b86f929cad7bafe Author: car Date: Thu Jul 21 18:13:13 2005 +0000 complex fabs Src/F_BaseLib/fab.f90 commit afebb410edfaa9cbdd328aceeeab37d660e86ce9 Author: lijewski Date: Wed Jul 13 19:56:31 2005 +0000 Some mods for Portland Group C++ compiler. I'm using PGI as a placeholder for the "appropriate" predefined compiler symbol. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/Thread.H commit 78b2ffb892fdb054312f7d2f4a54c9ab358bace1 Author: car Date: Mon Jul 4 23:12:22 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_types.f90 commit 594dc949113d9db39dcec412471af0550ff7b4fa Author: car Date: Mon Jul 4 22:52:01 2005 +0000 endian test Src/F_BaseLib/bl_types.f90 commit da12b8212456b0ebc3794cd875959ccb03e487bc Author: car Date: Thu Jun 23 16:50:22 2005 +0000 some multicomponent adjustments Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/multifab.f90 commit a38e65d09e62c5ac72cbfc74f782d4280beba5b2 Author: lijewski Date: Tue Jun 21 21:42:03 2005 +0000 added Plot_Files_Output() Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit e2edc891584b9d72762f6492f4774562177936d8 Author: lijewski Date: Tue Jun 21 20:09:47 2005 +0000 fixed the bug in the speed upgrades Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a55347dbfdc89a37902d547a2043890cb5bc7f16 Author: car Date: Sat Jun 18 19:04:36 2005 +0000 *** empty log message *** Src/F_BaseLib/test/t_boxlib.dsp Src/F_BaseLib/test/t_boxlib.dsw Tests/F_BaseLib/t_boxlib.dsp Tests/F_BaseLib/t_boxlib.dsw commit 61f6d42cf91247584884089a76de5cc0b20dd063 Author: car Date: Fri Jun 17 17:08:31 2005 +0000 OMP fix Src/LinearSolvers/F_MG/stencil.f90 commit 55214aac725effa2ab4fe1a5df16e4e8e8abc623 Author: car Date: Fri Jun 17 02:03:28 2005 +0000 new mech for intrisics Tools/F_mk/GMakedefs.mak commit 246f57fdac26bcdfc8a877f46d112a39ce6a4875 Author: car Date: Thu Jun 16 22:53:14 2005 +0000 box_projectable Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/ppm_util.f90 commit bb5ed4a3c51abed6647fba9c9105de1ecb44a3bb Author: car Date: Tue Jun 14 20:00:24 2005 +0000 support for Intel 9 Tools/F_mk/GMakedefs.mak commit 6434c20fdd3cb909e396c0640e32a1948590515c Author: car Date: Tue Jun 14 16:30:11 2005 +0000 not need external on iagc Src/F_BaseLib/f2kcli.f90 commit 7575538fb78aebe918ebfce661d41f8d6d4eb29f Author: car Date: Tue Jun 14 16:23:08 2005 +0000 Lahey checking Tools/C_mk/Make.Linux commit 4b37269a3e4754a13f34773e1b394078a1bfdf68 Author: car Date: Tue Jun 14 16:22:54 2005 +0000 icpc/ifort version 9 Tools/C_mk/Make.defs commit b19aeb4c36a85be853817571cc91f6725e8c7ef1 Author: car Date: Fri Jun 10 16:56:28 2005 +0000 reversion to April 1, 2005 Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 49dfd40399b7241b5200a2914e5b567137ff2dd6 Author: lijewski Date: Thu Jun 9 17:27:56 2005 +0000 some simplification Src/F_BaseLib/cluster.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 0379f0a83e467e90e52fd3f3095dbd3771bc3bd9 Author: almgren Date: Thu Jun 9 00:08:58 2005 +0000 Fix to the problem of one-cell thick domains getting the boundary nodes incorrectly set to nodal. Fix is in combination to fix to box_contains function... Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 14971bcda06e2384bd039183e0e1cdd6b144c933 Author: almgren Date: Thu Jun 9 00:08:04 2005 +0000 "Contains" now checks lo against lo and hi, and hi against lo and hi. Src/F_BaseLib/box.f90 commit f25d2ad4d593ba8cbcce7aa65cb4e79d6b409985 Author: lijewski Date: Wed Jun 8 21:50:04 2005 +0000 ml_nodal_restriction is now parallelized Src/LinearSolvers/F_MG/ml_restriction.f90 commit 7610d6792d8b173985afdbf6d2ce03bdd9dab927 Author: lijewski Date: Wed Jun 8 17:26:00 2005 +0000 added filtering ability to copy routines Src/F_BaseLib/multifab.f90 commit f619cf01a3166f11029c8db53abecd6bc91d0b36 Author: almgren Date: Tue Jun 7 18:23:10 2005 +0000 Change so that we only do interface updates if it is truly a crse-fine point, not a fine-fine point. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 6bc7525af61a9a68bf0e5853bd40c8477bf714f3 Author: lijewski Date: Tue Jun 7 18:09:53 2005 +0000 added nodal zero routines Src/LinearSolvers/F_MG/mg_restriction.f90 commit 8ff13e753dffaa7adfd0c4a82cb1045fc72e7a89 Author: almgren Date: Tue Jun 7 18:03:31 2005 +0000 Formatting... Src/LinearSolvers/F_MG/ml_nd.f90 commit f44ac78390dace21f28c62ddd80196230690c297 Author: almgren Date: Tue Jun 7 16:33:03 2005 +0000 Fix to how we zero the crse array before restriction. Src/LinearSolvers/F_MG/ml_restriction.f90 commit 159c4b7dfa432c74363bac3d2d8ab0d887102288 Author: car Date: Mon Jun 6 18:17:43 2005 +0000 lnc Src/F_BaseLib/multifab.f90 commit 6499825a90708e5a117d291da1fdf15cb766ca3d Author: almgren Date: Mon Jun 6 16:37:06 2005 +0000 Put the same changes in lin_cc_interp_3d as in lin_cc_interp_2d to get indexing thru crse and fine correct. Src/F_BaseLib/interp.f90 commit b5d1d90f5f3049556ec21c983182445461357ee9 Author: almgren Date: Sun Jun 5 21:06:58 2005 +0000 Fixed lin_cc_interp_2d...NOTE: 3d needs to be fixed as well!!! Src/F_BaseLib/interp.f90 commit 96bd11c1c44e6950c3620436a5b1eded2b6094d9 Author: lijewski Date: Fri Jun 3 22:49:05 2005 +0000 added error checks in dataptr routines Src/F_BaseLib/fab.f90 commit a4a386a264dcf098c9938d638dca27f39ede0f64 Author: lijewski Date: Fri Jun 3 21:35:02 2005 +0000 Got rid of bunch of redundant code by calling more general routines when possible. All the norms now use "mask" consistently. The "mask" is now always considered to be a 1 compolent multifab; i.e. it represents a geometric mask even in the case when we're interested in the norm of multiple components of a multifab at one time. Src/F_BaseLib/multifab.f90 commit b9630ae3b7e205c3b64bb25f8452a781bdd5cb6e Author: lijewski Date: Fri Jun 3 19:39:49 2005 +0000 parallelized ml_edge_restriction Src/LinearSolvers/F_MG/ml_restriction.f90 commit 7fb5e29716bd2dd554fe6bd5ad9a2293e035bd73 Author: lijewski Date: Fri Jun 3 19:16:51 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_restriction.f90 commit 172423f185724b88b0c7546304d297e38ce71164 Author: lijewski Date: Fri Jun 3 17:45:16 2005 +0000 moved destroy code to after final uses Src/LinearSolvers/F_MG/ml_cc.f90 commit b13c65472416f9062965df2bfedf04c8e1a174c6 Author: almgren Date: Fri Jun 3 05:16:26 2005 +0000 Pass "n" thru calling sequence instead of looping over. Note that multifabs coming in are now edge-based. Src/LinearSolvers/F_MG/ml_restriction.f90 commit 0c5bbe17525aa6905bd758059d8c1050dba61e15 Author: lijewski Date: Thu Jun 2 20:35:36 2005 +0000 a little cleanup Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 3da5758eb31967e6068331e03d28e415d1253422 Author: lijewski Date: Thu Jun 2 16:38:39 2005 +0000 out -> inout in a couple places Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 commit 6a7a2ca8064a3a78a7677c7d840ba8cdc9a69fb7 Author: vince Date: Thu Jun 2 00:28:08 2005 +0000 added support for jvn. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 5d811c4153f48c78f8fdc252c14ee91ef71705c6 Author: lijewski Date: Wed Jun 1 22:28:52 2005 +0000 some cleanup Src/LinearSolvers/F_MG/mg_restriction.f90 commit e5a63febfed9a878aee398c97ed841ecde034db9 Author: car Date: Wed Jun 1 21:40:35 2005 +0000 should read ml_boxarray with != rr properly Src/F_BaseLib/box_util.f90 commit 7185005aa5a40db46516c990006614c6ff81c480 Author: almgren Date: Wed Jun 1 21:08:56 2005 +0000 Fix problem in defn of jbot vs jtop. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 7c23a3aebc366ea719d62566c956f463d1d17806 Author: lijewski Date: Wed Jun 1 20:14:38 2005 +0000 parallelized ml_prolongation Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 8fa1f54aa452a1d63567056313c0ea749b0caeeb Author: lijewski Date: Wed Jun 1 16:44:16 2005 +0000 messed up something in ml_nodal_restricton Src/LinearSolvers/F_MG/ml_restriction.f90 commit 1c57233314a403be954765693538c3c1a2413385 Author: lijewski Date: Tue May 31 21:38:19 2005 +0000 some cleanup Src/LinearSolvers/F_MG/mg_restriction.f90 commit cc6242d557558efe269ccd2b83ca9acb0a398081 Author: lijewski Date: Tue May 31 21:38:04 2005 +0000 parallelized cell-centered restriction Src/LinearSolvers/F_MG/ml_restriction.f90 commit fea37d04355998fcfd1329156bb1de3c4c90cbc5 Author: marc Date: Tue May 31 18:11:22 2005 +0000 make sure filpatches called using amrlevels in hierarchy--required subtle change to regrid function Src/C_AMRLib/Amr.cpp commit 38ab5f4d72b380739efd31acef710eccfad0a90e Author: car Date: Tue May 31 17:21:44 2005 +0000 more ignorance Tests/LinearSolvers/F_MG/.cvsignore commit 7b985ab9c65bc946ca97607fc2c8d343d315ea0f Author: car Date: Fri May 27 21:59:23 2005 +0000 strengthen optimization on non amd systems Tools/F_mk/GMakedefs.mak commit 907f11ae1aceb42e69b17bb9db82dfc392acbd11 Author: car Date: Fri May 27 21:58:11 2005 +0000 BC_UNDEF Src/F_BaseLib/bc.f90 commit 344b56f08bfdfecf2497332b3178480e53fc2a90 Author: car Date: Fri May 27 21:57:21 2005 +0000 memory leak fix; pointer->allocatable Src/LinearSolvers/F_MG/ml_nd.f90 commit edd7aef60785ee0910652db73de73f42d95234fa Author: lijewski Date: Thu May 26 20:48:13 2005 +0000 Added WhereToStart(). Now do "fairer" job laying out multifabs across CPUs. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit a864af5f042006ac575bb7b7bee4855f43715d82 Author: car Date: Thu May 26 16:42:02 2005 +0000 memory leak Src/LinearSolvers/F_MG/ml_cc.f90 commit ddc90495568afb6beacb2e09bb4add9b1b7f97fa Author: almgren Date: Wed May 25 21:10:38 2005 +0000 Was bug in how we were computing ML residual within the iteration loop. Now appears to work on 2-level and 3-level problems. Src/LinearSolvers/F_MG/ml_cc.f90 commit 67a291c665e8c452a305d2f64803ad34ae9ad83e Author: colella Date: Wed May 25 18:29:23 2005 +0000 Comment out pretty_print. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit ae72f554f59ed39bd35c66958b761e614b7d67d4 Author: lijewski Date: Tue May 24 22:31:22 2005 +0000 added the_copyassoc_head Src/F_BaseLib/layout.f90 commit 13af223ac8e49c57348c1eaae1447864ddebb787 Author: lijewski Date: Mon May 23 21:21:44 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit a079cf144404e0f743ebdfa2743f7ee8ac949d19 Author: lijewski Date: Mon May 23 20:08:28 2005 +0000 ml_interp_bcs now calls ml_interp_bcs_c Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 263391b2da05d7ef7a6396cd64608f8a2922ff40 Author: lijewski Date: Mon May 23 19:43:11 2005 +0000 ml_cc_restriction now call ml_cc_restriction_c Src/LinearSolvers/F_MG/ml_restriction.f90 commit 0eae8af7d0f9f925360f043f9231c0ff91dd3d47 Author: lijewski Date: Fri May 20 21:30:11 2005 +0000 removed local_boxes stuff Src/F_BaseLib/layout.f90 commit 5f9faac679482c5d8176e85161d2f449c74756a0 Author: lijewski Date: Fri May 20 20:42:29 2005 +0000 added multifab_internal_sync_c Src/F_BaseLib/multifab.f90 commit 4146c3ef64f3455fc4cb48979c22e586f75f7295 Author: lijewski Date: Fri May 20 18:22:09 2005 +0000 more copyassoc stuff Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 commit 141259c6fa88d9614a90517023e4667ed6c9a552 Author: lijewski Date: Wed May 18 21:57:16 2005 +0000 some work toward a fancy parallel copy Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 commit a12746270ae70bbe18602b9afeb64d5021d9711e Author: car Date: Wed May 18 21:16:28 2005 +0000 try to get the alpha term right Src/LinearSolvers/F_MG/stencil.f90 commit 3302494e1ef3a7b972f9d1de97ab4805ebf96bd7 Author: lijewski Date: Tue May 17 22:03:17 2005 +0000 copy fixes Src/F_BaseLib/multifab.f90 commit 9ab1a0b838157be8023a767d7e6b35e9bd1d62ab Author: lijewski Date: Tue May 17 22:02:53 2005 +0000 added component to debug output Src/F_BaseLib/fab.f90 commit 1c6fd110369ee3c5b66e1b11acb0a5ca5a2f30da Author: car Date: Tue May 17 20:46:41 2005 +0000 false alarm Src/F_BaseLib/fab.f90 commit 8edc145fbfd0412863422a5920ab888db81e12ec Author: car Date: Tue May 17 20:19:05 2005 +0000 make sure multicomponet fabs print correctly in 1 and 2 dimensions Src/F_BaseLib/fab.f90 commit 286cd32dc7853d1323fd28f0d4cd7535131bf0c6 Author: car Date: Sun May 15 21:11:52 2005 +0000 more multicomponent fixes Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/multifab.f90 commit 5ad874f5cc5662ba176e7063ce2d7ea623528be6 Author: car Date: Tue May 10 22:11:41 2005 +0000 print generic for ml_multifab Src/F_BaseLib/ml_multifab.f90 commit fa7a599cf235f2bb15d48af05ded472bc89d219a Author: car Date: Tue May 10 22:11:11 2005 +0000 simple abec code Src/LinearSolvers/F_MG/stencil.f90 commit f621c287e2a5017435e8cbfabaf9b7f628e961b9 Author: car Date: Tue May 10 13:51:28 2005 +0000 single component applicators Src/LinearSolvers/F_MG/stencil.f90 commit c0724c04583a8da35f4b443781b8589abdbb591b Author: car Date: Fri May 6 19:59:11 2005 +0000 select bottom level Src/LinearSolvers/F_MG/mg.f90 commit 795823b6f32d23d5d4be46fcf9323c9c5513e2d6 Author: car Date: Thu May 5 22:32:58 2005 +0000 more suger Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 commit ba899d7a27f361cf8e7983f97e8d7027c0557ca4 Author: car Date: Thu May 5 22:32:47 2005 +0000 more options to output plotfiles Src/F_BaseLib/fabio.f90 commit fbd00787623906a173a813218675ad31b3b2fc35 Author: car Date: Thu May 5 22:32:14 2005 +0000 not needed modules Src/LinearSolvers/F_MG/ml_cc.f90 commit c3d3b2a725310e74461e8b765e94491e69ee30e4 Author: car Date: Thu May 5 20:29:11 2005 +0000 PROF only uses BLMpi.cpp Src/C_BaseLib/Make.package commit 69f311ac336d7314bce09a69676bbc2bd64f03d6 Author: car Date: Thu May 5 04:35:01 2005 +0000 more suger Src/F_BaseLib/ml_multifab.f90 commit b57e5463de579788e12cc0ba2eb377889cd6c848 Author: car Date: Wed May 4 21:06:15 2005 +0000 more helper fcns Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 commit 3d3c9432b252047b9f3657567d6633bd389e6247 Author: lijewski Date: Tue May 3 17:46:01 2005 +0000 oops Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 4ed8ed56dea30987586d112372d3f94891cb7a14 Author: car Date: Fri Apr 29 20:34:15 2005 +0000 layout lev 1 owns finer level layouts Src/F_BaseLib/ml_layout.f90 commit 08181a5a72175e1d78c4317090c37ecddcb9b139 Author: lijewski Date: Thu Apr 28 23:09:13 2005 +0000 memory cleanup Src/F_BaseLib/ml_layout.f90 commit 68c10b047da7d09ddb48976a65ca0e2521c495d5 Author: lijewski Date: Thu Apr 28 22:15:41 2005 +0000 memory cleanup Src/LinearSolvers/F_MG/ml_nd.f90 commit 0afaf239298b7884f52bd9c46cb1dc859c898c0f Author: lijewski Date: Thu Apr 28 18:29:49 2005 +0000 memory cleanup Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_layout.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 4fa42c1336d1a296f0d781a10c765dfe0c35ac02 Author: almgren Date: Thu Apr 28 16:54:25 2005 +0000 ml_layout_build can now take periodic flag pmask...(passes flag through into layout_build) Src/F_BaseLib/ml_layout.f90 commit d4867a5a0d53cd222c8cc696b571d47dc0295a69 Author: almgren Date: Thu Apr 28 16:54:04 2005 +0000 Need this change to make nodal work. Src/F_BaseLib/fabio.f90 commit 28f292c8e0cf7f55603c341ce292b961c1014efd Author: lijewski Date: Thu Apr 28 16:31:12 2005 +0000 simplification of buildFPB() Src/C_BaseLib/Geometry.cpp commit 0fcc79b5b99e7a973fd5fb9aba5f31dae4730115 Author: lijewski Date: Mon Apr 25 18:25:56 2005 +0000 nodal fix to set_bc_nodal Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 0f18844645e749193efdc40a8d2e0583afacd30c Author: car Date: Sat Apr 23 19:49:49 2005 +0000 sparse data distribution speed up Src/C_BaseLib/FabArray.H commit ddb0250e90a70570f07eec01d58d3917de1c9ff2 Author: lijewski Date: Fri Apr 22 20:59:22 2005 +0000 mods to speedup interface_residual Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H commit f0fcce6d1f0596d7d6952b14b236ef3d62c47b82 Author: car Date: Fri Apr 22 17:24:16 2005 +0000 added profiler Src/C_AMRLib/AmrLevel.cpp commit 405e170886c9bb1e3b56e862376f761c09452626 Author: lijewski Date: Fri Apr 22 02:35:30 2005 +0000 Array -> Array for did_work storage Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 178211150aa8b4e8a9ad299bd821e4d7699c6c69 Author: lijewski Date: Fri Apr 22 02:01:10 2005 +0000 speedup for fill_internal_borders Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit f6a058926d3d8e0b93f1c1996217f3f34defaf3c Author: lijewski Date: Thu Apr 21 19:53:49 2005 +0000 speedups to fill_interface() Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 0e9bfeff592e2e0ecdab0f5d4dc2c09c8d9be0e7 Author: almgren Date: Thu Apr 21 17:08:48 2005 +0000 Use ml_layout mla instead of array of layouts la_tower(:) Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 7a0ba01a53f5dbad00148f6da21b73c5247a878d Author: almgren Date: Thu Apr 21 16:22:21 2005 +0000 Add option to fix boundary conditions on solution so we can correctly compute the gradient afterwards. Src/LinearSolvers/F_MG/ml_cc.f90 commit 93225d4a6fb20a9e2b8c8af4808d808c8f3f7b12 Author: almgren Date: Thu Apr 21 15:12:44 2005 +0000 New ml_cc routine (called by cc_multi), and modifications to ml_cc and ml_nd so that we don't test on the full multilevel residual unless the fine residual is already converged. Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 16b0fbcd77109775f5e59938550a32450a7d2f1e Author: almgren Date: Thu Apr 21 14:45:57 2005 +0000 Add restriction of rh in beginning, and better convergence criteria. Src/LinearSolvers/F_MG/ml_nd.f90 commit b55a9127deb7ff8a53687e44c3dd0f44bbbaa439 Author: almgren Date: Wed Apr 20 18:04:41 2005 +0000 Fixed bug in stencil_flux_2d for lo-j sides. Src/LinearSolvers/F_MG/stencil.f90 commit e7175a3f20b83e28cd175c9cb47a4c9643928a4c Author: car Date: Tue Apr 19 21:04:20 2005 +0000 can no turn of all i/o; improves grid_places for large numbers of grids Src/C_AMRLib/Amr.cpp commit c8a336bfde9484d42f57b5366563b457083a7aa0 Author: car Date: Tue Apr 19 20:42:24 2005 +0000 fill_patch::restrict_level: seems to speed up cases with > 1000 grids Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 1adaf20986559744078121fcd9d267ea53743074 Author: car Date: Tue Apr 19 03:32:37 2005 +0000 hate assert Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/boxarray.f90 commit 49e954308372a4363b53f2aa13aaabb3bb438a00 Author: lijewski Date: Mon Apr 18 19:21:21 2005 +0000 fix to box_periodic_shift when nodal. ---------------------------------------------------------------------- removed automatically CVS: CVS: Committing in . ---------------------------------------------------------------------- Src/F_BaseLib/box.f90 commit 015caad98ec7596658daa483013f097b9d59fae2 Author: lijewski Date: Mon Apr 18 18:26:39 2005 +0000 Checked in some mask code for dealing with periodicity; not fully working. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 635b6487f4cafe262c8106c6d140791395dd08d4 Author: car Date: Mon Apr 18 16:25:57 2005 +0000 ml_nd Src/LinearSolvers/F_MG/GPackage.mak commit a6569b66e35c9e8c9c9474d5a451e7a9caa8ce6f Author: almgren Date: Mon Apr 18 00:51:20 2005 +0000 Use bl_constants_module instead of redefining constants. Src/LinearSolvers/F_MG/ml_nd.f90 commit 6ba07d0b1e01b912095c8600bca51fd3ecb93d7e Author: almgren Date: Fri Apr 15 21:05:54 2005 +0000 This contains the multilevel loop that does nodal multilevel multigrid solves. Src/LinearSolvers/F_MG/ml_nd.f90 commit 7588056419eba4ec7d841043c4cc18e58b4e80df Author: almgren Date: Fri Apr 15 17:06:14 2005 +0000 Intersect box with the problem domain in stencil_set_bc so that Neumann boundary conditions are not over-written by coarse-fine loop. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit bbddb66edc84f049fd7de2c848f129f35391070b Author: lijewski Date: Thu Apr 14 23:22:36 2005 +0000 fixed typo Src/F_BaseLib/multifab.f90 commit 28199bb57d864622093fc7f2c0ba7f6914a24599 Author: lijewski Date: Thu Apr 14 21:50:11 2005 +0000 Now pretty print nodal masks. Src/LinearSolvers/F_MG/stencil.f90 commit 48366dce8b6fb056600e6a8b91248bdf57b40f90 Author: lijewski Date: Thu Apr 14 18:22:17 2005 +0000 Just a little rearrangement; no substantive changes. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 8107e89514a9965accbce6b0daa63cce76aedcd2 Author: almgren Date: Thu Apr 14 17:49:27 2005 +0000 Make the same change for 1-d and 3-d. Src/LinearSolvers/F_MG/sparse_solve.f90 commit de06ac8d6c7799a1e2172b11a8ec4be4c74d78a1 Author: almgren Date: Thu Apr 14 17:41:38 2005 +0000 Changed order of operations in filling/copying index array for sparse solver on more than one grid. Src/LinearSolvers/F_MG/sparse_solve.f90 commit 80dce12eeee75a76966359a78c1dd77bbb79fa85 Author: almgren Date: Wed Apr 13 20:12:05 2005 +0000 Fixed a bug in the s_simple_2d_nodal (and probably the 1d and 3d as well) routine - the part which assigned BC_DIR to coarse-fine boundary nodes. New code is the same for all dimensions and more like the cc code. Tested on gr.2_19grids. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 35b1e4d39a831c0c8ff0bdf33681a7a7f4f33ee6 Author: lijewski Date: Wed Apr 13 15:59:26 2005 +0000 fixed some typos Src/F_BaseLib/parallel.f90 commit 46550e99b9bfbb9a7a8fb8cee8fe6050828b472e Author: car Date: Tue Apr 12 23:25:27 2005 +0000 fix for vector bcast Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 57881f5c121f214f906dc57bd4d55512cc3bc047 Author: car Date: Tue Apr 12 23:21:01 2005 +0000 bcast error condition Src/LinearSolvers/F_MG/mg.f90 commit cbb3b8292015f02497737e2882e64725f5ee7e50 Author: car Date: Tue Apr 12 23:20:23 2005 +0000 broadcast of scalars Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit b905169db92eda6f6864871dcd3e8088136243c8 Author: lijewski Date: Tue Apr 12 20:30:15 2005 +0000 Added call destroy(mm_grown) Src/LinearSolvers/F_MG/sparse_solve.f90 commit e95f6cc7f727a11e54ea157573a087e51930304d Author: lijewski Date: Tue Apr 12 18:22:29 2005 +0000 Some modest name changes due to adding support for single-level nodal solves. Tests/LinearSolvers/F_MG/makefile commit b8a69bd3c3fd9eb60d89931680b6f6867ae2b8dd Author: almgren Date: Tue Apr 12 17:00:45 2005 +0000 New interface routines which take fine mask as well as coarse. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 1e5185fe85856914fc84759624b5e8f997775a78 Author: lijewski Date: Mon Apr 11 17:57:26 2005 +0000 Fixed bug in copy() routines. Src/F_BaseLib/multifab.f90 commit e23597c07613182d77e47a4742edb05b081e6029 Author: car Date: Mon Apr 11 17:33:07 2005 +0000 parallel Src/LinearSolvers/F_MG/sparse_solve.f90 commit 1f88724f37d2a029a27f04428820f44b0d9f65ea Author: car Date: Mon Apr 11 16:31:47 2005 +0000 reclaim memory Src/LinearSolvers/F_MG/mg.f90 commit f8bd6f262e875b429eebc1c6edd965ede7f86853 Author: car Date: Sun Apr 10 00:50:14 2005 +0000 fix up that bottom solver... Src/LinearSolvers/F_MG/mg.f90 commit 56dca9e33d2de480fb7a8ff19bc7987be33983f0 Author: lijewski Date: Thu Apr 7 22:51:31 2005 +0000 -O4 buggy on AIX Tools/F_mk/GMakedefs.mak commit c9a7859b4c03ce22d12f20dc79e4e380665eafb4 Author: lijewski Date: Wed Apr 6 16:58:42 2005 +0000 Always do fill_boundary()s using asynchronous recv's. Src/F_BaseLib/multifab.f90 commit f666bd184c96230be05c500a531f8b53724ac769 Author: car Date: Tue Apr 5 16:54:47 2005 +0000 change of calling sequence to stencil_fill_cc; pxa and pxb are the locations of the 'physical boundary' relative to the celll geometry edge; normally, these are set to ZERO Src/LinearSolvers/F_MG/stencil.f90 commit d192027929f986b7d21555b9610cfcd37d39e99a Author: lijewski Date: Mon Apr 4 21:43:12 2005 +0000 Call fab_destroy() unconditionally to fix mem_stats bug. Src/F_BaseLib/multifab.f90 commit e8e39fd92b2342c6f2f0578dd868fc2b780c1a65 Author: almgren Date: Mon Apr 4 17:28:32 2005 +0000 Don't use mg_bc.f90 any more. Src/LinearSolvers/F_MG/GPackage.mak commit 565a8457fbcabb442903743123728b4e0443a8ad Author: car Date: Fri Apr 1 22:15:17 2005 +0000 seem to have 2nd order adaptive 'working' Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/test/t_main.f90 Src/LinearSolvers/F_MG/mg.f90 Tests/F_BaseLib/t_main.f90 commit e970741e7e175654c2ffa389c0d0802aad5a36b3 Author: car Date: Thu Mar 31 18:44:14 2005 +0000 ml operations added Src/LinearSolvers/F_MG/stencil.f90 Tools/F_mk/GMakedefs.mak commit f4e81cb22015789a11b82856491a5477089a49a3 Author: car Date: Thu Mar 31 18:43:57 2005 +0000 *** empty log message *** Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit 2294fdc72b8e0511b534566a6e87229d810252ca Author: welcome Date: Wed Mar 30 01:49:01 2005 +0000 Added "probStartTime" data member to Amr class to record the system time just before init/restart was called. Needed for "Time since start(restart)" value printed when dumping plotfile. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 365e125c177dab67b6aee00e8e9e532c9b4ad032 Author: lijewski Date: Thu Mar 24 21:39:23 2005 +0000 Got working on Jacquard with PathScale compiler. Src/F_BaseLib/mboxarray.f90 Tools/F_mk/GMakedefs.mak commit c54d80e9fdff354f0cc259142e0f838daa076002 Author: lijewski Date: Thu Mar 24 17:49:51 2005 +0000 Added pretty printing for mask arrays. Fixed a bug in the Z-direction stuff in *_aaa(). Src/LinearSolvers/F_MG/stencil.f90 commit 57d90871c0e0c7ec89b083b6afb0da034f2f146f Author: car Date: Tue Mar 22 22:59:07 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit 967818457ff13cf3ff0d3709874e0dc7e5025ab0 Author: lijewski Date: Tue Mar 22 21:40:32 2005 +0000 Just more goo from periodic testing. Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit 615d5ef108d4aad7e21a7434172e1e5e08980a26 Author: lijewski Date: Tue Mar 22 21:38:04 2005 +0000 Modified arguments to stencil_fill_bc_st() Tests/LinearSolvers/F_MG/t_stencil.f90 commit 7b1406aaa67bf6e670ea4afe2c60a3de903a0185 Author: lijewski Date: Tue Mar 22 21:23:18 2005 +0000 Set mg.v=2 & added ability to set periodicity. Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/in.2_big Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/in.2_3x2 Tests/LinearSolvers/C_CellMG/grids/in.2_big Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/in.2_small_a Tests/LinearSolvers/C_CellMG/grids/in.2_small_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d commit 536c2f7720a7758145b17e17694a3f476d107522 Author: lijewski Date: Tue Mar 22 21:22:53 2005 +0000 Changed the default tol & made dump_VisMF default to true. Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 8bbdd5db8e9797367ceae6e6ef715f266447359f Author: lijewski Date: Tue Mar 22 19:23:08 2005 +0000 Progress merging in periodic stuff. Src/LinearSolvers/F_MG/stencil.f90 commit 47b8626dbb199ef640b94e852cd2e79949e9854d Author: car Date: Thu Mar 17 23:34:52 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit 1ca69aacd95fe3204045f296f54d922239da5ddc Author: lijewski Date: Thu Mar 17 22:05:51 2005 +0000 Work needed to add "cross" argument to fill_boundary. Src/F_BaseLib/layout.f90 commit d4c52506612aaff6e0fda66460ba1ae10c5a92fa Author: lijewski Date: Thu Mar 17 21:57:25 2005 +0000 slight code rearrangment Src/F_BaseLib/boxarray.f90 commit 25ac3448396e62d6bbc9abefb497ac89d59edb7b Author: lijewski Date: Thu Mar 17 21:56:54 2005 +0000 Added optional cross argument to fill_boundary. Src/F_BaseLib/multifab.f90 commit dad342d0dce6cbd64e8c6ba92197de7358268e2e Author: car Date: Wed Mar 16 23:33:59 2005 +0000 corner/edge extrap Src/LinearSolvers/F_MG/stencil.f90 commit 7086b012b37363ed90c8be91b6702df607df1539 Author: lijewski Date: Wed Mar 16 21:56:00 2005 +0000 Added boxarray_box_corners() Src/F_BaseLib/boxarray.f90 commit 75b6304831786fec04e952c7cf8688b8a341a02c Author: car Date: Wed Mar 16 19:00:42 2005 +0000 OMP syntax fixes Src/F_BaseLib/multifab.f90 commit e2901289288454680b12d3d5ce59586043b96580 Author: car Date: Wed Mar 16 17:30:23 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit 19b76eaef7fab5cd81408b8fb28b11ab769e4778 Author: lijewski Date: Tue Mar 15 21:43:34 2005 +0000 Better test for early return from multifab_internal_sync_shift Src/F_BaseLib/multifab.f90 commit 7fd0ddf8cc0a3dcca3469976570fcf6e6faabeb0 Author: lijewski Date: Tue Mar 15 21:00:30 2005 +0000 internal_sync's now appear to work for periodic. Src/F_BaseLib/multifab.f90 commit d133f62ddf99eae8f4e87a4710d446cc738eac98 Author: lijewski Date: Tue Mar 15 20:59:38 2005 +0000 slight change in notation Src/F_BaseLib/box.f90 commit 20fa607f3e76a96cdf0a292f0dcdd2de68e796cd Author: car Date: Tue Mar 15 19:14:00 2005 +0000 think i've fixed ann's checkpoints Src/F_BaseLib/fabio.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit 8c88a056f3384b4353c2010687c06e62bb61976e Author: car Date: Mon Mar 14 22:56:37 2005 +0000 denodalize Src/F_BaseLib/box.f90 commit 80ace0b4e8224972c655888ef596a346cbcbc43d Author: almgren Date: Mon Mar 14 20:58:35 2005 +0000 Remove nodal from the writing of the bounding box in fabio_ml_multifab_write_d. Src/F_BaseLib/fabio.f90 commit ec031d2891aedf48504fbc0f42fdb55de9cdeb6a Author: car Date: Mon Mar 14 20:45:11 2005 +0000 add flux_reg.f90 Src/F_BaseLib/GPackage.mak commit 894be3f9ef0ab001436d9466217136184ca1789f Author: car Date: Mon Mar 14 20:44:50 2005 +0000 read nodal mf Src/F_BaseLib/box.f90 Src/F_BaseLib/fabio.f90 commit 410e40101dcf938ef7aa6b6886ad9dffc93a51f8 Author: almgren Date: Mon Mar 14 20:29:12 2005 +0000 New flux register code - this differs from boundary registers in that these are defined in fine index space at the boundaries of fine grids. Src/F_BaseLib/flux_reg.f90 commit 00df4da58c3bd47790eb3ca5cb78c0bda49d1a8d Author: car Date: Sat Mar 12 19:43:51 2005 +0000 cvs strings Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/timer_c.c commit a08d707a316ef4ea23bb129cc9630720531ee74f Author: car Date: Sat Mar 12 14:39:49 2005 +0000 mac i/o is like aix Src/F_BaseLib/fabio_c.c commit 9088e54c87e5b065b489eb8279428450e031062f Author: lijewski Date: Sat Mar 12 00:24:34 2005 +0000 Some work to make internal_sync periodic-aware. Needs to be tested. Src/F_BaseLib/multifab.f90 commit cfcb6534aeca1b4c535515d5a494ecc4b7d45cad Author: lijewski Date: Sat Mar 12 00:23:34 2005 +0000 A little simplification. Src/F_BaseLib/layout.f90 commit bc017ede278139672349222431c08199ea9c0bb9 Author: lijewski Date: Sat Mar 12 00:22:31 2005 +0000 periodic_shift() -> box_periodic_shift() Src/F_BaseLib/box.f90 commit a5fa5e09beeed3c28243ba40a682cb86e17e53c7 Author: lijewski Date: Fri Mar 11 22:28:16 2005 +0000 Added box_contains_strict() Src/F_BaseLib/box.f90 commit da87eb547544dda4c2cb6b4ab63ef075d136ad29 Author: lijewski Date: Fri Mar 11 19:20:37 2005 +0000 Didn't have easy() functions quite correct for nodal MultiFabs. Src/F_BaseLib/multifab.f90 commit 20b24e3e10d6ee940441f350786a41892a558107 Author: lijewski Date: Thu Mar 10 23:00:05 2005 +0000 Made the easy() functions in multifab fill_boundary periodic-aware. Src/F_BaseLib/multifab.f90 commit 0130c53384ae25331c815827ac753e20195ac416 Author: lijewski Date: Tue Mar 8 21:50:44 2005 +0000 Some progress on making fill_boundary periodic-aware. Src/F_BaseLib/layout.f90 commit 054e598ccab0dcaa32ea2e891071457aacead2cb Author: almgren Date: Tue Mar 8 17:29:13 2005 +0000 Fix for 3d so now works correctly with Neumann bcs. Src/LinearSolvers/F_MG/sparse_solve.f90 commit 198eb064268ae2e7dd28c0dca0e2cc141e1b4519 Author: lijewski Date: Mon Mar 7 23:11:41 2005 +0000 Looking good. Src/F_BaseLib/box.f90 commit 568bc33ecc980852fe33a8d30ae2ae8f45ecfffb Author: almgren Date: Mon Mar 7 22:16:01 2005 +0000 Works now in 3-d for Dirichlet bc's, still broken for 3-d Neumann. Src/LinearSolvers/F_MG/sparse_solve.f90 commit e62866d728a316f2152bc500ddae1be937809fb3 Author: lijewski Date: Mon Mar 7 21:52:39 2005 +0000 Rewrote a few things slightly differently. Src/F_BaseLib/box.f90 commit 5373c1de5bbd84edb5457ace26da53700ce22eb4 Author: almgren Date: Mon Mar 7 21:52:19 2005 +0000 Fix bug in setting coarse-fine interfaces to Dirichlet. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 543eff91b78db77f1e6b527bacfab177d27ad913 Author: almgren Date: Mon Mar 7 20:28:56 2005 +0000 Fixed Neumann bug in 2-d. Src/LinearSolvers/F_MG/sparse_solve.f90 commit a210f723b5fb73e264ce0f64be936e8daf1f8a11 Author: almgren Date: Mon Mar 7 19:57:04 2005 +0000 Now works with Neumann bc's in 2d. Still need to fix 3d. Src/LinearSolvers/F_MG/sparse_solve.f90 commit 1e2ca940323da3601271cb63b51360750c7efe8c Author: car Date: Fri Mar 4 20:27:10 2005 +0000 efactor is used in case doing a residual or an operator application Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 32497989040300afff9edb6a54cb204f3f427e24 Author: car Date: Fri Mar 4 20:25:48 2005 +0000 remove extraneous print statments Src/LinearSolvers/F_MG/stencil.f90 commit 96b3f58d706e3120da1effc44d3219787db1422f Author: lijewski Date: Thu Mar 3 23:35:38 2005 +0000 Added periodic_shift. Still got to test it a tad more. Src/F_BaseLib/box.f90 commit e6b3d3bbcc1044ceaaff1d40bf7c6fa371377efc Author: almgren Date: Thu Mar 3 19:18:31 2005 +0000 Fixed some bugs in order to run on more than one grid. Runs on multiple grids with Dirichlet bc's but not yet working for Neumann. Src/LinearSolvers/F_MG/sparse_solve.f90 commit a188430c467e8ea216979379839f5f51f91c23f9 Author: car Date: Thu Mar 3 02:25:05 2005 +0000 -C converts cvmgt to MERGE; as per f90 Tools/C_scripts/strip72 commit 77260d80c95d5a419ac6a9f07a50558094828338 Author: almgren Date: Wed Mar 2 22:35:36 2005 +0000 Cleaned up so it doesn't use the neighbors stuff, that was only used to generate an approximate size. Src/LinearSolvers/F_MG/sparse_solve.f90 commit d1c692eff764809bbfd89f850ab62c7aba7b26cb Author: almgren Date: Wed Mar 2 22:21:03 2005 +0000 Added sparse solver for nodal system. Tested on single grid as top-level solver and bottom solver for MG, works in both cases. Src/LinearSolvers/F_MG/sparse_solve.f90 commit 9c9d0edfdf3d1bdfea2562279c403b8a29ebb85b Author: almgren Date: Wed Mar 2 22:20:09 2005 +0000 Now allows for call of nodal sparse solver as bottom solver. Src/LinearSolvers/F_MG/mg.f90 commit 5082aa474e3201d6b7d06d59198c5695c271e1b7 Author: almgren Date: Wed Mar 2 21:35:08 2005 +0000 Bug in ml_interface_2d : should test on face +/- 1, instead was testing on +1 vs -2. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit e68a52893978775bd4c3691bb92f67347721ba73 Author: car Date: Wed Mar 2 17:42:56 2005 +0000 newest intel 8.1 fixes check shape pointer Tools/F_mk/GMakedefs.mak commit c346419fa7920319f8e5cabf969ceea95b8bb829 Author: almgren Date: Tue Mar 1 20:10:54 2005 +0000 Fixed the stencil for nx or ny = 2 (shouldn't be skewed). Added some new code for fluxes... Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit f6e940cdf231df8fea916a7b23d3da637faedd48 Author: almgren Date: Tue Mar 1 20:09:57 2005 +0000 Changes the way the mini-cycle is handled. Src/LinearSolvers/F_MG/mg.f90 commit e2c1ecb842189b27f22cb2346652fbf3094ba7c5 Author: almgren Date: Tue Mar 1 20:03:25 2005 +0000 Clean-up... Src/LinearSolvers/F_MG/sparse_solve.f90 commit c7071b7f95be2436e068ba3fa866f3a717600332 Author: car Date: Fri Feb 25 16:27:24 2005 +0000 somedebugging Src/F_BaseLib/GPackage.mak Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Tools/F_mk/GMakedefs.mak commit 0954314d324d0674b7fe6dcf1ea01736a539e0fc Author: car Date: Sun Feb 20 16:51:34 2005 +0000 fixes for dft Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/t_bx.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_bx.f90 Tests/F_BaseLib/t_main.f90 commit 883230ef9220bc19dfe8c24797ed653cf9098b35 Author: car Date: Sun Feb 20 16:50:57 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit 9e47ef623bb548418cefd8764ce2244f8caea125 Author: car Date: Fri Feb 18 14:25:53 2005 +0000 *** empty log message *** Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bx.f90 commit 1e35231daf5e154a2ee008291580565751454bbf Author: car Date: Thu Feb 17 23:21:09 2005 +0000 debug and opt flags for IBM on Mac Tools/F_mk/GMakedefs.mak commit e51763f3379d6d6400ab41070cdd2a73a51e2d84 Author: car Date: Thu Feb 17 22:03:31 2005 +0000 no stinking mutex's Src/C_AMRLib/AmrLevel.cpp commit 483438ce9fc979f0ace5801eb6b9b0d9b7b33d0e Author: car Date: Wed Feb 16 23:10:40 2005 +0000 more arithmetic in multifab Src/F_BaseLib/multifab.f90 commit a392809b0c92b49e386ccd34d31323aef991dfc1 Author: car Date: Tue Feb 15 21:54:19 2005 +0000 more dft debug changes Src/F_BaseLib/multifab.f90 commit 723a8e79e6c7bdce36a5c2bae225b72e09e54b51 Author: car Date: Sat Feb 12 20:15:43 2005 +0000 MPI_recv takes a status argument Src/F_BaseLib/pingpong.f90 commit 411d010e616d3447dd4c75a441a94ba3ff313625 Author: car Date: Thu Feb 10 23:37:21 2005 +0000 more fixes for dft Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit ff480a09feeab6887d102abf2156a5619c0c7ab4 Author: car Date: Wed Feb 9 23:35:33 2005 +0000 more progress Src/F_BaseLib/box_util.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Tools/F_mk/GMakedefs.mak commit fdedd0f5978587e7514857fa683606c8c214ba15 Author: car Date: Tue Feb 8 23:54:13 2005 +0000 fixes for eigensolvers Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/stencil.f90 Tools/F_mk/GMakedefs.mak commit dc0a913a33f6b40988919421d3f578b4d3b62c9b Author: lijewski Date: Wed Jan 26 23:20:51 2005 +0000 Got rid of std::pow() call. Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 010c0ef8da0fd0646c207649d2a8a25819b9c16d Author: lijewski Date: Wed Jan 26 23:20:30 2005 +0000 Got rid of std::pow(). Src/C_BoundaryLib/InterpBndryData.cpp commit 3bfb976d9f7109c3143ce75259c2d24ab83eb42a Author: lijewski Date: Wed Jan 26 22:52:54 2005 +0000 Fix for Jacquard. Src/C_BoundaryLib/InterpBndryData.cpp commit 6db487679515969366e1a44323dbbe1bec961943 Author: car Date: Wed Jan 26 16:33:15 2005 +0000 fancy gfortran Tools/C_mk/Make.defs commit 7233048b02e2b9876f95f80899c787092f3353b4 Author: car Date: Wed Jan 26 16:31:27 2005 +0000 fancy gfortran Tools/C_mk/Make.defs commit a5d45a5df5da028cd370146d1f7a3937fb5d630a Author: car Date: Wed Jan 26 00:20:31 2005 +0000 crafty way of getting path to libf95.a Tools/C_mk/Make.defs commit 6b1a36024fbc44b46141de901abfcffbf243b882 Author: lijewski Date: Tue Jan 25 21:27:19 2005 +0000 Mod for PathScale when USE_MPI=TRUE on jacquard. Tools/C_mk/Make.Linux commit a4ffedea1d8d792d3a66cf320e8661a437ac5328 Author: lijewski Date: Tue Jan 25 18:45:00 2005 +0000 Mods to PathScale to compile on NERSC's jacquard system. Tools/C_mk/Make.Linux commit 3ab6bf71e740f13179a0430ea6af10a5833c0b71 Author: car Date: Mon Jan 24 23:54:32 2005 +0000 *** empty log message *** Src/F_BaseLib/fabio_c.c Src/F_BaseLib/pingpong.f90 Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/test/main.f90 Tests/F_BaseLib/main.f90 commit 3d3d4288db34b01face3c2488856b293992a6819 Author: almgren Date: Tue Jan 11 21:48:30 2005 +0000 Put trim(names(i)) instead of names(i) so that amrvis can read the names of the variables without the extra white spaces... Src/F_BaseLib/fabio.f90 commit 40b02322bd161b124e92abd92c61c44194425045 Author: car Date: Mon Jan 10 22:04:45 2005 +0000 White Space Fix dos->unix Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit c294768193af601af1dec03d6acdc0e5d120a6f5 Author: lijewski Date: Fri Jan 7 17:38:55 2005 +0000 fix to operator= Src/C_BoundaryLib/BndryRegister.cpp commit 9072c2000ea574e7c746a9aad56a254494d0801b Author: lijewski Date: Thu Jan 6 22:18:50 2005 +0000 extra gunk for LAM Tools/C_mk/Make.mpi commit 71b10e49e2fa7ddc8e2cfa6ca43ff74457bd0832 Author: lijewski Date: Wed Jan 5 22:19:46 2005 +0000 fix to operator= Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp commit aedce090a628e6e5cbb1129ee98b4a53693a8338 Author: lijewski Date: Wed Jan 5 21:53:21 2005 +0000 fix to operator= Src/C_BaseLib/Tuple.H commit 7bef65ebbbabea43475bec11647869377a4674b8 Author: car Date: Tue Jan 4 23:33:22 2005 +0000 JEFF_TEST turns on mpi_waitall Src/C_BaseLib/ParallelDescriptor.cpp commit f68c181d66cf679eadfd5b673a20e1ddd38ac4dd Author: car Date: Tue Jan 4 22:36:15 2005 +0000 name map Tools/C_mk/Make.frank commit 72dae790503862f551bd104b0a1f42f07adf5fd3 Author: car Date: Tue Jan 4 22:10:41 2005 +0000 frank archive file Tools/C_mk/Make.frank commit 96297ec7da57b970c79b612774f61938b03af1b0 Author: car Date: Tue Dec 21 17:10:59 2004 +0000 g95 tweaks Src/F_BaseLib/filler.f90 Tools/F_mk/GMakedefs.mak commit e25d77ebfa822af5358e6d36f09d65e36e516f38 Author: car Date: Tue Dec 21 15:32:03 2004 +0000 darwin Src/F_BaseLib/GPackage.mak commit 1122e9d5f2d454b09b663ba333c45d0a2b93fbc0 Author: car Date: Tue Dec 21 15:22:58 2004 +0000 some minor fixes to silence warnings Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fabio.f90 Tools/F_mk/GNUmakefile Tools/F_mk/makefile commit 4437415232ae7ff0dd1a560ae194c4229353d395 Author: car Date: Fri Dec 17 21:53:05 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/mboxarray.f90 Src/F_BaseLib/parallel_stubs.f90 commit e53eb44c2b647b267343430b865b6f76a6e76ee8 Author: car Date: Fri Dec 17 17:33:53 2004 +0000 MF_DEBUG_FILL: untested Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 6c5f766b16e6af69793e9ef61bdf680a37d2603d Author: vince Date: Thu Dec 16 20:36:54 2004 +0000 this version works for me using CC. Tools/C_mk/Make.IRIX64 commit 397e49f0a045aefb7bafd3df84410c4aed15eed2 Author: car Date: Wed Dec 15 18:40:42 2004 +0000 can now read denfile to setup test case Src/LinearSolvers/C_NodalMG/proj.cpp commit 41829590fc4761ad8a893fb9d5607cda7a3b83d6 Author: car Date: Wed Dec 15 18:39:56 2004 +0000 changes: 1) now bottom toleranced decreased by a factor of 10 2) Expert mode is default and gone 3) failure to converge is not a BoxLib::Error; it sets the return code to 8 Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 3c62e472bee7b78059fd18b5bcab8cdf8d669ccb Author: car Date: Wed Dec 15 18:06:54 2004 +0000 stupid warning wrap w/ IOProcessor() Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 2e16292ac758e41f9d4feb4c50aeba49e98469a7 Author: lijewski Date: Tue Dec 14 22:39:07 2004 +0000 *** empty log message *** Src/C_BaseLib/test/tVisMF2.cpp Tests/C_BaseLib/tVisMF2.cpp commit 26e336ae547114b252b04742fc5d8c2b9162e782 Author: car Date: Fri Dec 3 18:54:52 2004 +0000 clean/realclean not as painful Tools/C_mk/Make.rules commit e13be4fbda9c630013644c7be4a6065f1d485de6 Author: car Date: Fri Dec 3 17:44:04 2004 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit 349932412a9d6fa20eebdf4bca86ae32f150d399 Author: almgren Date: Wed Dec 1 18:37:17 2004 +0000 Need change in setting up mba%rr in order to be consistent with new mboxarray_build_rr routine. Src/F_BaseLib/box_util.f90 commit c568d1421572876a79161421c50abde612d85826 Author: lijewski Date: Tue Nov 30 19:21:09 2004 +0000 added Compare class Src/C_BaseLib/IntVect.H commit 2b7b6a9c6206e717ed7e64055f4b6e5cbc370cb4 Author: almgren Date: Mon Nov 29 22:42:16 2004 +0000 Use bc_module as opposed to mg_bc_module. Src/LinearSolvers/F_MG/stencil.f90 commit 33ea3d8d1d2f858f05a97780fd6347ce639dacaf Author: almgren Date: Mon Nov 29 22:40:55 2004 +0000 Added edge restriction. Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit 0f16050c23c64a2917b0964d114a0df1c6b29fe4 Author: almgren Date: Mon Nov 29 22:40:30 2004 +0000 Removed print statements. Src/LinearSolvers/F_MG/mg_smoother.f90 commit bd9f69f63de6b5171330c0bcb9efe54e92e5ba43 Author: car Date: Mon Nov 29 20:53:24 2004 +0000 bc interp renewed Src/F_BaseLib/GPackage.mak commit 01c966c67de45165ca373caed8137b11dc401766 Author: almgren Date: Mon Nov 29 20:14:32 2004 +0000 bc.f90 holds the definitions of the bc type parameters. lincc_interp2d in interp.f90 has a bug fix. Src/F_BaseLib/bc.f90 Src/F_BaseLib/interp.f90 commit 007562a944b6a8727331db61a20b1e87af1e7a79 Author: car Date: Sat Nov 27 20:28:09 2004 +0000 fix for totalview Src/F_BaseLib/GPackage.mak Src/F_BaseLib/interp.f90 Src/F_BaseLib/mboxarray.f90 commit 5bf8b178ae798dce16c77ad7e85a9b7cfd0bd9ec Author: almgren Date: Fri Nov 19 20:28:22 2004 +0000 Bug in index loop for defining voffx. Src/F_BaseLib/interp.f90 commit e4a08abdc6ac9ecbb7a1abf49460583cb9afacaa Author: car Date: Thu Nov 18 17:55:46 2004 +0000 bipolar disorder Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile commit fcb99dde695b2a39c7728e254488d80d0ef9769e Author: car Date: Thu Nov 18 17:42:01 2004 +0000 XLC fixes Src/F_BaseLib/multifab.f90 Tools/F_mk/GMakedefs.mak commit 349020cee3cb868f5ffc1297a77b54c69a9e1be5 Author: almgren Date: Thu Nov 18 17:36:36 2004 +0000 Modified calling sequence of lin_cc_interp_3d so it matches that of 2d. Src/F_BaseLib/interp.f90 commit 08641960137e41430550b7a06cd084b5b182719a Author: car Date: Wed Nov 17 20:08:25 2004 +0000 using lbound,ubound should work Src/F_BaseLib/multifab.f90 commit e3c0b22e9310e4bd60e1e57387422acd96caa373 Author: car Date: Wed Nov 17 19:09:22 2004 +0000 multifab_fab_copy Src/F_BaseLib/multifab.f90 commit b86bd3eff421a50f85b72033d8e731cd5dd9e8a1 Author: car Date: Wed Nov 17 16:29:36 2004 +0000 FreeBSD Tools/F_mk/GMakedefs.mak commit 6e2f6720bf6999a3810e7f92363877ff4ba8d029 Author: car Date: Tue Nov 16 23:56:24 2004 +0000 order of include Darwin? Src/F_BaseLib/timer_c.c commit a910d0b28debaf706d61d75b726df8c59005232d Author: car Date: Tue Nov 16 23:21:19 2004 +0000 MacOS X Src/C_BaseLib/FPC.cpp Tools/C_mk/Make.Darwin commit f4710f69ca7e8dfce6541db7e62dff84da0fb8dc Author: car Date: Sun Nov 14 01:21:32 2004 +0000 *** empty log message *** Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/stencil.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit dd6968be77626a24457df0284d99f31ac8254789 Author: car Date: Fri Nov 12 20:55:33 2004 +0000 gotta go home Src/LinearSolvers/F_MG/stencil.f90 commit 9ea8a4fdd12e740228aa89d734bc60101a579f26 Author: car Date: Thu Nov 11 22:31:29 2004 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit 44d75da840402026d8fcc03867a0c4f31b2c1fe0 Author: car Date: Thu Nov 11 22:24:34 2004 +0000 *** empty log message *** Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/mboxarray.f90 Tools/F_mk/GMakedefs.mak commit d4c8d32c7e5b4a48e2c274b693ed900eb2c70b13 Author: car Date: Wed Nov 10 22:39:14 2004 +0000 minor tweaks Src/F_BaseLib/bl_constants.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 702f94fcebd51c1cde0a54228a13234a1f4767ba Author: car Date: Mon Nov 8 22:33:33 2004 +0000 minor tweaks for F Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/mt19937ar.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/pingpong.f90 Src/F_BaseLib/plotfile.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit acbc89095a3076284eca0fd3ebdd40b181f5a111 Author: car Date: Fri Nov 5 19:11:16 2004 +0000 MLW: barrier in glean prevents buffer overrrun Src/C_BaseLib/BLProfiler.cpp commit 761c53a4fcfce77cb0e9002382e4adbaa75df593 Author: car Date: Thu Oct 28 19:17:15 2004 +0000 tweak Tools/F_mk/GMakedefs.mak commit 2a7645fd7d1a296c31b1d58cb2d58f3111326dfa Author: car Date: Thu Oct 28 17:27:37 2004 +0000 *** empty log message *** Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit edec0da57c5934032707ea88bc95dab5ae0cb10f Author: car Date: Fri Oct 15 21:36:35 2004 +0000 *** empty log message *** Src/F_BaseLib/fabio.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit 6c48adeae0300a4659d5ac8a19aa14fcd1e69fb0 Author: car Date: Fri Oct 15 20:34:51 2004 +0000 more changes for eigenproblem Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 Tools/F_mk/GMakerules.mak commit 900b521804dc65d3f2fb4f876a9bce0f4116a1f2 Author: car Date: Fri Oct 15 20:31:58 2004 +0000 first cut at ml_multifab_read Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/list_box.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit 211a22360b6b3c0d9060180a18b9982dd66a182d Author: lijewski Date: Wed Oct 13 21:52:22 2004 +0000 Set default for "verbose" to true for the time being. Added "only_heaviest_cpu". Src/C_BaseLib/DistributionMapping.cpp commit be82e93bc00952c6cf5a63856ea5a9cd15b76b82 Author: lijewski Date: Wed Oct 13 20:57:03 2004 +0000 output a bit more stuff Src/C_BaseLib/DistributionMapping.cpp commit 5a895ca5af5ce1cb137aef524c08792773be5385 Author: car Date: Tue Oct 12 15:44:07 2004 +0000 If the number of processors is <= 8 then use the 'better' metis partitioner. Src/C_BaseLib/DistributionMapping.cpp commit 38dcdcc7606c4aefb89632ccd9d15d5d5b03f7fd Author: car Date: Mon Oct 11 23:26:35 2004 +0000 If metis_opt is != 0 then use edgeweights in addition to vertex weights. The edgeweights are equal to the volume of the intersection of the target box grown by one and the source boxs. Src/C_BaseLib/DistributionMapping.cpp commit 63fda6d1988e4d5535253a34a0e3be2e6827438e Author: lijewski Date: Mon Oct 11 22:45:37 2004 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 157f832a24b2d866c6c36a0b6cc4a23ec45ad1e5 Author: lijewski Date: Mon Oct 11 22:00:12 2004 +0000 Fixed Chuck's bug Src/C_BaseLib/DistributionMapping.cpp commit b6bc72726b3bb43fa21f32d2184c15677204c14e Author: lijewski Date: Mon Oct 11 21:57:09 2004 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit d586aaaa2059d7124709b3e7d28d895a166e4c17 Author: lijewski Date: Mon Oct 11 21:47:03 2004 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 327aeccdf4c7c6569e29889d6959e0db31142cc9 Author: car Date: Mon Oct 11 21:17:13 2004 +0000 for metis Tools/C_mk/Make.defs commit ed87788876392e69f7e10e351e04bc6f4828e8e3 Author: car Date: Mon Oct 11 20:33:17 2004 +0000 ops Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/test/GNUmakefile Tests/C_BaseLib/GNUmakefile commit b297203b266f906b52ecc758894ae66a57daf4dc Author: car Date: Mon Oct 11 20:20:47 2004 +0000 added metis Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 53ab355a2489dd434a8aacbd4417d355f12627eb Author: vince Date: Wed Oct 6 23:54:50 2004 +0000 zero pointer after delete so clear can be called on uninitialized fabs. Src/C_BaseLib/VisMF.cpp commit f2e9190bbe7f1a0d01ba22412a0b112998cb1b93 Author: car Date: Tue Oct 5 01:41:46 2004 +0000 minor fixes Src/F_BaseLib/fabio_c.c commit e82f3bc4d4e07b3ec4891ecac3bf3bb37a04f155 Author: car Date: Tue Oct 5 01:40:56 2004 +0000 windows fixes Src/F_BaseLib/plotfile.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil.f90 commit a7c1d24e824bbf5810e21b1f84f9432085cd1ee2 Author: car Date: Mon Oct 4 19:41:54 2004 +0000 ml changes Src/F_BaseLib/multifab.f90 commit 76fbff6c43747ebacd29c0f9d39ed0124ebfc3e0 Author: car Date: Sat Oct 2 22:49:41 2004 +0000 *** empty log message *** Src/F_BaseLib/filler.f90 Src/F_BaseLib/mt19937ar.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/test/main.f90 Src/LinearSolvers/F_MG/stencil.f90 Tests/F_BaseLib/main.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit 36a075224a260f71c3276661eeae83d758ef3cd9 Author: car Date: Thu Sep 30 19:02:41 2004 +0000 corrected fab dimensions Src/F_BaseLib/fabio.f90 commit 52b21666a78d0b774f48aebc82b2f69352a3729a Author: car Date: Tue Sep 28 17:56:35 2004 +0000 formatted io for plotfiles Src/F_BaseLib/fabio.f90 commit 94a89bf35c886af089170c85c5317cbd70c9440f Author: car Date: Wed Sep 22 17:53:41 2004 +0000 more constants Src/F_BaseLib/bl_constants.f90 commit b594a1f3cd2b78e498209957df555c51a40c9753 Author: car Date: Tue Sep 21 17:38:17 2004 +0000 fixes for ia64 Src/F_BaseLib/mt19937ar.f90 commit 01095cc2a388eb99ab20e1d25074502157b16119 Author: car Date: Mon Sep 20 21:49:34 2004 +0000 make extrap bc eat boundary value Src/LinearSolvers/F_MG/stencil.f90 commit c9487e3a5a96b99df307c0cbf71c0f3a3380c64c Author: car Date: Fri Sep 17 22:45:39 2004 +0000 minor thrashing Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/fabio.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 Tools/F_mk/GMakedefs.mak commit 6196a2b4ef881422608fccd10b8e497ccbf8a8b7 Author: car Date: Fri Sep 17 20:30:36 2004 +0000 Make.IRIX64 Tools/C_mk/Make.IRIX64 commit 3914f4b1da7b469dd526e71ae4b1a38697fe81af Author: car Date: Thu Sep 16 16:12:45 2004 +0000 intel8 bug fixes Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_util.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GNUmakefile commit 71082b1b66b5ca445881163de236f406d204eac4 Author: car Date: Wed Sep 15 22:22:18 2004 +0000 windows fixes Src/F_BaseLib/NPackage.mak Tools/F_mk/NMakedefs.mak Tools/F_mk/NMakerules.mak commit 4e9324af3363f4a5732fe4fdfd2c8fe92e58d9a1 Author: car Date: Mon Sep 13 19:55:34 2004 +0000 *** empty log message *** Src/F_BaseLib/f2kcli_crayx1.f90 commit 22edc03421c877e7662a4b9cb497e981633d5542 Author: vince Date: Mon Sep 13 19:02:23 2004 +0000 flags for cxx. Tools/C_mk/Make.OSF1 commit 5eb9e944c881b19365bd58ffe58b802189ae599d Author: car Date: Thu Sep 9 16:35:08 2004 +0000 more spinning Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 Tools/F_mk/GMakedefs.mak commit fad650ffe77d0a924784a805b7d34080bc0e08aa Author: car Date: Tue Sep 7 16:22:00 2004 +0000 minor changes Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 Tools/F_mk/GMakedefs.mak commit dfaa7e17b876648adba0af9f51a7f8aee123cf9d Author: vince Date: Fri Sep 3 23:59:19 2004 +0000 added check for capfinestlevel. Src/C_AMRLib/StationData.cpp commit 7186242283d9f921860bcb402eeb975e5238ec19 Author: welcome Date: Fri Aug 27 17:47:57 2004 +0000 Changed options for CRAYX1 removed -O in C++, does nothing Default C++ optimization is -O2 Added options for loopmark listings to see where vectorization happens. Tools/C_mk/Make.CRAYX1 commit 0721b1a6e9c54c08ce58884e36b2c39d3afa9cca Author: car Date: Wed Aug 25 19:32:27 2004 +0000 FCOMP=g77 Tools/C_mk/Make.defs commit 78227cec8f992cb727bd78f957002d229087993c Author: car Date: Tue Aug 24 22:33:16 2004 +0000 Intel/Lahey fix Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit b6b3876ce21d3c85c1fefa364086f3438c6ebf07 Author: marc Date: Mon Aug 16 22:40:50 2004 +0000 Add test for max ref ratio in PROTECT_INTERP Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 42213ab3e7f8f0f99dfd38007cee05fed2fa55f1 Author: car Date: Thu Aug 5 22:21:54 2004 +0000 slight changes Src/F_BaseLib/knapsack.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 commit d7c55d06cb4d582ba4080feb17071333b9283539 Author: car Date: Thu Aug 5 16:45:18 2004 +0000 windows fixes Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/cluster.f90 Src/LinearSolvers/F_MG/stencil.f90 commit a5e885339f38f1c37c64f826e6ce56a41bbfcf82 Author: car Date: Wed Aug 4 22:46:08 2004 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit f2cb29f722b89a083fe64e11b6c8496dac94f42f Author: car Date: Wed Aug 4 19:53:26 2004 +0000 more mboxarray stuff Src/F_BaseLib/mboxarray.f90 commit 756e43d7e5989346222168c84f4eece12fb89440 Author: car Date: Wed Aug 4 00:52:04 2004 +0000 windows update Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 9a5a2a140c7a1647969c29ac447d2299ffb0a486 Author: car Date: Tue Aug 3 22:47:17 2004 +0000 *** empty log message *** Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/stencil.f90 commit e15eba5661180ed9a116cf62c40e0aa123e736e3 Author: car Date: Mon Aug 2 22:11:38 2004 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit 8fdbc1627b54ab4cd4c36e0035cf2e729a599e33 Author: car Date: Fri Jul 30 18:01:29 2004 +0000 minor tweaks Src/LinearSolvers/F_MG/mg_smoother.f90 Tools/F_mk/GMakedefs.mak commit 3ff88aa9cf8c8b1fa856825bfb7be2b36c97696f Author: car Date: Fri Jul 30 17:46:49 2004 +0000 smaller files Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit c624c543ec9448bd9be99313e97208d3531acc55 Author: car Date: Thu Jul 29 20:32:23 2004 +0000 altrix Tools/C_mk/Make.defs commit a6abde51ce08d701a3f978f065ae43f4859e7a31 Author: car Date: Thu Jul 29 18:53:12 2004 +0000 altix Src/C_BaseLib/FPC.cpp commit 66444630a78fd470bff7a33d591cb367e610fe26 Author: car Date: Thu Jul 29 15:35:03 2004 +0000 crayx1 Tools/C_mk/Make.CRAYX1 commit 0a3ea4370183b38a1d24a15661279aa7fb37f961 Author: welcome Date: Wed Jul 28 20:48:30 2004 +0000 Modification for NEC SX6. Needed to explicitly strip-mine the main loops in hgrlxu. Brain-dead Sx6 compiler partially vectorizes the loop but needs to allocate temporary array. Makes an assumption about the max length of the loop and generates a run-time error if the actual length is larger than the assumption. Can request larger array with pragma, but only up to about 15000. New function only called on SX6, since not very well tested. Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit bcd9aa399274b832d785a63881f741262d593d71 Author: welcome Date: Wed Jul 28 20:20:24 2004 +0000 try again to update makefiles for NEC SX6 Tools/C_mk/Make.SUPERUX Tools/C_mk/Make.defs commit d55a7cd6eee2e8085271a117702a1c5aa085beee Author: welcome Date: Wed Jul 28 19:52:18 2004 +0000 Minor updates for NEC SX6 Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FPC.cpp commit 9b50bfe4844a7ff665dc40968bcc03780edc832a Author: car Date: Wed Jul 28 18:06:05 2004 +0000 fixes for X1 Tools/C_mk/Make.CRAYX1 commit 3109abab5c734ebbfda7e6ff83d6e87e952efa60 Author: vince Date: Tue Jul 27 22:51:25 2004 +0000 added std:: Src/C_AMRLib/DatasetClient.cpp commit 0a08b7a9e78466a69fa82e0e6d38ee53d3dc526d Author: vince Date: Mon Jul 26 22:24:29 2004 +0000 call fix for arrayview. Src/C_AMRLib/DatasetClient.cpp commit b6470af68cfe86d4d9767e556579a6d79f36a22a Author: car Date: Mon Jul 26 20:49:39 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit 72eb71b04bab1b3469925fe0943ecbefed88c197 Author: car Date: Mon Jul 26 20:49:09 2004 +0000 gfortran trial Tools/F_mk/GMakedefs.mak commit d8f0312c52423a26e21cb2d66f4c0c0c7fd1e453 Author: car Date: Mon Jul 26 20:48:18 2004 +0000 cray x1 fixes Src/F_BaseLib/f2kcli_crayx1.f90 Tools/F_mk/GMakedefs.mak commit 308db54d460fdb8dbad5403af95938440698fa97 Author: car Date: Mon Jul 26 19:37:21 2004 +0000 ihi->ilo Src/F_BaseLib/interp.f90 commit 20fedb2cbf8671afe781adf8651a3a5ab68f986a Author: car Date: Mon Jul 26 19:36:59 2004 +0000 pointer association, not Src/F_BaseLib/cluster.f90 commit f3bf137f66b946ad676032f6678fb56810ffb456 Author: car Date: Mon Jul 26 19:25:57 2004 +0000 broken unitialized variables on IRIX Tools/F_mk/GMakedefs.mak commit 97953be18556308271ff62f4a8f1951b4edde0ca Author: car Date: Fri Jul 23 23:37:28 2004 +0000 cray bug work around Src/F_BaseLib/boxarray.f90 commit 1888a52fa5ede2af987007a8e5c7ccd94cbf6ba3 Author: car Date: Fri Jul 23 22:04:22 2004 +0000 crayx1 Src/F_BaseLib/f2kcli_crayx1.f90 Tools/F_mk/GMakedefs.mak commit 46459cb7b8f6284cf822bf8af741d526d25e68b5 Author: car Date: Thu Jul 22 17:33:12 2004 +0000 CRAY X1 port Src/C_BaseLib/CoordSys.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Tools/C_mk/Make.CRAYX1 Tools/C_mk/Make.defs commit d5281354df394c07d44db1b9c9b0f3071d26cca5 Author: car Date: Thu Jul 22 17:31:33 2004 +0000 fix for CRAY X1 Src/C_BaseLib/FPC.cpp Src/C_BaseLib/winstd.H commit 348b0bf434400904cf7278c2011c85ec0e2088fa Author: car Date: Wed Jul 21 23:50:01 2004 +0000 Makes CRAY X1 a little happier Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Pointers.H commit 1362c09f91d617c59fa7e1e510a9fd18d83df8f5 Author: marc Date: Thu Jul 15 17:16:50 2004 +0000 Add BL_NOLINEVALUES to list of defines Tools/C_scripts/dsp.mak commit 133ce1eed5dd67ef9739913841fed502bc118ec6 Author: car Date: Fri Jul 2 19:59:25 2004 +0000 new types definitions Src/F_BaseLib/bl_types.f90 commit 78f388b9cd6870a2f51a89b84c82498d3eb0268d Author: car Date: Wed Jun 30 22:10:48 2004 +0000 testing purposes Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/multifab.f90 commit 0662eb229b121158dbe08197d2be39e53fdb97be Author: almgren Date: Tue Jun 29 20:19:45 2004 +0000 Removed some print statements. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 17c27aeec444f0e5418724f6fad9c0210c55ac12 Author: almgren Date: Tue Jun 29 19:58:48 2004 +0000 Removed print statements. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit bc5ce3c98e8c2ffa54cc56546866e1fe1f9e6452 Author: car Date: Mon Jun 28 16:00:30 2004 +0000 minor fixes Src/F_BaseLib/BoxLib.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/test/fornberg_weights.f90 Tests/F_BaseLib/fornberg_weights.f90 Tools/F_mk/GMakedefs.mak commit 2c963801d3556c895be08460ad0c907dd467801e Author: car Date: Mon Jun 28 15:57:33 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_IO.f90 Tools/F_scripts/coco/coco.pl Tools/F_scripts/coco/e1.FF Tools/F_scripts/coco/e1.II commit c4eff2651ec9e8ba6f9d224ba72bdb058ed807e6 Author: almgren Date: Fri Jun 25 22:38:30 2004 +0000 Typo: had ny instead of nx. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 3173d662efb5c335c65bc9f546e6c6f875af41e1 Author: almgren Date: Fri Jun 25 20:01:32 2004 +0000 Changes to accomodate Neumann bcs in the case of factor 4 refinement. Change also relevant for factor 2 but that already worked. This uses values inside the domain instead of those reflected outside by Neumann condition (which didn't exist for factor 4). Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 72277441416649dbd9ed2223111ae43f1ac21687 Author: almgren Date: Thu Jun 24 22:06:30 2004 +0000 Fix in nodal_restriction_2d which gives same (working) result for factor 2 refinement but fixes the (broken) factor 4 refinement. Only fixed in 2d for now. Src/LinearSolvers/F_MG/mg.f90 commit d9dcffe58a5fcca0ad26947c16ea89081614fc27 Author: almgren Date: Thu Jun 24 20:23:14 2004 +0000 Fixed code for Neumann boundary conditions in 2d and 3d. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit e5a97a70dd0385d345a25b2c3a5440bbc266343e Author: almgren Date: Thu Jun 24 20:22:32 2004 +0000 Typo mis-spelling corrected. Src/LinearSolvers/F_MG/stencil.f90 commit a8f52092276b16830a15c83e87106e59c875d2d7 Author: car Date: Wed Jun 23 17:23:42 2004 +0000 bl_kiss not needed Src/F_BaseLib/GPackage.mak Src/F_BaseLib/NPackage.mak Src/F_BaseLib/bl_kiss.f90 Src/F_BaseLib/test/.cvsignore Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/.cvsignore Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit 1debffcf8d56b68a72406d9f981e10ce1e0fd979 Author: car Date: Tue Jun 22 16:42:05 2004 +0000 *** empty log message *** Tools/F_scripts/coco/coco_e.FF Tools/F_scripts/coco/e1.FF Tools/F_scripts/coco/e1.II commit 002a20494cfd2fffaa1d87a1d37ac59c5689caa5 Author: car Date: Tue Jun 22 16:42:05 2004 +0000 *** empty log message *** Tools/F_scripts/coco/coco_e.II commit 05598a4b5e3ddf378d2818d3ba31b4c1849ac841 Author: car Date: Tue Jun 22 16:42:05 2004 +0000 *** empty log message *** Tools/F_scripts/coco/coco.pl commit cd47cacf990f681764392dd640f63c72e2097d59 Author: car Date: Tue Jun 22 15:11:43 2004 +0000 initial Tools/F_scripts/coco/coco.pl commit 08daff055e395e9b6396e385688b0109d0aa60ab Author: almgren Date: Fri Jun 18 17:18:18 2004 +0000 Need to check _comp instead of COMP Tools/F_mk/GMakedefs.mak commit 7c2c9a3724804c65febd18ba5c1d70c8d7e80626 Author: lijewski Date: Tue Jun 15 19:24:16 2004 +0000 Added -mp flag Tools/C_mk/Make.defs commit 67e8ca16a59070abfc328003c5e76a4fb9c70df7 Author: car Date: Fri Jun 11 21:42:21 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_timer.f90 commit d441d2ad5827c0cc10c433b8c8422a907c4ab0cf Author: car Date: Fri Jun 11 03:50:41 2004 +0000 timer Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Src/F_BaseLib/timer_c.c Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit 550399b831fe42849beee923bc8198964ebca937 Author: car Date: Tue Jun 8 18:14:34 2004 +0000 *** empty log message *** Tools/F_mk/GMakerules.mak commit f5e8ec7ad959a77bccb8d2e4b10b21da4f4a7b9f Author: car Date: Tue Jun 8 01:01:16 2004 +0000 *** empty log message *** Src/F_BaseLib/list_box.f90 Src/F_BaseLib/test/makefile Tests/F_BaseLib/makefile commit f3b08ec15b3d863aa0b82cc9eed8cc0f0c2c0ccf Author: car Date: Mon Jun 7 16:05:55 2004 +0000 *** empty log message *** Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/test/.cvsignore Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/def_knapsack.out Src/F_BaseLib/test/t_knapsack.f90 Tests/F_BaseLib/.cvsignore Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/def_knapsack.out Tests/F_BaseLib/t_knapsack.f90 commit 9deaadcc0d7dff926602a2f16d4d16a67e1a4216 Author: car Date: Mon Jun 7 15:56:59 2004 +0000 formatted output Src/F_BaseLib/test/knapsack.out Tests/F_BaseLib/knapsack.out commit b38c28277d814911d49d6b41e6be4394e44dfba4 Author: car Date: Sat Jun 5 16:23:08 2004 +0000 *** empty log message *** Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/test/knapsack.out Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/knapsack.out Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_scripts/f90doc/stmts.pl commit 30def42a45e9e77a5879014f3e37e4cafefd06f9 Author: car Date: Sat Jun 5 15:29:01 2004 +0000 conn_defs no longer uses processor defs Src/F_BaseLib/test/conn_defs Tests/F_BaseLib/conn_defs commit 544ae6e27c4192943b1d48cdf965be58db9bc928 Author: car Date: Sat Jun 5 15:07:18 2004 +0000 *** empty log message *** Src/F_BaseLib/GPackage.mak Tools/F_mk/GMakedefs.mak commit 32923c8d61b0594d4f7500f0c79625774c5429ba Author: car Date: Sat Jun 5 00:16:42 2004 +0000 Fixes for Intel8 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/inputs.domain Src/F_BaseLib/test/main.f90 Tests/F_BaseLib/inputs.domain Tests/F_BaseLib/main.f90 Tools/F_mk/GMakedefs.mak commit b86e8be454c12b06ab9730c6a4aa128db758b2fe Author: car Date: Fri Jun 4 17:03:19 2004 +0000 OMP typos Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit 7dda15991a1e9f703b74ed9e05c6b84498f06303 Author: car Date: Fri Jun 4 16:48:42 2004 +0000 OMP typos Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile commit 8ce4a8da7388c1c84b6641684befe8fc23c8861e Author: car Date: Thu Jun 3 21:10:20 2004 +0000 86 ieee Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_ieee.f90 Src/F_BaseLib/bl_ieee_c.c Src/F_BaseLib/bl_ieee_c.h Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/t_ieee.f90 Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/stencil.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/t_ieee.f90 Tools/F_mk/GMakedefs.mak commit a569d2c0255f18bb0529aa526ff416438280f8c8 Author: car Date: Tue Jun 1 04:46:59 2004 +0000 more refinements on windows makefiles Src/F_BaseLib/NPackage.mak Src/F_BaseLib/test/makefile Tests/F_BaseLib/makefile Tools/F_mk/NMakedefs.mak Tools/F_mk/NMakerules.mak Tools/F_scripts/mkdep.pl commit d93a11da628024d44d1c94a1eee2fda0a537a1d0 Author: car Date: Mon May 31 19:29:17 2004 +0000 *** empty log message *** Src/F_BaseLib/NPackage.mak Src/F_BaseLib/f2kgetcl.c Src/F_BaseLib/test/makefile Tests/F_BaseLib/makefile Tools/F_mk/NMakedefs.mak Tools/F_mk/NMakerules.mak commit 8365d270a128ceee7c4391dfba2254120d2d0127 Author: car Date: Sun May 30 04:09:53 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_ieee_c.c Src/F_BaseLib/bl_ieee_c.h Tools/F_mk/GMakedefs.mak Tools/F_scripts/mkdep.pl commit 9fe5839da5e4608cd5c083a6dee5c8c2f480bd43 Author: car Date: Sat May 29 22:07:59 2004 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_scripts/mkdep.pl commit 58bc4962376b68e9cfcf6683417d74e92f4a2431 Author: car Date: Sat May 29 19:02:46 2004 +0000 *** empty log message *** Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_ieee.f90 Src/F_BaseLib/bl_ieee_c.c Src/F_BaseLib/bl_ieee_c.h Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_ieee.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_ieee.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_scripts/mkdep.pl commit 098db076c129dc9f0bb60e5157721550b029d93e Author: car Date: Sat May 29 16:05:34 2004 +0000 *** empty log message *** Src/F_BaseLib/fabio_c.c Src/F_BaseLib/test/inputs.domain Src/F_BaseLib/test/main.f90 Tests/F_BaseLib/inputs.domain Tests/F_BaseLib/main.f90 commit 4782accff44a0f4cf304d29607c92d907c0f5c7f Author: car Date: Fri May 28 22:48:01 2004 +0000 john wants comments Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_kiss.f90 Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_parmparse.f90 Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile commit e06a3f12cbd66f0dd32cc7ba77402322593dbde0 Author: car Date: Thu May 27 22:32:25 2004 +0000 more makefile fixes Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit 27a86f6ad538b56412f29743adbc2c1a64616204 Author: car Date: Wed May 26 21:48:51 2004 +0000 *** empty log message *** Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit fc12903af2d0e16c470bf031403f679c4af7b2ec Author: car Date: Wed May 26 13:05:51 2004 +0000 *** empty log message *** Src/F_BaseLib/test/.cvsignore commit ef34454c74163d63f407ba9fc2fe3f65a90c9972 Author: car Date: Wed May 26 13:01:39 2004 +0000 *** empty log message *** Src/F_BaseLib/test/.cvsignore Tests/F_BaseLib/.cvsignore commit f875d0d5f67eca98a3d252d279e909c6210469db Author: car Date: Wed May 26 13:01:39 2004 +0000 *** empty log message *** Tests/F_BaseLib/.cvsignore commit 8be21aae9c6b61a34deaf56f6827a4c080e76c7e Author: car Date: Tue May 25 22:39:51 2004 +0000 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Src/F_BaseLib/filler.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/test/t_main.f90 Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/stencil.f90 Tests/F_BaseLib/t_main.f90 commit f3745eef3e58d5c07adb3db5f8be101bf731e03c Author: car Date: Mon May 24 22:10:10 2004 +0000 split files Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/bl_kiss.f90 Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_parmparse.f90 Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/bl_utility.f90 commit da197d87ad085003077387284a2bbb3f38e7a8f7 Author: car Date: Mon May 24 21:59:14 2004 +0000 *** empty log message *** Tools/F_scripts/ibm_sp_batch.poe commit 1aaf5c7151e8875fab661929d609700835dd26bb Author: car Date: Mon May 24 21:50:06 2004 +0000 Initial revision Src/F_BaseLib/BoxLib.f90 Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_space.f90 Src/F_BaseLib/bl_types.f90 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type fix. Src/C_BaseLib/BoxList.cpp commit 5908d8e24e300eb83d50efcf2383787efe67a632 Author: car Date: Tue Apr 27 17:04:05 2004 +0000 no longer builds by default Src/C_BaseLib/GNUmakefile commit b5b10e660c2dd68a205c9810be6600f272641623 Author: car Date: Tue Apr 27 17:00:44 2004 +0000 cout -->> std::cout needed by gcc 3.4.0 Src/C_BaseLib/FabArray.H Src/C_BaseLib/test/GNUmakefile Tests/C_BaseLib/GNUmakefile commit bfb44ed8c6eff8483d150bc1e28f61a367feb140 Author: car Date: Wed Mar 31 23:18:22 2004 +0000 some checks for vismf file correctnes Src/C_BaseLib/VisMF.cpp commit 48121aad6be2757996c87616fa0042340d824fcd Author: almgren Date: Tue Mar 16 20:50:52 2004 +0000 OOPS last time - should have deleted this line from every case, not added it for the i-face. Test that this is correct is that coarse residual sums to zero - only true for this line missing. Src/LinearSolvers/C_NodalMG/amr_real3d.f commit df3071e0c190d2c0ce8d53ad5b0928f4b25a73d9 Author: almgren Date: Tue Mar 16 20:00:49 2004 +0000 Missing line "fac0 = fac0 / (...)" in the case of faces in the i-direction only; this scaling was there for faces in the j- and k-direction. Would only affect multilevel solves in 3-d. Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 61c0dbd4e43129b6207a89de65667d5bc9d671a0 Author: car Date: Tue Mar 9 18:35:37 2004 +0000 PathScale support Tools/C_mk/Make.Linux commit 4526d09dda96c071aa9a356c8c1076b3f94b0a3f Author: car Date: Tue Mar 9 18:28:51 2004 +0000 cpp seems to the right way to invoke pre-processor Tools/C_mk/Make.Linux commit 9d0f54d13f5e3f0ff8597786e1180daa06a6314a Author: car Date: Mon Mar 8 23:06:36 2004 +0000 swap is never defined, but declared Src/C_BaseLib/Array.H commit b382a5a1f71010f2e2c7d9b8d8500230caab7e36 Author: car Date: Fri Mar 5 17:53:30 2004 +0000 obsolete Src/C_BaseLib/test/tThread.cpp Tests/C_BaseLib/tThread.cpp commit c457d0225eecaad35f3448288e859c0aa992e979 Author: car Date: Fri Mar 5 17:49:38 2004 +0000 make tests compile Src/C_BaseLib/test/t8BIT.cpp Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/t8BIT.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 105a26bc47c76a4a87498eccee926a84714e15c4 Author: car Date: Thu Mar 4 18:09:40 2004 +0000 PathScale Src/C_BaseLib/FPC.cpp commit 6a1ca0c41878d45dfe2f386fe23b52787d44ca57 Author: car Date: Thu Mar 4 18:09:01 2004 +0000 *** empty log message *** Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tMF.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tMF.cpp commit fdf90cb12a75a199755b2b1a5ee858792fa1da92 Author: car Date: Fri Feb 27 21:20:32 2004 +0000 We should care if the bottom solve fails, print a warning and break; what really should matter is that the composite solve itself converge. Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 91da88c2dc81ab9332f5705e516b70f30d2a979e Author: car Date: Thu Feb 19 18:17:54 2004 +0000 valgrind: tuples constructors have default values Src/C_BaseLib/Tuple.H commit f68c9820572b559c5d0069571833db77c1f7860d Author: car Date: Thu Feb 19 17:52:40 2004 +0000 valgrind says that dx is uninitialized, 0 is a reasonable bad value for dx Src/C_BaseLib/CoordSys.cpp commit e8bfcde9e87fd02585ddd506440f612f0119176c Author: car Date: Wed Feb 11 20:26:28 2004 +0000 SUPERUX is the sx-6 Src/C_BaseLib/Thread.H Src/C_BaseLib/winstd.H commit f8c8dea0dd284ffa6da9551b492b918bff4bae31 Author: car Date: Thu Feb 5 23:23:51 2004 +0000 SX-6 specific stuff, note that SUPER-UX ==> SUPERUX Tools/C_mk/Make.SUPERUX Tools/C_mk/Make.defs commit 8854279f81d19c994bac32fb4500ebfbc9440083 Author: lijewski Date: Wed Jan 21 21:04:13 2004 +0000 First version. Src/C_BaseLib/test/tParmParse.cpp Tests/C_BaseLib/tParmParse.cpp commit f4811db0cbaf970c658b7ab699e6c874b44d1956 Author: lijewski Date: Tue Jan 20 21:54:10 2004 +0000 Added tParmParse Src/C_BaseLib/test/GNUmakefile Tests/C_BaseLib/GNUmakefile commit f04fd6367f7ad54753abf6c4fae26d14509d6a11 Author: lijewski Date: Tue Jan 20 21:53:31 2004 +0000 fixed bug Src/C_BaseLib/ParmParse.cpp commit 0fe0fedd7925651f0264b6fdacdae52655faa144 Author: car Date: Wed Jan 7 21:45:03 2004 +0000 tweak for std::size_t Src/C_BaseLib/winstd.H commit 450004ef4fdb0a791fa84d5c414e3f250d0618dd Author: car Date: Wed Jan 7 21:44:20 2004 +0000 windows tweaks for std::size_t Src/C_BaseLib/Arena.H Src/C_BaseLib/winstd.H commit eb8e6571d31562f5b7c5d6750d6c9b702d45655d Author: car Date: Wed Jan 7 21:18:19 2004 +0000 for some compilers size_t, pow, sqrt, etc, need to be in the std namespace Src/C_AMRLib/Interpolater.cpp Src/C_BaseLib/Arena.H Src/C_BaseLib/Arena.cpp Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/Utility.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit e27febbc6acbd4508934d10c9afc08274fe28a90 Author: car Date: Wed Dec 10 18:09:43 2003 +0000 support for BGL and Intel 8.0 Tools/C_mk/Make.bgl Tools/C_mk/Make.defs commit 68c00965c66b9bb924e47795f05323f411a23850 Author: car Date: Mon Dec 8 23:13:46 2003 +0000 powerpc for BGL Src/C_BaseLib/FPC.cpp commit 9813060a6c43b7a9ff1bebee66b0c64f801e66d0 Author: marc Date: Wed Oct 15 18:01:33 2003 +0000 Add quarter time levels into which_time Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit ec5c20fcf529fc9cddc5c67e3ba9cd56bdf4d487 Author: lijewski Date: Thu Sep 18 19:21:00 2003 +0000 Got rid of cdir$ ivdep stuff Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f commit 169470300821c1ad281336e35fb388d650f65713 Author: almgren Date: Tue Sep 16 18:39:45 2003 +0000 Changes in FORT_LINCCINTERP so that in the case of being next to a HOEXTRAP or EXT_DIR boundary, but with xok or yok (or zok) not true, we now use a correct stencil to incorporate a wall-based value instead of defaulting to the centered stencil as before. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 94c8ff0a7b3b97865478053197ee1dba5abd8514 Author: lijewski Date: Mon Sep 15 21:17:03 2003 +0000 removed CellConservative Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit 952666bc8a067ba6345dcd87be6269d12cbadcec Author: lijewski Date: Mon Sep 8 22:22:38 2003 +0000 some bringing up-to-date Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/GNUmakefile Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit 1c7a99cc003251e1495e37760b72632d0ae8251d Author: lijewski Date: Mon Sep 8 21:07:45 2003 +0000 Make tags declaration & call of buffer() consistent. Src/C_AMRLib/Amr.cpp commit 1e1d43b7334b37d20d99253692dd1951a243eb16 Author: car Date: Thu Aug 28 17:17:27 2003 +0000 __amd64__ Src/C_BaseLib/FPC.cpp commit 612841a382e8b490e580aec7a28a9db25767edb9 Author: car Date: Tue Aug 19 15:19:42 2003 +0000 strip72 doesn't work with f90 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit f319bf324f6470179bd5495ee7fd0a1462cb0c5f Author: lijewski Date: Thu Aug 14 22:26:57 2003 +0000 some cleanup Src/C_AMRLib/TagBox.cpp commit af6b09665cba93e5642c47ed05e170f5046561f9 Author: lijewski Date: Thu Aug 14 19:18:14 2003 +0000 minimized comm costs in collate() Src/C_AMRLib/TagBox.cpp commit 89eb2fdcddd2955e69ef8ad326cefcbd02f12c04 Author: lijewski Date: Wed Aug 6 21:04:01 2003 +0000 added -cm to Intel Fortran Tools/C_mk/Make.defs commit 725503ff2357d7bfb877887e8d52efea02c9c1d1 Author: car Date: Wed Jul 30 15:07:34 2003 +0000 debugging changes Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit 53f9fdf292774dcd2b502ed49bf443ae6ac3b6b9 Author: lijewski Date: Mon Jul 21 21:22:26 2003 +0000 First cut -- can parse chemkin & therm files. Tools/C_scripts/ckread.pl commit 321d756216dd73561f7dc9f0e49994ff0e0cc58c Author: lijewski Date: Fri Jul 18 04:57:11 2003 +0000 Gather -> Alltoall Src/C_AMRLib/FluxRegister.cpp commit 5793060ba6707e44c4c1485f65bffa63f7a9d8b9 Author: lijewski Date: Fri Jul 18 04:51:46 2003 +0000 Gather -> Alltoall Src/C_BaseLib/FabArray.H commit 8df5e30497bb73be236b1e1239f8ca2ed30c4edb Author: car Date: Tue Jul 8 20:48:23 2003 +0000 cleanup Src/LinearSolvers/C_TensorMG/visc2d.m commit 338447b317701ee12a4f7064fa3fe9eeea7d0d8d Author: car Date: Tue Jul 8 20:19:30 2003 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/visc2d.m Src/LinearSolvers/C_TensorMG/visc3d.m commit e37180e343a793357618e8880811d089fdd42ca2 Author: car Date: Tue Jul 8 20:04:02 2003 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/visc3d.m commit bd20fd54deb9561905603611bf4c8d77cee9167e Author: car Date: Tue Jul 8 19:42:33 2003 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/visc3d.m commit c653260b3034564b2c8c933b086d48d4beb2ba33 Author: car Date: Tue Jul 8 19:10:52 2003 +0000 stripped out mathematica code for tensor solve generation Src/LinearSolvers/C_TensorMG/visc2d.m Src/LinearSolvers/C_TensorMG/visc3d.m commit 761f5559554cbf9328ae5f4e3ce2f87fab99f578 Author: car Date: Sat Jul 5 15:22:30 2003 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/Format.m commit 11fa162b784f7f4d045d850c0e9ab30c3d6b9f42 Author: car Date: Fri Jul 4 21:58:36 2003 +0000 Mathematica 5.0 fixes Src/LinearSolvers/C_TensorMG/Format.m commit d91b090bd1da8b2063466da4815723dd1fdd5491 Author: car Date: Fri Jul 4 17:24:27 2003 +0000 Mathematica packages need by the notebooks Src/LinearSolvers/C_TensorMG/Format.m Src/LinearSolvers/C_TensorMG/Optimize.m commit 589383930debbda375cfe936fd5986835e4e7369 Author: lijewski Date: Tue Jun 24 17:18:21 2003 +0000 merged in d_numPts() Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.cpp Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 33eec024160aa21341a80d672739022ba893a35f Author: car Date: Fri Jun 20 19:37:11 2003 +0000 *** empty log message *** Tools/C_mk/Make.IRIX64 commit 0e99f69af33816b1be198e9e5cfd37f01172c7a1 Author: car Date: Fri Jun 13 22:03:23 2003 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.H commit f921be8f91d44648345fdb2d8c529ad3484d8286 Author: car Date: Fri Jun 13 19:50:47 2003 +0000 inline out of order Src/LinearSolvers/C_NodalMG/interface.H commit 13b07d06cff803b6737df0fc097c5af84e596fb2 Author: car Date: Wed Jun 4 21:41:56 2003 +0000 redhat 7.1 fortran Tools/C_mk/Make.defs commit 734045541b9f06d521a81f7a39d1d6cab23e9c73 Author: vince Date: Wed May 21 22:47:52 2003 +0000 fix for escher Tools/C_mk/Make.defs commit 3c0e9051a96249d241467be1ec21d7f135968139 Author: vince Date: Wed May 21 22:47:13 2003 +0000 fix for escher. Tools/C_mk/Make.IRIX64 commit d5bbf378c33d37710b33c69d2f9cb90603e7b1d3 Author: lijewski Date: Thu May 15 22:01:01 2003 +0000 Removed the BL_PROFILE() line. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 2b8b11cd0c0a09e8c82474ad72eb0b449380d552 Author: car Date: Fri Apr 11 17:16:06 2003 +0000 redhat 7.1 Tools/C_mk/Make.defs commit 0d69768010566ab9650d1f8104367be68e1a50be Author: marc Date: Wed Apr 9 22:35:24 2003 +0000 change constant to a long Src/C_BaseLib/DistributionMapping.cpp commit b0b3ee7e639c67048b289fbad24b3bc91abb6bad Author: car Date: Thu Apr 3 18:44:31 2003 +0000 flush at end of grid log entry Src/C_AMRLib/Amr.cpp commit 715c0c9983f41a19129448c3cd8fafb97f5b7d38 Author: marc Date: Fri Mar 14 23:44:57 2003 +0000 fixes to be compatible with g++ 3.x in cygwin Tools/C_mk/Make.CYGWIN_NT Tools/C_mk/Make.defs commit 01d26baee407a99f8d9530091d720f41abaed912 Author: lijewski Date: Wed Mar 12 21:03:32 2003 +0000 fixed divide by zero in verbose output Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 3a37037c3b89cdf5e282e73073f926032aea8adc Author: lijewski Date: Wed Mar 12 20:54:59 2003 +0000 fixed divide by zero in verbose output Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit c588d28f1f27ee3569b66c8175693f688e5a2fd5 Author: lijewski Date: Fri Mar 7 17:39:39 2003 +0000 set_preferred_boundary_values() now takes a MultiFab Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 17934d081fd7d522d1766ea973bf2edbff08c6e4 Author: lijewski Date: Fri Mar 7 16:59:25 2003 +0000 ParmParse'd in max_efficiency Src/C_BaseLib/DistributionMapping.cpp commit 91f89ba86a00d3aaeb0480fc76e09390419b2a9d Author: lijewski Date: Thu Mar 6 23:57:38 2003 +0000 wrapped knapsack times in verbose Src/C_BaseLib/DistributionMapping.cpp commit 5d896e2d8930bc0746523723bf2741576f466418 Author: lijewski Date: Thu Mar 6 22:34:56 2003 +0000 print out some knapsack() timings Src/C_BaseLib/DistributionMapping.cpp commit cbbb293a5d960946077aaef80d7eff48d71137c6 Author: lijewski Date: Fri Feb 28 22:42:15 2003 +0000 removed the static collate space in TagBox Src/C_AMRLib/Amr.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit a4bd2b3b9c8b9498a32280d2e809db4140902f16 Author: lijewski Date: Wed Feb 26 18:07:08 2003 +0000 added verbose option Src/C_BaseLib/DistributionMapping.cpp commit 6ec44fc73e90b675e74635e08cf4868e224d42d7 Author: car Date: Fri Feb 21 22:49:10 2003 +0000 compiles, probably doesn't work in parallel Tools/C_mk/Make.defs commit 57ad6e6cdc0a616220dbbdcce393180a7eeeaf77 Author: almgren Date: Wed Feb 19 18:34:19 2003 +0000 New routine, pressure_project, to be used for initializing calculations with hydrostatic (from gravity) background. Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 62296b694eac8cfd44c13794a64e58aa1ec6718e Author: almgren Date: Tue Feb 18 21:13:18 2003 +0000 Removed all calls to writeMF. Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit d56befc9e41f49ab9a0ef8ca5838e6daf45819a6 Author: car Date: Tue Feb 18 20:55:00 2003 +0000 strstream -> sstream Src/C_AMRLib/AmrLevel.cpp commit d83b75735f561defddedeebd75d49938523b726b Author: car Date: Tue Feb 18 20:54:40 2003 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/ABec_UTIL.F commit ce6e0af8b5dbdf02eaee192e23bbc3a08f334674 Author: car Date: Wed Feb 12 22:31:53 2003 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 4c72b831d8b00afb33666f897ffae5349e78ae44 Author: car Date: Wed Feb 12 22:31:12 2003 +0000 *** empty log message *** Tools/C_mk/Make.defs commit f1637be2c6f96281767bf30868cbc7a261c1f41a Author: car Date: Fri Feb 7 17:42:26 2003 +0000 minor problem, periodic fillpatch Src/C_AMRLib/AmrLevel.cpp commit 161db21b36badb73074def18226a5a4cd6f9fb49 Author: car Date: Fri Feb 7 16:34:12 2003 +0000 some additional diagnostics; now don't solve the CGSolve if norm is initially zero. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 03715082ffcd77c6cc7e21fbc530642446e0e3ac Author: lijewski Date: Thu Feb 6 18:14:29 2003 +0000 more work on bunching fill operations Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit a679c7618e6747df72479af6bd726652a8a93784 Author: car Date: Wed Feb 5 16:33:24 2003 +0000 fixes, I think, for Intel compilers Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit fad563c0eeef71f93b763084a64c04482dd62ddc Author: marc Date: Tue Jan 28 20:55:35 2003 +0000 Modernize lib builder Tools/C_scripts/dsp.lib.mak commit 82b0803bb5bbe06388e88faa262602cacb7b625a Author: car Date: Mon Jan 27 17:10:36 2003 +0000 bl_pd_is_ioproc Src/C_BaseLib/ParallelDescriptor.cpp commit adad6f8e742b0a41d4d35bf4731ea82206a912ae Author: car Date: Thu Jan 23 20:10:01 2003 +0000 win32 hates templates Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 500ece7296685f2b84d19deadf9f62de43499d19 Author: lijewski Date: Wed Jan 22 22:39:44 2003 +0000 Mods to Fill_Boundary() multiple comps at once Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 2a3543ed41de014f1372678be3ad2a58fd63fa60 Author: car Date: Wed Jan 22 19:19:27 2003 +0000 optimization for Intel compilers Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit a5053aed5f5717b6b8a2ed38402ac5aa495d13e3 Author: car Date: Fri Jan 3 19:25:11 2003 +0000 foolish mistakes Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/ParmParse.cpp commit 30dadbe53189ff65b62b403be9f658f93d42cbbc Author: car Date: Thu Jan 2 22:30:26 2003 +0000 libpthread Tools/C_mk/Make.Linux commit acd76cf215c915b954a166f04af5d232bba44cc9 Author: car Date: Thu Jan 2 14:59:30 2003 +0000 *** empty log message *** Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 7865f7e58332280a1dadcc65ea37bd5da8c3229b Author: almgren Date: Mon Dec 30 22:09:45 2002 +0000 Making area(i,j) = abs(a) instead of area(i,j) = a in FORT_SETAREA for the r-z case. NOte that FORT_SETVOL and all other cases of FORT_SETAREA already return guaranteed-positive values. Src/C_BaseLib/COORDSYS_2D.F commit 26a212be6b475b0f2d0c32264acf3bcc31ca3e3e Author: car Date: Fri Dec 20 23:05:39 2002 +0000 fix for FluxRegister::ADD Src/C_AMRLib/FluxRegister.cpp commit fd11da5ca05136380eb4db57b50231f378647b75 Author: lijewski Date: Wed Dec 18 18:44:23 2002 +0000 fixed comment Src/C_BaseLib/FabArray.H commit 2674c6524d33b6a6b1740743cb6fe730f37f0ead Author: almgren Date: Tue Dec 17 22:19:56 2002 +0000 Fix for inflow on hi-side boundaries...was screwing up before, all better now. Src/LinearSolvers/C_NodalMG/boundary.cpp commit 5a07382eef110431ae4aea1a7d0d7f1b43f4e0d6 Author: almgren Date: Wed Dec 11 20:43:22 2002 +0000 In the case where the fine cells didn't cover all of the coarse cell being interpolated from, there was an index bust. It has been fixed so that the fine correction is only modified on cells where it actually exists. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 2152679bba5b03276479a979f683970aca9ce2b9 Author: almgren Date: Wed Dec 11 18:33:45 2002 +0000 Should have used cvol instead of ratiox*ratioy for denominator in icase=1. Src/C_AMRLib/INTERP_2D.F commit d9fdc4b91ab6904f3880bcde5d402a0e385609fd Author: lijewski Date: Wed Dec 11 17:02:16 2002 +0000 removed an assertion that isn't correct in serial Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit a1fd088bf66c550635412b84b9ac65a9a30a5e54 Author: lijewski Date: Tue Dec 10 20:31:14 2002 +0000 Commented out HeaviestCPU() stuff used by MinimizeCommCosts(). Src/C_BaseLib/DistributionMapping.cpp commit e6ecdbf163d9743b5be30f2698d12052cc7d165a Author: lijewski Date: Sat Dec 7 16:25:26 2002 +0000 fixed syntax error Src/C_AMRLib/INTERP_3D.F commit 38d05ddbe20c614e4bf49e02f32390b936b8fc1e Author: lijewski Date: Sat Dec 7 16:09:16 2002 +0000 increased the cache hit rate Src/C_BoundaryLib/FabSet.cpp commit 3361b505a057f66ec163a6b015c4c694423780e3 Author: almgren Date: Sat Dec 7 05:59:35 2002 +0000 Do the right thing for icase=1 when fine_state is zero to start with. Same as the recent fixes in 3d. Src/C_AMRLib/INTERP_2D.F commit c1eb130b1c8baba1282201b0b55b845701c7102f Author: almgren Date: Sat Dec 7 05:57:09 2002 +0000 Same problem as before for icase=1; the correction wasn't being zeroed out first for states which were 0 at first. Src/C_AMRLib/INTERP_3D.F commit caa3d5539d4a1ed310d2fb6ba5161f446304db48 Author: lijewski Date: Wed Dec 4 23:06:53 2002 +0000 same error in plus() as in copy() in CrseInit Src/C_AMRLib/FluxRegister.cpp commit 756ac6a78d2c01c820b6c220bd268506ee22f10e Author: lijewski Date: Tue Dec 3 18:35:38 2002 +0000 improved FillPeriodic cache hit ratio Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit be231ae5b2c5c69d9f6853e46baa37f4404a1827 Author: lijewski Date: Tue Dec 3 18:03:27 2002 +0000 improved FillBoundary cache hit ratio Src/C_BaseLib/MultiFab.cpp commit 2b16013bf7c7a9f506c8cd766001596d3028303d Author: lijewski Date: Tue Dec 3 00:02:42 2002 +0000 added new accessor functions Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H commit 69746209bd0f94cdcf56f1c4625030a32561c497 Author: jbb Date: Mon Dec 2 20:45:01 2002 +0000 Need to restrict the copy in FluxRegister::CrseInit to be only on the region that was just filled from the coarse grid, NOT from the whole fab, some of which is still unfilled. This was causing errors and core dumps. Src/C_AMRLib/FluxRegister.cpp commit 8b7ad15d4a2a5c72df75493e79a739e077e50894 Author: car Date: Fri Nov 29 22:12:18 2002 +0000 no trailing semicolons Src/C_BaseLib/SPECIALIZE_F.H commit 01657d478e04e6736165273f03c5faba75eb554b Author: car Date: Wed Nov 27 21:54:19 2002 +0000 replace a stop Src/C_AMRLib/SLABSTAT_2D.F Src/C_AMRLib/SLABSTAT_3D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F commit 2e4b7ba23737dfc13a1d2987ab9e0a0a458cd36b Author: lijewski Date: Tue Nov 26 22:47:22 2002 +0000 modest performance improvement Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 97cb4a4633e4e46627e2abc43aa8f55dbc2f3352 Author: lijewski Date: Tue Nov 26 22:37:40 2002 +0000 modest performance improvement Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BoundaryLib/FabSet.cpp commit 49dc138c33d022d8176e1fd4907123783dc6d2eb Author: lijewski Date: Wed Nov 20 16:55:55 2002 +0000 additional arg to compFlux() Src/LinearSolvers/C_CellMG/ABecLaplacian.H commit cc80d6936585ba1a8d61adc7fbe08d234f81a890 Author: lijewski Date: Wed Nov 20 16:52:07 2002 +0000 Added addition signature for compFlux() that avoids applyBC() call. Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 8eb4eaee414420b7bc28d6b49622201955e0f753 Author: lijewski Date: Thu Nov 14 23:04:56 2002 +0000 using bl_abort() in place of stop Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_BaseLib/COORDSYS_1D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F commit f85903cd850607675118e37d0cbce3fcf818bc43 Author: lijewski Date: Thu Nov 14 21:13:08 2002 +0000 removed statics from template functions Src/C_BaseLib/FabArray.H commit 4be714ff3257d058f54acae86af32c4f8be68c45 Author: car Date: Thu Nov 14 18:43:29 2002 +0000 *** empty log message *** Src/C_BaseLib/BLBoxLib_F.f Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.cpp commit 7193e1d202abd89e4876800059de5c5ac2ea3d9f Author: marc Date: Thu Nov 14 07:08:32 2002 +0000 Add option to add instead of copy on CrseInit operations Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 08de9f413e94f40128b6cc4c70d3979ccdcf2cef Author: marc Date: Thu Nov 14 00:13:23 2002 +0000 fix Mikes extra arg fix Src/C_AMRLib/AmrLevel.cpp commit 480e6fe980f95598113389e298afa55a3fec6988 Author: lijewski Date: Wed Nov 13 17:15:20 2002 +0000 quiet valgrind Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp commit 53d6cbcea42557e63ce3a00377dce9aacd0223ed Author: lijewski Date: Wed Nov 13 05:04:58 2002 +0000 tad rearrangment Src/C_AMRLib/AmrLevel.cpp commit 36d8c65a5a033c010e1941622da3de95e5b02159 Author: lijewski Date: Tue Nov 12 20:49:35 2002 +0000 to shut up valgrind Src/C_BaseLib/PArray.H commit 505c846edac761e2ae386fb5ddb80e1811b7dec8 Author: lijewski Date: Tue Nov 12 17:08:48 2002 +0000 fixed mismatched deltes Src/C_BoundaryLib/InterpBndryData.cpp commit 254736d9c60ceec0f69583f0fb3e7b0832992b30 Author: lijewski Date: Mon Nov 11 17:49:53 2002 +0000 can now do some semblance of tracing Src/C_BaseLib/BLProfiler.cpp commit ff96744ce6912a7306142a91196ec4dd5d8188f1 Author: almgren Date: Sun Nov 10 14:57:54 2002 +0000 Modified icase=1 in PROTECT_INTERP to fix a problem with case 1, which wasn't setting the correction to zero for states that were zero, it was leaving the previous value in there. Now the correction is set to zero there. Src/C_AMRLib/INTERP_3D.F commit 31f98fee1409d5f0a09608026e42d3c7216b3281 Author: lijewski Date: Sat Nov 9 02:15:52 2002 +0000 more BL_PROFILE()s Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/StateData.cpp commit 18019d63ac055e084bc890ae5c813017fa6e8ccf Author: lijewski Date: Fri Nov 8 22:00:51 2002 +0000 added some BL_PROFILE()s Src/C_AMRLib/Interpolater.cpp commit b7bd003484aca82bf97ee5dbb22cd7e36417a523 Author: car Date: Fri Nov 8 18:34:42 2002 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/lo_bctypes.fi commit 4012fb309c2b49d6f7773d381f1d4f4f2c8fbae0 Author: lijewski Date: Thu Nov 7 19:04:01 2002 +0000 specialized performCopy() for Reals Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit f91b2f0b39b94c85e20ebbd1e528b637df571060 Author: lijewski Date: Wed Nov 6 20:51:41 2002 +0000 tad bit o cleanup Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 3d7a8aa0c950c1223c3db89646dd3356d47e9045 Author: almgren Date: Tue Nov 5 21:21:58 2002 +0000 Restored cmax and cmin seeing the corner data (we believe it should be there). Put a test for alpha > 1. Protected against divide by zero in computation of alpha. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit b40fc4bfda877c01e2cb246501490e04b059ea43 Author: lijewski Date: Tue Nov 5 21:06:17 2002 +0000 +K2 -> +K1 Tools/C_mk/Make.AIX commit aa9585bcd7f92a98a327ea3bbd94310c8404c8c1 Author: lijewski Date: Tue Nov 5 05:34:21 2002 +0000 removed extraneous end do Src/C_AMRLib/INTERP_3D.F commit 4cbc9c55ff3f7d923ed19a6f415fde1366f6e48e Author: almgren Date: Mon Nov 4 18:43:06 2002 +0000 Modified calculation of cmax/cmin in CCINTERP so that it doesn't see corner values, which may not be filled since they aren't used in the actual slope calculation. Src/C_AMRLib/INTERP_2D.F commit 9e609e50c1ae1b3c9e072335a0eb56ca584dd3f0 Author: almgren Date: Mon Nov 4 18:39:50 2002 +0000 Modified the calculation of cmax/cmin in CCINTERP so that it doesn't see corner values (since they may not be filled, they aren't used in the slope calculations.) Src/C_AMRLib/INTERP_3D.F commit e17587188be2c1708ec9b9e169e9e6fa5a747a66 Author: lijewski Date: Thu Oct 31 21:59:21 2002 +0000 Added -qrtti=all when debugging. Tools/C_mk/Make.AIX commit 484e5fbc9f7d6c0de13e80b7e58dcacee6dbb14a Author: lijewski Date: Thu Oct 31 21:56:33 2002 +0000 removed excess profiling gunk Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 346cf29ced1c7b6ad64a48c83574bcefddc34a4c Author: lijewski Date: Thu Oct 31 21:01:30 2002 +0000 removed excess profiling gunk Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 1a01907925bcea1b0edaded06326db47523f4ac5 Author: car Date: Thu Oct 31 18:44:00 2002 +0000 fixes for microsoft Src/C_BaseLib/ParallelDescriptor.H commit aeea97f88c55acf1792879eedc951fcd5f7a8cac Author: car Date: Thu Oct 31 18:09:00 2002 +0000 some inlineing Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit fae73cc1d989ae2102e1b33a0aaabb8d3dc1e565 Author: lijewski Date: Thu Oct 31 17:01:50 2002 +0000 more profiling stuff Src/C_BaseLib/BaseFab.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 5ba370a33ce47756edf8b54202b95a2ae9a5597b Author: lijewski Date: Wed Oct 30 21:33:13 2002 +0000 added some profiling calls Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit d45db96ffb9d19a087a8066f32daf960c2346c54 Author: lijewski Date: Fri Oct 25 22:21:44 2002 +0000 speed improvements Src/C_BaseLib/Utility.cpp commit 95e0a7e42a1dc4feb7861f6f97e620cf88a2ceac Author: lijewski Date: Thu Oct 24 21:56:00 2002 +0000 added InvNormDist stuff Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit ae1e9ee145564c4bd377cbad07b5bc9a48d9fe8c Author: car Date: Sat Oct 19 18:33:28 2002 +0000 silence warnings Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/LO_UTIL.F commit ba0d87804b39ccba24e503052bed9510617709da Author: almgren Date: Fri Oct 11 18:23:00 2002 +0000 Missed a subcase in the first logic case. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 0e8cd2ad4039e70c27ce33732b9d0833c989045f Author: car Date: Fri Oct 11 18:20:44 2002 +0000 improved error message Src/C_BaseLib/BLProfiler.cpp commit 9fdbf9c3bcf98fbbe7792b7fcd5b8ed6c0f7a20c Author: car Date: Fri Oct 11 18:20:29 2002 +0000 profiling fix Src/C_AMRLib/TagBox.cpp commit a502f5fb4a927bf78e35d6caab01a76b891341ba Author: car Date: Fri Oct 11 13:28:27 2002 +0000 more profiling Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp commit 66be8b254fbeb8cea6247c11a4158ebb50ab268e Author: car Date: Wed Oct 9 21:43:20 2002 +0000 *** empty log message *** Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp commit c6fa60fa81389130aa69826919ed2f242bd93aca Author: car Date: Wed Oct 9 13:59:04 2002 +0000 more timers Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/TagBox.cpp commit 5203e34cd5a4f28080a30fc14e2bd7ddb0fef229 Author: vince Date: Tue Oct 8 21:33:28 2002 +0000 added ,n to a few crse reference. Src/C_AMRLib/INTERP_3D.F commit cca8c37fb9813fdd3497641bf619d59d5a59531c Author: almgren Date: Mon Oct 7 20:44:37 2002 +0000 Fixes to CCINTERP which require that the new fine-grid values interpolated conservatively from the coarse grid not exceed any max's or min's of the local coarse grid values. Does this by modifying the slopes which are used in the cell if a max/min would be violated by the slopes as first calculated. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.cpp commit 8c69b84cb072ea0e7f114fdb27f1f57387c771aa Author: lijewski Date: Mon Oct 7 20:28:10 2002 +0000 remove MISMATCH stuff ... Src/C_AMRLib/INTERP_2D.F commit 531d19cd170b46a317dc9deb7e9f1327ab6db1b7 Author: car Date: Sun Oct 6 18:02:43 2002 +0000 more profiling Src/C_BaseLib/DistributionMapping.cpp commit f7504138cd96c300c9f302846dbdababd7cc21fe Author: car Date: Wed Oct 2 22:26:12 2002 +0000 silence some warnings Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f commit 3dd2ce3a374ef9d005daa055f5c82c5e116a19d6 Author: marc Date: Tue Oct 1 23:56:07 2002 +0000 Allow ratio up to 4 in protected interp func Src/C_AMRLib/INTERP_3D.F commit 32a6116cfa48df5044e6d3b94223bf58504431f1 Author: lijewski Date: Tue Oct 1 22:38:42 2002 +0000 ensure sprintf() buffer big enough Src/C_BaseLib/Utility.cpp commit ca36981fded0c3b7e18e4e278394e4c3e8ed7aa2 Author: lijewski Date: Sat Sep 28 19:03:35 2002 +0000 silenced compiler warnings Src/C_AMRLib/Interpolater.cpp commit 3d485d29b5ac39401f2a3ea10683e0ec9c2a87e6 Author: lijewski Date: Sat Sep 28 19:03:07 2002 +0000 bug fix for AIX Src/C_AMRLib/INTERP_F.H commit ecf4f98604ca827c01d5df3d390ea594486a40f3 Author: almgren Date: Fri Sep 27 19:20:00 2002 +0000 New interpolation code which allows one to modify the interpolated corrections to a field in order to keep that field non-negative as much as possible. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit d5999ba19e7245fb9e21b1318dd95d824b84df53 Author: lijewski Date: Mon Sep 23 19:06:21 2002 +0000 *** empty log message *** Tools/C_scripts/compressor commit 5bb7f3784a3351a69c47c26f76003096fc6b4319 Author: car Date: Mon Sep 23 17:02:45 2002 +0000 compressor has a lock file Tools/C_scripts/compressor commit 086a9ed12c1dc17afc6d52add8d21f5ef77d9e32 Author: car Date: Mon Sep 23 16:57:36 2002 +0000 testing new compressor Tools/C_scripts/compressor commit 1cb7030bd95b4d6f2729a59b8630101feb0fc319 Author: car Date: Thu Sep 19 21:02:14 2002 +0000 do'h Src/C_BaseLib/Utility.cpp commit 80bc721221b65ae9880de59b7927475da313de08 Author: car Date: Thu Sep 19 19:26:22 2002 +0000 fort call to initrand Src/C_BaseLib/Utility.cpp commit ec727fe1794be20fc6d9bebc983cc78662c5e0e2 Author: lijewski Date: Fri Sep 13 19:19:41 2002 +0000 Added MinimizeCommCosts() Src/C_BaseLib/DistributionMapping.cpp commit f20e5d2404fe54f82a41aaade32decf6cace5d09 Author: car Date: Fri Sep 13 14:00:47 2002 +0000 say GPROF=TRUE to got F/C/C++ -pg Tools/C_mk/Make.defs commit c6dbc5074154088b5363e7a0be4e53f3d08ce310 Author: car Date: Tue Sep 10 19:41:59 2002 +0000 3d corrected Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/inputs commit fda9d4e22853bad18d7e98676d76a93d394ab1f1 Author: car Date: Tue Sep 10 18:25:27 2002 +0000 oops Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 0d14836dddbbd156d01f2d26f26a270ae0664393 Author: car Date: Tue Sep 10 18:19:57 2002 +0000 more debugging output Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit a87adc8fbfce9e8364ca121f575b2afc5e3cf28d Author: car Date: Tue Sep 10 16:03:05 2002 +0000 3d re-rolled, un-rolled Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f commit 437e526cd7704d9961fc514adec9a1a826073cd5 Author: car Date: Tue Sep 10 14:07:14 2002 +0000 re-rolled, unrolled routines Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 3518e7520b27a1639f3373c60b81d3fa31c7541e Author: marc Date: Mon Sep 9 22:30:33 2002 +0000 remove __kcc... define-it breaks compiles on brainerd Tools/C_mk/Make.defs commit 1130991912e375e12edb34a06fd8c05a96a41c9b Author: car Date: Mon Sep 9 22:00:57 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 95abb36d22ce1895e05da54bb3b94e153e384740 Author: car Date: Mon Sep 9 20:52:24 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 87cf8b49d59d3759f3ad7d13ffdb1caa03b5dcea Author: car Date: Thu Sep 5 20:59:10 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.f commit 8aa42d2f46d65d00d3112b67e49194e5501d1aa0 Author: car Date: Thu Sep 5 16:34:41 2002 +0000 e200 might have been to fierce, changed 'infinity' to e50 (should still be ok for sne Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 131984a6d0c1cf9e834102ba4591d852c61c5ba3 Author: car Date: Wed Sep 4 15:29:53 2002 +0000 use .f not .F Src/LinearSolvers/C_NodalMG/GNUmakefile commit daa43ff468f2048cd1a2cb0c6133ac24a431928e Author: car Date: Tue Sep 3 19:07:05 2002 +0000 left in some debugging cruft Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 45b519044aaeb29a39df57191caedaf7647acf09 Author: car Date: Tue Sep 3 18:10:30 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_avg2d.f Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_proj2d.f Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 892780a36164a4bab07f60a6564dee6e37db8fcf Author: car Date: Tue Sep 3 16:42:40 2002 +0000 let fortran be fortran Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/hg_avg2d.f Src/LinearSolvers/C_NodalMG/hg_avg3d.f Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f Src/LinearSolvers/C_NodalMG/hg_proj2d.f Src/LinearSolvers/C_NodalMG/hg_proj3d.f commit b50c054236c09a15d7d97b6b5068497ba25d1a01 Author: car Date: Tue Sep 3 16:34:54 2002 +0000 useless Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgdebug.F Src/LinearSolvers/C_NodalMG/hgdebug_F.H Src/LinearSolvers/C_NodalMG/proj.cpp commit f448aaad728b09ae23d8285d4a0cb781c2261946 Author: lijewski Date: Fri Aug 30 22:10:34 2002 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit 6e9698914e0dbf3f5d14ca0f7b00236455571964 Author: car Date: Thu Aug 29 22:17:09 2002 +0000 silence a warning on int<>bool Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 1cfc1524c40272f7248febdb84d3cf44f15d0ed9 Author: car Date: Thu Aug 29 22:14:34 2002 +0000 single precision constants in fortran Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_BoundaryLib/LO_UTIL.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit 75e851aea6c5803ab879246ac644e3beb6c10297 Author: car Date: Thu Aug 29 18:03:15 2002 +0000 some single precision constants Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 5fb0f316ff16b4cf62bea9902b19f9b7163ad892 Author: car Date: Wed Aug 21 20:12:40 2002 +0000 more e20/e30-->e200 changes Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp Src/C_BoundaryLib/BndryRegister.cpp commit a25fd324826516cdca86733c95c2ff59c4ba74fa Author: lijewski Date: Tue Aug 20 21:00:55 2002 +0000 Increased data size ... Tools/C_mk/Make.AIX commit 2b2d5666aa603fbddee25430162a693b56e63e2d Author: car Date: Fri Aug 16 23:15:27 2002 +0000 change infinity from e20 to e200 Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit e2c51d309533bfa2f0f548b0af324e53904ecc8f Author: car Date: Fri Aug 16 22:07:07 2002 +0000 Intel 7.0 support Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 3a7515b0f9c8d68bca3189f40d0bbc5598179ced Author: car Date: Wed Aug 7 17:23:56 2002 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit d8f2bdc455d31edf768d12dd27951cd2ac63db79 Author: car Date: Tue Aug 6 18:09:06 2002 +0000 *** empty log message *** Src/C_AMRLib/AmrLevel.cpp commit d870ef0a36f6dcb19b93beaf2f927a2ec5e657f0 Author: car Date: Mon Aug 5 15:41:22 2002 +0000 remove intel temp files Tools/C_mk/Make.rules commit 7427a4a7866eebcfe980cb7e84b5288f6eefc087 Author: lijewski Date: Wed Jul 31 22:32:02 2002 +0000 got formulas consistent Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F commit 9fa61cd28ad07414990b1d8986b34302a84f2694 Author: car Date: Wed Jul 24 23:42:57 2002 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 6782ca0fe1b7c19a1bb2857ce210a1bdfb063b9c Author: car Date: Wed Jul 24 21:18:16 2002 +0000 changed bicg so that if the solution criteria is met before the iteration begins, we return Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 2368bb7149d361939260ae5f8bb1a908585501d5 Author: lijewski Date: Thu Jul 18 21:28:15 2002 +0000 *** empty log message *** Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F commit b48618e7202859294e216e9fcaa10f06deaebcbf Author: lijewski Date: Fri Jul 12 23:07:38 2002 +0000 was NOT right Src/C_BaseLib/DistributionMapping.cpp commit 4d5a8e5d0cd18780d68c0b1337e785d827098efd Author: marc Date: Wed Jun 26 18:06:44 2002 +0000 Add lf to result file Tools/C_scripts/dsp.mak commit 98379250a4fdb114636d94cc8bba4baca924f07d Author: marc Date: Wed Jun 26 00:02:01 2002 +0000 Fix up dsp generation to allow config changes, ie independent/concurrent Release and Debug builds Tools/C_scripts/dsp.mak commit ca798c2bc5a2048b5ac256645935c51a3d1cbe96 Author: car Date: Thu Jun 20 18:28:00 2002 +0000 another fortran header file Src/C_AMRLib/bc_types.fi commit 6b219edf149a7e7f0a9869544a2de1b83c3d7ab3 Author: car Date: Thu Jun 20 15:59:36 2002 +0000 allow upper/lower case in fortran INCLUDE Tools/C_scripts/mkdep commit c5ef9fbed828d9d5dfbfaf589d354083f580c7d6 Author: car Date: Wed Jun 19 22:21:38 2002 +0000 *** empty log message *** Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/ParmParse.cpp commit 4c58c90be78480141c334b3b47004f0a719c6ea6 Author: car Date: Wed Jun 19 20:49:44 2002 +0000 *** empty log message *** Src/C_BaseLib/BLutil_F.f Src/C_BaseLib/ParmParse.cpp commit 06922d8e36d12d16952b98ab83cdedd511746ca0 Author: car Date: Tue Jun 18 16:28:28 2002 +0000 cvs strings Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/BLutil_F.f commit 870972d45e985d3e259c261235ff73f843dbf62e Author: car Date: Tue Jun 18 14:26:24 2002 +0000 better support for \.f files Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 7f4aa43a363242269f7a4b0fe721dfa3b25c9874 Author: car Date: Mon Jun 17 22:00:17 2002 +0000 added arrays Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/BLutil_F.f Src/C_BaseLib/ParmParse.cpp commit b474e39c9d1b750c2fa2d7a06b184ff439f77a7f Author: car Date: Mon Jun 17 19:40:42 2002 +0000 Fortran includes with -fortran flag Tools/C_mk/Make.Linux Tools/C_mk/Make.rules commit 3410838317d865b756d8175b3e7f9fd8ae97fc76 Author: car Date: Mon Jun 17 19:40:27 2002 +0000 mkdep now parsers fortran includes when the -fortran flag is thrown Tools/C_scripts/mkdep commit a0fd7606d21641f8eceadc4886d75acb9b3838d9 Author: lijewski Date: Mon Jun 17 19:36:46 2002 +0000 *** empty log message *** Src/C_BaseLib/BLParmParse_F.f commit 13ae96f51edc13c50ded158c5ab718d2f678005c Author: car Date: Mon Jun 17 19:34:49 2002 +0000 *** empty log message *** Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/Make.package commit cc816f44390244e5c1bd98c9b22aeb7949ae4296 Author: car Date: Mon Jun 17 17:01:27 2002 +0000 isStateVariable, is a bool Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 9f3af684759e38a1e41dd82d120a7ee009815876 Author: car Date: Mon Jun 17 17:00:40 2002 +0000 *** empty log message *** Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/BLutil_F.f Src/C_BaseLib/Make.package Src/C_BaseLib/ParmParse.cpp commit 62487cd895f2cf4451e5a98f8bb414410f8f9ced Author: car Date: Tue Jun 4 17:42:37 2002 +0000 Some support for GCC 3.1 Tools/C_mk/Make.defs commit e52f1864c6678726d8a9f68348849a17fd6b3f52 Author: car Date: Tue Jun 4 16:48:48 2002 +0000 add DIMARG; Use BL_USE_FORT_STAR_PRECISION to get real*8 and real*4 instead of DOUBLE PRECISION and REAL Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BLFort.H Src/C_BaseLib/REAL.H commit 85f8184c54e8e692c2a2c988806fd5dd92daefe7 Author: car Date: Wed May 29 22:37:47 2002 +0000 gcc 3.1 needs to include Src/C_BaseLib/BLProfiler.cpp commit 3c5ff8414379af709c801bf0a0225a7356925de6 Author: marc Date: Tue May 28 23:21:12 2002 +0000 Add a routine to hoextrap to cc Src/C_AMRLib/FILCC_2D.F commit 60d35a70847e39cdfa239074de9099a2b50c003c Author: car Date: Thu May 23 22:22:49 2002 +0000 set BL_FORT_STRICT_REAL_T if you want REAL_T to be DOUBLE PRECISION or REAL depending on BL_USE_FLOAT setting Src/C_BaseLib/REAL.H commit 856e6b2015d110bf03e88c8204a885ff0b512a5a Author: car Date: Thu May 23 19:10:38 2002 +0000 BoxLib\BLFort.H Src/C_BaseLib/BLFort.H commit 9a9c90382cfb5664fbdd0e96b0fc8c3a0f896618 Author: car Date: Thu May 23 18:22:13 2002 +0000 *** empty log message *** Src/C_BaseLib/Make.package commit 8f0b24e39552727029ee606c3d0d09c9a9ea37bf Author: car Date: Thu May 23 18:21:48 2002 +0000 BLFort macros useful for FORTRAN calls Src/C_BaseLib/BLFort.H commit 940fa27cf58e1e99db878aa4faae4b52dbe26756 Author: vince Date: Thu May 23 18:21:10 2002 +0000 some changes for opal. Tools/C_mk/Make.OSF1 Tools/C_mk/Make.mpi commit 12035cc561613134cf8fdb30535f37176f39b287 Author: lijewski Date: Mon May 20 22:14:20 2002 +0000 -O3 -> -O2 due to xlF bug in tranfit_d.f Tools/C_mk/Make.AIX commit 040acc7ddd42fcc9a548b94e8324b4bd31de235e Author: car Date: Wed May 1 03:37:32 2002 +0000 The *.dsp files were not maintained Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/BoxLib.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_CellMG/mglib.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 8b695acb730f697a2562acfce08438fc50499b4e Author: marc Date: Sat Apr 27 07:10:24 2002 +0000 generalize a bit Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp commit f1cad0030afae6d6d8c33daa35f9f910520aa5e7 Author: marc Date: Sat Apr 27 07:07:41 2002 +0000 Allow making a geom without needing a ParmParse file Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 5e821ad28503e7c5d09c38b76c33deb981f168e2 Author: car Date: Fri Apr 26 22:40:00 2002 +0000 BL_USE_SETBUF removed from command line; set in BoxLib/winstd.H, if needed Src/C_BaseLib/winstd.H Tools/C_mk/Make.defs Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp commit 6af280487e478bd9528929dd624b6b92766a3fa3 Author: car Date: Fri Apr 26 22:24:43 2002 +0000 *** empty log message *** Tools/C_mk/Make.Linux Tools/C_mk/Make.rules commit 2db9f68924721cbd7fd41c7dbdd98a39660e8e78 Author: lijewski Date: Fri Apr 26 22:10:01 2002 +0000 defaulted BL_LANG_CC Src/C_AMRLib/BC_TYPES.H Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_AMRLib/SLABSTAT_F.H Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/SPACE.H Src/C_BoundaryLib/INTERPBNDRYDATA_F.H Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/MG_F.H Src/LinearSolvers/C_TensorMG/DivVis_F.H Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/MCLO_F.H Src/LinearSolvers/C_TensorMG/Test/main_F.H Tests/LinearSolvers/C_TensorMG/main_F.H Tools/C_util/Convergence/AVGDOWN_F.H commit 72a1d03386fae19231022abd12ea0779d778c05e Author: car Date: Wed Apr 24 22:25:20 2002 +0000 another fix for ICC Src/C_BaseLib/winstd.H commit 574ef73b4a28fcfdbca7ba053edd12dbcb1fea5e Author: car Date: Wed Apr 24 17:55:30 2002 +0000 support for 6.0 Intel compilers Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit f8ce7a3781f013ec24040b7beadafc917d94c884 Author: vince Date: Wed Apr 17 22:22:19 2002 +0000 added flag for null KCC version parse. Src/C_BaseLib/VisMF.cpp Tools/C_mk/Make.defs commit 077213ebc1d162afde9b9123616d9eed2d3a26da Author: vince Date: Tue Apr 16 18:06:28 2002 +0000 added synchronization of random tables in parallel. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/PROB_AMR_F.H commit fd04f5708d0d9d0d1af9471074494d80d804a3a3 Author: lijewski Date: Tue Apr 16 15:20:28 2002 +0000 forgot to update LDFLAGS earlier Tools/C_mk/Make.AIX commit 1b64dbd23147c7fc0f1ae0e0debdec575df98a4d Author: car Date: Mon Apr 15 20:12:26 2002 +0000 oops Src/C_BaseLib/BLThread.cpp commit 20080f70db77a30681a8ffa25b7f888f9b10a37c Author: car Date: Fri Apr 12 17:24:52 2002 +0000 tweak for f77/g77; if you compile COMP=Intel then FCOMP=Intel seems necessary for now. This is not enforced Tools/C_mk/Make.Linux commit 5c7a2c0773e02c3a28bb62feac1ebef7924098bb Author: car Date: Fri Apr 12 17:09:17 2002 +0000 better support for icc Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 927d79f73ae31265e184fad78757ac48e3562620 Author: car Date: Thu Apr 11 19:40:29 2002 +0000 icc support Src/C_BaseLib/Thread.H Src/C_BaseLib/winstd.H Tools/C_mk/Make.Linux commit 03fb68a4c4694d283440640e67e9805521a8f31c Author: car Date: Mon Apr 8 20:51:36 2002 +0000 *** empty log message *** Src/C_BaseLib/Thread.H commit abe496899780e8f5ae9b05ca854feb51b9524c3a Author: car Date: Mon Apr 8 20:46:46 2002 +0000 max_threads is now unsigned long Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Thread.H commit ad5823674063b7226307993933b3738b7d29db5e Author: car Date: Mon Apr 8 17:25:05 2002 +0000 f90 and f no longer preprocess, F90 and F do Tools/C_mk/Make.rules commit 9a8a1b911f93d255f5a447b6841a5332ee54226b Author: car Date: Sun Apr 7 17:00:44 2002 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Tools/C_mk/Make.FreeBSD commit 7149fc2b9e8c8ac5799f322c687cc6f9c74405fb Author: lijewski Date: Thu Mar 28 21:00:12 2002 +0000 *** empty log message *** Tools/C_mk/Make.OSF1 commit 3164f52618fcd60f386c41419f895ef982f4dfd1 Author: car Date: Wed Mar 27 23:58:50 2002 +0000 std::abs on BL_OSF1 Src/C_BaseLib/winstd.H commit e27cf9367d12fd77093e94a7ad7d2feac8994d18 Author: lijewski Date: Wed Mar 27 23:49:07 2002 +0000 *** empty log message *** Tools/C_mk/Make.OSF1 commit 7333878ad4b08164f9b9482c928f01657bfe3ebf Author: car Date: Wed Mar 27 21:35:59 2002 +0000 *** empty log message *** Tools/C_mk/Make.OSF1 Tools/C_mk/Make.mpi commit f2721443b77418f19aeb312d70d1afe8bccfe20b Author: lijewski Date: Wed Mar 27 19:21:54 2002 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit aa3f0c2f3f32939b775485482478b146415b98f9 Author: lijewski Date: Wed Mar 27 17:54:34 2002 +0000 mods to quiet xlC Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 87c77ee0ceb96093f54748c90cb80f1f0946211b Author: lijewski Date: Wed Mar 27 17:10:20 2002 +0000 *** empty log message *** Src/C_AMRLib/AmrLevel.H commit 24365ae040453080244bd4778051eed292bb64dd Author: lijewski Date: Tue Mar 26 23:59:29 2002 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit 3b8ed4dc17b8888ebe53ab6018f9fb9b41a946ae Author: lijewski Date: Tue Mar 26 22:23:58 2002 +0000 *** empty log message *** Src/C_BaseLib/Utility.cpp commit cf175d9315d0bcf95c1a2bb4d92c3caa1fcd9c6e Author: car Date: Tue Mar 26 22:15:43 2002 +0000 different support for f90/f/F/F90 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit a7fc7b553a9c663f1bfb486b873d88de50c2221b Author: car Date: Tue Mar 26 22:14:33 2002 +0000 only sleep Src/C_BaseLib/BLThread.cpp commit e2c3315aad6ba866765ce5d44d22c0d0b59013e9 Author: lijewski Date: Tue Mar 26 21:50:49 2002 +0000 *** empty log message *** Tools/C_mk/Make.AIX Tools/C_mk/Make.defs commit 27820ad64fc914af3c60a5a28b59d09b43ba5f06 Author: lijewski Date: Tue Mar 26 20:47:02 2002 +0000 changes to work with xlC Src/C_BaseLib/ParmParse.cpp commit 591aac8ab77eec16da762a4197127acec5447cf3 Author: lijewski Date: Tue Mar 26 20:04:06 2002 +0000 changes to work with xlC Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/ParallelDescriptor.cpp commit 6e33ce42d26632a009bff83ef841a941372410b9 Author: car Date: Fri Mar 22 23:29:24 2002 +0000 Small change: Only print unused ParmParse variables if there are any unused ParmParse variables. Src/C_BaseLib/ParmParse.cpp commit 4ac41070023867262f02359288533f11e67c8e91 Author: vince Date: Thu Mar 21 00:41:08 2002 +0000 added -ieee flag for opal. Tools/C_mk/Make.OSF1 commit 1c99f4700776d8fd2fb36f6ad09013b5939f84f7 Author: almgren Date: Mon Mar 18 22:31:54 2002 +0000 Modifications needed to correct for the fact that the scalings of Du, S and DGphi are different between the v5 and v9 versions. Src/LinearSolvers/C_NodalMG/hg_avg2d.F commit 371fb5fcf915e402c611cf1147bfb617630b5bbf Author: almgren Date: Fri Mar 15 20:47:52 2002 +0000 Modified the weighting of the source term in hgavg, hgfavg, hgcavg for use with the 9-pt instead of 5-pt stencil. Src/LinearSolvers/C_NodalMG/hg_avg2d.F commit f1a3087cf7e8179f3903f6d800fdd1153b20106f Author: marc Date: Fri Mar 15 20:20:32 2002 +0000 Rework frac calc to avoid using domain.numPts Src/C_AMRLib/Amr.cpp commit 159a754e6c3950ec0e05cbab6ae20e639ac39744 Author: marc Date: Fri Mar 15 19:01:47 2002 +0000 dsp maker for libs Tools/C_scripts/dsp.lib.mak commit aeb78d0fa91c09a26738658c6d8fcb54cb2fa227 Author: car Date: Thu Mar 14 23:56:07 2002 +0000 fix for gcc3 and KCC Tools/C_mk/Make.defs commit bf27a7bdf755fa1001528656c824d999bcae062a Author: car Date: Thu Mar 14 23:05:16 2002 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 6f6956a84f0220fd334eede179441ee21bd54c4f Author: vince Date: Thu Mar 14 01:48:58 2002 +0000 changes for kcc 3.9 Tools/C_mk/Make.defs commit f333f2ca4ca3ee5fc1da96df89133dcc6b94657c Author: vince Date: Thu Mar 14 00:27:03 2002 +0000 changes for brainerd. Src/C_BaseLib/VisMF.cpp commit 35b44a3dd1dedb52f5ebf1906a5b1ef57ec5b466 Author: almgren Date: Wed Mar 13 22:07:49 2002 +0000 Updated version of test results with 2-d test cases. Src/LinearSolvers/C_NodalMG/files.2d commit 6a881c0fbf5525170fef671094f809e5703bc7f4 Author: almgren Date: Wed Mar 13 21:54:59 2002 +0000 Improved version of the test code. Fixed some bugs even. Src/LinearSolvers/C_NodalMG/proj.cpp commit c3fd2b5eeb434ecacad645994c44135704c61162 Author: almgren Date: Wed Mar 13 21:54:24 2002 +0000 We dont do factor of 8 refinement. Src/LinearSolvers/C_NodalMG/tests/gr.19s8 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s8 commit 8f3977005c22bcbcd14aec0562f50ede7242ba66 Author: almgren Date: Wed Mar 13 21:52:54 2002 +0000 This test case fails because it needs an absolute tolerance in the CG solver. Not worth worrying about here. Src/LinearSolvers/C_NodalMG/tests/gr1rick Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick commit ed17fe6adf38cfb09b8f02d0d57ebc8f08e77cd2 Author: almgren Date: Wed Mar 13 21:49:16 2002 +0000 A grid 201 long does not coarsen! Try making this 0-199 instead of 0-200... Src/LinearSolvers/C_NodalMG/tests/gr1rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick2 commit 0065503662bca6788bbc5100e4482368a7a6899b Author: vince Date: Wed Mar 13 21:43:58 2002 +0000 Added FabArray shift for hchem support. Src/C_BaseLib/FabArray.H commit 536c4207daf1c8604fafb010a1915d4abad3b958 Author: almgren Date: Wed Mar 13 21:39:03 2002 +0000 This grids file assumes a factor of 8 refinement - get rid of it! Src/LinearSolvers/C_NodalMG/tests/gr2a8 Tests/LinearSolvers/C_NodalMG/test_grids/gr2a8 commit 718142363728c68eb446843edc21b53ac7c799ec Author: almgren Date: Wed Mar 13 21:32:34 2002 +0000 Make this a 3-level instead of 1-level test case, with same grids at finest level. Src/LinearSolvers/C_NodalMG/tests/gtclearsmall Tests/LinearSolvers/C_NodalMG/test_grids/gtclearsmall commit 83d30e01fddac9cac5fd48a2aebce37d975cc872 Author: almgren Date: Wed Mar 13 21:31:41 2002 +0000 Previous grids file had files not contained in domain. Src/LinearSolvers/C_NodalMG/tests/gt12.2 Tests/LinearSolvers/C_NodalMG/test_grids/gt12.2 commit 6f14f6fff4598ef26acd388be78e8a6e350e3fc6 Author: almgren Date: Wed Mar 13 21:30:37 2002 +0000 Latest update on what works of the 3-d test cases. Src/LinearSolvers/C_NodalMG/files.3d commit 3042d947a7b10a26735721a710af10f4547b46e9 Author: almgren Date: Wed Mar 13 21:17:25 2002 +0000 Too small to be interesting. Src/LinearSolvers/C_NodalMG/tests/gt2t2 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t2 commit 13b9720a56865176f6cd6f8531447a2371def5da Author: lijewski Date: Wed Mar 13 19:07:00 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/files.2d commit d52f759cd2949216375e99d52141bec569532f16 Author: lijewski Date: Wed Mar 13 18:31:42 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/files.2d commit 65a475d43dfce70923c06d18a95b9bcfff2b86ad Author: almgren Date: Wed Mar 13 18:29:38 2002 +0000 Fixes for 2d only: length --> size, etc... Src/LinearSolvers/C_NodalMG/proj.cpp commit 4ef872bcd816669d49ca315921b4f31370f0a1b9 Author: almgren Date: Wed Mar 13 00:57:35 2002 +0000 New test problem which failed with previous code but now works. A smaller version of the critical grids of this problem are in gtclearsmall. Src/LinearSolvers/C_NodalMG/tests/gtclearlarge Tests/LinearSolvers/C_NodalMG/test_grids/gtclearlarge commit d026a97c59c48a4f5b97827459a59ba6dba917a6 Author: almgren Date: Wed Mar 13 00:56:56 2002 +0000 New test problem which failed with the previous version of the code. This is extracted from gtclearlarge. Src/LinearSolvers/C_NodalMG/tests/gtclearsmall Tests/LinearSolvers/C_NodalMG/test_grids/gtclearsmall commit de15f205daf94846ac0e1f7b164d24d2b37b9ade Author: almgren Date: Wed Mar 13 00:56:02 2002 +0000 Updated list of which of the tests/gt* files are 3-d problems, and whether they work with the current version of the code. Src/LinearSolvers/C_NodalMG/files.3d commit 1ac4aa00e3e26bba19492fba58a49b60c4349bff Author: almgren Date: Wed Mar 13 00:55:33 2002 +0000 Fixed a bug in the construction of the level interface objects - code used to fail on test code gtclearsmall and now works. Replaced "contains" by a box by "contains" by a BoxArray. Src/LinearSolvers/C_NodalMG/interface.cpp commit 22cb2a162e9d3ab0ad191dda67755e2ebc29b43d Author: lijewski Date: Mon Mar 11 23:05:53 2002 +0000 added Src/LinearSolvers/C_NodalMG/proj.cpp commit e78669da0c4ce41c58698ed4506601ad31281ebf Author: car Date: Mon Mar 11 21:53:57 2002 +0000 Now an empty BoxList is constructed from an empty BoxArray. Src/C_BaseLib/BoxArray.cpp commit 920f4c3ac07f46bf3c467e2fd4cf4b87bf93bbfd Author: lijewski Date: Mon Mar 11 19:24:08 2002 +0000 got rid of unsigned on aux() -- it's an int Src/LinearSolvers/C_NodalMG/interface.H commit 6b47b8cca0eb2ecbac281f9b26d46711653bad23 Author: car Date: Tue Feb 26 23:41:45 2002 +0000 gcc 3 Tools/C_mk/Make.defs commit 1f7c145e18913074a71367b6d05a792d2dde8bbe Author: car Date: Tue Feb 26 23:41:31 2002 +0000 some systems require explicit include of pthread Src/C_BaseLib/BLThread.cpp commit bf9d3afd1b24fe7037708991b9c3049b5a58a939 Author: car Date: Mon Feb 25 20:59:43 2002 +0000 UnitBox was implemented as a 2x2x2 box. Src/C_BaseLib/Box.cpp commit 4b74e6143fe04257dd7cb4d9abebe0980e989cce Author: lijewski Date: Fri Feb 22 20:53:54 2002 +0000 Fixed FixUpPyhsCorners() bug Src/C_AMRLib/AmrLevel.cpp commit 942781915ec62e5e1950717a7df366b895a6bdfe Author: car Date: Tue Feb 19 23:36:06 2002 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit df06e6982db379987476cd6ae951536e062aba12 Author: car Date: Wed Feb 6 18:14:46 2002 +0000 Fixed random number seeding. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit a3680ce81de37fd1c18ae8872194b24541708765 Author: car Date: Tue Jan 8 16:30:24 2002 +0000 no message Src/C_BaseLib/BLProfiler.cpp commit cba564c6e21582eeb0d94249d049f8052f85d44c Author: car Date: Fri Jan 4 00:17:23 2002 +0000 no message Src/C_BaseLib/BoxLib.dsp commit fe97f51e9993427ecfc6c9ac6e65b4b30d176a20 Author: car Date: Thu Dec 13 23:46:08 2001 +0000 properly initialize m_used Src/C_BaseLib/CArena.cpp commit 614bae79406e6958960389c78b38511f54b7fb45 Author: car Date: Thu Dec 13 18:24:59 2001 +0000 makefile system knows fortran Tools/C_mk/Make.defs commit c5aa18122aefb54b890d8fb0ec1249faeb824f8e Author: car Date: Tue Dec 4 21:28:17 2001 +0000 OSF1 now discriminates between V3 and all others Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs commit bacab6a12cb31b6566bc2e743540fffb891ba460 Author: lijewski Date: Mon Dec 3 22:35:54 2001 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp commit 0cc079ff0e59d78175f57040cd7e30bb80598ec5 Author: lijewski Date: Mon Dec 3 22:24:54 2001 +0000 removed mpi_data_type() stuff Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/ccse-mpi.H Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp commit cbccf3a46f5d71d4be324e1e332cccf6ae988667 Author: car Date: Mon Nov 26 18:17:58 2001 +0000 fix for max_threads Src/C_BaseLib/BLThread.cpp commit aa45c741ae3d028c098c669fb502841b77bef51c Author: car Date: Mon Nov 26 18:14:26 2001 +0000 refinement of BLThread.cpp for WINNT Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Utility.cpp commit b2aab7ac284e4ad60874d64999f16b116731150f Author: car Date: Wed Nov 21 19:50:44 2001 +0000 CriticalSections seem to work better for mutex's Src/C_BaseLib/BLThread.cpp commit 8c08667ffba905dd0e42311d98608f4e61d2a733 Author: car Date: Mon Nov 19 19:10:49 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BoxLib.dsp commit 4079c9cd80d7ebfedd0cd8e35354cca78bb71c2c Author: car Date: Fri Nov 16 18:19:33 2001 +0000 cv needs to be mutable Src/C_BaseLib/WorkQueue.H commit 0280ec49a92b18536b822258f938a37744502aee Author: car Date: Fri Nov 16 18:05:16 2001 +0000 numthreads needs a lock Src/C_BaseLib/BLWorkQueue.cpp commit 214d02d44a7f9576ac0b91d10399086c46d375bf Author: car Date: Tue Nov 13 00:08:29 2001 +0000 KCC doesn't always like PTHREAD_STACK_MIN? Src/C_BaseLib/BLThread.cpp commit b7adaf6e3a63ebbc19c81101c862f4272749f991 Author: car Date: Mon Nov 12 23:28:03 2001 +0000 Windows fixes Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Utility.cpp commit 43c985a15582bb48320594e8314ee27664733bdd Author: lijewski Date: Mon Nov 12 21:38:21 2001 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit ccf5488c49da10a6f294c107fbc4feb794a7504a Author: car Date: Fri Nov 9 14:33:10 2001 +0000 fix for unix threads Src/C_BaseLib/BLThread.cpp commit ee80a04348de98aba8f4b1ddf89caf1cf07fbe6d Author: car Date: Wed Nov 7 22:00:57 2001 +0000 More WIN32 support Src/C_BaseLib/BLThread.cpp commit a4a35f4d821e2db7f7332f2ecf02a448946564f5 Author: lijewski Date: Wed Nov 7 19:05:01 2001 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit 859a479709e7aed287e87e349f02263ca90b5c7b Author: car Date: Thu Nov 1 23:52:50 2001 +0000 restored a user-specified TSD destructor Src/C_BaseLib/Thread.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tWorkQueue.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tWorkQueue.cpp commit b7817598a6e9d912ff867a12444d1d216f04eb1c Author: lijewski Date: Thu Nov 1 23:21:34 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp commit ebce6425de3beca53ef11912330dabdfe6c6501e Author: car Date: Thu Nov 1 18:53:15 2001 +0000 baseThread Src/C_BaseLib/BLThread.cpp commit 468a31f35ddd97823af4714943f42149fa08fc89 Author: car Date: Thu Nov 1 18:46:37 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp commit 30627b1b8177f978707f85b92d5662676c5e16c6 Author: lijewski Date: Thu Nov 1 17:57:30 2001 +0000 re-added BLMpi.cpp Src/C_BaseLib/FabArray.H commit 461389f6c773904d2045cd36d047d8c31085f75b Author: car Date: Thu Nov 1 17:08:41 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp commit 7f907f1e10b2964816e30648887dedf51999a0aa Author: lijewski Date: Thu Nov 1 16:50:38 2001 +0000 *** empty log message *** Src/C_BaseLib/BLMpi.cpp commit 8ef6ee3851b343d90bc9d50c4a8db4ddbeba7e3f Author: lijewski Date: Wed Oct 31 22:42:01 2001 +0000 re-added BLMpi.cpp Src/C_BaseLib/Make.package commit a10fc2dbfbbb8729a47467c520309fb99d527493 Author: lijewski Date: Tue Oct 30 22:03:42 2001 +0000 more threading work Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit a13824bcc5e09a3bf974ce7a5659c8d5f6477d1b Author: lijewski Date: Tue Oct 30 20:26:29 2001 +0000 removed no-threadsafe constructs Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit 70090192584334f12af5d94d6fff31a349e322e5 Author: car Date: Wed Oct 24 19:48:44 2001 +0000 PGI C++, which doesn't work Tools/C_mk/Make.Linux commit ff8b20d4ed0164dfc1d0e73076fae3d3f347c0fb Author: lijewski Date: Tue Oct 23 17:31:02 2001 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp commit 16813e44d01096e385aed62a4052662111b1bd1d Author: lijewski Date: Tue Oct 23 17:01:02 2001 +0000 added BoxLib::ResetArena() Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Arena.H Src/C_BaseLib/BaseFab.cpp commit 3fd8f79a9a35676cd3111da5ba3632f7631628f4 Author: car Date: Mon Oct 22 22:49:53 2001 +0000 Fix for windows Src/C_BaseLib/BLThread.cpp commit e405a8bc77c5bb6420747740cbd41883b9f3015c Author: lijewski Date: Mon Oct 22 21:12:45 2001 +0000 thread stacksize stuff Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/Thread.H Tools/C_mk/Make.OSF1 commit 4c93567682ac951c6d29282bd84096bffcfe0f97 Author: car Date: Sat Oct 20 22:45:32 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/Thread.H commit c36187ce4827f48113addec285ba9f4d6d0924a6 Author: car Date: Thu Oct 18 21:54:13 2001 +0000 Added BaseFab.cpp Src/C_BaseLib/BoxLib.dsp commit b37f4962c6a3de9a7a5a570f93eebe3d05e0bfd0 Author: lijewski Date: Thu Oct 18 17:55:31 2001 +0000 some thread fixes Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Thread.H commit eade3ab0d2c60df5f707b435947731a18c4293a5 Author: lijewski Date: Wed Oct 17 17:53:33 2001 +0000 removed unneeded BL_USE_SETBUF and BL_USE_NEW_HFILES Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tFB.cpp Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tFB.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tools/C_mk/Make.CRAY Tools/C_mk/Make.CYGWIN_NT Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.Linux Tools/C_mk/Make.T3E Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffPlot.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFdiff.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp commit a903c0e29dcce2007a34c37347a5eefa57764a42 Author: lijewski Date: Wed Oct 17 16:49:27 2001 +0000 Need BL_USE_SETBUF for g++ Tools/C_mk/Make.defs commit 1e455959ef9aee95373ade78ebb4111171754319 Author: lijewski Date: Wed Oct 17 16:43:22 2001 +0000 always use pubsetbuf() Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.cpp commit 75fc152526b42d710802400726b1471d1f2ce06c Author: lijewski Date: Tue Oct 16 22:45:34 2001 +0000 got rid of libmiranda.a Tools/C_mk/Make.AIX commit 71ba288b4c5619ebc3b7cdda1c29ab85d76192cc Author: lijewski Date: Tue Oct 16 19:59:51 2001 +0000 Integrated in BoxLib::The_Arena() Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Arena.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/FabArray.H Src/LinearSolvers/C_NodalMG/proj.cpp commit 3f6a2a5193636707e846fd1f1889e8becfaa3dd3 Author: car Date: Mon Oct 15 23:01:27 2001 +0000 debugging flags for PGI Tools/C_mk/Make.Linux commit b91f04de32b27321fd556cc0c941d43b8e2b8dfd Author: lijewski Date: Mon Oct 15 21:01:50 2001 +0000 Set up PGI to use pgf90. Tools/C_mk/Make.Linux commit fdf18a0c6cd69c46732b54b20881891db342c527 Author: car Date: Mon Oct 15 18:37:35 2001 +0000 Don't need the timespec declaration anymore. Src/C_BaseLib/winstd.H commit b7183a8eed30bb1891d7dd1e493a90ca5785b722 Author: car Date: Mon Oct 15 18:17:51 2001 +0000 just replicate the data members of timespec in our Timer Src/C_BaseLib/Utility.H commit 13eba0c7d0bad0de0647a78a1d1edbee49e4ca31 Author: lijewski Date: Mon Oct 15 18:15:22 2001 +0000 Removed COALESCE_FABS stuff and NEW_HFILES stuff. Tools/C_mk/Make.AIX commit b8c06326b62459f6c3c104b8f7fb8a5722004aa2 Author: lijewski Date: Fri Oct 12 17:44:25 2001 +0000 added Mutex Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 688f396d5c8c8f6e08e4722f3ac9bb20ff8973de Author: lijewski Date: Thu Oct 11 16:33:38 2001 +0000 add tread.cpp Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tread.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tread.cpp commit 559ea361fa609b3e0a6395fc88f94b25d2fb10aa Author: car Date: Wed Oct 10 20:12:44 2001 +0000 mpi typemaps for some BoxLib types Src/C_BaseLib/Box.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit b2512af21f8ed04ab0dd289749b12deb3394d1e2 Author: car Date: Wed Oct 10 15:44:41 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp commit 61f1ebe1090c9d34ce41184d0fe346cc7dd494c4 Author: car Date: Tue Oct 9 22:37:46 2001 +0000 MINGW32, a minimal gnu under win32 Src/C_BaseLib/winstd.H commit 7ce56e29638eba89e732593f73196d38aa0289dc Author: lijewski Date: Fri Oct 5 19:47:55 2001 +0000 Up'd -bmaxdata size ... Tools/C_mk/Make.AIX commit 2afe53654513189bdfc71f906841249edf49f6ec Author: marc Date: Fri Oct 5 07:19:55 2001 +0000 iAdd check for instability (due typically to case where initial residual is very small). this code was basically copied from the scalar solver stuff, except that the expert setting to turn it on was put into the cg parm parse stuff. Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit 103188b07bea3ccf6e8723d43dd23906c3036861 Author: lijewski Date: Wed Oct 3 19:53:51 2001 +0000 output maxthreads only if verbose Src/C_BaseLib/BLWorkQueue.cpp commit 5da536222afb59c9459107d8ffb86a9158a505bd Author: lijewski Date: Tue Oct 2 16:30:41 2001 +0000 mods to get working with KCC Src/C_BaseLib/ParallelDescriptor.H commit 34f09082fb182d45885dd48fe6f9fb7f667340c8 Author: lijewski Date: Thu Sep 27 21:54:13 2001 +0000 removed the default arguments Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 951888185f71268a7add80ae65d388f3dc454ec5 Author: lijewski Date: Thu Sep 27 21:05:15 2001 +0000 got it right (I think) ... Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit a5e1e556fc63c40d1e1ee54fe8967c42cf1657bf Author: lijewski Date: Thu Sep 27 19:52:14 2001 +0000 oops -- had a parallel bug in there somewhere Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 33419539c950928cb0acda0275bed4eb24633256 Author: lijewski Date: Thu Sep 27 18:03:26 2001 +0000 some std stuff Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 1a6dfb1c0d23d66f25d651e470f93672360c2745 Author: lijewski Date: Thu Sep 27 17:57:21 2001 +0000 removed more BL_USE_MPI stuff Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 3ba787581441db36d983b02a55e197bb3ffa6ea9 Author: car Date: Thu Sep 27 16:11:49 2001 +0000 -DBL_KCC_VERSION added Tools/C_mk/Make.defs commit bb5e8e2e119f1c0b9f5543ba9500172d454bd8a4 Author: lijewski Date: Wed Sep 26 16:59:53 2001 +0000 removed unused variable Src/C_AMRLib/FluxRegister.cpp commit fff524dd362d28cd15dd0298a87f50e733af9613 Author: lijewski Date: Wed Sep 26 15:47:54 2001 +0000 for clarity ... Src/C_BaseLib/FabArray.cpp commit 80817573ffa5a82cd360175e9d150fa26deaadd7 Author: car Date: Wed Sep 26 15:43:31 2001 +0000 debugging of MFIters taken from HG removed 2 static array decls in Collect Data that broke MSVC. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit da09a91423e9d8771213d282ef33fabd0e4f1fd0 Author: car Date: Wed Sep 26 02:16:58 2001 +0000 HG_is_debugging is only defined in IAMR CollectData not in macros triggers a bug in VC++ Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit a56ca1ee9ffa5c55ac519a809ffaf6c0c015a73d Author: lijewski Date: Tue Sep 25 22:45:40 2001 +0000 more hiding of MPI-specifics Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 2c8f75e97db7fb85d09f7322c266ef61ad879925 Author: car Date: Tue Sep 25 21:02:54 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 5ba9149aea3f46f7b580d91ccda79cd27a830494 Author: lijewski Date: Mon Sep 24 20:31:35 2001 +0000 output wallclock time since start(restart) Src/C_AMRLib/Amr.cpp commit a70f10677c599e1905d99f597c99eb2d1d6581bb Author: lijewski Date: Mon Sep 24 19:10:03 2001 +0000 *** empty log message *** Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit b64429b28f91db6c8528cf70e11573799e254af5 Author: lijewski Date: Fri Sep 21 21:38:21 2001 +0000 removed some BL_USE_MPI blocks Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/VisMF.cpp commit 54d3f11c6cf1be5dbed521c57aad38bc7b45466f Author: car Date: Wed Sep 19 17:04:43 2001 +0000 no dependencies in real fortran Tools/C_mk/Make.rules commit 6c48d5bcd05331279341ab3b3a44f3b071776f5d Author: car Date: Wed Sep 19 17:03:58 2001 +0000 in serial ParallelDescriptor::second now returns wall clock time Src/C_BaseLib/ParallelDescriptor.cpp commit 02a8bc93775d340dbeb6cbe1ad3205239fa63a2f Author: lijewski Date: Wed Sep 19 16:54:05 2001 +0000 Added stuff to get threading to work. Tools/C_mk/Make.AIX commit 2f9b4a7152a17cebe4036b3440b99ba31a609952 Author: car Date: Wed Sep 19 02:39:53 2001 +0000 -CB loses mostly Tools/C_mk/Make.Linux commit 187dd78339c2bfb7ee68166400a73971f26c83d8 Author: car Date: Wed Sep 19 02:37:20 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit daa9c28e32db761d311088ae49028d1fb2d9cc0d Author: car Date: Wed Sep 19 02:36:47 2001 +0000 need header Src/C_BaseLib/BLWorkQueue.cpp commit 54f0aba6a9aff378da116131ee289f62f43a7d92 Author: lijewski Date: Tue Sep 18 20:40:27 2001 +0000 Wrapped an I/O statement appropriately. Src/C_BaseLib/BLWorkQueue.cpp commit 241971920e8d0878774e9d5975c63329c50968f2 Author: marc Date: Tue Sep 18 18:15:03 2001 +0000 Split out tests for defined junk. Src/C_BaseLib/std/limits commit 203a3d5d4dea875acf2c7fc67fd31433b66d07ac Author: car Date: Tue Sep 18 03:34:49 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit ea590d2ea3b8b0e5120da18ab45bae1fdb211edc Author: lijewski Date: Mon Sep 17 22:03:03 2001 +0000 add thread_safe for mpKCC Tools/C_mk/Make.defs commit 095d92dd0c0120fa8f2b09441e6a1f4ab889b56b Author: car Date: Sun Sep 16 16:44:24 2001 +0000 more support for Intel, must upgrade set gigan:/var/tmp/RPMS/extra Tools/C_mk/Make.Linux commit 9aeb80a366953faa9b052afceeeb79656c7597cd Author: marc Date: Sat Sep 15 05:29:29 2001 +0000 Fix for little-f files Tools/C_mk/Make.Linux commit 44f094c67a9cc04782ba921df79a7e657d43c375 Author: lijewski Date: Fri Sep 14 21:03:06 2001 +0000 Now always print out workqueue.maxthreads at startup ... Src/C_BaseLib/BLWorkQueue.cpp commit 303ee73a16d38cd5bf948c2390204c083d19dfae Author: car Date: Fri Sep 14 04:03:39 2001 +0000 fixes for KCC Src/C_BaseLib/Thread.H commit 9742d8c8ba60bdfd4ce867bb071c6ca426ae253f Author: lijewski Date: Thu Sep 13 23:09:16 2001 +0000 Now print out # of cells advanced at each level as we go ... Src/C_AMRLib/Amr.cpp commit 921ace7223dc53eb18cb76354acd1fc44f343062 Author: lijewski Date: Fri Sep 7 23:06:44 2001 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp commit 807c18d7623407f9d8af19b8175f4fbb8cfe3d01 Author: car Date: Fri Sep 7 22:03:21 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp commit 32de1352383526bd89ec871e91ef65723b4b4ee4 Author: car Date: Fri Sep 7 00:35:02 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 4d8e0bbd247eb9aa7143b71dc083a02ab2d5e8fe Author: lijewski Date: Thu Sep 6 22:49:19 2001 +0000 added a default getID() for USE_THREADS=TRUE. Src/C_BaseLib/BLThread.cpp commit 6b3e88b9ed15bc169b1fa25f1892fb3f70a75739 Author: car Date: Wed Sep 5 19:29:59 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 92371bcfeb8a7148e464490dc75dca3d011439f1 Author: car Date: Tue Sep 4 16:59:41 2001 +0000 Threading Fixes Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Thread.H commit 6ba19a0dda3bddcfed07b30f56b2d1b57fd402a5 Author: car Date: Thu Aug 23 21:58:04 2001 +0000 simplify thread Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Thread.H commit 9faef0875e130afd8a6a32c9b8aa5293809ed897 Author: car Date: Thu Aug 23 21:44:32 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxLib.dsp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Thread.H commit 04c1effe3ef4aa4ccbf01bc0173edae4ace82982 Author: lijewski Date: Thu Aug 23 20:07:43 2001 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp commit eeed082d0f9f47063d57fc0f5637d474c9c3de68 Author: lijewski Date: Wed Aug 22 21:35:25 2001 +0000 removed an assert() Src/C_AMRLib/AmrLevel.cpp commit 8b0b392947b22ce54b07bec8a2704e5bb6c4222c Author: lijewski Date: Wed Aug 22 20:18:14 2001 +0000 made probin_file default to probin Src/C_AMRLib/Amr.cpp commit ecc5eb267d2f63085747112264695200bbfe8100 Author: lijewski Date: Wed Aug 22 19:21:00 2001 +0000 reverted to older style copy constructor Src/C_BaseLib/Geometry.cpp commit 4502658b9100a4a8bf0629be3168aeff38ff1d47 Author: car Date: Tue Aug 21 22:15:37 2001 +0000 revitalized threads Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/WorkQueue.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tWorkQueue.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tWorkQueue.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 922025d0b7524dd1359cb8ff097cac255e536458 Author: car Date: Tue Aug 21 20:30:02 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Thread.H commit 8f913f72c868e5c7c74f25906efcd7ce10cf90ea Author: lijewski Date: Tue Aug 21 19:01:51 2001 +0000 simplification Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 0db707ac0e68f5002b6a705f44242671c762d0ff Author: lijewski Date: Tue Aug 21 18:08:46 2001 +0000 simplification Src/C_BaseLib/FArrayBox.cpp commit 4eeb606df24f0501b8c9cff3187f34e47ca2eb97 Author: car Date: Tue Aug 21 17:10:31 2001 +0000 minor leak Src/C_BaseLib/BoxLib.cpp commit 7b10c4391585fa26dd4a5b7764d6a6d6e2224261 Author: car Date: Mon Aug 20 02:48:50 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 01d19ee174dae26d5f40f9897bafb019d0f1006e Author: car Date: Sat Aug 18 23:39:10 2001 +0000 added souce numega filters. Src/C_BaseLib/.cvsignore commit 833ff7fce0f90515b2a792d4161d9c5cce603e7d Author: lijewski Date: Fri Aug 17 15:41:33 2001 +0000 Reverted out the greeno stuff; shouldn't have been checked in :-( Src/C_AMRLib/Amr.cpp commit df78fd8d0ef5e48f74292ee83ecb7b1d073ed894 Author: lijewski Date: Thu Aug 16 23:06:47 2001 +0000 Modifications as per greeno. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/FILCC_1D.F Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/Interpolater.cpp commit 0694402c6eb4351b225eaab7f7601876ae1a79d7 Author: lijewski Date: Thu Aug 16 20:11:38 2001 +0000 Refined the way we call ParmParse::Initialize(). Src/C_BaseLib/BoxLib.cpp commit f0f99427b9805afb406ff5277ff56fd55403feda Author: lijewski Date: Thu Aug 16 17:57:43 2001 +0000 some simplification ... Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/REAL.H commit a0719c9333e650d46dc5febfd4d916be19ec5186 Author: almgren Date: Wed Aug 15 21:51:55 2001 +0000 Dont define spherical_origin_fix with 0.0 (double) but with 0 (int). Src/C_BaseLib/Geometry.cpp commit 37190422efe52e9137860b78f7e83a0c834bbf96 Author: lijewski Date: Wed Aug 15 19:23:55 2001 +0000 stuff needed by greeno Src/C_BaseLib/COORDSYS_1D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 6e3a077753a84845b508a5474fa5dadaa949bb02 Author: lijewski Date: Wed Aug 15 16:25:21 2001 +0000 Removed some _GNUC_ stuff. Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BaseFab.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 51e58097e0ba4d0609df5cf66c173edcc33b9798 Author: lijewski Date: Tue Aug 14 22:21:08 2001 +0000 Can now turn off profiling via ParmParse with "profiler.profiling=0" Src/C_BaseLib/BLProfiler.cpp commit d2b572ff3919e296faf36f9e6dfd0e92f31ac4c3 Author: car Date: Tue Aug 14 22:14:00 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 9ab69eac956799ef451257ce772981d8e9d57560 Author: car Date: Tue Aug 14 16:07:31 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 641bcc3cea102cb2f027b2cb40625238d8a82ab0 Author: car Date: Mon Aug 13 22:34:45 2001 +0000 MSVC fixes Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxLib.dsp Src/C_BaseLib/FArrayBox.cpp commit ee8888269112f92c7afab76b74783886a00c8f41 Author: car Date: Mon Aug 13 01:54:26 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit f0b50192cab0981403c429151e3d7d957f0c6461 Author: car Date: Sat Aug 11 21:19:04 2001 +0000 MSVC fix Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 7c12f23ebef1bd4920ffe559bbb5e5f29f46e069 Author: car Date: Sat Aug 11 21:14:20 2001 +0000 Fix for WIN32 Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit d7b601a7a989c333c9d197fc08742a335913a17d Author: car Date: Sat Aug 11 20:50:14 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 5b4c7b9b277cd43dcd7e504445aa8aa0c2042f0f Author: car Date: Sat Aug 11 20:45:55 2001 +0000 Added ParmParse 'Record' types Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit c3d96db94e8c77bef1cbb5e0833307fc8c6fc991 Author: almgren Date: Fri Aug 10 19:57:53 2001 +0000 Changed the way we input periodic. Src/LinearSolvers/C_NodalMG/inputs Src/LinearSolvers/C_TensorMG/Test/inputs2D Tests/LinearSolvers/C_TensorMG/inputs2D commit 510203f3b86658f7f75313de2bb3fe588386aa0a Author: almgren Date: Fri Aug 10 19:52:21 2001 +0000 Changed the way we input periodic. Src/C_BaseLib/Geometry.cpp commit 1e9e3c0ffe16b85528ee66a34101e2bf373a91df Author: marc Date: Thu Aug 9 22:50:20 2001 +0000 change fwd declare from class to struct Src/C_BaseLib/Geometry.H commit f15617af995c9766097ff3552027ff7926a2d085 Author: marc Date: Thu Aug 9 22:41:59 2001 +0000 added winstd for MSVC debug builds Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StationData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/SPACE.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Tools/C_scripts/dsp.mak commit f46244821e146a930a0387824ae0e3f7e49fff4c Author: marc Date: Thu Aug 9 16:21:26 2001 +0000 Change concat function to satisfy DVF compiler Src/C_BaseLib/REAL.H commit f13db4d2d431d33df1715d0bba8a60b78139bc34 Author: marc Date: Thu Aug 9 16:20:37 2001 +0000 Minor fixes to satisfy MSVC compiler Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateDescriptor.cpp commit 32a5c830f884c24cc09be0023538e8e86598506c Author: car Date: Mon Aug 6 19:40:27 2001 +0000 Box constructor/user defined conversion Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit b5fa0066ace065562a35b323611c8e544fd5cdf5 Author: car Date: Mon Aug 6 19:39:59 2001 +0000 ParmParse hacks Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 9f66ae669f1a780a5f9edccaa6583418b7da398c Author: car Date: Mon Aug 6 19:39:25 2001 +0000 windows Src/C_BaseLib/VisMF.cpp commit 27000a1ce9d27b694061b2d0ebebfdc50d1eabd8 Author: car Date: Thu Aug 2 16:37:49 2001 +0000 Typo Src/C_BaseLib/CONSTANTS.H commit 80f58685eac367875da2caeacb5c0946e4b6c848 Author: car Date: Thu Aug 2 16:18:15 2001 +0000 CONSTANTS change, use BL_REAL Src/C_BaseLib/CONSTANTS.H commit 2b88faef7d8f2811348ca61c57e73ed0dae5d4b0 Author: car Date: Thu Aug 2 16:04:11 2001 +0000 append->push_back Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/SlabStat.cpp Src/C_BaseLib/RealBox.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp commit 67bb16c6d219abafd7823ac9deb1cfa8e0251f44 Author: car Date: Thu Aug 2 16:01:43 2001 +0000 append->push_back, prepend->push_front, Fab[] stubs, Fab=, MultiFab= Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 23cfe8ffef90ca6bab57ca8a8e5b23cd8907f4e6 Author: car Date: Thu Aug 2 01:23:44 2001 +0000 BL_REAL macro to make constants Src/C_BaseLib/REAL.H commit 256bf8109271d43d1dbebbe060e880eddf92bc8d Author: car Date: Thu Aug 2 01:22:48 2001 +0000 removed fwd decl of ConstFabArrayIterator Src/C_BaseLib/FabArray.H commit b2f85c9b2732d08c562211c6f0d5dbf722307a42 Author: car Date: Thu Aug 2 01:11:36 2001 +0000 MSVC fixes Src/C_BaseLib/Array.H Src/C_BaseLib/FabArray.H commit 56a303c681ed86cc8bb6765ee692ab38555c20d6 Author: car Date: Wed Aug 1 22:32:23 2001 +0000 make fixes for g++ Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit cde8b520e11627317e95acfd1c4adb8781100832 Author: lijewski Date: Wed Aug 1 21:50:44 2001 +0000 now using BoxLib Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DatasetClient.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/Mask.H Src/C_BoundaryLib/Mask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/grids/gr.2_19boxes Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/grids/gr.2_19boxes Tests/LinearSolvers/C_CellMG/main.cpp Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp commit 137e3e506d093440489565eaac8419bead99eef6 Author: lijewski Date: Wed Aug 1 20:24:21 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/VisMF.cpp commit 908cb19809d92e8d6405575f67e3f817e0c6afeb Author: lijewski Date: Wed Aug 1 18:14:13 2001 +0000 now include where needed for std::abs() Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Utility.H commit 955d70fc0788aef8ea807c91fd2fa869610f991d Author: lijewski Date: Tue Jul 31 22:43:16 2001 +0000 Inlined trivial functions. Without inlining I was 20% slower than old code on my example. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/UseCount.cpp commit 8050d4ed2ce12de3cbdb5ae13f898c35b423c0e5 Author: lijewski Date: Tue Jul 31 19:24:10 2001 +0000 No more RunStats. Src/C_BaseLib/Make.package Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit a1a940f520174eef366403090bb5f51c15837e4d Author: lijewski Date: Tue Jul 31 17:56:24 2001 +0000 Some cleanup Src/C_BaseLib/Arena.H Src/C_BaseLib/Array.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BLMpi.cpp Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 3107dd516e9a903da30c83a87cb01a24b210a43b Author: lijewski Date: Tue Jul 31 15:03:42 2001 +0000 Got rid or old Iterator stuff Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H commit 2fa0036583b2388714cb40844631cc0ddcd29ce2 Author: car Date: Thu Jul 26 20:50:05 2001 +0000 more winstd.H uses Src/C_BaseLib/CArena.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/ccse-mpi.H Src/C_BaseLib/winstd.H commit a2e8afc08f647d2a3f8b25e6aa580bccfcdc0ae7 Author: car Date: Thu Jul 26 20:31:38 2001 +0000 include file tweaks; Utility.H need iostream defns Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/Utility.H commit 9f1077891eb46e66f031242e2b3bdde7fdd32669 Author: car Date: Thu Jul 26 20:27:27 2001 +0000 *** empty log message *** Src/C_BaseLib/BLWorkQueue.cpp commit 8491ef3da2e8db7c77766af56910439f04e83bf6 Author: lijewski Date: Thu Jul 26 20:08:43 2001 +0000 More forward declaration including Src/C_BaseLib/Array.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabConv.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H commit 63d7ad859f8c18cf0b6fc266ee6d46b832162a29 Author: lijewski Date: Thu Jul 26 14:55:25 2001 +0000 *** empty log message *** Src/C_BaseLib/FabArray.cpp commit 1c95994de2f4c09ba88e7c321dc6816789b33379 Author: car Date: Thu Jul 26 13:51:54 2001 +0000 Removed redundant member Src/C_BaseLib/FabArray.H commit 98f542eccff2276d5a015cfc2d0930f0059428fc Author: lijewski Date: Wed Jul 25 23:42:02 2001 +0000 *** empty log message *** Src/C_BaseLib/FabArray.H commit cecd2fa2a5264e0326f2104fecb8eb6236c39fbd Author: lijewski Date: Wed Jul 25 23:39:18 2001 +0000 oops Src/C_BaseLib/FabArray.H commit 36ac9c9caa33616cd1e650ce33ebb9b0cc279366 Author: lijewski Date: Wed Jul 25 23:36:15 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 14357803bd1c77b55a7d5400914990e431eb3b0b Author: car Date: Wed Jul 25 05:22:56 2001 +0000 BL_NO_LEGACY_ITERATORS Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.cpp commit a7173323431a168b9ffe894018273cc8ade071a5 Author: car Date: Wed Jul 25 04:45:55 2001 +0000 MFIter Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 0b86f20a476fee7df1ed82947403120a1082aa71 Author: car Date: Wed Jul 25 01:15:13 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.cpp commit 0f6c5e637daea01565b1cef3da344f26b214cb01 Author: car Date: Tue Jul 24 22:42:12 2001 +0000 MFIter... Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit a5c844d943f2dc4307e977e978273969c5610e4b Author: lijewski Date: Tue Jul 24 22:04:47 2001 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 75f1cda463aed16ca7bceaca14a07e8c83fec011 Author: lijewski Date: Tue Jul 24 20:15:38 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.cpp commit 44b3c392387dbe230f9d61b0577fd9f2a7a413f0 Author: car Date: Tue Jul 24 19:47:17 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 9203a74a0b57bf946aeb2254f67a31ca07415427 Author: lijewski Date: Tue Jul 24 18:16:51 2001 +0000 Now use size() instead of length() Src/C_BaseLib/Array.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 191e9dc98b43056199b5a15e8cd7ea577ade3bcb Author: car Date: Tue Jul 24 18:16:26 2001 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H commit 62286bc3732ebcf195fe980e407e49afef5212ea Author: car Date: Tue Jul 24 18:12:34 2001 +0000 Fab Copy constructor Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 4374dfec2d25539b40793cf93261de540cb496a8 Author: car Date: Tue Jul 24 14:38:21 2001 +0000 removed 'options' Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit a8d59f5611bbdc8e6f1cbac2ba333c0da47abde1 Author: car Date: Tue Jul 24 05:12:47 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 8949f4f4f2d0b0d69fa7429f388191f056006498 Author: lijewski Date: Mon Jul 23 23:07:36 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp commit ba547e81817cd175d9cf1ff462cb3d8cfd0f44af Author: car Date: Mon Jul 23 22:30:23 2001 +0000 minor changes Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H commit 71c3373282a772ddd3b9f12bcee21e42af72f6fb Author: car Date: Mon Jul 23 21:32:38 2001 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit ba437c4a83eab55cc0d9bee897c8ddc841e6d7be Author: car Date: Mon Jul 23 21:15:16 2001 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 52c59cabee7d644263f16f92d4d6988b37f9e00c Author: lijewski Date: Mon Jul 23 20:07:14 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 7c3e80cd2c273e08b7d39f7515db936993942806 Author: vince Date: Mon Jul 23 20:06:06 2001 +0000 Added derived quantities. Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit f69355a70ebbe4beff590074ceb4bb8f5f677bb0 Author: lijewski Date: Mon Jul 23 19:34:23 2001 +0000 *** empty log message *** Src/C_BaseLib/WorkQueue.H commit d333f2664e8575be6a1d898a7695410cfe8e0cac Author: car Date: Mon Jul 23 19:33:36 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 69ea9cdec781223e39b27007246b2e9c76ba803e Author: lijewski Date: Mon Jul 23 18:15:21 2001 +0000 aString is gone for good Src/C_BaseLib/ParmParse.cpp commit 410b354dd297fbd563f3d08a5b976b8b753219c7 Author: lijewski Date: Mon Jul 23 17:55:32 2001 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit 70b94ecede13d4f41b84e26f05b4d7a8cef3ed3a Author: lijewski Date: Mon Jul 23 17:39:00 2001 +0000 asdfdfasdfkasdf asdf Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Utility.H commit db68d076df99d485f657545ae2efc64523216443 Author: car Date: Mon Jul 23 04:31:03 2001 +0000 *** empty log message *** Src/C_BaseLib/.cvsignore Src/C_BaseLib/BoxLib.dsp Src/C_BaseLib/GNUmakefile Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/GNUmakefile.tCArena Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/GNUmakefile.tCArena Tests/C_BaseLib/tCArena.cpp commit 0a43f9e1c815b703c6039c43f53db3994ddf8bb3 Author: car Date: Mon Jul 23 04:25:47 2001 +0000 *** empty log message *** Src/C_BaseLib/test/.cvsignore Tests/C_BaseLib/.cvsignore commit b5b5179d0b162049c94b1af286462f0cd0b06062 Author: car Date: Mon Jul 23 04:16:52 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/ParallelDescriptor.H commit fdf4d4ada8f77237c4e4ef311b2dc63ca5ba8251 Author: car Date: Sun Jul 22 23:46:40 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.cpp commit cbd5c543e1a6658937860ea287ecfebaf08fec4b Author: car Date: Sun Jul 22 23:41:27 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 3af39cdf1a53bf588b834b27ada84f6753a631f2 Author: car Date: Sun Jul 22 23:25:24 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Profiler.H commit 7556cfb3a2469154b6804227b25528ab12941a62 Author: car Date: Sun Jul 22 22:12:22 2001 +0000 WIN32 Fixes Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/test/tProfiler.cpp Tests/C_BaseLib/tProfiler.cpp commit 2f2534d6ae580134652d01a2e52b543509b9a011 Author: car Date: Sun Jul 22 22:12:10 2001 +0000 Hides Profiling stuff in Initialize Src/C_BaseLib/BoxLib.cpp commit 68eb7780ae14ca0094419a39bb0516640f800f5e Author: car Date: Sun Jul 22 22:11:43 2001 +0000 parm parses into std::string instead of aStrings Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 4b9015ae6a5bf2c3666b41d4c0c2af87853970ca Author: car Date: Sun Jul 22 20:44:30 2001 +0000 *** empty log message *** Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.cpp commit 5a927ceaf541211f91db06d4b528d7057dc10585 Author: car Date: Sun Jul 22 20:21:16 2001 +0000 *** empty log message *** Src/C_BaseLib/test/tRan.cpp Tests/C_BaseLib/tRan.cpp commit 0b72a64ac5dcd8965e795e5db54bf3c1edc748f7 Author: car Date: Sun Jul 22 19:38:15 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Thread.H commit fa244b61362767249add884bdef02ed75be8e0f7 Author: car Date: Sun Jul 22 18:52:16 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/ParallelDescriptor.H commit 684ea5b2df1b5fec1e160288aa3eea074d0dfc33 Author: car Date: Sun Jul 22 18:25:48 2001 +0000 upto BoxLib spec Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tDir.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tProfiler.cpp Src/C_BaseLib/test/tThread.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BaseLib/test/tWorkQueue.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tDir.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tThread.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tWorkQueue.cpp commit 80c46df23ca54b8c96f20cbbf5105f7c187a7f04 Author: car Date: Sun Jul 22 18:11:02 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/test/GNUmakefile Tests/C_BaseLib/GNUmakefile commit 09a55d0a23d9474287fd35f19c032ce8dee82473 Author: car Date: Sun Jul 22 18:10:45 2001 +0000 Random number validation file Src/C_BaseLib/test/mt19937int.out Tests/C_BaseLib/mt19937int.out commit 4579913949ab03f8b0c3d7b870eb88c48681b685 Author: car Date: Sat Jul 21 17:37:09 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/winstd.H commit 90c4b072801eb6ae25a01fe3c160ca2ae30bea56 Author: car Date: Sat Jul 21 17:37:09 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp commit 20de776b38c869f375563ad7ecfd8937cc35860c Author: car Date: Sat Jul 21 01:17:25 2001 +0000 *** empty log message *** Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 34e0fd6d29b66e9f3a17ef1489886ad1afb56bd4 Author: car Date: Sat Jul 21 00:53:50 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Thread.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tProfiler.cpp Src/C_BaseLib/test/tThread.cpp Src/C_BaseLib/test/tWorkQueue.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tThread.cpp Tests/C_BaseLib/tWorkQueue.cpp commit cbeecaa3966b3c27c386cccf0f5f077ad34879e6 Author: car Date: Sat Jul 21 00:33:15 2001 +0000 *** empty log message *** Src/C_BaseLib/BLWorkQueue.cpp commit 8b076f91240b0bef56b2587dc54057b996e90f53 Author: car Date: Sat Jul 21 00:32:37 2001 +0000 *** empty log message *** Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/WorkQueue.H commit 9f41823161690d7b27713caa04ef7aa1cc97744e Author: car Date: Sat Jul 21 00:32:37 2001 +0000 *** empty log message *** Src/C_BaseLib/WorkQueue.H commit 0964e060bf456c0c474dabd1b756d6a6b2de186d Author: lijewski Date: Fri Jul 20 23:06:17 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/PArray.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Thread.H Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit f2b4670f94fa5bc0166906bbc41b6aba4825f5fe Author: car Date: Fri Jul 20 19:52:54 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp commit a591e253890f0b136bf976b1b6799b7e32983ac6 Author: car Date: Fri Jul 20 19:44:24 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Thread.H Src/C_BaseLib/Utility.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tProfiler.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp commit 960659929b14cfe5657d5f95f90e1a2f05198709 Author: car Date: Fri Jul 20 19:37:36 2001 +0000 *** empty log message *** Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tProfiler.cpp Src/C_BaseLib/test/tThread.cpp Src/C_BaseLib/test/tWorkQueue.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tThread.cpp Tests/C_BaseLib/tWorkQueue.cpp commit 0341fc65b804dcf538b93eb2e00e21e217971fd3 Author: car Date: Fri Jul 20 19:31:06 2001 +0000 Parallel Fixes Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit cfb67175f0662ed73b39e02ffc061df95232253c Author: car Date: Fri Jul 20 18:18:42 2001 +0000 *** empty log message *** Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit b82e95e66822450c785b93d077381e5ebc7bebef Author: car Date: Fri Jul 20 17:57:27 2001 +0000 Fixes for Parallel Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp commit 33f2abe03cb1fda11725885c431b5850612f863c Author: lijewski Date: Fri Jul 20 17:28:16 2001 +0000 Removed index>=0 checks ... Src/C_BaseLib/aString.cpp commit 9fc149a9c5d940e5d128cee6c679d9b1cd398b27 Author: car Date: Fri Jul 20 17:24:30 2001 +0000 windows normalization Src/C_BaseLib/winstd.H commit 578c057a618d30ac7a6c04d7ce372079713cc769 Author: car Date: Fri Jul 20 17:20:48 2001 +0000 FabArray takes only one template arg Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 09a7778333455c3f80f6f786cad07031b14ef92a Author: car Date: Fri Jul 20 17:01:44 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLTimer.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/SPACE.H Src/C_BaseLib/Thread.H Src/C_BaseLib/Timer.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/ccse-mpi.H commit e1d65f30503f2a7c18ea0c97d69b75f3865a7570 Author: lijewski Date: Fri Jul 20 16:54:07 2001 +0000 Merged BaseFab among other tweaks. Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H commit 6b3e02fd2176f805fcf35fce7b355bc77c76ec98 Author: car Date: Fri Jul 20 04:46:21 2001 +0000 profiling works in serial Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLTimer.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Thread.H Src/C_BaseLib/Timer.H Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit d1dc9f1e2c2507c5d240583983ce8c4f8166feec Author: car Date: Fri Jul 20 01:45:48 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/PArray.H commit 025f52d8040a31eaafb1aad75084eb281c1d1021 Author: lijewski Date: Thu Jul 19 21:31:09 2001 +0000 Fixed a small bug we introduced. Src/C_BaseLib/IntVect.cpp commit 85dc53c3222cc684a2bdbe8ffc6ea4039b07ed42 Author: lijewski Date: Thu Jul 19 21:11:50 2001 +0000 *** empty log message *** Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/VisMF.cpp commit 7e6f6699614d04710573c4077973769c0ad104cb Author: lijewski Date: Thu Jul 19 20:02:43 2001 +0000 *** empty log message *** Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/UseCount.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit 5b16bd096eb25cb4812c4bef71c42854977667e8 Author: lijewski Date: Thu Jul 19 19:02:42 2001 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/MultiFab.cpp commit b46652ee1209765713186022e5aee6ff50711b77 Author: lijewski Date: Thu Jul 19 17:51:48 2001 +0000 Mods due to BoxLib:: namespace Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/FabArray.H commit 3131f06b1e991d0386d3fca31eea9d8e72065216 Author: car Date: Thu Jul 19 17:19:33 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxList.cpp commit 15e45842e56f40ab7c03b05d608ca8ed0f1f2023 Author: car Date: Thu Jul 19 17:19:32 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Thread.H commit 263f6398443b2fe2f80694b3befccb9b860187b1 Author: lijewski Date: Thu Jul 19 16:57:30 2001 +0000 Got rid of namespace. Src/C_BaseLib/Arena.H Src/C_BaseLib/Arena.cpp Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/SPACE.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/ccse-mpi.H commit 1c5d3b6a195234d4477880b368d43a1f81d82b04 Author: car Date: Thu Jul 19 16:51:22 2001 +0000 *** empty log message *** Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp commit 117d6849f5e917583a2a483aa7a1016a6391bce3 Author: lijewski Date: Thu Jul 19 15:26:47 2001 +0000 We've now got an Arena.cpp. Src/C_BaseLib/Arena.H Src/C_BaseLib/Arena.cpp Src/C_BaseLib/Make.package commit 1bb6d252d4935ad16c6ebc1c1c737ac6ba67ff2e Author: lijewski Date: Wed Jul 18 23:07:06 2001 +0000 More work toward the one true BoxLib ... Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit ab3e5275f8626d22f558fc6176bea1b2f0eb0cf2 Author: car Date: Wed Jul 18 22:21:15 2001 +0000 Profiling stuff Src/C_BaseLib/BLMpi.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp commit bfb513574868b478185973e0528ff14e51b17e66 Author: car Date: Wed Jul 18 22:20:29 2001 +0000 Initial loads, don't work Src/C_BaseLib/BLMpi.cpp Src/C_BaseLib/BLMpi.w Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Thread.H commit 43315a02bd97e0f8875a129bbf39770c5188b071 Author: car Date: Wed Jul 18 20:41:04 2001 +0000 Max->std::max Src/C_BaseLib/MultiFab.cpp commit dbf9f2dcf11e3598c1548f3c64db9128beedbc30 Author: car Date: Wed Jul 18 20:40:29 2001 +0000 Abs->std::abs Src/C_BaseLib/NormedFab.H commit 529033c6124606a1b20941e2b105faf3a1710e8d Author: lijewski Date: Wed Jul 18 19:37:19 2001 +0000 A few more tweaks ... Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp commit 3a827d1ba3a45ae646fa65c1cc9bb0caea08044c Author: car Date: Wed Jul 18 17:33:04 2001 +0000 another Max Src/C_BaseLib/RunStats.cpp commit 0f2140dc731783bb1538cc72a62dc57ab5ecb25e Author: lijewski Date: Wed Jul 18 17:31:06 2001 +0000 2-D bug Src/C_BaseLib/FArrayBox.H commit b899136954c04b12fbf4f91b16807dc91c0f8988 Author: car Date: Wed Jul 18 16:46:09 2001 +0000 fix for KCC 4.0f Tools/C_mk/Make.defs commit 9a39f08ba20feb6ff5e2cef76c6143ff9eddf2d7 Author: car Date: Tue Jul 17 23:40:08 2001 +0000 Fortran process // comments Src/C_BaseLib/CONSTANTS.H commit 8745cb3484ca919486144e2742c081680a61a6ed Author: car Date: Tue Jul 17 23:14:38 2001 +0000 Fortran can't process // comments Src/C_BaseLib/REAL.H commit ddf319374930edff9cb1ac65339049c2709fa0d5 Author: car Date: Tue Jul 17 23:14:13 2001 +0000 inline changes Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit 494b32562c2cfcd035d6d5821324cfd5215ca5b1 Author: lijewski Date: Tue Jul 17 23:02:17 2001 +0000 numerous changes Src/C_BaseLib/Arena.H Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BLassert.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Make.package Src/C_BaseLib/Misc.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/SPACE.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/ccse-mpi.H commit f7104d8b032b8ab4f99f26a7ce6bcb05fc44628b Author: marc Date: Tue Jul 17 21:21:12 2001 +0000 Remove Wimplicit for little-f files, as they are generally written by 'someone else', and we don't want to rewrite everything... Tools/C_mk/Make.Linux commit 2d518f0351e88bd7129f1d09a9f9eeae61ecedf7 Author: lijewski Date: Tue Jul 17 16:58:05 2001 +0000 Added for GNU Src/C_BaseLib/std/limits commit 41f3ac2599bf462a839a39e5f54bc4a620549249 Author: lijewski Date: Tue Jul 17 16:47:35 2001 +0000 Getting rid of some stuff. Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Specialize.cpp Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tracer.cpp commit dbe000a5a3d3513f9f6659ccd727d46751130244 Author: car Date: Fri May 18 16:49:24 2001 +0000 ampersand is a better continuation character, RE: Fortran standard Tools/C_scripts/strip72 commit b8e376401f6b38daa495a5cea09d389ec8f60ba1 Author: car Date: Thu May 17 21:52:13 2001 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 196cf06d299b221868ec826cfa415bce08a002eb Author: car Date: Tue May 15 16:31:23 2001 +0000 changes in flags Tools/C_mk/Make.Linux commit aeadde2a9cac3431fb3c7efd397896151112c6b1 Author: lijewski Date: Mon May 14 17:48:12 2001 +0000 Removed tar_and_rm_files stuff. The compressor utility seems to work fine. Src/C_AMRLib/Amr.cpp commit 7d543992601b1cd57c1024cc9266ef7ff905bbea Author: wyc Date: Fri May 11 19:44:24 2001 +0000 added small change to handle PGI compiler Tools/C_mk/Make.Linux commit 501733762dc0b3e3510ccc0339cea7d13574292e Author: lijewski Date: Thu May 10 17:16:40 2001 +0000 No longer compile in Tracer.[H,cpp] Src/C_BaseLib/Make.package commit 542ce34e712bcd440513e68c49eceda4dd0e6303 Author: lijewski Date: Wed May 9 22:42:22 2001 +0000 Simplified report(). Src/C_BaseLib/RunStats.cpp commit b9db89229893876b5408f2018bc34eca944a5dd9 Author: lijewski Date: Wed May 9 22:41:45 2001 +0000 Removed more RunStats stuff. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit c35feab8a16c6b2a1bd805bf8a77c377e4cbf98f Author: lijewski Date: Wed May 9 22:30:59 2001 +0000 Simplified how RunStats is used in code. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp commit 313fbd308caadbbed752ffdb221cc75ade6a0ad9 Author: lijewski Date: Wed May 2 20:20:40 2001 +0000 New -L option for mpi on OSF1 Tools/C_mk/Make.mpi commit 8160d45db5a5859dd9a2c8e500e2fa46e25ad62d Author: car Date: Fri Apr 27 20:07:11 2001 +0000 Added support for Intel compiler Tools/C_mk/Make.Linux commit 41b7d20f27251ac5ad65f8bafe3533ef6ead031b Author: car Date: Wed Apr 25 22:54:09 2001 +0000 minor bugs Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp commit 73a9e0d1078e8197bb67b43660ed784f5e64f84d Author: car Date: Wed Apr 25 04:16:20 2001 +0000 isDouble should return bool Src/C_BaseLib/ParmParse.H commit bff785c93ece49ba4795ab27ff3dc2ab8ab84176 Author: car Date: Tue Apr 24 19:42:19 2001 +0000 quiet warnings Src/C_BaseLib/CArena.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.cpp commit c6b075ca39f4eea4807194adb11d92f40f69e9e3 Author: car Date: Mon Apr 23 20:08:20 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 9eac80e95fe459241bdac9d7e26bfb428e45064e Author: car Date: Mon Apr 23 19:33:30 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit c13320f5ff9f1b5ee8f144f88a76a2a57c669de9 Author: car Date: Fri Apr 20 14:25:30 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 91c4ea8d3f8068ac58659643767f8dba610e78d2 Author: lijewski Date: Thu Apr 19 22:24:19 2001 +0000 Removed some RunStats. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/FabSet.cpp commit 7d954501c735a4724e842566ab361897e93abb99 Author: car Date: Mon Apr 16 22:38:17 2001 +0000 *** empty log message *** Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/wrappergen.c commit af4166b6529eb71ce145eda2ce90506beeda326c Author: car Date: Mon Apr 16 22:20:49 2001 +0000 *** empty log message *** Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/args.c Tools/C_util/wrappergen/readproto.c Tools/C_util/wrappergen/wrappergen.c Tools/C_util/wrappergen/wrappergen.h commit 7f567212cf6d3fb2823f8d60b336b500eef61bcc Author: car Date: Mon Apr 16 21:32:55 2001 +0000 *** empty log message *** Tools/C_util/wrappergen/wrappergen.c commit e88d8d4da2f7a36001d875d725f2a2548e5b1a1d Author: car Date: Fri Apr 13 17:18:54 2001 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit b7456cc3a8fd9966eadc8a3c5e66ec4afe17cb9e Author: lijewski Date: Wed Apr 11 18:11:04 2001 +0000 Further simplification to copy(). Src/C_BaseLib/FabArray.H commit a4ba6c4c6970b689d76a74ff55354e91b5085cd7 Author: car Date: Fri Apr 6 20:27:52 2001 +0000 *** empty log message *** Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/PROTO Tools/C_util/wrappergen/README commit d7fcf120d314f5abf03cb214a745f4673001b696 Author: car Date: Fri Apr 6 20:17:03 2001 +0000 minor changes Tools/C_util/wrappergen/.cvsignore Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/PROTO commit 3a3d84e372f5544a91d683dd41219c2b3898d3e4 Author: car Date: Fri Apr 6 20:12:14 2001 +0000 Initial revision Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/PROTO Tools/C_util/wrappergen/README Tools/C_util/wrappergen/args.c Tools/C_util/wrappergen/args.h Tools/C_util/wrappergen/doc.c Tools/C_util/wrappergen/doc.h Tools/C_util/wrappergen/driver.c Tools/C_util/wrappergen/expandingList.h Tools/C_util/wrappergen/mpifn Tools/C_util/wrappergen/petsccfg.h Tools/C_util/wrappergen/prof.c Tools/C_util/wrappergen/prof_wrapper.c Tools/C_util/wrappergen/readproto.c Tools/C_util/wrappergen/sample.c Tools/C_util/wrappergen/sample.w Tools/C_util/wrappergen/system.c Tools/C_util/wrappergen/system.h Tools/C_util/wrappergen/tools.h Tools/C_util/wrappergen/wrappergen.c Tools/C_util/wrappergen/wrappergen.h Tools/C_util/wrappergen/write_proto.c commit 7191f0a5ea9e05f47293e9cb4722c8b9f12d5e08 Author: car Date: Fri Apr 6 20:04:52 2001 +0000 MPI off fix Src/C_BaseLib/VisMF.cpp commit c03b1479ce6402cf0f3a4be346ff39bd6ca92d0c Author: lijewski Date: Mon Apr 2 17:58:59 2001 +0000 Now use MPI_Waitsome() instead of MPI_Wait() ... Src/C_AMRLib/FluxRegister.cpp commit c74e9c3c57bf04136aa1dc116d2311bd16328dc7 Author: lijewski Date: Mon Apr 2 16:48:31 2001 +0000 Simplified and improved the MPI stuff ... Src/C_BaseLib/VisMF.cpp commit dea06748ad81966ce21ee62aff4709ad2a16e5c4 Author: lijewski Date: Fri Mar 30 23:25:31 2001 +0000 Now use MPI_Waitsome() instead of busy-waiting with MPI_Test(). Src/C_BaseLib/FabArray.H commit dbfa17a899f0d47fe8e36f96c33ac1fbc823666e Author: car Date: Wed Mar 28 21:22:20 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 674c5e649f8235ca860e58dc911ed08eb6ddfa35 Author: car Date: Wed Mar 28 21:08:51 2001 +0000 Removed FPU code, wasn't useful Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Tools/C_mk/Make.CYGWIN_NT Tools/C_mk/Make.Linux commit 6322e52d1d5da20ee6b04263089f7a4518bb229a Author: car Date: Wed Mar 28 20:25:53 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit fe718320981a1d0b6604e81f4006ad0b9c89b922 Author: car Date: Wed Mar 28 19:36:44 2001 +0000 Makefile tweaks Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 7e5d160b118e4b3806803635a293c930c0de5bd2 Author: lijewski Date: Fri Mar 23 21:10:21 2001 +0000 More asynchronicity in fab_copy. Now use MPI_Send() instead of MPI_Ssend() as well. Src/C_BaseLib/FabArray.H commit cf7f7f01269ea358e600e0b0bb059d6ebf7b7860 Author: lijewski Date: Fri Mar 23 18:23:20 2001 +0000 Some additional asynchronous computation in CollectData(). Definite improvement when running 2-D iamr on many CPUs. Src/C_BaseLib/FabArray.H commit 09301a90ca439075a3cd61eedca8297611785ae7 Author: lijewski Date: Thu Mar 22 22:58:40 2001 +0000 Adde SeqNum() for use by CollectData(). Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 019046932671708913fcb8e5d8c0452861638447 Author: car Date: Wed Mar 21 14:58:59 2001 +0000 makefile tweaks; CPP-->FORT_CPP Tools/C_mk/Make.AIX Tools/C_mk/Make.CRAY Tools/C_mk/Make.CYGWIN_NT Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.Linux Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E Tools/C_mk/Make.rules commit cc6d436c141bdd48b55e611a058a399ba954bec6 Author: car Date: Tue Mar 20 19:42:02 2001 +0000 maxorder flag Src/LinearSolvers/C_CellMG/LinOp.cpp commit e5a8716c56af13c262dfcf237b8ece12ba11bbd0 Author: car Date: Tue Mar 20 19:41:42 2001 +0000 verbose flags Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 2a740254626e6b1ebb10f0e7ec694ac155631725 Author: car Date: Tue Mar 20 19:40:43 2001 +0000 namespace correction Src/C_BaseLib/ParallelDescriptor.cpp commit e02d57b123630225f5f2eafa65fd16ab2cb1abfe Author: lijewski Date: Wed Mar 14 22:02:29 2001 +0000 Removed some virtual calls and other simplifications. Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit dddacbb297e64d041a41881e049a9f2e8af92414 Author: wyc Date: Thu Mar 1 21:17:34 2001 +0000 added preprocessor foobah to protect squirrelly namespace stuff Src/C_BaseLib/ParallelDescriptor.cpp commit 354753c2df0f51e59bf528ccc9c15140abcebe47 Author: lijewski Date: Wed Feb 28 18:07:31 2001 +0000 Removed FORT_FLUSH stuff ... Src/LinearSolvers/C_NodalMG/hgdebug.F commit 031a96bad2e9b25aa1c83af5d0ed64da69ab3fcb Author: lijewski Date: Tue Feb 27 18:49:14 2001 +0000 Rearranged some HG_DEBUG stuff. Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit b7fa8451ae1ba45a1e882abdf97904fd96ce698c Author: marc Date: Sat Feb 17 01:17:36 2001 +0000 A little more fixup for Athlon compile of stuff. Tools/C_scripts/dsp.mak commit 827042311f109d6cd90ccb83f7d5ecb082cbe149 Author: almgren Date: Fri Feb 16 22:59:51 2001 +0000 Don't need this declaration. Src/C_BaseLib/COORDSYS_2D.F commit 73e0ff6fe7939a9063aec7bef90a708a74a3106f Author: lijewski Date: Wed Feb 14 19:05:44 2001 +0000 Deprecated BL_USE_ARLIM junk Src/C_BaseLib/ArrayLim.H commit 60bd10ee5700606ddd06f6cb54877d0b168242c1 Author: lijewski Date: Wed Feb 14 17:57:57 2001 +0000 Deprecated BL_USE_ARLIM ... Src/C_BaseLib/ArrayLim.H commit 0d2faeaa0d3ff54377bf467fcbfb4463de819f38 Author: lijewski Date: Thu Feb 1 23:39:35 2001 +0000 Removed AlternateApplyBC junk. Src/LinearSolvers/C_CellMG/LinOp.cpp commit 65bf0193a85def70207df7aeb1b2706a446a732f Author: lijewski Date: Thu Feb 1 23:17:57 2001 +0000 BiCG is now default CG solver. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 8b012e3614bcc8e08e0b7978fdbeaa502bfe0cbf Author: vince Date: Thu Feb 1 21:28:27 2001 +0000 Added support for cygwin under nt. Tools/C_mk/Make.CYGWIN_NT commit b1dc57a913d5cda718e50346507e859640a48c6c Author: vince Date: Thu Feb 1 00:49:02 2001 +0000 Added support for cygwin. Tools/C_mk/Make.defs commit 33173521f94bae0684c181eb4ad7f3c92c2b25a3 Author: lijewski Date: Fri Jan 26 18:08:14 2001 +0000 Forgot the non-MPI section Src/C_BaseLib/ParallelDescriptor.cpp commit 57ad6f0be0267a3d05d041b2a71091dad3ccdfb7 Author: lijewski Date: Thu Jan 25 23:53:23 2001 +0000 Removed a BL_ASSERT() ... Src/C_BoundaryLib/FabSet.cpp commit 00592b4f5c4f4f6eb50194cf9e6c31c3dc979129 Author: lijewski Date: Thu Jan 25 23:52:36 2001 +0000 Added NProcsCFD() to ParallelDescriptor. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit ea2b90f65e1f18fc34cbce9bb7300a881ea740a5 Author: lijewski Date: Wed Jan 24 22:50:47 2001 +0000 Now compiles. Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/tCArena.cpp commit caaf0e2e2d4d34246cf62fc6314416c91ab3a2b0 Author: marc Date: Fri Jan 19 22:57:48 2001 +0000 Incorporate larger stencil in tang interp at c-f Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/InterpBndryData.cpp commit b12571515b3ab4cd345f7d4cabd655257660084b Merge: 7a69181e3 24e3d0b53 Author: Matthew Emmett Date: Thu Jan 4 06:52:45 2001 -0800 Merge branch 'master' of gamera.lbl.gov:/home/CCSE/gitroot/BoxLib commit 7a69181e354761fd68906024d6139fda1b626571 Author: Matthew Emmett Date: Thu Jan 4 06:51:17 2001 -0800 PyBoxLib: Fix int size bug. Src/Python/F90/fboxlib/boxarray.py commit 30bff5876cc34e213e1302a304e9f2193e127f9a Author: Matthew Emmett Date: Fri Nov 14 03:54:34 2014 +0300 PyBoxLib: Flesh out a few more things. Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/fboxlib/multifab.py Src/Python/F90/src/fboxlib_c.c commit b78150934753d56b662d28b879aae35aa67dc4e4 Author: marc Date: Thu Jan 4 00:49:52 2001 +0000 Fix up script a little more... Tools/C_scripts/dsp.mak commit 711bef5d80f53d096ce90efcf7b24372171427d6 Author: car Date: Mon Dec 11 18:45:53 2000 +0000 main.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit ed60313c3db7ae82747a2e5e71be2b19ce909a18 Author: marc Date: Thu Dec 7 17:39:05 2000 +0000 Small mod to script for opt Tools/C_scripts/dsp.mak commit 4ee38a2aebf2347489ed235068bda3c238106137 Author: marc Date: Wed Dec 6 23:44:28 2000 +0000 Set maxmem stuff to be unlimited Tools/C_mk/Make.AIX commit dc2b57a8614778113a32991329b0a2445bb36a5e Author: almgren Date: Wed Dec 6 23:13:58 2000 +0000 Modified AddFPB to allow the Geometry::FillPeriodicBoundary call to handle edge-centered as well as cell- and node-centered data. Src/C_BaseLib/Geometry.cpp commit 84bbec8bf1eecf948d64895c084d5111445f2426 Author: marc Date: Tue Dec 5 01:05:29 2000 +0000 Fix up to build on Athlon with W2K + MSVC 6 Tools/C_scripts/dsp.mak commit 3ee17ff6c345e4a5bdc5aa556a5b5ce3952eb353 Author: marc Date: Fri Dec 1 23:35:19 2000 +0000 Move stop tests to avoid relax/print if incoming problem already solved. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit ba7d284f4c46e29a876a39e6de65f21ede3d8d51 Author: lijewski Date: Fri Nov 17 18:01:09 2000 +0000 Consolidated some duplicated code. Src/C_AMRLib/StateData.cpp commit b9ec7dfb8d3f1f02a0c8cad489ced54859d28320 Author: lijewski Date: Fri Nov 17 18:00:55 2000 +0000 Little simplification ... Src/C_AMRLib/Interpolater.cpp commit cbf36fd7621c4ad9d8c3ca3e5359bcd7d6799f53 Author: car Date: Wed Nov 15 20:12:02 2000 +0000 D_PICK expands to 1st, 2nd, or 3rd argument dependinging on BL_SPACEDIM; Happy Compiling Src/C_BaseLib/SPACE.H commit 3bafa86d56fe5595708f65c1affa29455934db8f Author: car Date: Sun Nov 12 17:26:12 2000 +0000 added a NumPts to BoxArray Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 8ae3ea420ec6979b1194c171f614591d23dfb7a9 Author: car Date: Wed Nov 8 22:01:50 2000 +0000 book != bool Src/C_BaseLib/BaseFab.H commit 7473a058fb82b34bac68b550f0439b267d15000b Author: lijewski Date: Wed Nov 8 21:48:21 2000 +0000 Added bool isAllocated () ... Src/C_BaseLib/BaseFab.H commit 4b68a52a723d59cf91e54d818e4e8151650b3ca7 Author: lijewski Date: Thu Nov 2 23:07:27 2000 +0000 A tad simplification ... Src/LinearSolvers/C_TensorMG/DivVis.cpp commit f56f3aadea4b9ae9c5bf131af4cc3d03bdc5e759 Author: lijewski Date: Wed Nov 1 18:29:37 2000 +0000 A little simplification ... Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/RealBox.cpp commit c399cc572fe52df454d6731de8a375297805cfc1 Author: lijewski Date: Wed Nov 1 18:06:14 2000 +0000 A little simplification ... Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp commit 4ad8bad8e3951ccd140511e1a2cf97ca9849d0cd Author: lijewski Date: Tue Oct 31 21:11:21 2000 +0000 Minimized memory overhead in MF -> FAB copy(). Src/C_BaseLib/FabArray.H commit bf024155c2114ec5938913b5a00e115d8c54f756 Author: vince Date: Fri Oct 27 00:50:18 2000 +0000 Added setbuf ifdefs. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.cpp commit 23e08015c22f1b30878c0410da72634a20ed0dbb Author: lijewski Date: Thu Oct 19 18:04:17 2000 +0000 Removed "nproc" stuff from DistributionMapping interface. Added specialized DistributionMapping constructor. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit cb140d92bd123e84e5a641f1317bc665c770f813 Author: lijewski Date: Tue Oct 3 20:26:49 2000 +0000 Small change for BL_AIX Src/C_BaseLib/Utility.cpp commit fd1d53df7b936948085152c99f83f57291d6e7b7 Author: lijewski Date: Tue Oct 3 18:17:27 2000 +0000 Added an explicit type Src/LinearSolvers/C_CellMG/LP_2D.F commit 07c7708e31ba6104946e9bc83eea82c1fe75cbcc Author: lijewski Date: Mon Oct 2 21:08:52 2000 +0000 Removed copyright macro. Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffPlot.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp commit 3592610112e3a0b14e24a1d89402695ed30f5756 Author: lijewski Date: Mon Oct 2 20:48:40 2000 +0000 Removed copyright macro. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DatasetClient.H Src/C_AMRLib/DatasetClient.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Arena.H Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BLassert.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Misc.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/SPACE.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tracer.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/ccse-mpi.H Src/C_BaseLib/test/t8BIT.cpp Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tDir.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/Mask.H Src/C_BoundaryLib/Mask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Tests/C_BaseLib/t8BIT.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tDir.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tVisMF.cpp commit 48d075f85212df62d1f7c1fc3908119f09fc7b8a Author: car Date: Mon Oct 2 18:13:08 2000 +0000 Lab Sanctions Source License Src/C_AMRLib/OpenSource.txt Src/C_BaseLib/OpenSource.txt Src/C_BoundaryLib/OpenSource.txt Src/LinearSolvers/C_CellMG/OpenSource.txt Src/LinearSolvers/C_NodalMG/OpenSource.txt Src/LinearSolvers/C_TensorMG/OpenSource.txt commit 6f8d126016270098bccfa68e039069491163eab6 Author: car Date: Tue Sep 26 18:19:25 2000 +0000 helper macro for FORTRAN calls Src/C_BaseLib/ArrayLim.H commit cae0639e68fcdc971217177bca90628851e2911b Author: car Date: Tue Sep 26 18:18:57 2000 +0000 fix for min max Src/C_BaseLib/MultiFab.cpp commit 118a1ed36f71dc39dcbc167f2fe575f14a7a9907 Author: almgren Date: Thu Sep 14 19:44:06 2000 +0000 Changes to allow for multiple datalog files if more than one file name is specified in the inputs file. It's up to the user to not try to access more files than names are given. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 955d586719336163f41861ba8086d828f6af319f Author: lijewski Date: Thu Sep 14 15:25:26 2000 +0000 Cut down on sleep time. Tools/C_scripts/compressor commit 5c199a6a9c35feef5b1048ceb1809f22076f6e1d Author: lijewski Date: Wed Sep 13 20:09:12 2000 +0000 BiCG is now the default ... Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit ff26cfa8f53b2bfdd11a0ae26985cb50fbe4560a Author: almgren Date: Mon Sep 11 22:03:57 2000 +0000 Fix to propp's re-write of build_sigma...we need to copy the zeros in ghost cells when for_sync_reg != 0. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 588f412f902f3dd3ac70620c69f0bd40dc3e6ee9 Author: car Date: Tue Sep 5 17:40:54 2000 +0000 filter profiling files Src/LinearSolvers/C_CellMG/Test/.cvsignore Tests/LinearSolvers/C_CellMG/.cvsignore commit d4ac45668618b23c755b955b056504ed19e53444 Author: car Date: Wed Aug 30 19:19:13 2000 +0000 New convergence criteria: relative tolerances may need to be reduced by a factor of 5 or 10. Absolute tolerances may not be needed at all. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit b63dbf4bd185c3a2957b6ea0fbadcaba3cb8d09b Author: car Date: Mon Aug 28 15:54:01 2000 +0000 Use new convergence criteria by default; must still select BiCGStab in ParmParse Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit c10ea96b199cf0f8b29945a06baab7e2575e01c6 Author: car Date: Sat Aug 26 19:41:00 2000 +0000 3D Norm Src/LinearSolvers/C_CellMG/ABec_3D.F commit 515ac65331fd8d6ce6fc898936ef79ff6792748b Author: car Date: Fri Aug 25 19:23:28 2000 +0000 fix for bicg with initial zero residual Src/LinearSolvers/C_CellMG/CGSolver.cpp commit cad579b09909ed449e464d949643fc530e6477df Author: car Date: Fri Aug 25 17:50:25 2000 +0000 annotation tweak Src/LinearSolvers/C_CellMG/CGSolver.cpp commit eec21b74546a041493a2cd89044c808291696be9 Author: car Date: Thu Aug 24 22:45:46 2000 +0000 profiling fix Src/LinearSolvers/C_CellMG/LinOp.cpp commit 2c766543e9ae4dac9d8e3f4acb3eb22869c232f5 Author: car Date: Thu Aug 24 22:39:02 2000 +0000 solver selection, timing Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 5916df9f1c67cd544cf2e9d8e008f4ad31ec8f35 Author: car Date: Thu Aug 24 20:28:28 2000 +0000 fix initialize, add norm Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit d0c9b7eb949c6f9bfe9dde87155945ed0df7c7f2 Author: car Date: Thu Aug 24 16:02:46 2000 +0000 Added BiCGStab Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 0e52c05fb01a457116c45cb72b30751ec9e8e579 Author: lijewski Date: Wed Aug 23 20:16:29 2000 +0000 Fixed some PlotVar stuff ... Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit c120731e880d3062eedf8be1ab5fa6c72da05437 Author: marc Date: Thu Aug 17 17:31:00 2000 +0000 Enable array of blocking factors. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 5b4150a2454052ed39b52aefd85c64e7ad9b1059 Author: car Date: Tue Aug 15 19:37:31 2000 +0000 Make.mpi Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit c45957611a526efc02469edfcb6b44cde3dfe92d Author: car Date: Tue Aug 15 19:24:29 2000 +0000 a new way of making MultiFabs: pass in a Distribution Mapping; changes to Distribution mapping to aid access to knapsack Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit 04e613e552499c6acad6221efc9e2b1a095b057f Author: lijewski Date: Wed Aug 9 20:23:04 2000 +0000 Removed an unnecessary parallel reduction. Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit dd207f25c2473fe55a7f41abe704b232b2d2b145 Author: lijewski Date: Wed Aug 9 15:38:50 2000 +0000 Removed unnecessary paralllel reduction. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit e10b3969f9de6d1352e1d4cf292dfdbdaeb2a68a Author: car Date: Fri Aug 4 18:06:22 2000 +0000 another Profile Src/C_BaseLib/FabArray.H commit db2b930e3f7db971d18db297be097cd3e1d09aa7 Author: lijewski Date: Fri Aug 4 18:00:58 2000 +0000 Removed need for MPI_Gather() in copy(). Src/C_BaseLib/FabArray.H commit 1708d99978ee8a0c7b444c10f8cc6583cadfb755 Author: car Date: Thu Aug 3 18:27:51 2000 +0000 c++ comments in fortran Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F commit a5c907246bc286d520969b38cce832ca731ee322 Author: almgren Date: Wed Aug 2 21:03:50 2000 +0000 Modified LinOp::applyBC to take src_comp and num_comp arguments. Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit 20f1b7c9c1c2db6dfc522ddcf3e02da5124af016 Author: car Date: Wed Aug 2 16:11:53 2000 +0000 BoxLib3 Profiling code and threading Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit ad87a29e2f431e0cd282fbe18657eb8b556bbf50 Author: car Date: Wed Aug 2 16:09:45 2000 +0000 MPICH 1.2.0 Support Tools/C_mk/Make.mpi commit a6fd7a57338fec0ac44abe27479f9b17430ccbce Author: car Date: Wed Aug 2 16:08:35 2000 +0000 Thread Safety Support Tools/C_mk/Make.defs commit 6363b8688b4f538e4523ae0eac1f95c5ed4890da Author: car Date: Wed Aug 2 16:08:10 2000 +0000 profiling support Tools/C_mk/Make.Linux commit 1088a1cc4ce321135d342051044d6bc4a0b70a68 Author: car Date: Wed Aug 2 16:06:32 2000 +0000 BoxLib3 Profiling code; commented out Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 60a0f20762b431ba53fe10c8c537d7f70caba90e Author: car Date: Wed Aug 2 16:00:53 2000 +0000 Added Profiling Code; ParallelDescriptor::StartParallel fixed to allow multiple calls with no error Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit 58f54c0cf16bd6cef44142e26298a0593cb04fb6 Author: lijewski Date: Tue Jul 25 19:10:38 2000 +0000 which_time() now asserts that time is in (oldtime,newtime) interval Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 8c26eead709d86ca4e964ee6dc05b5fff55c8de2 Author: almgren Date: Fri Jul 21 22:45:04 2000 +0000 Added code to take a velocity field and return the stream function. This is done by computing the vorticity and solving Laplacian(phi ) = vort. Called from Projection::getStreamFunction in iamrlib. The computation of vorticity and inversion of the Laplacian are full multilevel operations. Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit ab1cea3ad27b3df75cf30c545f6a6947f5502d84 Author: lijewski Date: Fri Jul 21 20:45:21 2000 +0000 Added AmrHalfTime to support rho_half in NS. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit a1e056bd4c58bb9902c9a21919cb01663847f68d Author: lijewski Date: Wed Jul 19 19:53:36 2000 +0000 Removed some unused foo ... Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F commit 2fb89c322ba1e99f81de6fc20e0457c574cace38 Author: sstanley Date: Mon Jul 17 16:58:03 2000 +0000 Mudified the logic in MultiGrid::coarsestSmooth() so that when the CG solver fails (presumably due to the stability criterion), that the standard bottom end smoother is called instead. This has the potential to make the MG solves more robust. Also, it will allow the CG solver to be used on the bottom end of the diffusion solve while allowing the regular smoother to help the solution of the mac projection. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 9610bf28c8bb1e6a7f11be40d10f3f4c1dcd7014 Author: sstanley Date: Mon Jul 17 16:26:19 2000 +0000 Minor changes to the mac projection input and grid files. Src/LinearSolvers/C_CellMG/Test/grids/gr.3_mac_tst Src/LinearSolvers/C_CellMG/Test/grids/in.3_mac_tst Tests/LinearSolvers/C_CellMG/grids/gr.3_mac_tst Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst commit 6c2f61fee06e140e3b1040d5487262c26be06e34 Author: sstanley Date: Sat Jul 15 00:13:42 2000 +0000 Added the input and grid files for the mac projection test code. Src/LinearSolvers/C_CellMG/Test/grids/gr.3_mac_tst Src/LinearSolvers/C_CellMG/Test/grids/in.3_mac_tst Tests/LinearSolvers/C_CellMG/grids/gr.3_mac_tst Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst commit f23315df232116a81295cb14fded21e836401d92 Author: sstanley Date: Sat Jul 15 00:12:23 2000 +0000 Added a test routine to read the information for a specific mac projection and set up and solve this problem. Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/macprojTest.cpp commit 13ada30311fda85cdbb10b8c5944a8dfd752c9c5 Author: sstanley Date: Sat Jul 15 00:11:01 2000 +0000 Added writeOn and readFrom routines to dump and read boundary data objects. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 80094a8248857a9c5a3aa746a2d16248f3532eec Author: almgren Date: Fri Jul 14 23:37:06 2000 +0000 Added the code for line solvers in each direction in FORT_GSRB. The default is still set to do Gauss-Seidel red-black, but the code is now in place to do line solves if wanted. Src/LinearSolvers/C_CellMG/ABec_3D.F commit 5bd49aabf35284ed264202429b8bc0c56b9ce6d8 Author: almgren Date: Thu Jul 13 23:26:55 2000 +0000 Handle the case differently where t < t1-teps...require that the flag extrap be set in order to allow this, then extrap backwards, instead of just setting to the "old" value. Src/C_BaseLib/MultiFab.cpp commit 87c58e23156e4cd66f8a985bdacc882721ae900d Author: sstanley Date: Thu Jul 13 23:10:03 2000 +0000 Added this new routine which checks all interior ghostcells in a multifab to insure that they are consistent with the cells in the valid region. This utility only works with disjoint multifabs. Tools/C_util/ViewMF/checkMFghostcells.cpp commit 3daf32fdac35dcf696601bb18f6cb3361ef1641a Author: sstanley Date: Tue Jul 11 21:03:55 2000 +0000 Modified the interface to SlabStats::checkPoint so that the AmrLevels are passed in. This allows the problem domain and the grid spacing to be output in the header files for the SlabStats. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp commit 4113ee63cd44dbaaf9abbcd1c415fbfde23e05af Author: lijewski Date: Tue Jul 11 20:47:48 2000 +0000 Move which_time() from HeatTransfer to here. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 76c4eff5b15e6bb08193d1f3f91043ca46546025 Author: lijewski Date: Thu Jul 6 17:03:57 2000 +0000 Protected a couple cout's with IOProcessor() checks. Src/C_BaseLib/ParmParse.cpp commit d2520949f6f98c9f1a1fe0804eb7cc2b4006de0b Author: lijewski Date: Mon Jul 3 23:40:02 2000 +0000 Tad more simplification ... Tools/C_scripts/compressor commit af08316afdea887242d3b10fbac64262c39a893e Author: lijewski Date: Mon Jul 3 22:02:50 2000 +0000 Removed couple declarations that were never defined. Src/C_AMRLib/FluxRegister.H commit 74828a19968debb80987a6dfd1cef8b592f0218d Author: sstanley Date: Thu Jun 29 21:14:42 2000 +0000 Shifted the maxdata option over to LDFLAGS since it is a load time option. Tools/C_mk/Make.AIX commit 211e88440549142a097ea90ff9abc98e11cde2f5 Author: lijewski Date: Tue Jun 27 20:54:50 2000 +0000 Removed "inline" from isBoolean() definition. Src/C_BaseLib/ParmParse.cpp commit 25b4eacb16a20304150f9e2d54dffef5ec091600 Author: lijewski Date: Fri Jun 23 16:48:00 2000 +0000 Uped maxmem for optimization a tad more. Tools/C_mk/Make.AIX commit d3ad8f5cf70e5965489587953cdd8380aa88cced Author: car Date: Thu Jun 22 22:52:28 2000 +0000 decrease size of temporarys in ABEC's GSRB Src/LinearSolvers/C_CellMG/ABec_2D.F commit 24a3ad81817c2a47f59046396a491b00fa580901 Author: car Date: Thu Jun 22 20:56:22 2000 +0000 ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit aa5492fea12e45af8cdafd576c283887562889a9 Author: car Date: Thu Jun 22 20:00:15 2000 +0000 Threading... Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 3058772b0ed78d0b5e87d6694d93d0e7b9f82682 Author: car Date: Thu Jun 22 18:34:50 2000 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LinOp.cpp commit 8a632bef35c50d59556d8d0ad13adbefb38d0599 Author: car Date: Thu Jun 22 18:33:45 2000 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit 01dcf85674a46af6c51bb3059a195e9cde4a7d8d Author: lijewski Date: Thu Jun 22 16:07:32 2000 +0000 ::intersect() of two BoxLists wasn't right. Src/C_BaseLib/BoxList.cpp commit 529e3ef777d9bc41ba9d83377a6bda07b76a6e26 Author: sstanley Date: Wed Jun 21 22:07:34 2000 +0000 Added a global include file defining the fortran flush() function. Changed a few routines to use this global function, FORT_FLUSH. This was done because the flush fucntion call is different on different machines. Src/C_AMRLib/FLUSH_F.H Src/LinearSolvers/C_NodalMG/hgdebug.F commit f37b81d218b4245abdc983cfb1f148a1412dd4a5 Author: sstanley Date: Wed Jun 21 18:27:45 2000 +0000 Added the options to use up to 1Gb of memory per node. Tools/C_mk/Make.AIX commit 19a58e2a196e7b1cc31db34adb53048b882fe04f Author: sstanley Date: Tue Jun 20 23:43:22 2000 +0000 Changed the compile options for lower and upper case fortran files. Lower case .f files compile with 80 columns and uppercase compiel with 72 columns. Tools/C_mk/Make.T3E commit 2421967db59848b52f1b942e6743142c1ce8fd09 Author: marc Date: Tue Jun 20 23:28:59 2000 +0000 Allow separate options for f and F files. Tools/C_mk/Make.AIX Tools/C_mk/Make.CRAY Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.Linux Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 7203478afe2f3543d7e2f23d172a559c79ccd955 Author: lijewski Date: Tue Jun 20 21:44:11 2000 +0000 A little more finagling with sleeps. Tools/C_scripts/compressor commit 3bcb28b594e480c0154b47bd404bb76e463e912d Author: lijewski Date: Tue Jun 20 20:45:51 2000 +0000 Changed sleep interval. Tools/C_scripts/compressor commit 8333abeb675ad1ac1357733dabcc3f9e8e3e77cf Author: lijewski Date: Fri Jun 16 17:39:49 2000 +0000 Fixed bug in grid_places(). Probably needs more testing, but ... Src/C_AMRLib/Amr.cpp commit fcd694569afd9e4382f050c63ee395b1c65a84bd Author: lijewski Date: Thu Jun 15 17:29:01 2000 +0000 Got rid of CXXFLAGS; moved stuff to CXXOPTS & CXXDBG. Tools/C_mk/Make.AIX commit 31206d21724bdc6c10ba9f4753311556a581ff16 Author: lijewski Date: Thu Jun 15 16:57:41 2000 +0000 Now print grid info to cout as well as gridlogout. Src/C_AMRLib/Amr.cpp commit 9c6526776d2334f8525891dd3d3e68e392e2184e Author: lijewski Date: Tue Jun 13 16:52:28 2000 +0000 Don't tar up last plotfile. Wait till next one is written. Tools/C_scripts/compressor commit b8ba728d5a2d426f6148a7da00928dbc4fcca2f9 Author: almgren Date: Mon Jun 12 23:43:03 2000 +0000 Now pass iteration into post_timestep so it will eventually get passed into the sync project in IAMR. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit a2bdaf19aafe3f159b55ed258d39585b48f15688 Author: sstanley Date: Fri Jun 9 21:25:51 2000 +0000 Changed errorEstimate to work properly on all levels, not just level 0. Midfied the logic slightly when dumping residuals in the bottom smoother. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit b6ee7e90669d8244eedf3aa80e97cdb03adf195e Author: lijewski Date: Fri Jun 9 21:10:31 2000 +0000 Use CXXFLAGS instead of XTRADEFS in one case. Tools/C_mk/Make.AIX commit 74b7efbe2ccdc885d55584108fd88d743805f22f Author: sstanley Date: Thu Jun 8 20:26:33 2000 +0000 Added a few constants that I needed. Src/C_BaseLib/CONSTANTS.H commit 6a8bc584fda84cf70e34b172d16a0ff73ff37ac2 Author: lijewski Date: Thu Jun 8 17:38:02 2000 +0000 Increased maxmem a tad more. Tools/C_mk/Make.AIX commit 3f21ad65aa9873bd77994c8c3363a891c48e50e8 Author: marc Date: Wed Jun 7 23:18:11 2000 +0000 Reverse order of define and namespace close Src/C_BaseLib/Specialize.cpp commit e7fc2dd919d8dac341f2d34e31ea0444f621b6be Author: lijewski Date: Wed Jun 7 20:59:16 2000 +0000 Turn on coalescing memory manager. Bump memory used by C compiler for optimization. Tools/C_mk/Make.AIX commit a7384b4a3d3358379a34d84456996995ef158d52 Author: sstanley Date: Wed Jun 7 00:33:23 2000 +0000 Added writing of the residuals when using the simple smoother on the bottom end of the multigrid. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit e8d3b282ab4585fd4671c7da9f135462c5cdcd62 Author: lijewski Date: Mon Jun 5 22:37:37 2000 +0000 Removed no_overlap arg from FillPeriodicBoundary(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit f6026456d7e63defa8f09408f2cd1b7e34f48ef4 Author: car Date: Mon Jun 5 19:11:16 2000 +0000 namespace fix Src/C_BaseLib/ParallelDescriptor.cpp commit fdf923bc84fb1df967ba4dda655a806d177dc355 Author: car Date: Mon Jun 5 18:56:08 2000 +0000 another bc buster Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_3 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3 commit 58e6f0e68137486b29a65912b86bb303778cd203 Author: car Date: Mon Jun 5 18:39:31 2000 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit f316413e577735a6c49ffc09b1bb4727a49dd67c Author: marc Date: Fri Jun 2 22:58:53 2000 +0000 extern c chuck you moron Src/C_BaseLib/ParallelDescriptor.cpp commit 75d98742aa9a6df5f9ae49e52f06887735342117 Author: lijewski Date: Fri Jun 2 22:37:40 2000 +0000 Added new intersect() functions. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 35732d7921c118a83e1a21681c9e5a1ac3dbd043 Author: almgren Date: Fri Jun 2 17:59:53 2000 +0000 Chnage the time interpolation so it allows t >= t1-teps instead of just t > t1-teps. This matters in the case where t1=t2 so teps = 0. Src/C_BaseLib/MultiFab.cpp commit 6e81a72e84923d05f9c4ea2fa846ac3152eb35dd Author: lijewski Date: Fri Jun 2 17:09:16 2000 +0000 Cleaned up a bit. Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 62e6d4674853db8e66e7c617018c0bb9d5bef44b Author: car Date: Fri Jun 2 01:04:12 2000 +0000 Bad BL_PD_ABORT defn Src/C_BaseLib/ParallelDescriptor.cpp commit 0d117db551eac58f15d9115ab7c494a6e6a6a25a Author: car Date: Thu Jun 1 23:10:36 2000 +0000 Support for KCC 3.4, Thread, and Strict compilation Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 37513f0f9c1e1408a196ef0f9869d210028ecc66 Author: car Date: Thu Jun 1 23:09:28 2000 +0000 use ksh in Make Tools/C_mk/Make.OSF1 commit 99afd6379661a166e071e17568573df7ccea61dc Author: car Date: Thu Jun 1 22:59:47 2000 +0000 g++ fixes Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/inputs commit 6405a8810dd04aa65f915dd828b02fc72b897e3f Author: car Date: Thu Jun 1 21:39:54 2000 +0000 using ParallelDescriptor::Communicator() Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit a615409c5c64a930458f6ad796acd8516cf71c12 Author: lijewski Date: Thu Jun 1 21:28:57 2000 +0000 Added extrap() member to StateDescriptor & integrated into code. Really only used in FillPatch(). Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit c0b66371ba7f1b9c3342d0e65fc0caffda1bf74c Author: car Date: Thu Jun 1 21:22:31 2000 +0000 using ParallelDescriptor::Communicator() Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/PltFileNormB.cpp commit 7316a9200cb77307d4beb76899ac048384a15e0a Author: car Date: Thu Jun 1 21:07:51 2000 +0000 Two Parallel Changes: 1) ParallelDescriptor::Communicator() should be used instead of MPI_COMM_WORLD. This will allow us to mix other libraries that use MPI without message passing tag collisions. 2) Added a few FORTRAN bindings to ParallelDescriptor calls: BL_PD_ABORT BL_PD_COMMUNICATOR BL_PD_NPROCS BL_PD_IOPROC BL_PD_MYPROC BL_PD_BARRIER Its probably not worthwhile to add any others. Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/ccse-mpi.H commit cf5b97ec92b0538ae19f8b8bee55320e8b39a581 Author: car Date: Thu Jun 1 20:59:38 2000 +0000 not needed here: --one_instantiation_per_object Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit 7a6a7b8dde7996820d87dc640c5a4b21f40ee873 Author: sstanley Date: Thu Jun 1 16:41:14 2000 +0000 Fixed a problem with how quoted strings were broken up. This caused file name problems on the SP machines. Tools/C_scripts/strip72 commit 0dc4369ec3ea34aec46b26228cf3426a5952446c Author: car Date: Thu Jun 1 15:39:16 2000 +0000 boolean values are now parsed 'true', non-zero numerics ---> true 'false', zero numerics ---> false Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit e68fd92c5225f1eb6e940126f8625b8de0aa3153 Author: car Date: Wed May 31 20:35:25 2000 +0000 const-ness issue Src/C_BaseLib/Geometry.H commit c04ae6ec75c77061ca35576225a79213ad369ea6 Author: car Date: Wed May 31 20:33:40 2000 +0000 Silence a warning Tools/C_util/WritePlotFile.cpp commit 88f9a8d5be2d6696f3c2e66ebbb5c24b33a43fc1 Author: car Date: Wed May 31 20:33:14 2000 +0000 KCC 4.0 support Src/C_BaseLib/Utility.H Src/C_BaseLib/VisMF.H commit 072fc09a3bdf7feb66bc1ea9f9a30df2107219c4 Author: lijewski Date: Wed May 31 17:44:24 2000 +0000 Removed FillCoarsePress() -- figured out how to reuse FillCoarsePatch(). Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 2b26a51ff9f179a487274bf597b84fa850522873 Author: almgren Date: Tue May 30 21:10:47 2000 +0000 Added SetNewTimeLevel and SetOldTimeLevel calls in StateData. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 8d9e6e139f138bc30ea270753f2e0389e6068189 Author: almgren Date: Tue May 30 20:24:54 2000 +0000 Added AmrLevel::FillCoarsePress routine which is willing and able to fill ghost cells as well as valid region of NODAL data only. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit ce819493c933fa34e7497ce63c2a4eeee2a73d8e Author: car Date: Thu May 25 15:49:25 2000 +0000 .cvsignore Src/LinearSolvers/C_CellMG/Test/.cvsignore Tests/LinearSolvers/C_CellMG/.cvsignore commit 5d996ce17a1c6c4d7d61d34a8cf1779debda2e6e Author: car Date: Thu May 25 15:40:03 2000 +0000 Removed unused variables Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Looping.H Src/C_BaseLib/VisMF.cpp commit 873edddc223cc35dcdb5dec7ecbd4338aa18f038 Author: car Date: Thu May 25 15:39:28 2000 +0000 RealDescriptor needs virtual destructor Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp commit 580e4b26bf4205bb17f1038e3e998c3d98d5e2de Author: lijewski Date: Wed May 24 17:19:53 2000 +0000 Added some more of scott's test cases. Src/LinearSolvers/C_NodalMG/files.3d commit 222d55e97901b9a35852b43c4f8cc6db9bcba010 Author: car Date: Mon May 22 23:19:24 2000 +0000 support for hypre Tools/C_util/Make.package Tools/C_util/WritePlotFile.cpp commit 680c76358c79078bc8529c673db8ace8afec6f52 Author: car Date: Mon May 22 23:18:51 2000 +0000 revamped to test hypre Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/main.cpp commit 42e27523608c7dfd98f25f908c6ad0d04327eb48 Author: lijewski Date: Mon May 22 20:14:25 2000 +0000 Added gt.sas. Src/LinearSolvers/C_NodalMG/files.3d commit d46e2c6910203a38e70a257495733b31f34b78c3 Author: lijewski Date: Mon May 22 20:13:45 2000 +0000 Tests some doubly-periodic stuff. Src/LinearSolvers/C_NodalMG/tests/gt.sas Tests/LinearSolvers/C_NodalMG/test_grids/gt.sas commit 213a8f547360e8c8825d604d50dadd97621b11ad Author: sstanley Date: Mon May 22 19:54:00 2000 +0000 Minor changes to the slabstat files. Added $Id: $ fields to the fortran and changed the #define variable to force only single inclusion of the header file. Src/C_AMRLib/SLABSTAT_2D.F Src/C_AMRLib/SLABSTAT_3D.F Src/C_AMRLib/SLABSTAT_F.H commit 8e19ce7c7eae53a8063da94c42b12f410b0d70f5 Author: lijewski Date: Thu May 18 20:13:42 2000 +0000 More periodic fixes. Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 074e91290acfd191c46b4cd1046293f65df62f1f Author: lijewski Date: Thu May 18 20:02:16 2000 +0000 Added some comments on how to set boundary conditions. Src/LinearSolvers/C_NodalMG/inputs commit 7c7d1a2f58cf0ee9be86e7440e606d02d1471968 Author: lijewski Date: Thu May 18 19:55:44 2000 +0000 Made the stencil default to cross. Src/LinearSolvers/C_NodalMG/inputs commit 9c06593c48723267cbd146a9d0453022c83c0d45 Author: car Date: Mon May 15 19:45:17 2000 +0000 trying to fix fill_border Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 13af3eda2241cfa7efb423cd3eec99b42ffb27af Author: lijewski Date: Mon May 15 16:47:50 2000 +0000 Fixed a bug in task_bdy_fill::ready(). Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 36d26d3c746f163b1fa719a4517de79abd7e123e Author: lijewski Date: Fri May 12 18:08:45 2000 +0000 Added task_local_base(). Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 0062a35de7ef0c645679d1818d95256fa2b247de Author: lijewski Date: Fri May 12 16:36:30 2000 +0000 Strenghens the depens_on_q() test in task_copy_local(). Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 840a9f39e9bc42519f955e9fc3c33b3448752b5b Author: car Date: Thu May 11 16:38:18 2000 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/proj.cpp commit 2ceefb21deda4f1757876dfc31517005c1ba5dda Author: sstanley Date: Mon May 8 22:17:52 2000 +0000 Initial commit of the utility intersectGrids. This one reads a fixed_grids file and checks to see which grids intersect a specified box. All of the grids intersecting the box are written out in a fixed_grids format. Care should be taken when using this for more than 2-level cases since it doesn't insure proper nesting. Tools/C_util/dbgTools/intersectGrids.cpp commit fac3126bf2329258cd25da613c78623282948f4a Author: propp Date: Thu May 4 23:43:49 2000 +0000 reordered build_sigma a little bit Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit e84220d55baa78d51aa7c469fc0fa9d2a0175234 Author: car Date: Thu May 4 20:16:44 2000 +0000 integer promotion? Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F commit 38c68b9a583280ee78888e3824120ae94067c2a2 Author: sstanley Date: Wed May 3 22:32:45 2000 +0000 Corrected a mistake I committed yesterday where zero was used instead of 0.0d0. Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F commit 774d4a0ce2eb2a62589c75c6ae3228998697e692 Author: almgren Date: Wed May 3 21:08:47 2000 +0000 Fill_borders call should have been boundary.terrain_sigma() call to start with, before fill_borders became fill_sync_reg_borders. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 37646207c6caca32fa474a0ac3aaf09907a1403c Author: almgren Date: Wed May 3 18:27:16 2000 +0000 Changes in order to handle periodic boundaries correctly when defining the coarse contribuation to the sync registers, i.e. Sync_resid_crse. We used to fill ghost cells at periodic boundaries; now we don't fill them at all (i.e. we use fill_sync_reg_borders calls instead of fill_borders calls), and the periodic stuff is taken care of in SyncRegister::CrseInit instead. Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 52e25159ad000d24ff2e222636a86eb43fa5c453 Author: propp Date: Wed May 3 17:12:11 2000 +0000 changed default for NAMESPACE to be FALSE Src/C_BaseLib/GNUmakefile commit d5119e7fb4f1af0297f838214408db2c6a11c926 Author: propp Date: Wed May 3 03:36:40 2000 +0000 fixed bug so libraries would be built correctly Src/C_AMRLib/Make.package commit 7305ac0d6b64408ef25753088c8e4f1baf61edcc Author: sstanley Date: Tue May 2 22:13:59 2000 +0000 Further fix to how the values in the cen array are calculated and dealt with. Added logic in thew hgcen_full and hgcen_terrain to set cen=0 when the sigmas sum to zero. Changed logic in hgres_terrain and hgres_full to deal properly with the zero values in the cen array. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F commit 12cb88100c871e9ba95a5b8165e66af273ec499b Author: car Date: Tue May 2 17:17:41 2000 +0000 add fp exceptions for Linux Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Tools/C_mk/Make.Linux commit bf8b824a247e42668561fe3d763be71673cfe49f Author: car Date: Tue May 2 15:55:33 2000 +0000 modified hgcen to give cen=0 when sigma's are zero Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 72b673e5fc29dfc61d8c45b1f82a1c80f6c01700 Author: sstanley Date: Mon May 1 22:06:38 2000 +0000 Fixed a problem in build_sigma when for_fill_sync_reg==1. Turns out you don;t need to calculate cen for this case since it never gets used. Also, it can not be calculated since the sigma_node is set up so it is zero on all covered cells and we divide by sigma_node when calculating cen. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 63ee35b277ed03fa5345efca94e226b6af47eca5 Author: car Date: Mon May 1 17:53:24 2000 +0000 Remove Assert.H from Make.package Src/C_BaseLib/Make.package commit 68f3ca4db893f9d195db7cc33e9ffd2d0b9f0088 Author: car Date: Tue Apr 25 18:03:39 2000 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 223f2b457a74ff12c638530bc6a1f6c44ae09975 Author: car Date: Tue Apr 25 16:29:56 2000 +0000 more namespace fluff Src/C_BaseLib/FabArray.H commit 7eb68527ecf32de33166b3420e4ed8f9294f2b8f Author: car Date: Mon Apr 24 18:00:52 2000 +0000 missed one Src/C_BaseLib/SPACE.H commit 6c9471bc26bcd83858fba4281366e7e2c9ee246e Author: car Date: Mon Apr 24 17:52:32 2000 +0000 Minimal namespace support. The changes here should have no impact on user code. Two c-preprocesor symbols are used to control the changes: 1) BL_NAMESPACE: if defined, BoxLib code is wrapped within a namespace whose name is given by the BL_NAMESPACE macro. 2) BL_NO_USING_DIRECTIVE: if defined, no 'using namespace BL_NAMESPACE;' is implicitly given in for each module. The Makefile system was made namespace aware about a month ago. If you say 'NAMESPACE = TRUE' you will get the effect of saying: BL_NAMESPACE=BoxLib2. The default is 'NAMESPACE=FALSE' The intent is that two versions of BoxLib can be used within the same program. I don't expect that apart from a forced recompile that there will be any changes required to user code. Src/C_BaseLib/.cvsignore Src/C_BaseLib/Arena.H Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/Assert.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/GNUmakefile Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Misc.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Specialize.cpp Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tracer.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/ccse-mpi.H commit 26cc56728ca50ecfee528b8d2d1423867ac79711 Author: sstanley Date: Sat Apr 22 00:34:14 2000 +0000 Moved the storage of the statistics data from being in the checkpoint files to being in their own directory, 'slabstats'. The data for each level 0 timestep where it is saved is stored under subdirectories, 'slabstats/stats0000', etc. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp commit e388160e98462a9251e7e5a46db1fb54a21efa1c Author: sstanley Date: Sat Apr 22 00:16:26 2000 +0000 Modified the constructors for SlabStatList and SlabStatRec so that if the boxes are read form the file, then the level is read from the file as well. If the boxes are included in the constructor, then the level is included in the constructor. Makes sense since the boxes are defined on a specific level and are generally not valid except on this level. Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp commit 2dc1da1b77b2d392135afc9493ce1805f7eeef91 Author: sstanley Date: Fri Apr 21 22:31:04 2000 +0000 Corrected a couple of problems with the derive function which takes a multifab to be filled. There were a few things still in place which assumed you were working with the level multifabs. Src/C_AMRLib/AmrLevel.cpp commit 3e075be8fcfa4297d38715beeeb4f131ee254fb3 Author: sstanley Date: Fri Apr 21 22:29:39 2000 +0000 Corrected a problem with the ordering of the variables passed into the running statistics fortan routines. Src/C_AMRLib/SLABSTAT_2D.F Src/C_AMRLib/SLABSTAT_3D.F commit e34ded7b35b43767689d25f78c6ba422f129ca43 Author: sstanley Date: Fri Apr 21 22:28:16 2000 +0000 Elaborated on the documentation for SlabStatRec. Src/C_AMRLib/SlabStat.H commit cb803de49e63ca3342ca0660f5888476c650b6a0 Author: car Date: Fri Apr 21 18:46:06 2000 +0000 fix for g++ Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit 5d3f8018ad97044d35a0784b9410adb3404c987d Author: sstanley Date: Fri Apr 21 16:26:15 2000 +0000 Added a couple of general SlabStat statistics routines that save the values required to calculate the first four moments of whatever state components are passed in. Routines were added to do this using Reynolds averages and Favre averages. These are likely to be used in NS, HT as well as HCAll, so they were added here. Src/C_AMRLib/Make.package Src/C_AMRLib/SLABSTAT_2D.F Src/C_AMRLib/SLABSTAT_3D.F Src/C_AMRLib/SLABSTAT_F.H commit 8b48ec51af9df3d9d1e6ed20f48e7822e0cbd216 Author: sstanley Date: Fri Apr 21 16:24:02 2000 +0000 Corrected a typo in an error message about the format if the ParmParse inputs. Src/C_AMRLib/SlabStat.cpp commit b4819bc9f630f424a3cc884b62d23bc62214e95f Author: car Date: Fri Apr 21 16:23:32 2000 +0000 *** empty log message *** Src/C_BaseLib/CoordSys.H commit 1a80d848da57621a306894819f23cdf7be825479 Author: sstanley Date: Fri Apr 21 16:20:21 2000 +0000 Added ARRAYLIM_2D.F and ARRAYLIM_3D.F to amrlib. These contain a couple of helper fortran routines that convert back and forth from the DIMDEC type cpp defined array dimensions to dimensions stored in arrays, lo(SDIM) and hi(SDIM). Src/C_AMRLib/ARRAYLIM_2D.F Src/C_AMRLib/ARRAYLIM_3D.F commit eeb075118c78c04fa34b38d01c93ff4473fa9e91 Author: car Date: Fri Apr 21 14:22:24 2000 +0000 fixes for fill_sync_reg memory allocation problems Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgdebug.F Src/LinearSolvers/C_NodalMG/hgdebug_F.H Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 66440d3036b98d8d77dfd6e24605b4afe09c004f Author: car Date: Thu Apr 20 17:46:47 2000 +0000 noquotes in fortran Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit 049b3c8828d3ff1fc207b9de595166687f299d25 Author: car Date: Mon Apr 17 21:16:10 2000 +0000 partial backout fix for fill_sync_reg Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 670237f751deec3b55e2ed23b33b3a979262ce51 Author: car Date: Mon Apr 17 20:53:29 2000 +0000 partial backout fix for fill_sync_reg Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit e82962200eddeb930c2c125e7187ad3ec38d7d09 Author: car Date: Mon Apr 17 17:58:37 2000 +0000 I think a fix for fill_sync_reg allocation Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/inputs commit bb8aa30d316591a8368da55c772e1844e6701b52 Author: propp Date: Fri Apr 14 20:56:12 2000 +0000 deleted extra arguments Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F commit 6c23f9321fa2a911d1b5281c0d6f36411a8bbc5a Author: lijewski Date: Fri Apr 14 20:45:48 2000 +0000 Fixed some bugs. Src/LinearSolvers/C_NodalMG/proj.cpp commit 89e5ea0e9eca411800a878bae79c67d7ec22b0d2 Author: sstanley Date: Wed Apr 12 16:14:23 2000 +0000 Added a newline at the end to eliminate a warning message on mothra. Src/C_BaseLib/Utility.cpp commit 13954427cdd7b6144ddd9486a58234c5e11ace89 Author: sstanley Date: Thu Apr 6 17:05:39 2000 +0000 Changed some comments from // to /* */ since cpp on cobalt isn't stripping the // comments. Src/C_BaseLib/SPACE.H commit 54158faa00e4cfa7f642fd6965f6d6750bc5560f Author: sstanley Date: Wed Apr 5 18:22:02 2000 +0000 Rewrote the nodal interpolation routines in 2-d and 3-d. This was done in order to make them give the same results for nodes which are periodically duplicated. The new interpolation does not give identical results to the old however the changes are extremely small (<1.0e-14). Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.cpp commit 75dda74e0883980334ea42485077f15afa2719d7 Author: sstanley Date: Tue Apr 4 18:28:59 2000 +0000 Changed the box definitions. Tools/C_util/ViewMF/viewMFdiffHardWire.cpp commit 5952d06fc098630c64b70864434ee76ee054293b Author: vince Date: Tue Apr 4 00:20:13 2000 +0000 Added a denormal fix option. Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp commit c8257f87e742b32f4ef2d8119a03c2614cdf4bdb Author: marc Date: Mon Apr 3 23:13:03 2000 +0000 ifdef out os stuff...see Utility.[H,cpp] Src/C_AMRLib/Amr.cpp commit 92fd212b98bd1834a5f7d0a298842d9bbd74b371 Author: marc Date: Mon Apr 3 23:11:40 2000 +0000 ifdef out pid stuff for WIN32...there's probably a way to implement this, but it's low priority. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit ecf14e5d305381dd0f366a67e17d018c94a4725e Author: sstanley Date: Wed Mar 29 23:05:54 2000 +0000 Added the ability to build in place. Tools/C_util/ViewMF/GNUmakefile commit f490e05240c7950be0cb26ac868616ba673b59ea Author: sstanley Date: Wed Mar 29 23:05:30 2000 +0000 This is a variation on the viewMFdiff routine. THis allows boxes to be specified for the two multifabs to be compared. THis allows the same multifab to be passed in twice and to be compared periodically. Tools/C_util/ViewMF/viewMFdiffHardWire.cpp commit eeca8b87a3fd2380b45beed2cc359ac129ee17f1 Author: lijewski Date: Wed Mar 29 21:42:38 2000 +0000 Now can specify boxes via ParmParse. Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp commit ff26049e830ad6d2a54d40c48629c7987c401bff Author: marc Date: Mon Mar 27 20:23:18 2000 +0000 Changes to port to mahler.ca.sandia.gov Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.defs commit 5a15738f9fd4f8b24c16d13ca3e8081520c55638 Author: car Date: Mon Mar 27 20:06:07 2000 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgdebug.F commit 0b2742982ed9c802db4aa8b6663d75089f0a75b2 Author: lijewski Date: Mon Mar 27 16:26:13 2000 +0000 Added some copy constructors and copy assignment operators. Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/InterpBndryData.H commit 051c96748877c67e5a021fc616f8947a312aa8ef Author: lijewski Date: Fri Mar 24 22:10:01 2000 +0000 Some mods for AuxBoundayrData ... Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 64388a33b24f8d3da8c8f5cd5e885d58aaf2e5ce Author: car Date: Fri Mar 24 18:13:19 2000 +0000 Removed path dependence of tarch, tdevice. Tools/C_mk/Make.mpi commit 181dd17654ca6cc42523ef388a58853eb76b50c8 Author: car Date: Fri Mar 24 18:12:36 2000 +0000 uses tarch, tdevice in mpich: must be on path. Tools/C_mk/Make.mpi commit ef7965b436e9ae8cf1419b00f2e13d1a819861d2 Author: sstanley Date: Thu Mar 23 22:09:44 2000 +0000 Added a new tool to the utils directory which will read a fixed_grids type grid format and coarsen. Tools/C_util/dbgTools/GNUmakefile Tools/C_util/dbgTools/Make.package Tools/C_util/dbgTools/crsGrids.cpp commit 36bdabd0166d3f8ecdd24cd2cb22b33e8e3e56c0 Author: lijewski Date: Thu Mar 23 21:39:06 2000 +0000 Turned off a couple things. Src/LinearSolvers/C_NodalMG/GNUmakefile commit 10afa9880c51e364726b0c1bfb7584ada634a69f Author: lijewski Date: Thu Mar 23 21:38:27 2000 +0000 These are 3d test cases that are known to work with periodic bcs. Src/LinearSolvers/C_NodalMG/files.3d commit 1a29774ee886ff868b8fabf22ea7568073ba0cd4 Author: car Date: Thu Mar 23 21:16:59 2000 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit eab12d8334af8063364971e9e7ebb3760308fabb Author: car Date: Wed Mar 22 21:10:11 2000 +0000 inflow bug fix: grow the srcbox Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit b842f9f34a707879629e3ccd3c7489f2f196c849 Author: lijewski Date: Wed Mar 22 15:51:45 2000 +0000 Some mods for g++ and cxx. Don't use -lm_sqrt with V4 OSF1 Tools/C_mk/Make.OSF1 commit 4c2997f5479a337ab14147e97ed9092c64237062 Author: lijewski Date: Tue Mar 21 19:24:04 2000 +0000 Added INCLUDE_LOCATIONS stuff for OSF1 Tools/C_mk/Make.mpi commit 00248f5efb2bec44481e4b4904d90478116bacaf Author: marc Date: Fri Mar 17 22:01:01 2000 +0000 Add slashes around saved common block name Src/LinearSolvers/C_NodalMG/hgdebug_F.H commit 18a1e3dc4212bdc0bfe9e507893d04cd9346ab1d Author: car Date: Fri Mar 17 21:58:59 2000 +0000 k Src/LinearSolvers/C_NodalMG/hgdebug.F commit 00063bcc15cb2401c858c23062d67141b075eebc Author: car Date: Thu Mar 16 23:15:07 2000 +0000 Added BL_NAMESPACE support Tools/C_mk/Make.defs commit f7dccaafc216512d298d5106ecda1f429a3a4f11 Author: car Date: Thu Mar 16 23:13:40 2000 +0000 clean is now a double colon rule Tools/C_mk/Make.rules commit 74e5cfd9c883a4803a1b72c3f45e74a18ff0c846 Author: car Date: Thu Mar 16 23:11:32 2000 +0000 fixes an inflow bug, might not break the periodic code Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgdebug.F Src/LinearSolvers/C_NodalMG/hgdebug_F.H Src/LinearSolvers/C_NodalMG/inputs Src/LinearSolvers/C_NodalMG/proj.cpp commit 075c1167471dd7d7d1d72f937035c9a41b907b91 Author: car Date: Thu Mar 16 16:43:34 2000 +0000 Linux fixes for mpich/lam and Vince's WHICHLINUX Tools/C_mk/Make.mpi commit a92ec23120cee45d77be71bd8382a68139d5ef70 Author: lijewski Date: Wed Mar 15 16:51:23 2000 +0000 Some changes to MPI environment on mothra due to mpich1.1.2 install. Tools/C_mk/Make.mpi commit c4f28d9ad9f9ebe6be226fbdc8df9348b372292c Author: sstanley Date: Wed Mar 15 00:03:06 2000 +0000 Fixed a bug with how data was filled from the AmrData object. The wrong level was used. Tools/C_util/Convergence/DiffPlot.cpp commit 046ecb4d410dd90039dff0433c8ce83b276bafa6 Author: car Date: Mon Mar 13 18:25:20 2000 +0000 trivially different from sstanley_2.32 Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_3.32 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3.32 commit 656403f3eb4987f09b6df74cb97391794e21aab9 Author: car Date: Mon Mar 13 17:19:17 2000 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_2.32 Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_2.64 Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_3.32 Src/LinearSolvers/C_NodalMG/tests/gt2t4 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.32 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.64 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3.32 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t4 commit 33a0df4e16587824b057df3993e4afd7e80952e1 Author: lijewski Date: Wed Mar 1 21:58:51 2000 +0000 Upped the precision in checkPoint(). Src/C_AMRLib/SlabStat.cpp commit 5c36e7ed0dfe22b902df232cf0ca9a1318eb54cd Author: lijewski Date: Wed Mar 1 20:19:02 2000 +0000 More work getting SlabStats going. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/SlabStat.cpp commit 43f3191577a8a3de3bcc5b41d81dd629ce277a96 Author: lijewski Date: Wed Mar 1 15:43:34 2000 +0000 Stuff for checkPoint()ing SlabStat stuff Src/C_AMRLib/Amr.cpp Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp commit 6593ff78eddee49eea0638d6e5c08e37c9188016 Author: lijewski Date: Wed Mar 1 15:43:03 2000 +0000 Defaulted another argument. Src/C_BaseLib/VisMF.H commit a31b4e7eed16cbedeb2c5981bce77fb2effce68f Author: lijewski Date: Mon Feb 28 23:27:00 2000 +0000 Some mods for the statistics stuff ... Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 78278d020db26012cbcabb5d2e825b11c46c1ec0 Author: lijewski Date: Mon Feb 28 23:26:36 2000 +0000 Mods for some statistics stuff ... Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Make.package Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 00d87edc8cfed0528cec888f7a0eb1455c918826 Author: sstanley Date: Fri Jan 28 01:14:05 2000 +0000 Modification to the doc++ stuff to make it work properly. Src/C_AMRLib/StateDescriptor.H commit 28db038b55dbb9da26d8e858ca4ad717bf3942eb Author: vince Date: Mon Jan 10 23:55:15 2000 +0000 Added support for yukon (ARSC). Tools/C_mk/Make.defs commit 248a7d8b86d1d252685e045c77459f9bbe45a253 Author: lijewski Date: Thu Jan 6 19:03:27 2000 +0000 Fixed docxx comments to compile with latex. Src/C_AMRLib/AmrLevel.H commit 053c755e04a956f0d919f17ed12aab25805a743b Author: lijewski Date: Thu Jan 6 18:26:40 2000 +0000 Updated docxx documentation so it can be latex'd. Had to add a '\' to some BL_ASSERT()s and BL_SPACEDIMs. Src/C_BaseLib/BLassert.H Src/C_BaseLib/BoxLib.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Orientation.H commit 35201aebda195e8f14d1ffe1be1546abd7b45480 Author: lijewski Date: Thu Jan 6 18:14:36 2000 +0000 The docxx style file we use for latex. Src/C_BaseLib/docxx_squish.sty commit 52f6a58475d9f47d48a191c2d1db65c2e4858e10 Author: dailey Date: Mon Jan 3 14:02:56 2000 +0000 Make.IRIX64 modified for use with SGIs at the Univ. of Wisconsin 01-03-00 Sara Bauman Tools/C_mk/Make.IRIX64 commit fbb861952eb5989b5bffd2d39380d3f9586ddefc Author: lijewski Date: Thu Dec 9 22:06:08 1999 +0000 Now use Mersenne Twister random number generator. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit e2b10fe46c5ade3c93742366228f2c1879b80d0e Author: sstanley Date: Thu Dec 2 07:43:05 1999 +0000 Modified the logic in HT::manual_tags_placement() to fix the problem with to many cells left uncovered near the outflow. This, unfortunately required a change in the interface to this routine, and thus a change in the header which fed all the way back to AmrLevel.H. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit a9ecef303a79116c9aa57b15d9db00a4d377471f Author: lijewski Date: Wed Dec 1 16:37:24 1999 +0000 Shut up a warning on SGI ... Src/C_BoundaryLib/BoundCond.H commit d512bb98258a673429c22c64a7ee244f79dcd8a2 Author: lijewski Date: Wed Dec 1 16:17:10 1999 +0000 Shut up a warning ... Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.H commit e184b43e43fb3c293cd34ed40aa9701d025976e4 Author: lijewski Date: Wed Dec 1 16:16:45 1999 +0000 Shut up warnings ... Src/C_BaseLib/BoxList.H Src/C_BaseLib/MultiFab.cpp commit fc2a3fa18344a39c826d4da0883ca6774235b045 Author: lijewski Date: Sun Nov 28 19:48:51 1999 +0000 Don't try to read .profile Tools/C_scripts/compressor commit 82416729ec829d3341a0c56c7138fcbf62b03fa1 Author: lijewski Date: Sun Nov 28 19:48:22 1999 +0000 Mod to fix bug on T3E Tools/C_scripts/compressor commit 8aaee9d05d0c35292b8885b5d31e8e78e7822e21 Author: lijewski Date: Fri Nov 26 20:02:41 1999 +0000 Strip out any possible tar files. Tools/C_scripts/compressor commit c61f8af88e1edfd9307390253fb76abe86851221 Author: lijewski Date: Sat Nov 20 19:41:38 1999 +0000 Direct error output of `ls' commands to /dev/null. Tools/C_scripts/compressor commit 6d4bc5c7eba894ff86d63274bd0340984a0f8608 Author: lijewski Date: Sat Nov 20 00:09:12 1999 +0000 Beefed it up a bit so job chaining will work. Tools/C_scripts/compressor commit b553d176f50dce1cd8ebc01f5ac6c1450c7afe78 Author: car Date: Thu Nov 18 22:19:43 1999 +0000 We think we fixed inflow on the high side of an idim. Src/LinearSolvers/C_NodalMG/boundary.cpp commit 2706753f5e18072191fa9754871a2385a4449233 Author: sstanley Date: Thu Nov 18 21:29:57 1999 +0000 Minor change to fix a documentation problem. Src/C_BoundaryLib/FabSet.H commit 55053973ad6330f5b2ba864d5306ea156637b68e Author: car Date: Thu Nov 18 00:27:51 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit 6aa2df8970d3bef121acbf4668ab14e468e2b0b6 Author: car Date: Thu Nov 18 00:09:07 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/tests/gr.ann.1 Src/LinearSolvers/C_NodalMG/tests/gr.sstanley.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.ann.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.sstanley.1 commit 80fdf472afe8cdbe99af1d69765e872986da5296 Author: lijewski Date: Fri Nov 12 21:37:54 1999 +0000 A ksh script to tar up and rm chk and plt directories. Mostly useful in batch scripts :-) Tools/C_scripts/compressor commit accd3b0b982fcca08f1a85f8e7ee6f1add58200e Author: lijewski Date: Thu Nov 11 21:26:08 1999 +0000 Make the default for tar_and_rm_files to false, even on T3E ... Src/C_AMRLib/Amr.cpp commit ade581fc599964f11d880e9736e08711512850a6 Author: propp Date: Wed Nov 3 16:33:25 1999 +0000 eliminated inlined function to make totalview happy Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit eb90c821cd904eac1590c662363a9b9aefdd76e0 Author: propp Date: Sat Oct 30 00:01:36 1999 +0000 moved static function to appease totalview Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 9e3e5dd223fe3648ab76e4a58699601d024b9af6 Author: sstanley Date: Fri Oct 29 17:31:48 1999 +0000 Fixed a problem with the level used from the exact data. The old code is still intact. Tools/C_util/Convergence/DiffUniform.cpp commit 084127e37bfcf2cf2e1065f216514807d5763669 Author: sstanley Date: Fri Oct 29 16:36:03 1999 +0000 Small modifications to DiffSameGrid.cpp (all documentation) and added the routine DiffSameGridRefined.cpp which does the same thing as DiffSameGrid.cpp but allows the two plotfiles to have different levels of refinement, as long as they have the same physical region refined. Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/GNUmakefile commit 883704896b63daa6390be56a77626e788ae776e9 Author: lijewski Date: Thu Oct 28 21:49:52 1999 +0000 When amr.tar_and_rm_files is true ... We now stagger deleting the ckfiles to support restart() and job chaining. Src/C_AMRLib/Amr.cpp commit f725a9b56aaa2c8dac02935a6e79a0c063b9722f Author: vince Date: Wed Oct 27 21:24:40 1999 +0000 Moved a flag. Tools/C_mk/Make.T3E commit 4a2cd8feb361a0b86b1d0665236f1af0451ff195 Author: marc Date: Mon Oct 25 18:31:33 1999 +0000 Do explicit C-style caststo shut gcc up on my Linux box Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 6007231e5c6502bf291135698471fa98dfee9d06 Author: marc Date: Mon Oct 25 18:29:54 1999 +0000 Add optimization to FFlags for opt. Tools/C_mk/Make.Linux commit e14b601aa3c2a335958292b6d0bd23b339b1b7c3 Author: lijewski Date: Thu Oct 21 17:27:21 1999 +0000 Now remember pid for chk and plt tar_and_rm commands so can grok them. Src/C_AMRLib/Amr.cpp commit 94057b43d3d8567be6e8861943154a89223a84f1 Author: sstanley Date: Wed Oct 20 22:35:37 1999 +0000 Added volume factor to the norms in DiffSameGrid.cpp. Added the routine PltFileNormB.cpp which just does the norms of the values in a plotfile. Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/PltFileNormB.cpp commit 3d8a1bcc3e45209a2811a422b67ca3d58839c713 Author: sstanley Date: Wed Oct 20 20:08:35 1999 +0000 Marc's changes to the DiffUniform.cpp routine (along with minor documentation of my own). Similar documentation in PltFileNorm.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp commit 2bbdecf32c72338e4d2c8c2d06a8011afa0a12b2 Author: lijewski Date: Wed Oct 20 18:25:13 1999 +0000 Added Execute(). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 8fb12379ba7cabb362905037d3dc429011bbd9a4 Author: lijewski Date: Wed Oct 20 18:24:58 1999 +0000 Added amr.tar_and_rm_files ability. Src/C_AMRLib/Amr.cpp commit 78795f93137186c5db52b9b17a52eba17fc29f65 Author: vince Date: Fri Oct 15 23:44:29 1999 +0000 Additions for the LBNL Alpha cluster. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 611d895ca174907959d536805358a46820ab8a9c Author: propp Date: Fri Oct 8 20:54:50 1999 +0000 added plotfile_on_restart option Src/C_AMRLib/Amr.cpp commit e1b2a38844a329c50bf8255890b33d067a3d52a4 Author: sstanley Date: Thu Sep 30 15:55:12 1999 +0000 Minor change to doc++ stuff, but it seemed like a good time... Src/C_BaseLib/BoxArray.H commit a653e49cac0224a61d38a70a118517a21f40ee07 Author: lijewski Date: Thu Sep 30 14:56:19 1999 +0000 Removed cached MultiFabCopyDescriptor stuff ... Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 9a9c8cdfa347027d4720f26c491d1b081e58ac32 Author: lijewski Date: Thu Sep 30 14:55:53 1999 +0000 Removed cached MultiFabCopyDescriptor junk from MultiFab. Src/C_BaseLib/Geometry.cpp commit 955b3b13cf88873baa4310d4b346675cb59e2276 Author: sstanley Date: Wed Sep 29 21:46:08 1999 +0000 Modification to fix compiling on the T3E Tools/C_util/ViewMF/GNUmakefile commit c99e646157f4a1780db9d5373c4349c66b98b76e Author: sstanley Date: Fri Sep 24 21:26:34 1999 +0000 Fixed a problem with doing the max norm. Tools/C_util/Convergence/DiffSameGrid.cpp commit e4f116ff32331c1cc48fb136af98d93b8e6eb7d4 Author: marc Date: Thu Sep 23 21:06:56 1999 +0000 Surround output func by ifdef HG_DEBUG to satisfy compiler Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit fde0e1f1afffbf0c171deaa40b24d41fd1ad3530 Author: vince Date: Sat Sep 18 00:50:34 1999 +0000 Added changes for the vis server (escher, an sgi) and n2001 (the pc linux cluster). Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit b01845fe869124ccd77d8ccf8bf2359fcbb2e76d Author: lijewski Date: Fri Sep 17 23:32:45 1999 +0000 Fix to make level 0 regridding work with fixed grids. Src/C_AMRLib/Amr.cpp commit 858a7e0f25969b57c35dbfcf1f3b8005bee2e33b Author: lijewski Date: Fri Sep 17 21:45:06 1999 +0000 amr.regrid_on_restart=1 will force regrid() on 1st timestep on restart. Src/C_AMRLib/Amr.cpp commit ed75327bc9dc63fcf957b2b1a37ee3a4dbab496d Author: car Date: Fri Sep 17 17:22:47 1999 +0000 tweak Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 1bfca1886f13e45f9e4d1b99a2c68002b049aa8d Author: lijewski Date: Thu Sep 16 23:12:41 1999 +0000 Some mods to allow regridding at level 0 if max_grid_size changes. Src/C_AMRLib/Amr.cpp commit ecd836abc0eda24b0afe3378817644b42fbccb44 Author: car Date: Wed Sep 15 16:58:32 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 90972fdb4aa4c95b6edb84af2be3571ef0803521 Author: car Date: Tue Sep 14 18:26:56 1999 +0000 support for dense stencils is added Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 2628e3af5b882904ff97ea351875ae423c595ca8 Author: lijewski Date: Fri Sep 10 21:07:30 1999 +0000 Added -qdpc to promote FP constants to double precision ... Tools/C_mk/Make.AIX commit 95f64c92a2d14031fdf5b1a406e0bedc77f2f9f7 Author: lijewski Date: Fri Sep 10 20:53:01 1999 +0000 Added -fpconstant to FOPTF and FDEBF Tools/C_mk/Make.OSF1 commit bcb82edfb22f96845ccc7fbe7e1c38de16225168 Author: almgren Date: Thu Sep 2 22:00:27 1999 +0000 Removed the is_sync flag. Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit e8666ebb35efb458479c676635dd8871c6de1e70 Author: sstanley Date: Thu Sep 2 00:12:38 1999 +0000 Corrected the definition of the grids for this case. They were improperly defined, although it doesn't show up for this test case. Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_a commit 6531cf9525df7b348a7c8fe2e217df6b3475bfb5 Author: sstanley Date: Sat Aug 28 00:43:57 1999 +0000 A couple of small changes to allow it to compile. Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/Make.package commit 4bcfbb85e3951dced1e48981a0a77f1913701322 Author: sstanley Date: Fri Aug 27 15:10:53 1999 +0000 Removed the nprocs from the StartParallel call. Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 1bde6bd72097f909f8eaa1acb335305e267b733e Author: lijewski Date: Thu Aug 26 18:10:47 1999 +0000 Now recognizing leading ! character as a comment. Don't currently allow any preceding space before the ! ... Tools/C_scripts/strip72 commit 7986ee17bd089acb747b34810c9d3624040da1d2 Author: lijewski Date: Thu Aug 26 17:19:58 1999 +0000 Changed test for KCC to also recognize mpKCC and newKCC ... Tools/C_mk/Make.defs commit bf46a75523ca15b5ce1882185e43e7b035ccc455 Author: propp Date: Wed Aug 25 18:03:58 1999 +0000 added BL_FORT_USE_LOWERCASE option Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BoundaryLib/INTERPBNDRYDATA_F.H Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/MG_F.H Src/LinearSolvers/C_TensorMG/DivVis_F.H Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/MCLO_F.H commit 638bc20e8078dd5c7d320c47aae7cda6efaecd27 Author: lijewski Date: Wed Aug 25 17:52:33 1999 +0000 Fixed bug regarding usage of ConstFabSetIterator. Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 899267ead6cab5f902ed1c9f2d88e2356b71a83a Author: lijewski Date: Tue Aug 24 21:02:22 1999 +0000 Use new hfiles with KCC ... Tools/C_mk/Make.AIX commit 4bc0d7f462212d65e9dac2a54f2c7d186ec622f3 Author: lijewski Date: Tue Aug 24 20:08:46 1999 +0000 Simplified some settings. Tools/C_mk/Make.AIX commit d64996046cbb9c654611dfb8f71944050a6eb2d1 Author: lijewski Date: Tue Aug 24 16:28:29 1999 +0000 Cleaned up the FillPatch stuff a tad more. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 7f6f1a5fafdf435c7522e5b77bcc6a3355cefc40 Author: lijewski Date: Mon Aug 23 21:19:58 1999 +0000 Added tokenize() ... Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit d82600e2c5561c5361b19d96a95e7381c102346a Author: car Date: Mon Aug 23 21:16:49 1999 +0000 support for Geometry Src/LinearSolvers/C_NodalMG/inputs commit 3b1c9e8e3553c23212a697d255bd787c17ea8804 Author: lijewski Date: Fri Aug 20 21:54:22 1999 +0000 Oops -- needed to define FillPatch::operator++() ... Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 576b85e752adb18047bdb1e491e45ef2794791b2 Author: lijewski Date: Fri Aug 20 17:52:55 1999 +0000 Removed --no_restrict; Crays header files use it :-( Tools/C_mk/Make.T3E commit 1e028f327af6182e42ed48c78e83e3595b0febc0 Author: lijewski Date: Fri Aug 20 17:38:02 1999 +0000 Added --no_restrict Tools/C_mk/Make.T3E commit 5b100cfe47edd987820a94e56507c100ac4b70b9 Author: lijewski Date: Thu Aug 19 20:16:32 1999 +0000 Fixed yet more memory leaks ... Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 527b7e2fe7b7c2bc63d9139433ea7d899c254736 Author: lijewski Date: Wed Aug 18 21:53:01 1999 +0000 FillPatchIterator now uses the appropriate Iterator for each of the components at a specified StateDescriptor index. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit ef4b189092dc9ddfd154a25bca0fbda6473cd0ba Author: propp Date: Mon Aug 16 18:21:53 1999 +0000 *added ability to derive multicomponent data with separate names for each component *added ability in heat transfer to derive mole fracs Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 649441d3c4868e6ca18b93c3604ca72885a4654e Author: propp Date: Fri Aug 13 16:28:57 1999 +0000 fixed up writePlotFile routines added setPlotVariables routine Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 13da5ce51c55a91b4bde4d22ea41dddde085288a Author: lijewski Date: Wed Aug 11 19:52:05 1999 +0000 Added FOPTF+=-O for default case Tools/C_mk/Make.Linux commit c70246a83e9e900aafb8feb6feafc58c0d426103 Author: marc Date: Tue Aug 10 00:12:42 1999 +0000 Generalize for prversion/parallel junk Tools/C_scripts/dsp.mak commit 3db1051a4e2ac26d89a816b2f6b470a7cdeb1229 Author: car Date: Mon Aug 9 16:44:41 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit 0c9ae1133e391435d6b455f637ffd074daeeb76d Author: car Date: Fri Aug 6 23:10:05 1999 +0000 bndrylib is now needed Src/LinearSolvers/C_NodalMG/GNUmakefile commit ca56a92d5bea4b5ed200f47022f0a363871540aa Author: sstanley Date: Fri Aug 6 22:45:28 1999 +0000 Fix to BoxArray::contains(BoxArray ). Src/C_BaseLib/BoxArray.cpp commit a8617ab87ba92adc36655d3af99021ed9a94282c Author: propp Date: Fri Aug 6 21:48:35 1999 +0000 deleted parmparse variable verbose, now must use parmparse variable v Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 322b73f941caafcc9889a7fbe2928447b0e65184 Author: propp Date: Fri Aug 6 18:20:16 1999 +0000 eliminated verbose ParmParse argument; it was being overwritten by v ParmParse argument Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 6ce859c8a51b8687e1e713f4d21e0251390ef18b Author: almgren Date: Tue Aug 3 07:03:37 1999 +0000 Need to include bndrylib now because we're using a Geometry object. Src/LinearSolvers/C_NodalMG/GNUmakefile commit e741a0420ba5c99d4ec478eca4cb367993f2cae9 Author: almgren Date: Tue Aug 3 07:02:35 1999 +0000 A different paradigm for doing Sync_resid_fine - the previous way just wouldnt work for periodic in 3d. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit e4d3f616295db94cf29d9f5b3328bdcfa44fe358 Author: propp Date: Tue Aug 3 00:37:24 1999 +0000 Fixed bug in FORT_APPLYBC where 1st component of bc array was used to determine bc type instead of the dir-th component of bc array. This change has already been made in the 2D version of the code. Src/LinearSolvers/C_TensorMG/DV_3D4.F Src/LinearSolvers/C_TensorMG/DV_3D4.mF commit 336dd86c0775724213a57ae60e1421a459a81571 Author: almgren Date: Mon Aug 2 20:24:16 1999 +0000 Need to fill rhs_local periodically as well in fill_sync_reg. Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 915d575ab54b9a728040cf34b864d38a5b8e865d Author: sstanley Date: Mon Aug 2 19:22:16 1999 +0000 Minor changes in the location of the doc++ information. Put it after the forward declarations instead of before. Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/MultiFab.H commit 623060614c2bf705f1cddb787915127e94ff6e99 Author: almgren Date: Sun Aug 1 15:11:44 1999 +0000 Changes in order to get periodic right. Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit d9d818fb08aa8722b4cb9cd9c0ee248f6e543584 Author: almgren Date: Fri Jul 30 23:46:06 1999 +0000 Warning message in hgfres. Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit b149f468fc3f4e4ad6955d079187be2a974f32b4 Author: marc Date: Thu Jul 29 01:07:06 1999 +0000 Add options for specifying serial hgproj and prversion....note that this is all still a little flimsy... Tools/C_scripts/dsp.mak commit 14f31e18ed501200aaa52b016a81a9978349ed3c Author: almgren Date: Wed Jul 28 17:19:24 1999 +0000 Should only do the special r-z stuff if i+m=0, not just i=0. Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 04acd2f8e3f48e4fdd77b80b2746ae7d2bd370c0 Author: marc Date: Tue Jul 27 17:35:51 1999 +0000 Remove manual_grid_placement in favor of tagbox processing Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 7f3c3131962957e104d18c54d47afe1f2ab2e7eb Author: marc Date: Tue Jul 27 17:34:59 1999 +0000 Make const args const in signature Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 29ee23c01b926a5e0fa2dfdfcf6e3d8cb7ee11bf Author: marc Date: Tue Jul 27 17:34:06 1999 +0000 Make physicalBndryTrpes available to Fortran Src/C_AMRLib/BC_TYPES.H commit aa7cf471c93ac8513f657de1fec1cea7dbda0505 Author: lijewski Date: Mon Jul 26 16:59:42 1999 +0000 Updated a comment :-( Src/C_BaseLib/ParallelDescriptor.H commit 7463973514f1824bf87e69a702666a18f75e9f19 Author: almgren Date: Fri Jul 23 23:56:13 1999 +0000 Made a bunch of changes having to do with how the sync register stuff is computed. In this new version, the contributions to the sync registers are computed in hgproj, not in SyncRegister... Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit c12f46ed39e620e3225a49725193613b0c7796d4 Author: car Date: Fri Jul 23 21:29:13 1999 +0000 test case for inflow bust Src/LinearSolvers/C_NodalMG/tests/gr2.inf Tests/LinearSolvers/C_NodalMG/test_grids/gr2.inf commit b41b1e70dfe617f349b48c9a25600746bf08d5c6 Author: car Date: Fri Jul 23 21:28:31 1999 +0000 saves work in serial Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit c200fd1124b651939512d1f356fb4a5646ef6e6a Author: car Date: Fri Jul 23 21:28:00 1999 +0000 fix for array bounds bust Src/LinearSolvers/C_NodalMG/boundary.cpp commit 4c470e17126830a544d2e73d8f5d6e3e47eb8a8d Author: car Date: Fri Jul 23 17:56:40 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit e906ce17eb869fef4b1195a62038f358c3312a0d Author: sstanley Date: Wed Jul 21 21:09:20 1999 +0000 Modified the location of the call to manual_tags_placement(). Src/C_AMRLib/Amr.cpp commit a53ac631a79fdedb1be5ac3fa59a3ec1664c2d74 Author: lijewski Date: Wed Jul 21 21:07:38 1999 +0000 Output CArena stats ... Src/LinearSolvers/C_NodalMG/proj.cpp commit a6ee7c2f903360d900c37043d443b1cfbafc9e0b Author: lijewski Date: Wed Jul 21 21:06:08 1999 +0000 Oops -- forgot to remove a commented out #if Src/C_BaseLib/CArena.cpp commit d9b9cb5fecc5dd548bdc0a4d841e28e0722378b5 Author: lijewski Date: Wed Jul 21 21:02:49 1999 +0000 Added heap_space_used(). Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit d77bc85c9ace4869a1b5cb0a936682161ade435a Author: lijewski Date: Wed Jul 21 21:02:40 1999 +0000 Added extra newline to an output message for additional separation ... Src/C_BaseLib/RunStats.cpp commit fb1977fa968669df499dcd9880a9eca5403c1fa9 Author: lijewski Date: Wed Jul 21 17:26:08 1999 +0000 Removed commented out line ... Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 182ad4ba8abff1284d89602c3f43a4cbf79d6426 Author: lijewski Date: Wed Jul 21 17:20:34 1999 +0000 Got memory mods working with periodic. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit cbc4d4187ec5e48d34f9ffa375d991a8bd0e1f6c Author: lijewski Date: Wed Jul 21 15:28:00 1999 +0000 Some mods to minimize communication when in parallel. Src/LinearSolvers/C_NodalMG/restrictor.cpp commit d9aaf9b152c07a41d36f2099367e1ebeb7947ffb Author: lijewski Date: Tue Jul 20 23:45:02 1999 +0000 The restrict_level stuff wan't quite right ... Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 22776294825c0933889c8d4393903771eefbfc59 Author: almgren Date: Tue Jul 20 20:42:13 1999 +0000 Added manual_tags_placement which will replace manual_grid_placement. It is only virtual here, to be defined in applications. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 26d12136bc66e833a4ae5bb4a5645c57b7ebb1cf Author: lijewski Date: Tue Jul 20 17:13:59 1999 +0000 Slight mod of what I checked in yesterday. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 50ea5699d6ad04b14bde8a5fe2db3685fd287a3f Author: lijewski Date: Tue Jul 20 15:45:04 1999 +0000 Made restrict_level() more memory efficient in parallel. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 639fb6b7b9c8400861b7ead8df33d70c8e6fe9b1 Author: lijewski Date: Mon Jul 19 23:05:06 1999 +0000 Added some statistics to track parallel data transfer. FillPatch routines now transfer less data in parallel. Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a63e8b9b6002941a4e697c6b4b0e7dcfb8aa45a7 Author: almgren Date: Mon Jul 19 19:54:24 1999 +0000 Fixed code for r-z with 5-point stencil, also removed some routines which weren't being used. Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 2394d192f585fb5902f0171cc69ebf1186238961 Author: propp Date: Mon Jul 19 17:40:48 1999 +0000 added 3d fortran routines... Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/Make.package commit dff87ccfc229cb9b3045829ea124b525504e4d3f Author: sstanley Date: Fri Jul 16 18:23:49 1999 +0000 Increased the precision at which the Header in plotfiles and checkpoint files gets written. We were losing precision in the timestep. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/StationData.cpp Tools/C_util/WritePlotFile.cpp commit 7ba8d555ed89718372bdc11d7a233dddf4a71678 Author: almgren Date: Fri Jul 16 17:14:46 1999 +0000 Fix in hgcdiv to correctly do 5-point stencil at r=0 (for r-z only!). Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 10b4c950c8edd3a22ede041aa30c60f33970c6ed Author: lijewski Date: Thu Jul 15 17:07:04 1999 +0000 Got rid of all those computeBoxLen() calls. Now only call it when length() is called. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit b5f30e424dd86b111dc02a3d0d898e18e94b1a7b Author: sstanley Date: Thu Jul 15 01:37:02 1999 +0000 Corrected a couple of the Docs. Src/C_AMRLib/StateData.H commit 22d11c8156a5de1ebd86c7f2caf3f49e51f52689 Author: lijewski Date: Wed Jul 14 23:06:15 1999 +0000 Did copy constructor correctly. Src/C_BaseLib/Geometry.cpp commit 31daf4b127624887bafd1d727ab423d477b581fd Author: lijewski Date: Wed Jul 14 19:20:44 1999 +0000 Added malloc_stats(0) call for BL_T3E in OutOfMemory(). Src/C_BaseLib/Utility.cpp commit a6e62aca5dce9fc1ee09ea7dc0f94a6b5653d03e Author: marc Date: Tue Jul 13 01:30:48 1999 +0000 Fix a few little problems...still work-in-progress Tools/C_scripts/dsp.mak commit 5b99a235ba824f5247d498cffa697c0e5d369d97 Author: lijewski Date: Mon Jul 12 16:42:11 1999 +0000 Fix for periodic-nonperiodic boundary cells. Also moved more heap-based stuff into FillPatchIterator data member area. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 42721987c552042544e968efa8d900414234123e Author: car Date: Wed Jul 7 22:48:33 1999 +0000 MPI type safety Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 00f832f2aaf9b75ec54d78f135e96482537054a5 Author: almgren Date: Wed Jul 7 21:45:12 1999 +0000 IsRZ() only exists if BL_SPACEDIM == 2. Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit a91891178cc0292b1a5af791f8cdcd13628deeee Author: almgren Date: Wed Jul 7 18:30:43 1999 +0000 IsRZ() is only defined in 2-d Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 04c03acd88da01bb807faa189c4e2a617f093b8c Author: almgren Date: Thu Jul 1 23:18:31 1999 +0000 Modifications to correct the 5-point stencil in r-z at r=0. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 241413d1079cbc11aa4906772e158e1efe01f651 Author: lijewski Date: Thu Jul 1 20:12:24 1999 +0000 Changed how RunStats stuff was done ... Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 06561a4541f7fc07da67929188e401194f6ea9af Author: lijewski Date: Thu Jul 1 19:44:49 1999 +0000 Added ReduceIt() to fix bug with how the List is reduce()d. Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit a7b36ea5ab45c52e7e88143feb6dc17a451a0316 Author: lijewski Date: Thu Jul 1 19:44:04 1999 +0000 Got rid of old-style cast. Src/C_BaseLib/VisMF.cpp commit 3bb8f8713b44b2c4d3d1567776c6b8a7d53f0166 Author: lijewski Date: Thu Jul 1 16:36:00 1999 +0000 Fixed bug in readStats(). Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit 9efd4eec1fc333a4f0f65ee1286bd650f55d73a6 Author: marc Date: Wed Jun 30 23:46:38 1999 +0000 Fix a few random (and mysteriously uncovered) bugs in the averaging routines/calls Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit bccc7132e9a507de4983858e626a280438dc6c60 Author: almgren Date: Wed Jun 30 21:46:14 1999 +0000 Corrected the averaging of cell-centered source terms onto nodes at r=0. Src/LinearSolvers/C_NodalMG/hg_avg2d.F commit 63343a1279647ff3f3dc5faead17f3a3d9c2e161 Author: almgren Date: Wed Jun 30 21:43:29 1999 +0000 Removed already-commented-out code. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit e2aa51919f0d3dc93936491dda0e7ccf49d6a49a Author: marc Date: Tue Jun 29 18:09:53 1999 +0000 Externified typedef fixed up for 2D by Chuck. Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 95af0492c21fc5a49b2a5db477cd53da412c7961 Author: car Date: Mon Jun 28 20:37:00 1999 +0000 changes for KCC version 3.4, should be innocuous for 3.3 Src/C_AMRLib/StateDescriptor.H Src/C_BaseLib/Arena.H Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/MultiFab.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Src/LinearSolvers/C_TensorMG/DivVis_F.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp commit 8b7b6eeda6532431016d9a2747b5920e9799b50a Author: car Date: Thu Jun 24 22:09:47 1999 +0000 Bone headed IntVect usage Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit fdcdf4a7b7a03592e2ce2a450374af5ab8910986 Author: marc Date: Thu Jun 24 21:21:55 1999 +0000 Oops! src was written as rc... Src/LinearSolvers/C_NodalMG/hg_avg2d.F commit 0bca89193a4eed732bff4fdcf31f50ed4b7a896c Author: car Date: Wed Jun 23 17:59:40 1999 +0000 changes to support KCC 3.4 Src/C_BaseLib/VisMF.H Tools/C_mk/Make.defs commit b4020cfbaf9a3bc3ee6388510c7129d186816a37 Author: lijewski Date: Tue Jun 22 20:06:43 1999 +0000 Redid how HG RunStats are setup to work around RunStats bug. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit b99ac16b153c33458f0dd02ced45200a2e0265cc Author: car Date: Sat Jun 19 03:57:55 1999 +0000 added hg_{irecv,isend,test} to runstats Src/LinearSolvers/C_NodalMG/inputs commit 1c6c9d2e93c01fe6058e5ca473d087f069d84d9d Author: lijewski Date: Fri Jun 18 19:16:28 1999 +0000 Added RunStats for MPI_IRecv() MPI_ISend() and MPI_Test() Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 80f8663a7f6a8fb897db6371abd1a714248f9f35 Author: lijewski Date: Fri Jun 18 16:01:57 1999 +0000 Some cleanup. Src/C_BaseLib/Geometry.cpp commit f282940d221960bc04698721527da94f02e00f83 Author: almgren Date: Wed Jun 16 22:51:16 1999 +0000 The extra terms for r-z should only be used with the 9-point stencil. Src/LinearSolvers/C_NodalMG/hg_avg2d.F commit 4661577f2b382fe060f1421fee0450dc9ebc1866 Author: lijewski Date: Wed Jun 16 22:13:03 1999 +0000 Removed some dead code. Src/C_BaseLib/RunStats.cpp commit abd7c9f36289741412dedf1fef600d8334ee1173 Author: car Date: Mon Jun 14 17:07:26 1999 +0000 defused loop Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 706a7f7450def2cc2bb9452121cbe564f24a7ccb Author: marc Date: Sat Jun 12 00:10:14 1999 +0000 First cut at a script to make MSVC project input file. Tools/C_scripts/dsp.mak commit 0374a8c479c07766f29a729847d2fa2dc4319c40 Author: almgren Date: Wed Jun 9 18:25:35 1999 +0000 We don't want to use the additional rz terms for the five-point stencil. These terms *should* be included for the nine-point stencil only. Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit fb24ff9b4d30dd3eb65fc87840202eb0f41619b7 Author: car Date: Tue Jun 8 14:39:54 1999 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit 7af1da817b6becc24652c469f4b786d244d536c1 Author: marc Date: Tue Jun 8 00:57:37 1999 +0000 Hack a little more on the derive_plot_vars junk. Src/C_AMRLib/Amr.cpp commit 7aecfd4739c6baaf1f167ce643cf032d859c45b3 Author: marc Date: Mon Jun 7 20:57:38 1999 +0000 Remove rz assertion Src/LinearSolvers/C_NodalMG/amr_multi.H commit d66e2e3282655675fc9066fefdb211995ba22cba Author: car Date: Sun Jun 6 19:07:42 1999 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 86f95c3bab7ac56d919675f8d84e5205815cddd9 Author: sstanley Date: Fri Jun 4 17:03:52 1999 +0000 Changes to make it work properly in parallel. Tools/C_util/Convergence/DiffSameGrid.cpp commit 6f8a074f32efce5dc68b5170b6c942b9069f0519 Author: sstanley Date: Fri Jun 4 01:03:25 1999 +0000 Modification to make it work on the T3E. Tools/C_util/Convergence/GNUmakefile commit 7f9d3a1644d76ca536c5e34c5fa0b2b78d2450fe Author: sstanley Date: Thu Jun 3 23:38:43 1999 +0000 Converted to allow building in place. Also removed nProc from ParallelDescriptor::StartParallel() call. Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp commit 3438b0e35456a2febd751fb37879bb04207d8740 Author: lijewski Date: Thu Jun 3 22:57:14 1999 +0000 Changed way MPI message tags are calculated. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit d95d67c05aba6fbb7f0f9907666ac2d727817ef4 Author: lijewski Date: Wed Jun 2 20:09:00 1999 +0000 Don't add MPI_HOME/include to INCLUDE_LOCATIONS if MPI_HOME is null Tools/C_mk/Make.mpi commit 5b4f18ba2152ee22b7c9c6f9538e0bb9e625d854 Author: lijewski Date: Wed Jun 2 19:20:53 1999 +0000 Tightened up some assert()s Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 6eef4cf3df0f3df0aeb9f17366f13deab91d5481 Author: sstanley Date: Thu May 27 20:55:59 1999 +0000 Added the bit of logic to allow derive_plot_vars[0]="ALL" force inclusion of all derived fields in the plot files. Src/C_AMRLib/Amr.cpp commit 7cbc22bf3ef19153f2a0cda483347054e2bb1eb4 Author: sstanley Date: Thu May 27 19:15:54 1999 +0000 Added the logic to allow the inclusion of derived quantities in plotfiles. Added a new Array, derive_plot_vars, which controls which derived fields are included in plotfiles. Also made the lists static and added hooks addPlotVar and addDerivePlotVar to allow variables to be added to the lists from within the code. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 48e9c1382d888bdf9a2bc994fe1fb317e5cc5033 Author: marc Date: Wed May 26 19:33:33 1999 +0000 Remove implicit cast to shut up the MSVC compiler Src/C_BaseLib/FArrayBox.cpp commit 9ace929a2871b87a36f1de61dd4fbf3f1b9db71d Author: marc Date: Tue May 25 23:09:02 1999 +0000 Fix include for WIN32 Src/C_BaseLib/CoordSys.cpp commit 4ed2a853ae1e2518906016879949243e072ba7fd Author: lijewski Date: Tue May 25 22:02:20 1999 +0000 small bug fix ... Src/C_BaseLib/FArrayBox.cpp commit 76df1cbc5583b10b5f2a1adce3d32f54f8337b17 Author: car Date: Mon May 24 18:11:44 1999 +0000 Makefile system now MPI aware Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_TensorMG/GNUmakefile Tools/C_mk/Make.defs Tools/C_util/Convergence/GNUmakefile Tools/C_util/ViewMF/GNUmakefile commit 7c71fe7bf417e457b657e250720eb47c9e149fb9 Author: car Date: Mon May 24 17:51:57 1999 +0000 mpi support Tools/C_mk/Make.Linux Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 9ae8b698eb3253ce8d25b286e7a2654928bb6440 Author: lijewski Date: Tue May 11 17:42:59 1999 +0000 Got rid of remove(int) and clear(int) -- they're weren't parallel safe. Src/C_BaseLib/FabArray.H commit 0f58b8f480aace0742b0f7a96a7b17e3d3a9f9f6 Author: car Date: Mon May 10 21:32:52 1999 +0000 tune for absoft, g77 Tools/C_mk/Make.Linux commit 27b513c4aa5703ddd572feb70fca0e988ccd27d2 Author: car Date: Mon May 10 21:26:31 1999 +0000 tune for absoft, g77 Tools/C_mk/Make.Linux commit 6ce554832ccb10a663f14e80e0b5574ed2d05be0 Author: car Date: Mon May 10 21:25:32 1999 +0000 Added LOWERCASE Fortran Types Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 92b32d8ec37983f141c4e9ce1d99d804a010b0a4 Author: lijewski Date: Mon May 10 20:44:50 1999 +0000 DBL_MIN -> -DBL_MAX and likewise for FLT_??? Src/C_BaseLib/MultiFab.cpp commit ce868a5930e2480b690e13a34f5d76fa7d5b99be Author: marc Date: Mon May 10 20:31:14 1999 +0000 Move logical reset inside loop to behave correctly. Src/C_AMRLib/Amr.cpp commit 72f4ff12abb769940f991d0ef47f430de87527d7 Author: car Date: Mon May 10 18:54:07 1999 +0000 BLassert -->> BL_ASSERT. Good luck typing it. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DatasetClient.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/BLassert.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Specialize.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/Mask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tVisMF.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffPlot.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit 3e48456e3452678a0faa598a4389673e95654b1f Author: car Date: Mon May 10 17:18:27 1999 +0000 Replace all asserts with BLassert. Replace all #include Assert.H with #include BLassert.H This avoids incompatiblities on systems which insist on using the system assert in their library header files. Assert.H will be removed soon. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DatasetClient.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/Assert.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Specialize.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/Mask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tVisMF.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tools/C_mk/Make.Linux Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffPlot.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit 06fcc22b6d996c1dfdd3669291f1ac481649db5f Author: marc Date: Fri May 7 20:39:40 1999 +0000 Add manual grid placement function in grid_places routine for hacking with grid distributions during regrid operation. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit c1e4af58b959e032ea46f0890117461b42e3be1b Author: lijewski Date: Fri May 7 15:36:56 1999 +0000 We now output list of unused variables on final destructor call. Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit f36a2575ca18c7a99f800e9f9079775fe0870953 Author: car Date: Thu May 6 16:57:28 1999 +0000 Allows quiet_nans even when running ndebug Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit 4688abe7847ff0f1cea3c650ad3a64ebe9e5b7e4 Author: lijewski Date: Thu May 6 16:31:41 1999 +0000 Hack to work around array bounds error ... Src/LinearSolvers/C_NodalMG/boundary.cpp commit 00b3069252d7ecf7f465d3ccba80beed83f093b4 Author: car Date: Tue May 4 17:59:06 1999 +0000 assertion for intersection of src,dest boxes Src/LinearSolvers/C_NodalMG/boundary.cpp commit 5c5031c41e3865fabf5d9320d1dd40f21a0b8081 Author: car Date: Tue May 4 17:58:59 1999 +0000 ofstream truncate??? Src/LinearSolvers/C_NodalMG/proj.cpp commit cb99647384c552276f8165d38f87758b357bf4f5 Author: lijewski Date: Tue May 4 17:54:22 1999 +0000 periodic in x & z and refWall in y Src/LinearSolvers/C_NodalMG/proj.cpp commit 5d1674c1dd8c85b68e045353b92bf9cfb46f7a7c Author: car Date: Mon May 3 21:32:00 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/tests/gt.jbb.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.jbb.1 commit 3de42cba2ef3b99ecc6bba972518a17d5e3ead74 Author: lijewski Date: Thu Apr 29 20:41:45 1999 +0000 Now properly call constructor and destructor of T. Src/C_BaseLib/BaseFab.H commit ec5844fd3fbcbb3b6c58bdf16a80c20a9bd72d59 Author: car Date: Wed Apr 28 15:41:52 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit ecb8d76db051a27719175d42b4eb75cf85ca693b Author: car Date: Wed Apr 28 00:01:26 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/tests/gt.scott.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.scott.1 commit edaf9633ab645cf1925a4a23e62d9418c9da90f1 Author: lijewski Date: Tue Apr 27 21:38:04 1999 +0000 Removed BoxAssoc ... Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxAssoc.cpp Src/C_BaseLib/Make.package commit 079fdf215fea12bc0a761edab3735ad84502811e Author: lijewski Date: Tue Apr 27 18:24:45 1999 +0000 Made proj_project() a static member function. Added hack to add back in level 0 procmap after regrid at level 0. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 5e8e17ed6b8ae07a56a7f2fce7fd61b0f3ed0a93 Author: lijewski Date: Mon Apr 26 20:09:56 1999 +0000 Removed MaxSizeBox() -- it's now BoxList::maxSize(const IntVect&). Src/C_AMRLib/Amr.cpp commit 43f9d7d00312a8eb90626a8052c250f6bc779e32 Author: lijewski Date: Mon Apr 26 20:09:22 1999 +0000 SpaceDim -> BL_SPACEDIM. Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Orientation.H commit a26186aa33080f94a8899572588a50820fe5de75 Author: lijewski Date: Mon Apr 26 20:09:11 1999 +0000 Added maxSize(const IntVect&); maxSize(int) calls it. Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit ba799c21ab78131594f32d878e3ad3d297a53228 Author: lijewski Date: Fri Apr 23 18:42:26 1999 +0000 Removed the BoxList data member from FillBoxId -- wasn't used. Src/C_BaseLib/FabArray.H commit 2d0b11b58e271eec338d06e6a6194cb6092a4903 Author: lijewski Date: Fri Apr 23 18:06:48 1999 +0000 Set CPP=KCC -E if have KCC Tools/C_mk/Make.IRIX64 commit 74f27e491a5436faa36531b62da286dd4888b1c7 Author: sstanley Date: Fri Apr 23 17:47:07 1999 +0000 Modified so that the fabs in the boundary registers are assigned values of BL_SAFE_BOGUS after they are generated. This is done to be safe since FORT_APPLYBC in the tensor operator uses these values before checking the masks to see if they are needed. So, they are used before being assigned. Src/C_BoundaryLib/BndryRegister.cpp commit bd93103d86fd173e44013497f7cb067b0b9be7b1 Author: marc Date: Thu Apr 22 17:13:19 1999 +0000 YAAF: yet another access function. Src/C_AMRLib/Amr.H commit 0de72076f9137b4ab8fa20a1ead3490a6357f833 Author: sstanley Date: Tue Apr 20 23:54:55 1999 +0000 Fixed a 3-d bug in compFlux. yflux was passed into the fortran instead of zflux. Src/LinearSolvers/C_TensorMG/DivVis.cpp commit 8992df0435df6f1e6178f740087d92b269ba0d7a Author: car Date: Tue Apr 20 01:26:16 1999 +0000 added BLassert.H, will remove Assert.H later Src/C_BaseLib/BLassert.H Src/C_BaseLib/Make.package commit 20325c7d4022e75d9415521624c025f2f21783cc Author: lijewski Date: Mon Apr 19 23:17:03 1999 +0000 Some mods to CollectData() ... Src/C_BaseLib/FabArray.H commit 1d42dbf9d40c7e9625ab95b0e856df7dd2d4648a Author: car Date: Mon Apr 19 00:42:12 1999 +0000 CRAY --> BL_FORT_USE_UPPERCASE, and tweaks Src/C_BaseLib/Make.package commit d9d68e665bd3d0240f5aa499f628321cf39c2da0 Author: lijewski Date: Fri Apr 16 19:19:48 1999 +0000 tune ev5 -> tune host Tools/C_mk/Make.OSF1 commit 4ff1eeda46cf7e7a7dd41f0d991cfd61786c81b4 Author: propp Date: Fri Apr 16 18:17:55 1999 +0000 added -C and -u flags for debugging on mothra. Note that -u only produces a warning for undeclared variables Tools/C_mk/Make.OSF1 commit 85ca26d22f03cc8b57978d88be306e0406a787a5 Author: lijewski Date: Fri Apr 16 17:38:06 1999 +0000 Reverting out random_shuffle() stuff -- not a big win. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.cpp commit b01f8d004df56e50ae1de10ab6cc3c727c16c5e0 Author: lijewski Date: Fri Apr 16 00:19:05 1999 +0000 Didn't get the optimization options quite right. Tools/C_mk/Make.T3E commit 1e025e4371e2be1415b0eafe63fe18c9db351940 Author: lijewski Date: Fri Apr 16 00:09:23 1999 +0000 More CXXOPTF options for backend C compiler with KCC. Tools/C_mk/Make.T3E commit e090803579600f003e2a664fe5d76ef765b86fa2 Author: lijewski Date: Thu Apr 15 23:29:12 1999 +0000 Updated to make random_shuffle() stuff in knapsack work. Src/C_AMRLib/Amr.cpp commit 95d5d81be69a9226bc0276821a05e098543bc47e Author: lijewski Date: Thu Apr 15 23:28:37 1999 +0000 Added random_shuffle() stuff to knapsack. Src/C_BaseLib/DistributionMapping.cpp commit 92b9c89c81985a08a594d5ad7d7d81bc97a2e1ee Author: lijewski Date: Thu Apr 15 23:27:58 1999 +0000 Removed all virtual functions. Inlined some more stuff. Src/C_BaseLib/ArithFab.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H commit 0eafc29bab97f3f11a821ad5da07edf066845be8 Author: sstanley Date: Tue Apr 13 21:37:36 1999 +0000 Modified so that the norm of the residual get calculated over all components instead of just the first one. Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit e484f5347ffff410e070a7d90305ec567c003376 Author: sstanley Date: Tue Apr 13 21:36:11 1999 +0000 Modified CGXDOTY to calculate the multicomponent dot product in 3-d the same as in 2-d. Ie. sum the dot product over components. Src/LinearSolvers/C_CellMG/CG_3D.F commit a05253a16b584b7dbfeb3b140f30b06ce22a71ba Author: lijewski Date: Tue Apr 13 15:28:19 1999 +0000 Removed GNUG hack junk. Src/C_AMRLib/BCRec.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/RealBox.H commit f26b14af0bd577215f0de33be30a6bc8d321f2e1 Author: lijewski Date: Tue Apr 13 00:09:14 1999 +0000 Modest simplification of FabArray -> FabArray copy(). Src/C_BaseLib/FabArray.H commit 7a5280a87f917114b24516e828bbbd47f4e8325e Author: marc Date: Tue Apr 13 00:09:11 1999 +0000 Remove ProxyGeometry class, in favor of "explicit" modifier to Geometry ctr preventing auto-type-conversion Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 38393ab30a7e6c338df611803723c3064317c29b Author: marc Date: Tue Apr 13 00:08:05 1999 +0000 Prohibit auto-type-conversion from box to Geometry, enable removal of ProxyGeometry class. Src/C_BaseLib/Geometry.H commit bf9eaa611971b278b02a2789695b60dbf84ae54a Author: lijewski Date: Mon Apr 12 20:31:47 1999 +0000 Added additional assert() in ::Copy(). Src/C_BaseLib/MultiFab.cpp commit af5ce3607e48fb58cd34024eee18b986bd990786 Author: lijewski Date: Sun Apr 11 23:31:22 1999 +0000 Added truesize data member to make resize() really work as expected. Also inlined some more stuff. Src/C_BaseLib/BaseFab.H commit f1a0a0a6b062d1a9c9239abb3d536f3afbf7cf73 Author: lijewski Date: Sun Apr 11 23:30:47 1999 +0000 Simplified FabArray -> FArrayBox copy(). Src/C_BaseLib/FabArray.H commit 644073afa02f1fec0a16a4057020060b75635c59 Author: lijewski Date: Sun Apr 11 23:30:26 1999 +0000 Inlined some more stuff. Removed unnecessary new of length 1 in default constructor. Src/C_BaseLib/Array.H commit bf699b69c917cf0db71dd286b27736d62c4a17c9 Author: lijewski Date: Sun Apr 11 23:29:58 1999 +0000 Inlined some more stuff. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit db288b8306703d3b3fbc416f634020840f188564 Author: car Date: Thu Apr 8 21:00:56 1999 +0000 rename hgparallel.h --> hgparallel.H Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 527780e8bca5c89ec474605efcf42b018f47fce3 Author: lijewski Date: Thu Apr 8 20:52:11 1999 +0000 Fixed problem with INFINITY macro being redefined on Suns. Src/C_BaseLib/MultiFab.cpp commit 6ca65e786c9c51d6869b6baf2e26502db7e1aff9 Author: lijewski Date: Thu Apr 8 20:22:43 1999 +0000 Also now cache FasSet/MultiFab BoxArray intersection junk. Src/C_BoundaryLib/FabSet.cpp commit eff09b56dbb09fd8b0cd1fc63047a74aefda16a7 Author: marc Date: Thu Apr 8 17:49:12 1999 +0000 Remove unnecessary copy-on-intersect when loading boundary data objects Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp commit 12b413887b84cbe8aa2edf4b0986388425923c93 Author: lijewski Date: Thu Apr 8 17:01:45 1999 +0000 Fixed latent bug in plusFrom() Src/C_BoundaryLib/FabSet.cpp commit 22b36b2aacbf78a9d003aa52c58eea8df3aa2c61 Author: lijewski Date: Wed Apr 7 17:11:45 1999 +0000 Devirtualized task_fab::fab() and inlined it as well. Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 6bb4a4f5cbcecb16923d3fb347220dc9beb60223 Author: lijewski Date: Tue Apr 6 18:15:59 1999 +0000 Some cleanup. Src/C_BaseLib/Array.H commit 1f98466c9ae8ba32b9aff223192e41cd962117c0 Author: lijewski Date: Tue Apr 6 16:53:37 1999 +0000 Added -M 1110 to FC Tools/C_mk/Make.T3E commit 9cb6cd547f00a77279f2b89a8a573f2d66b7b385 Author: lijewski Date: Tue Apr 6 16:41:18 1999 +0000 Ignore additional warning 7212 Tools/C_mk/Make.T3E commit b8f897719a633e2c3d7556901fa245ba1ef7ccb3 Author: car Date: Mon Apr 5 17:39:20 1999 +0000 BL_AIX --> BL_FORT_USE_LOWERCASE, where appropriate. Makefile tweaks in pAmrvis and DataServices. Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_BaseLib/COORDSYS_F.H Src/LinearSolvers/C_NodalMG/GNUmakefile Tools/C_mk/Make.AIX commit 0c8dab8d914958b768c43cb0406cb66be51d9b9a Author: car Date: Mon Apr 5 16:49:25 1999 +0000 fix non-inplace compile Src/LinearSolvers/C_TensorMG/Make.package commit 10e767836e9ad9b154c2589266252229a2117d5e Author: sstanley Date: Fri Apr 2 20:47:23 1999 +0000 Added a -r in one of the $(RM) lines under clean: to allow removing a directory. Thsi didn't work properly on the T3E. Tools/C_mk/Make.rules commit bba81c1978d70368410995e2523548579377389f Author: lijewski Date: Thu Apr 1 23:52:55 1999 +0000 A special FORTPREP for T3E ... Tools/C_mk/Make.T3E commit f0eee2d211fa6c2e95401863b01c2842530489cc Author: lijewski Date: Thu Apr 1 22:31:01 1999 +0000 Fixed bug in FabArray::copy(FabArray). I had a improperly nested parallel loop :-( Src/C_BaseLib/FabArray.H commit 71baf54fef82c8fe1af30e7659f66ea276ec41c5 Author: car Date: Thu Apr 1 21:43:10 1999 +0000 harmless, I think, makefile thrashing Src/C_AMRLib/Make.package Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_TensorMG/Make.package commit a3d7d7de5a31be320086930352b2aa29d206d382 Author: car Date: Thu Apr 1 21:42:49 1999 +0000 FORT_FLUX added Src/LinearSolvers/C_CellMG/LP_F.H commit 501af9c686f2c173567d565b56d48183f57e4597 Author: car Date: Thu Apr 1 16:57:48 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile commit f777586315e842ab6676bb11416fb03a7d72d884 Author: car Date: Wed Mar 31 22:52:27 1999 +0000 Linux updates Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_TensorMG/GNUmakefile commit 0d23d065c1377ed9cdb405834df89151dc2666ae Author: car Date: Wed Mar 31 18:19:37 1999 +0000 linux changes Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_TensorMG/GNUmakefile Tools/C_mk/Make.Linux commit cb2ac2e025bfbf2a52674de8c0c75aa21eba2bbf Author: lijewski Date: Wed Mar 31 18:19:03 1999 +0000 Turn off message warning 1135 Tools/C_mk/Make.T3E commit 0237ef895d3fbe6d4cf55e9e150dd44087aabd3d Author: lijewski Date: Wed Mar 31 17:04:48 1999 +0000 Now also call FabSet::FlushCache() to clear some cached CollectData() stuff. Src/C_AMRLib/Amr.cpp commit 3bc61b18687238f500eaee7fc77beafcb66d4b57 Author: lijewski Date: Wed Mar 31 17:04:17 1999 +0000 FabSets now cache some CollectData() stuff. Now use CommDataCache for the cache in question. Src/C_BaseLib/Geometry.H Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 46d5a48aa7c8fe87f32f9e69046c92748ee1f579 Author: lijewski Date: Wed Mar 31 17:03:47 1999 +0000 Fixed deadlock I introduced in CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit a8ba1bb8882b7ad1dde8f41abc4b327e4382a6c2 Author: car Date: Tue Mar 30 00:54:06 1999 +0000 New defines for linux Src/C_BaseLib/FPC.cpp commit 486c722df8d14eaee3058c16e2dfcb34a9fd78bd Author: car Date: Tue Mar 30 00:49:50 1999 +0000 A first approximation to a Make.Linux Tools/C_mk/Make.Linux commit 6f0568c5d0d85a5588d8a5ff766c8c038346ee5e Author: lijewski Date: Mon Mar 29 23:26:46 1999 +0000 Removed OneFilePerFab option. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 14a505e1260fa1cbdddba0ea343d23ed32dacf0e Author: lijewski Date: Mon Mar 29 22:27:57 1999 +0000 Turn off message 191 when using KCC on T3E. Tools/C_mk/Make.T3E commit a2550c164b7aea90a79f502e6910fb065b4a9e34 Author: lijewski Date: Mon Mar 29 19:27:52 1999 +0000 Yet another bug fix to CollectNumPts(). Src/C_BaseLib/RunStats.cpp commit 60a005eb61e0dfe001a8a3421c6d5de18369eb01 Author: lijewski Date: Sat Mar 27 01:00:58 1999 +0000 Mods to cache some CommData stuff in CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit c7e242c3e2779f604deb117df3504b0f997149f0 Author: lijewski Date: Sat Mar 27 01:00:23 1999 +0000 Added operator<<() for CommData. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 13b3f55ba8259c66f953c9a13b1aa521058c3f97 Author: lijewski Date: Fri Mar 26 19:19:34 1999 +0000 Added operator==() and operator!=() for CommData. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit a4112e7e0d04c5fc21a74e32ca48be20e0f3530f Author: marc Date: Mon Mar 22 21:31:27 1999 +0000 Minor fixups to support ngrow option. Tools/C_util/ViewMF/viewMF.cpp commit 35666fd20c85fee89cdad04d62c3eda4bf45d51a Author: marc Date: Mon Mar 22 21:19:02 1999 +0000 Add a couple options, and make mfab ins manditory Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit 8326bac86e8cf3a0b6d4312d81e7a4f78ae6a7c8 Author: lijewski Date: Mon Mar 22 15:57:48 1999 +0000 Arguments to clear(int,int) in declaration & definition were messed up. Src/C_BaseLib/VisMF.H commit 76b4140025bd786c0fcc806a64d5590d02a60d52 Author: marc Date: Fri Mar 19 23:08:46 1999 +0000 Add support for diffing MultiFabs having different box arrays Tools/C_util/ViewMF/MFNorm.H Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit 79a72542d9d649728af3f25f85cc2e995e8c8a2d Author: lijewski Date: Fri Mar 19 17:57:35 1999 +0000 The per-processor allocation of FABs wasn't being output. Src/C_BaseLib/RunStats.cpp commit e6a44ef88640e5420494c82bdc32a142c5c52094 Author: lijewski Date: Thu Mar 18 22:12:01 1999 +0000 Restored clear(int) and remove(int) for Vince. Src/C_BaseLib/FabArray.H commit 1af6289f6e60adc313578e7877fb883bd6c83a67 Author: lijewski Date: Thu Mar 18 17:05:35 1999 +0000 Added dt_min to checkpoint files, maintaining upward compatibility. Src/C_AMRLib/Amr.cpp commit 59c804e8c811b051c4d5a7c09b115cbf401b0e1f Author: lijewski Date: Thu Mar 18 00:13:01 1999 +0000 Spiffed up message coming from coarsestSmooth(). Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 473f1b528ffb424b358fdfecc0d81d73407043f2 Author: lijewski Date: Wed Mar 17 21:58:46 1999 +0000 Added init() to consolidate copy ctor and assignment operator. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit eef7d07ce1799b88524fc642a1db6958b4e773f6 Author: lijewski Date: Wed Mar 17 21:58:13 1999 +0000 Added init() function to consolidate copy constructor and assignment operator. Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit db41d569bed49454540c21eed51423ca0af235dd Author: lijewski Date: Wed Mar 17 21:57:45 1999 +0000 Removed a couple dangerous member functions: clear(int) removeFab(int) clearUnmanaged() Src/C_BaseLib/FabArray.H commit 3eef76804438f839b148de4dbd20eaff5aed6250 Author: lijewski Date: Wed Mar 17 21:49:13 1999 +0000 Fixed bug in dumpReport() regarding wall clock time. Src/C_BaseLib/RunStats.cpp commit 5d4675d6a3eac1013de15d206b00ec7f8e76845b Author: lijewski Date: Fri Mar 12 21:17:12 1999 +0000 Removed limits on cache size. Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 1e1b3f0e5bbf93e546ca01fe1263399e6d304462 Author: sstanley Date: Fri Mar 12 20:09:07 1999 +0000 The makefiles now point to the versions of these files which are stored elsewhere. DataSetClient is gotten from pAmrvis/. Tools/C_util/ArrayView.H Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffPlot.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/DatasetClient.H Tools/C_util/DatasetClient.cpp commit 13395408a55bff603b19a1d4b580394cefa40f16 Author: sstanley Date: Fri Mar 12 18:55:48 1999 +0000 Modified so that the compile is done against the libraries. Added the seperate routines viewMF.cpp viewMFdiff.cpp which have been extracted from main.cpp and view and diff multifab files. viewMFdiff.cpp has the option for the validbox only or defaults to the fabbox for comparisons. Tools/C_util/ViewMF/GNUmakefile Tools/C_util/ViewMF/MFNorm.H Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/Make.package Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit ff4e5a927a0da1666bb2d119b3abdf8367120ab3 Author: lijewski Date: Fri Mar 12 03:27:07 1999 +0000 Tab cleanup. Src/C_BaseLib/test/tFB.cpp Tests/C_BaseLib/tFB.cpp commit b7627e94ead81e6f642b19fa8c9a1bdf22cbe194 Author: lijewski Date: Fri Mar 12 02:55:43 1999 +0000 Beefed up the test case a bit. Src/C_BaseLib/test/tFB.cpp Tests/C_BaseLib/tFB.cpp commit 55eb0633c192c00c85d38ffd71bf75556b579208 Author: lijewski Date: Fri Mar 12 02:55:26 1999 +0000 Some cleanup and simplification. Src/C_BaseLib/MultiFab.cpp commit 7a0cd5ccb6e28930fc722253a78ee3fe9b83ce15 Author: lijewski Date: Fri Mar 12 01:09:24 1999 +0000 Mod for T3E. Src/C_BaseLib/Utility.cpp commit 37d5a9d4448e9934c5b783f523079451a062817c Author: lijewski Date: Thu Mar 11 17:56:58 1999 +0000 Added Concatenate(). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit c7aa4bbb4e00c0ece0f7ddfa0b56d374e599be19 Author: lijewski Date: Thu Mar 11 17:56:44 1999 +0000 Merged in Utility::Concatenate() and some cleanup. Src/C_AMRLib/Amr.cpp commit 4b02a6f9d071effb0df01ea125737c0e07750028 Author: marc Date: Thu Mar 11 17:48:39 1999 +0000 Make initial dt something so that old and new time are always different Src/C_AMRLib/Amr.cpp commit f2f771be47b5054a21ca8e1398b4eba738f10591 Author: marc Date: Thu Mar 11 17:48:07 1999 +0000 Add def for virtual function used by FillPatch Src/C_AMRLib/AmrLevel.H commit 7e6195bd6f074c3c5f9ce7ebdd9e99826720daad Author: marc Date: Wed Mar 10 16:54:15 1999 +0000 Add a virtual called to intercept FillPatch allowing for application- specific overwrite of FillPatched boundary data. Defaults to no-op. Src/C_AMRLib/AmrLevel.cpp commit c1bbb1c62801664a9cbfd8fb8f8a6fe51f47eecc Author: lijewski Date: Wed Mar 10 16:33:31 1999 +0000 Added flag to ignore double precision constants on T3E. Src/LinearSolvers/C_TensorMG/GNUmakefile commit 0f798fdb80af752ca9d2172cfa41f463d68a9d91 Author: almgren Date: Fri Mar 5 23:18:37 1999 +0000 Add AmrLevel::okToRegrid() flag which asks whether this level should go ahead and allow the regridding tests. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit fafad54941a2e46c52f0834a5e1a49dc1808106b Author: lijewski Date: Thu Mar 4 22:18:37 1999 +0000 Added static void Copy(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit d91015f4c7c8dc327b3e1b2e762b1f1a43e39078 Author: car Date: Thu Feb 25 17:35:35 1999 +0000 re-name again, BOX->Box REAL->Real Src/C_BaseLib/CoordSys.cpp commit f446015dd715356d483da0b6f1e6427c90193ac3 Author: sstanley Date: Wed Feb 24 23:31:20 1999 +0000 Added utilities for convergence studies. Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffPlot.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/GNUmakefile.temp Tools/C_util/Convergence/Make.package Tools/C_util/Convergence/Make.package.SAVE Tools/C_util/Convergence/Make.package.temp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp commit 0ac0c4402a28ba3c912146be02ffa2fa40443873 Author: car Date: Wed Feb 24 18:36:24 1999 +0000 Changed the way holy_grail_amr_multigrid constructor is invoked. Previously, three bool's were used to select either full, cross, or terrain stencils. Now an enum is used: holy_grail_amr_multigrid::stencil, which has three values (terrain, cross, full). There still is no full stencil support. Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 434c219a956bbeed0f5bcd504bbccc2956bff50a Author: lijewski Date: Wed Feb 24 16:50:31 1999 +0000 Simplified the FabSet interface. Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit f92167986ffec3642d2bb6835e3796dc02fa43f8 Author: propp Date: Wed Feb 24 01:56:04 1999 +0000 fixed some 2D to 3D bugs in BndryData added bcComponentsNeeded function to MCLinOp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 6378d7d0bb8fa741b3b0e0fe78d33fbf771b3805 Author: lijewski Date: Wed Feb 24 01:03:47 1999 +0000 Fixed some bugs and added FabSet::copyFrom(FabSet). Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit cb2c2d6b08f61e55a6c76ae20537975f0b3c57a9 Author: sstanley Date: Tue Feb 23 00:34:46 1999 +0000 Changed sign on the fluxes calculated in DV_2D.F and DV_3D2.F to be consistent with this in the scalar viscous terms. Added the new notebook files for mathematica. Should use the new, but I left the old ones for safety sake. Src/LinearSolvers/C_TensorMG/DV_2D.F Src/LinearSolvers/C_TensorMG/DV_2D.mF Src/LinearSolvers/C_TensorMG/DV_3D1.F Src/LinearSolvers/C_TensorMG/DV_3D2.F Src/LinearSolvers/C_TensorMG/DV_3D2.mF Src/LinearSolvers/C_TensorMG/DV_3D3.F Src/LinearSolvers/C_TensorMG/DV_3D4.F Src/LinearSolvers/C_TensorMG/visc2d.nb Src/LinearSolvers/C_TensorMG/visc3d.nb commit df12a443c2db434d76737e4ca26a39574dc96181 Author: lijewski Date: Wed Feb 17 21:44:17 1999 +0000 Added Lp.alternateApplyBC flag. Src/LinearSolvers/C_CellMG/LinOp.cpp commit a2db8d81c8c700326ce149ac39311912f60cd801 Author: lijewski Date: Wed Feb 17 00:10:35 1999 +0000 Explicitly turn off exceptions. Tools/C_mk/Make.T3E commit d521c406843ce5df6278c0fab3499c4936ebe177 Author: lijewski Date: Fri Feb 12 00:07:05 1999 +0000 +K2 -> +K3 when COMP=KCC Tools/C_mk/Make.T3E commit 004e7adf51d487a435f2be8e1d6466701a70058f Author: marc Date: Thu Feb 11 18:07:23 1999 +0000 Modernize driver Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/testVI.cpp commit 740410da8592ee4d90be260d7e56b7c3cde17f3b Author: marc Date: Thu Feb 11 18:06:59 1999 +0000 Remove area multiplies in compFlux fortran. Extensive fluxes obtained by setting transport coefficient to include local areas. Fix up Mma and fortran manually. Src/LinearSolvers/C_TensorMG/DV_2D.F Src/LinearSolvers/C_TensorMG/DV_2D.mF Src/LinearSolvers/C_TensorMG/DV_3D2.F Src/LinearSolvers/C_TensorMG/DV_3D2.mF commit d451a6af58902b0625c5fcb2f98122a8a85ea95c Author: car Date: Thu Feb 11 17:07:01 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile commit 8b995402949699319c803bd159999a73d9c10889 Author: lijewski Date: Wed Feb 10 21:09:44 1999 +0000 Boolean.H has been removed from Parallel BoxLib. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Boolean.H Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CArena.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/Make.package Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.H commit 50e17cf12afb342f9b1423d693a8ab815058787b Author: lijewski Date: Tue Feb 9 21:21:45 1999 +0000 Little cleanup suggested by Bill. Src/C_BaseLib/Boolean.H commit 916f33fb4a8febcc4ad315ad872bb1e812fa2f7b Author: lijewski Date: Mon Feb 8 17:49:37 1999 +0000 From Matt Bettencourt. Tools/C_mk/Make.IRIX64 commit 972434d151f8add9b8fa09a904ccea11c4467a06 Author: lijewski Date: Fri Feb 5 18:56:06 1999 +0000 Some cleanup. Elided some do-while loops in Iterators when !BL_USE_MPI. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit 1a7029a1a742fe884ec675b01886c5041a178b14 Author: lijewski Date: Fri Feb 5 18:54:29 1999 +0000 Forgot to comment out 3rd stuff. Src/LinearSolvers/C_NodalMG/GNUmakefile commit 084636948fc33b0de97b6c16e4fef5c5cd784cd8 Author: car Date: Wed Feb 3 23:31:36 1999 +0000 backed out CONSTANT REAL_T Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 5a8b703e80f9ee18a2ab171e9af9860c7132f117 Author: lijewski Date: Wed Feb 3 22:50:28 1999 +0000 Added -M 1110 to f90 options on T3E to quiet warnings re: double precision. Src/LinearSolvers/C_NodalMG/GNUmakefile commit 0e1f3076f831cdfe887072425b555a9dd932aa2d Author: lijewski Date: Wed Feb 3 21:56:58 1999 +0000 Fixed typo. Src/C_BaseLib/RunStats.cpp commit 7d080100a5c841430f0fb60e3f7501d0e18d9128 Author: lijewski Date: Wed Feb 3 21:55:32 1999 +0000 Made some RunStats objects static. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 30cabfd8aeedfecd59326de6259215e71fd2060b Author: lijewski Date: Wed Feb 3 21:55:15 1999 +0000 *** empty log message *** Src/C_BaseLib/RunStats.cpp commit ce66b928f7f69b3e81630280ac60cff4a743c34d Author: lijewski Date: Wed Feb 3 21:48:51 1999 +0000 Removed RunStats junk. Src/C_BaseLib/CArena.cpp commit 4183be4bfe3836ab27eae062e5d836d1f47bdf50 Author: lijewski Date: Wed Feb 3 19:29:57 1999 +0000 Fixed bug in CollectNumPts(). Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit f24c20db3b263358f997bc84c3e369783dfb16b6 Author: lijewski Date: Wed Feb 3 19:29:26 1999 +0000 Cleaned up checkPoint() a bit. Src/C_AMRLib/Amr.cpp commit e7fcda0c6743e0c09cf85f049cf6c39a87a40be1 Author: lijewski Date: Wed Feb 3 00:39:25 1999 +0000 Needed to include Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/MG_2D.F commit a96b009f12c4cdb1807a3ac25309bd31feeadbb9 Author: lijewski Date: Wed Feb 3 00:16:31 1999 +0000 Replaced some fp constants with macros. Src/C_BaseLib/COORDSYS_2D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/MG_2D.F commit b2464e778ca239dd423cf85d51d77e81ff4b7fa0 Author: lijewski Date: Tue Feb 2 23:36:05 1999 +0000 Removed FORT_SCALADDTO Src/C_AMRLib/FLUXREG_2D.F commit e69122613b0e5c3d73e92e29ddd3f3eaa3b1c634 Author: car Date: Tue Feb 2 23:24:41 1999 +0000 d comment line! Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 581078fe1325a52995f257fcb61d18f0658d30a9 Author: car Date: Tue Feb 2 17:14:57 1999 +0000 no 2d rz Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/interface.H commit fcfa49321742f32c6cbb83989b89b6620e67101e Author: lijewski Date: Tue Feb 2 00:24:03 1999 +0000 Substituted BL_SPACEDIM for some numbers. Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit b2aeb40f498049cef2ed03adb74bef60a45e1b24 Author: car Date: Mon Feb 1 18:17:35 1999 +0000 Make task_proxy a friend of task so that it can access protected members. Is this a bug in MSVC5? Src/LinearSolvers/C_NodalMG/hgparallel.h commit 3e34b3a6d19c2c88db708a9730ff2be6674b860c Author: lijewski Date: Sat Jan 30 17:57:00 1999 +0000 Simplified task_proxy. Cuts way down on heap allocations. Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 7077a495d5a0656a47f492078238513f48879f69 Author: lijewski Date: Fri Jan 29 23:20:25 1999 +0000 Removed CVS ID string. Src/LinearSolvers/C_NodalMG/hgparallel.h commit 026ef02ce4733529e150e4d2f8d41279e38151c5 Author: lijewski Date: Fri Jan 29 23:19:50 1999 +0000 Yet more performance enhancements. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit e0704bcd5874dbbffdf115dbf2fe9950962feaf7 Author: car Date: Fri Jan 29 20:13:52 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 3a34e8c12f28ed0337ebda55d71a2ca2b8b62e4f Author: lijewski Date: Fri Jan 29 19:23:57 1999 +0000 Some cleanup and copyright macro insertion. Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit ab39e610317b72b9aeed83a052f63a6535ccbd9a Author: car Date: Fri Jan 29 19:09:56 1999 +0000 minor changes to quit warnings Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit ef0b6774b63733dd06b1c671352b4f8e7bef506e Author: car Date: Fri Jan 29 18:33:46 1999 +0000 fixes for 2D Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit a9da2412907cfe24ee7096ba7bc52ab54377d3d1 Author: car Date: Fri Jan 29 17:50:10 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit d1f37dda3bd7e88d0240036ad3370052bc2908be Author: car Date: Fri Jan 29 00:20:27 1999 +0000 more 2d Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 2a869db5b8fc7ac629a0a32384e93f0a6f6979b9 Author: car Date: Thu Jan 28 23:36:13 1999 +0000 changes for 2D Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a92eb85e02f1bbcdcff293accb3baf7d27023264 Author: lijewski Date: Thu Jan 28 21:00:49 1999 +0000 More performance enhancements. Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 35b6114e0e7403d287c7641a5e751f051ab683f3 Author: lijewski Date: Thu Jan 28 18:50:38 1999 +0000 More performance enhancements. Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 0a80acacd0b15a09ddf5ad15f74b256aedba1bcc Author: lijewski Date: Thu Jan 28 16:58:28 1999 +0000 More performance enhancements. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a2caca1104c77e584d63468711ebd9912e6317bb Author: lijewski Date: Wed Jan 27 17:35:51 1999 +0000 Some performance enhancements. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit cac50d225dab90e11a84b083d0456d0041167bc9 Author: marc Date: Fri Jan 22 21:34:16 1999 +0000 Prettier still... Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 59fd9eb94d1b91b4ce4d0e6fe6441a2fa57f856f Author: marc Date: Fri Jan 22 21:24:41 1999 +0000 Make verbose out a little prettier...nothing significant here... Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 45c8fb4e8cc354d58bf6982eaaeddfb6cfe03b2f Author: vince Date: Fri Jan 22 21:05:07 1999 +0000 Deleted an assertion in copy(...). It was causing problems in parallel. The assertion is checked later, so it was also redundant. Src/C_BaseLib/FabArray.H commit 6d03c1acf63a73e56524fab60d93185c500960f1 Author: lijewski Date: Thu Jan 21 22:03:14 1999 +0000 FillCoarsePatch() was still doing some ghost cells when didn't need to. Src/C_AMRLib/AmrLevel.cpp commit 84dbec77527199db3971e8714c4314a6444ffc0a Author: lijewski Date: Thu Jan 21 20:27:05 1999 +0000 Fixed bug in and added argument to FillCoarsePatch(). Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 2a92076e5afd769f02171c3cb1bdcdb574108cc9 Author: lijewski Date: Wed Jan 20 19:24:00 1999 +0000 Must do physical bndry conditions after periodic junk in isValid(). Src/C_AMRLib/AmrLevel.cpp commit 9785d598ea532c6d58092d9d46d177865213ab33 Author: lijewski Date: Wed Jan 20 04:41:36 1999 +0000 Fixed bug in FillPeriodicBoundary(). Src/C_BaseLib/Geometry.cpp commit cee40cba249c2a71d5b2d9c324c1deb5b03b9cd2 Author: lijewski Date: Fri Jan 15 21:44:22 1999 +0000 Dealt with periodic nodal quantities in FillPatchIterator::Initialize(). Src/C_AMRLib/AmrLevel.cpp commit 3a48c6de77ca4de91d3f68dbc589ea1d18000105 Author: car Date: Thu Jan 14 22:48:47 1999 +0000 Really old comments Src/LinearSolvers/C_NodalMG/README Src/LinearSolvers/C_NodalMG/Rewrite commit 61e5972d15c270b70b80db0b7a86b455265b1a28 Author: lijewski Date: Wed Jan 13 04:14:19 1999 +0000 Removed the hash junk. Simplified things a bit. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 1d7f977d956650b1192452425f3b8e28a4850055 Author: lijewski Date: Tue Jan 12 19:00:18 1999 +0000 Added carena RunStats for CArena::alloc() and CArena::free() Src/C_BaseLib/CArena.cpp commit 83a84b6a60d7371aeda7dde9dc76d44f8062e391 Author: lijewski Date: Tue Jan 12 17:56:46 1999 +0000 Added RunStats for regrid. Src/C_AMRLib/Amr.cpp commit c9d4d68c2f7951b81a92c99845cf5d20d530944c Author: lijewski Date: Wed Jan 6 21:27:58 1999 +0000 Changing how the DatasetClient stuff is wired into the code. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/DatasetClient.H Src/C_AMRLib/GNUmakefile Src/C_AMRLib/Make.package commit dee30e43182f75f22bd93d45a9821c06133ebf28 Author: lijewski Date: Wed Jan 6 20:06:56 1999 +0000 Some cleanup. Always compile in TagBox stuff. Src/C_AMRLib/DatasetClient.cpp commit 4b9c0fc420af4ba0e7079cd023b2b7eca6956226 Author: marc Date: Wed Jan 6 00:32:37 1999 +0000 Update makefile stuff, and member args for IBD, also make test runnable in 2D. Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/Make.package Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.H Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Src/LinearSolvers/C_TensorMG/Test/main_3D.F Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/main_3D.F Tests/LinearSolvers/C_TensorMG/testVI.cpp commit 3009caf1c31ab3ca3ca8dbb902f5ee85611f9ca2 Author: marc Date: Wed Jan 6 00:31:42 1999 +0000 Make this stuff look more like the mglib stuff...nothing really new here... Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp commit 210192197f86ca539cc55852dfb600344e7b5727 Author: marc Date: Wed Jan 6 00:30:52 1999 +0000 Fix bug to shift back mask box after periodic crud. Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 93e3b4cd20a53d18952a1f25375bb2312d4bdae8 Author: lijewski Date: Wed Jan 6 00:15:06 1999 +0000 Had to move header file so FArrayBox was properly declared. Src/C_AMRLib/DatasetClient.cpp commit 78c05aeae0471fa192049ada450d1aa3ba1a9e32 Author: lijewski Date: Mon Jan 4 21:31:48 1999 +0000 Just some cleanup -- must have been bored over holidays. Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 632b34039889991598c67c19922335bb7589c443 Author: marc Date: Mon Jan 4 19:01:07 1999 +0000 Add include for constants. Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F commit 3accef59ea611754a4f2c3944788f9a85df0c185 Author: marc Date: Mon Jan 4 18:28:45 1999 +0000 Add code for pure fort files (.f) Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit c19c8d16294636e90b4175cd0d3a867eff895f30 Author: marc Date: Mon Jan 4 18:27:14 1999 +0000 Add target Src/C_AMRLib/GNUmakefile commit 0b1dc3e9377b540866f192310e9684190c03df6a Author: marc Date: Mon Jan 4 18:26:32 1999 +0000 Add arg for lib make Src/LinearSolvers/C_TensorMG/GNUmakefile commit 7e79e820de634cb70a3c87af4a54012e2d43cba6 Author: marc Date: Mon Jan 4 18:12:08 1999 +0000 Make it better Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 3124202b504746b1d3dc84a45caa76b757627386 Author: marc Date: Mon Jan 4 18:11:45 1999 +0000 Add code for flux compute member, similar to that in tensor stuff. Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H commit 6f469852056b84fd9f044ba86b9f84cf45c459fe Author: marc Date: Mon Jan 4 18:11:14 1999 +0000 Add multicomponent stuff. Make first stab at output function for ||. Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp commit ff8114f5d4e1351e643b128e538996b2dfe7bd55 Author: marc Date: Mon Jan 4 18:10:22 1999 +0000 Increase verbose output, for mg add code for mg.v>2 to dump mg levels Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 0b9d62de22573c6c97fe08f3b4d82344bdba5c9c Author: marc Date: Mon Jan 4 18:09:36 1999 +0000 Add multi-component stuff. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 51808d173ea770febf25e584e26a57a2e984f6ea Author: marc Date: Mon Jan 4 18:09:00 1999 +0000 Add flux compute member function, similar to that in the tensor stuff. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H commit d971f96dba5c8dea3272b83481440602f315bf42 Author: lijewski Date: Fri Dec 25 18:58:09 1998 +0000 Minimized more heap allocations in FillPatchIterator. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit eb5c068ea916fdf4859d6e37359b5f9702fd9e09 Author: lijewski Date: Wed Dec 23 23:14:07 1998 +0000 FillPatch now does periodic correctly. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 11815f426348a68ca4aba76a48ae586d73ab30f4 Author: almgren Date: Tue Dec 22 22:42:56 1998 +0000 OOPS - pc_domain was a coarsened domain, what I really wanted was geom[levf].Domain() Src/C_AMRLib/Amr.cpp commit a8e9818bf2cbc5091a217dcc924310c1c1f4580f Author: lijewski Date: Fri Dec 18 16:47:52 1998 +0000 Added catenate(). Src/C_BaseLib/BoxList.H commit 0f64e6b7d2ad491a54bb4e3b729b29be1d422e07 Author: wyc Date: Fri Dec 18 00:40:41 1998 +0000 Its miraculous that this bug never was noticed before. ncx and ncy were declared as logicals, despinte being used as integers...... Src/C_AMRLib/INTERP_2D.F commit a1127c24bf3824da5fdef07b4fc3c2be9f7ad184 Author: lijewski Date: Wed Dec 16 22:27:39 1998 +0000 Fixed memory leak. Src/LinearSolvers/C_NodalMG/hgparallel.h commit ee7bcfadef03ca09aa5d9b16853fd4b9cf3e144e Author: car Date: Wed Dec 16 20:51:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/machinefile.mpi commit 2369ae8e9ab66d2127cd12b8521ee0c8ee0ed3c3 Author: car Date: Wed Dec 16 18:54:14 1998 +0000 a new bad grid set Src/LinearSolvers/C_NodalMG/tests/gt.inputs.3d.spin.grids Tests/LinearSolvers/C_NodalMG/test_grids/gt.inputs.3d.spin.grids commit 8f7ea7db942e0f155fe0630b3a54b959b15f9022 Author: car Date: Wed Dec 16 18:42:53 1998 +0000 test infrastructure Src/LinearSolvers/C_NodalMG/inputs Src/LinearSolvers/C_NodalMG/proj.cpp commit 38977095bcbf3493bd3e08cca116bd023f4ca16a Author: car Date: Wed Dec 16 17:51:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit e0374a8b0987208f6b700d92d9c76daf801374fd Author: car Date: Wed Dec 16 17:33:42 1998 +0000 fix for task_copy::depends_on_q Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 148facd45956bd4a9d276205fcc9615659b48737 Author: car Date: Tue Dec 15 23:34:56 1998 +0000 more checking options Src/LinearSolvers/C_NodalMG/proj.cpp commit f19d728a18bc0191735cca9b2cd006e16e18f2f2 Author: lijewski Date: Tue Dec 15 18:51:27 1998 +0000 Attempt to speed up processing of local tasks. Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit cb3f1798954309c57ff840c122f19f559f560692 Author: lijewski Date: Tue Dec 15 18:13:24 1998 +0000 Had a bug in task_list::execute(). Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit d023deac1615242ad57b9fff9512bf15cb55ff43 Author: lijewski Date: Tue Dec 15 17:32:32 1998 +0000 Prepended cout's with "HG:" Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit ae2a4ce955a74c654d28c8daca0da9759286ca0e Author: lijewski Date: Tue Dec 15 17:22:47 1998 +0000 An improvement to task_list::execute() loop. Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 744046ce9bea4b970cb20ade2fe664bcd466c1f0 Author: car Date: Tue Dec 15 17:01:30 1998 +0000 better execute loop Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit d6677935513e9fb9861560a47a1e49337cbd485c Author: car Date: Tue Dec 15 04:01:33 1998 +0000 Fix for explosion in number of tasks. The ParmParse parameter HG.max_live_tasks, limits the number of tasks that can be pending in a task loop. The default limit is 50. Since tasks always are issued in pairs, and the tasks are asynchronous sends/recvs this should not deadlock. The fortran change is to get the line length of a few lines back down to 72 or smaller. Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit ecd84eaa4e55399ea9e27e8da060f753a6b1c06d Author: lijewski Date: Mon Dec 14 22:43:11 1998 +0000 Integrated in and . Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 5b3bfbaecdc99519d3ada4774259f6137c6ecc6e Author: lijewski Date: Mon Dec 14 20:23:47 1998 +0000 Got rid of hard-wired double-precision constants to snuff T3E warnings. Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit 6c8428f5dc823729c0e5af725a45faa9209b7759 Author: car Date: Sun Dec 13 01:21:38 1998 +0000 sleep flag Src/LinearSolvers/C_NodalMG/proj.cpp commit f8f6cea88b05c878f66c2fc7222f867e69286560 Author: car Date: Fri Dec 11 21:55:40 1998 +0000 T3E KCC change Src/C_BaseLib/Utility.cpp Tools/C_mk/Make.T3E commit 3109fab39676b61e5b5414fc24e10c2191d5e602 Author: car Date: Fri Dec 11 21:54:25 1998 +0000 T3E change in prototype for _rtc Src/C_BaseLib/Utility.cpp commit 29f9715bf6c03c85dac0787a18c3c66f8d95f99a Author: car Date: Fri Dec 11 19:21:26 1998 +0000 fix for rwtime == 0 Src/C_BaseLib/RunStats.cpp commit b5e7339e44a2faec21b4d16157ad3b3e9cc0143c Author: car Date: Fri Dec 11 18:55:32 1998 +0000 added inputs file Src/LinearSolvers/C_NodalMG/inputs commit 6bb89d44eed4c0d43628ca7cc3db5f33a5818b9f Author: car Date: Fri Dec 11 18:54:57 1998 +0000 Additional ParmParse support Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 46097abc203e14b37a09c2452adeaf402c109830 Author: car Date: Fri Dec 11 18:37:46 1998 +0000 ParmParse and RunStats support Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 15ebcf27453a9b081bfef9d9a939bab13302d330 Author: lijewski Date: Fri Dec 11 02:47:14 1998 +0000 Removed IncrementPeriodicBoundary(). Shouldn't have been checked in. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 48f54f611d3323d3d25750a1a42ff0f939d9de4d Author: lijewski Date: Fri Dec 11 02:46:18 1998 +0000 Removed the FillFabPlus() stuff. Shouldn't have been checked in. Src/C_BaseLib/FabArray.H commit 47ce67b42ed048df638d432bd02abed4f735c0d8 Author: car Date: Fri Dec 11 00:26:57 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit e21b11c90090a3d7f68cab7d3eca485c2b1d2752 Author: car Date: Fri Dec 11 00:01:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit c60621052e25c6eacfae586ca486ebf9e3ebe977 Author: lijewski Date: Thu Dec 10 23:34:58 1998 +0000 Added FillFabPlus(). Src/C_BaseLib/FabArray.H commit 215baf4dc64fc2bc361dee28c56d2b56f92d9cf0 Author: lijewski Date: Thu Dec 10 23:31:58 1998 +0000 The node centered stuff in buildPIRMMap() wasn't quite right. Src/C_BaseLib/Geometry.cpp commit ebd146f918f3c74e8f69bcd9bda9a06165e2904d Author: lijewski Date: Thu Dec 10 23:24:14 1998 +0000 Fixed a bad assert(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 9c0e817e6768625b40921d75c5678cbdb079330c Author: car Date: Thu Dec 10 23:16:01 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 3a49a6d1cb4d31d2b4cc8f7f2ddf3b8f69d7b7d9 Author: car Date: Thu Dec 10 23:10:41 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit ca151403edcbf85ebd9a5819044a3538d0c7a44d Author: car Date: Thu Dec 10 22:54:32 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 675ccfe039f99027a441c91634fc8c8813332193 Author: lijewski Date: Thu Dec 10 22:16:07 1998 +0000 Changes to buildPIRMMap() for nodal MultiFabs. Src/C_BaseLib/Geometry.cpp commit 652b41bb651c16999887ccde22b1019d14908149 Author: car Date: Thu Dec 10 20:57:39 1998 +0000 non MPI projection Src/C_BaseLib/FabArray.H Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 214bfa9b2e236bd28e526296d790f5aa9a0f5650 Author: car Date: Thu Dec 10 18:41:21 1998 +0000 remove extraneous dependency check Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 407893736ef7357fbde6bf31f77b965c7efb0008 Author: car Date: Thu Dec 10 01:02:38 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 7352e2b085b96080eb3566d61491ab4af7c9fb9b Author: car Date: Thu Dec 10 01:00:32 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 554ee2c892142019edc04ea8b7bed5d769a1e403 Author: car Date: Wed Dec 9 23:13:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/tests/gt.bill1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.bill1 commit 8b846f69fed2fe768c36c5e74ea6b15a91711e68 Author: wyc Date: Wed Dec 9 21:56:28 1998 +0000 Mike put some T3E defines where he meant BL_T3E. Src/C_BaseLib/Utility.cpp commit f0d8674cda46bf500da12b0d729aee74acbc3b1a Author: lijewski Date: Wed Dec 9 20:21:30 1998 +0000 In buildPIRMap(), restrict src box to be in Domain(). Src/C_BaseLib/Geometry.cpp commit da3594b74983b20a53d198f42be874b5b295d47d Author: wyc Date: Tue Dec 8 18:25:44 1998 +0000 These changes allow CGSolver to recognise a loss-of-accuracy event and deal with it gracefully. By default, CGSolver will act in the old-die- horribly mode. However, you can activate expert mode which will allow CGSolver::solve() to return an integer indicating status. MultiGrid.cpp has been modified to use expert mode. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 7216b4df5520a35c561099894c97570551ad082d Author: lijewski Date: Tue Dec 8 18:13:20 1998 +0000 A fix to task_copy::depends_on_q(). Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit f2fcfa6cc98531f791cc723bf1f0c3877d8c91d1 Author: lijewski Date: Mon Dec 7 18:39:21 1998 +0000 Mods to compile on T3E. Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 35cb695ef97068a27cf267a1d56cae27a51a7e55 Author: almgren Date: Sat Dec 5 00:39:44 1998 +0000 This contains the fix to the previous regridding "fix" submitted by Almgren - the grow by n_proper had been neglected in the earlier "fix". Src/C_AMRLib/Amr.cpp commit 2985ee7acfc29fb11156ebe90cb3d81f3ad4617c Author: car Date: Fri Dec 4 21:32:48 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit a66bade541a23229cd6672d50b4a4eb115e71b33 Author: car Date: Fri Dec 4 21:19:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 3f1a7b913d48aa8fad04231e2810c7305bd8c48e Author: lijewski Date: Fri Dec 4 17:33:24 1998 +0000 time -> time+dt_level[level] in station.report() call. Src/C_AMRLib/Amr.cpp commit ed8122d464be1cd3046e221e0eb14be57de1b4be Author: lijewski Date: Wed Dec 2 18:36:45 1998 +0000 Removed bad assert(). Src/C_AMRLib/AmrLevel.cpp commit 800a79387b3a165f3733428d25df7797b9689805 Author: lijewski Date: Wed Dec 2 17:52:55 1998 +0000 Fixed another periodic bug in FillPatchIterator. Src/C_AMRLib/AmrLevel.cpp commit 0c30d99f7178b829644533f22c92e4922ac4307f Author: car Date: Wed Dec 2 05:58:57 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile commit fda145647f8512827b3ca35ddd2769db43554978 Author: lijewski Date: Wed Dec 2 00:04:37 1998 +0000 Added poe junk ... Src/C_AMRLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_TensorMG/GNUmakefile commit 14761830d8f30b27a1ec9e48f44e750902942f1f Author: lijewski Date: Wed Dec 2 00:04:06 1998 +0000 A tad cleanup. Src/C_BaseLib/GNUmakefile commit 5320f6f09e6982e578c68a0719326b2a79c35781 Author: lijewski Date: Tue Dec 1 21:56:39 1998 +0000 Reverted out the cache stuff. Not a significant win. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit bc0ef05de8d897c7232fe03713a8431e8de5a863 Author: lijewski Date: Tue Dec 1 21:56:23 1998 +0000 Reverted out the cache junk. Not a significant win. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 137ed14f2e1b3e1bd74d5632bcd8a9eb2fbe5994 Author: lijewski Date: Mon Nov 30 21:30:09 1998 +0000 Added more assert()s in operator() per Dan Graves. Src/C_BaseLib/BaseFab.H commit 47ea150f8e0047f322cd076726ce0ca1d5cbe90c Author: lijewski Date: Mon Nov 30 21:13:38 1998 +0000 Mod to get to run on T3E. Src/C_AMRLib/StationData.cpp commit f58051a1e30a381daea397a126db4c588d289442 Author: lijewski Date: Mon Nov 30 18:52:05 1998 +0000 Now use getType() of StateDescriptor to get appropriate IntVect into FAB. Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit 5d5c7d4af158fdcc9341aac1b35ff52a012506c1 Author: lijewski Date: Mon Nov 30 02:12:35 1998 +0000 Some cleanup. Almost done ... Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit 77bd244bfd391b5f26b97992f4c31f3ebeb737fe Author: lijewski Date: Sun Nov 29 01:33:53 1998 +0000 Now support putting station files in sub-directory. Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit 0e9f7b3e4dbd87c3c42df89a9ab6edd76a5368db Author: lijewski Date: Sun Nov 29 00:22:36 1998 +0000 Merged in DataStation junk. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Make.package commit f6446d518e1e87b372c5520b37a8ee81bdba3cfa Author: lijewski Date: Sun Nov 29 00:22:09 1998 +0000 Added some const versions of member functions. Src/C_AMRLib/AmrLevel.H commit 673ea017871e511dbcdd28307588d3f6c23e3b8a Author: lijewski Date: Sun Nov 29 00:21:41 1998 +0000 Looking pretty good ... Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit 2371e215d251dba7897c75e6f1eb444ad67fb0c8 Author: lijewski Date: Sat Nov 28 21:58:43 1998 +0000 More work bring up-to-date with amrlib structures. Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit 634fe9676c4914fa27ee6554462e863f39d8be64 Author: car Date: Thu Nov 26 20:30:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 9a419ce039efb70c68434c1943323567e470901d Author: lijewski Date: Wed Nov 25 23:58:22 1998 +0000 Progress moving from AmrSS to current amrlib ... Still a work in progress though. Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit ed97a42f642a776dbf8939ae7113de23c20e0875 Author: car Date: Wed Nov 25 23:52:34 1998 +0000 Fixes for HGPROJ MultiLevel Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 81a960034e4d89d556bdcbbe970f09a050df91b3 Author: lijewski Date: Wed Nov 25 19:14:16 1998 +0000 From very old amrSS code ... Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit 04484597bc05be0afca914a597249313b3895d74 Author: wyc Date: Tue Nov 24 23:17:52 1998 +0000 added chuck's patch for a problem which was causeing hg not to converge Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit cc9f455bb7d273aec9e60c54c98b320333764f55 Author: lijewski Date: Tue Nov 24 19:22:57 1998 +0000 Now caching Snds stuff for CollectData(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit d72f57972860fc2b47ea757a0bca1d98ab31a52d Author: lijewski Date: Tue Nov 24 19:22:38 1998 +0000 Now cacheing Snds stuff in CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit f149eb1ca35cd9b2e45895e12757917e9bf6c1e0 Author: lijewski Date: Tue Nov 24 01:01:14 1998 +0000 Merged in new Reduce() functions. Src/C_AMRLib/Amr.cpp commit a476cee54cbd94a01b2eb5943e7c9a0027e924b5 Author: lijewski Date: Tue Nov 24 01:00:54 1998 +0000 Merged in new Reduce() functions taking cpu to reduce to. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RunStats.cpp commit 69f93808df85ca2aa3fd25910920ba8862346360 Author: lijewski Date: Mon Nov 23 22:39:26 1998 +0000 Added const versions of newData() and oldData(). Src/C_AMRLib/StateData.H commit 4f7c5424927c98a5427ebcb4bdad90621c322db6 Author: lijewski Date: Mon Nov 23 18:27:01 1998 +0000 Removed canned procedure. Was proving too much trouble. Tools/C_mk/Make.rules commit d4402fb05b72889d6731a7a0e156bf95f72c14d8 Author: lijewski Date: Mon Nov 23 17:56:42 1998 +0000 Fix for busted gmake on T3E. Tools/C_mk/Make.rules commit 9cea9858941b4d255513367be9285c2c98c6ce18 Author: car Date: Mon Nov 23 17:31:36 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp commit 5d99e5686c60b6c33caf66d448b13b2dd724d56a Author: car Date: Mon Nov 23 00:50:23 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp commit 1840e58b09c5cbb451aca513b513cd5811532c7e Author: lijewski Date: Sun Nov 22 17:42:54 1998 +0000 Wrapped the closelib junk into a canned procedure. Tools/C_mk/Make.rules commit aca54123ad14184bfa4e8b00abd9bb3b9f78081e Author: lijewski Date: Sat Nov 21 19:34:19 1998 +0000 Added ti_files directory for cleaning. Tools/C_mk/Make.rules commit 1b879d1d798aaac8c6b2fe96ebbd87623e06d0a4 Author: lijewski Date: Sat Nov 21 19:02:54 1998 +0000 Reverting out the simplification of *OUTPUT_OPTION junk. Tools/C_mk/Make.AIX Tools/C_mk/Make.CRAY Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit fe7a068e01c43b878aaf5d0a1bd5318c4568a3b7 Author: lijewski Date: Sat Nov 21 03:12:10 1998 +0000 Some simplification. Tools/C_mk/Make.AIX Tools/C_mk/Make.CRAY Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 9c36ad7bc13a49d4da47aa2733cc65d899259cef Author: lijewski Date: Sat Nov 21 02:49:39 1998 +0000 Simplified the library closure junk. Tools/C_mk/Make.rules commit 12e47901f995acdd3db39b60d6242e7d8f82ccd4 Author: lijewski Date: Sat Nov 21 00:27:43 1998 +0000 Yet more OUTPUT_OPTION mods. Tools/C_mk/Make.defs commit 3dede12c2847f54fcf111203975d77b2c81abdd1 Author: lijewski Date: Sat Nov 21 00:24:14 1998 +0000 Bug fix to form of *LIB_OUTPUT_OPTION. Tools/C_mk/Make.defs commit f7712f479806974297203ca0400135a5f908b8de Author: lijewski Date: Sat Nov 21 00:15:40 1998 +0000 Now have four *_OUTPUT_OPTION variables. Tools/C_mk/Make.AIX Tools/C_mk/Make.CRAY Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit ba1426892584a371d5297fbd0990f37a4ab2c3d7 Author: lijewski Date: Fri Nov 20 23:18:02 1998 +0000 Some fixes relating to OUTPUT_OPTION & FORT_OUTPUT_OPTION Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit dd7980708b23b2150a417a37ecd5a7fae9017d70 Author: lijewski Date: Fri Nov 20 21:58:24 1998 +0000 Added real time clock routines for second() & wsecond() on T3E. Src/C_BaseLib/Utility.cpp commit b3e9db76635425680ba004baca4f4f37d7c7c5bf Author: car Date: Fri Nov 20 21:42:41 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit ce086bafcc58dffc33d833e626e8dbe1d29971e6 Author: lijewski Date: Fri Nov 20 21:23:36 1998 +0000 ld -> d on an sprintf() call Src/C_BaseLib/VisMF.cpp commit 8fdc243e6b20d4ebbe7812511e319ff5c34828b8 Author: car Date: Fri Nov 20 20:34:10 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 2545e19028236c2c51c8eb4f3256eb9cc1463dd3 Author: car Date: Fri Nov 20 20:29:45 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 7209bceffdc49e305c0d9da531f42cad5b7c9784 Author: car Date: Fri Nov 20 19:09:48 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 9e11b0e72c623ab58b57496e69a12022589a210c Author: car Date: Fri Nov 20 05:01:10 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 686c3f8e9edb61de99c8a9447056039557dcc381 Author: car Date: Fri Nov 20 00:01:03 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 92718d63278d50dfa6760967849828a3430cf953 Author: car Date: Thu Nov 19 22:32:45 1998 +0000 fixed task_fecdiv_2 Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit cb308943e034691d9f2a775ac1b8d52bb9782d30 Author: car Date: Thu Nov 19 22:10:17 1998 +0000 parallel hgproj changes Src/C_BaseLib/FabArray.H Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 95aeaeb56a5fb5b46b4356f0d4308050983d5724 Author: car Date: Thu Nov 19 18:09:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/bl_abort.cpp Src/LinearSolvers/C_NodalMG/matherr.f90 commit d48cbe6634be9b4737c7c814c0953c36787cf4e0 Author: car Date: Thu Nov 19 16:48:23 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/bl_abort.cpp Src/LinearSolvers/C_NodalMG/matherr.f90 commit 9a8face422e16d09d69b0ac5e3b51dfd584efd53 Author: car Date: Thu Nov 19 02:20:46 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp commit fd7cbf1a209f47fb25310224b7fca717b92811d2 Author: car Date: Wed Nov 18 23:01:23 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit d9c4419aced54b1831f2b75ad5ccf129b9b4cec4 Author: car Date: Wed Nov 18 21:46:44 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 9eac975ce10ce3718b270bb2254081aeb88dc5e5 Author: car Date: Wed Nov 18 21:08:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit cd64c24f0d0be4d676b065175e3c2ff12caa9ca5 Author: lijewski Date: Wed Nov 18 20:47:05 1998 +0000 Updated to reflect new Make.defs. Src/LinearSolvers/C_NodalMG/GNUmakefile commit d95ac2f79d755983112bd80a08de6017bed9e596 Author: car Date: Wed Nov 18 20:40:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 190eea1c4b35224f8fe32d720486bf2f76a31393 Author: lijewski Date: Wed Nov 18 20:34:50 1998 +0000 Updated to reflect MPI in machineSuffix. Src/LinearSolvers/C_TensorMG/GNUmakefile commit f7f0d21379d1bc88363e829e337f2a9931262040 Author: lijewski Date: Wed Nov 18 20:33:02 1998 +0000 Updated to reflect MPI in library names. Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BaseLib/test/GNUmakefile.test Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Tests/C_BaseLib/GNUmakefile.test commit 4d9159f93dd4827fd15684d6d2345ad75a3702fa Author: lijewski Date: Wed Nov 18 20:32:40 1998 +0000 Now distinguish between libraries built w/ or w/o MPI. Tools/C_mk/Make.defs commit c7277c2565e9b0de682c6552d21977d16160e10d Author: lijewski Date: Wed Nov 18 20:31:56 1998 +0000 Removed the unneeded first argument to StartParallel(). Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c51ed2d4d40f30cddadf81baa60c3a8d4648641b Author: car Date: Wed Nov 18 19:19:30 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit b538c4a016b3e3c7cbda18d7c1ab85548c5a38d6 Author: car Date: Wed Nov 18 17:59:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 6f8879cfa745425a3e1465e329771304e6edabba Author: car Date: Wed Nov 18 17:57:45 1998 +0000 fixed up for LIB AND EXE support in same directories and Makefiles. Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 4e2f9a9cd9ee5088d9ca8cd8132e0292dca8ada2 Author: car Date: Wed Nov 18 01:30:51 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit 28c0e238bf1d8e8f7d5b08ab6b6318b79f25edad Author: car Date: Wed Nov 18 01:00:24 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit e8a8f5ee7c9e581e36c4062273bd982c4656ed32 Author: car Date: Tue Nov 17 20:07:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/restrictor.H commit 0549ef2184c451d68d1b2fa9bb0943dfbcc7dcb3 Author: lijewski Date: Tue Nov 17 19:15:39 1998 +0000 Small touchup. Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 9801a3865fe1c57711956c09f0c7cd74bc2b605f Author: lijewski Date: Tue Nov 17 19:11:09 1998 +0000 Brought up-to-date with latest Parallel stuff. Src/LinearSolvers/C_TensorMG/GNUmakefile Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLO_F.H Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/Make.package commit a987979f41f7028cd36fb80df6a7eb62981a90db Author: car Date: Tue Nov 17 18:00:49 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 6e3d5c2a02dafeee26340965f09d1ded86116700 Author: car Date: Tue Nov 17 17:48:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit bda064809210ef07a0912ab8226e6dca7b4a94cc Author: car Date: Tue Nov 17 00:51:16 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 6bcee24182428f7e127da031576a7da3ac4c7f53 Author: car Date: Tue Nov 17 00:48:50 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 5d1e371d034bb857802962d6801f92a4b894f4c9 Author: car Date: Tue Nov 17 00:38:05 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 7a25a20a4a2c96cd655ecf6c3cabdb6a2c844c45 Author: car Date: Tue Nov 17 00:18:14 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit e866f5934bed57dbb8b033ae0c164737af13ac43 Author: car Date: Mon Nov 16 23:52:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit bc78f849927692fdcfa34badb33148277b4781b5 Author: car Date: Mon Nov 16 22:54:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit dd8e601e6a394fdd46aefc16f67bdd22d207046b Author: car Date: Mon Nov 16 21:57:23 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 8660b414355ca4267539462760ce432abfef51b2 Author: car Date: Mon Nov 16 21:44:10 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 150f8d9ab68d126728e837c3d711fab0fbb96acf Author: car Date: Mon Nov 16 18:11:49 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit ffe557787fdfd669a361e1ca6e51d32a063a5d11 Author: car Date: Mon Nov 16 17:47:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 88dcf21ef42d9beefb871823a2e7044442e6823c Author: car Date: Mon Nov 16 17:31:01 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit c2f9eaaaadfffea0c382ce477b19c46b499ae1b4 Author: car Date: Mon Nov 16 15:53:17 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit 1f9c06522f7540c5995db64ed8e91b4e00d5b4fd Author: car Date: Mon Nov 16 03:52:11 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 756f5b26f5a418331f2bd6097b33daed7ee8221b Author: car Date: Mon Nov 16 00:47:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 59e5863bbe7a3d73a083a3099e1456fac84c031f Author: car Date: Sun Nov 15 23:40:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 90759a068cbfcbf932bd44e48adb1a649734afb0 Author: car Date: Sun Nov 15 00:01:27 1998 +0000 win32 support Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit e26c775b52b693ace9b7fd54720481ea9d2e3a98 Author: car Date: Sat Nov 14 19:38:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 7f8c59df1a1b973d819540114f0254547c0f30a9 Author: car Date: Sat Nov 14 00:34:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit d70d1d2ddcce8380f20a57d1dda5cc01c0e71609 Author: car Date: Sat Nov 14 00:34:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp commit c9d14f4aa2c588a4335e281b68562fd691a83a13 Author: car Date: Fri Nov 13 22:14:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit ce53dcef7361791f2814becacdc0797fbfe0c7f1 Author: car Date: Fri Nov 13 20:09:28 1998 +0000 Temp file name. Src/LinearSolvers/C_NodalMG/.cvsignore commit 204c320c37707b42d4c3261121685d13d5f4e442 Author: car Date: Fri Nov 13 20:08:45 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 79887a9f0ff5b487ac07cd44c4870a4bf314b5ae Author: car Date: Fri Nov 13 17:25:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 8cf6188c40514a2be04df50651d4741fba504f30 Author: car Date: Fri Nov 13 16:03:51 1998 +0000 EBASE should be null Src/LinearSolvers/C_NodalMG/GNUmakefile commit 63fffad6de2c1ceb8c47c40c5d8eac68f9b2ea92 Author: car Date: Fri Nov 13 16:03:07 1998 +0000 quiet some warnings Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 3dec428241494354a5e476b29a52a84620eb7429 Author: car Date: Fri Nov 13 00:25:01 1998 +0000 fixes for parallel, throws find bugs Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit dd8acc29bddb258c2311d05dd4014e9682ebf337 Author: marc Date: Fri Nov 13 00:16:14 1998 +0000 Fix up a couple of 1D-specific bugs. Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Looping.H commit 8dfac2f530f32b5288853284e4cacefb0fb1384c Author: car Date: Tue Nov 10 02:21:59 1998 +0000 libs target Src/LinearSolvers/C_NodalMG/GNUmakefile commit 597132aca6d68dab7a89265745cf274886ddee0f Author: car Date: Mon Nov 9 23:13:14 1998 +0000 Makefile tweaks: no type make COMP=... EBASE=proj to buildlocally Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package commit 8e290e6ac51cc2ed7425c48ba99d76a5255ac0db Author: car Date: Sat Nov 7 21:42:14 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6395377f863b78c04eabeca8eda600364390d590 Author: car Date: Sat Nov 7 21:34:16 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit f4cb1fc354a1293c2207ee5847e9f88ee0c4e94f Author: car Date: Sat Nov 7 21:19:56 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 9369bb81ed060ae3c888e2be3e79b012fc8a9358 Author: lijewski Date: Sat Nov 7 02:51:08 1998 +0000 Updated to reflect FillPeriodicBoundary() mod. Src/LinearSolvers/C_CellMG/LinOp.cpp commit 1442b1c951daf09dfbde165ad2ae459dc36fd78c Author: marc Date: Sat Nov 7 01:45:11 1998 +0000 Remove indenting whitespace. Uglier f77 generated, but guaranteed correct Tools/C_scripts/strip72 commit b54fa72ac384ad1f924d6449c40d79b08ed241f0 Author: marc Date: Sat Nov 7 01:14:42 1998 +0000 Remove whitespace that was inserted on a continuation line, since that is space that may be inserted into a character string. Tools/C_scripts/strip72 commit b70719b72912842e07cc9e8b97db5aa5f02ea27d Author: lijewski Date: Sat Nov 7 00:35:19 1998 +0000 Added do_corners boolean to FillPeriodicBoundary(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 9f2486cad8b853f3080b1ecd4792c52b067c0695 Author: lijewski Date: Sat Nov 7 00:30:43 1998 +0000 Mods for FillPeriodicBoundary(). Src/C_BaseLib/MultiFab.H commit 6d9693da92a3947b8a29bd1f73d8232da0c88477 Author: car Date: Fri Nov 6 21:35:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/RegType.H commit e0ba793e94e2976687a3f91687171da47e29f001 Author: car Date: Fri Nov 6 21:31:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 890f2e145a16012f73cb0fb127df45474434ff89 Author: car Date: Fri Nov 6 04:22:35 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 187c2b6e41ca15a444aa09eef201ab2ae8c5814a Author: car Date: Fri Nov 6 04:03:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit b2022bb37bdd364ee1585782e82d127847e3d6c6 Author: almgren Date: Thu Nov 5 06:42:59 1998 +0000 Fixed a bug in the recent fix to not buffer the buffer cells - we can't assume that grid cells next to a domain boundary were buffer, not tagged, cells... Src/C_AMRLib/Amr.cpp commit c4fc5e93ccdd9c6fd93371df70a5618b501ffb88 Author: almgren Date: Wed Nov 4 20:30:22 1998 +0000 Removed the following snippet of code: if (!sub_cycle) { // must adjust regridding trigger int factor = 1; for (k = max_level-1; k >= 0; k--) { factor *= MaxRefRatio(k); regrid_int[k] = ri*factor; } } which for no subcycling did funny things to regrid_int. Now regrid_int at each level is just what is set in the inputs file, which means effectively you will now regrid every regrid_int time steps with lbase = 0. Src/C_AMRLib/Amr.cpp commit 58e30546bf8aa08ce5940f643891034034b4b2a1 Author: lijewski Date: Wed Nov 4 00:45:16 1998 +0000 Added DataLog() ... Src/C_AMRLib/Amr.H commit 2d43c22b3e4b31bf9af87bd04f8721894d631d10 Author: marc Date: Tue Nov 3 21:56:08 1998 +0000 Add write for AmrData object as well. Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp commit 14e4ba8752a5a6a053f1470d5f965584458972c9 Author: almgren Date: Tue Nov 3 21:53:05 1998 +0000 Two changes are made in regridding: first, an "intersect with domain" is added to a loop which tests whether fine grids are properly nested within coarser grids. Second, the way that fine grids affect coarse grids is modified in that only the boxes around fine *tagged* cells are coarsened to re-tag at the coarser levels, not the boxes around tagged *and* buffered fine cells. Src/C_AMRLib/Amr.cpp commit 0cbc23859d84dbacb8b803a15334b5278ba023de Author: lijewski Date: Tue Nov 3 18:16:36 1998 +0000 Sync'd with serial _amr. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/MAKESLICE_3D.F Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit ef4301f4c03c23f6ba0756abcaa6bca752228dd4 Author: lijewski Date: Mon Nov 2 18:35:55 1998 +0000 HG_DEBUG is defined only when building executable. Src/LinearSolvers/C_NodalMG/GNUmakefile commit 8760d4e059791eb89af78847bb9fe6f39ddee4a5 Author: lijewski Date: Mon Nov 2 18:19:48 1998 +0000 Added PROB_AMR_F.H Src/C_AMRLib/Make.package commit e413163c6b2f0d86c4a716b2cfae36bf1cc73de9 Author: lijewski Date: Mon Nov 2 18:16:13 1998 +0000 Forgot about amr_defs.H Src/LinearSolvers/C_NodalMG/Make.package commit 39922cbee5e0e922b435789ab2c516e1347f40e0 Author: lijewski Date: Mon Nov 2 17:13:25 1998 +0000 Added LevelBld.H. Src/C_AMRLib/Make.package commit 2cbcc552d47bef2575b682d797623b2aa960a563 Author: lijewski Date: Fri Oct 30 19:02:44 1998 +0000 Mods to get doc++ to build proper TeX. Src/C_AMRLib/Amr.H Src/C_AMRLib/TagBox.H commit 72c80ea3e29b3a3c5e5dd676bcc7ab44603529e8 Author: lijewski Date: Thu Oct 29 21:56:56 1998 +0000 Fixup for doc++ DVI generation. Src/C_BaseLib/VisMF.H commit 4c37ddbcef3a2e020079df79a840bdec5886ec33 Author: car Date: Thu Oct 29 21:56:26 1998 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 0dcb6499259183f9702bec05b516c58bc10d03c5 Author: lijewski Date: Thu Oct 29 17:33:53 1998 +0000 More work on Parallel GNUmakefile consistency. Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package commit 6ccc46f7d47d17eb6b5f9d450416e6de5857c481 Author: lijewski Date: Thu Oct 29 16:54:03 1998 +0000 More work on Parallel GNUmakefile consistency. Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile commit 37b12d3af4ec2b12930d24d761e3cdbc8b8421d2 Author: lijewski Date: Thu Oct 29 16:33:39 1998 +0000 Simplified decision regarding how to set QNAN. Src/C_BaseLib/FArrayBox.cpp commit 368cfec05948214aa6a72e57b1c1d0a3ec3baee2 Author: lijewski Date: Wed Oct 28 22:47:55 1998 +0000 More readily build standalone library. Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 26874b5e907546934d32a9b4047d41e266407499 Author: lijewski Date: Wed Oct 28 22:03:45 1998 +0000 Now can build the library standalone. Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_CellMG/Make.package commit d559ba83eff0b4d7111e6c8531dc6347b846e618 Author: lijewski Date: Wed Oct 28 22:01:15 1998 +0000 Forgot BC_TYPES.H Src/C_AMRLib/Make.package commit 83c6589a270d82fed5635a7d3756c5cd5171eda0 Author: car Date: Wed Oct 28 18:43:04 1998 +0000 __GNUC__ Src/C_BaseLib/FArrayBox.cpp commit b7eca13f4c64f5498cdd8390da6fb58211733832 Author: lijewski Date: Wed Oct 28 18:15:13 1998 +0000 More work on getting standalone library to build. Src/C_AMRLib/GNUmakefile Src/C_AMRLib/Make.package commit 9927643059493bc21547276bc8c5f4f7645125d9 Author: lijewski Date: Wed Oct 28 17:49:32 1998 +0000 More work on building standalone libraries. Src/C_BoundaryLib/GNUmakefile Src/C_BoundaryLib/Make.package commit 1eeb056c5f0d3d8ff4e216ec6b97fc05556049fb Author: lijewski Date: Wed Oct 28 17:42:16 1998 +0000 More work on building and installing library. Src/C_BaseLib/GNUmakefile commit 26416c5ec92f0b02cb9b536ad42804e02b667d4c Author: marc Date: Wed Oct 28 02:01:56 1998 +0000 Change the name of the function Utility::CreateDirectory to Utility:: UtilCreateDirectory. Tools/C_util/TV_TempWrite.H Tools/C_util/WritePlotFile.cpp commit cb86bf203eb932cf69632fe39ebfd9bcbdabe854 Author: lijewski Date: Tue Oct 27 22:07:10 1998 +0000 Redid previous fix in a slightly clearer way. Src/C_BaseLib/FabArray.H commit a57311e7e247857f9403321f75c6b9a5391e2010 Author: lijewski Date: Tue Oct 27 21:58:25 1998 +0000 Forgot to set dataAvailable = true on early return in CollectData(). Src/C_BaseLib/FabArray.H commit 8861008c91b65122688ade95a2fb1f289caa0258 Author: almgren Date: Tue Oct 27 19:22:09 1998 +0000 Put if (sub_cycle) around loop Vince added for multifluid, and set parameters correctly for no subcycling. Src/C_AMRLib/Amr.cpp commit aae5628e8e06075b22196e0c91eb095bef017547 Author: lijewski Date: Tue Oct 27 17:33:05 1998 +0000 Simplified reflux() slightly & worked around g++ 2.8.1 bug. Src/C_AMRLib/FluxRegister.cpp commit 8418a4cc861b16dbeea68802bd23f613b5d22853 Author: lijewski Date: Mon Oct 26 23:58:50 1998 +0000 __GNUC -> __GNUC__ Src/C_BaseLib/FArrayBox.cpp commit 70ddcc88ea63f4ef232a50991b85cca99b8d1b98 Author: lijewski Date: Mon Oct 26 20:51:38 1998 +0000 mpi_waitall -> mpi_wait for RunStats. Src/C_AMRLib/FluxRegister.cpp commit 154d59e0a02af0c1c8aaa6384b4678d993ace934 Author: lijewski Date: Mon Oct 26 20:51:15 1998 +0000 Optimized MPI communication in copy(). Src/C_BaseLib/FabArray.H commit 0e8f7bddd429ce584722a0a7c3a598a09cc04d03 Author: lijewski Date: Mon Oct 26 20:50:53 1998 +0000 Added tFAC.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tFAC.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tFAC.cpp commit 9bc15016e0704a622b230cbfd78a7e617cce5bd7 Author: lijewski Date: Sat Oct 24 22:26:42 1998 +0000 Figured out the bug in 1.49 -- Yes! Src/C_AMRLib/FluxRegister.cpp commit 41a8c1d43283a508d6735fc3385fe427f7664214 Author: lijewski Date: Sat Oct 24 20:24:49 1998 +0000 Reverting to previous version; something's not quite right :-( Src/C_AMRLib/FluxRegister.cpp commit f83a60e5f86b82b6f15cf2cb003ffa341df74620 Author: lijewski Date: Sat Oct 24 16:49:25 1998 +0000 Optimized communication in CrseInitFinish(). Src/C_AMRLib/FluxRegister.cpp commit 97be32ddce0a379ccff062a3e55cfb48d0c9471c Author: car Date: Fri Oct 23 23:46:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 797dc4a69cbf1be0158fa737eabc9985457f0e46 Author: lijewski Date: Fri Oct 23 16:54:00 1998 +0000 A little cleanup. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/VisMF.cpp commit fec5a6d1cc7564e11076c3cf1497f49088c22aa3 Author: lijewski Date: Fri Oct 23 01:59:35 1998 +0000 Added immediate return in CollectData() if NProcs() == 1. Src/C_BaseLib/FabArray.H commit 6cec58a510b105378c5e7c4ffe6049943825527f Author: lijewski Date: Thu Oct 22 17:27:56 1998 +0000 Added a few strategically placed ios::binary in open() calls. Src/C_BaseLib/VisMF.cpp commit db24e6b2ed64af6736d829bf5230d0170013e947 Author: lijewski Date: Sun Oct 18 03:48:16 1998 +0000 Now use coalescing FAB heap for FAB data in CollectData(). Src/C_BaseLib/FabArray.H commit 0ef28cda87996de992f48ef893684e953f13be57 Author: lijewski Date: Sun Oct 18 01:44:17 1998 +0000 Added new cut at CollectData() minimizing # of communications. Src/C_BaseLib/FabArray.H commit 5e10cd5941729faf0b93cbe9876019b7035dcb8f Author: lijewski Date: Sun Oct 18 01:43:50 1998 +0000 Added copy constructor and assignment operator for CommData. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 682d013f01be9044775f2b61dbbc5c618763eb4b Author: lijewski Date: Thu Oct 15 21:53:02 1998 +0000 Now cache the AddBox() info in the CopyDescriptor. Src/C_BaseLib/Geometry.cpp commit d5faa92d5b5913b5f548817e491f37f87acc149f Author: lijewski Date: Thu Oct 15 21:52:40 1998 +0000 Now cache the AddBox() gunk in the CopyDescriptor. Src/C_BaseLib/MultiFab.cpp commit fea6f72d48cc15ef5146432d45363af21dadf594 Author: lijewski Date: Thu Oct 15 21:52:15 1998 +0000 No longer clear fabComTagList() in CollectData(). This allows caching of CopyDescriptors between calls to CollectData(). Src/C_BaseLib/FabArray.H commit ef6864568fff909f40a68a9f918736913b20c7c0 Author: lijewski Date: Thu Oct 15 17:14:32 1998 +0000 Added instrumentation code. Src/C_BaseLib/FabArray.H commit a8de30a57c775abab46fea62e01f603b3eadcd03 Author: car Date: Tue Oct 13 18:20:32 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 1ea9dd65da922838d55e72817124062070bc70b5 Author: car Date: Tue Oct 13 18:19:34 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 24eed233ff7d9e9c39f10a4a8015f154b215bb82 Author: sstanley Date: Mon Oct 12 23:22:54 1998 +0000 Replacement of EXTRAP with FOEXTRAP to be consistent with change in amrlib/BC_TYPES.H from v.1.3 to v.1.4. Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp commit 055e020c9d6fb033c3718dfa7d20c4db10af6298 Author: car Date: Thu Oct 8 20:23:57 1998 +0000 minor refinement of message Src/C_BaseLib/BoxLib.cpp commit b4c1daa14e2009baa874dce58d7fc8fe34ce5e47 Author: car Date: Thu Oct 8 18:19:42 1998 +0000 oops Src/C_BaseLib/BoxLib.cpp commit f1a225648adcabc17759a33c58e21f222d142191 Author: car Date: Thu Oct 8 18:05:45 1998 +0000 id string for abort/error Src/C_BaseLib/BoxLib.cpp commit 3f4d614d4ea79f084800c571f4632cbc32ef3d13 Author: vince Date: Wed Oct 7 21:18:18 1998 +0000 Added modifications for Multifluid and a few changes for the pc. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BC_TYPES.H Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/test/tDir.cpp Tests/C_BaseLib/tDir.cpp commit acf9a6105dd719c9382c214272c7f7a33bcf15da Author: vince Date: Wed Oct 7 20:51:59 1998 +0000 Added Make.AIX for blue. Tools/C_mk/Make.AIX commit 6f580f6637f117c44d2403213e781fec2683be44 Author: lijewski Date: Tue Oct 6 23:00:10 1998 +0000 Don't need -DBL_SETBUF_SIGNED_CHAR with KCC Tools/C_mk/Make.T3E commit 6c4938bdae79fb5a10653e0e26403dee4d03e09f Author: lijewski Date: Tue Oct 6 22:56:47 1998 +0000 Removed -e I option to FC. hgproj needs more cleanup before it'll pass this. Tools/C_mk/Make.T3E commit f8424bca35680f1d70c1c1d77edddb0e73a84b1b Author: lijewski Date: Tue Oct 6 22:54:08 1998 +0000 Removed a unary plus that killed T3E compiler. Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F commit a0172ff961339f4d919932410be67a650761f58c Author: car Date: Tue Oct 6 20:11:01 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit d536964040d0080f45c5747da2ec4009cf25bd0e Author: lijewski Date: Fri Oct 2 19:36:48 1998 +0000 Relaxed a couple assert()s in copy() Src/C_BaseLib/BaseFab.H commit 4f0a47600552556b41da5f010d031303a4a24cf8 Author: car Date: Fri Oct 2 18:42:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit 2a180ce12e7623463b5901d2f4f72c619f19c3e5 Author: car Date: Thu Oct 1 17:17:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 20d6e043848a784f697a62c29f61fb565e8139f8 Author: lijewski Date: Wed Sep 30 20:07:18 1998 +0000 Added tad more useful error output for bldTable(). Src/C_BaseLib/ParmParse.cpp commit 2d1842d76141ecd1f4ed97d191391e8746649581 Author: lijewski Date: Wed Sep 30 19:28:56 1998 +0000 Fixed bug in & simplified FillPeriodicBoundary(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.H commit 422f2f2ced6d2a3832a6bf5fc608d6be64d8bcd9 Author: lijewski Date: Wed Sep 30 17:07:39 1998 +0000 Added tFB.cpp. Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tFB.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tFB.cpp commit 4d9367c8dd3277520ba2d9dd03cd89d612cbe7ff Author: lijewski Date: Wed Sep 30 17:05:55 1998 +0000 Fixed bug in FillBoundary() in parallel. Simplified it as well. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 52c01626b4bb2adf1391842bbc24fb297c78afca Author: lijewski Date: Tue Sep 29 20:08:27 1998 +0000 Added copyright macro. Src/C_AMRLib/DatasetClient.cpp commit 835b56f9a7ced1211f57414c9ceb1f4b17b7dd65 Author: car Date: Tue Sep 29 18:05:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit ad2346a5d88aded12c346f385109a352706f5b8f Author: car Date: Fri Sep 25 23:00:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit d778c8264d80860b16c45a92b5ca435acef5aaae Author: lijewski Date: Fri Sep 25 17:57:13 1998 +0000 Added t8BIT.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/t8BIT.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/t8BIT.cpp commit 29b662953d300251bb07baaeb2b1971d5fa221bc Author: car Date: Wed Sep 23 22:46:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 54f1564b8e446c3645085978c5ef111226a0e0fd Author: lijewski Date: Wed Sep 23 22:00:10 1998 +0000 Needed to use finest_level instead of max_level in bldFinestLevels(). Src/C_AMRLib/Amr.cpp commit 67a17ed4329ca690059f4e32f7bb7b007f2c7207 Author: lijewski Date: Wed Sep 23 20:19:38 1998 +0000 bldFineLevels() now iterates through regrid() till grids don't change. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 5d4a46984efffd845cd920c2179f2ddfb6a2d3e4 Author: lijewski Date: Tue Sep 22 23:42:59 1998 +0000 Removed Amr_Auxil.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Amr_auxil.H commit 85e6ca293f9ab425d6a93d7b9d83aa372038a067 Author: car Date: Tue Sep 22 20:29:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit acbdd5c0c1d38ba91da2a11c4ecf4244c6e9aa9f Author: car Date: Tue Sep 22 18:06:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit a68590e7b43a3ce4a343559fbd43fc030715b1dd Author: car Date: Fri Sep 18 20:26:12 1998 +0000 proj.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c7e8c0d1de6d488ef2b0c096b80d5dc6cf9e6a95 Author: car Date: Fri Sep 18 18:03:46 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 83e5edbd908679fd230b35df8120a795d1277d7f Author: car Date: Fri Sep 18 00:09:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 0cf16f9f713937ab65b59667ed1d86fd696a60d9 Author: car Date: Thu Sep 17 17:05:35 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 35c60ff37010fc06a0b0a9ac55f1037d4d4c39e8 Author: car Date: Thu Sep 17 16:46:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 0c1390c58ea8ae1c5d3e58c055c46e9dfd091827 Author: car Date: Wed Sep 16 18:18:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit bfdee9deb76faf9bdd162f526d92fcc244bb7e0b Author: car Date: Wed Sep 16 03:36:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit e118923bab13acb3b58af8ef4262a721e6c30a73 Author: lijewski Date: Tue Sep 15 22:31:40 1998 +0000 Added amr.plot_vars ParmParse variable and a couple supporting functions. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit a6be4fd5be0fef81741db00d3f211954bf771dab Author: lijewski Date: Tue Sep 15 00:11:06 1998 +0000 Undid 1.20. Src/C_AMRLib/StateData.cpp commit e7b5e5ef62a9ad1234f1ec562a893d75d1e3d4c3 Author: lijewski Date: Mon Sep 14 23:28:56 1998 +0000 Ability to set ghost cells to average of min/max in Write() Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 302812ca9c915b49b2955adcca1862e41bb49b74 Author: lijewski Date: Mon Sep 14 23:28:13 1998 +0000 Set ghost cells to average of min/max on VisMF::Write() in checkPoint(). Src/C_AMRLib/StateData.cpp commit d0b844f051748e7c9868065c36981b65b42da557 Author: lijewski Date: Mon Sep 14 21:50:34 1998 +0000 format and fabio weren't in sync after an init() or setFormat(). Src/C_BaseLib/FArrayBox.cpp commit af6d02f2301daee7cde747271ecc72f238c9563f Author: lijewski Date: Mon Sep 14 21:49:56 1998 +0000 checkPoint() always used fab.format=NATIVE Src/C_AMRLib/Amr.cpp commit 2d3a211dc6b93e676d214e3221e1ea038bce10bd Author: car Date: Fri Sep 11 21:15:42 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit c2bc44d6f4ae18358eec8569c8debc49f602ccfb Author: lijewski Date: Fri Sep 11 20:04:17 1998 +0000 Added some stat output stuff in #if 0 ... #endif block. Src/C_BaseLib/DistributionMapping.cpp commit e25dd8cf18b4e4c9ff49cb478270f907650f0c22 Author: lijewski Date: Fri Sep 11 19:58:15 1998 +0000 Minor cleanup to linInterp stuff. Src/C_AMRLib/StateData.cpp commit fa7cc9cc9b2c1df62de041b8303f69371c4ac410 Author: lijewski Date: Thu Sep 10 17:59:13 1998 +0000 StartParallel() now does a MPI_Barrier() as a last step. Src/C_BaseLib/ParallelDescriptor.cpp commit 985322b6979b312a11e3e9e592689b955094451c Author: car Date: Wed Sep 9 23:49:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit eb8b67681682234dcc4e4d5fa8817779880576f4 Author: car Date: Wed Sep 9 19:57:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 4af929bddfbaee3c288e24472952603563bc120e Author: car Date: Wed Sep 9 17:17:45 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 62e6edac25cf23b391b12b640cc31b3a7ab99bf7 Author: car Date: Tue Sep 8 23:12:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hglib.dsp commit 257d3ab6d6deed0462924c8c6cb63cf4d1ba1ce1 Author: car Date: Tue Sep 8 23:06:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 650523ad16728d91a41c3a69f486af2d1c8fb6f7 Author: car Date: Tue Sep 8 23:00:04 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp commit 7f1494300d4f88d94eaeff9ddba54f2cb38f96d5 Author: car Date: Tue Sep 8 22:59:40 1998 +0000 cleanup Src/LinearSolvers/C_NodalMG/GNUmakefile commit 3bf7e93acfe4b05a803f2c2bf6a0ff8fd8578922 Author: car Date: Tue Sep 8 22:35:55 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 5996557a649deafd8fad29bcb65a94ccee635fd5 Author: car Date: Tue Sep 8 21:07:32 1998 +0000 counted pointer Src/LinearSolvers/C_NodalMG/hgparallel.h commit 824bcf47faaf417e94bd9bc1bd6fa4e224309de1 Author: car Date: Fri Sep 4 22:31:12 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interface.H commit 7095a143e5d8bcec7ab98da64a11bb5aaebf78b8 Author: car Date: Fri Sep 4 19:30:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 55762bf78fa33fbd006df781476d63330fe94542 Author: car Date: Thu Sep 3 18:30:15 1998 +0000 Really No changes. Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 607e8fc5575bbdd9a3b27743516859f99f12d05f Author: car Date: Wed Aug 26 17:48:15 1998 +0000 added back graph stuff Src/LinearSolvers/C_NodalMG/interface.cpp commit 3191a1c839dfb5212152049c00c1dcf1a57c7229 Author: car Date: Tue Aug 25 23:44:25 1998 +0000 added some more temporary files to .cvsignore Src/LinearSolvers/C_NodalMG/.cvsignore commit 4709c5015dca56fae449aa28a65df694dc7f02d2 Author: car Date: Tue Aug 25 23:43:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 06327110839ebbf3185ba828f415ab762eddf51b Author: car Date: Fri Aug 21 23:19:14 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit c19075340e0079120848835c53068f63a545edd3 Author: car Date: Fri Aug 21 22:20:19 1998 +0000 ErrorString Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 45d05ed57c8098fc3cdc896b5a2cadd51e71283d Author: car Date: Fri Aug 21 18:06:08 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/test/GNUmakefile.tCArena Tests/C_BaseLib/GNUmakefile.tCArena commit 8d61a344aa51fd913b0a489c2f7ac18299ecd0b8 Author: car Date: Fri Aug 21 17:58:28 1998 +0000 More Abort changes Src/C_BaseLib/GNUmakefile Src/C_BaseLib/test/GNUmakefile.test Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_NodalMG/GNUmakefile Tests/C_BaseLib/GNUmakefile.test commit d66922bcbaad2fb941e83280a41fb6b2cb27dba3 Author: car Date: Thu Aug 20 23:53:47 1998 +0000 Abort switch Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 726e54da09e9f7e183dd5b4e8440a2d9d419dc46 Author: car Date: Thu Aug 20 17:53:59 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit d19e7d7b33acef67215a4e157a8df39e7ee5e706 Author: car Date: Thu Aug 20 17:40:09 1998 +0000 Support for KCC_VERSION Src/C_BaseLib/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Tools/C_mk/Make.defs commit ccd97c33c15ba9ccaaa30fd16e2fd17bb46126f3 Author: car Date: Wed Aug 19 17:52:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit a02ac89b0f454c2abe83d406e6fda108b0bdb822 Author: car Date: Wed Aug 19 17:35:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_defs.H commit dc50a5c868fd8a9f0b3b0c1bc0ab2d14fe51c99a Author: car Date: Wed Aug 19 17:22:00 1998 +0000 Minor changes. Src/LinearSolvers/C_NodalMG/amr_defs.H commit bc7d03bd4c54a0d247780ac260e3228da8a7f5a2 Author: car Date: Fri Aug 14 22:51:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 1ed79ac89cce0ac1524d3d04ff4d66020ef32a1c Author: car Date: Fri Aug 14 17:26:39 1998 +0000 Fix for g++, no limits header file Src/C_BaseLib/FArrayBox.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit e6a26f2c37074ef67fd4339ed21044dfa66bc28a Author: car Date: Fri Aug 14 16:37:34 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit 79b91b27c1055ad58c4f827c72e3f16a14c03900 Author: car Date: Fri Aug 14 16:36:19 1998 +0000 Fixes for WIN32 Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit 06c750c9d41ce73655ba57e98051f88cc2f382ff Author: car Date: Fri Aug 14 16:28:19 1998 +0000 added portable support for quiet_NaN Src/C_BaseLib/FArrayBox.cpp commit fff2d0a47e52bccd965ddf7c02a9f7f95be13a8e Author: car Date: Fri Aug 14 14:31:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 53133428a9ad67a1e157999ec82828d1eab8bff7 Author: car Date: Fri Aug 14 00:22:09 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6fb62a945f0ee51337b1f55947d068ae868ccbe5 Author: car Date: Thu Aug 13 22:54:40 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 2fd5c5fad63bfe55dacb96c4d9a9cf7ee0bc35a1 Author: car Date: Thu Aug 13 22:48:56 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit c0dff225aa2d87d00fb02f8c3f10ebd520d8497a Author: lijewski Date: Wed Aug 12 18:00:53 1998 +0000 Added more MPI RunStats. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit dc2af11173335094a73afd58229064e23e000e42 Author: lijewski Date: Tue Aug 11 20:33:38 1998 +0000 Added mpi RunStats Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit 6145a17da30e1f3064ea3493b25ca1a933f5ec20 Author: lijewski Date: Tue Aug 11 20:33:20 1998 +0000 Added mpi RunStats. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit f5d2ab0ffc2e5018fa3b010947441ae29b0efb68 Author: lijewski Date: Mon Aug 10 17:03:57 1998 +0000 Didn't get BL_T3E & BL_CRAY stuff quite right. Src/C_BaseLib/CONSTANTS.H commit cdc81e29d3180f9269b37d6288a88087c0d913c8 Author: lijewski Date: Sat Aug 8 17:25:23 1998 +0000 Merged in BL_OLD_STL Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp Tools/C_mk/Make.CRAY Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E Tools/C_mk/Make.defs commit e2b5ceb880f51fb002c99a11c8d4e0a89571d43e Author: car Date: Fri Aug 7 17:46:59 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 6252cf4b10923a9fdc1f70a46648b40b5bb6c3f3 Author: car Date: Thu Aug 6 23:12:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit e1655d8e7f2eb2617e2c89cccd9d3610e01c1d0c Author: car Date: Thu Aug 6 20:56:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H commit 24f124b44efbf90c7dfdaaeba74eb74206eb43d5 Author: car Date: Thu Aug 6 20:31:09 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H commit 782b4485715d3f101764f39a64115164ab325457 Author: car Date: Thu Aug 6 20:30:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 8d098dc8a691205a3481257e1f82dacffd630f40 Author: car Date: Thu Aug 6 03:46:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit e064629091a034ef081578db5eaff3ab09158dd6 Author: car Date: Wed Aug 5 21:42:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 8ae87928b523a8f9b55021e25c6aa51d0ac7311a Author: car Date: Wed Aug 5 21:24:42 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit e6f8a740c9430cec2d5ecfb435156ece44214fa5 Author: car Date: Wed Aug 5 20:57:59 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 055d94fea9b6ae37df597d8e0feda81120166086 Author: car Date: Wed Aug 5 19:21:34 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/proj.cpp commit 314cba5060e343e2fc7e351e4a7d4c5c8b14c6dc Author: car Date: Wed Aug 5 17:49:25 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 35096a6fe2509ecdaf21a8d61899e83aa47ef5e1 Author: car Date: Wed Aug 5 17:38:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 6f2e25b736f15cb538e13debc93f9996b45e3667 Author: car Date: Tue Aug 4 22:57:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/hgproj.pg commit f04343d72d21afe2369b0ac432cde0eb88227bff Author: car Date: Tue Aug 4 21:48:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 9880d1c1619ee3e18b467df34e2863abd92b415f Author: car Date: Tue Aug 4 18:25:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit aa711f5b1f6302c9c7ad68088b3904b4a1db1116 Author: lijewski Date: Tue Aug 4 16:41:55 1998 +0000 Removed verbose output referring to flushing various caches. Open gridlog, datalog and runlog in append mode. Src/C_AMRLib/Amr.cpp commit 9d1a221f3ec1eac0adb1c6d63e09c1b911d33aea Author: car Date: Mon Aug 3 20:35:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 7a865d336a17fa2c6e4b0daebaee5b3b7b74504c Author: car Date: Mon Aug 3 20:02:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit ad27d2c1702d98e30fafb8e64f4cf1c7f82da3d8 Author: car Date: Mon Aug 3 19:26:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit caf87eb1a45bab6ccf73ffcaf6fcb043eb4d888e Author: car Date: Mon Aug 3 18:01:56 1998 +0000 Some parallel fixes for single level. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 2d64b23f1c1bf932972940ac67ad49a6b169200f Author: car Date: Fri Jul 31 17:23:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 7eafaa7d5c0e2a8f8b80c5e3628b8e9c24939320 Author: car Date: Thu Jul 30 23:14:14 1998 +0000 Removing BSP Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/main.cpp commit 32978dd30013a48b5ba02b7f6df8a5835f33cbaf Author: car Date: Thu Jul 30 23:13:45 1998 +0000 more preload removal mods Tools/C_util/README commit 3aa8d5a9499020e7f9a9013652cb1537c2bd6676 Author: car Date: Thu Jul 30 23:06:43 1998 +0000 Rid ourselves of BSP files... Tools/C_util/preload.cpp commit 5a0a4653370ebe8d60ddd1d09ca7e602f75079e1 Author: car Date: Thu Jul 30 21:01:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 4f8c64e3585136790ce0b832d1dbd30c0f1c4cd1 Author: lijewski Date: Wed Jul 29 20:44:12 1998 +0000 Use Barrier() instead of Synchronize() to sync across processors. Tools/C_util/WritePlotFile.cpp commit 54f73a5ab9351ea864396b5c1ac0020e8a3227a8 Author: lijewski Date: Wed Jul 29 20:25:55 1998 +0000 Brought up-to-date with latest ParallelDescriptor mods. Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp commit b587af721b78200a3d1c15bf19181e4813133153 Author: lijewski Date: Wed Jul 29 20:04:35 1998 +0000 Added back in Broadcast() -- needed by some vis code. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit b05b5b4acd261cc3c64c643e4189020a9bfedcd5 Author: lijewski Date: Wed Jul 29 19:26:39 1998 +0000 Only use cache if BL_USE_MPI && !BL_NO_PROCMAP_CACHE Src/C_BaseLib/DistributionMapping.cpp commit 6023333a3d42059ea569d5ff4c8c2e6527472fdf Author: lijewski Date: Wed Jul 29 19:09:30 1998 +0000 Brought up-to-date with new ParallelDescriptor and FabArray.H. Src/C_BoundaryLib/FabSet.cpp commit 91333ecfc6805411105ad30ca446d1f5a20ba566 Author: lijewski Date: Wed Jul 29 19:09:05 1998 +0000 Brought up-to-date with new ParallelDescriptor and FabArray.H Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 78483c3c480b79a757c93f72367937b03c010f69 Author: car Date: Wed Jul 29 17:21:30 1998 +0000 Added comment for Windows. Src/C_BaseLib/Utility.H commit 546589ac41e0a59ebbc3cef467fc839165843702 Author: car Date: Wed Jul 29 00:06:04 1998 +0000 Dosify. Src/C_BaseLib/Utility.cpp commit e8a485fc0adb43b654d4f6c61c5037fd718fd499 Author: lijewski Date: Tue Jul 28 17:47:49 1998 +0000 Undid the static RunStat -- T3E had a bug. Src/C_BaseLib/DistributionMapping.cpp commit f77e226b5eeb656262b548de2e75116e849982d0 Author: car Date: Tue Jul 28 17:16:06 1998 +0000 Added ccse-mpi.H as a T_source. Src/C_BaseLib/Make.package commit caa642b152f12f2982ba021302729ced586acce3 Author: car Date: Tue Jul 28 03:21:17 1998 +0000 windows fixes Src/C_BaseLib/ccse-mpi.H Src/C_BaseLib/pBoxLib_2.dsp commit c4ff8ac29c2f9b25ac8ed98ecfd80c9b4bb69cce Author: lijewski Date: Mon Jul 27 21:33:36 1998 +0000 Now using instead of Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 8186fe09c17d8b69589c55c667ee541cc50b2dee Author: lijewski Date: Mon Jul 27 21:33:06 1998 +0000 Now using Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/VisMF.cpp commit 3c5cdb66510427444320d0231f403ad8d2178090 Author: lijewski Date: Mon Jul 27 21:32:46 1998 +0000 Encapsulates making it slightly easier to change from using BL_USE_MPI or not. Src/C_BaseLib/ccse-mpi.H commit 1f558f6a85761f365401b3276d0c035fb18ab1a3 Author: lijewski Date: Mon Jul 27 21:14:16 1998 +0000 Made RunStats(fabarray_copy) a static object. Src/C_BaseLib/FabArray.H commit 599aa935f3277f4fe54e8d5a4485c31e8a2f1c73 Author: lijewski Date: Mon Jul 27 20:43:37 1998 +0000 Added BL_NO_PROCMAP_CACHE to enable the turning off of caching. Src/C_BaseLib/DistributionMapping.cpp commit 4200f76071b449f32ff63e288ce4af5d48f07230 Author: lijewski Date: Fri Jul 24 22:40:46 1998 +0000 RunStats object is now static. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit 957e1b0d135bcdde93e0e78f0b132000316ce910 Author: lijewski Date: Fri Jul 24 01:25:37 1998 +0000 Constructor now takes aString instead of char*. Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit dfde8ef42eccc07c6d310f0c0f63bf30fe86d7e7 Author: lijewski Date: Fri Jul 24 01:24:51 1998 +0000 Brought up-to-date with latest RunStats mods. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit e6baf45ee0a4758feda3ea245af5898b5d7217bb Author: lijewski Date: Thu Jul 23 20:53:10 1998 +0000 Some code rearrangment to fix g++ 2.8.1 bug on Solaris. Src/C_BaseLib/DistributionMapping.cpp commit 2c77613f47bfba5dcba24d31f2837bbe0beca17a Author: car Date: Thu Jul 23 16:34:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit e9fa9a876377e1d431cd1aaf730945af2423ebaa Author: car Date: Thu Jul 23 02:49:27 1998 +0000 Not needed Src/LinearSolvers/C_NodalMG/Notes.doc commit 6d3cbd65c3e82e3cf03f6ba49ba8b4acc96c4491 Author: car Date: Wed Jul 22 21:23:33 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit edfd0b923ce8e64ef6f3772be5f12e7e80a32681 Author: car Date: Wed Jul 22 19:45:25 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 1945b59ab07f0ea61169f8f6512609abd604e2ae Author: car Date: Tue Jul 21 17:44:45 1998 +0000 MSVC change Src/C_AMRLib/TagBox.cpp commit 9b192d4aa4059a202d4fea38ce1cbff83463b503 Author: lijewski Date: Tue Jul 21 15:23:40 1998 +0000 Now can use this stuff in serial w/o calling Start & Stop routines. Src/C_BaseLib/ParallelDescriptor.cpp commit e820238b3f1959e2fb6403021954c2cb7b02d428 Author: car Date: Fri Jul 17 17:59:07 1998 +0000 Testing. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit c83cc4c53616704f8295bb5a781316f48df5f2ca Author: car Date: Fri Jul 17 17:32:59 1998 +0000 Minor changes. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit f1e6548f2967355eabebe683734b2f66646a9969 Author: lijewski Date: Thu Jul 16 18:19:18 1998 +0000 Make sure CoarseBox() for NodeBilinear doesn't produce degenerate boxes. Src/C_AMRLib/Interpolater.cpp commit af7c64b42c4ca1711f62378e7f447f89c5b1f3dc Author: car Date: Thu Jul 16 17:34:59 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Notes.doc Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 589fed441fdf27bdd663a56d10fd118db4cb4fb2 Author: lijewski Date: Wed Jul 15 22:42:09 1998 +0000 Removed TagBoxArray::mergeUnique(). TagBoxArray::collate() now removes the duplicate IntVects. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit fb196b286b5e7e11493fc2799aff8e060d512432 Author: car Date: Tue Jul 14 20:47:26 1998 +0000 test Src/LinearSolvers/C_NodalMG/Notes.doc commit 861afdafbd14142f23bbd7e15eb39bd6d007dd8e Author: car Date: Tue Jul 14 20:23:41 1998 +0000 Anal changes Src/LinearSolvers/C_CellMG/ABec_UTIL.F Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F commit 6108eca8693b0beb5389a4bb93547319ee3e23a5 Author: car Date: Mon Jul 13 21:40:42 1998 +0000 First CHeckin Src/LinearSolvers/C_NodalMG/Notes.doc commit abba5e1ed8c99d59d012c421d027f109cf4232fb Author: car Date: Mon Jul 13 18:17:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit bcb3ab2259ae975d9409ab4a941b6344a8a5fc31 Author: car Date: Fri Jul 10 22:32:05 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit e8a0deeea75cfb6d2b44a16b8b00921f43a716d8 Author: car Date: Fri Jul 10 21:56:16 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 8d52ae5f18fec55134f680e3b5dcf1dcd34facb7 Author: car Date: Fri Jul 10 20:13:51 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 11ba2d0688a643e92d0d040c329bc6e2667d629d Author: lijewski Date: Thu Jul 9 18:27:33 1998 +0000 Added back in dest_comp argument to FillCoarsePatch(). Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit a79d76c5ed2011f9a7d6da961d96b02e061750cd Author: lijewski Date: Thu Jul 9 17:59:24 1998 +0000 Assume dest_comp==0 in FillPatchIterator and FillCoarsePatch Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 3783cf499f9ac199245fc67131b9b55f3a8e8c1b Author: car Date: Thu Jul 9 00:53:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 02575940f1b7ffb2157a94d80ad5bce079e41001 Author: car Date: Thu Jul 9 00:50:19 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 007d89bbea2baad2c094df354c334ac829d0a187 Author: lijewski Date: Wed Jul 8 22:26:37 1998 +0000 Modest speedup in how we build PIRMMap. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit dcd43befce5f7c84bb62cc5da099fdf55c2cface Author: lijewski Date: Wed Jul 8 21:56:21 1998 +0000 Fixed very subtle bug in FillBoundary() caching mechanism. Src/C_BaseLib/MultiFab.cpp commit 73286732a57c1b6f1e6087a0d5d9fc39dcf3282b Author: car Date: Wed Jul 8 20:19:57 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 9794a496ed3611ed63643573eb8f2f03219940f2 Author: car Date: Wed Jul 8 19:59:19 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp commit a8f19728a4f40c6f39162b3527c23710d2171eff Author: lijewski Date: Wed Jul 8 19:17:51 1998 +0000 Added updated version of self-intersection caching for FillBoundary(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit ae4740d6f79aaf73160d55d66bea39b7bf0abfc1 Author: lijewski Date: Wed Jul 8 19:17:16 1998 +0000 Added MultiFab::FlushSICache() in appropriate place. Src/C_AMRLib/Amr.cpp commit 9a3632319996d411b67088a789fe1b7e867b7084 Author: lijewski Date: Wed Jul 8 16:36:12 1998 +0000 Added a sentinel value to m_procmap in DistributionMapping. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 78fc43e1c1b7e4d095fe3d99de637477f501db28 Author: lijewski Date: Wed Jul 8 16:33:56 1998 +0000 Removed ProcessorMap() from FabArray. Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit 2289e3ec70113ed1d986473dbf8a0e7fcf3b0995 Author: lijewski Date: Wed Jul 8 16:33:36 1998 +0000 Removed ProcessorMap() from FabArray Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp commit 0a4aaadc089f46ecfae9955567a2959997e674e0 Author: car Date: Wed Jul 8 00:20:23 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit d28873e74df0928ea5dc9d9cfde44431cdc64281 Author: lijewski Date: Tue Jul 7 20:04:56 1998 +0000 Added fpb_cache_size to geometry ParmParse in Setup(). Src/C_BaseLib/Geometry.cpp commit 3d59f6db53ebde2b47d2282d26ad8d85136c0d7d Author: lijewski Date: Tue Jul 7 19:43:28 1998 +0000 Merged the four readFAB()s into one. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 7df4b362411e8556ea1a144e7cc277449e0efc5f Author: lijewski Date: Tue Jul 7 17:25:11 1998 +0000 Added BL_COPYRIGHT_NOTICE macro. Substituted spaces for TABs. Some generic code cleanup. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/Mask.H Src/C_BoundaryLib/Mask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 0e01d1aee96b3d280ade8437f1ae0a8ad639ecc7 Author: car Date: Tue Jul 7 15:41:52 1998 +0000 Support for g++ 2.8.1 Tools/C_mk/Make.defs commit 7186cd1cc733035165e0a2517dfac1b60d4bc257 Author: lijewski Date: Mon Jul 6 21:17:24 1998 +0000 Got the sense of a #ifdef wrong. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.cpp commit d3da773e59f0a774943cf250bd7099447f420a65 Author: lijewski Date: Mon Jul 6 20:44:47 1998 +0000 Now use pubsetbuf() by default instead of setbuf(). BL_USE_SETBUF now means to use setbuf() instead of pubsetbuf(). Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E commit 459d20e3276eb14a511422a09fdd12a92d9b4bdd Author: lijewski Date: Mon Jul 6 20:44:18 1998 +0000 Now use pubsetbuf() instead of setbuf() by default. Src/C_BaseLib/VisMF.cpp commit 5b8c80317cb49b2f792654a0f564bf0185ff06c8 Author: lijewski Date: Mon Jul 6 20:44:00 1998 +0000 Now use pubsetbuf() by default. Src/C_AMRLib/Amr.cpp commit cada317fc69798637b4115dbbc5952a2b620b65b Author: lijewski Date: Mon Jul 6 18:05:03 1998 +0000 Removed a setVal(0). Inverted a swith statement and a for loop. Src/LinearSolvers/C_CellMG/LinOp.cpp commit 434c5c69e320e3923039435f1c89cdf91af01591 Author: lijewski Date: Sat Jul 4 03:35:14 1998 +0000 Fixed bug in FillCoarsePatch(). Src/C_AMRLib/AmrLevel.cpp commit f58e9da9c926e374b5feaf28a1dae3c3925f8ea5 Author: car Date: Thu Jul 2 20:17:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/interface.H commit 8a837b3bc92ffc3727748f66fba70f0e637fcf43 Author: vince Date: Wed Jul 1 20:43:52 1998 +0000 Added distinction between OSF1 versions 3 and 4. Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs commit 3a132e375641790b623af42799ac0740d056114f Author: lijewski Date: Wed Jul 1 19:20:39 1998 +0000 Removed FPMINBOX stuff as well as SerialFillPatch() gunk. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 4df6e72642fb0bc9258515571a08b79793925638 Author: lijewski Date: Tue Jun 30 23:43:45 1998 +0000 More simplification to FillPatchIterator. Src/C_AMRLib/AmrLevel.cpp commit 2e28220e08879d6f147b403702a1ae05925e411b Author: lijewski Date: Tue Jun 30 15:11:21 1998 +0000 Make sure not to call SerialFillPatch if NProcs != 1. Src/C_AMRLib/AmrLevel.cpp commit 17484ca0af66241cd873a943c273a719197e5e8b Author: lijewski Date: Tue Jun 30 04:33:56 1998 +0000 Fixed bug in FillPatchIterator. Left in some fill patch debugging code. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 4f3e8ba67809b643dc090c24f8a4464a9bb0ff81 Author: lijewski Date: Tue Jun 30 04:08:16 1998 +0000 A tad bit of cleanup. More needed. Src/C_AMRLib/Interpolater.cpp commit 1cd8050ca2d2f88b7d058da73ad8e03b98e836ad Author: car Date: Mon Jun 29 17:03:29 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 4e51b918da634a34a28ac3119d03033269cceaac Author: car Date: Mon Jun 29 17:01:54 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit c5ed2f04341ebf44840e129042d277f8a0134cde Author: car Date: Mon Jun 29 16:44:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 522589b17c7a58b042bf6c2df911b3afd00644bb Author: car Date: Mon Jun 29 16:34:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit acf789a10b86df783dfe588c1c1744cf9e38c9af Author: lijewski Date: Sat Jun 27 21:34:42 1998 +0000 Some cleanup in FillPatch() FillCoarsePatch() is now more memory efficient. FillPatch() now sets course ghost cells outside of physical boundary. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 329113b6dc60d222d12d8d91bac10ad9ece9cd30 Author: car Date: Fri Jun 26 20:09:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 6a79874822f9d798364523b78ba691761686f6d7 Author: car Date: Fri Jun 26 19:54:02 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit b695555bb809e9b0b50c7e5bcc14daefafdb3d08 Author: car Date: Thu Jun 25 21:54:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit 5fbc9ef19bdae609667d23300f04574d3c992cd3 Author: car Date: Thu Jun 25 21:26:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit b3743151376b29b69b8ef4144d1b71e605a78e9e Author: car Date: Thu Jun 25 16:34:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit ea451921df41c1d1bc392de4da90e198f9de5095 Author: car Date: Thu Jun 25 15:54:12 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 4cce7c3b128b5ccb8cf9fb25fdf95074d582fa2c Author: car Date: Thu Jun 25 00:15:55 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit b1b26653a1392d1cf1f539205922ed5b67bb4d98 Author: car Date: Wed Jun 24 23:46:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit ade3a0ef1ec57858f777b72e2923bcd4dcc38aa7 Author: car Date: Wed Jun 24 20:49:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 4235eda301043d0343b4880f45522c2ec6d981a2 Author: car Date: Wed Jun 24 17:34:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/restrictor.cpp commit c67a198fd430ede7cef3f8852a58ac9d2bf8f82e Author: car Date: Wed Jun 24 17:26:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit 7994afbbbb1a2cf3fa601aa5490636d2b68e589d Author: car Date: Tue Jun 23 23:57:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit ea66c56bd38d34d5213e9efa9f80b7f22a9e1443 Author: car Date: Tue Jun 23 21:52:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit deca473695175c5ac6be40aba50b0e99ca9cb514 Author: car Date: Sun Jun 21 22:10:35 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit 1e6f48fdf3af3ef7c27e62c16e12c3df6ce4d4a8 Author: car Date: Sun Jun 21 21:53:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 297e34e72608d47510e0073e12b575c6f5a72b3d Author: lijewski Date: Sun Jun 21 18:02:39 1998 +0000 Added additional assert()s re: AddBox() return values. Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit d8e143ffdec5f91079936452a48bcb40f81da331 Author: lijewski Date: Sun Jun 21 17:56:23 1998 +0000 Added additional assert()s re: AddBox() return values. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 4b4852854c915a0c945cc58d12bc6ef7b1422b3c Author: lijewski Date: Sat Jun 20 16:16:09 1998 +0000 Added copyright notice macro. Src/C_AMRLib/Interpolater.H commit ad5a1968f7cbdb7de33f17c54c17e8305f11b03f Author: lijewski Date: Sat Jun 20 03:20:02 1998 +0000 Fixed bug in mapPeriodic(). Src/C_AMRLib/TagBox.cpp commit e60a3898d4a02076aa0da1fc0cd9aeae2f383a98 Author: car Date: Fri Jun 19 22:47:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit b690fc7abda317a22f772b29a020f85c209af38a Author: car Date: Fri Jun 19 19:06:45 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 475223d4f8e8121b4c3e4ae9fec5a3c759a87fde Author: car Date: Fri Jun 19 18:18:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/restrictor.cpp commit cd36cc80c6becd95dca68349e68650f7b0899668 Author: car Date: Fri Jun 19 18:18:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 43e1badb4e0459a737037fce43b1fdd580f1bde5 Author: lijewski Date: Thu Jun 18 23:45:52 1998 +0000 Added another assert(). Src/C_BoundaryLib/FabSet.cpp commit 4b62b801fd3549309b84739be7a89de805b8754d Author: car Date: Thu Jun 18 19:44:50 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 8abc89b589405f61b629598e9d21267a8d25abaa Author: car Date: Thu Jun 18 18:09:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a4cfcc34e6eb6d2bbfce0e65f047841ed1b037e8 Author: car Date: Thu Jun 18 17:54:29 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6486b5da0e17423f4b6b4e9b10d5e04ea4fdfd31 Author: car Date: Thu Jun 18 15:36:57 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 9cbaa9f73bbe6f20924e6eaa38d5e0ab32e5fc06 Author: lijewski Date: Thu Jun 18 04:12:41 1998 +0000 Fixed a bug in the caching of FPBs. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit a7ffe122990c6ad885b4d5876843392a5ceb4bd4 Author: car Date: Wed Jun 17 23:20:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 1b967c15927e3e04394b347be294cd9df4713b52 Author: car Date: Wed Jun 17 19:15:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 2e523afd81ad6df3ecad1275a0620667cd7c7091 Author: car Date: Wed Jun 17 18:16:57 1998 +0000 2D Changes.2D Changes. Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 812b8d86e822387bac39147a363acab6058c778b Author: car Date: Wed Jun 17 18:15:55 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 7038ddfd411b3f0dce5b7a59fb355c304d8b522e Author: car Date: Wed Jun 17 17:23:25 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 88a4a19509a84705d4089fa85cbe13633862a380 Author: car Date: Wed Jun 17 17:00:43 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 84879686ccd296e438da29ab8ebbe9bb23855edc Author: car Date: Tue Jun 16 23:30:05 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit 6579ceb48e8aa10386ccee388087ec06117a760b Author: car Date: Tue Jun 16 20:53:48 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 305766b357b44b52bd37ce840987204d55f2dd21 Author: lijewski Date: Tue Jun 16 18:02:04 1998 +0000 Slight change regarding how we get MFCD from MultiFab. Src/C_BaseLib/Geometry.cpp commit 05f416afb7c5e4e7d79f1e0ba60268761739ddd4 Author: lijewski Date: Tue Jun 16 18:01:37 1998 +0000 Removed call to FlushSICache(). Src/C_AMRLib/Amr.cpp commit 73c54960c1b8ca320b47a9d134dbfd615813e299 Author: lijewski Date: Tue Jun 16 18:01:13 1998 +0000 Removed the self-intersection cache. Doesn't look to have been really useful. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 17806c67378bb437400d7b7e065eedab47b392f7 Author: lijewski Date: Tue Jun 16 18:00:46 1998 +0000 Made FabArrayCopyDescriptor::clear() really work. Src/C_BaseLib/FabArray.H commit 73517b11504a57c83c0f5b259a1e5e6789544d4d Author: car Date: Tue Jun 16 16:02:03 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 51cf3787dc9b72dbaba0daa8867dc01178e1e8f7 Author: car Date: Tue Jun 16 16:01:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 62c546deb23a4b2393744a398106a3fbcc99f690 Author: car Date: Tue Jun 16 15:59:43 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit b63539ae98ecaa5f185fc28c20f684fe1f1c5970 Author: car Date: Tue Jun 16 15:41:38 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 421b290c5f5e468e9d774f1a2f1556c99cbf2158 Author: car Date: Tue Jun 16 03:39:03 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit d880d98cc10b06bab9c0a6d0fd1fe7bad5d77d0f Author: car Date: Tue Jun 16 00:04:49 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 310fee123bfaf8bc89844b41403609a702d42731 Author: lijewski Date: Mon Jun 15 23:55:36 1998 +0000 Added MultiGrid::FlushSICache(). Src/C_AMRLib/Amr.cpp commit 7263d88fda53239acfe6bda7c8e36d530b38757a Author: lijewski Date: Mon Jun 15 23:55:13 1998 +0000 Decreased size of cache. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit ef25fff04a690610423d492b546536debd9ff0b0 Author: lijewski Date: Mon Jun 15 23:54:24 1998 +0000 Added grid self-intersection cache for FillBoundary(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit e3c441a779c0eb04ee27ff08ec9129c716a984a6 Author: lijewski Date: Mon Jun 15 23:53:44 1998 +0000 Inlined operator==()s. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit aeb04c8786b5839fb8336264f53a0c46729b92be Author: lijewski Date: Mon Jun 15 23:52:57 1998 +0000 Simplified operator==() a tad. Src/C_BaseLib/Array.H commit e6dfcf9b0894e75ffab7d7e63f03e831c456eb01 Author: car Date: Mon Jun 15 21:18:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit d71cba396249d71527cfae046073f71d0a0a9b2d Author: lijewski Date: Mon Jun 15 20:06:16 1998 +0000 Rearranged how FPB stuff is done. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit f769ce551cc84f8374bd50a44cf7cd11f26eb0d8 Author: car Date: Mon Jun 15 16:07:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6a38903106911a536d1fae3a44c9ade0386a211c Author: lijewski Date: Mon Jun 15 15:13:25 1998 +0000 Added fabarray_copy RunStat. Src/C_BaseLib/FabArray.H commit ab4564201577041b650133aa0e9eba8b16b42261 Author: lijewski Date: Sun Jun 14 22:05:38 1998 +0000 Removed default size initializer on cache. Src/C_BaseLib/Geometry.cpp commit 48c4cad790ad4f88b930a0b301ee99fc26d1a2ca Author: lijewski Date: Sun Jun 14 06:10:40 1998 +0000 Fixed some bugs I introduced. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 779364e3052fcd59a4033912832bb1614f7714c4 Author: lijewski Date: Sat Jun 13 21:12:28 1998 +0000 Added more RunStats. Src/C_BoundaryLib/FabSet.cpp commit 7630694b76263dbbf634a1455ea08cf55a75a4fc Author: lijewski Date: Sat Jun 13 21:07:34 1998 +0000 Added reflux RunStat. Src/C_AMRLib/FluxRegister.cpp commit 97b5b81ea0099a85e844bbe3462a36a811874ef4 Author: lijewski Date: Sat Jun 13 21:00:35 1998 +0000 Use vector instead of List for cache. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 76632f51bb2f39aa411e9f35ea7daf038026e0fd Author: lijewski Date: Sat Jun 13 21:00:09 1998 +0000 Some performance mods and additional RunStats. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit 9b9a823b656aca6c229f298fac08f62c402eb066 Author: lijewski Date: Sat Jun 13 17:28:58 1998 +0000 Added theFPBmfcd() for cacheing FillPeriodicBoundary info. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 8ad2dbf6ba68648156d11bbf17ec7bb00aac44dd Author: lijewski Date: Sat Jun 13 17:28:30 1998 +0000 Now use MultiFab::theFPBmfcd() Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 3f0da15e7f7f8efed143bcd3a2f848e685c00653 Author: lijewski Date: Sat Jun 13 15:50:01 1998 +0000 Geometry now caches PIRM stuff. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit f48c3fdf54933a99fb8ed38b5e43a4ad68380642 Author: lijewski Date: Sat Jun 13 15:49:43 1998 +0000 Added a CacheSize() member. Src/C_BaseLib/DistributionMapping.H commit 0c91232aa61cce893ce29e1ba7ac11659fa8b29d Author: lijewski Date: Sat Jun 13 15:49:08 1998 +0000 Now cache PIRM stuff. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 00e9124d72155b93d40617b9f7eea08458c717f6 Author: lijewski Date: Sat Jun 13 15:48:11 1998 +0000 Now flush PIRM cache at appropriate time. Src/C_AMRLib/Amr.cpp commit 51bb5ec6a3cd570e43bf5749e1774a925fe55ae6 Author: lijewski Date: Fri Jun 12 20:34:36 1998 +0000 Moved FillBoundary() to MultiFab. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit cca0556395601a7d54c5178cb4f6467e97185734 Author: lijewski Date: Fri Jun 12 19:39:53 1998 +0000 Now only use coalescing fab arena if BL_COALESCE_FABS. Src/C_BaseLib/CArena.cpp commit e12c6dbbfacb20d3caa58812bd725f05a13cce81 Author: lijewski Date: Fri Jun 12 16:47:08 1998 +0000 Added BL_COALESCE_FABS. Tools/C_mk/Make.T3E commit 9b860d8e60047b613f4354939e5c2a90eb342063 Author: lijewski Date: Fri Jun 12 16:37:57 1998 +0000 Unary + and - operators are now const. Src/C_BaseLib/IntVect.H commit 89b230199e736e2667e1661a0426a359e7055952 Author: lijewski Date: Fri Jun 12 16:25:18 1998 +0000 Performance mods for second Reflux(). Src/C_AMRLib/FluxRegister.cpp commit 8d03de2760511975d21af83bcc68f90f5e0b4e07 Author: lijewski Date: Fri Jun 12 00:11:14 1998 +0000 Performance enhancement to first Reflux(). Src/C_AMRLib/FluxRegister.cpp commit b90d7db247f59c109a790b0f7766c945ce28bd42 Author: lijewski Date: Thu Jun 11 22:37:45 1998 +0000 Performance mods for mapPeriodic(). Src/C_AMRLib/TagBox.cpp commit 558208994da77641ccbaa15232b3c55c792dd6c7 Author: lijewski Date: Thu Jun 11 21:24:25 1998 +0000 Performance enhancement to CrseInit(). Src/C_AMRLib/FluxRegister.cpp commit e55809379ffda85f1720dc4a052fba48839f1b57 Author: lijewski Date: Thu Jun 11 18:21:29 1998 +0000 Some FillBoundary() optimizations (hacks?). Src/C_BaseLib/FabArray.H commit d119c97c2bcd9fe889e863c3232456f4971266cc Author: lijewski Date: Thu Jun 11 17:23:10 1998 +0000 Some performance enhancements to copyFrom() and plusFrom(). Src/C_BoundaryLib/FabSet.cpp commit 9a19cdccd1605873d1fa1e03ed08d6400323c18c Author: lijewski Date: Thu Jun 11 00:06:16 1998 +0000 Fixed little bug I just introduced. Src/LinearSolvers/C_CellMG/LinOp.cpp commit 00078cf80f874994c34de77f3b63d06548b9fc7e Author: car Date: Wed Jun 10 23:30:13 1998 +0000 windows fix Src/C_BaseLib/FabArray.H commit 65a2004078af80f40cee8e04196c917aef70ba2f Author: lijewski Date: Wed Jun 10 22:24:32 1998 +0000 Added RunStats to FillBoundary. Src/C_BaseLib/FabArray.H commit 16f2e824443ec3e78e65ae9849da6e9f07c09c60 Author: lijewski Date: Wed Jun 10 22:19:49 1998 +0000 Use std::vector instead of Array. They're much more efficient when resize()d often. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit dcfcb8f1714432999a67022805d3e4e9877fb8d9 Author: lijewski Date: Wed Jun 10 22:18:58 1998 +0000 Reverted out latest FillPeriodicFabArray mods. Got to be a better way ... Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 097335334dd289705945393e829e1ca37c9f9c28 Author: lijewski Date: Wed Jun 10 19:40:49 1998 +0000 Added second version of FillPeriodicFabArray(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit b034f201fa33f926742f7a04d2051334a5f5c647 Author: lijewski Date: Wed Jun 10 19:20:00 1998 +0000 Now use std::vector instead of Array<> in FabArrayCopyDescriptor. Src/C_BaseLib/FabArray.H commit 2d2c86ae8a738ccd4d19e2bdb5d6fd4e36ca0f8a Author: lijewski Date: Wed Jun 10 18:23:01 1998 +0000 Added test for periodicity in FillPeriodicFabArray(). Src/C_BaseLib/Geometry.cpp commit e45ca4f1657370b4190cb1ceb3e75d0149d59b8c Author: car Date: Wed Jun 10 17:40:45 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 896adae9663807efaf58113ccad6759a91d00192 Author: car Date: Wed Jun 10 17:29:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 2660bc84a2e4764021a6f019999f0378af381422 Author: lijewski Date: Tue Jun 9 23:04:48 1998 +0000 Added fill_patch RunStats variable. Src/C_AMRLib/AmrLevel.cpp commit 9536294693807a36c235922b4c66280acfc6eecf Author: lijewski Date: Tue Jun 9 21:41:39 1998 +0000 Put ifdef USE_BSP around the sync in isValid(). Src/C_BaseLib/FabArray.H commit 34cd0bc3919b0e058e000b0d6d671e66adc23fe6 Author: lijewski Date: Tue Jun 9 15:02:43 1998 +0000 Enable BL_USE_SETBUF for OSF1. Tools/C_mk/Make.OSF1 commit ae082ece64cc1142337df97fd02b4174f7c2d360 Author: lijewski Date: Thu Jun 4 17:12:38 1998 +0000 Dealt with multifab copies taking nghost. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit f5a6cc8e58f681c85b316ae1b7ff4867dfd32bab Author: lijewski Date: Thu Jun 4 00:16:32 1998 +0000 MF-MF copy never mucks with ghost cells. Src/C_BaseLib/FabArray.H commit 5f4676a515289e902b0c3bb0764d3bba628d431a Author: lijewski Date: Wed Jun 3 23:11:19 1998 +0000 Reverted back to old version of copyFrom(MF) since we no longer support nghost argument to MF-MF copy. Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 1b61be54e86e1d39ffcb1f1ff7351180f5e97328 Author: lijewski Date: Wed Jun 3 23:10:38 1998 +0000 No longer take nghost argument for MF-MF copy. Src/C_BaseLib/FabArray.H commit 477da0f7fe012673d969051e08cdc0c38c3c968f Author: lijewski Date: Fri May 29 20:58:28 1998 +0000 When !NDEBUG & BL_OSF1 we hide BaseFab::resize(). What we do is call BaseFab::resize() and then setVal() with invalid floating-point values. Should help find erros quicker. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit 40a239b764bad703d74a675ec8ef13f04318d046 Author: lijewski Date: Fri May 29 19:46:52 1998 +0000 Removed a couple unnecessary lines. Src/C_AMRLib/TagBox.cpp commit 6683a15815b31d9df33ce529e463c362c6fd5317 Author: lijewski Date: Fri May 29 18:01:37 1998 +0000 Added toDouble(), toInteger() and toLong(). Src/C_BaseLib/aString.H commit 805fe73c74e29a0b4761e039d197781af52ac65e Author: lijewski Date: Thu May 28 21:34:29 1998 +0000 Parallel copy() now generalized to accept num_comp, src_comp & dest_comp. Src/C_BaseLib/FabArray.H commit f2a4973e86318984f6c80104d3a50de2ed24d90d Author: lijewski Date: Thu May 28 21:34:01 1998 +0000 A little cleanup. Src/C_BaseLib/MultiFab.cpp commit 27f16269442e3ca642bf6f6a0c0c4b241f118c0e Author: lijewski Date: Thu May 28 21:33:45 1998 +0000 copyTo(MultiFab) & copyFrom(MultiFab) implemented in terms of FabArray copy Src/C_BoundaryLib/FabSet.cpp commit b47788850682a35f2034a2ec20cdbe85ebec06b2 Author: lijewski Date: Thu May 28 21:32:03 1998 +0000 Some more cleanup. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 7d4180504a0cff75b4f7a9dc29364127a132ef0f Author: lijewski Date: Thu May 28 18:19:29 1998 +0000 boxarray is now mutable so FabSet can change it in const member functions. Src/C_BaseLib/FabArray.H commit 809f7adbadb35b0ac26dce0843f69b7eda0880c3 Author: lijewski Date: Thu May 28 18:18:55 1998 +0000 copyTo(MultiFab) is now implemented with FabArray::copy(FabArray). Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit db57b0ffdae080b83f916b2402d8b8785e7ba950 Author: lijewski Date: Thu May 28 02:50:44 1998 +0000 Using different FabArray::copy() in copyTo(). Src/C_BoundaryLib/FabSet.H commit 30c04f363a762cb5a23202463b679bf32f43076f Author: lijewski Date: Thu May 28 00:11:22 1998 +0000 Removed some assert()s that didn't really make sense. Src/C_BoundaryLib/FabSet.H commit 842e37c120c921a0085abfc61ed8e9c5f6a7c0e1 Author: vince Date: Wed May 27 22:46:11 1998 +0000 Added Broadcast for MPI. Src/C_BaseLib/ParallelDescriptor.cpp commit 4304a13afa5fcc392db4ffec990a6168a843d671 Author: lijewski Date: Tue May 26 22:58:40 1998 +0000 Merged in new FillFab() routine. Not so fast-n-loose with FillBoxId copying. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit f0eae46b3757d6e8d08c3137a3de5f45a3cda594 Author: lijewski Date: Tue May 26 22:58:17 1998 +0000 Merged in second FillFab() routine. Not so fast-n-loose with FillBoxId copying. Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit 29d335cf2be752e1808d13a173b355f479fa8dca Author: lijewski Date: Tue May 26 22:57:43 1998 +0000 Added second FillFab() taking a destination Box. Merged common code in two AddBox()s into AddBoxDoIt(). Src/C_BaseLib/FabArray.H commit e3325ed1d40f79b6dcaa5507bbae196f97d844e8 Author: lijewski Date: Tue May 26 17:08:54 1998 +0000 Integrated in vector::iterator. Src/C_AMRLib/FluxRegister.cpp commit e74ba3766676db312b1d0899770a8bfd613a325e Author: lijewski Date: Tue May 26 16:17:16 1998 +0000 Oops. Didn't check BSP. Src/C_BaseLib/FabArray.H commit 40745951f2388f6e84861cebc670400f51707bc2 Author: lijewski Date: Tue May 26 00:27:07 1998 +0000 Now use the form of AddBox() in Reflux() taking FabArray grid index. Src/C_AMRLib/FluxRegister.cpp commit eed99680b045c454a5666b43e3f71c7471531ef7 Author: lijewski Date: Tue May 26 00:01:48 1998 +0000 Optimized size of temp FAB used in CrseInit(). Src/C_AMRLib/FluxRegister.cpp commit 3c7ceda8e9314101565ff2573972cb6ab1c9387b Author: lijewski Date: Mon May 25 22:55:24 1998 +0000 Optimized away the temp FAB in copyFrom() and plusFrom(). Src/C_BoundaryLib/FabSet.cpp commit f8c117e4b7ba7cea674d94942d9f2756c865ff1d Author: lijewski Date: Mon May 25 06:01:24 1998 +0000 Fixed bug in FillBoundary(). Src/C_BaseLib/FabArray.H commit 5a568f6e567899ff3e9a39760656648e1a9d6600 Author: lijewski Date: Mon May 25 05:06:25 1998 +0000 Fixed some latent bugs in AddBox() calls. Did some simplification. Src/C_AMRLib/FluxRegister.cpp commit b17e1efa3c62007dd6694d87096ec289d6115f26 Author: lijewski Date: Mon May 25 05:01:10 1998 +0000 Minor fixup. Src/C_AMRLib/TagBox.cpp commit eac12aa28099c47c4efd22432f55f45d17129c91 Author: lijewski Date: Mon May 25 05:00:19 1998 +0000 Fixed some bugs in srccomp/destcomp in AddBox() calls. Src/C_BoundaryLib/FabSet.cpp commit b6a6cfa04b8e10d38b27eecee8b9c91aca3e348d Author: lijewski Date: Fri May 22 23:52:27 1998 +0000 Moved more FABs out of inner loops. Using resize() instead. Src/C_BaseLib/FabArray.H commit 2fe7e36c68fb10246020eb576cd4506f252d3437 Author: lijewski Date: Fri May 22 23:31:31 1998 +0000 Only communicate overlap in copyFrom() and linComb(). Src/C_BoundaryLib/FabSet.cpp commit 62f5e80c81efd59e365c84c0b4e21c5c24bb33ed Author: lijewski Date: Fri May 22 22:30:28 1998 +0000 Removed a couple assert()s that didn't look OK. Src/C_BoundaryLib/FabSet.cpp commit 2a887085ad7107986197b3503f091bfdcd119c4e Author: lijewski Date: Fri May 22 22:08:41 1998 +0000 Moved some FAB constructors out of inner loops. Use resize() instead. Src/C_AMRLib/AmrLevel.cpp commit ecc1f453b7556a515ef995c43a40585b41df4631 Author: lijewski Date: Fri May 22 22:03:14 1998 +0000 Moved FAB construction out of inner loops. Use resize() instead. Src/C_BaseLib/FabArray.H commit 4393d3bc48bec8b78afbb69d530ff81151d1158f Author: lijewski Date: Fri May 22 21:52:49 1998 +0000 Added copyTo(MultiFab). Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 045b3203e6975062a0e816042d2c9b5767b30108 Author: lijewski Date: Fri May 22 21:46:29 1998 +0000 Moved some FABs out of inner loops. Use resize() instead. Src/C_BaseLib/Geometry.cpp commit 266e4afb963a61a26e2b00f9a3c7e11ebbe6e828 Author: lijewski Date: Fri May 22 21:46:01 1998 +0000 Added ncomp argument to resize(). Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 02a2499619ac40ae141ff8c57bf551829121d023 Author: lijewski Date: Fri May 22 21:45:47 1998 +0000 Moved some FAB constructors outside of loops. Use resize() instead. Src/C_AMRLib/FluxRegister.cpp commit dc5321fd53f3f96288d59e3c9c1373fa1aea6b00 Author: lijewski Date: Fri May 22 17:47:11 1998 +0000 Reverted out previous change; shouldn't have been checked in. Src/C_AMRLib/DatasetClient.cpp commit 0a0364f8c4e6ee6b56ce60f26c2906d7bbbd7425 Author: lijewski Date: Fri May 22 17:45:14 1998 +0000 Now using setComplement() on FABs instead of setBndry() on MultiFabs. Src/C_AMRLib/DatasetClient.cpp commit 24eaf7d16e257d0cefc11e73c0289057b78e2c1a Author: lijewski Date: Thu May 21 22:44:51 1998 +0000 CXXOPTF=+K2 Tools/C_mk/Make.T3E commit 12a182baa04a68f8e7b1cdc34ce7231c47f6d7fc Author: car Date: Thu May 21 21:28:43 1998 +0000 assert foolishness Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 4c4e44fed2d8d44ce53542b0778023bdf2c13af4 Author: lijewski Date: Thu May 21 18:16:52 1998 +0000 Added final newline in file to quiet KCC Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit bb8a6297234eab5b74eae97365723ecfa92d7f0b Author: lijewski Date: Thu May 21 16:48:39 1998 +0000 DependentFabArrayIterators now check for equality of processor maps. Src/C_BaseLib/FabArray.H commit 35dbc72e3c40e016854763e73a82a93d5a508ee8 Author: lijewski Date: Thu May 21 15:04:29 1998 +0000 Removed DependentMultiFabIterator stuff from FillBoundary(). Src/C_AMRLib/StateData.cpp commit 73640750c048a2cbdc785c22b95b50af3294c16e Author: car Date: Wed May 20 18:10:05 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit 415b1bd51c9446d6e81536cae4c8f3673c1fc06f Author: marc Date: Wed May 20 00:10:45 1998 +0000 Make contains() const Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp commit 2285511c59d677551fad1ea21d38d867b3b53416 Author: marc Date: Tue May 19 21:08:35 1998 +0000 Fix a couple of little errors. Src/C_BaseLib/Geometry.cpp commit 14d82a76c5568d6679f9a75612b6e6a8ca9ab83e Author: lijewski Date: Tue May 19 20:27:03 1998 +0000 Added no_ovlp argument to FillBoundary stuff for SyncRegister code. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 997dc7062627c80effd9971e549ea4728854d239 Author: lijewski Date: Tue May 19 17:10:52 1998 +0000 Moved allocation of pshifts outside of all loops. Src/C_BaseLib/Geometry.cpp commit 8ae6e89d91a060b31af3451224d930dbc840d04b Author: lijewski Date: Mon May 18 17:52:20 1998 +0000 Some cleanup/simplification ... Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp commit 0ccff42f46df50de43cd3ce9e1fb17113babaa54 Author: car Date: Mon May 18 01:20:10 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 73136f067f1e8954b124cbb0099d5e69b0d53c61 Author: lijewski Date: Sun May 17 00:57:23 1998 +0000 Added FillPeriodicBoundary() taking src_comp and num_comp. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 938932d4f0bc7f7d435ec9d4399330c80f03e58c Author: car Date: Fri May 15 22:31:29 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit 7c546102472b9624a5f8a3be0de5f7852f9bb56e Author: car Date: Fri May 15 22:28:48 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 4910eb18ba70096b013dded6b861df96db598d3c Author: lijewski Date: Fri May 15 18:13:12 1998 +0000 Fixed bugs in TagBoxArray::mapPeriodic() and TagBoxArray::coarsen(). Src/C_AMRLib/TagBox.cpp commit 0211e7104de736d6e05828f5f33777be693287ba Author: car Date: Fri May 15 16:36:06 1998 +0000 some 2D fixes Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit edcaaf68f0f3197a32d842fec399f8c60f03e993 Author: car Date: Fri May 15 16:16:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit 4fff2af87318afdaba7a9d565223e81f02d62558 Author: car Date: Fri May 15 16:05:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit bbd9c6131bcecb00608e82b08f90155ea652d041 Author: car Date: Fri May 15 00:32:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit ea58e78ff0f4e4183fc1a67aa1e09138dfb83c72 Author: car Date: Fri May 15 00:31:48 1998 +0000 3D only, sorry Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 89344527f0781c9252228dc34841ed004d3c0d96 Author: vince Date: Thu May 14 22:23:04 1998 +0000 Fixed minor bug due to TagBox changes. Src/C_AMRLib/DatasetClient.cpp commit ed129f3a991384f20f89bf62b2b3fe35e6f4e206 Author: almgren Date: Thu May 14 22:08:50 1998 +0000 Modified main.cpp. Amr.{H,cpp} to allow the user to specify a starting time for the calculation (strt_time, read in the inputs file like stop_time). Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 7325167a8d67186e6b302d51f246e718e9a537b0 Author: lijewski Date: Thu May 14 22:06:03 1998 +0000 -O5 -> -O in FOPTF. Compiler has problems with few routines. Tools/C_mk/Make.OSF1 commit d0bcee9a5febd8514c5956b9758aba9f4f9a9ef6 Author: almgren Date: Wed May 13 23:15:03 1998 +0000 Changes necessary to pass stop_time through to the applications (NavierStokes, HyperClaw, e.g.) so that it can be used for time step control. Also allow only one of max_step and stop_time to be set in inputs with the other not affecting the time step control. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 9f7c2a82232daab9f1b61c79ff1ff6dd6fc008a4 Author: almgren Date: Wed May 13 18:57:09 1998 +0000 Changed some ParmParse get's to query's and modified the plot test in Amr::init() so that it will make plt0000 if plot_int > 0 OR plot_per > 0. Src/C_AMRLib/Amr.cpp commit 442daa7b5e63cb14588e1ec9ac4f603b96345fb6 Author: lijewski Date: Tue May 12 22:12:42 1998 +0000 Can now pass name of probin file to Fortran. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/PROB_AMR_F.H commit f12fd16dad227a17c3087d42f50fc8d2ed5f5726 Author: car Date: Tue May 12 19:38:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 86a8cf1aa1e5175962b91f33f8ca9c033a97655d Author: car Date: Tue May 12 15:36:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 7a7519751512c641fbeecb22395fb0bb36cc07c6 Author: lijewski Date: Mon May 11 17:45:46 1998 +0000 -O2 -> -O for CXXOPTF when using g++. The former yields some nasty optimization bugs. Tools/C_mk/Make.defs commit 02404fcf90a9a2e1d870421d6433cb6915d5d1ab Author: lijewski Date: Mon May 11 17:06:24 1998 +0000 Removed some doc++ comments that didn't translate to html well. Src/C_AMRLib/Derive.H Src/C_AMRLib/ErrorList.H Src/C_AMRLib/StateDescriptor.H commit 7ad339e6c6f5a1ff0f14364991626e7b6ad99b9f Author: car Date: Fri May 8 22:25:19 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 02e74468af9c2232ddb62acc30355ca1d30377f6 Author: car Date: Fri May 8 17:47:03 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/interface.cpp commit 86bff1dbe3df0bc33e6e4862c0b1c6102956df90 Author: lijewski Date: Fri May 8 15:58:50 1998 +0000 Added more Doc++ comments. Src/C_AMRLib/FluxRegister.H commit 3daabeeda6935b050198ecc0bb91b1e8a66fc21a Author: lijewski Date: Fri May 8 15:57:12 1998 +0000 Updated Doc++ comments. Src/C_BaseLib/Box.H commit a543fb636b2b07d62a738f98b99e23358930cdac Author: marc Date: Fri May 8 00:23:56 1998 +0000 Fix up stuff in Reflux that was wrong for certain combinations of src_comp/dest_comp/etc. Src/C_AMRLib/FluxRegister.cpp commit f42be05ec8cb72da14fa2ff96e7642197d420ee5 Author: lijewski Date: Thu May 7 22:26:09 1998 +0000 Added ResetWallClockTime(). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit c2e50d6c3f96855499cfa7981dac6f628d866698 Author: car Date: Thu May 7 19:39:38 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit aa127c43c81579dd22b51f18e14ad7a472b740f2 Author: car Date: Thu May 7 18:28:59 1998 +0000 Microsoft VC++ bug with nested classes Src/C_BaseLib/Geometry.H commit 8e66035e94f7805e8f0eea7c45149ea05cfdabe3 Author: lijewski Date: Wed May 6 22:36:14 1998 +0000 Added doc++ comments. Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/FabSet.H commit 96a6be0aef77c841645d730d20e21e3b1c7ea5ca Author: car Date: Wed May 6 22:21:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 2a0447b292c785b132d735694aa1d02deb99b81e Author: car Date: Wed May 6 20:11:54 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 042f08fc0aaca7f500be693e9f7807e71224a072 Author: lijewski Date: Wed May 6 17:52:43 1998 +0000 Gunk for doing doc++ Src/C_BoundaryLib/GNUmakefile commit c314ea5979524c87706b22bcf52bd13138d3a04a Author: lijewski Date: Wed May 6 17:50:44 1998 +0000 Added doc++ comments. Src/C_AMRLib/Amr.H Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/BCRec.H Src/C_AMRLib/Cluster.H Src/C_AMRLib/Derive.H Src/C_AMRLib/ErrorList.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/TagBox.H commit 4da161f2317d6adcb4c2b8bed4203406956e94a3 Author: lijewski Date: Wed May 6 17:50:30 1998 +0000 Gunk for doing html and ps from Doc++ comments. Src/C_AMRLib/GNUmakefile commit c4c7094080429ad7cddcece84107506033bfc094 Author: car Date: Wed May 6 03:33:49 1998 +0000 *** empty log message *** Src/C_AMRLib/.cvsignore Src/C_BaseLib/.cvsignore Src/C_BoundaryLib/.cvsignore Src/LinearSolvers/C_CellMG/.cvsignore Src/LinearSolvers/C_NodalMG/.cvsignore commit 7a33c2d28a6be7ae83d636593163fc8069d268de Author: car Date: Tue May 5 00:25:29 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 779ffa56232870e248e3b39a4b1262d3e609be34 Author: lijewski Date: Mon May 4 23:13:13 1998 +0000 Implemented ReduceBoolAnd() and ReduceBoolOr() for MPI. Src/C_BaseLib/ParallelDescriptor.cpp commit f7923952cfa21b74e91448752be7eb9abbe2e90e Author: lijewski Date: Mon May 4 21:24:53 1998 +0000 Added doc++ comments. Src/C_BaseLib/Array.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CArena.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/VisMF.H commit 31b397cc33c62fdc30667a28b075109fd1377c68 Author: car Date: Mon May 4 17:36:56 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 3133bc231a2528d010f6b5c892729d75eab50ad0 Author: car Date: Fri May 1 19:18:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 7dfae3d4c3a5017927669d5bf57e138e1b941df1 Author: car Date: Fri May 1 18:23:58 1998 +0000 *** empty log message *** Src/C_BaseLib/GNUmakefile Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 6bdc6e942b23045ad199191cbd3b14498750b197 Author: lijewski Date: Fri May 1 17:12:32 1998 +0000 Mods to FillFab() so g++ 2.8.1 will compile. Src/C_BaseLib/FabArray.H commit 09e18dbb6c31845225873da9a7fe3e4c1274bb1f Author: lijewski Date: Thu Apr 30 18:04:33 1998 +0000 Removed member template OpMin(). Src/C_BaseLib/Utility.H commit 1637ab5b15aef54384b987b721df5ce22db52b84 Author: lijewski Date: Thu Apr 30 16:35:03 1998 +0000 Mods to quiet g++ 2.8.1 Src/C_AMRLib/Amr.cpp Src/C_BaseLib/ArithFab.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/Utility.cpp commit 8eec662d54356745473741990bee19a9a53bef98 Author: lijewski Date: Thu Apr 30 15:51:19 1998 +0000 Removed BL_AUTO_INSTANTIATE Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs commit 856bbdde82198f01ab360aaae1a4be97e29667eb Author: lijewski Date: Wed Apr 29 23:12:37 1998 +0000 fixed typo for GNUG workaround Src/C_BaseLib/Geometry.H commit 4abead740996163b37b52e0509d0ac9fce318ec7 Author: car Date: Wed Apr 29 22:39:44 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 5884a75b7c9984551ae2eb9736f36f9e1a92b1ff Author: lijewski Date: Wed Apr 29 20:06:10 1998 +0000 Changed way GNUG workaround was coded. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 920b98a57bf26b430aed7ba7ad47f20196595721 Author: car Date: Tue Apr 28 15:43:09 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit 223211f8288421dfa2e70e1559a5ca01c8c6e811 Author: car Date: Mon Apr 27 21:27:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 48d25fd663db95fdcbb17b686c350dae4834932a Author: car Date: Mon Apr 27 20:27:18 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 86d514b9333aca0da7f7ffeced04d8d9916253d6 Author: lijewski Date: Mon Apr 27 19:43:46 1998 +0000 The BoxList argument to AddBox is now passed as a BoxList*. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 41998f167708da8abd3071eb75aafee095116a93 Author: lijewski Date: Mon Apr 27 19:43:19 1998 +0000 The BoxList argument to AddBox is now passed as a BoxList* Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit 8b4a73c136b2252d2000e9d28c3de44a606c3eec Author: lijewski Date: Mon Apr 27 19:42:54 1998 +0000 The BoxList argument to AddBox is now passed as a pointer to make it easier to deal with the case where we aren't interested in the BoxList. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp commit 537dfdce0cc1d4c4e30acef878daed6202e85a76 Author: car Date: Mon Apr 27 17:37:40 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/restrictor.cpp commit fd2b7b4fdc1d59a3bc09b148c44d2589e7d6e137 Author: car Date: Mon Apr 27 17:30:25 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6bb3101efb4050986b225ece9bf817a04a404dd6 Author: lijewski Date: Mon Apr 27 16:31:42 1998 +0000 Mods to work on non-standard conformant compilers. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 14416136c7817e9fb6bdf1947852c379a5d4aeda Author: car Date: Fri Apr 24 21:23:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.cpp commit 7bc1f484a28ccec35fd0f5903f390a94fb1269f7 Author: car Date: Fri Apr 24 21:19:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.cpp commit e07a031177d103eb3223ab889c010260857251bc Author: lijewski Date: Fri Apr 24 17:52:19 1998 +0000 Now maintain NProcs() and MyProc() in static data members. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 9c5d007076675d5f5639858ee50c44b75d9411b7 Author: lijewski Date: Fri Apr 24 17:10:18 1998 +0000 Collapsed a number of data members of FabComTag. Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H commit 05d86397ef796da57c9db8838a22d53c882904ad Author: lijewski Date: Fri Apr 24 16:28:57 1998 +0000 Fixed typo. Src/C_AMRLib/FluxRegister.cpp commit 958170a51bc76d62152acd24d311601f38ead464 Author: lijewski Date: Fri Apr 24 16:23:58 1998 +0000 Use query() instead of contains() to set amr.v Src/C_AMRLib/Amr.cpp commit e7cbe8c869950ca62cc1ebe359c6b77b16505749 Author: car Date: Fri Apr 24 01:03:30 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/interface.cpp commit 184b42b94aabc4302e7d3982210a20dcfb10076c Author: lijewski Date: Fri Apr 24 00:11:38 1998 +0000 Got CrseInit()/CrseInitFinish() working with MPI. Src/C_AMRLib/FluxRegister.cpp commit 97506424b51bc1a088f3027e26c3a79905d4d453 Author: car Date: Thu Apr 23 22:37:48 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/interface.H commit 72bcb0544026fe306348e2ccaaa757d462a9298b Author: car Date: Thu Apr 23 21:13:51 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 15cf84779e46fbedda76e02eb3e67d133f234cb9 Author: car Date: Thu Apr 23 17:24:18 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 4f0a1fdc9ba91628b9664d9af931bfac1bef83f0 Author: lijewski Date: Thu Apr 23 16:37:32 1998 +0000 MPI_Send() -> MPI_Ssend() Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/VisMF.cpp commit 0dc2b0f7a67e6297900c3dc58d7a4a8f4dc3158e Author: car Date: Thu Apr 23 05:07:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit cc549725f601d3ef94df81b6984aa6d7189891d6 Author: car Date: Thu Apr 23 04:48:44 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit 9c7eb639b3a877cdaade59aab021713f4c75f671 Author: car Date: Thu Apr 23 04:46:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit be5cba063b9c6bba49550372936f36289d501b0c Author: car Date: Thu Apr 23 04:31:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit d7fa0d5b05a82669a6f6cccf3e4e3afe0574adfd Author: car Date: Thu Apr 23 04:13:12 1998 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 7db1d5cc7fa9f8793f6a44ba0bafd216ce53e667 Author: almgren Date: Wed Apr 22 23:56:20 1998 +0000 Removed the trace, debug and silent flags, and replaced them with the verbose flag. Also made verbose be defined by pp.contains("v") rather than pp.contains("verbose"). This is in keeping with how verbose is defined in the IAMR files. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 964861b3c4436f4ca45327765e02f61bc95b2c4d Author: car Date: Wed Apr 22 23:48:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LinOp.H commit 564e3a292908aa94ab7eee639b470e47cb41bd55 Author: marc Date: Wed Apr 22 23:39:31 1998 +0000 Added info for periodic boundaries. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit b072e19262ec3d6585a00ec3e726ea8465b27f67 Author: car Date: Wed Apr 22 23:39:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6c15caa335b167bae3d7c60ebced363cbe1096cc Author: car Date: Wed Apr 22 22:51:24 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a2783df5a9be469d53366e4ae50e4418474ff0f4 Author: lijewski Date: Wed Apr 22 22:40:37 1998 +0000 Bug in TagBoxArray::collate(); used sizeof(IntVect) instead of BL_SPACEDIM. Src/C_AMRLib/TagBox.cpp commit 9e174c4a86be597195498c2cf71dcc04808f7041 Author: lijewski Date: Wed Apr 22 21:02:48 1998 +0000 Wasn't erase()ing fabComTagList in MPI case. Src/C_BaseLib/FabArray.H commit 4d1458dc693bbbce3760d1e27d2e1e72783d28db Author: car Date: Wed Apr 22 19:58:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit c94c80536c0b25198fb976b7036ab07ca523dd1b Author: lijewski Date: Wed Apr 22 19:39:06 1998 +0000 Add setVal() to bad value when debugging on OSF1. Src/C_BaseLib/FArrayBox.cpp commit 2ce37c009ca9930f84af2564f134913ff0e8117c Author: lijewski Date: Tue Apr 21 23:09:42 1998 +0000 Added TRACER objects to all code making direct MPI calls. Src/C_BaseLib/VisMF.cpp commit 40493e15bc24859b598b1116601423a5bdd3d13f Author: car Date: Tue Apr 21 22:24:25 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit fbbed0fdaca707fe89c052b181ba04498af4d9ac Author: almgren Date: Tue Apr 21 22:22:41 1998 +0000 Slight cleanup. Src/LinearSolvers/C_NodalMG/proj.cpp commit ee8fcab2b6ade4f870cff523058f4dc3b8613e06 Author: almgren Date: Tue Apr 21 22:16:50 1998 +0000 Modified proj.cpp to add init calls for m.length() = 3 before each test of the projection so that each test would have the right initial conditions. Also modified the timing routines so they would time the projections and not the initializations. Src/LinearSolvers/C_NodalMG/proj.cpp commit 32a047481ec70bc25b4190a40bbc069d6ec79e23 Author: car Date: Tue Apr 21 21:04:03 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/restrictor.H commit 7faaecd4624943030a62bb06ebf6fe8195d5b254 Author: marc Date: Tue Apr 21 19:32:43 1998 +0000 Limit optimization reduction to terrain file. Possibly to remove this if we split up the terrain code further Src/LinearSolvers/C_NodalMG/GNUmakefile commit 3b9a6e77cdd0fe4b39f4c81e07645d07040be859 Author: car Date: Tue Apr 21 16:40:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit 75b62c164f5403a9f6af749969919de8503132ab Author: lijewski Date: Tue Apr 21 05:21:08 1998 +0000 Made parallel-aware. Src/C_BaseLib/Tracer.cpp commit b0333b1cf8f93fec60d3e29eddbc59eb2a436be3 Author: lijewski Date: Tue Apr 21 05:20:27 1998 +0000 Commented out TRACER in StartParallel(). Src/C_BaseLib/ParallelDescriptor.cpp commit 018dbc6008ebe705368b294e9890e00c6e0692cf Author: car Date: Tue Apr 21 02:01:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 0b9c3c984f6bcd9ef5e92d4ea936e828aa8d3232 Author: marc Date: Tue Apr 21 01:44:55 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 109a7c8d99bfe5a18e0e11e39bbe2a45f6d79713 Author: car Date: Mon Apr 20 23:44:01 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit c6944dee7961335fd4462d037341fba8c6aeeec3 Author: car Date: Mon Apr 20 22:57:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.H commit 2f5098661ce89ac74aadfa1ebf9198f98666d1b5 Author: lijewski Date: Mon Apr 20 22:43:03 1998 +0000 Added a few TRACER objects in functions making MPI calls. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit a90ccae964270446692d3bd8a21304270deb4a06 Author: lijewski Date: Mon Apr 20 22:34:09 1998 +0000 Added a few TRACER objects for functions that make MPI calls. Src/C_BaseLib/FabArray.H commit 909974fb8248f082c4659f5d5c3ed08882e8b3a6 Author: lijewski Date: Mon Apr 20 22:18:29 1998 +0000 Added TRACER objects to MPI calls. Src/C_BaseLib/ParallelDescriptor.cpp commit 0186aa8854aed268a39948e038f2c34a4c0ce122 Author: car Date: Mon Apr 20 22:17:10 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 4f4bcf73e6ba8437ac3a31b8b5bd3943adf05240 Author: lijewski Date: Mon Apr 20 22:16:38 1998 +0000 Added fflush(stdout) after printf(). Src/C_BaseLib/Tracer.cpp commit 8f0f988b36e9354d6b13506a8757a168d7b918b3 Author: car Date: Mon Apr 20 20:24:56 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 12679c698478eb4ee599538391d8e1fe59fcd589 Author: car Date: Mon Apr 20 19:14:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp commit 1bb07f853ccbb0a9238c7fc56de60f3ac5c28919 Author: car Date: Mon Apr 20 19:14:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp commit dff86a55f0ccac8bcf4c86fbe5dcf8b9133ad0d6 Author: lijewski Date: Mon Apr 20 04:18:54 1998 +0000 The sense of an Assert() was backwards. Src/C_BaseLib/ParallelDescriptor.cpp commit 330ba38cc92413f18b53b9394316d000905d03c3 Author: lijewski Date: Mon Apr 20 04:18:14 1998 +0000 Fixed some MPI-specific bugs. Src/C_BaseLib/VisMF.cpp commit 69aac649455fc86b32f6d01f6ae4bfac798fb64f Author: lijewski Date: Sun Apr 19 03:46:41 1998 +0000 Added SetMessageHeaderSize(), ShareVar() and UnshareVar() in MPI as no-ops. Src/C_BaseLib/ParallelDescriptor.cpp commit e357907feb377d831e0ddf5d6b1ecbca26165d37 Author: lijewski Date: Sun Apr 19 03:46:05 1998 +0000 MPI-specific code for FabArray::Copy(FAB). Src/C_BaseLib/FabArray.H commit e23034df536f9477aba111e2f29e57b1c5f9e0c0 Author: lijewski Date: Sat Apr 18 21:24:58 1998 +0000 Added MPI-specific code for TagBoxArray::collate(). Src/C_AMRLib/TagBox.cpp commit 59651f4c39dc176254067fa38b1077eb0da57819 Author: car Date: Fri Apr 17 23:25:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit f16bade4715f43abd22bec03200c4d3e5adb00dc Author: car Date: Fri Apr 17 23:25:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit cc921c1f6b2d78573034da47af6c88773fb50e99 Author: lijewski Date: Fri Apr 17 22:22:06 1998 +0000 Added three more integers to CommData. Wrote MPI-specific code for CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 4962def3da2adc91bb7b0a4a842408c29768ede1 Author: lijewski Date: Fri Apr 17 22:21:31 1998 +0000 Added three more integers to CommData. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit c7d90031f6a3c5f09ee2117cff7dd310e1da3a8f Author: car Date: Fri Apr 17 20:57:04 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit a0200c6d2fc02f0a1c40203e0abfb1bde4b16266 Author: car Date: Fri Apr 17 19:22:41 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 7ed45149c087a9fd60b725888bea54be009dfb49 Author: lijewski Date: Fri Apr 17 18:14:12 1998 +0000 Added fromproc() and id() to CommData. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 6f1df7a930e3a9eb95db1c4c8ec3a093e85a1d28 Author: lijewski Date: Fri Apr 17 18:13:51 1998 +0000 Added fromproc() and id() to CommData. Now use the combination of these two values to match up fab boxes and the data on those fab boxes that are sent separately. Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 1802928b39c5fa771d2ad54a5b4f84f6e2a6bbbf Author: car Date: Fri Apr 17 16:40:11 1998 +0000 check for non-existent test file Src/LinearSolvers/C_NodalMG/proj.cpp commit bcf531b09601a0f729d6b8705f4258b959d7222e Author: marc Date: Fri Apr 17 00:30:48 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit 6a9611cf33aaf6fc0da42ccedb9575d0908f6a30 Author: car Date: Thu Apr 16 23:54:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 17423de807783dde0e6607fc77799a9cc54a86ce Author: lijewski Date: Thu Apr 16 23:07:09 1998 +0000 Merged in template<> mpi_data_type(T*) Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit 2ee12323d451fb459db57fb162c74f127fb58ccf Author: car Date: Thu Apr 16 22:50:12 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit b2a520b6e7868cb797098109acce68bd5162180e Author: lijewski Date: Thu Apr 16 22:36:15 1998 +0000 Moved CommData to ParallelDescriptor. Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit d0f4fafb7b1ef5df478fd64ec970f3a2528369e7 Author: lijewski Date: Thu Apr 16 22:05:13 1998 +0000 Now use CommData from ParallelDescriptor for MPI communication. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 5515cf8dd82c59c22d2ade43ca895ccb79eb987f Author: car Date: Thu Apr 16 21:29:05 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit d8ee97aa071883eedbe28eeec1b0714a4c70aa0b Author: lijewski Date: Thu Apr 16 20:31:47 1998 +0000 Fixed minor nit found by dbs. Src/C_BaseLib/IntVect.cpp commit 62cef72d90b81f547446a8f6b959d5ecdb4cad60 Author: lijewski Date: Thu Apr 16 20:27:03 1998 +0000 Some simplification in preparation for MPIification ... Src/C_BaseLib/FabArray.H commit e5e2d7e52aec6c0ec6fc688a430b0fbcd141cd89 Author: lijewski Date: Thu Apr 16 18:00:41 1998 +0000 List<> -> vector<> ... Src/C_BaseLib/FabArray.H commit 4da74f5fc6f62b6737646f62fe5f4a6eb1d1838c Author: car Date: Thu Apr 16 16:15:48 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit ec4e872ddeac699273e8e4be1730df8e75a48d6c Author: lijewski Date: Thu Apr 16 00:12:29 1998 +0000 List -> vector. Src/C_BoundaryLib/FabSet.cpp commit e753ccd2177ee071fb17ea971eac0494474670d5 Author: marc Date: Wed Apr 15 23:47:53 1998 +0000 reinstate files Tools/C_util/DatasetClient.H Tools/C_util/DatasetClient.cpp Tools/C_util/README commit 787b450d6fe7d8709f9238691a62409b5aada986 Author: car Date: Wed Apr 15 23:42:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit aba086ff6ab102dd05ffc03c53d4709f811c8e87 Author: lijewski Date: Wed Apr 15 23:31:28 1998 +0000 List<> -> vector<> ... Src/C_AMRLib/TagBox.cpp commit b023c86848d36eb34847fb5ec270159d8cb62147 Author: marc Date: Wed Apr 15 23:29:14 1998 +0000 Oops! these were already in DataServices Tools/C_util/README commit db08156535b6d8705dd60917ac158ea5ace7e39a Author: marc Date: Wed Apr 15 23:25:30 1998 +0000 Clean up file Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/Make.package commit 9d18f79dec0de6a0a6a1ad1ddb54de3d905ddd08 Author: marc Date: Wed Apr 15 23:19:05 1998 +0000 Clean up the file a little Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/Make.package Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package commit 0118d847c6c94cefe328bc1ce2465a4f6efaa6e1 Author: marc Date: Wed Apr 15 23:17:40 1998 +0000 Initial revision Tools/C_util/ArrayView.H Tools/C_util/README Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/GNUmakefile Tools/C_util/ViewMF/Make.package Tools/C_util/ViewMF/main.cpp Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp Tools/C_util/preload.cpp commit 392090f32793f530f69e4b243185d8aab0b45f5a Author: lijewski Date: Wed Apr 15 22:49:54 1998 +0000 List -> vector List -> vector. Src/C_AMRLib/FluxRegister.cpp commit 3e25f275a2c7f0f4896962fe7379dd08ff699ca0 Author: marc Date: Wed Apr 15 22:36:20 1998 +0000 Move to util directory Src/LinearSolvers/C_CellMG/Test/WritePlotFile.H Src/LinearSolvers/C_CellMG/Test/WritePlotFile.cpp Src/LinearSolvers/C_CellMG/Test/preload.cpp Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.H Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.cpp Src/LinearSolvers/C_TensorMG/Test/preload.cpp Tests/LinearSolvers/C_CellMG/WritePlotFile.H Tests/LinearSolvers/C_CellMG/WritePlotFile.cpp Tests/LinearSolvers/C_CellMG/preload.cpp Tests/LinearSolvers/C_TensorMG/WritePlotFile.H Tests/LinearSolvers/C_TensorMG/WritePlotFile.cpp Tests/LinearSolvers/C_TensorMG/preload.cpp commit 28799f46a0f78a7794b8f66fd11bd5e020cfdbef Author: marc Date: Wed Apr 15 22:14:58 1998 +0000 Update to properly extend to multiple components Src/LinearSolvers/C_CellMG/Test/WritePlotFile.cpp Tests/LinearSolvers/C_CellMG/WritePlotFile.cpp commit 7c7d4cf87e105ad2e72440e6dcb188109e7cc9ba Author: marc Date: Wed Apr 15 21:48:09 1998 +0000 Enter changes necessary for multiprocessor solves. Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCBndryData.H Src/LinearSolvers/C_TensorMG/MCBndryData.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit c1ef9edb340526c8b3eff59f3b64f480577d0f2c Author: marc Date: Wed Apr 15 21:34:44 1998 +0000 Add test files for multiprocessor version of tensor solve Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/Make.package Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.H Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.cpp Src/LinearSolvers/C_TensorMG/Test/amrvis.defaults Src/LinearSolvers/C_TensorMG/Test/inputs2D Src/LinearSolvers/C_TensorMG/Test/inputs3D Src/LinearSolvers/C_TensorMG/Test/inputs8 Src/LinearSolvers/C_TensorMG/Test/main_2D.F Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Src/LinearSolvers/C_TensorMG/Test/vpramps.dat Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package Tests/LinearSolvers/C_TensorMG/WritePlotFile.H Tests/LinearSolvers/C_TensorMG/WritePlotFile.cpp Tests/LinearSolvers/C_TensorMG/amrvis.defaults Tests/LinearSolvers/C_TensorMG/inputs2D Tests/LinearSolvers/C_TensorMG/inputs3D Tests/LinearSolvers/C_TensorMG/inputs8 Tests/LinearSolvers/C_TensorMG/main_2D.F Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/C_TensorMG/vpramps.dat commit 6bd8cade091d432c48501119d57d1d0a7f5ecd97 Author: marc Date: Wed Apr 15 21:28:32 1998 +0000 Add a couple of test grids. Src/LinearSolvers/C_TensorMG/Test/grids/gr.3_2x3x4 Src/LinearSolvers/C_TensorMG/Test/grids/gr2D Tests/LinearSolvers/C_TensorMG/grids/gr.3_2x3x4 Tests/LinearSolvers/C_TensorMG/grids/gr2D commit bcf3b46bb48cc850daa63202cb8105e2ab76d4f9 Author: marc Date: Wed Apr 15 21:25:55 1998 +0000 Commit cosmetic and other changes to (nearly) complete the port to parallel. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/Mask.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/WriteMultiFab.H Src/LinearSolvers/C_CellMG/WriteMultiFab.cpp commit 0101b7781fd3476a39edebacd6f99a8de00efa77 Author: lijewski Date: Wed Apr 15 21:18:31 1998 +0000 Finished with MPI-specific code for now. Src/C_AMRLib/FluxRegister.cpp commit 30ae225d948ff32063f1c63ef9b3eec1af5c99d9 Author: marc Date: Wed Apr 15 20:59:25 1998 +0000 Convert test codes to multiple processors Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/WritePlotFile.H Src/LinearSolvers/C_CellMG/Test/WritePlotFile.cpp Src/LinearSolvers/C_CellMG/Test/amrvis.defaults Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/WritePlotFile.H Tests/LinearSolvers/C_CellMG/WritePlotFile.cpp Tests/LinearSolvers/C_CellMG/amrvis.defaults Tests/LinearSolvers/C_CellMG/main.cpp commit ef34c7f5f435449b6a31c2532b12a05aebc4faf6 Author: marc Date: Wed Apr 15 20:50:28 1998 +0000 Add input files checking periodic boundary conditions Src/LinearSolvers/C_CellMG/Test/grids/in.2per_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.3per_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.2per_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.3per_2x3x4 commit f49fc08e0c1d2c3de965250fb1af7ecf35636ede Author: lijewski Date: Wed Apr 15 18:04:11 1998 +0000 More MPI-specific code. Src/C_AMRLib/FluxRegister.cpp commit 313f0ae9dd1e2232e5d382cc3a46deb82b7b0b48 Author: lijewski Date: Wed Apr 15 16:50:45 1998 +0000 Some MPIification .... More to come. Src/C_AMRLib/FluxRegister.cpp commit 32984e1036c8b3838853c0a61b99874dc141a383 Author: lijewski Date: Wed Apr 15 16:50:26 1998 +0000 A tad bit of const'ification. Src/C_AMRLib/TagBox.cpp commit 56940968355d6528d39cf3a6fcbfff643adef737 Author: lijewski Date: Tue Apr 14 23:57:43 1998 +0000 Changed a few names to more mnemonic ones ... Src/C_AMRLib/TagBox.cpp commit 170e1da5e5e2681159747a9e156a1a2f05163b4d Author: lijewski Date: Tue Apr 14 23:01:50 1998 +0000 Rearranged CrseInit() to facilitate MPI implementation. Src/C_AMRLib/FluxRegister.cpp commit 7846eec604e26c2accc75012b9aca8d28ddf5854 Author: lijewski Date: Tue Apr 14 21:01:45 1998 +0000 Some more simplification and cleanup before doing MPI work. Src/C_AMRLib/FluxRegister.cpp commit e5b1627644a814fe2d47f62ed4385965b98d6346 Author: lijewski Date: Tue Apr 14 20:24:03 1998 +0000 Now pass integer and Box in MPI as int[1+3*BL_SPACEDIM]. Src/C_AMRLib/TagBox.cpp commit eb50ede5a8e71c617f9025a01959a17b989b4eb1 Author: lijewski Date: Tue Apr 14 19:38:49 1998 +0000 Optimized a few setVal() calls. Src/C_BaseLib/FabArray.H commit d09ef4af3b1446d7f18accc9c62f77b1c870d693 Author: car Date: Tue Apr 14 17:30:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.cpp commit 598323aa1821b86d3139260f1f722f1317e3f705 Author: car Date: Tue Apr 14 17:07:24 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.cpp commit 265996dce789d49d629f40001711648ca31bc853 Author: lijewski Date: Tue Apr 14 16:51:39 1998 +0000 Added some (as yet untested) MPI-specific code. Src/C_AMRLib/TagBox.cpp commit f7ba0a31e21e85f8bdd3f7ba46eb2cb38d6432fe Author: lijewski Date: Tue Apr 14 16:50:53 1998 +0000 Fixed some syntax errors in MPI-specific code. Src/C_BaseLib/VisMF.cpp commit 7eaf492854b2d5a05bfb88f4801bc0d476b47c2d Author: lijewski Date: Mon Apr 13 21:50:13 1998 +0000 Some more (as yet untested) MPI-specific code. Src/C_BaseLib/VisMF.cpp commit 7c814b7b1aaad1efb1d1a3deff5cdba8e127603b Author: lijewski Date: Mon Apr 13 19:44:42 1998 +0000 Added some (as yet) untested MPI-specific code. Src/C_BaseLib/VisMF.cpp commit 18c713475faa1f08aadca8d1f83d007949daf90e Author: lijewski Date: Mon Apr 13 19:44:26 1998 +0000 Added Abort(int) for MPI. Now check the return code of MPI calls. Src/C_BaseLib/ParallelDescriptor.cpp commit ea05fe6cf65f6fcb750af0938e6c7e2122b8367a Author: lijewski Date: Mon Apr 13 19:44:04 1998 +0000 Added Abort(int) for MPI use. Src/C_BaseLib/ParallelDescriptor.H commit 966a44f08bc5e7b14b64c7f9269a8eb405b827c9 Author: car Date: Thu Apr 9 22:37:27 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit 6ff233cdace6e699243f195b5f83b430b0f73042 Author: car Date: Thu Apr 9 19:27:54 1998 +0000 fixed makefiles Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/Make.package commit 33321ebf257cebc442b8887120403f15d0d0b572 Author: car Date: Thu Apr 9 16:18:10 1998 +0000 added serial Gather Src/C_BaseLib/ParallelDescriptor.cpp commit 29ec0b4872a99382c5025e0940336172c2b830c3 Author: lijewski Date: Wed Apr 8 23:42:52 1998 +0000 Some more simplification. Src/C_AMRLib/TagBox.cpp commit a2005f6e4827d2073f1abf1f5647e07fd8355a94 Author: lijewski Date: Wed Apr 8 23:29:16 1998 +0000 Some simplification. Src/C_BaseLib/VisMF.cpp commit 692ff903aedd718fb2cd5e2747c51ae3bd375729 Author: lijewski Date: Wed Apr 8 21:04:28 1998 +0000 Added ParallelDescriptor::Gather(). Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RunStats.cpp commit b51e452b24e25fe1da3003712b8d5c6eb29fd0b7 Author: car Date: Wed Apr 8 19:45:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 0fee43962b7e164d169cdbd27dc3eab3a30d08da Author: car Date: Wed Apr 8 17:51:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 7ad78315ad1cc1a636d4be4f7b7837a0adebbedf Author: lijewski Date: Tue Apr 7 23:10:18 1998 +0000 Only compile in core of knapsack if BSP or MPI is being used. Src/C_BaseLib/DistributionMapping.cpp commit c42ceca619e9169b0ec6d7d7021312dd00b4071b Author: lijewski Date: Tue Apr 7 22:24:44 1998 +0000 More simplification. Src/C_BaseLib/FabArray.H commit 18828dfd65865198361daeaccb0c036fc3eceff0 Author: lijewski Date: Tue Apr 7 20:13:48 1998 +0000 Simplified mergeUnique() a tad. Src/C_AMRLib/TagBox.cpp commit 6985108df97844650c8c2587c013c579fb4bf629 Author: car Date: Tue Apr 7 20:03:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 767b57e72be37c77d8be34ca2df71f976fe27233 Author: car Date: Tue Apr 7 19:43:54 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 7b25059162e5fb24867ada3aca8236baaf52f346 Author: car Date: Tue Apr 7 17:36:02 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 556b45bcad378427221e091611aeb14b49ccff42 Author: car Date: Tue Apr 7 17:24:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 4647e605d2aa1a321f187fdf68d9d261c98997f9 Author: lijewski Date: Tue Apr 7 15:52:23 1998 +0000 Some minor things found by KCC --strict_warnings. Src/C_AMRLib/Derive.H Src/C_AMRLib/ErrorList.H Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_AMRLib/StateDescriptor.H Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit bcd1e7475d2f0ff5334a0c34a32b998aed9c42df Author: car Date: Mon Apr 6 22:43:19 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 631768943c8aad2839958074b6caf65ca0f10903 Author: lijewski Date: Thu Apr 2 00:14:07 1998 +0000 Removed cacheRemoteData data member; it was always true. Removed faName data member and the two access functions. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H commit 6a6f5db6775304c7e495736fd00b409ddd998dfb Author: lijewski Date: Thu Apr 2 00:13:02 1998 +0000 Updated to reflect mods to FabArray. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit bc6e5cf43200c843706e2ae294f9139ff94db90f Author: lijewski Date: Wed Apr 1 18:22:27 1998 +0000 Removed commented out Synchronize() calls. Src/C_BaseLib/FabArray.H commit 4d76767748f04b89803338e9314448c9aa090085 Author: lijewski Date: Wed Apr 1 18:21:50 1998 +0000 Merged in Barrier(). Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 8bf34974f3f5e24bbe98c7600cce127a353c76fd Author: lijewski Date: Wed Apr 1 17:52:37 1998 +0000 Added Barrier() to the interface. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 5da597e9725998ade522789c151643d5d854108c Author: car Date: Wed Apr 1 17:38:35 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit a88344d39e43fe356d041f522c80580b5036b5bb Author: lijewski Date: Wed Apr 1 17:34:25 1998 +0000 Added Banner.html for doc++ users. commit 34f21601c09afe51e276b7664f102aefa0b0620e Author: car Date: Wed Apr 1 17:01:55 1998 +0000 *** empty log message *** Src/C_BaseLib/test/tVisMF.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Tests/C_BaseLib/tVisMF.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 09f6fbb6b238095dc66b235ad74eaf7b888be8e0 Author: lijewski Date: Wed Apr 1 16:55:04 1998 +0000 Cleaned up code. Implemented Synchronize() for MPI using MPI_Barrier(). Src/C_BaseLib/ParallelDescriptor.cpp commit fd9d4b8767526bdd70aafe429dc6a2ecf415f85e Author: car Date: Wed Apr 1 00:34:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp commit dbf7eef80773688866ef21c5409fc25b46814338 Author: car Date: Wed Apr 1 00:32:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp commit effe4482e8d2c52baa8c7daa1d59f94cdb4c559d Author: car Date: Wed Apr 1 00:29:43 1998 +0000 Made Start/EndParallel static Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/test/tVisMF.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Tests/C_BaseLib/tVisMF.cpp commit 501126c3081c37821739ed8c34a697aa147ccf09 Author: marc Date: Wed Apr 1 00:27:32 1998 +0000 Move forward declarations to fix Doc++ doc generation. Src/C_BaseLib/MultiFab.H commit db32bc53c3f404ae8f38161401f6455b6d596f33 Author: car Date: Tue Mar 31 22:58:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 6f6868db0b09e2f644cb75bef18eed4f133a46d5 Author: car Date: Tue Mar 31 20:43:12 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 8802d6ce0152cc6234e9c5373d86d3c46a0199fe Author: car Date: Tue Mar 31 18:43:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 9251f066547a179b1d14c69c2382bb7510857a20 Author: car Date: Tue Mar 31 18:25:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 679baf2c91d5c6dae1097e4df72b0360f56eb5f7 Author: lijewski Date: Tue Mar 31 00:23:59 1998 +0000 Some reformatting ... Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/MAKESLICE_3D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F commit 423bef95a2313b969916a4ba11d84a40bc9fe25b Author: lijewski Date: Mon Mar 30 21:57:32 1998 +0000 Cleaned up the code for release. Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H commit e6faecbcc1723d43513c5b52f7ef5f9abf0e0336 Author: lijewski Date: Mon Mar 30 20:45:51 1998 +0000 Removed print() and two unimplemented CrseInit()s. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 2e5ccce351605e8b01e8bd4a83d58d44deaeabcb Author: lijewski Date: Mon Mar 30 20:23:45 1998 +0000 Removed copyTo(MultiFab). Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 75ae0db1a89fcf0669c232266a0fe3088ecfc74d Author: lijewski Date: Mon Mar 30 20:05:34 1998 +0000 Removed I/O functions. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 67a14231d13b0d4a1a889d59d6b94c6910fe29f9 Author: lijewski Date: Mon Mar 30 20:04:18 1998 +0000 Removed linInterp(). Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 6d0bcaafd93d7ecb19c8cf39393bf5706798f09f Author: lijewski Date: Mon Mar 30 18:59:27 1998 +0000 Removed linInterp(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit cdfec93638f4f6efb5f8f9f12769f4cfd4a1f7da Author: car Date: Mon Mar 30 18:35:57 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_CellMG/mglib.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 3474716fcda8d2bc90f17c8e40caef8612fbffd4 Author: lijewski Date: Mon Mar 30 18:14:49 1998 +0000 Removed operator<<(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit cbfd49040eaee2c3ea913104f358530c91cd2dfa Author: lijewski Date: Mon Mar 30 18:03:00 1998 +0000 Removed MultiFab(istream). Removed readFrom() and writeOn(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 80ce96576533c95076feb9918307323312b4b8aa Author: lijewski Date: Mon Mar 30 17:28:57 1998 +0000 Removed FillPatch(). Removed FillCoarsePatch(FAB). Removed USEUNRAVELEDFILLPATCH define. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit afd277debb8c5a73a028e1d625292024e46ef7be Author: car Date: Sun Mar 29 16:46:11 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_CellMG/mglib.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 8f6861223b52ea34179fa3cd6ded89b2eb82b176 Author: car Date: Sun Mar 29 16:25:55 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_CellMG/mglib.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 5b28850c79690d9b3ae704bb2e132243c89d1b18 Author: lijewski Date: Sat Mar 28 00:45:04 1998 +0000 NEWFPMINBOX -> BL_NEWFPMINBOX Src/C_AMRLib/AmrLevel.cpp commit 72302898b276f59704c360a816981d364651b4f7 Author: lijewski Date: Fri Mar 27 23:53:20 1998 +0000 Removed BL_PARALLEL_IO define. Removed USEOLDFILLPATCH define. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit c1119048349a6656814bc5229911966298e0ebbc Author: vince Date: Fri Mar 27 18:34:00 1998 +0000 Minor additions. Tools/C_mk/Make.T3E commit 8d2ee8f94a3e9b66b87f7e1f73c5f345107b19e7 Author: marc Date: Fri Mar 27 00:41:26 1998 +0000 Remove extra copy of tridiag routine Src/LinearSolvers/C_CellMG/ABec_2D.F commit e989933a8fc150cc8344bc58d07306bce83b1f56 Author: lijewski Date: Fri Mar 27 00:06:39 1998 +0000 Removed unused rangeType() and corresponding member data. Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 09043219e1bcdceac254114ab7c1a8b9f6ac1b2d Author: lijewski Date: Thu Mar 26 22:40:26 1998 +0000 A useless commit ... Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 54927ebd36f6d65358717f9c32b6fe95c0e4bc90 Author: marc Date: Thu Mar 26 22:24:04 1998 +0000 Add PBOXLIB def Src/C_BaseLib/GNUmakefile Src/C_BaseLib/test/GNUmakefile.tCArena Src/C_BaseLib/test/GNUmakefile.test Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_TensorMG/MCBndryData.H Src/LinearSolvers/C_TensorMG/MCBndryData.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Tests/C_BaseLib/GNUmakefile.tCArena Tests/C_BaseLib/GNUmakefile.test Tools/C_mk/Make.T3E Tools/C_mk/Make.defs commit efb5d9a489d249fdcbdcb4fbe7c85d53a3d4471d Author: marc Date: Thu Mar 26 19:31:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/gr.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/gr.2_big Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_d Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_e Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_d Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2boxes_a Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2x3x4 Src/LinearSolvers/C_CellMG/Test/grids/gr.3_big Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/gr.3_shiftedUp Src/LinearSolvers/C_CellMG/Test/grids/gr.3_small_a Src/LinearSolvers/C_CellMG/Test/grids/gr.3_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/in.2_big Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d Src/LinearSolvers/C_CellMG/Test/grids/in.3_2boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_2x3x4 Src/LinearSolvers/C_CellMG/Test/grids/in.3_big Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.3_shiftedUp Src/LinearSolvers/C_CellMG/Test/grids/in.3_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_stack_a Tests/LinearSolvers/C_CellMG/grids/gr.2_19boxes Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/gr.2_3x2 Tests/LinearSolvers/C_CellMG/grids/gr.2_big Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/gr.2_small_a Tests/LinearSolvers/C_CellMG/grids/gr.2_small_b Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_a Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_b Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_c Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_d Tests/LinearSolvers/C_CellMG/grids/gr.3_2boxes_a Tests/LinearSolvers/C_CellMG/grids/gr.3_2x3x4 Tests/LinearSolvers/C_CellMG/grids/gr.3_big Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_a Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_b Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_c Tests/LinearSolvers/C_CellMG/grids/gr.3_shiftedUp Tests/LinearSolvers/C_CellMG/grids/gr.3_small_a Tests/LinearSolvers/C_CellMG/grids/gr.3_stack_a Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/in.2_3x2 Tests/LinearSolvers/C_CellMG/grids/in.2_big Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/in.2_small_a Tests/LinearSolvers/C_CellMG/grids/in.2_small_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.3_big Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp Tests/LinearSolvers/C_CellMG/grids/in.3_small_a Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a commit 54906dbca6fda685521cc67f1ea1a1fb92185c2d Author: marc Date: Thu Mar 26 19:15:27 1998 +0000 Add tensorMG to Parallel repo Src/LinearSolvers/C_TensorMG/DV_2D.F Src/LinearSolvers/C_TensorMG/DV_2D.mF Src/LinearSolvers/C_TensorMG/DV_3D1.F Src/LinearSolvers/C_TensorMG/DV_3D1.mF Src/LinearSolvers/C_TensorMG/DV_3D2.F Src/LinearSolvers/C_TensorMG/DV_3D2.mF Src/LinearSolvers/C_TensorMG/DV_3D3.F Src/LinearSolvers/C_TensorMG/DV_3D3.mF Src/LinearSolvers/C_TensorMG/DV_3D4.F Src/LinearSolvers/C_TensorMG/DV_3D4.mF Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/DivVis_F.H Src/LinearSolvers/C_TensorMG/MCBndryData.H Src/LinearSolvers/C_TensorMG/MCBndryData.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_2D.F Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLO_3D.F Src/LinearSolvers/C_TensorMG/MCLO_F.H Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/Make.package Src/LinearSolvers/C_TensorMG/Test/Palette Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.H Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Src/LinearSolvers/C_TensorMG/Test/amrvis.defaults Src/LinearSolvers/C_TensorMG/Test/doit Src/LinearSolvers/C_TensorMG/Test/dotest Src/LinearSolvers/C_TensorMG/Test/grids/gr16.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr16x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr32.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr32x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr64.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr8.dog Src/LinearSolvers/C_TensorMG/Test/inputs Src/LinearSolvers/C_TensorMG/Test/main_2D.F Src/LinearSolvers/C_TensorMG/Test/main_3D.F Src/LinearSolvers/C_TensorMG/Test/main_F.H Src/LinearSolvers/C_TensorMG/Test/preload.cpp Src/LinearSolvers/C_TensorMG/Test/probin Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Src/LinearSolvers/C_TensorMG/Test/vpramps.dat Src/LinearSolvers/C_TensorMG/visc2d.ma Src/LinearSolvers/C_TensorMG/visc3d.ma Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package Tests/LinearSolvers/C_TensorMG/Palette Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/amrvis.defaults Tests/LinearSolvers/C_TensorMG/doit Tests/LinearSolvers/C_TensorMG/dotest Tests/LinearSolvers/C_TensorMG/grids/gr16.dog Tests/LinearSolvers/C_TensorMG/grids/gr16x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr32.dog Tests/LinearSolvers/C_TensorMG/grids/gr32x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr64.dog Tests/LinearSolvers/C_TensorMG/grids/gr8.dog Tests/LinearSolvers/C_TensorMG/inputs Tests/LinearSolvers/C_TensorMG/main_2D.F Tests/LinearSolvers/C_TensorMG/main_3D.F Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/C_TensorMG/preload.cpp Tests/LinearSolvers/C_TensorMG/probin Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/C_TensorMG/vpramps.dat commit 51466191c70b6e0f1e4be55945cf84afd2ae2def Author: marc Date: Thu Mar 26 18:58:17 1998 +0000 Added test directory files Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/Palette Src/LinearSolvers/C_CellMG/Test/amrvis.defaults Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_CellMG/Test/preload.cpp Src/LinearSolvers/C_CellMG/Test/vpramps.dat Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/Palette Tests/LinearSolvers/C_CellMG/amrvis.defaults Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_CellMG/preload.cpp Tests/LinearSolvers/C_CellMG/vpramps.dat commit d2012999fb58b439a60f6e8dbbfaec0767d0ce25 Author: marc Date: Thu Mar 26 18:55:51 1998 +0000 Incorporate changes from Bill's tensor solve directory Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F commit 9ea73fed1be32867a0a71a635db7fca0c84d7312 Author: almgren Date: Thu Mar 26 17:51:58 1998 +0000 Remove geom from setBndryConds call. Src/C_BoundaryLib/InterpBndryData.cpp commit 27aceb303de91d1d15f7416e9279ffc5a570dcc8 Author: almgren Date: Thu Mar 26 17:51:33 1998 +0000 Remove geom from the setBndryConds call. Src/C_BoundaryLib/InterpBndryData.H commit 494156ce680b792910a36b9b6c6b9a5fc9b2412b Author: lijewski Date: Thu Mar 26 17:32:16 1998 +0000 Added new convert() function. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 6dfbcb7295ad7412d9a11ca6531f377da1b24aca Author: lijewski Date: Thu Mar 26 17:31:50 1998 +0000 Uses new BoxArray::convert() function. Src/C_AMRLib/AmrLevel.cpp commit d60730e7b8a18b0a97f707f5e32862c1b36c044f Author: lijewski Date: Wed Mar 25 21:32:18 1998 +0000 First cut at parallelized AmrLevel::derive(). Needs to be checked out better. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 42f7b8c782cf8b9e12184a405a2afe72f34dff67 Author: car Date: Wed Mar 25 20:59:54 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit fa287ca43aab056bfcdd5f8344a9a6438a603e1a Author: car Date: Wed Mar 25 20:54:31 1998 +0000 *** empty log message *** Src/C_BaseLib/GNUmakefile Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/LinearSolvers/C_CellMG/WriteMultiFab.cpp commit cbb89488c4064c612ec55c1df0af76ced40ee085 Author: car Date: Wed Mar 25 19:20:50 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit 69287608d46a6b3d28e275e048f17f5f4f060809 Author: car Date: Wed Mar 25 19:17:47 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit b80eb3e3c7460bd9523c66a7c247744c5a41645f Author: car Date: Wed Mar 25 19:03:06 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c552012402c2bd395db846b09a428c16598d49b5 Author: car Date: Wed Mar 25 18:23:08 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/pBoxLib_2.dsp commit ed078c269f69e382ed28feab5f9132398aa67532 Author: car Date: Tue Mar 24 23:45:14 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/.cvsignore Src/LinearSolvers/C_CellMG/mglib.dsp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit d8c225f640708d95fc60f8f8289da557c6587851 Author: car Date: Tue Mar 24 20:18:49 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp commit 9971aec3582f9b51fde496bcf79d2209e384dc1b Author: lijewski Date: Tue Mar 24 19:08:41 1998 +0000 Commented out bunch of cout's in old FillPatch routines. Src/C_AMRLib/AmrLevel.cpp commit e1942293c0be7a47ae80aaa2e1af721d5db7a11d Author: lijewski Date: Tue Mar 24 18:28:29 1998 +0000 Some work in preparation for parallelizing FillDerive(). Src/C_AMRLib/AmrLevel.cpp commit 993f07b149f3f4673b8928614528dcb5790e1109 Author: almgren Date: Tue Mar 24 07:05:10 1998 +0000 Moved this file from ../IAMRAll. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_F.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/LO_BCTYPES.H Src/C_BoundaryLib/LO_UTIL.F Src/C_BoundaryLib/Mask.H Src/C_BoundaryLib/Mask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/ABec_UTIL.F Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F Src/LinearSolvers/C_CellMG/MG_F.H Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/WriteMultiFab.H Src/LinearSolvers/C_CellMG/WriteMultiFab.cpp commit 18dd515c42ab7847eb2f640c2b187ae27d403a89 Author: almgren Date: Mon Mar 23 23:36:17 1998 +0000 Moving this file from ../IAMRAll. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit d06c8e8ec64b18fb1909079f100118c6a57d8fe1 Author: lijewski Date: Mon Mar 23 21:03:17 1998 +0000 Now maintain DeriveRec in List instead of List Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 9de50888e7e7ea480229214ec169ac4393f3402f Author: lijewski Date: Mon Mar 23 21:02:56 1998 +0000 Now maintain ErrorRec in List not List Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit b823cc551e8037d7eaf09d78517ced580412f9aa Author: lijewski Date: Mon Mar 23 20:20:14 1998 +0000 Removed default constructor and DeriveFuncSrc stuff. Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit e06890b6773064c664a03153c8ece3a885e47b75 Author: lijewski Date: Mon Mar 23 17:23:58 1998 +0000 Cleaned up the code ... Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 500f80b5d940ee5b35f34b9a2081e101ff33edcf Author: car Date: Thu Mar 19 19:02:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit ed2f3d02c3db7603aa902e140671ccccadc18548 Author: car Date: Mon Mar 16 18:26:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/proj.cpp commit 78cad0cf04d5dadc1576576f9c0359691b7640d8 Author: car Date: Sun Mar 15 23:44:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit 061a52241c3255ff6eb4f32993b8c31afd4822f5 Author: car Date: Sun Mar 15 20:41:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit d1c3ee873995175bf0d1d5a81a5c9f1a77f397fb Author: car Date: Fri Mar 13 23:10:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit cadf06710b601e167485c418c76d51922b8a4eb6 Author: car Date: Fri Mar 13 22:18:43 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 3db41b0e97acff5837d93fd5f4e3ca97a9bca63e Author: car Date: Fri Mar 13 20:50:30 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit c85294e902d5f40f0f0bc8ebf8870c0fd998bc45 Author: car Date: Thu Mar 12 23:21:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6970820bc9a7f6d71d7c56dfdfea039162ab0307 Author: car Date: Thu Mar 12 21:07:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 8be5b29236e3468e034411c1ba575a046ae7555d Author: car Date: Wed Mar 11 21:31:05 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 8a60655758cf1c23673f083b6857ab613a18b0d5 Author: car Date: Tue Mar 10 23:31:12 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 58ef77c733899e23ca2cf6133395e9bcace0fb83 Author: car Date: Fri Mar 6 00:28:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit ebb64b1d69c3142654d3890b90e2d785105a666b Author: car Date: Thu Mar 5 00:40:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 352d330720256f90bf32558458243afc0006b221 Author: car Date: Wed Mar 4 22:44:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 75b92dedf7566b09530d4f82e00257cb09744f88 Author: car Date: Wed Mar 4 21:16:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 21878921bdbbe06dd8304b87fe4a4d3883c955ba Author: car Date: Wed Mar 4 03:05:19 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 3cf9a5e9667aa56135deb03a46e35eb975f8cf2d Author: car Date: Wed Mar 4 02:31:23 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit d3204a9d42cc08a726f6e0c8bcec78cc44299e7d Author: car Date: Wed Mar 4 00:55:42 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit ad21d479ebd8e34dfbe4aed8578993deb248d6c2 Author: car Date: Tue Mar 3 23:19:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 84032fab90e533e6068e24bdb975500a16ec03b9 Author: car Date: Mon Mar 2 17:57:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp commit 30a32794f0af360ed93f9e5b9840e8fabd692019 Author: car Date: Sun Mar 1 22:17:46 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 53a1e97f0def542902a922f992aaf076e1dadfee Author: car Date: Sun Mar 1 21:58:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F commit 9fba3e2fb35260266b531312956e15edeb8ad08e Author: car Date: Sun Mar 1 21:51:51 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit 6a52dfb6666a010b61c2873c79f5341c1a7e02d1 Author: car Date: Sat Feb 28 17:56:51 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 18ff5814921f13fa454e553ef4a5090b756925de Author: car Date: Fri Feb 27 22:49:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 040c4955055a835aa1e2edb9b42f0cd4471383f4 Author: car Date: Fri Feb 27 21:03:44 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit 0398cf30094464180464c32a7b1dcbf5f43af0ef Author: car Date: Fri Feb 27 21:01:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit a0565f3f87cbee8af57f78825fb2a549aac6d0f8 Author: car Date: Fri Feb 27 20:59:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit d7ab03739737010b94d4fb22d180406feef80901 Author: lijewski Date: Thu Feb 26 22:07:57 1998 +0000 Made isStateVariable() static. Src/C_AMRLib/AmrLevel.H commit c38372b5d6f5474df5301bf23164cb6b000c7483 Author: car Date: Wed Feb 25 23:24:16 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit 72ed30f6a11b06e4439257dc08e70818243a49cd Author: car Date: Wed Feb 25 22:27:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 04e17e6fff4a524e8873937a4145f5c2f3cfd77e Author: car Date: Wed Feb 25 21:05:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 6a16fca94e170e366f74dca7c9b32af05fe885b2 Author: car Date: Tue Feb 24 19:25:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit e9b1951bda3b8fa68fa781f360c6ad0dda440175 Author: car Date: Tue Feb 24 00:27:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 62a1db5165620770bf04945b538a6076dcdffe9d Author: car Date: Mon Feb 23 22:55:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit 20359df7d47d23fe26c73c10ab801c797161e8b6 Author: car Date: Sun Feb 22 20:50:10 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 199545865962fd9e9b72326db5b4f1ad22e363d6 Author: car Date: Sun Feb 22 19:24:25 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 0e2eebe0744aabdf9613bf9b89865de8d4b7fc1b Author: car Date: Sun Feb 22 19:06:57 1998 +0000 anal changes to fortran Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/MAKESLICE_3D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F Src/C_BaseLib/GNUmakefile Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F commit 21a6a7678fee732eedec6b76472cf94fa408b81f Author: car Date: Sun Feb 22 17:29:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 4126cbd50d6a9e0af61cb7433c30b5a87116f78d Author: car Date: Sun Feb 22 04:16:19 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit e6bc0ed5fa4185457a26beb2ad6162c37bfc725a Author: car Date: Sun Feb 22 01:36:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit c7c57052a1d62e6ced9fe59c09b0a73930b28f4e Author: car Date: Sun Feb 22 01:35:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit eb32a57e2feb407515678c1b7cf1a3fc18ebb53b Author: car Date: Sun Feb 22 01:32:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 0a51bb21226c81586d647f8b8ad9e3b952575c20 Author: car Date: Sun Feb 22 01:30:02 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 7c77304daba83b6ca60b4f868570c08232e6b1c5 Author: car Date: Fri Feb 20 23:00:55 1998 +0000 *** empty log message *** Src/C_BaseLib/FabArray.H Src/LinearSolvers/C_NodalMG/hgproj.dsp commit e3d53f27fcf21cec025d32de3d6c352d4b0ba05d Author: car Date: Fri Feb 20 22:53:09 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 21c149ea3be4767d1b99e4c02afe32125e342f71 Author: car Date: Fri Feb 20 21:49:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit d3bcb9cab2afcdf74b7dd8ee98b52b5f8cf0161d Author: car Date: Fri Feb 20 21:46:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit c769567ce01d62880f0dfd8d32514802c5a9f0b6 Author: car Date: Fri Feb 20 21:42:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit e40ee2c7831c132431b95f1aa3205ed59b89407b Author: car Date: Fri Feb 20 21:37:14 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F commit 4c40f6be906b881eff9c35bff5f79e6e66db39e8 Author: car Date: Fri Feb 20 21:07:11 1998 +0000 changes Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 16f8272630399bdb20ae851d25bec0bf7ebf47e8 Author: vince Date: Fri Feb 20 18:30:47 1998 +0000 Optimized FillFab and fabCopyDescList. Src/C_BaseLib/FabArray.H commit 25c020128bd956dcf07eb6c1f0e78b9b162357ad Author: car Date: Thu Feb 19 23:26:40 1998 +0000 fiddle: Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 914588858e15f1dcdc746f2ef14306535d8628cd Author: lijewski Date: Thu Feb 19 18:10:46 1998 +0000 Added default constructor to TagBoxMergeDesc. Src/C_AMRLib/TagBox.cpp commit 64833abe26920c9f796f1660f983b28f285b216f Author: lijewski Date: Thu Feb 19 17:15:52 1998 +0000 Added default constructor to FabComTag so that all values get set to some valid value; i.e. I wanted to shut up 3rd about reading unset values when BSP does a memcpy() of a FabComTag. Src/C_BaseLib/ParallelDescriptor.H commit 332e670a47e3e88973cf4a5dfa94e88e866b66ca Author: car Date: Thu Feb 19 01:51:35 1998 +0000 fixes 2 d Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 64f3d2d2b8f0e83de0fa0e45bd06dd003bb7ece5 Author: car Date: Wed Feb 18 23:09:55 1998 +0000 fiddle Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 60a41e742bc4a3ab78617a8aa94877ace0417e84 Author: vince Date: Wed Feb 18 21:38:11 1998 +0000 Removed fortran apprentice flag. Tools/C_mk/Make.T3E commit 03bbc3c5d1060720fcdd181c664a1f88d0ae8ef0 Author: vince Date: Wed Feb 18 21:35:32 1998 +0000 Removed unnecessary syncs. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.cpp commit a6b3b7adbb1238c1b88cb85c2a92885bb3132a99 Author: lijewski Date: Wed Feb 18 21:34:37 1998 +0000 Only FlushCache when at lbase==0 Src/C_AMRLib/Amr.cpp commit a9fa8447e30df9f7cc15d70f2840c2a18c483ffe Author: vince Date: Wed Feb 18 21:31:12 1998 +0000 Removed unnecessary syncs and added functionality to support amrvis. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/Utility.cpp commit b970099acba6d2b86dd3019b86fc2d6ab1c38284 Author: lijewski Date: Wed Feb 18 16:14:42 1998 +0000 Had to remove parallel_sync RunStats stuff. Can't do that since RunStats::report() uses ParallelDescriptor::Synchronize() which leads to inconsistencies and weird numbers. Src/C_BaseLib/ParallelDescriptor.cpp commit d94013ece9266715ff2842b09e1b8a2a935b65fd Author: car Date: Tue Feb 17 23:02:16 1998 +0000 nothing Src/C_BaseLib/CoordSys.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit e2237736f5375680a911b371330f7c9b82863ba4 Author: lijewski Date: Tue Feb 17 22:42:04 1998 +0000 Added a RunStats variable for parallel sync time. No longer need to include in . Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 6255667f18e56878cc262b6f42e82a773605afd4 Author: car Date: Tue Feb 17 17:29:13 1998 +0000 small changes Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 42df6f40c9b3b2579cbadc82eeeb1f02a74f8910 Author: lijewski Date: Fri Feb 13 21:13:07 1998 +0000 Added rules for .f90 that exectly mirror those for .F files. Eventually we'd like to remove the need for FORTPREP (split77) for .f90 files. Tools/C_mk/Make.rules commit c65613de80f4e54028e7103f59e0ec2ac13ace26 Author: car Date: Thu Feb 12 22:47:46 1998 +0000 tweaks Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp commit c6deab694c84b0c67d250ef5cccc2df889c3f3ce Author: wyc Date: Thu Feb 12 22:37:13 1998 +0000 fixed a bug in VisMF.H where there was ambiguity about which index was what in the clear(int,int) function. Src/C_BaseLib/VisMF.H commit 24c29e0d25d67d56ca3de3297198b2d64e79dea5 Author: vince Date: Thu Feb 12 22:16:24 1998 +0000 Initialized m_pa. Src/C_BaseLib/VisMF.cpp commit 00571d09626ce3a98a5fe324d94dc3d521851f47 Author: lijewski Date: Thu Feb 12 18:13:27 1998 +0000 Added calloc() and realloc() so can emulate malloc(3) functionality. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 133ad8afe411a42541a311819a77425275858d6b Author: car Date: Thu Feb 12 17:32:10 1998 +0000 win32 changes Src/C_BaseLib/Utility.cpp commit c36759a831238ee7427d7d62b1b0c7a9a4d0db9c Author: lijewski Date: Thu Feb 12 16:56:08 1998 +0000 Fixed bug in getline(). Src/C_BaseLib/aString.cpp commit e304a4e09dbd0a086ffcf5f1f8d967f6b62ec1d3 Author: car Date: Wed Feb 11 21:41:12 1998 +0000 Small changes. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 277ec8c4dfd06731c7fd6faec309ff05ff6d5c4f Author: car Date: Tue Feb 10 15:15:33 1998 +0000 win32 change Src/C_BaseLib/CArena.H Src/LinearSolvers/C_NodalMG/proj.cpp commit 7ee2df6eeaeb73a9d6009673c9db7e27ee0db33b Author: lijewski Date: Mon Feb 9 22:45:58 1998 +0000 Mods for T3E and g++. Src/C_BaseLib/CArena.cpp commit 15611985d70f567879568b465b10497ee49fdfd2 Author: lijewski Date: Mon Feb 9 22:02:14 1998 +0000 Added a couple more insert() hints. Src/C_BaseLib/CArena.cpp commit 1e1fbf25e56da12fd1a1bd3fdc598784c74836ce Author: lijewski Date: Mon Feb 9 22:01:27 1998 +0000 Fixed using declaration: using std::list -> using std::set Src/C_BaseLib/CArena.H commit 31515f5379a847561769b1104fdfd5b34b7cca18 Author: lijewski Date: Mon Feb 9 20:46:52 1998 +0000 We're now using the CArena stuff. Src/C_BaseLib/Arena.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/tCArena.cpp commit 71869768d73f85d47725d086fb58a64c1bb58ca2 Author: car Date: Mon Feb 9 20:33:29 1998 +0000 doodle Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit 92090db6522a5207d7b2dbeac6e0a97c3555e313 Author: lijewski Date: Sun Feb 8 21:13:31 1998 +0000 Increased the count on a few for loops to up test strength. Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/tCArena.cpp commit 4c545e4a876ea148f8ad8b66b8b4a6a0167c0e84 Author: lijewski Date: Sun Feb 8 20:03:59 1998 +0000 Free()d blocks are now coalesed with lo and hi neighbors. Src/C_BaseLib/CArena.cpp commit fa8220ec6b22c99f7cf11d8ae9985b3bd5a97033 Author: lijewski Date: Sun Feb 8 18:19:48 1998 +0000 Test code for CArena Src/C_BaseLib/test/GNUmakefile.tCArena Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/GNUmakefile.tCArena Tests/C_BaseLib/tCArena.cpp commit a6e042e77145dd8e45d6ad7fed1155df58bda17d Author: lijewski Date: Sun Feb 8 18:19:28 1998 +0000 A start at a rewrite using STL. Doesn't do compact()ing yet. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 7bc488840836e6651bb01828067c2710e3892bc1 Author: lijewski Date: Sun Feb 8 17:52:07 1998 +0000 Added a function pointer to Word union. Src/C_BaseLib/Arena.H commit b7b6a26435c2ce7ce6211b6c1ea7c1fdddaf0375 Author: lijewski Date: Sat Feb 7 23:41:55 1998 +0000 Still doesn't work. Looks like I need to rewrite this. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 914719adf92a079b89ea7a0cf02a1688f35c394e Author: lijewski Date: Fri Feb 6 23:44:09 1998 +0000 Closer to working code. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 4e37176e7af7724850337bebd9e4dd9f264fbd00 Author: car Date: Fri Feb 6 22:26:26 1998 +0000 some fixes for win32 Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/pBoxLib_2.dsp commit 466d7f721dd6c8eaf3993c699d81da49d0f7f184 Author: car Date: Fri Feb 6 22:19:19 1998 +0000 CleanUp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 80d5bfbaed2b0599d96240f62afa723b084dd9cf Author: vince Date: Fri Feb 6 22:09:13 1998 +0000 Deleted warning for deprecated FArrayBox::setOrdering() and FArrayBox::getOrdering(). (amrvis needs these). Src/C_BaseLib/FArrayBox.cpp commit 08031b6e6aef590e6cd0011db5ecfce8a1848dc2 Author: lijewski Date: Fri Feb 6 18:22:03 1998 +0000 Uses ::operator new and ::operator delete instead of new and delete. Src/C_BaseLib/BArena.cpp commit d2b47d8cc9473abe4036f7d838e8b9d4a1c84a75 Author: lijewski Date: Fri Feb 6 18:21:34 1998 +0000 The initial cut. Hasn't even been compiled. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 289c256767ed83fe616f671fb02349f958551f01 Author: car Date: Fri Feb 6 16:53:10 1998 +0000 Array bust Src/LinearSolvers/C_NodalMG/amr_real3d.F commit ea263bbdb882b15f46b627d76dd003cf75db315e Author: vince Date: Thu Feb 5 23:01:34 1998 +0000 Changed VisMF to use an I/O granularity of a single component of a fab in a multifab and to not store data. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 12a8a67226460c56cacf386ce8d01afba274e4fd Author: car Date: Thu Feb 5 22:18:10 1998 +0000 Frob Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 48d4276946b5b321bf419c1a3b6b64188afc82b0 Author: vince Date: Thu Feb 5 22:15:55 1998 +0000 Fixed a typo. Src/C_BaseLib/COORDSYS_3D.F commit ce8e8875aaa54119fc5223e0300bc22a452e5295 Author: lijewski Date: Thu Feb 5 17:02:28 1998 +0000 Removed cout call when bumping collate space size. Src/C_AMRLib/TagBox.cpp commit 14ec52da85a4a0208ecc61d206cce6283dbf03a8 Author: car Date: Thu Feb 5 00:38:19 1998 +0000 Fiddling. Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/restrictor.H commit 45fb895cbbb28355927dcccd82b6c60086de6bee Author: car Date: Thu Feb 5 00:37:59 1998 +0000 Fiddling Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 80293e5f80e68a315f1f8b4a5897f5b590b5c73a Author: lijewski Date: Wed Feb 4 16:25:50 1998 +0000 Fixes for Visual C++. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit bf9998d4c4db7f00c3a8a9de265ef8172d224ae2 Author: lijewski Date: Wed Feb 4 01:03:20 1998 +0000 We're now reference-counted. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 5e109466e0da9ec7cd720e6eaab0d7b7ca29a40d Author: lijewski Date: Tue Feb 3 19:33:53 1998 +0000 In copy, check that the processor maps are equal, not the boxarrays. Src/C_BaseLib/FabArray.H commit 7553bebf1777d585d63cac104778816447d8e64e Author: lijewski Date: Tue Feb 3 19:33:12 1998 +0000 We now only flush the processor map cache in regrid if we're at the coarsest level. Otherwise we can run into problems in LevelAdvance. Src/C_AMRLib/Amr.cpp commit a741ddf34570d42ea25dea51027cc931c8982fbc Author: car Date: Sat Jan 31 00:12:26 1998 +0000 Minor Changes. Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit db51f51aeea00f50ae54dcd46e33e442c7bb6a53 Author: lijewski Date: Thu Jan 29 18:59:36 1998 +0000 Lowered the size of ChunkSize. Src/C_AMRLib/TagBox.H commit 9ea937d02230e09230daea9ecc46f9a8f94fd56d Author: car Date: Wed Jan 28 22:54:23 1998 +0000 Minor changes Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 5f4de625b3196fc2dc35761db626339befabea2f Author: car Date: Wed Jan 28 22:29:15 1998 +0000 A little more general, another stupid fill_patch fix. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 196bba89948a18ed325201eda957028d26a0b552 Author: car Date: Wed Jan 28 22:11:15 1998 +0000 Stupid fix in fill_patch. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 199d81602aa1069825f86af64bbf3e58da4f2196 Author: car Date: Wed Jan 28 21:58:32 1998 +0000 Thrashing. Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit f2d1de6e75c0de276c0815f124737b7e6608e00f Author: lijewski Date: Wed Jan 28 18:35:07 1998 +0000 Latest mods to Cluster have now been ported to T3E. Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 822e3a00d9e271118d6f584f2e9921aed4adef1f Author: lijewski Date: Wed Jan 28 04:55:10 1998 +0000 First cut at having the Cluster code work exclusively with a hardwired IntVect array built and maintained by the TagBox::collate() code. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 06eafb51535cb9abdc4f440fb6036431e157c79e Author: car Date: Tue Jan 27 00:15:05 1998 +0000 Fixes cleanups. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 43a7536450459ff4e1bae7b2caae11014a527cd1 Author: car Date: Tue Jan 27 00:14:50 1998 +0000 Fixes, cleanups. Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 36374282171f75c1e5b4a28a6adeb8e70b78fe53 Author: car Date: Mon Jan 26 23:27:00 1998 +0000 No longer need cbasics.H, and updated .cvsignore to ignore louis's lib directory. Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/cbasics.H commit 8935fa74e5deccc5b00787fa45e2ff9e8d705fa6 Author: lijewski Date: Mon Jan 26 23:16:20 1998 +0000 Removed unused function. Src/C_AMRLib/Cluster.H commit 1283da021cd32ef3581fcd626b6c4f0eff7b6832 Author: lijewski Date: Mon Jan 26 22:00:00 1998 +0000 Cleaned up the code a bit. Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp commit d621d1ec8511a6451c3e0a710be1a052f8891a40 Author: lijewski Date: Mon Jan 26 21:57:18 1998 +0000 We're now derived from BaseFab Added tags() and tags(Array) to support Fortran. Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 92cfb5d77a6ce97826b8a16ccba328c747852823 Author: car Date: Mon Jan 26 20:56:19 1998 +0000 Fixes. Src/LinearSolvers/C_NodalMG/GNUmakefile.main commit 0c8d38d2efd648d98d406865f649ac5809efeb09 Author: car Date: Mon Jan 26 20:20:55 1998 +0000 for loop index Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 3f9d86f2c7ef25aa91fb662bed03e15ee7c05105 Author: car Date: Mon Jan 26 19:18:19 1998 +0000 Changes for 2 D. Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 2807adec0d82d3286093e0af6835e14cd92533e1 Author: lijewski Date: Sat Jan 24 01:35:58 1998 +0000 Forgot a 'endif' in the previous merge. Src/C_AMRLib/INTERP_2D.F commit 4755b9df6a7f81ae1ea2f51c8f8174d3c8cc194e Author: lijewski Date: Fri Jan 23 22:48:38 1998 +0000 bsp_put() -> bsp_hpput() bsp_get() -> bsp_hpget() Src/C_BaseLib/ParallelDescriptor.H commit 00ded7dab63a03132f215a5f995ed6f88043bbc5 Author: car Date: Fri Jan 23 18:34:00 1998 +0000 Changes. Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 0f95128dc20326fbe55cbfeb48097973fce4d1de Author: lijewski Date: Fri Jan 23 17:51:31 1998 +0000 Reduced memory usage in colate(). Src/C_AMRLib/TagBox.cpp commit f2e77a3fe0028db1bb5e80d8395894e7bdaa1c8f Author: car Date: Thu Jan 22 23:25:31 1998 +0000 Const correctness... Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit bcfe5b1079d12c7364d5fa5a454d059aa4e57c8e Author: lijewski Date: Thu Jan 22 16:39:53 1998 +0000 Added [] to delete in a few places. Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/Interpolater.cpp commit ea8a9a5689e9ae1a0e4b8c6a52f59aba5fa1ca52 Author: car Date: Wed Jan 21 22:57:52 1998 +0000 Caching removed. Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 3a6802b773dc2e15ed9e50def231b79dc077d623 Author: car Date: Wed Jan 21 22:57:38 1998 +0000 Removed caching. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 1515006855aba48d472f5bf09e7a74010edcdb91 Author: car Date: Wed Jan 21 22:57:21 1998 +0000 Removed caching Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/restrictor.H commit 4a6da3ee9b07976eca40502ea2d257af84afa368 Author: car Date: Wed Jan 21 22:56:52 1998 +0000 Removed include Files Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 9ab04286ebba7f75ac30eba243160d3478ee1af5 Author: car Date: Wed Jan 21 21:39:20 1998 +0000 Removed more useless stuff. Src/LinearSolvers/C_NodalMG/mall_info.cpp commit 61d280f3f0c3429dbb20d0086dc702a443011e85 Author: car Date: Wed Jan 21 21:35:50 1998 +0000 Removed graphics. Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_graph.H Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/cont2d.F Src/LinearSolvers/C_NodalMG/cont3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit e66b4a82793437cd2db8599549a8cc2c7a3c1603 Author: car Date: Wed Jan 21 20:57:54 1998 +0000 Changes for Parallel. Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_graph.H Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 04d5f5a28de9f57f9e6e051742c934797547395d Author: vince Date: Wed Jan 21 19:32:12 1998 +0000 Minor change for the cray. Src/C_AMRLib/DatasetClient.cpp commit cb75afca46ce7b18430e6d9f2813854612a297e8 Author: lijewski Date: Fri Jan 16 23:14:23 1998 +0000 Merged in some fixes Ann added to _amr. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/Interpolater.cpp commit 33eeb22fea7df2ad8dbe82cca743be21e64a084d Author: lijewski Date: Fri Jan 16 22:53:01 1998 +0000 Mods to compile with g++ 2.8.0 Src/C_BaseLib/DistributionMapping.cpp commit 2d87fde7c686efb60dc38d11fb888b1553a2da45 Author: car Date: Thu Jan 15 20:37:18 1998 +0000 Changes for WIN32 Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/hglib.dsp commit 6760927a889f6827ea3646e97574403e9c5d9032 Author: car Date: Thu Jan 15 19:15:59 1998 +0000 New files for WIN32 and cvs bookkeeping. Bug Fixes for WIN32. Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit 0ab68793ee5ccf234611183c3db02a9d68569eba Author: lijewski Date: Thu Jan 15 18:52:35 1998 +0000 Removed references to Arena stuff ... The Arena junk still exists, it just isn't used or referenced anywhere. Src/C_BaseLib/Make.package commit f4b1741d6f30bd056dc5ac0fae090a137dde4956 Author: car Date: Wed Jan 14 21:56:49 1998 +0000 Don't need Src/LinearSolvers/C_NodalMG/amr_grav2d.F Src/LinearSolvers/C_NodalMG/amr_grav3d.F Src/LinearSolvers/C_NodalMG/amr_gravity.H Src/LinearSolvers/C_NodalMG/amr_gravity.cpp Src/LinearSolvers/C_NodalMG/hg_elliptic.H Src/LinearSolvers/C_NodalMG/hg_elliptic.cpp commit f554eb86590e351feaaf108c5f95570a17fd66e9 Author: car Date: Wed Jan 14 21:51:02 1998 +0000 Parallel BoxLib_2 compatible first cut. Remove elliptic and other. Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/driver.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/poisson.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a2662247c9141341c55a73a2ca83132f74e45c80 Author: car Date: Mon Jan 12 21:21:46 1998 +0000 Turned on browser. Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp commit b9f7ca673b5f8efe52d003e64a4349a6cd8eb3d0 Author: vince Date: Thu Jan 8 23:06:04 1998 +0000 Added ReduceBoolOr. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.H commit 00f672699c71006d5c77769a34285363ad1e9c82 Author: lijewski Date: Thu Jan 8 18:59:59 1998 +0000 Now up-to-date with _amr. Had to add in Steven's new stuff. Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit 603443b53d94e8518f8e0101e9cea7b6347aba57 Author: lijewski Date: Tue Jan 6 23:43:56 1998 +0000 Brought into line with stuff in _amr. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 391c896479aac886fb2f0b53458e0971595acf1e Author: car Date: Tue Dec 23 19:22:34 1997 +0000 VC++ changes. Src/C_AMRLib/amrlib.dsp Src/C_BoundaryLib/bndrylib.dsp commit a1a0ac5a53aa194d881420f2854d2245f3d924e8 Author: car Date: Tue Dec 23 05:15:52 1997 +0000 Fix for win32. Src/C_BoundaryLib/bndrylib.dsp commit 9473074d92c11a725ce89060e0726e3cfc07441d Author: car Date: Tue Dec 23 05:15:15 1997 +0000 Change for Win32. Src/C_AMRLib/amrlib.dsp commit 1249c6591b446e9c0902092644a64d75d90ee257 Author: car Date: Mon Dec 22 23:12:04 1997 +0000 Updates for Win32 Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp commit 61e8f6ffd62167301124c561045c3afdf3105f9b Author: lijewski Date: Fri Dec 19 22:21:39 1997 +0000 operator&() is now implemented in terms of operator&=(). Likewise for the friend versions of surroundingNodes() and enclosedNodes(). Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 5bdc6dfdaadf33eb1544ca2bb94ff62595c12d4f Author: lijewski Date: Fri Dec 19 21:54:45 1997 +0000 Removed List::copy(). Just a memory leak waiting to happen. Src/C_BaseLib/List.H commit 681924cacad520171cc2d8f8f88d0808a19ebb7f Author: lijewski Date: Fri Dec 19 19:08:55 1997 +0000 Got rid of the ugly and dangerour (int*) cast. Src/C_AMRLib/Interpolater.cpp commit b1edb225eff063539eb70f4bc8b776944691064a Author: lijewski Date: Fri Dec 19 18:43:51 1997 +0000 getBCArray() now returns Array not int*. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit fcf695131501679e53d72e44cb0fde25017848c1 Author: lijewski Date: Thu Dec 18 18:44:38 1997 +0000 These are specialized versions of performCopy() and setVal(). They're being checked in only for informational purposes at the moment. That is, they're aren't integrated into the code. Turns out, they don't buy you anything on the DEC Alpha. They do though on a vector machine such as the Cray. Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Specialize.cpp commit f13ea356e3e9f1a8151468253dbfbf76aadf4814 Author: lijewski Date: Wed Dec 17 23:04:53 1997 +0000 Now need Src/C_AMRLib/AmrLevel.cpp commit f352fec4d8eb703e3e1b3afbd6a043a3dc931ccd Author: lijewski Date: Wed Dec 17 23:04:32 1997 +0000 Removed need for Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RealBox.cpp Src/C_BaseLib/VisMF.cpp commit 021cb575ad5915e0057c73aa06830e6b74f0b4e3 Author: lijewski Date: Wed Dec 17 18:09:33 1997 +0000 Don't allow Mersenne prime as seed. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit a1c009ce34a57cebf12483cc121368bfd712d568 Author: vince Date: Tue Dec 16 23:34:14 1997 +0000 Added pierre.nersc.gov (the T3E-600). Tools/C_mk/Make.defs commit 95f6693518a56f14211ab81a9825feee3fcc2228 Author: vince Date: Tue Dec 16 19:05:51 1997 +0000 Changed the profile tool from apprentice (which is broken) to pat. Tools/C_mk/Make.T3E commit 1ed7f8b7e0c9f5d2c6fa62f8510a3a5a44648c6f Author: lijewski Date: Tue Dec 16 16:44:54 1997 +0000 I've made it clearer in the code that only processor #0 writes to or does anything useful with the plotfile or checkpoint file header. Src/C_AMRLib/Amr.cpp commit 7c9896f0ac62d8fbe932547f6ac1e4f34de79375 Author: car Date: Tue Dec 16 15:27:47 1997 +0000 Make a warning go away. Src/C_BaseLib/RunStats.cpp commit fa0ef937808dc73214eb9a10f457dd217bdb8358 Author: lijewski Date: Tue Dec 16 00:41:28 1997 +0000 DIMV -> DIMENSION DIMV macro conflicted with the one in ArrayLim.H. Src/C_AMRLib/MAKESLICE_3D.F commit 17b3dbbf54051e26084d7f54aad368e3400aafc1 Author: lijewski Date: Mon Dec 15 17:00:52 1997 +0000 utilrand() -> blutilrand(). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit e62ad3c067a13ec0a61485aad0bf0e2f19d5cb9b Author: lijewski Date: Sun Dec 14 23:34:59 1997 +0000 Added Random(), InitRandom() and Fortran entry points for Random(). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 302e9a2796342c636dca4b9499073f79fc15ce9a Author: lijewski Date: Sun Dec 14 23:34:14 1997 +0000 Added CVS ID in C comment. Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_BaseLib/COORDSYS_F.H commit 647d2727d72d7bbfbf855e0b12ecd5e392f3c3fa Author: lijewski Date: Sun Dec 14 01:05:52 1997 +0000 Reverted out the merged of FAB stuff in BaseFab. It tickles a bug with the Cray CC compiler on the T3E. Quite pernicious. Src/C_BaseLib/ArithFab.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H commit a37fa9cae782a4c4f8d753928ad0d7fe1120d1e7 Author: car Date: Sat Dec 13 21:09:28 1997 +0000 Compile rule changes. Src/C_AMRLib/amrlib.dsp commit 0a499e0803a493c0ca5adddc4eb347505878e82d Author: lijewski Date: Sat Dec 13 19:53:07 1997 +0000 Fixed some inconsistencies between declarations in the _F.H file and the definition/usage. Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/Interpolater.cpp commit 2ac9a7c7226b48c009e3e1c0917a40bf2c943fa6 Author: lijewski Date: Sat Dec 13 19:48:03 1997 +0000 Mod to keep T3E quite re: usage of real*8 Src/C_AMRLib/FLUXREG_3D.F commit 605213228d415d6bab0a44fb00eeb5948e564a6a Author: lijewski Date: Fri Dec 12 23:23:40 1997 +0000 Only the I/O processor tries to build the required directory tree. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 18788d705427dafc3064380d1b9ca1091168703b Author: lijewski Date: Fri Dec 12 22:44:54 1997 +0000 DIMS.H has been merged in. Src/C_BaseLib/ArrayLim.H commit c1c2ce6a09b6bca8ec3e5db780f4e0e70702fd0f Author: lijewski Date: Fri Dec 12 22:42:42 1997 +0000 DIMS.H has been merged into ArrayLim.H All .F files now have leading comment containing CVS ID. Src/C_AMRLib/DIMS.H Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/MAKESLICE_3D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F commit e85bc2df3102bda72a4bd16ba4a1b0adffb28aae Author: lijewski Date: Fri Dec 12 16:10:14 1997 +0000 Now use f90 instead of f77. Tools/C_mk/Make.OSF1 commit 935d811fa8891e5ccaec9fb350052eb3ff75a742 Author: car Date: Fri Dec 12 00:17:15 1997 +0000 Changes for VC++ Src/C_AMRLib/.cvsignore Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/MAKESLICE_3D.F Src/C_AMRLib/amrlib.dsp commit 96a8a983fc82bb0a21f3975d37a45b3a2d326138 Author: car Date: Fri Dec 12 00:15:57 1997 +0000 VC++ fixes. Src/C_BaseLib/COORDSYS_3D.F Src/C_BoundaryLib/.cvsignore Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/bndrylib.dsp commit c6e44f8fa73ce93a38fe6c78e152bb53a7015be2 Author: car Date: Fri Dec 12 00:14:57 1997 +0000 Changles for VC++ Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/pBoxLib_2.dsp commit 16aa03f3b1f8b7235f5037208f44d468fbba0d35 Author: lijewski Date: Thu Dec 11 23:26:58 1997 +0000 Removed all checks on the return value of new. We now rely on a set_new_handler() being installed. See Parallel/HCAll/main.cpp for details. Brought up-to-date with the serial version of BndryLib. Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 174ae4a6f67c5648d78bde2487850264fc3ee234 Author: lijewski Date: Thu Dec 11 23:25:38 1997 +0000 Removed all checks on the return value of new. We now rely on a set_new_handler() being installed. See Parallel/HCAll/main.cpp for details. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/BC_TYPES.H Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DatasetClient.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxAssoc.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/List.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Tracer.cpp Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit 073b10ae7e3d6767e5b5cf7bc1a013461ce496d7 Author: lijewski Date: Thu Dec 11 06:14:02 1997 +0000 A few more endls added. Src/C_AMRLib/Amr.cpp commit 611e3a3d57d80e13fc2f0708c1514d790d26b911 Author: lijewski Date: Thu Dec 11 06:07:47 1997 +0000 Added some strategically placed endl's. The T3E iostream library doesn't flush on newline :-( Src/C_AMRLib/Amr.cpp commit 5df40bb4168d53c00db762cf974cc80d0d25b328 Author: lijewski Date: Thu Dec 11 05:01:08 1997 +0000 Brought up-to-date with servial version of BndryLib stuff. Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 2ff8299f66f1621d39f03fab4f4fbafb8fca7945 Author: lijewski Date: Wed Dec 10 22:04:42 1997 +0000 Added DIMS==1 stuff. Src/C_AMRLib/DIMS.H commit 941c34764fdce5a833861ed1591a436c1ec63709 Author: lijewski Date: Wed Dec 10 21:56:01 1997 +0000 Merged in mods from IAMRAll. Inlined all FabSetIterator gunk. Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/RealBox.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit d622c9c131c70a12ccad7e91fdc09f1e0f34e321 Author: lijewski Date: Wed Dec 10 19:07:38 1997 +0000 Moved from HCAll. Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 5f003658c365112a12258ac3825e4f401e06213f Author: lijewski Date: Tue Dec 9 23:29:59 1997 +0000 ArithFab, NormedFab and OrderedFab have been merged into BaseFab. BaseFab is no longer a virtual baseclass of FArrayBox. Removed the maskLT-type operations. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package commit bc51b60088e7011f61acc22c8f9d8b471bdca318 Author: lijewski Date: Tue Dec 9 21:54:52 1997 +0000 TagBoxArray::numTags() now returns long. Merged in TagType typedef everywhere. TagBox::numTags(Box&) now calls TagBox::numTags(). Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit b2f43254817e87dcd6021a324ef594ff706ba105 Author: lijewski Date: Tue Dec 9 17:46:20 1997 +0000 Delayed some of the new's until after sync()s as much as possible. Src/C_AMRLib/TagBox.cpp commit d15fb5d669354198bdde126ea7d54d9413709509 Author: lijewski Date: Mon Dec 8 23:12:59 1997 +0000 The define() functions now have a guard that checks to see if we're running in parallel or not. Also, the one that returns PArray* now returns MultiFab* Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit ec10bf416228adf4d62f11e3f7a0b93ad46ad0f3 Author: lijewski Date: Sat Dec 6 01:04:47 1997 +0000 Added in Marc's fix for non-nested grids. Src/C_AMRLib/Amr.cpp commit 5b31a6c2e087b856a33b7f7a520e424bcc7b8974 Author: lijewski Date: Fri Dec 5 22:07:31 1997 +0000 Some consolidation. Tools/C_mk/Make.T3E commit 73822ae6714999728658448baccaf85b36fb90b4 Author: car Date: Fri Dec 5 19:07:30 1997 +0000 Give an argument to ::time() Src/C_BaseLib/Utility.cpp commit 041888b9739ec659c8e5a6cf0a69146730f0a9bb Author: lijewski Date: Fri Dec 5 17:59:25 1997 +0000 Merged couple more mods from IAMR. One was a setVal() in isValid() that had been removed -- it's needed in IAMR. Src/C_AMRLib/AmrLevel.cpp commit 06abebbad7523ba283fee6222e867f2be63123d6 Author: lijewski Date: Fri Dec 5 16:18:22 1997 +0000 Added clear() and clear(int). Src/C_BaseLib/VisMF.H commit d814232dc3a7f7da34ce84fb069cfb1e9e990f94 Author: lijewski Date: Fri Dec 5 00:07:31 1997 +0000 If not BL_USE_SETBUF setbuf -> pubsetbuf Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.cpp commit cbed681d37f6aa4355b2220152120eed9a520068 Author: lijewski Date: Thu Dec 4 22:57:08 1997 +0000 Using .isNull() instead of == "". Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.cpp commit a7482eb8f13bb825f8bb4185dcbca80adc30160c Author: lijewski Date: Thu Dec 4 22:33:20 1997 +0000 Fixed weird requirement that ParmParse must be init'd from command line. Src/C_BaseLib/ParmParse.cpp commit 40ee356ed8994303486ca644e4bec0be668a64e9 Author: lijewski Date: Thu Dec 4 21:32:06 1997 +0000 Moved from amrlib. Src/C_BaseLib/Make.package Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit 609c3231920fd66265b515ccd27aa3e819df4e9a Author: lijewski Date: Thu Dec 4 21:31:52 1997 +0000 Moved to pBoxLib_2 Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit e91598b114acb9e481c054faa791e7a1a316b739 Author: lijewski Date: Thu Dec 4 20:58:48 1997 +0000 Changed plotfile and checkpoint file formats slightly to facilitate reading and writing them to directories different from the one in which you're running. Merged more gunk from IAMRAll. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit d43432b60b1b500f976ff3c000471133691eb70f Author: lijewski Date: Thu Dec 4 20:11:01 1997 +0000 Mods to allow writing of plotfiles and checkpoint files in directories other than the one in which you're running. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 062fc873b23ccf26d68bea215849aca5319ae743 Author: lijewski Date: Wed Dec 3 23:26:11 1997 +0000 chkfile -> chfile when not using BL_PARALLEL_IO. Src/C_AMRLib/Amr.cpp commit 6522fc97765ebc19f0e15e3713d1afd03f794145 Author: lijewski Date: Wed Dec 3 21:09:54 1997 +0000 Cleaned up a tad. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit d5d40ca423116d44fabde4856d67ca109410580b Author: vince Date: Wed Dec 3 19:24:54 1997 +0000 Added a variable to distinguish between the NERSC T3E and the NAVO T3E. Tools/C_mk/Make.defs commit d9eec7e93e4b6e5256fa3e904614b04858e533f2 Author: lijewski Date: Wed Dec 3 03:26:57 1997 +0000 Performance modification to performSetVal(). Src/C_BaseLib/BaseFab.H commit b9d9755a1441e78a36b7d7252e284ac3d7fcaede Author: lijewski Date: Tue Dec 2 23:59:29 1997 +0000 Merged in from IAMRAll. Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F commit aca53b646f5b030c636c16c9248c287b5383eda7 Author: lijewski Date: Tue Dec 2 23:40:32 1997 +0000 Merged with one from IAMRAll. Src/C_AMRLib/FluxRegister.cpp commit dcaba019a2fd0d31427420f46d3336a3a1e3d933 Author: lijewski Date: Tue Dec 2 23:05:28 1997 +0000 Merged with IAMRAll. Src/C_AMRLib/TagBox.cpp commit 3cc8b18f0d6eb3ed26891ea45ec2f832e6fcbf28 Author: lijewski Date: Tue Dec 2 21:30:56 1997 +0000 Updated from IAMRAll. Src/C_AMRLib/StateData.cpp commit a211f6340f445ba6a77b020c09761aaa8717764a Author: lijewski Date: Tue Dec 2 21:15:47 1997 +0000 Updated from IAMRAll. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit b3e9cce89a07963e0ed3e3bcaf25f6ccc047480f Author: lijewski Date: Tue Dec 2 19:12:17 1997 +0000 ErrorType and ErrorFunc are now member of ErrorRec. Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit bdc75be87999dab12a261d04ccc2d71a1518ea21 Author: lijewski Date: Tue Dec 2 00:08:55 1997 +0000 Added virtual aString thePlotFileType() const. Removed an extraneous include directive. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 9a49fb840866a5c3dcb4888ab7cfcc763a04ba2d Author: vince Date: Mon Dec 1 21:01:29 1997 +0000 Moved BSP defines to the appropriate Make.machine file. Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E commit b8498d60b70124f9e5da6a89a37d13cd5f59c4b2 Author: vince Date: Mon Dec 1 20:49:58 1997 +0000 Added ifdefs for the T3E. Src/C_BaseLib/CONSTANTS.H commit bdbd2a0966e7027277119d5c831377780c7add9a Author: lijewski Date: Mon Dec 1 18:23:11 1997 +0000 Mods to compile with Cray compiler on T3E. Src/C_BaseLib/DistributionMapping.cpp commit bcf073c9c4f7686dcdb40526adc585921c249c04 Author: lijewski Date: Fri Nov 28 18:30:25 1997 +0000 Removed maximum cache size mumbo-jumbo. The cache must now be flushed manually. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 6d2120e6876df2a34915fb4a49c942180001f7e2 Author: lijewski Date: Fri Nov 28 18:14:42 1997 +0000 Call DistributionMapping::FlushCache() in regrid() after grid_places(). Src/C_AMRLib/Amr.cpp commit 0a1c87390b127de07f8023f0159f87f4dc461a39 Author: lijewski Date: Fri Nov 28 17:27:37 1997 +0000 Bypass the processor cache when using ROUNDROBIN. Src/C_BaseLib/DistributionMapping.cpp commit f93718ec08ebe1f09cd17646961f86b6e23b720c Author: lijewski Date: Fri Nov 28 16:45:13 1997 +0000 Added assert(rwtime > 0). Now that we're using wsecond() this shouldn't happen, but ... Src/C_AMRLib/RunStats.cpp commit a0c694a9f73c331d3e354c343f56aafe3a64f27d Author: lijewski Date: Fri Nov 28 00:00:45 1997 +0000 Am now caching processor maps. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 710697e5ad818b19abb8170f622298aaa0c04719 Author: lijewski Date: Wed Nov 26 20:51:36 1997 +0000 CLUSTER -> Cluster Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp commit dc7efde597f5e2f7be1d2b06a0f9b4b186843236 Author: nazgul Date: Wed Nov 26 20:46:17 1997 +0000 Testing errors in divergence of a linear velocity field Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c5d04257975f57cda908e22201800e12cc88d6ec Author: nazgul Date: Wed Nov 26 20:44:08 1997 +0000 Grids for convergence test with single refined patch Src/LinearSolvers/C_NodalMG/tests/gr2r1 Src/LinearSolvers/C_NodalMG/tests/gr2r2 Src/LinearSolvers/C_NodalMG/tests/gr2r3 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r3 commit 875e4cf3add35beaed7a90cf0eb42230e3fb831e Author: lijewski Date: Wed Nov 26 20:41:41 1997 +0000 The return value of all "new"s is now checked. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/TagBox.cpp commit 43c49db0947ea7a55dc0c8a1232fba1a2093192c Author: lijewski Date: Wed Nov 26 19:18:46 1997 +0000 BOX -> Box REAL -> Real TAGBOX -> TagBox INTVECT -> IntVect FARRAYBOX -> FArrayBox Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/ErrorList.H Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit d35e1c6a9cc6b6db290b737a0bbb5c2d4c88242b Author: lijewski Date: Wed Nov 26 18:27:45 1997 +0000 setTimeLevel() now takes three arguments. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 909029aaab141527b8d9c59575ac5134efc8f654 Author: lijewski Date: Wed Nov 26 17:46:22 1997 +0000 enum TimeCenter is now nested in StateDescriptor. Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 10e5b26984d8391b48badf150356992e293db849 Author: lijewski Date: Wed Nov 26 06:26:45 1997 +0000 Made wsecond() initializers explicitly extern. Don't want anyone to think they should be static :-) Src/C_BaseLib/Utility.cpp commit e173ec034764e9e29755b5e909030a1e2417b10d Author: lijewski Date: Wed Nov 26 05:07:25 1997 +0000 init() is now protected. The constructors call it if it hasn't already been called. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit ff669c441728a23f4ab81774d965e633679b9833 Author: lijewski Date: Wed Nov 26 04:22:34 1997 +0000 Don't call knapsack code if on 1 cpu -- use roundrobin. Guarantee that all versions of wsecond() get initialized at program startup. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 741d07df888ffa7adfa3dc0db507d3ec9f48221f Author: lijewski Date: Wed Nov 26 04:21:46 1997 +0000 init() is now protected. It's called by the constructor if it hasn't already been called. Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit 090da2f19dc49617370b4ecfb56fc80254bc071b Author: lijewski Date: Tue Nov 25 22:17:51 1997 +0000 Added four types of create functions. Call them through a static pointer to member function. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 966bcb45cc7c113576d08c8bfbd3989aa843d9f9 Author: car Date: Tue Nov 25 19:55:15 1997 +0000 Assertion for nprocessors > 1 Src/C_BaseLib/DistributionMapping.cpp commit e343caa0f06827f5ad07b57e1aed6a9c06be2f14 Author: lijewski Date: Tue Nov 25 19:23:31 1997 +0000 Regularized os.precision() mumbo-jumbo a tad. Src/C_AMRLib/RunStats.cpp commit 9e1091c89357c16a7905d2dce40c01aacab92524 Author: lijewski Date: Tue Nov 25 19:09:42 1997 +0000 Different way to guarantee wall clock time gets initialized. Src/C_BaseLib/Utility.cpp commit 65fd1ea0ff17a71e0339ece4c461dfe68a17ea7a Author: car Date: Tue Nov 25 19:00:36 1997 +0000 Improvements in DistributionMapping for Knapsack Src/C_BaseLib/DistributionMapping.cpp commit dbaffef3482714b2aa5279b0eccfb7fc6c22d7fa Author: lijewski Date: Tue Nov 25 18:47:05 1997 +0000 Added init() and strategy(). Turned on knapsack(). Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 2a4d5a0869b1b90cf48d31e4f4ce23a02e7c3e06 Author: lijewski Date: Tue Nov 25 17:08:25 1997 +0000 Small changes ... Src/C_BaseLib/DistributionMapping.cpp commit 68fa915dfbc2338a1e6c57fa9a09c358d55e8db2 Author: car Date: Tue Nov 25 14:49:30 1997 +0000 Removed use of member template. Src/C_BaseLib/DistributionMapping.cpp commit 07c667a8064c45af21efc3b105b3c94482d8cb13 Author: lijewski Date: Mon Nov 24 23:45:51 1997 +0000 Added initializer for wsecond(). Src/C_BaseLib/Utility.cpp commit d713dc76066ff10d8180db70214104cb995a8a03 Author: car Date: Mon Nov 24 22:05:10 1997 +0000 Commiting some knapsack code, to see if it compiles on T3E. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/GNUmakefile commit 47c36e3f35abcc63b00f57b54cbfd534b088cf16 Author: lijewski Date: Mon Nov 24 21:04:37 1997 +0000 Am now using Utility::wsecond() in place of ParallelDescriptor::second(). Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit 30b300234dddd73ff35d87c877869e537e629290 Author: lijewski Date: Mon Nov 24 18:52:26 1997 +0000 Merged in BL_COPYRIGHT_NOTICE macro. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Amr_auxil.H Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/BC_TYPES.H Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 03a1edc77cfe304eb20a15dbb6c1f4403dab42eb Author: lijewski Date: Mon Nov 24 18:40:53 1997 +0000 Minor mod to output formatting. Src/C_AMRLib/RunStats.cpp commit 2d82e5ad5a4d6db9004cf9cff738e996bba85906 Author: lijewski Date: Sun Nov 23 21:42:50 1997 +0000 Removed m_numpts stuff. It's now in RunStats. Src/C_BaseLib/FabArray.H commit 927df7ff08765882c95dd7c3118e2e383683ef68 Author: lijewski Date: Sun Nov 23 21:42:31 1997 +0000 NumPts() stuff from FabArray::AllocFabs() is now in here. Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit 4acbf7cb9f02a0106d17b0bd0b22b7d82c09e1e5 Author: lijewski Date: Sun Nov 23 18:19:59 1997 +0000 We now return # of bytes written to disk. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 1ac4be59b81ef4dbef44a7adf63376379fa4a13d Author: lijewski Date: Sun Nov 23 18:18:49 1997 +0000 RunStats now accumulates bytes written to disk. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp Src/C_AMRLib/StateData.cpp commit 1223356c10c46af6ea34b84421af5108b5f7ad56 Author: lijewski Date: Sun Nov 23 00:12:08 1997 +0000 Don't print out stats if the particular stat is 0. Src/C_BaseLib/FabArray.H commit 972bf74ed43f8cf8d61a0ed0cd0a2c13df086c14 Author: lijewski Date: Sun Nov 23 00:10:55 1997 +0000 Merged in a saner RunStats. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit d287254ecf1008f08a69bcf26ee8b8bc8b553854 Author: lijewski Date: Sat Nov 22 17:52:06 1997 +0000 Moved FileOpenFailed() to Utility. Added CreateDirectoryFailed() to Utility. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 35f09d2306022d65900f0bc0f7f109fe2747bccd Author: lijewski Date: Sat Nov 22 17:51:31 1997 +0000 Moved FileOpenFailed() and CreateDirectoryFailed() to Utility. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 254c7f4c0205435dec780b6cac6e305655f3d874 Author: lijewski Date: Sat Nov 22 01:10:41 1997 +0000 Merged in VisMF::FileOpenFailed(). Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit d61c5cbf2174d79225ef99fa57f15535b1f0071d Author: lijewski Date: Sat Nov 22 00:44:44 1997 +0000 Merged in I/O statistics stuff. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 80b42b44834d0175d518a45e2e14b3478eaebe75 Author: lijewski Date: Sat Nov 22 00:44:22 1997 +0000 Merged in I/O statistics. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 3a29dc686b6c227c96d1b1114799e0940f9e4c80 Author: lijewski Date: Fri Nov 21 20:33:25 1997 +0000 Added typedef to describe first argument of bsp_fold(). Src/C_BaseLib/ParallelDescriptor.cpp commit d7c140a2b36bf60ea5f45ed33ee9d407a5a4c3a3 Author: lijewski Date: Fri Nov 21 03:50:35 1997 +0000 Now accumlate numPts() in m_numpts. Src/C_BaseLib/FabArray.H commit 273e77e9682043b051ce8fa8ab14ea43f32ec972 Author: lijewski Date: Fri Nov 21 03:50:10 1997 +0000 Fixed a bug in RunStats. Still needs work. The name of WritePlotFile RunStats variable didn't match that in inputs. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit b6259f73d32732e0f2187202b66f00d0f892ecc8 Author: lijewski Date: Thu Nov 20 18:26:59 1997 +0000 Small changes Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E commit 14ea1a3b9bfee6907b4d30e11a5ddf1bf975db69 Author: lijewski Date: Thu Nov 20 18:14:32 1997 +0000 Removed a `return' following a `stop' that compiler warned was unreachable. Src/C_AMRLib/INTERP_3D.F commit ebde3cbef4316373d3f53360e10de25a88312d56 Author: lijewski Date: Thu Nov 20 17:05:10 1997 +0000 Small mod to compile on T3E. Src/C_BaseLib/VisMF.cpp commit d1144ac0f339e530ca652fa427ad8a7d75f740cd Author: lijewski Date: Thu Nov 20 17:04:57 1997 +0000 Small mod to get to compile on T3E. Src/C_AMRLib/Amr.cpp commit f93dce4316880b343263c358a1c8490f204d2931 Author: lijewski Date: Thu Nov 20 16:13:38 1997 +0000 A small simplification. Src/C_BaseLib/ParallelDescriptor.H commit 3b1715cd2d8567bb8161758b1dcf21e051413a2a Author: lijewski Date: Thu Nov 20 00:49:42 1997 +0000 ParallelDescriptor::SetMessageHeaderSize() now takes int not int&. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit 26f5efae06b0e670322d2d2ef0c8e55b222c93b7 Author: lijewski Date: Thu Nov 20 00:19:50 1997 +0000 Added PrintStats() to FabArray. Src/C_BaseLib/FabArray.H commit 69d07d5b9af87d1a4313555ae1b6f5d918958d4d Author: lijewski Date: Thu Nov 20 00:19:30 1997 +0000 Prettified report() a tad. Src/C_AMRLib/RunStats.cpp commit 235c008475187c04dd7ae36eb8f520deded123b9 Author: lijewski Date: Wed Nov 19 17:31:19 1997 +0000 Removed some unused arrays in FabArrayCopyDescriptor and general cleanup. Src/C_BaseLib/FabArray.H commit fc1aebf5a3a40ccded9a994bdc6f5c376c631b1d Author: lijewski Date: Wed Nov 19 16:25:54 1997 +0000 Added write_pltfile and write_chkfile RunStats. Moved some RunStats functions inline. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit e93560b695d6d4509d99f56e101b34eb4955e7d0 Author: lijewski Date: Wed Nov 19 04:42:27 1997 +0000 Simplified a tad bit of code. Src/C_AMRLib/RunStats.cpp commit 706190ebc65e593fd47687703c81e3752f7a4cf4 Author: lijewski Date: Wed Nov 19 00:01:26 1997 +0000 Modified to deal with bsp_time() possible returning zero. Src/C_AMRLib/RunStats.cpp commit 411ed2fc60c77998ad4c5970761e3040f3a8296b Author: car Date: Tue Nov 18 21:45:28 1997 +0000 Start some changes. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 88a4eaf6e05cdf6172364fe40dfb55d13e884cac Author: lijewski Date: Tue Nov 18 19:30:19 1997 +0000 Copied from Parallel/HCAll Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Amr_auxil.H Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/BC_TYPES.H Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DIMS.H Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/MAKESLICE_3D.F Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 7580dbc50250fc98c65d6287899469a168b556df Author: lijewski Date: Tue Nov 18 18:51:53 1997 +0000 PerFile -> PerFab Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit b1b43805e1d22020c38aa4e7f205657818871126 Author: lijewski Date: Tue Nov 18 18:48:13 1997 +0000 Fixed a bug. Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 2bed7fd7983f1060808bd0b38f3607313e42e485 Author: lijewski Date: Tue Nov 18 18:22:24 1997 +0000 Mods to compile on NAVO T3E. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit b4c40aa369442e197db0fd969f3636726bedd8c8 Author: lijewski Date: Tue Nov 18 00:04:45 1997 +0000 Added explicit to all single-argument constructors. Removed IntVect::operator const int * Wrote BoxList::contains(BoxArray). Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/aString.H commit da5f8ca65647b43377ab0c0250333b5fdc16b9a4 Author: lijewski Date: Mon Nov 17 21:09:30 1997 +0000 Removed ToString(). Got rid of GetTheChar(). Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit be34251f063aae0ba8373b5b0065b3d93c923b47 Author: car Date: Mon Nov 17 19:05:31 1997 +0000 A little better way: just pass in a dummy mode variable in WIN32. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 02be1b6435f232df319cc65b3cfcc03b56bfcbba Author: car Date: Mon Nov 17 19:02:03 1997 +0000 Fix for WIN32 not supporting mkdir. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit da2dca39383022b04afc87f7c728283a761f0b5a Author: lijewski Date: Sat Nov 15 00:52:38 1997 +0000 Added VisMF::Read(). Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit a55ffec0d73f28c2ad91559bf836b35f719cb9ba Author: vince Date: Fri Nov 14 21:43:35 1997 +0000 Added better optimization flags. Tools/C_mk/Make.T3E commit 42f1aeaee1b13f53c6dba9329afa8d4224b6b43e Author: lijewski Date: Fri Nov 14 20:22:40 1997 +0000 The IO_Bufffer object needs to be created before the [io]fstream one! Src/C_BaseLib/VisMF.cpp commit 171470f55904913285ebfadbb1ee003299edbea4 Author: lijewski Date: Fri Nov 14 00:59:55 1997 +0000 Removed Large_IO_Buffer() and replaced with Array usage. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 93d90f6eb05e1fd98ebda7e80c851c0348d47b54 Author: lijewski Date: Thu Nov 13 23:55:44 1997 +0000 Made IO Buffer stuff public so Amr could use it as well. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 627d0ed0a2a41ba363d9626167273d917bc8ec81 Author: lijewski Date: Thu Nov 13 21:47:46 1997 +0000 Removed ios::binary junk. Integrated in BL_USE_SETBUF and BL_SETBUF_CHAR_SIGNED. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit dcbcb4aa1f46879a8733fdff360e506e3e77866f Author: lijewski Date: Thu Nov 13 21:41:23 1997 +0000 Added BL_USE_SETBUF. Tools/C_mk/Make.T3E commit 8bf2453b733cc05f0dc021a7de03d5e2c32e9813 Author: lijewski Date: Thu Nov 13 21:28:01 1997 +0000 Added -DBL_SETBUF_SIGNED_CHAR when using CC. Tools/C_mk/Make.T3E commit 36023a9e0532dc4dbb50e1375ea48066b3c583cf Author: lijewski Date: Thu Nov 13 18:45:14 1997 +0000 Now uniformly use BoxLib::Error() for error reporting. It now uses ParallelDescriptor::Abort() internally, when needed. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.cpp commit 8fe14ed9529726e90c08c6bfd1bf68fa6c0bcab1 Author: lijewski Date: Thu Nov 13 16:38:54 1997 +0000 Replaced abort() with BoxLib::Abort(). Src/C_BaseLib/ParallelDescriptor.H commit 6f6535f7e59c6cb39deb231ee6499dfeec634d69 Author: lijewski Date: Thu Nov 13 16:34:00 1997 +0000 Maxed out the precision when outputting the Header. Replaced BoxLib::Error() with ParallelDescriptor::Abort(). Src/C_BaseLib/VisMF.cpp commit 3e4f7350c5ebdc3cacf3fc4433c1a2b7aff00419 Author: lijewski Date: Thu Nov 13 15:47:34 1997 +0000 Bug in the relative path portion of CreateDirectory() Src/C_BaseLib/Utility.cpp commit 0e7688ec40ee9c57120f60205799349f4bc2e004 Author: vince Date: Thu Nov 13 01:14:43 1997 +0000 Make definitions for the T3E. Tools/C_mk/Make.T3E commit 34c3ce53861205acf3f172113da3aed1cd192bcf Author: lijewski Date: Thu Nov 13 01:05:12 1997 +0000 Signatures of Abort() were not consistent in sequential/parallel code. Src/C_BaseLib/ParallelDescriptor.H commit 9deac822f6de4d5afa4c1ce513f5fe0989d37f6e Author: nazgul Date: Wed Nov 12 22:10:30 1997 +0000 fiddling with test problems Src/LinearSolvers/C_NodalMG/proj.cpp commit ea17c0a6c99aacaa2f5f90d2ac06e4c7ddbd54bd Author: lijewski Date: Wed Nov 12 21:57:26 1997 +0000 Added Utility:CreateDirectory() and a test case. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tDir.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tDir.cpp commit 974ebd6a6402d98bd84879e9d24a1cc2cb1143ea Author: nazgul Date: Wed Nov 12 21:42:33 1997 +0000 New tests for 3d terrain stencils Src/LinearSolvers/C_NodalMG/tests/gt2t1 Src/LinearSolvers/C_NodalMG/tests/gt2t2 Src/LinearSolvers/C_NodalMG/tests/gt2t3 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t1 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t2 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t3 commit d5405f554e8fa7292d1344340eb07c40e7707898 Author: nazgul Date: Wed Nov 12 21:39:29 1997 +0000 Fix to problems with sigmas in terrain stencils? Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 6eafa3faf7a3a63e0442c7aac32bb7ef9df9fdce Author: lijewski Date: Wed Nov 12 17:40:33 1997 +0000 VisMF.cpp currently compiles on T3E. Added -nboxs flag to test case. Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit c3b2b9decf9bed0c9cebc7a2a1f17827651a4e70 Author: lijewski Date: Wed Nov 12 04:12:24 1997 +0000 Made the open modes I expect explicit. Now longer clean up previous output files in test case. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 8477ccb607366879f486ff382f8e6a724229d993 Author: lijewski Date: Wed Nov 12 00:22:57 1997 +0000 Added .cvsignore Src/C_BaseLib/.cvsignore commit 7b0886b7799558836552352318143a04261bea94 Author: lijewski Date: Wed Nov 12 00:16:56 1997 +0000 Added some code to use large I/O buffers on T3E. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit b2a4849bd98ec80bc920200f1c98c648dafabfef Author: lijewski Date: Tue Nov 11 22:18:59 1997 +0000 Needed a ParallelDescriptor::Synchronize() between writing and reading. Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 1d2d9c7f876b9ae83a21881650a8f0e4119cb4c1 Author: lijewski Date: Tue Nov 11 21:38:37 1997 +0000 Added a call to MultiFab::setBndry(0). Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 6efd06bd71aacccf2e7fe7e0ab8ab68daed64c99 Author: lijewski Date: Tue Nov 11 21:22:50 1997 +0000 Consolidated some of the code into larger routine. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 05dd332fe75a4cb053c9de15d88b0de4b521c900 Author: vince Date: Tue Nov 11 21:04:52 1997 +0000 Added sync argument: FabArrayIterator::isValid(bool bDoSync = true); Src/C_BaseLib/Box.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp commit 1cec386f02ec5642acf31469fe3f77a9d5b140dd Author: lijewski Date: Tue Nov 11 21:02:19 1997 +0000 Now the OneFilePerFab is working in Parallel. Src/C_BaseLib/VisMF.cpp commit ce90c46d9f36c971a0c99753ffe77e6765d5ba8d Author: nazgul Date: Tue Nov 11 20:51:05 1997 +0000 Added compiler options necessary to get optimization to work with KCC 3.1a and 3d terrain level solves. (Cannot use higher than +K2). Src/LinearSolvers/C_NodalMG/GNUmakefile.main commit 7ea8288dc1d5e51f9d5caf8af9702155e569d23c Author: lijewski Date: Tue Nov 11 20:29:56 1997 +0000 Added -how flag. Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit e1e01db38ee3abd6a9cf5f6d27d910d90dacb444 Author: lijewski Date: Tue Nov 11 19:20:05 1997 +0000 Got the VisMF::OneFilePerCPU working in Parallel. Had to Change the signature of ParallelDescriptor::SendData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/GNUmakefile Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tVisMF.cpp commit 69ba94f24fa738ddcdcbfe61b9885fc21d29f5fc Author: lijewski Date: Tue Nov 11 01:18:13 1997 +0000 Added some more parallel code. Yet more to come. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 4a85cfa5eb28722d7b729beb300a73fb11769a06 Author: lijewski Date: Mon Nov 10 22:41:21 1997 +0000 Did the MultiFab loops using proper Parallel construct. All that remains is to do the reduction of the VisMF::Header. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 28b1d733eece835af8947f32f9deef7af6fb994e Author: almgren Date: Mon Nov 10 22:22:33 1997 +0000 These files now have the correct subroutines for the 3-d multilevel terrain stencils (faces / edges / corners) for residual and divergence. They are ifdef'ed for TERRAIN. Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 917a5935e1339560e318e7762442f5bf340fb02d Author: lijewski Date: Mon Nov 10 22:14:47 1997 +0000 Added length() member to VisMF.H Now test reading and writing both ways at once. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit e0511943b7c79a843f58a3bdf20a68794e3586aa Author: car Date: Mon Nov 10 21:36:17 1997 +0000 Some changes for parallel file I/O. Src/C_BaseLib/Box.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/pBoxLib_2.dsp commit 42fc8aca600e7d443e836e807c733361a6a34f81 Author: lijewski Date: Mon Nov 10 21:29:48 1997 +0000 Got working for -DUSE_NEW_HFILES macro. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit e9fda6fc2ba520eeef6937b9d5fa0fe55862609e Author: lijewski Date: Mon Nov 10 21:17:10 1997 +0000 Got OneFilePerFab working. Parallel to come .... Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 1f3f0335cc9c42666dcc88444a4ef099483238cd Author: lijewski Date: Mon Nov 10 19:30:12 1997 +0000 The OneFilePerCPU stuff seems to work. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tVisMF.cpp commit 319f3a350a8b72b3e98e939024107c93036638f7 Author: lijewski Date: Mon Nov 10 17:54:40 1997 +0000 BoxArray(istream&) wasn't implemented. Now can read the VisMF::Header that has been written to disk. Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit d90e806f32a69eacb746ce65e5aa5a5bd0002ce6 Author: lijewski Date: Mon Nov 10 03:55:46 1997 +0000 Forgot about the ghost cells :-( Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 1cba5e03c9ab1744917afd85365f1713d946a920 Author: lijewski Date: Mon Nov 10 03:37:29 1997 +0000 Wrote the stream extraction operators. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit c915e63bbd7e6df69b00621ca657334e050b0b1c Author: lijewski Date: Sun Nov 9 20:31:40 1997 +0000 OneFilePerCPU output is more or less done. Now for the testing. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit d2639f853837afbfac5d509a4e247b69c6fd8ef9 Author: lijewski Date: Sun Nov 9 20:11:25 1997 +0000 Just cosmetic guff. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 5c2d5d466f4e3b8e5ef92adc066d15897ec27c7d Author: lijewski Date: Sun Nov 9 19:45:29 1997 +0000 Slight cosmetic changes -- no more static stuff in .cpp file. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 0168fa96dd8c6b533f83b746594dfd07a59ab040 Author: lijewski Date: Sun Nov 9 00:58:56 1997 +0000 Added some more code. Lots more to follow. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 7450ac6ba2d45882ffd2d2e2cb0371873b53af3f Author: lijewski Date: Sat Nov 8 23:24:16 1997 +0000 Added VisMF stuff -- just getting started with it. Src/C_BaseLib/Make.package Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit b6a549645833f8e7a91bd753baa11ebad0d6ab96 Author: jbb Date: Sat Nov 8 01:42:02 1997 +0000 Fixed nested comments Src/C_BaseLib/Utility.H commit 9e289e25a32fda9c0bf218d99f2b66a2320861ae Author: almgren Date: Thu Oct 30 22:44:32 1997 +0000 Added subroutines hgfdiv, hgediv and hgcdiv for TERRAIN defined. Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 61c404f39f962c7079aa6908f789cb7385de8a89 Author: almgren Date: Thu Oct 30 22:44:13 1997 +0000 Cosmetic changes only. Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 6cd1d16687afdf6e5465cc44323f4c35c4d37cde Author: vince Date: Tue Oct 21 22:00:52 1997 +0000 Bug fixes for parallel multilevel IAMR (minus the nodal projection). Also other fixes and code cleanup. Src/C_AMRLib/DatasetClient.cpp commit 70e92eff9aac7b20539be29a390d0a5b616cf076 Author: vince Date: Tue Oct 21 21:55:53 1997 +0000 Minor changes to AddBox interface. Src/C_BaseLib/Box.H Src/C_BaseLib/FabArray.H commit 15b8ce2bab58de1b394fb1c2634e6aba90ecb577 Author: car Date: Thu Oct 9 18:23:10 1997 +0000 Added more access functions to the iterators: more STL like. Src/C_BaseLib/FabArray.H commit 7bff2a1aa5af7fbef7a9848b58034a1bf02c9c0b Author: car Date: Thu Sep 25 21:57:17 1997 +0000 Small changes. Src/C_BaseLib/pBoxLib_2.dsp commit 949841b53c75d1a257cc5db73618a1155deb50c9 Author: lijewski Date: Wed Sep 24 22:06:41 1997 +0000 Replaced most endl's with '\n'. Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxAssoc.cpp Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParmParse.cpp commit fea6a8fd2fd994433230de2174cdc937f9e4d4da Author: lijewski Date: Wed Sep 24 04:24:50 1997 +0000 Removed the BoxList intersect with BoxList function. It wasn't implemented properly. Will add a correct one if the need arises. Removed ostrstream usage from BoxLib.cpp. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 328fb178b241ca4a5ef2e36272078cbcada758d9 Author: car Date: Wed Sep 24 03:01:20 1997 +0000 Removed a strstream.h file inclusion, not needed. Src/C_BaseLib/ParmParse.cpp commit 2688be7c705eb08803aea6d09ef471eff637cceb Author: lijewski Date: Tue Sep 23 19:25:39 1997 +0000 Merged in BL_USE_NEW_HFILES. Removed many unnecessary #include directives. Removed a couple more instances of RASTER and CONTOUR usage. Src/C_AMRLib/DatasetClient.cpp commit 5e700a0626be21d946af44dde9b1b618535c7c9a Author: nazgul Date: Tue Sep 23 18:13:44 1997 +0000 Minor modifications occasioned by the 4 level test problem, and letting the convergence test see the norm of the coarse_source. Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 41ba3fc0532f526083919b4f456c54fdf9a6efb6 Author: nazgul Date: Tue Sep 23 18:11:24 1997 +0000 4 level test problem Src/LinearSolvers/C_NodalMG/tests/gr4level Tests/LinearSolvers/C_NodalMG/test_grids/gr4level commit 0a58d792af5203d76118b7de867caf3ed626c901 Author: car Date: Fri Sep 19 18:20:02 1997 +0000 Quiet down a warning about conversion of long to bool. Update the Project file. Src/C_BaseLib/FabArray.H Src/C_BaseLib/pBoxLib_2.dsp commit 29bcd0f20dd53cfb57133ed6472464de7189838c Author: vince Date: Fri Sep 19 18:04:34 1997 +0000 Bug fix for T3E (ReduceBoolAnd problems). Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.H commit c5fa29a9b4d3e3d87cb797108451e28b3e9956c4 Author: car Date: Fri Sep 19 16:17:30 1997 +0000 Change Comment. Src/C_BaseLib/ArrayLim.H commit 111550f24a68ea03c41d1098dd55de0b050e3340 Author: lijewski Date: Thu Sep 18 23:34:18 1997 +0000 Only output continuation line count if > 19 of them. Tools/C_scripts/strip72 commit e90fb1730737fa0b457463be6b821356ce3808a9 Author: lijewski Date: Thu Sep 18 22:09:24 1997 +0000 Changed a few functions that took `const int' to take simply a `int'. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H commit c8450b894ea404e3bf808210f0ee49a2c324cdff Author: lijewski Date: Thu Sep 18 21:22:19 1997 +0000 Removed some lines that had been commented out. Src/C_BaseLib/PArray.H commit f225a6529dfa29d22f9c0b740debbf04f0dabed2 Author: lijewski Date: Thu Sep 18 20:12:42 1997 +0000 Added BL_USE_NEW_HFILES macro. Src/C_BaseLib/Arena.H Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Tracer.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit 86435a01bb3b77326b190f9d6e9e1da616314109 Author: car Date: Thu Sep 18 18:25:19 1997 +0000 Added some stuff. Src/C_BaseLib/pBoxLib_2.dsp commit 2dd0ee07696f36f5b6bf3400857e317ebfcefd6a Author: car Date: Thu Sep 18 18:18:01 1997 +0000 Broke a comment. Src/C_BaseLib/Utility.H commit cb25311b3520630c59588f83a55157e4913dd78e Author: car Date: Thu Sep 18 18:03:33 1997 +0000 C++ style comments can't be in fortran include files. Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/REAL.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Utility.H commit 1f40f94399e7412e75333277525647f9bed65bdc Author: lijewski Date: Wed Sep 17 22:51:11 1997 +0000 Enforced all files having a copyright macro. Prepended all file inclusion macros with BL_ Src/C_BaseLib/Arena.H Src/C_BaseLib/Array.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/Assert.H Src/C_BaseLib/BArena.H Src/C_BaseLib/Boolean.H Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FPC.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Misc.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/SPACE.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/aString.H commit 99622cae738f6bbc75e357a7a772f552eba5f178 Author: lijewski Date: Wed Sep 17 22:22:49 1997 +0000 Inlined the constructors. Prepended BL_ to file inclusion macros. Src/C_BaseLib/BaseFab.H commit 66551db6f06b7bfc85866db12c71673cd5e30304 Author: lijewski Date: Wed Sep 17 17:46:31 1997 +0000 Inlined the constructors. Regularized the indentation. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 066bb95aeba8b0191008de0b02df29ed36dae9d2 Author: lijewski Date: Wed Sep 17 17:15:59 1997 +0000 Inlined all the MultiFabIterator stuff. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit bac52e53c8d6289c982089535d698a2b0d43166e Author: lijewski Date: Wed Sep 17 00:03:49 1997 +0000 Now check assignments of Box::numPts() to integers. Src/C_AMRLib/DatasetClient.cpp commit 35b9afb0a67b852b8a53164aba70e5ffb155081d Author: lijewski Date: Wed Sep 17 00:03:26 1997 +0000 Check assignments of Box::numPts() to integers. Src/C_BaseLib/FabArray.H commit 847fc06b03eec118f13783e69ad0eeaa654fa99e Author: lijewski Date: Tue Sep 16 22:28:14 1997 +0000 Removed `inline' from class definitions. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/List.H Src/C_BaseLib/PArray.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/Tuple.H commit e03036067d3b0f437fa6dc36e9770ad34cb25f4f Author: lijewski Date: Tue Sep 16 22:12:43 1997 +0000 The previous virtual stuff that was removed consisted only of the stuff in FabArrayIterator. This mod removes all the virtual stuff from the three remaining Iterators in this module, as well as the virtual stuff from FabArrayCopyDescriptor. Src/C_BaseLib/FabArray.H commit ccc3769a13049b3460aaa750596c0c517633a30d Author: lijewski Date: Tue Sep 16 21:11:34 1997 +0000 Removed all virtual stuff. Src/C_BaseLib/FabArray.H commit 980dde8029d140ae76d2d05700648d63159e2d93 Author: lijewski Date: Tue Sep 16 19:18:11 1997 +0000 Some cleanup and code simplification. Inlined more stuff. Src/C_BaseLib/Array.H Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FabArray.H commit 673ec7d486b8830c16b6ef68674375adafd104ab Author: lijewski Date: Tue Sep 16 16:04:59 1997 +0000 Removed all DPtr stuff. Src/C_BaseLib/AliasedDPtr.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/DPtr.H Src/C_BaseLib/Make.package Src/C_BaseLib/SimpleDPtr.H commit 3e687e8125c007bc433b3516f46555ebf67927ff Author: lijewski Date: Tue Sep 16 03:30:36 1997 +0000 Removed all aliasing stuff from BaseFab. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Looping.H commit 536217df33fa117181fd3a1d19481209c7e841e8 Author: lijewski Date: Mon Sep 15 23:33:19 1997 +0000 Removed aliasing stuff. Removed LPARX stuff. Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/DPtr.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H commit 18db379740d74a888d2946a9160a5cb99ae2c099 Author: lijewski Date: Mon Sep 15 22:24:10 1997 +0000 From Guthamr release. Tools/C_scripts/install-sh Tools/C_scripts/mkdep Tools/C_scripts/strip72 commit a8e7104301a3df86d54708c4964a4934017e3b8d Author: lijewski Date: Mon Sep 15 21:53:51 1997 +0000 Now assumes there is ../scripts directory. Tools/C_mk/Make.defs commit dcaa46f8a809e222b61ad27a01b4b511779f36ee Author: lijewski Date: Mon Sep 15 20:46:01 1997 +0000 Now assume things at ../mk Tools/C_mk/Make.defs commit 296a7d000fe41bc59e4b42fa1f3ba2b2a5ec2196 Author: lijewski Date: Mon Sep 15 20:45:43 1997 +0000 Now assume ../mk existance. Src/C_BaseLib/GNUmakefile commit 1c282a382a7493b9332146ca3a08220cb1374021 Author: lijewski Date: Mon Sep 15 20:37:04 1997 +0000 Moved from IARMAll directory. Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 4b417c9677f32d29e5c8813d176d1f3085186baa Author: lijewski Date: Mon Sep 15 19:45:24 1997 +0000 Removed Tuple.cpp and rearranged some things. Src/C_BaseLib/Make.package commit 12c046f524fc5d203748dc36a37d2da7b206750a Author: lijewski Date: Mon Sep 15 19:40:05 1997 +0000 Brought some stuff up to the indentation style of previous boxlib. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit ad1c15eb80c200afabbd3559f95935d870fa1e63 Author: vince Date: Mon Sep 15 16:39:38 1997 +0000 Added files. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 75deac98e0431fa3322aa21ab9f75e3513659f58 Author: lijewski Date: Fri Sep 12 17:59:59 1997 +0000 Moved from IAMRAll directory. Src/C_BaseLib/AliasedDPtr.H Src/C_BaseLib/Arena.H Src/C_BaseLib/Array.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/Assert.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Boolean.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxAssoc.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/DPtr.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Make.package Src/C_BaseLib/Misc.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/SPACE.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/SimpleDPtr.H Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tracer.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit afb9a89932bb568e849656b2aca95cb63feb8549 Author: car Date: Mon Aug 11 23:45:38 1997 +0000 Fortran tweaks. Src/C_AMRLib/DatasetClient.cpp commit dd6443e646e9f29410d9c7ff897a43bbbc280159 Author: nazgul Date: Tue Aug 5 03:26:59 1997 +0000 Yet more test grids. Src/LinearSolvers/C_NodalMG/tests/gr2.0 Src/LinearSolvers/C_NodalMG/tests/gr2.1 Src/LinearSolvers/C_NodalMG/tests/gt010 Src/LinearSolvers/C_NodalMG/tests/gt012 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.0 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt010 Tests/LinearSolvers/C_NodalMG/test_grids/gt012 commit 67e0489383acac4ceeea54af5758ff197f3da3d4 Author: nazgul Date: Tue Aug 5 03:24:54 1997 +0000 Level project now works in the t27 stencil (no line solves yet). Line solves work in any direction in the v7 stencil. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit bbb2dd4d390208db69facd61f2fa460ea3cb7571 Author: car Date: Mon Jul 28 23:16:02 1997 +0000 Make _OSF_... complient for KCC-3.2b Src/C_AMRLib/DatasetClient.cpp commit f157f5d78378df1e8cf0cfdc0dc8431dd9cc9e45 Author: nazgul Date: Sun Jul 27 06:11:46 1997 +0000 A simple 16 cube Src/LinearSolvers/C_NodalMG/tests/gt016 Tests/LinearSolvers/C_NodalMG/test_grids/gt016 commit 1f57183141ec47999aec76e91ea7c9bbcfcef59a Author: vince Date: Thu Jul 24 20:31:14 1997 +0000 Added more FillPatchIterators. Src/C_AMRLib/DatasetClient.cpp commit 3976a1d77302700e9b5717fe6712f60c2578f5ea Author: nazgul Date: Sat Jul 12 06:10:39 1997 +0000 2d 9-point terrain stencils now working fully. line solves implemented, fixed bug in sync project. Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c75230faf043996fcee66a2e1aa2cc265dd188b8 Author: nazgul Date: Fri Jul 11 22:02:56 1997 +0000 2d 9-point terrain stencils appear to work for level and sync project, except that line solves are not yet implemented. Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit bbabf6d5f39a13d17f4ef25ec2f0d62be585c126 Author: nazgul Date: Thu Jul 3 21:44:21 1997 +0000 test file for 2 small level 0 grids Src/LinearSolvers/C_NodalMG/tests/gr0b Tests/LinearSolvers/C_NodalMG/test_grids/gr0b commit 197f0fa7276b0152fc83f02191a036cfcaaabf0d Author: nazgul Date: Thu Jul 3 21:43:56 1997 +0000 terrain now implemented for level project Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 8722964b1385f26566d2c489c227c1c6d6fb9681 Author: nazgul Date: Fri Jun 27 21:54:00 1997 +0000 integration form of restriction for terrain stencils declarations added Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/cont3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit ebbaf3120c60bc03aef836660a8c09146b7b7c59 Author: nazgul Date: Thu Jun 26 23:19:35 1997 +0000 Beginnings of terrain additions. Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 5b809cac28f31826f5a42f235aba46640dda8596 Author: nazgul Date: Thu Jun 26 23:17:46 1997 +0000 Declarations added to fortran. Beginnings of terrain additions. Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/cont2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 5829c65425db170a84df9b2ad5390f2e3a773f53 Author: nazgul Date: Thu Jun 26 23:05:43 1997 +0000 Test grids which exceed the size the cg bottom solver can easily handle Src/LinearSolvers/C_NodalMG/tests/gr1rick Src/LinearSolvers/C_NodalMG/tests/gr1rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick2 commit 73897d51f8a7c0a69bac0a2b6c7372b6338e26bc Author: nazgul Date: Tue Jun 10 21:50:31 1997 +0000 Extend line solves to rz and dimension 0 in 2d. Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 7bae9431fcf243eecf446eedb0675699386ec75b Author: nazgul Date: Tue Jun 10 00:50:17 1997 +0000 Minor fixes: forward line solve made vectorizable, conjugate gradient failure made non-fatal, just prints an error message (if pcode >= 2) and goes on. Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 7acc39a95d9f35073c84419212b1d9285274b36e Author: nazgul Date: Fri Jun 6 16:59:08 1997 +0000 Full-level line solves, in dimension BL_SPACEDIM - 1, for stencils v5, v9 and v7, in Cartesian coordinates only. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/proj.cpp commit 2cb536d60338abae0b1fbf19629c168fc29b8fef Author: nazgul Date: Fri Jun 6 16:49:29 1997 +0000 Yet another test grid Src/LinearSolvers/C_NodalMG/tests/gt05 Tests/LinearSolvers/C_NodalMG/test_grids/gt05 commit e7c2f6c4c99cd7c38f01326be4a9b208d3128c76 Author: nazgul Date: Mon Jun 2 20:56:14 1997 +0000 Test for case where domain can't be coarsened but a grid (apparently) can. Src/LinearSolvers/C_NodalMG/tests/gr2dave Tests/LinearSolvers/C_NodalMG/test_grids/gr2dave commit 588e910984fa921a0891b02b645817b0111e6f73 Author: nazgul Date: Mon Jun 2 20:55:51 1997 +0000 Bug fix for case where domain can't be coarsened but a grid (apparently) can. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 0221b7d7797f7fcccc64081bfa6664c66b0f5a18 Author: nazgul Date: Fri May 30 20:55:08 1997 +0000 Fixed a routine that isn't used yet so that the file will compile. Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 180f1301d3af355a06bc8cee7813505b5ac5d487 Author: nazgul Date: Fri May 30 20:32:54 1997 +0000 Corrections to handle (4,1) refinement correctly. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit 4842b6e5470bf7b21457af87a793e7d6e36e1ee3 Author: nazgul Date: Fri May 30 20:32:11 1997 +0000 Adding (4,1) test grids. Src/LinearSolvers/C_NodalMG/tests/gr.19s4.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4.1 commit 8206143d920174ac0ab88e14dc1e357510246696 Author: nazgul Date: Wed May 28 19:16:03 1997 +0000 Adds changes to support IntVect refinement ratios. Minor: fixes bug where cell-based source average trashes some interface divergence values that were already calculated. Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_graph.H Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/amr_gravity.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cont3d.F Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit bb56e75a5fff449325f871ed0c70285fd8f0f831 Author: nazgul Date: Wed May 28 19:12:32 1997 +0000 Tests for variable refinement ratios. Src/LinearSolvers/C_NodalMG/tests/gr.19s2.4 Src/LinearSolvers/C_NodalMG/tests/gt4s2.4.4 Src/LinearSolvers/C_NodalMG/tests/gt4s4 Src/LinearSolvers/C_NodalMG/tests/gt4s4.2.4 Src/LinearSolvers/C_NodalMG/tests/gt4s4.4.2 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2.4.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.2.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.4.2 commit c3ca852054668ca71425ea5c4950cac13b3a11e6 Author: nazgul Date: Wed May 14 20:33:27 1997 +0000 line solve bug fix for degenerate case of 1-point line solves Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit ccf827a86e46802ea327329177ff0cb1ab824a02 Author: nazgul Date: Thu May 8 15:18:17 1997 +0000 Removed the function type(const PArray& a). It was too prone to errors caused by partially-filled arrays. Use type(const FabArray& r) instead. Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit d54a21c35d4f3cb5f27d0371773cdc75f00afef6 Author: nazgul Date: Wed May 7 22:24:26 1997 +0000 fix type index bug Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 44bc484391ff0051173bbfcc8674a5f20ef5363b Author: nazgul Date: Wed May 7 21:35:06 1997 +0000 fix to sync source correction Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 8e8bc933eeba15314d227303c8e9b30cca05e59c Author: nazgul Date: Wed May 7 21:29:19 1997 +0000 sync source solvability correction Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 93c2d649c1627732aedae0ffa64483674110b569 Author: nazgul Date: Wed May 7 01:37:55 1997 +0000 adding line solve Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 5bca72009eeb1c3d2f869563ae4261a411f18a97 Author: nazgul Date: Wed May 7 00:35:43 1997 +0000 adding line solve Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c0c90778cefc358ca49b6132afc6e7ffde36d79c Author: nazgul Date: Tue May 6 03:11:18 1997 +0000 fix index bug Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit bad568c5614578c49cbee45558f823110a6ab6e9 Author: nazgul Date: Mon May 5 22:18:35 1997 +0000 Bug fix to build_index Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 37257f0bd58dd5c3099205e98974e1daa0fb6877 Author: nazgul Date: Fri May 2 22:06:26 1997 +0000 Fixed memory leak in test program Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/proj.cpp commit c0b6bc499b3f85c4a7821027396d181cc57f7e6c Author: nazgul Date: Fri May 2 17:35:14 1997 +0000 Fixes for variable density now work. Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/Rewrite Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 97e6e31d7d751d014563aabcec43b390fa0b0d1f Author: nazgul Date: Wed Apr 30 22:04:33 1997 +0000 Corrections for 3D. Src/LinearSolvers/C_NodalMG/Rewrite Src/LinearSolvers/C_NodalMG/amr_graph.H Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit e4f0a563c5d1dd000ec4903229699b9a1c2525f1 Author: nazgul Date: Wed Apr 30 20:28:51 1997 +0000 adding GNUmakefile manually since import ignores it. 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20:41:56 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c686e8eb909d6bc9e1470687eba613f8979febe1 Author: nazgul Date: Tue Apr 29 20:38:16 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/fill_patch.H commit 5e43618b9ba22ff0405611be875aed141fb2971a Author: nazgul Date: Tue Apr 29 20:15:56 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit ba18f4dd9f6dfa86e00df173cf66154acc1ead2e Author: nazgul Date: Tue Apr 29 18:29:40 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 94ffd818a9bf1ab6c86ec18e6e4565395f40ff4e Author: nazgul Date: Mon Apr 28 21:51:56 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_multi.H commit a498100b0a43479409605ec9eaa464600fe1621b Author: nazgul Date: Fri Apr 25 23:30:33 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/Make.package commit 0f2561a87bce705882fc6124212c47013f79abea Author: nazgul Date: Wed Apr 23 22:34:37 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/GNUmakefile.main commit f686b4bc929214d97a8b0588608fe3b6731e46dc Author: nazgul Date: Thu Mar 27 22:05:28 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_multi.H commit 52d19b7261ae7399004472ae95a884a86413590c Author: nazgul Date: Thu Mar 27 21:24:11 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_projector.H commit 6b3d4c19412bdbce7f963ddded8121c512d600c1 Author: nazgul Date: Wed Mar 26 17:38:08 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr2ann.p5 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p6 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p5 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p6 commit 8ff71095cc689bc66f398bc1ee37ae130abe0c75 Author: nazgul Date: Tue Mar 25 18:58:20 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H commit 1d73e974b0ad30060d63baa15439940bbbfff0a3 Author: nazgul Date: Fri Mar 21 20:13:36 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_gravity.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a3cf04d3be4853c18b48d3189cb7d77c1e01860d Author: nazgul Date: Fri Mar 21 20:09:06 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/interface.H commit 92deacad1bee7c78f20a98ca485ca87363e4a677 Author: nazgul Date: Thu Mar 20 21:13:29 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/Rewrite commit 2e93f82c5955ee9919b5c73c2a318745843ac9f0 Author: nazgul Date: Tue Mar 18 23:51:41 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/cache.H commit 003ce6b53e5b81ecd219bc5a44af8d244e71f26a Author: nazgul Date: Tue Mar 18 20:16:26 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gt3ann2 Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann2 commit 007298ac68b21503d37eaf44a9cae210ad49c333 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Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb commit 6830436830288f40cd9ae3c8829073031ee040db Author: nazgul Date: Thu Apr 25 16:46:17 1996 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 1f04efac2dc02158cf22a7c3d2f3f87082487dc6 Author: nazgul Date: Wed Mar 13 22:28:35 1996 +0000 Initial revision Src/LinearSolvers/C_NodalMG/cbasics.H Src/LinearSolvers/C_NodalMG/tests/gr0a Tests/LinearSolvers/C_NodalMG/test_grids/gr0a commit f87f1b2d83b7fe9c512ddc0ca43ae9bcd434670f Author: nazgul Date: Tue Nov 7 22:26:32 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_grav2d.F Src/LinearSolvers/C_NodalMG/amr_grav3d.F Src/LinearSolvers/C_NodalMG/cont2d.F Src/LinearSolvers/C_NodalMG/cont3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit c139797864292915ccc5ebea761e68615309b970 Author: nazgul Date: Mon Oct 30 22:35:09 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/README commit cfefdf25849ecf2ab5a5b2b6573a4f2bc43a21dd Author: nazgul Date: Mon Sep 18 20:37:46 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/poisson.cpp commit d3a6d7bfeffcf89aa95b004c4aabb44f9243f13c Author: nazgul Date: Mon Sep 18 18:20:14 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_elliptic.cpp commit e7ab65e98df0bd6814dab6ea6bb540296b1b4677 Author: nazgul Date: Thu Aug 24 21:25:02 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr2ann.l2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l2 commit ef57898a17aac4dd83b5457c8f70d6b4c4e42a2e Author: nazgul Date: Thu Aug 24 21:12:20 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr2ann.l1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l1 commit 642554a3d74ed89dfdb89c9049612fbcfb061494 Author: nazgul Date: Thu Aug 24 21:02:50 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr2ann.l0 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l0 commit 6603ce60473f65e14e871c323ac0c2fb4fda9df8 Author: nazgul Date: Fri Nov 4 23:35:41 1994 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr.11 Src/LinearSolvers/C_NodalMG/tests/gr.15 Src/LinearSolvers/C_NodalMG/tests/gr.16 Src/LinearSolvers/C_NodalMG/tests/gr.19 Src/LinearSolvers/C_NodalMG/tests/gr.19s2 Src/LinearSolvers/C_NodalMG/tests/gr.19s4 Src/LinearSolvers/C_NodalMG/tests/gr.292.11 Src/LinearSolvers/C_NodalMG/tests/gr.292.25 Src/LinearSolvers/C_NodalMG/tests/gr.7 Src/LinearSolvers/C_NodalMG/tests/gr.8 Src/LinearSolvers/C_NodalMG/tests/gr.8a Src/LinearSolvers/C_NodalMG/tests/gr0 Src/LinearSolvers/C_NodalMG/tests/gr1 Src/LinearSolvers/C_NodalMG/tests/gr1mike.thin Src/LinearSolvers/C_NodalMG/tests/gr2 Src/LinearSolvers/C_NodalMG/tests/gr2a2 Src/LinearSolvers/C_NodalMG/tests/gr2a4 Src/LinearSolvers/C_NodalMG/tests/gr2ann Src/LinearSolvers/C_NodalMG/tests/gr2ann.p1 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p2 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Src/LinearSolvers/C_NodalMG/tests/gt0 Src/LinearSolvers/C_NodalMG/tests/gt1 Src/LinearSolvers/C_NodalMG/tests/gt12 Src/LinearSolvers/C_NodalMG/tests/gt12.2 Src/LinearSolvers/C_NodalMG/tests/gt12.3 Src/LinearSolvers/C_NodalMG/tests/gt2 Src/LinearSolvers/C_NodalMG/tests/gt3 Src/LinearSolvers/C_NodalMG/tests/gt4 Src/LinearSolvers/C_NodalMG/tests/gt4s2 Src/LinearSolvers/C_NodalMG/tests/gt4s2a Src/LinearSolvers/C_NodalMG/tests/gt5 Src/LinearSolvers/C_NodalMG/tests/gt5s2 Src/LinearSolvers/C_NodalMG/tests/gt5s4 Src/LinearSolvers/C_NodalMG/tests/gt6 Src/LinearSolvers/C_NodalMG/tests/gt6s Src/LinearSolvers/C_NodalMG/tests/gt6s2 Src/LinearSolvers/C_NodalMG/tests/gt6s4 Src/LinearSolvers/C_NodalMG/tests/gt7a Src/LinearSolvers/C_NodalMG/tests/gt7aa Src/LinearSolvers/C_NodalMG/tests/gt8 Src/LinearSolvers/C_NodalMG/tests/gt8a Src/LinearSolvers/C_NodalMG/tests/gt8b Src/LinearSolvers/C_NodalMG/tests/gt8c Src/LinearSolvers/C_NodalMG/tests/gt8ms2 Src/LinearSolvers/C_NodalMG/tests/gtbig Src/LinearSolvers/C_NodalMG/tests/gtbig2 Src/LinearSolvers/C_NodalMG/tests/gtbig3 Src/LinearSolvers/C_NodalMG/tests/gtbig4 Src/LinearSolvers/C_NodalMG/tests/gtbig5 Src/LinearSolvers/C_NodalMG/tests/gtgrav2 Src/LinearSolvers/C_NodalMG/tests/gtgrav4 Src/LinearSolvers/C_NodalMG/tests/gtpfail Tests/LinearSolvers/C_NodalMG/test_grids/gr.11 Tests/LinearSolvers/C_NodalMG/test_grids/gr.15 Tests/LinearSolvers/C_NodalMG/test_grids/gr.16 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4 Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.11 Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.25 Tests/LinearSolvers/C_NodalMG/test_grids/gr.7 Tests/LinearSolvers/C_NodalMG/test_grids/gr.8 Tests/LinearSolvers/C_NodalMG/test_grids/gr.8a Tests/LinearSolvers/C_NodalMG/test_grids/gr0 Tests/LinearSolvers/C_NodalMG/test_grids/gr1 Tests/LinearSolvers/C_NodalMG/test_grids/gr1mike.thin Tests/LinearSolvers/C_NodalMG/test_grids/gr2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2a2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2a4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p3 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2b Tests/LinearSolvers/C_NodalMG/test_grids/gr2c Tests/LinearSolvers/C_NodalMG/test_grids/gr2cross Tests/LinearSolvers/C_NodalMG/test_grids/gr2d Tests/LinearSolvers/C_NodalMG/test_grids/gr2d2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2d4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2e Tests/LinearSolvers/C_NodalMG/test_grids/gr2f Tests/LinearSolvers/C_NodalMG/test_grids/gr2g Tests/LinearSolvers/C_NodalMG/test_grids/gr2h Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike3 Tests/LinearSolvers/C_NodalMG/test_grids/gr3.rz Tests/LinearSolvers/C_NodalMG/test_grids/gr3a Tests/LinearSolvers/C_NodalMG/test_grids/gr3b Tests/LinearSolvers/C_NodalMG/test_grids/gr3c Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike.3 Tests/LinearSolvers/C_NodalMG/test_grids/gr4 Tests/LinearSolvers/C_NodalMG/test_grids/gt.32 Tests/LinearSolvers/C_NodalMG/test_grids/gt0 Tests/LinearSolvers/C_NodalMG/test_grids/gt1 Tests/LinearSolvers/C_NodalMG/test_grids/gt12 Tests/LinearSolvers/C_NodalMG/test_grids/gt12.2 Tests/LinearSolvers/C_NodalMG/test_grids/gt12.3 Tests/LinearSolvers/C_NodalMG/test_grids/gt2 Tests/LinearSolvers/C_NodalMG/test_grids/gt3 Tests/LinearSolvers/C_NodalMG/test_grids/gt4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2a Tests/LinearSolvers/C_NodalMG/test_grids/gt5 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d9792e7e53274b898d907a0f08452bef75669031 Author: nazgul Date: Tue Oct 4 22:13:47 1994 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_gravity.H commit b06aef4481e3612148772e1a6e0aa59c3be684e4 Author: nazgul Date: Wed Mar 23 23:31:05 1994 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_elliptic.H commit 1fc596b76899cdd13da6cd2998ba4f362c5b3130 Author: nazgul Date: Tue Oct 5 18:46:17 1993 +0000 Initial revision Src/LinearSolvers/C_NodalMG/driver.cpp commit 93dbd8bb612ee031f19d5659b3b8aac4afb85511 Author: nazgul Date: Fri Mar 12 19:37:55 1993 +0000 Initial revision Src/LinearSolvers/C_NodalMG/RegType.H